# Our understanding of genetics is changing



## deknow

1. Perhaps you could explain this in your own words at least to some extent.....you claim this as "our" understanding...if you understand it and you think it is important it seems that telling people to read a whole book is a poor way to accomplish your goals (more people understanding something you think is important they understand.

2. It seems to me that there is a glaring omission in blurb....the vertical transmission and heritability of the microbial cultures that support larger life. The ability of Japanese humans to digest raw nori seaweed is a great example.
3. You might want to have this discussion with our own jwchestnut...from a recent thread:


> [Is there **any** evidence that "regression" is a biological state. This screams Lamarckian (or Stalinist Lysenko) fallacy. By "regression" I am referring to the popular internet meme that bees may be conditioned to grow into smaller sizes. This is "the heritability of acquired traits" that people should of learned in 7th grade was an alternative to Darwinian evolution proposed by Lamarck (Giraffes stretching their necks). The theory is complete bunkum.
> 
> As a member of a biological community that has to contend with folklore and disbelief about the Darwinian principles, I am uncomfortable when "regression" is presented as an established fact based solely on the anecdotes of Internet Gurus.
> 
> I do not believe that acquired traits are heritable in any meaningful way. I have more than a century of scientific trials to back me up.


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## peterloringborst

> 1. Perhaps you could explain this in your own words at least to some extent.....you claim this as "our" understanding...


By "our understanding", I mean the general consensus view of what genetics is and what it does. Understanding in the sense of what we think we know, not in the sense of a complete understanding, which we don't have and may never have.



> if you understand it and you think it is important it seems that telling people to read a whole book is a poor way to accomplish your goals


My desire was to initiate a discussion, not to accomplish a goal of any kind. I have suggested that most of the discussions of bee breeding assume that breeding of bees is understood, and that it consists of simple genetics as understood by grade school kids.



> 2. It seems to me that there is a glaring omission in blurb....the vertical transmission and heritability of the microbial cultures that support larger life.


That should have been in the blurb? I didn't write the blurb but it was intended to summarize the book in some way. No summary would contain everything. As far as microbial cultures, that certainly is the part of an organismal inheritance system that a comprehensive view of evolution would include. 

It may be also, and we have discussed this, that the process of requeening omits the passage of microbial communities that making splits does. In other words, as Charles Mraz suggested, it may be far better to make one or two splits directly from each of the most vigorous hives, instead of just busting up everything and adding queens from an outside source.

But this is the beginning of this thread and there are many more questions than answers, if you are interested. By the way, I didn't start this to get into a harangue with anyone.


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## JWChesnut

Eva Jablonka is not a "crank", but her claims are dubious.

Anyone should read Thomas E. Dickins critical review of her work cited below -- his core illustration is that natural selection is central, and proximal influences to the genetic control of phenotype explains her epigenetic and behavioral effects.

Plasticity in phenotype is under genetic control. Anyone who studies plants appreciates that plasticity of response has a component of heritable, evolutionary fitness.

http://rspb.royalsocietypublishing....5/10/rspb.2012.0273.full.pdf#page=1&view=FitH


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## Phoebee

I did a little casual research this morning on something that's been bothering me ever since I combined a hive of Carniolans with a hive of Italians, and wondered just how universal waggle dances are. Evidently this whole topic is subject to some "discussion" as of yet, but clearly waggle dances are used by bees and seem to convey some information about direction and distance to forage, and bees must develop an innate understanding of this "language" due to genetics.

Apparently there are "dialects" which vary somewhat between subspecies, although this is one of those "discussed" areas. There is some suggestion (again with a lot of discussion) that bees can learn to understand each others dialects.

There's a lot in bee behavior that is more flexible than one would expect of little biological automata. They can be trained and they do learn. They're notably adaptable in their behavior. Underneath all this are genes, but this flexibility is a level of function that is in the "whole is greater than the sum of the parts" that one might expect if genes are a hard script that totally define the creature.


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## deknow

There is a graph in the Gould/Gould book (I think it's called The Honeybee) from the scientific American library that shows the duration of parts of the dance as they vary between races.

Many traits do clearly follow the pattern of simple straightforward Mandelian genetics (a study that comes to mind is one where low and high pollen hoarding behaviors were selected from the same population).

One of the things that doesn't fit simply into the model is aggressiveness....mmixtures of bees that are all reasonably gentle have often been observed to be overly aggressive. I've often wondered if this had to do with conflicting dialects within the hive....the tower of babble effect.
The Gould book is well worth finding. Out of print, and I've never heard/seen anyone else recommend it.

Deknow


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## Phoebee

My limited experience with gentleness so far is this. My Carniolans are as gentle as lambs, as advertised. They didn't even get upset when the one hive lost its queen. I can stand right in front of the hives unprotected, and don't even bother with a veil for feeding or other simple tasks. We rarely use smoke, and if we do it is to get them out of a place where we're working.

The nuc with the replacement queen came from our mentor, and his bees have attitude. They will attack if you come within 15 feet of the hive entrance. But the nuc was gentle, and is now combined with the queenless hive and I see no difference in aggressiveness with the other hive. 

So far I've seen one factor that seems to explain all. Our hives are located inside a fortress, a strong fence with electric fencing on the outside. Skunks, bears, and other bee-botherers can't get in. But our mentor's hives are in skunk country, with no protection.

Another example of adaptability.


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## peterloringborst

> Many traits do clearly follow the pattern of simple straightforward Mandelian genetics (a study that comes to mind is one where low and high pollen hoarding behaviors were selected from the same population).


This is an example of how hereditary mechanisms can be forced to produce something that perhaps nature never would have done. Essentially, plants and animals with single traits that have been artificially intensified are "freaks." Natural selection simultaneously selects and reinforces a range of traits the increase the survival of the population. A bee that did nothing but hoard pollen wouldn't last long in the wild.


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## peterloringborst

> Eva Jablonka is not a "crank", but her claims are dubious.


This is certainly one of the most oblique put-downs I have ever seen. She is not a crank (implying that she could be regarded as such) but her claims are dubious. All of them? Granted, a lot of her work is speculative; much of genetics is speculative. Evolution is one of the hardest things to prove empirically. The field produces almost no testable theories. For example, given one million years -- but we don't have one million years. Can we even predict the evolutionary pathway of an organism in the next twenty?

The reason I conjured up Jablonka's work is because it is an example of the current thinking that there is a lot more to heredity than DNA (which by the way, I work with on a daily basis). Not to discuss the fringe ideas but to reflect on the inadequacy of common thinking regarding bee breeding. She wrote:



> Recognizing that there is more to heredity than DNA has implications for medicine and agriculture, as well as for evolutionary theory. For example, we know that some environmental insults and stresses, such as temporary starvation, can affect future generations. In evolutionary studies, because heritable non-genetic variations are often induced by the environment, we have to expand our notion of heredity and variation to include the inheritance of acquired variations, the once disparaged idea that was part of Lamarck’s theory.
> 
> In a sense, we have to go back to Darwin’s original, pluralistic convictions. Darwin, unlike many of his more dogmatic followers, saw a role for induced variation in evolution. Today, in the light of the newly discovered epigenetic mechanisms, Darwinian evolution should include descent with epigenetic as well as genetic modifications, and natural selection of induced as well as random variations. Certainly, it should not be reduced to “selfish genes.”


Read more at http://www.project-syndicate.org/commentary/the-pillars-of-darwinism#HCE2OCKLw340jkBX.99

Other authors have written extensively on this topic:



> We need to rethink how the genome functions as a cellular memory device (Wilson, 1928). Conventional evolutionary theory treats the genome as the source code for cell and organism characters -- essentially as a read-only memory (ROM) with no active input and subject to change through copying errors. The 21st Century alternative view is to treat the genome as a readewrite (RW) memory system, more like an iPod than a blueprint or even a DVD.


Rethinking the (im)possible in evolution. by James A. Shapiro
Progress in Biophysics and Molecular Biology 111 (2013) 92e96


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## peterloringborst

Deleted by author, off topic


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## Michael Johnston

So it turns out that the Lamarchian (I don't remember the spelling) theory of evolution is correct. A giraffe stretching to eat higher leaves passes on the genes for a longer neck rather than just the long necked giraffes are the ones that survive. Darwin's theory of natural selection selection is common sense and shouldn't be disputed but genes changing according to life's experience adds a more complex layer.


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## peterloringborst

No, it's not that Lamarck was right or Darwin was right. They were pioneers who paved the way. Did you know that Mendel was a beekeeper? He learned the basics of heredity by breeding peas. If he had studied bees instead, he wouldn't have figure out anything. We still haven't figured out bee heredity, isolated examples notwithstanding. 

In fact, Heather Mattila and others have shown that multiple matings produce better colonies than single ones. This leads us to suppose honey bees have evolve a system to prevent line breeding and the reinforcement of single traits. Of course, University academics look down their noses at beekeepers like Charlie Mraz but he thought modern bee breeding was headed in the wrong direction. 

But back to Eva Jablonka, and her book "Evolution in Four Dimensions", she points out that organisms that modify their environment create new selective pressures on their offspring. For example, if an animal creates a long term lair, then they are selecting for offspring that tolerate living long term in that sort of lair. Offspring that wander off may not be able to survive and reproduce. 

You can view selection on a spectrum ranging from simple natural selection, the survivors in the struggle of nature all the way to highly bred livestock which could not survive two days in the wild. In reality, organisms are the product of many influences, including climate, symbiotic relationships, and dumb luck.


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## Phoebee

Michael Johnston said:


> So it turns out that the Lamarchian (I don't remember the spelling) theory of evolution is correct. A giraffe stretching to eat higher leaves passes on the genes for a longer neck rather than just the long necked giraffes are the ones that survive. Darwin's theory of natural selection selection is common sense and shouldn't be disputed but genes changing according to life's experience adds a more complex layer.


Its not stretching the neck that passes the genes, so much as not stretching the neck to reach forage does NOT pass the genes. I've said for years that behavior obviously can steer evolution. It is the most easily changed adaptation in higher animals, and it is strongly driven by positive and negative reinforcement. The giraffe can't will its neck longer, but the behavior of reaching for forage is certainly a selective pressure favoring the individuals who are built for it.


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## peterloringborst

Genes discredited:



> Except in a small number of cases, the notion of genes, however they are defined, coding for an organism’s characteristics has been discredited. Referring to genes as being adapted to the environment no longer makes any sense. Adaptation is at the level of the phenotype. These considerations have profound implications for what should be regarded as the appropriate units for evolutionary biology and how cooperation should be treated.


Bateson, P. (2014). Evolution, epigenetics and cooperation. Journal of biosciences, 39(2), 191-200.


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## Michael Johnston

I actually have the opinion that genes will change based on life's experience. Many fundamentalist Christians refute the existence of any kind of evolution even though survival of the fittest is basically common sense. I have the view that this is a system created by god but that the genotype can actually change based on experiences during life; it gives god credit for creating a much more complex system. I have run into examples of what I considered changing genotypes but didn't write them down.
The whole idea of life evolving from a primordial soup violates the Law of Entropy.


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## peterloringborst

> I actually have the opinion that genes will change based on life's experience.


Patrick Bateson writes:



> To look at an individual’s behaviour and ask, ‘Is it genetic or is it learned?’, is to ask the wrong question. All behaviour patterns require both genes and an environment in order to develop. They emerge as a result of a regulated interplay between the developing individual and the conditions the conditions in which it lives. Moreover, like the records in a jukebox, different genes may be expressed in different environmental conditions. For that reason, the individual’s behaviour cannot be divided into two types – those patterns caused by internal factors (often referred to as ‘genetic’ or ‘innate’ behaviour) and those caused by external factors (‘acquired’ behaviour).
> 
> -- Bateson, P. (2014). Evolution, epigenetics and cooperation. Journal of biosciences, 39(2), 191-200.


James Shapiro:



> Because genome evolution is multilevel, amplifying, and combinatorial
> in nature, the end results are complex hierarchical structures with
> characteristic system architectures.
> 
> Genomes are sophisticated data storage organelles integrated into the cellular and
> multicellular life cycles of each distinct organism. Thinking about
> genomes from an informatic perspective, it is apparent that systems
> engineering is a better metaphor for the evolutionary process than
> the conventional view of evolution as a selection-biased random walk
> through the limitless space of possible DNA configurations.
> 
> -- Shapiro, J. A. (2011). Evolution: a view from the 21st century.


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## peterloringborst

I received a request to expand a bit on Charlie Mraz's ideas. Here is an essay he wrote in 1973:

The Genetic Vulnerability
CHARLES MRAZ
Middlebury, Vt.


> “A remarkably small number of plants feed mankind. On a global basis, five crop species—rice, wheat, corn, sorghum and barley—account for some 60 percent of the human caloric intake, with 25 percent coming from rice alone. It is thus a matter of concern that our major crops have increasingly become genetically vulnerable to attacks by pests and diseases.
> 
> “Crop epidemics are as old as history. The most recent record, for example, includes the ravages of the potato blight in Ireland during the 1840’s, the coffee rust of Ceylon in the 1870’s and, in this country the wheat stem rust of 1954 and the southern corn blight of 1970. In modern times the risk of epidemics has increased greatly as agriculture—responding to demands of consumers and the market place—creates vast monocultures wherein billions of plants of a single crop species sweep across thousands of acres, the plants all genetically similar. The narrowness of his genetic base helps make possible today’s high crop yields. Should a genetically uniform variety become susceptible, however, a bounteous banquet nay ensue for pest or pathogen. Man would lament yet could survive the loss of a cultivated crop such as coffee. The loss of rice, wheat, or corn, many observers note, would be as devastating to civilization as atomic warfare.
> 
> “Plant scientists, faced with these genetic threats to crops, already bear an awesome responsibility in helping feed the world’s burgeoning population. Of the steps they can take to safeguard our crop heritage, three loom particularly important. First, to obtain germ plasm for genetic diversity, plant scientists must vigorously collect or conserve till existing plant life—including the world progenitors of our cultivated crops—before they are gone forever. Second, these plants must be maintained, either in world collections such as those of ARS, or in isolated preserves set aside and protected against genetic dilution by cultivated varieties. Third, they must breed and release varieties that incorporate a diversity of genes, enabling them to better withstand epidemics.
> 
> “Plant scientists are in for trying times. Even with valiant exertions in fostering the genetic diversity of crops, the prospect for some years is for an uncomfortably close race between the stork and the plow. But with the know-how of agricultural science and public interest and support, neither crop plant nor man need become an endangered species.”
> 
> Everything said in the above message can be translated into beekeeping, in every respect. It is this message I have been trying to get across to beekeepers in my 40 years of effort to establish a diversity of genes in bees to establish and maintain vigor, health and resistance to disease. Beekeeping is now in this dilemma of a very narrow genetic base and lack of genetic diversity. Through years of inbreeding and the consequent loss of many old genetic lines, queen breeders now find themselves without new blood lines to restore vigor and resistancy that were found in strains of bees years ago.
> 
> The races of bees that we had 50 years ago were completely different from these same races in the U. S. today. All races of bees in the U. S., Italians, Carniolans, Caucasians, are really no longer like the stock that came over here originally. No new blood has been added to the genetic pool for almost 50 years from the country of origin of these different races. Practically all of them through constant inbreeding and genetic degeneration have become susceptible to one or more diseases. Many strains of bees today cannot survive except under constant medication of drugs for Nosema, EFB, AFB, paralysis, etc. This is a dangerous situation. Drug therapy can never be a substitute for resistance to disease.
> 
> We now have a station in the U. S. that is supposed to be a bank for preserving genetic strains of bees for future use. Unfortunately, so far as I have been able to observe, most of the strains being preserved are various degenerate freaks. What we need is a storehouse of vigorous, hardy bees with completely new blood lines to create that genetic diversity to select and crossbreed new vigor and resistance into the bees which are now lost. To my knowledge, such genetic stock cannot be found in the U. S. at the present time.
> 
> In the article it mentions that to accomplish this we will need the know-how of agricultural science and public interest and support. Here is the stumbling block to the whole problem. This problem of genetic diversity with bees in the U. S. has neither the support of our beekeeping scientists nor of the beekeepers themselves. Both seem content to solve the disease problem with “magic drugs”, an easier solution to the problem than the complexities of restoring the natural resistance bees have maintained on their own over their millions of years of existence. After 40 years of effort I have not succeeded in getting any cooperation from large queen breeders to help produce and perpetuate this diversity of genes for resistance and to make it available to the many beekeepers who may be interested. Perhaps we will have to wait until an epidemic of disease resistance or immunity to drugs threatens to wipe out beekeeping.
> 
> EFB resistance to drug therapy is already becoming a serious problem in parts of the U. S., Mexico and Argentina. Recently, news of bees dying off in Virginia has been carried by the press. Its cause and cure appear, according to reports, to be a mystery. There is nothing mysterious about it; it is a sudden manifestation of genetic degeneration in certain strains of bees now used quite extensively. The cure is simple; it only needs requeening with resistant queens. In one operation of requeening, the problem can be completely solved, as was my experience in Mexico some years ago. It is a form of paralysis and in Mexico was called “Rock & Roll Disease”. In the U. S. it even sometimes was called “Farrar’s Disease” because of the high susceptibility of this strain of bees to this problem.
> 
> The big problem is to find resistant stock with which to requeen. As long as there is no interest in looking for it, it will never be found. Every beekeeper should read the above article from Agricultural Research; it may mean the survival of our beekeeping business for the future.


Gleanings in Bee Culture, December 1973, Page 381


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## Saltybee

Aah, the arrogance of knowledge. It is kind of fascinating that people continue to claim an understanding of the cutting edge of science. Areas where more is unknown in the future, than has discovered in the present. Men of knowledge and education have always argued one point or the other as fact. History tends to prove later understandings disagree with both sides. 
Maybe it stems from the habit of reporting experiments as "Conclusions". "Appearances" or "steps of progress" usually are proven more descriptive over time.
Maybe human genetics has made a huge leap of advancement in the current generations and history will support "facts" understood today are indeed truths. If that is true, then a few are beating the historical odds.

Genetics, instinct, memory, evolution. I am more comfortable with the concept of "scientific appearances" more than the concept of "fact". Are you?

In slang; I don't know what I don't know.


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## Richard Cryberg

Michael Johnston said:


> I actually have the opinion that genes will change based on life's experience. Many fundamentalist Christians refute the existence of any kind of evolution even though survival of the fittest is basically common sense. I have the view that this is a system created by god but that the genotype can actually change based on experiences during life; it gives god credit for creating a much more complex system. I have run into examples of what I considered changing genotypes but didn't write them down.
> The whole idea of life evolving from a primordial soup violates the Law of Entropy.



Life most definitely does not violate any of the laws of thermodynamics and anyone who says it does clearly has never learned any thermodynamics and learned what a closed system is. Do not ever even hint at saying life violates any laws of entropy as you are simply showing your ignorance on the topic. I will add it is not an easy topic. Without math such as calculus and at least a bit of differential equations you will never have the slightest understanding of thermodynamics. It generally takes one undergrad thermo course and one or more grad level courses in the subject before anyone really understands it.

Dick


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## Michael Johnston

Well, Richard,
I guess you want to dismiss my statement about entropy on the basis that you're smarter than I am. You probably are. If you google Entropy and Evolution, you'll find some people that are smarter than you that agree with my statement.

Just so we don't get kicked off the site for going off topic, I'd like to comment on Charlie Mraz's ideas. I don't believe that inbreeding is a major factor in bee breeding. It's really hard for any beneficial old genes to disappear when a queen is mating wit around 16 drones. The system of haplodiploidy will make some deleterious genes disappear because the haploid drones with bad genes will be less fit for mating - good riddance to those genes. Inbreeding is prevented because a bee larvae with identical sex alleles will become a sterile drone. I would like to know how fast mutations occur in the bee genome leading to new genes. Maybe Peter can answer that.


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## mike bispham

Phoebee said:


> So far I've seen one factor that seems to explain all. Our hives are located inside a fortress, a strong fence with electric fencing on the outside. Skunks, bears, and other bee-botherers can't get in. But our mentor's hives are in skunk country, with no protection.


If you live in an area containing effective predators, the gentler characteristics have been removed from the population. Only hot bees get to make more bees.



Phoebee said:


> Another example of adaptability.


Yes. 

Mike (UK)


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## mike bispham

peterloringborst said:


> The reason I conjured up Jablonka's work is because it is an example of the current thinking that there is a lot more to heredity than DNA (which by the way, I work with on a daily basis).


There's that 'work with' again. Again, can you tell us:

a) your qualifications

b) your job description.

Mike (UK)


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## mike bispham

peterloringborst said:


> We still haven't figured out bee heredity, isolated examples notwithstanding.


Depended what you mean by 'figured out.' Pretty much all but the simplest life forms are too complex for us to say we know everything about them. But that's not to say we know nothing about them.

For example, we know that every single bee is in the first instance the product of the instructions provided by its mother and father. Period. There is further variation of a minor sort supplied by environmental factors (conditions while developing for example), and there may be further epigenetic shifts.

But the core fact remains: the mother and father supply the core instructions that build every single bee. 



peterloringborst said:


> You can view selection on a spectrum ranging from simple natural selection, the survivors in the struggle of nature all the way to highly bred livestock which could not survive two days in the wild. In reality, organisms are the product of many influences, including climate, symbiotic relationships, and dumb luck.


The reality is they are the product of their inherited dna. No dna, no orgamism. Wrong dna, poorly functioning organism; etc etc.

Nothing you can add to that picture alters that. Parenthood is the major author of all qualities, traits etc.

Natural selection continually winnows out the poorer parents, accelerating mechanisms (like competitive mating) continually boost the better fitted genes. 

Those are the foundations Peter. They always remain true, despite what else is true. You can't take natural selection out of the picture just because there might be an epigenetic element. Inheritance remains, and any epigenetic factors will also be subjected to natural selecton.

Proper husbandry works with the fact of inherited principles. No amount of waffle is going to alter that fact.

Mike (UK)


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## Phoebee

mike bispham said:


> If you live in an area containing effective predators, the gentler characteristics have been removed from the population. Only hot bees get to make more bees.


And yet our mentor's hot bees are tame once moved to our protected apiary. So the "hot" behavior switches on and off as the bees sense they need it. Maybe because there is more survival benefit in killing yourself in defense of the colony _only when needed_, Even africanized bees can be gentle if you don't trigger their notoriously touchy defensive behavior.


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## mike bispham

Phoebee said:


> And yet our mentor's hot bees are tame once moved to our protected apiary. So the "hot" behavior switches on and off as the bees sense they need it. Maybe because there is more survival benefit in killing yourself in defense of the colony _only when needed_, Even africanized bees can be gentle if you don't trigger their notoriously touchy defensive behavior.


Hmm. Yes, that makes sense, but only in an ordinary way. I don't think you need to posit a complex explanation. 

Mike (UK)


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## mike bispham

peterloringborst said:


> "This problem of genetic diversity with bees in the U. S. has neither the support of our beekeeping scientists nor of the beekeepers themselves. Both seem content to solve the disease problem with “magic drugs”, an easier solution to the problem than the complexities of restoring the natural resistance bees have maintained on their own over their millions of years of existence. After 40 years of effort I have not succeeded in getting any cooperation from large queen breeders to help produce and perpetuate this diversity of genes for resistance and to make it available to the many beekeepers who may be interested."
> Gleanings in Bee Culture, December 1973, Page 381


Turkeys don't vote for Christmas. Rather, they spend large amounts of money devising and promulgating stories that promote their own interests.



peterloringborst said:


> [Cont.] "Perhaps we will have to wait until an epidemic of disease resistance or immunity to drugs threatens to wipe out beekeeping."


Then they'll just look for ways of making money out of that. Isn't liberal capitalism a great thing?

Mike (UK)


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## Phoebee

mike bispham said:


> Hmm. Yes, that makes sense, but only in an ordinary way. I don't think you need to posit a complex explanation.
> 
> Mike (UK)


Oooookay. I thought I was keeping things simple. You're offering the essays. 

But I might counter that there is nothing simple about life, and simple life has not been prevalent since stromatolites were the dominant life form.


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## Rader Sidetrack

mike bispham said:


> There's that 'work with' again. Again, can you tell us:
> a) your qualifications
> b) your job description.


Mike seems to have an obsession about qualifications and training. That is pretty funny since _his _seems to have been rather .... mmm ... _informal_!



mike bispham said:


> I grew up in a farming community. From countless conversations in pubs, on buses, by the side of the road, about dogs, horses, ferrets, cattle, sheep, ****erels, and much more I learned about breeding.
> 
> My interest in living things extended to reading Richard Dawkins' The Selfish Gene when I was in my early twenties, and discovering the wonder of the magic mechanisms of life. Fascinated, I read more about evolution, all the while marrying this with the understanding I had of stock keeping. I kept joining the dots. This was 40 years ago.
> 
> In the interim I've continued to learn about the processes and mechanisms of health-seeking natural selection through independent reading and study, and as part of a university degree.


I just quoted a part of the long post - you can read the rest by clicking the blue arrow at the top of the quote. Oh, and that 'university degree' that Mike has - my understanding is that it is in _Philosophy_.




:gh:


... don't those _pubs _lead to hangovers ...


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## mike bispham

Phoebee said:


> Oooookay. I thought I was keeping things simple. You're offering the essays.
> 
> But I might counter that there is nothing simple about life, and simple life has not been prevalent since stromatolites were the dominant life form.


Didn't mean to be rude Pheobee. In the context of the topic I thought it worth pointing out that there might be a relatively simple explanation. Ockham's razor and all that. 

Mike (UK)


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## Barry

mike bispham said:


> b) your job description.


Mike, you have heard of Google haven't you?

http://cornell.academia.edu/PeterLBorst
https://plus.google.com/100095840744292753146/about
https://plus.google.com/100095840744292753146/posts : 


> Peter L Borst commented on a video on YouTube. Shared publicly - Mar 4, 2014. I just want to comment that I am not a Dr. This is a misunderstanding. I have no degrees. You can call me Pete.﻿


http://peterloringborst.com/
http://www.youtube.com/watch?v=ZlOGUpkNbZo
http://www.vet.cornell.edu/biosci/people/staff.cfm - Technician IV

Perhaps Nick is his brother?

Couldn't wait on Rader anymore.


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## Phoebee

mike bispham said:


> Didn't mean to be rude Pheobee. In the context of the topic I thought it worth pointing out that there might be a relatively simple explanation. Ockham's razor and all that.
> 
> Mike (UK)


Ockham's Razor isn't a proof, its more, what ya might call a "guideline".

The simplest explanation for life is that God created it. The more complicated one is that it arose by billions of years of trial and error, in absolute violation of the laws of thermodynamics, creating order from random physics and chemistry. 

But genes are proven to exist and to carry the blueprints for life. So, back to William of Ockham's rule of thumb that the simpler explanation is more likely to be true, surely genes are just a simple set of instructions for building an organism, right?

The more science delves into the complexities, the more surprises we find. Ockham's razor would delude us. _ Modus ponens_ and_ modus tollens_ are more the rules of science. 

BS, Biology, Va Tech, 1975


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## jbeshearse

mike bispham said:


> If you live in an area containing effective predators, the gentler characteristics have been removed from the population. Only hot bees get to make more bees.
> 
> 
> 
> Yes.
> 
> Mike (UK)


That is a very inaccurate and short sighted view. Prey adjusts behaviors to overcome unacceptable/unsustainable predation. These adjustments do not require that the prey become overly defensive. It only requires an effective countermeasure. That can take the form of extra defensiveness, but it can also take many other forms that have nothing to do with guarding/physical repulsion. A few that come to mind are:

Co-existence with a protective/protector species
Inaccessible location
Camouflage
Mimicry

This is said just to highlight that HOT bees are not the only ones to survive. I am sure you are aware that there are stingless bees are you not?


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## mike bispham

jbeshearse said:


> That is a very inaccurate and short sighted view. Prey adjusts behaviors to overcome unacceptable/unsustainable predation.


That's a bit backwards. Natural selection locates the most effective response/s to predation. In the case of the honey, that's largely the sting. 



jbeshearse said:


> These adjustments do not require that the prey become overly defensive.


Not if there are equally effective alternatives, sure. But we're talking about the honeybee. Running away isn't an option for a colony. The sting has evolved because it is effective. The behaviours with which the bees use it, the same.



jbeshearse said:


> It only requires an effective countermeasure. That can take the form of extra defensiveness, but it can also take many other forms that have nothing to do with guarding/physical repulsion. A few that come to mind are:
> 
> Co-existence with a protective/protector species
> Inaccessible location
> Camouflage
> Mimicry


Again, we're talking about honeybees. Sure an inaccessible location is great - and honeybees will take advantage. Coexistence with skunks and bears - a symbiotic relationship? hasn't happened. Camouflage - yes, bees are fairly well camouflaged. Mimicry: nope; but other insects do mimic them.

Honey bees major defensive mechanism is their sting. And... if a large proportion of the gentler strains within a local population are removed by predators, those with more effective responses will tend to make up the population.

Its simple. Don't overcomplicate things.

Mike (UK)


----------



## peterloringborst

> Mike seems to have an obsession about qualifications and training.


I have tried to _Ignore_ the constant haranguing about credentials. It is an _ad hominem attack _to say that so and so isn't qualified to speak on such and such a topic. Any one can talk about these issues, any one is free to make mistakes. I do it all the time, that's how I learn.


----------



## jbeshearse

I suppose that is why the german black bee is almost non-existant in the US then, because it was too gentle.

You are simply wrong in this Mike, and the one that is a bit backwards. 

Feral honey bees most effective response to predation is structure within a tree high above the predators. Managed honey bees most effective response is gentleness to their keepers.

There are much better predatory escapes than the suicide that is required of the Honey bee sting.


----------



## mike bispham

Phoebee said:


> Ockham's Razor isn't a proof, its more, what ya might call a "guideline".


It suggests that we'll make best progress if we avoid positing unnecessary entities. 



Phoebee said:


> The simplest explanation for life is that God created it.


If you think that's an adequate explanation, fine. I don't. I like the alternative.



Phoebee said:


> The more complicated one is that it arose by billions of years of trial and error, in absolute violation of the laws of thermodynamics, creating order from random physics and chemistry.


I think if life violated the laws of thermodynamics the physicists might have noticed that by now, and bought it to the attention of the evolutionary biologists. I'd double-check your sources if I were you.



Phoebee said:


> But genes are proven to exist and to carry the blueprints for life. So, back to William of Ockham's rule of thumb that the simpler explanation is more likely to be true, surely genes are just a simple set of instructions for building an organism, right?


Ockham's Razor is, as you say, a rule of thumb to use in the formulation of hypotheses. Not a yardstick by which different explanations can be judged on the basis of simplicity alone. Come on Phoebee. 



Phoebee said:


> The more science delves into the complexities, the more surprises we find.


Twas ever thus. 



Phoebee said:


> Ockham's razor would delude us.


Only if we're applying it in the wrong sort of way. Without Ockham's Razor (used properly) there wouldn't be any science. 



Phoebee said:


> _ Modus ponens_ and_ modus tollens_ are more the rules of science.


I don't think there are any specific rules of science, other than the obvious: explanations must be logically consistent and agree with observation.



Phoebee said:


> BS, Biology, Va Tech, 1975


You have Bsc in Biology and you're moaning about 100 words being an 'essay'? You should try the Humanities!

Mike (UK)

BA Philosophy, University of Kent (UK) about 6 years ago.


----------



## mike bispham

jbeshearse said:


> Feral honey bees most effective response to predation is structure within a tree high above the predators. Managed honey bees most effective response is gentleness to their keepers.


Think about this: managed bees, bred for gentleness, breed wth feral bees , who (in some locations) rely on strong responses. What happens to the feral bees? 



jbeshearse said:


> There are much better predatory escapes than the suicide that is required of the Honey bee sting.


Sacrifice of one of many individuals is a very effective strategy. And don't forget there is no genetic cost, no evolutionary cost - the stinging worker was never going to pass on her genes anyway. 

Mike (UK)


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## USMCEOD

jbeshearse said:


> You are simply wrong in this Mike, and the one that is a bit backwards.


I don't have a degree, but I have found that there is something about natural selection... Dead bees don't pass on their genes....
In my backyard, if a hive dies from the environment, pests, whatever.. they are dead and will not propagate. If a hive is overly aggressive, I kill the queen and they will not propagate.. so, as I see it the strong or the ones who adapt survive.

I have been all over the world, and I love the British, they are always so, Imperial...:applause:


----------



## Phoebee

Mike,

I certainly am no creationist. I'm pointing out that creationists like the argument that the simplest explanation for life is that God created it. They'll cite Ockham's Razor: http://creation.com/occams-razor-and-creation-evolution

Physicists have problems with the laws of thermodynamics. Life is one of them. Creation is another. Most physicists and cosmologists accept the Big Bang, which is a violation of every conservation law they ever formulated, plus the laws of thermodynamics, plus the Special Relativity, plus ....

As for 100 words being an essay, don't get me started. I'm a writer and I come in to my own at around 20,000 words (novella length).

I said, "_Modus ponens_ and _modus tollens_ are more the rules of science." You said "I don't think there are any specific rules of science, other than the obvious: explanations must be logically consistent and agree with observation." _Modus ponens_ and _modus tollens_ are fundamental rules of schoolman's logic (I learned this in a _philosophy_ course), taught as foundations of logical argument for at least a thousand years. Science grew from this sort of rigorous logical proof. Science very much DOES have rules. And careful observation is the challenge that will prune away any incorrect rules.

Reading your responses it becomes clear to me that you could do with reading the others with a bit more patience and depth. You are assuming we believe one thing when a more careful reading would suggest we believe the opposite.


----------



## peterloringborst

> it can also take many other forms that have nothing to do with guarding/physical repulsion.


This is correct. Tropical honey bees deal with predation by absconding or migrating. Many other examples could be named. Survival of the fittest never meant the survival of the meanest. Each organism expresses fitness in its own way; it fits. 

Reminded me of this:


> How flowers changed the world / essay by Loren Eiseley ; photographs by Gerald Ackerman.


----------



## Lauri

I've got no time to read all the comments here at this moment, but thank you peterloringborst for your suggestion. I've got the new and improved version in my Amazon cart. 
Going hunting in a wall tent for 2 weeks soon..No phone, no lights, no motor car-not a single luxury...

I need reading material!


----------



## snl

Lauri said:


> No phone, no lights, no motor car-not a single luxury...


Sounds like the song from "Gilligan's Island!"


----------



## JWChesnut

Michael Johnston said:


> It's really hard for any beneficial old genes to disappear when a queen is mating wit around 16 drones. The system of haplodiploidy will make some deleterious genes disappear because the haploid drones with bad genes will be less fit for mating - good riddance to those genes. Inbreeding is prevented because a bee larvae with identical sex alleles will become a sterile drone. I would like to know how fast mutations occur in the bee genome leading to new genes.


Bee's are accumulating new alleles (polymorphisms) at a very rapid (almost unprecedented) rate. ( I will edit this post with a downloadable citation to this from a European DNA study).

Bee's can accumulate polymorphisms because unlike breeding systems with "one man and one woman", bees have evolved a very specialized system of one woman and "20 gametes from a grandmother". This mean that bad genes are not lethal -- the colony/superorganism trucks on just as always, unless the bad allele is so lethal that the drone (gamete bearing) cannot fly.

Bee's have substituted high polymorphism, high polyandry as a substitute for classical fitness. It is the "portmanteau" strategy --- you throw everything into a steamer trunk, and carry it all along just in case any of it is needed. The allele that might be piss poor in Finland, will prove glorious in Serbia, the strategy of accumulating everything and never throwing any of it away, is what allows the bee's to remain fit across whole continents.

Eusociality and haploid polyandry are very rare -- and for good reason -- it is hard to evolve, because fitness pressures are diluted in the haploid system. Sin qua non, Bee's resist evolving (speciating) because to do so would initiate a specialization race with flower coevolution. They however need to make accommodations to their environment, the synthetic substitute derived in the breeding system is to accumulate the contributions of many, many fathers-- and each father sires a small portion of the nestmates, meaning a dozen or more sub-lineages all contributing some increase in fitness.


----------



## peterloringborst

> I've got no time to read all the comments here at this moment,


Yeah, sorry. I created this thread because the one I was on was hijacked. There seems to be a pack of dogs that follows me everywhere, barking as loudly as they can. Enjoy the peace while it lasts!


----------



## peterloringborst

> Eusociality and haploid polyandry are very rare


Not sure why you would suggest that a system that is found in ants, bees and wasps is rare. Reminds me of the statement made by a friend of mine that four leaf clovers were common. I have spent a whole afternoon looking for one, and not found it. On the other hand, I can pretty quickly find an ant, wasp or bee.


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## USMCEOD

peterloringborst said:


> Yeah, sorry. I created this thread because the one I was on was hijacked. There seems to be a pack of dogs that follows me everywhere, barking as loudly as they can. Enjoy the peace while it lasts!


Don't bee sorry, I for one like different points of view, it's the autocrats that suppress opinions and responses. I have been told that this is the way of forum discussion. I am still a novice beekeeper at best, I have small hive beetles that I fight all the time. I enjoy beekeeping and studying beekeeping, it is a way for me to put what I learn to practical use. As I stated, I don't have a degree, my profession does not have a college, I am an Explosive Ordnance Disposal Technician... I teach at the EOD school, so I guess you could say that I am a Professor at the University of Bombs and Bullets. I am allergic to bee stings, I swell up. 
Thank you for sharing, I learn from people like you, the others I dismiss.


----------



## Phoebee

Aha! As I understand it, bees can be trained quite quickly to detect explosives, so maybe there's some opportunity between your profession and your hobby.

The fact that bees can be trained to sniff out something so foreign to their needs as explosives fascinates me. They are obviously capable of greater shifts in behavior than one would expect of organisms viewed as simple automata. One would expect, in the simple view, that they would respond to their own pheromones and to floral scents, and might not even be wired to recognize chemical smells, much less learn to associate them with reward.


----------



## USMCEOD

Yes, due to the dangers of the world, they are trying all sorts of things for detection. I have read the reports, and it is interesting... I just don't know how practical it will be on a large scale. But, you are right bees have a lot more going on than we think, pretty sure you can't train a grasshopper...HaHa


----------



## Lauri

snl said:


> Sounds like the song from "Gilligan's Island!"


Yes sir! Now that song is going to play in your head all day


----------



## JWChesnut

peterloringborst said:


> Not sure why you would suggest that a system that is found in ants, bees and wasps is rare. ...I can pretty quickly find an ant, wasp or bee.


Peter,
Consider the universe of insects -- the eusocial pattern is very restricted within that universe.
Consider the universe of wasps and bees --- the eusocial pattern is restricted to just a few genera -- most bees and wasps are strictly solitary, some have hibernating queens with a colony of annual workers, some spp. overwinter with larvae in diapause. 
Ants and termites, bless them, are the exception -- they are strongly social. However, not all ants are polyandrous. One of the long running debates in evolutionary entomology concerns the relative fitness of polyandrous ants vs. polygynous ones (colonies with multiple reproductive females).

The correct frame of reference for my comment is the pollination guild of bees. In that, solitary bees dominate by any measure vs. the social ones.

Viz: http://books.google.com/books?id=lj...0CHwQ6AEwCQ#v=onepage&q=ant polyandry&f=false


----------



## peterloringborst

> The fact that bees can be trained to sniff out something so foreign to their needs as explosives fascinates me.


The way it is done is to train them with sugar syrup that has the odor of explosives. So they associate the odor with food. In the real world, there are hundreds of thousands of different smelling flowers, some with food for bees, some not. It would be no use for them to only go to certain smells and not others. What they can do is to learn to associate odors, colors, etc. with rewards. Then they seek those cues, instead of looking for new sources every day. Unfortunately, they don't seem to be able to learn the concept of danger. They often fly into vats of hot syrup or honey.


----------



## peterloringborst

> In that, solitary bees dominate by any measure vs. the social ones.


Quite. It doesn't matter really, the eusocial system is marvelous whether rare or ubiquitous.


----------



## Phoebee

peterloringborst said:


> The way it is done is to train them with sugar syrup that has the odor of explosives. So they associate the odor with food. In the real world, there are hundreds of thousands of different smelling flowers, some with food for bees, some not. It would be no use for them to only go to certain smells and not others. What they can do is to learn to associate odors, colors, etc. with rewards. Then they seek those cues, instead of looking for new sources every day. Unfortunately, they don't seem to be able to learn the concept of danger. They often fly into vats of hot syrup or honey.


I have a motto I stole from Robert Heinlein.

_A human being should be able to change a diaper, plan an invasion, butcher a hog, conn a ship, design a building, write a sonnet, balance accounts, build a wall, set a bone, comfort the dying, take orders, give orders, cooperate, act alone, pitch manure, solve equations, analyze a new problem, program a computer, cook a tasty meal, fight efficiently, die gallantly.

Specialization is for insects._

Bees are generalists in a superclass of specialists. If I recall correctly, the most sensitive sense of smell known to science is possessed by an insect. However, that insect can only smell one thing, the sex attractant pheremones of the females of its species. I expect the general trend of insects is to be wired to only detect odors relevant to them. 

I'm hardly disagreeing with what you say, but to me this generalist ability is just _way cool!_

To which we might say for bees, they can nurse, cooperate on a robbing party, design and build comb, communicate with dance, kick out the sick, bake bee bread, prepare honey, navigate to distant forage, cooperate, act alone, fight (clumsily), and die gallantly.


----------



## JWChesnut

Bees learning to detect danger:
http://www.sciencedaily.com/releases/2014/04/140429205823.htm

In the context of the superorganism, bees detect danger by foragers dieing before returning to the nest, thus extinguishing the discovery, and eliminating recruitment. The evolved need to have forager recruitment reoccur daily is a mechanism of evolved fitness to avoid lethal attractants. How bees can avoid pesticides in otherwise hyper-toxic environments.


----------



## JWChesnut

Phoebee said:


> Bees are generalists in a superclass of specialists


This is no accident. It is a function of the breeding system. The breeding system mitigates against rapid selection and speciation. Consequently, Flowers which depend on bees for pollination evolve more quickly -- converging towards a generic nectar, pollen and design. This reinforces the fitness of the "generalist" strategy.

The generalist conservatism of the honeybee conditions its environment, but cripples its ability to rapidly evolve. The bee has substituted an ever more energetic polyandry to incorporate more and more genetic variation into its superorganism. This is similar to plants that when stressed become polyploid species -- many desert impacted species are the triploid to 8x chromosome parallel of a 2x species from a moderate environment. Having 15 fathers in the superorganism is functional equivalent of polyploid.


----------



## Richard Cryberg

Phoebee said:


> The simplest explanation for life is that God created it. The more complicated one is that it arose by billions of years of trial and error, in absolute violation of the laws of thermodynamics, creating order from random physics and chemistry.


All thermo says is if you have a closed system and that system has matter in it with greater than zero point energy and that matter does work the disorder of the system will increase if you look long enough. Life does not violate this statement in any way any more than crystals forming from a solution or charging a battery violates the statement. I realize you are trained in biology rather than a rigorous science but that is no excuse to lie about what thermo says.

I became a scientist to learn how God did his job. Religions, in general, tell God how he had to do his job. Religions have much larger egos than mine.

Dick


----------



## peterloringborst

If you aren't convinced yet of the outdatedness of 20th century biology



> In a recent book, _Evolution: A View from the 21st Century_, ]ames Shapiro
> has used a systems biology approach to the structure and activities of
> the genome to argue forcefully and convincingly that what we have learned
> about cells and their sensory, communicative, and information-processing
> capabilities makes the twentieth-century view of evolution through the
> natural selection of random mutations with small effects hopelessly inadequate.
> 
> He backs up his argument with a huge amount of old and new
> data showing that natural genetic engineering is part and parcel of all living
> organisms, and that, in Barbara McClintock's words, the genome is a very
> dynamic "organ of the cell." Using a computer analogy, he concludes that
> we must change our view of the genome from that of a "read only memory
> system (ROM)," subject only to accidental changes, to that of a "read-write
> (RW) memory organelle" in which existing information can be modified
> and into which new information can be inscribed.


----------



## peterloringborst

A little bit about life and its relation to entropy:



> What is entropy? Simply put, it is a measure of the orderliness of a physical system. States of low entropy are ‘highly ordered’ in something very like the everyday sense of the phrase. Picture a tidy desk, papers neatly stacked, pens in the pot. As order decreases and the desk gets messier, entropy increases.
> 
> Now, suppose that every possible arrangement of the desk is equally probable (perhaps your way of cleaning up is to take the whole room and shake it). There are of course vastly more ways to be messy than there are to be tidy – so the chances are high that your desk is messy. After all, the messy states outnumber the tidy ones. The weight of numbers is on the side of messiness. What’s more, any random change to the arrangement is likely to make it even messier. Now, random changes, in the form of bumps and jiggles, happen constantly. So things get more stable (and messier) over time. As the Universe undergoes change, entropy increases.
> 
> High entropy and low energy, however, are just one manifestation of stability. Does nature offer others? It does. It turns out that stuff can be highly persistent even when it is highly unstable energetically. Indeed, that’s precisely what we find in the world of replicators.
> 
> Living things are low-entropy and energy-consuming, so they are unstable in the thermodynamic sense. Nevertheless, they can still be remarkably stable in the sense of persisting over time. Some replicating populations (certain bacterial strains, for example) have maintained themselves with little change over astonishing periods – millions, even a billion, years.


Life’s restlessness, by Addy Pross

http://aeon.co/magazine/nature-and-cosmos/stability-how-life-began-and-why-it-cant-rest/


----------



## JWChesnut

peterloringborst said:


> James Shapiro says:....


Even handed but fundamentally dismissive review:
http://gbe.oxfordjournals.org/content/early/2012/01/24/gbe.evs008.short

I am unconvinced by the folk PLB trots out trying to upset the applecart of the Darwinian synthesis.


If you are tired of the polite and evenhanded, here's a bomb throwing dismissal of Shapiro
http://whyevolutionistrue.wordpress.com/2012/12/02/james-shapiro-gets-evolution-wrong-again/


----------



## peterloringborst

> I am unconvinced by the folk PLB trots out trying to upset the applecart of the Darwinian synthesis.


Just how does a statement like this advance a discussion? "Trots out"?

And what do you mean by "folk"? These are reputable scientists respected in their field. Why would you refer to them as "folk", if not to disparage them. And why disparage them, and not just their ideas.


----------



## peterloringborst

In the review you cite:



> The argument is thought-provoking and the range of findings described, to support it, should be of interest to all cellular, developmental and evolutionary biologists. There are, however, some counter-arguments to be made to the general thesis or, at least, caveats to be registered.


That's all I said: it was thought provoking and there are many counter arguments to be made. There is no one evolution; evolution has many paths, some more fruitful than others. I am not trying to trash people's cherished ideas, but to expand them. Why the hostility?



> We do not see changes in ways of thinking in biology in terms of
> Kuhnian paradigm shifts, but the approach that we advocate does require
> extensions of evolutionary theory. Obviously, our conviction that changes
> are needed does raise the hackles of those biologists and philosophers of
> biology who maintain that the last foundational words about evolutionary
> theory were said more than 60 ago by the architects of the Modern Synthesis.
> 
> They genuinely believe that all of the last half century's developments
> in biology can be comfortably accommodated within the neo-Darwinian,
> gene-centered framework that we described in chapter 1. Since we think
> that a constructive response to these defenders of orthodoxy is more useful
> and interesting than a deconstruction of their position, we will start with
> what we see as the necessary extensions to the twentieth-century version
> of Darwinism. -- Jablonka & Lamb (2014)


----------



## mike bispham

Phoebee said:


> To which we might say for bees, they can nurse, cooperate on a robbing party, design and build comb, communicate with dance, kick out the sick, bake bee bread, prepare honey, navigate to distant forage, cooperate, act alone, fight (clumsily), and die gallantly.


Bees are often described as 'social' insects. There is an important sense in which this is untrue and misleading. The unit of reproduction is a colony. That, which can be reduced to the queen, is the individual.

Now neither queens nor colonies help other queens or colonies. They don't, as you put it, "nurse, cooperate on a robbing party, design and build comb, communicate with dance, kick out the sick, bake bee bread, prepare honey, navigate to distant forage, cooperate, act alone, fight (clumsily), and die gallantly" as brave bands of colonies. 

All these things happen only within what is effectively a single organism, or 'super-organism'.

In this sense then, there is no group level in which social behaviour can take place. And the evolutionary advantages of being part of a group - the 'social' advantages that you list - cannot come into play.

Mike (UK)


----------



## mike bispham

JWChesnut said:


> In the context of the superorganism, bees detect danger by foragers dieing before returning to the nest, thus extinguishing the discovery, and eliminating recruitment. The evolved need to have forager recruitment reoccur daily is a mechanism of evolved fitness to avoid lethal attractants. How bees can avoid pesticides in otherwise hyper-toxic environments.


A good point, but the mechanism is only useful where the pesticide effect is instant. Its no defence against 'sub-lethal' effects. Does the paper point that out?

Mike (UK)


----------



## mike bispham

JWChesnut said:


> Bee's have substituted high polymorphism, high polyandry as a substitute for classical fitness. It is the "portmanteau" strategy --- you throw everything into a steamer trunk, and carry it all along just in case any of it is needed. The allele that might be piss poor in Finland, will prove glorious in Serbia, the strategy of accumulating everything and never throwing any of it away, is what allows the bee's to remain fit across whole continents.
> 
> They however need to make accommodations to their environment, the synthetic substitute derived in the breeding system is to accumulate the contributions of many, many fathers-- and each father sires a small portion of the nestmates, meaning a dozen or more sub-lineages all contributing some increase in fitness.


JW, would you say there was anything inconsistent between these statements and Manley's approach to apiary health?

""In most farm stock stress is laid particularly on the male because he may
sire a large number of offspring, whereas the direct progeny of the
female are very limited in number. Now we breeders of hive-bees
have the great advantage over those who have to do with most
domestic animals in that from one desirable breeding queen we can
readily produce a virtually unlimited number of young queens.
Though in a state of nature a honey-bee queen would only produce
half a dozen or so daughter queens, and maybe a couple of thousand
drones, in the hands of a competent breeder she can be made to give
an almost unlimited number of both.

It is usually considered that too much in-breeding may lead to
deterioration in the stamina and fecundity of animals, though about
this there is some disagreement. When there is no trace of any bad or
degenerate strain in the stock, in-breeding does no harm, I think; but
unless one is quite sure that this is the case, it is probably better to
arrange, as far as possible, in our breeding apiaries, that the drones
flying there shall be produced by queens of the very highest
character, while the young queens with which they are expected to
mate shall be derived from breeder queens of a different strain, but
equally outstanding qualities. In this way, although it is impossible to
be certain that all matings will be as desired, yet it can be managed
that a very large proportion of our young queens will be the product
of the male and female parents from which we wish them to be
derived."

R.O.B. Manley, Honey Farming, page 62 of the pdf, 83 of the book
http://www.biobees.com/library/gener...gROBManley.pdf 

Its worth bearing in mind Manley's biological understanding was limited - he didn't know of multiple matings. It was empirical - he had extensive experience of what worked, and was, as he shows, familiar with with the traditions of genetic husbandry.

This describes the foundational method of bee husbandry still practiced by bee breeders the world over - whether as breeder-keepers or specialist breeders (though some specialist breeders will try to control drone input with AI - Manley doesn't). 

So I'm interested to know just what you think is wrong with it.

Mike (UK)


----------



## mike bispham

peterloringborst said:


> If you aren't convinced yet of the outdatedness of 20th century biology [:"In a recent book, Evolution: A View from the 21st Century, ]ames Shapiro
> has used a systems biology approach to the structure and activities of
> the genome to argue forcefully and convincingly that what we have learned
> about cells and their sensory, communicative, and information-processing
> capabilities makes the twentieth-century view of evolution through the
> natural selection of random mutations with small effects hopelessly inadequate."


Do dead individuals mate?

Do less fit individuals produce more sucessful offspring (ceteris patribus) than fitter ones?

Has natural selection for the fittest strains gone away as description of the basic mechanism of natural population shaping? 

The answer to all those questions is no. If you think otherwise, I'd love to hear your reasoning. 

Bear in mind too (and this applies to you as well I think JW) as we have these conversations: evolution works on many levels simultaniously. What concerns us here, as beekeepers and husbandrymen is not the creation of new species, nor even new behaviours by mutations - which is what your quote addresses.

_It is the day-to-day, generation-to-generation effect of the removal from breeding populations of the genes of the least fit, and the promotion of the genes of the more fit. _

That is a form of evolution, and over time it can reshape populations dramatically. But its also an essential short-term acting mechanism that maximises fitness continually. And it is the part of evolution that is of special interest to husbandrymen. Natural selection maintains health and vitality in populations at the local level by these means. 

Husbandrymen copy the process and thus reduce natural wastage and improve yields. It's the most fundamental aspect of farming, its what organic husbandry 'is'.

That's all. It isn't complicated. Don't blind yourselves with unnecessary science.

Mike (UK)


----------



## mike bispham

peterloringborst said:


> Just how does a statement like this advance a discussion? "Trots out"?


Why do the words 'pot', 'kettle' and 'black' come to mind?

Mike (UK)


----------



## mike bispham

peterloringborst said:


> That's all I said: it was thought provoking and there are many counter arguments to be made. There is no one evolution; evolution has many paths, some more fruitful than others. I am not trying to trash people's cherished ideas, but to expand them. Why the hostility?


On my part: it is because you present these things as counter-arguments to the standpoints of others, when they are nothing of the kind. You make statements like 'anyone who still thinks 20th views of evolution are relevant is an idiot', then throw some cutting-edge piece of writing at us with the clear implication that that supports your statement. In short you repeatedly try to 'blind us with science'. 

It isn't helpful. 

Helpful would be engaging in the low-level arguments that we make against your positions. Try for example tackling #65 above properly. Address the actual questions in a sraightforward way - or say why you think they cannot be addressed in a straightforward way. Critique the statements properly - with reasoning given.

Mike (UK)


----------



## peterloringborst

> You make statements like 'anyone who still thinks 20th views of evolution are relevant is an idiot'


I never made any such statement. However, I wish you would stay out of the discussion. You have attempted to hijack every thread I have started. Fortunately, I don't have to read all of your blather, but it makes it difficult for others who haven't learned to _ignore you_


----------



## peterloringborst

> Eva Jablonka is not a "crank", but her claims are dubious.


In response to this I asked, what claims? All of them? You seem to be content to dismiss the work of Jablonka and Shapiro on the basis of the fact that others have dismissed them, but what is it that you actually object to? I mean, actual examples of their dubious claims.


----------



## JWChesnut

mike bispham said:


> So I'm interested to know just what you think is wrong with it.
> Mike (UK)


Mr. Bispham,
There is nothing wrong with the slow, exacting practice of selective husbandry. This is not an either/or proposition. The point I have tried to impress on you, and the effort I have abandoned only to get dragged back into the fray is: "In bees, it ain't that easy".

You report selecting 3 or 4 breeder queens. In population biology, we model extinction probabilities for pops under 50 -- they increase dramatically as deleterious combination are expressed with greater frequency. Trying to breed fitness starting from the hives in a backyard is a nearly hopeless proposition. Look at the reported success to the BeeWeaver queens, they trialed (tens of) thousands of colonies to secure a modicum of resistance.

It ain't that easy in bees, 'cause unlike breeding poodles, bees have strong mechanisms in place to normalize the genome. Rather than a dead colony, its a dead horse I've been beating for your edification -- The ecological imperative of bees is constancy -- and selection for that strategy mitigates *against* maintaining artificial and highly derived gene combinations.

My suggestion to you is to avoid the classic pitfall of the auto-didact, and learn from others rather than lecturing them.


----------



## JWChesnut

Peter:
Both these authors have thrown bombs at the Darwinian synthesis. Wasn't Jablonka original popular book subtitled "The Lamarckian Dimension"? She is trolling for a reaction.

Shapiro has utterly lost sight of the the relative importance of the natural selection process in promoting the inchoate idea that cells are "engineering" their own self-improvement. Cells are imbibed with self-directed intelligence -- how is that?

Both of these authors ignore the established ecological principle that plasticity --- phenotype variation --- is a naturally selected fitness mechanism. Some species are "brittle" and some species have broad and rapid mutations. The response to Jablonka is that she is elevating the proximal -- behavioral variation absorbed and encoded by the selected genome specific to the fitness of the species -- into its own process.

I would suggest you read the enormous skeptical literature in response to both these authors before you elevate their ideas to that of a Kuhnian revolution. Serious scientists have spent serious efforts reviewing and explaining their thesis and the limits to them. Feigning hurt feelings 'cause I use words like "trot" isn't debate, but preening.

Here's a wonderful review of the collected papers from a symposium Jablonka organized on Lamarck: http://dash.harvard.edu/bitstream/handle/1/9131556/lamarck_ascending.pdf?sequence=1 I find the review interesting because it places the philosophica/theological imperative of the Neo-Lamarckians in poetic context.


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## peterloringborst

> I would suggest you read the enormous skeptical literature in response to both these authors before you elevate their ideas to that of a Kuhnian revolution. Serious scientists have spent serious efforts reviewing and explaining their thesis and the limits to them.


Didn't I just say : _We do not see changes in ways of thinking in biology in terms of Kuhnian paradigm shifts_? Further, I am not promoting the theses of Shapiro and Jablonka, but holding them out as examples of how the field of genomics is changing, based upon new information. 

See also




> First the ‘Weismann barrier’ and later on Francis Crick’s ‘central dogma’ of molecular biology nourished the gene-centric paradigm of life, i.e., the conception of the gene/genome as a ‘central source’ from which hereditary specificity unidirectionally flows or radiates into cellular biochemistry and development. Today, due to advances in molecular genetics and epigenetics, such as the discovery of complex post-genomic and epigenetic processes in which genes are causally integrated, many theorists argue that a gene-centric conception of the organism has become problematic.
> 
> From DNA- to NA-centrism and the conditions for gene-centrism revisited
> Alexis De Tiege • Koen Tanghe • Johan Braeckman • Yves Van de Peer
> Published online: 6 July 2013


See also



> Natural selection provides feedback through which information about the environment and its recurring challenges
> is captured, inherited, and accumulated within genomes in the form of variations that contribute to survival. The
> variation upon which natural selection acts is generally described as “random.” Yet evidence has been mounting
> for decades, from such phenomena as mutation hotspots, horizontal gene transfer, and highly mutable repetitive
> sequences, that variation is far from the simplifying idealization of random processes as white (uniform in space and
> time and independent of the environment or context)--
> 
> In _Darwinian evolution, feedback from natural selection leads to biased mutations_ Lynn Helena Caporale and John Doyle


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## Michael Johnston

I am hoping that JWChesnut can post the citation to which he alluded concerning the development of new genes in the honeybee genome. Here is his quote:
_Bee's are accumulating new alleles (polymorphisms) at a very rapid (almost unprecedented) rate. ( I will edit this post with a downloadable citation to this from a European DNA study)._


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## JRG13

Problems with aggressiveness, we don't understand all the triggers aside from the genetics. Often breaking up a large aggressive colony into smaller nucs can calm them down for a time, some even say sometimes just introducing the right queen immediately caused the bees to be gentle, there's a lot of chemical signalling involved within a colony that we have yet to understand let alone map pathways back to heritable traits. You can quote 'learned' responses, but looking at the life cycle or life span of a bee, it's hard to make that connection of individual bees learning new responses and passing it on, yet colony mechanics as a whole seem to contradict that statement at times.


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## peterloringborst

> Problems with aggressiveness, we don't understand all the triggers aside from the genetics.


Precisely. Often we have heard, "I requeened the hive and right away it settled down." I used to dismiss this as uninformed, since it takes a month or two for the new bees to replace the old. But -- if the queen somehow regulates the temperament of the colony, that would give an explanation to what some people have observed. Or, to put it more scientifically, the queen may produce pheromones controlling behavior or quite possibly RNA that controls gene expression in workers. Obviously, this would not be heritable through the workers, since they don't reproduce, but altered gene expression could be passed from colony to colony (epigenetic inheritance).


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## Saltybee

peterloringborst said:


> I used to dismiss this as uninformed,


You are not the only one who should consider whether that is a genetic or learned behavior. I try to reflect on that tendency within myself.


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## mike bispham

peterloringborst said:


> I wish you would stay out of the discussion.


I'm sure you do! Then you could carry on pretending to be a scientist! 



peterloringborst said:


> You have attempted to hijack every thread I have started.


I don't hijack. I ask simple questions (usually the same simple question) which you refuse to address - probably because you know the only acceptable answer will also require your eating a vast amount of humble pie.

There's a way to be wrong Peter. Fess up quick and move on. You're a living example of how not to do it.

Come on, bite the bullet, get it over with. Post #65 above....



peterloringborst said:


> Fortunately, I don't have to read all of your blather, but it makes it difficult for others who haven't learned to _ignore you_


Characterising my imput 'blather' and asserting that others should ignore me is as good a form of ad hominem as any. Its no good Peter - its useless saying I'm wrong. You have to say _why_ I'm wrong! You have to _show_ I'm wrong.

Anything else is for the playground.

Mike (UK)


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## mike bispham

JWChesnut said:


> Mr. Bispham,
> There is nothing wrong with the slow, exacting practice of selective husbandry. This is not an either/or proposition. The point I have tried to impress on you, and the effort I have abandoned only to get dragged back into the fray is: "In bees, it ain't that easy".


JW (if you tell me you first name I'll call you that; then could we get over the passive-aggressive use of formal names?) - I think perhaps we should look more closely at that 'it' of yours. Just what is 'it' that isn't easy?

Are we both talking about the same 'it'?



JWChesnut said:


> You report selecting 3 or 4 breeder queens. In population biology, we model extinction probabilities for pops under 50 -- they increase dramatically as deleterious combination are expressed with greater frequency.


'we' in population biology eh? Could you possibly let us have your qualifications, the places you earned them, and your job description? Last I asked you'd learned your stuff from an pre-war chicken feather farmer, trying to make things sound hard to dissuade competitors.

To your point: I'm not sure you've said anything there until you attach figures to those statements. But bear in mind: I'm not taking '3 or 4 'breeder' queens and re-queening the whole apairy from them. I'm replacing the lower 25% or so. I'm also making increase from the next 3 or 4 best looking queens. I'm bringing in more locally adapted varroa resistant swarms too. And I'm open mating, hoping to get reasonable strikes from a good enough percentage of varroa my and feral resistant drones. So talk of concetration leading toward extinction is way off the mark. 'Your' models simply don't apply.



JWChesnut said:


> Trying to breed fitness starting from the hives in a backyard is a nearly hopeless proposition. Look at the reported success to the BeeWeaver queens, they trialed (tens of) thousands of colonies to secure a modicum of resistance.


They didn't have the advantage from the outset of locally adapted varroa resistent ferals. (When you say 'fitness' I'm guessing you mean 'fitness' toward the number 1 health problem of late - varroa)



JWChesnut said:


> It ain't that easy in bees, 'cause unlike breeding poodles, bees have strong mechanisms in place to normalize the genome.


Tell me why I should listen to you rather than Ruttner, Manley, Michael Palmer, Michael Bush, Adam Finkelstein, John Kefuss, Marla Spivak, Francis Ratneiks and others. Why should I listen to your theories when they conflict with the evidence of my own eyes?



JWChesnut said:


> Rather than a dead colony, its a dead horse I've been beating for your edification -- The ecological imperative of bees is constancy -- and selection for that strategy mitigates *against* maintaining artificial and highly derived gene combinations.


Your theory might be well and good at some level of the evolutionary game, but my bees and many other very well qualified people tell a story that suggests that, whatever merits it might have, being applicable at the level of husbandry isn't one of them. 

We're not trying to change bees for all time JW. Just trying to work with natural selection to raise and maintain resistance to a parasite, and press for productivity while we're at it. Just as soon as we stop all our work will fade back into the ambient population. We know that.

To make this clearer for you; why don't you try taking The Loring Borst Test. Address the questions in post #65 above.



JWChesnut said:


> My suggestion to you is to avoid the classic pitfall of the auto-didact, and learn from others rather than lecturing them.


Happy to. But I'll choose 'others' whose words make sense in the context of my knowledge and experience thanks.

Mike (UK)


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## Saltybee

Maybe skunks are scratching Mikes door or he is in a dearth.


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## mike bispham

Saltybee said:


> You are not the only one who should consider whether that is a genetic or learned behavior. I try to reflect on that tendency within myself.


Just Nature vs Nurture eh? Aren't we supposed to include these newfangled factors as well now?

Mike (UK)


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## Barry

mike bispham said:


> JW (if you tell me you first name I'll call you that;


Just call him "John."


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## peterloringborst

Ever since Barbara McClintock discovered transposable mobile genetic elements, people have stopped regarding the genome as inviolable. (Barbara McClintock's discovery of these jumping genes earned her a Nobel prize in 1983.)



> The DNA serves as a stable information storage medium and every protein which is needed by the cell is produced from this blueprint via an RNA intermediate code. More recently it was found that an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on RNA transcripts. Natural genome editing on one side is the competent agent-driven generation and integration of meaningful DNA nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing on the other side designates the integration of all RNA activities acting on RNA transcripts without altering DNA-encoded genes. If we take the genetic code seriously as a natural code, there must be agents that are competent to act on this code because _no natural code codes itself as no natural language speaks itself._ -- Witzany, G. (2011). The agents of natural genome editing. Journal of molecular cell biology, mjr005.


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## peterloringborst

So, Mr. Chesnut is right, a lot of the ideas I have put forth are speculative and in dispute. I never denied that. What I was trying to show is that the whole field is in upheaval and it is changing faster than any of us can follow. However, there is new stuff that has an immediate impact on honey bee breeding. The goal of any bee breeding should be improved bee health. We have already seen how livestock that is bred solely for productivity generally is unhealthy and requires expensive inputs to maintain. On the other hand, wild types may not be productive enough to be even marginally profitable. There is some evidence of this with bees. The bees of Gotland were found to be mite resistant but the colonies stayed small and generally did not produce much surplus. For the purposes of honey bee conservation, these colonies might be ideal but as livestock, maybe not.



> Behrens et al. (2011) described honey bee populations from the island of Gotland, Sweden, that survive mite infections and performed QTL mapping for this trait. Parasitised and non-parasitised drones were separated, and the genome was screened for potential QTLs using a total of 216 microsatellite markers. Three candidate target regions were found on chromosomes 4, 7, and 9, but the strong epistasis among these three loci complicated application in a breeding programme.


Now this paragraph requires a little explaining. QTLs are what the average person calls genes. It stands for qualitative trait locus, which means that the trait seems to be linked to that part of the genome. So they found 3 possible QTLs (genes) but they found _epistasis_. This means the genes were linked in some way so that one has an inhibitory effect on another, such that selection for the one suppresses another. All the same:



> We have found specific gene variants that have a major impact on the mechanisms of behavioural resistance to ￼Varroa mites. These results suggest that it should be possible to select for resistance traits in bees through a simple genotyping assays in the future. In addition, it is important to identify the genes and specific causal mutations to obtain a better understanding on how these affect innate immunity in bees.


What this says is that there be mite resistant mechanisms that can be selected for, but that it is just as important to focus on immunity in general. Were it not for the viruses vectored by mites, their effect might be far less. At the same time, if bees were affected less by the viruses, mites would be less of a problem. The question is not whether mite resistant traits exist but how to propagate them.

REF:
Genetic bases of tolerance to Varroa destructor in honey bees (Apis mellifera L.)
E. Zakar • A. Ja ́vor • Sz. Kusza Insect. Soc. (2014) 61:207–215


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## JWChesnut

For Michael Johnston

Exceptionally high levels of recombination across the honey bee genome
http://genome.cshlp.org/content/16/11/1339.short

Unusually High Recombination Rate Detected in the Sex Locus Region of the Honey Bee (Apis mellifera) 
http://www.genetics.org/content/153/4/1701.short


Linkage Map of the Honey Bee, Apis mellifera, Based on RAPD Markers
http://www.genetics.org/content/139/3/1371.short


Comparative Linkage Mapping Suggests a High Recombination Rate in All Honeybees
http://jhered.oxfordjournals.org/content/101/suppl_1/S118.short

Variation in genomic recombination rates among animal taxa and the case of social insects
http://www.nature.com/hdy/journal/v98/n4/abs/6800950a.html
"The high rates are compatible with current hypotheses suggesting that sociality in insects strongly selects for increased genotypic diversity in worker offspring to either meet the demands of a sophisticated caste system or to mitigate against the effects of parasitism."

Insights into social insects from the genome of the honeybee Apis mellifera
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2048586/

Review copies of these documents, msg me.


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## mike bispham

Barry said:


> Mike, you have heard of Google haven't you?
> 
> http://cornell.academia.edu/PeterLBorst
> https://plus.google.com/100095840744292753146/about
> https://plus.google.com/100095840744292753146/posts :
> 
> http://peterloringborst.com/
> http://www.youtube.com/watch?v=ZlOGUpkNbZo
> http://www.vet.cornell.edu/biosci/people/staff.cfm - Technician IV
> 
> Perhaps Nick is his brother?


So we have a 'Lab manager' (his account) 'doing' 'Biomedical research' at Cornell

Or a Technician IV according to the university pages - is that one of those 4-6 week courses? 
(He's only 'Borst' there, not double-barrelled 'Loring Borst')

He's worked in a bee stuff shop, looked after the bees for a university department (that teaches beekeeping - not one doing research)... how many apiarists were there under this senior apiarist?

Do you think someone has arranged for him to have journal access, and to be paid to talk down the prospects of simple fixes for bee problems - since that notion, if it gained ground, would tend to cost them work/careers/sales? 

Who is Nick?

Mike (UK)


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## mike bispham

peterloringborst said:


> However, there is new stuff that has an immediate impact on honey bee breeding. The goal of any bee breeding should be improved bee health. We have already seen how livestock that is bred solely for productivity generally is unhealthy and requires expensive inputs to maintain. On the other hand, wild types may not be productive enough to be even marginally profitable. There is some evidence of this with bees. The bees of Gotland were found to be mite resistant but the colonies stayed small and generally did not produce much surplus. For the purposes of honey bee conservation, these colonies might be ideal but as livestock, maybe not.


Well done Peter. You have arrived at last at the position you've been arguing against for the last 6 months or so. 

No one suggests 1st generation natural survivors are suitable for beekeeping. What is suggested is that they have the essential qualities supplying mite management ability which, when combined with more productive bees, will result in productive bees that manage their own mites.

And/or they might be improvable themselves.

There is no single answer to the question of which of these is the better route. Each feral population is different, each will be coming to its own accomodation with varroa through co-evolution (by natural selection, as if that should need saying).

It is the case that each will be attuned to some degree to its local environment, and that might be a plus. (For exaple if you want to keep bees in that locality)



peterloringborst said:


> Now this paragraph requires a little explaining.


Yeah, maybe - actually I found your explation useful. However, lets note your conclusion:



peterloringborst said:


> What this says is that there be mite resistant mechanisms that can be selected for, but that it is just as important to focus on immunity in general.


... is bog standard husbandry practice. Its teaching your grandmother to suck eggs. When you pick as parents - carefully, with skill and knowledge of your organism and its ailments - those that are strongest and most productive without having assisted that health through medication and/or jiggery-pokery, what you are getting is 'best general health'. That subsumes 'immunity in general'.



peterloringborst said:


> Were it not for the viruses vectored by mites, their effect might be far less. At the same time, if bees were affected less by the viruses, mites would be less of a problem.


Interesting, but not stuff you need to know. How to do selective propagation skilfully is stuff you need to know. In my view the best way to gain insights into how it works is to look at Nature's most wonderful health-gaining mechanisms. The healthiest reproduce the most. 



peterloringborst said:


> The question is not whether mite resistant traits exist but how to propagate them.


I'm less than convinced this is going to last, but for now at least I really am genuinely pleased to see you writing this. 

Perhaps now we can stop arguing about whether improvement is possible, and get on with talking about the best ways to go about it.

Mike (UK)


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## Michael Johnston

Mike Bispham is very hung up on Peter Borst's credentials. Peter works in a lab doing genetics research at Cornell University. He's a technician. He does the work and the head of the lab ("the Scientist") gets to take credit for all of Peter's work and gets to publish in the journals.
Peter has every right to have an intense interest in all of the current research in apiculture. Unlike many of us that spend their evenings watching TV, Peter is on the internet researching. Randy Oliver uses Peter to do much of the research that goes into Oliver's articles and Randy thanks him often in the American Bee Journal. Peter is extremely knowledgeable and I would put his knowledge of current happenings in beekeeping against any university professor.


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## peterloringborst

> I am hoping that JWChesnut can post the citation to which he alluded concerning the development of new genes in the honeybee genome.


It's not that new genes form, the genetic structure is essentially the same or they would no longer be honey bees. Or at the very least, a new species which is genetically incompatible with the original. What JW is referring to is new alleles, which are variants of the genes required by the organism. A certain amount of recombination is allowed by the genetic machinery, this produces new variants of the genes and presents the possibility of improvements coming about. Without variation, there could be no evolution, no breeding improvements, no adaptation. 

The observation that the honey bee has an extremely high rate of recombination has still not been adequately explained. The original paper came out in 2006. In it they say:



> Recombination improves the efficacy
> of selection in the presence of genetic drift. The magnitude
> of genetic drift is dependent on the effective size of a population.
> The honey bee has a small breeding population and an increased
> recombination rate, consistent with theoretical expectations.
> 
> The number of colonies that contribute to the pool of males
> available to mate with honey bee queens is estimated to be no
> more than 238 (Baudry et al. 1998), resulting in an estimated
> effective population size of ∼500.
> 
> Higher levels of genetic variation and genetic associations could
> slow the spread of parasites and pathogens in colonies or provide
> the basis for more task specialization, leading to an increase in
> colony performance and fitness (Gadau et al. 2000).


In short, there is no real evidence (yet) that this high rate of recombination causes significant function. Most alleles are simply different and do not produce differences in the organism. Wikipedia : "_Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation. However, most genetic variations result in little or no observable variation._" 

In other words, the difference is only observed at a molecular level. It may be that most of the variation occurs in regions of the genome that have little or no overt function. Meanwhile, _DNA repair mechanisms_ are present that prevent serious alterations to the genome. 

Currently, the lab in which I work is studying DNA repair mechanisms and their role in meiosis. This is the stage of life where the chromosomes of the parents are separated and recombined to produce the eggs from which the next generation develops. A lot can go wrong at this point. Most copy errors produce fatal results and so are not passed on. Some errors do slip through causing various defects. Why this happens is what we are studying.


----------



## peterloringborst

As a follow up to my previous post:



> Our GLM shows that segments with high recombination rate have
> also a high ratio of CpG/GpC, indicating a low level of
> methylation, while fragments with low recombination rate
> are apparently highly methylated.
> 
> (Sigurdsson et al. 2009) proposed that methylation could either
> precede recombination to favor it or follow recombination
> to avoid another event in the vicinity (resulting in positive
> crossover interference). --Mol Genet Genomics (2014) 289:11–24


What does this mean? Going straight to Sigurdsson:



> Inter-individual and regional variability in recombination rates cannot be fully explained by the DNA sequence itself. Epigenetic mechanisms might be one additional factor affecting recombination. -- Genome Res. 2009 19: 581-589 originally published online January 21, 2009


This takes us back to epigenetics. There may be external factors which are controlling the rate of recombination, hence an external effect on the germline.



> Our results suggest that differences in methylation provide
> an explanation for a previously unexplained phenomenon of
> inter-individual differences in recombinational activity despite
> identical DNA sequence, as well as different locations of recombination
> hot spots between species with high sequence homology


DNA Methylation is a way the cell machinery has of control the gene expression. Wikipedia states: "_Some methylation modifications that regulate gene expression are heritable and cause genomic imprinting._"


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## peterloringborst

> Peter has every right to have an intense interest in all of the current research in apiculture.


Thanks for the kind words. Many of us "seniors" feel that time is running out, and we want to contribute something to the next generation. I have been studying the honey bee for forty years now, but feel as if we are just finding stuff out. One of the most exciting developments is the formation of the

_Center for Pollination Research at Penn State_ http://ento.psu.edu/pollinators 

_BeeInformed Partnership_ http://beeinformed.org

More information is available now than ever before, but it can be somewhat daunting, even to those of us who obtained their daily vitamin requirements from reading obscure journals. By the way, I watch TV. Anyone seen "Annika Bengtzon"?


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## squarepeg

Michael Johnston said:


> Peter is extremely knowledgeable and I would put his knowledge of current happenings in beekeeping against any university professor.


yep, plb is an amazing encyclo-pete-ia of beekeeping. 

this has been an interesting thread, many thanks to all for contributing.


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## peterloringborst

Mike Bispham writes:


> Or a Technician IV according to the university pages - is that one of those 4-6 week courses? (He's only 'Borst' there, not double-barrelled 'Loring Borst')


I am only going to respond to this because he is the second person on this forum to call attention to my family name. The last time it was d--- and I quit posting at that point for several years. He said some about "he's The Loring," alluding to The Lorax. It is a family surname so if you insult it, you insult my family. I use three names in the tradition of such writers as Henry David Thoreau, Ralph Waldo Emerson, Edgar Rice Burrows, Louisa May Alcott, David Foster Wallace, to name a few. Get over it.

About my position at Cornell, going after that is even more petty than attacking my name. As a matter of fact, when I first started posting online about the myth of small cells as a management technique D--- tried to get me fired for criticizing her. I was working as the Senior Apiarist at the Dyce Lab at the time. I had to stop posting. I worked there for 7 years and then as a NYS bee inspector for 3. I have actually been working at Cornell since 1995. I have been promoted numerous times, I have supervised dozens of students. 

None of this has any bearing on the topic at hand. I have been interested in honey bee breeding from the first summer I worked with bees in 1974. I raised queens for sale by 1978. I worked for one of the largest queen producers in California in 1982, with Mike Johnston, who stayed on a lot longer than me. I purchased breeders and raised queen bees at the Dyce Lab. Right now, I am not raising queens, and I have nothing for sale that any of you can buy. I don't even sell advertising.


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## Barry

peterloringborst said:


> None of this has any bearing on the topic at hand.


I agree. I was going to delete Mike's post (#85) but decided it was better to leave it and let his foolishness shine.


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## peterloringborst

One more thing: there is nothing wrong with being an amateur. It means doing things for the _love of it._ Which I do.


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## Rader Sidetrack

On the topic of Mike and ... ummm ... his _judgement _..... you really shouldn't miss his Honey Melter thread:

http://www.beesource.com/forums/sho...ar-for-melting-out-honey-directly-from-frames

In my view, it is relevant here as that thread can help you evaluate Mike's values and point of view.


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## Kosta Zhelev

Hello colleagues.I want to continue the theme.So far all comments are understandable and justified.With minor exceptions.Profession bees about 20 years.Last 10 with a selection of bee strains.My work is mainly applied in practical beekeeping.Whether a sign is falling apart or are resistant strain is just my opinion.This is before my eyes.I want to ask here if all pundits have checked his claims in practice.It is a measure of fidelity.I believe in scientific thought.I can assure you that VSH is a fact.Also that external / non-genetic / factors influence the behavior of a colony and it is transmitted as an inheritance.Whatever the purpose, the way they can be different.All however, should be of practical value.I'm practicing and trying to figure out the veracity of scientific publications.I want to ask - This is all done in the name of the bees and the people right?If "YES" then why do I see all criticism?It will be very interesting to read the opinions of colleagues who have practical observations on the genetic traits of bees.I'll be glad to continue the theme.


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## peterloringborst

> This is all done in the name of the bees and the people right?If "YES" then why do I see all criticism?


Greetings Kosta! The answer is yes, I am writing in the name of the bees and the people. Try to tune out the static, there is an important thread here. You have nicely summarized it. We know that some traits like VSH or hygienic behavior can be strengthened through conventional breeding practices. But not very much, and they seem to fade quickly when the queen is superseded. Since queens bought from breeders these days seldom last a year, it is a poor investment to buy good stock only to watch the qualities you bought it for disappear so soon. 

Meanwhile, we are trying to get a handle on what is passed on from colony to colony when the hive swarms, or when the beekeeper makes splits. There are a lot of possibilities here: DNA methylation which leaves marks on the chromosomes which are passed on; microbial colonies which in healthy colonies may transmit health benefits to the offspring; behavioral traits which may be learned by each generation from the previous. The practical side of this might be that the better way to propagate bees is to follow Charlie Mraz's model from the 1960s.

He recommended selecting your best hives and splitting those, allowing them to raise their own queens. This is the most reliable way of obtaining another colony with the traits of the former. The splits can be made on top of the parent hive using only a sheet of plastic to separate them. If the split is successful it can be place on a stand of its own. If not, the sheet of plastic is removed and the bees reunite, nothing lost.


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## Saltybee

peterloringborst said:


> The splits can be made on top of the parent hive using only a sheet of plastic to separate them. If the split is successful it can be place on a stand of its own. If not, the sheet of plastic is removed and the bees reunite, nothing lost.


The best sheet of plastic for this is a $3 queen excluder.


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## mike bispham

peterloringborst said:


> Greetings Kosta! The answer is yes, I am writing in the name of the bees and the people. Try to tune out the static, there is an important thread here. You have nicely summarized it. We know that some traits like VSH or hygienic behavior can be strengthened through conventional breeding practices. But not very much, and they seem to fade quickly when the queen is superseded.


Seem to fade?! Of course they do! The next generation has to mate with a sufficient number of drones carrying genes for the traits in order for them to (ceteris paribus) come through. If you're mating with drone from treatment-dependent stock that simply won't happen. This is basic husbandry. 

You haven't mentioned the feral contribution. Whether vsh, hygenic or other - brood breaking for example - they traits they convey are also desirable. Summing them up under 'mate-management capabilities' is useful to the discussion.

Your 'conventional breeding practices' covers a lot of ground, from traditional selective husbadry to hi-tec high intensity breeding. We've learned here its best to be specific to avoid confusion.



peterloringborst said:


> Since queens bought from breeders these days seldom last a year, it is a poor investment to buy good stock only to watch the qualities you bought it for disappear so soon.


Much better to have a sound and thoroughgoing plan to maintain, embed, enhance and balance the traits.

Of course, if you're surrounded by excellent ferals you can sit back a bit!



peterloringborst said:


> Meanwhile, we are trying to get a handle on what is passed on from colony to colony when the hive swarms, or when the beekeeper makes splits. There are a lot of possibilities here: DNA methylation which leaves marks on the chromosomes which are passed on; microbial colonies which in healthy colonies may transmit health benefits to the offspring; behavioral traits which may be learned by each generation from the previous. The practical side of this might be that the better way to propagate bees is to follow Charlie Mraz's model from the 1960s.
> 
> He recommended selecting your best hives and splitting those, allowing them to raise their own queens. This is the most reliable way of obtaining another colony with the traits of the former. The splits can be made on top of the parent hive using only a sheet of plastic to separate them. If the split is successful it can be place on a stand of its own. If not, the sheet of plastic is removed and the bees reunite, nothing lost.


One drawback with splitting best coloies is that you unsettle the balance between colony and mites, thus losing a 'true reading' of the colony's capabilites. You also reduce the drone output from that hive - a consideration worthy of plenty of attention. 

These things can be overcome, but in my view its worth maintaining your best hives as stand-alone big colonies that can be re-evaluated at intervals. At some point, if you're sure the queen is excellent, and developing an impression that she makes good offspring, it may well be worth sequestering her in a small hive where you can preserve her eggs, access them easily, see that she doesn't fly off, and have her fill lots of drone comb. 

Another drawback is that often it will be urgent to make dramatic increase, to bang up your numbers quickly in order to give you stocks to cover likely high losses (early in the game) and to select from. To influence the male side may also require a good number of colonies. This way of making increase might be too slow in that scenario. 

Mike (UK)


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## squarepeg

mike bispham said:


> One drawback with splitting best coloies is that you unsettle the balance between colony and mites, thus losing a 'true reading' of the colony's capabilites. You also reduce the drone output from that hive - a consideration worthy of plenty of attention.


you may have a point there mike considering that you are in the earlier stages of the winnowing process and are primarily concerned with varroa resistance and frank survival. once you have achieved that it may become a secondary consideration.

i find that my ferally derived survivors will almost without exception swarm every spring and sometimes even issue more than one swarm. i interpret this behavior as a part of what has allowed them to survive the introduction of varroa here. perhaps it's the multiplying effect, the brood break, some other reason, or some combination of reasons; but they are very good at swarming.

since they are bound and determined to split themselves anyway, it makes more sense from a management perspective to split them on my terms for making increase and for swarm prevention.

my usually method is to remove the queen with three frame of bees and mixed resources just prior to swarm season and allow the stronger parent colony to make the new queen.

i have had very good luck in getting strong new colonies when splitting from my strongest ones. the laggards are also split, but requeened with grafts from the stronger ones. from what i can tell, the overall vigor and production in my apiary is improving with each season, although the improved production could just as well be attributed to having more drawn comb.


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## Kosta Zhelev

Hello peterloringborst.Every word written by you is true.Thanks in advance to all who work in the service of bees and humans.I am an example of how Resistance mite protect my colonies.The reason I came to this conclusion is untreated colonies long time./ very bad effect of the treatment /And because I have not changed my queens to anyone dare say that VSH alleles are approved in my area.I must clarify, however, to spend the winter there well my colonies have changed dramatically in terms hive.I had to change the direction of development and growth of my colonies.Top downwards.Classical development is the opposite.Here non-genetic causes of behavior modification.It is interesting that the queens are forced to lay hard.There is a high laying activity.This creates excellent conditions for mite.But provoked VSH ​​expression.The role of scientific experts is to understand these issues.Our job is to trust them.I'm talking about mites because he is an enemy № 1.Not irrelevant and other issues affecting the genetic potential of the bees.You do not think there is anyone who knows what is going on in the hive?If it is only one hive Yes.What about the whole apiary?Bees are exchanged constantly by themselves and beekeeper.Definitely this is reflected.Even in the production of queens.It is not good to look at bees as a constant.They are variable.Most - it is important to have a common denominator.I believe in science.And in itself.Thank you Peter.


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## peterloringborst

> Hello peterloringborst. Every word written by you is true.


Thanks for your kind words, but I assure you that I don't believe every word I write is true. I have been trying to present new ideas, and some of them certainly ring true when compared to experience. In English the word "true" has many meanings. My favorite is in this example: "his aim is true." That is, in archery, for example, when one's aim is true, one will nearly always hit the center of the target. One may also miss for various reasons, but with a true aim, one will score most of the time. An unsteady hand may indicate an unsteady mind, and an unsteady mind can not consistently produce clear ideas.

Anyway, please continue to write and share your ideas and experiences. I will too.


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## peterloringborst

> The best sheet of plastic for this is a $3 queen excluder.


I was thinking about the plastic that comes in rolls. You can cut this into rectangles and it is a lot cheaper than $3 each. The plastic queen excluders are complete junk as far as I am concerned. If you want to spend money, an inner cover with the hole screened over makes a good divide board. There has to be a top entrance of some sort, usually just a notch in the inner cover. Many of these are sold with notches already cut.


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## Kosta Zhelev

Hello Peter!Always insure somehow.For me it is important what happens to my apiary.And if it is economically feasible.So far, no one speaks with which characteristics associated VSH​​.So far, in all publications reflect only the levels of mite in the tests.No mention of the other features that characterize these colonies.I can remove the mite levels in a completely mechanical way.The question is how the genetic approach is reflected.Not without significance is the age of the queen.And whether it is natural or instrumental insemination.In my area grazing is 60 days.My entire practice is subject to this period.My choice is those who manage to cope until then.I have a problem, however after this period.To figure out which ones have the most - high% VSH.Depriving the colonies of flying bees.Those colonies that have a high% of infestation in this period do not develop properly in time.Attention to them anymore.Others remain in the reproduction.They are classified according to the goals that I have in their program.Here each characteristic prevails.Of course everyone is entitled to their valuation method.Paying attention to the production method of the queen.I find differences in the results of this indicator.In traditional ways to industrial production of queens occurs - often high% of mite.It shows the relationship of the result in terms of quantity.It also shows that there are external factors that influence the result.For example, assessment of the bee itself.My opinion is that I find the right choice of the bees.Greetings from me!


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## peterloringborst

I already talked about "DNA Methylation". This is a way that the genes of an organism can be modified in real time, turning this or that one on or off. There is evidence that these modifications can be passed on to subsequent generations, and also that the modifications can be wiped clean, reverting the genome. 

DNA methylation underlies the difference between worker and queen; it is brought about externally through the larval food. This food is different for worker and queen. We don't fully understand the differences, they are not simply nutritional but other substances may be added by the nurse bees which send the larvae down one or the other developmental pathway. Meanwhile, studies have uncovered another way to regulate gene expression, RNA interference. Small RNAs can affect gene expression, essentially telling directing the development. 

You can think of the genome as a blueprint in the hands of a construction crew. Different crews may produce different results using the same blueprint, depending on their skill, the resources, and their ability to improvise. Depending on how specific the blueprint is, they may need to improvise a lot. For example, the blueprint may indicate the roof and that it should be covered with shingles, but it won't dictate the size and shape of every shingle, where it is placed, what kind of nail to use, etc. So the genome contains general instructions but not specific instructions on how every cell must be constructed. The cells develop along pathways which are directed by the cell machinery. 

What follows is an abstract of a presentation at the recent _International Union for the Study of Social Insects International Congress_ 13 - 18 July 2014 | Cairns Convention Centre | Queensland, Australia



> Non-coding RNAs in honeybee caste determination
> Regan Ashby, Sylvain Foret, Iain Searle, Ryszard Maleszka
> 
> In honeybees (Apis mellifera), three contrasting adult castes (phenotypes) are produced from the
> same genome; two diploid females (a sterile worker and the highly reproductive queen) and the
> haploid male (drone). While sex determination is genetically controlled, phenotypic differentiation
> between the two female castes has recently been shown to be associated with changes in the
> epigenome, specifically changes in DNA methylation patterns, in response to dietary composition
> (royal jelly). In more recent times, the role of another class of epigenetic modifiers, that of small
> non-coding RNAs, has become an area of major interest in regards to the regulation of phenotypic
> and developmental plasticity. This talk will discuss present findings from our laboratory concerning
> the expression profile of microRNAs between the three major castes using next-generation high
> throughput sequencing, and how differences in these profiles may relate to phenotypic output.
> Mature miRNAs are 20-24 nucleotide long molecules which form part of a larger RNA-induced
> silencing complex (RISC), providing sequence-specific targeting of mRNA molecules. Most commonly,
> the binding of a RISC-complex to a target mRNA sequence induces translational repression or mRNA
> degradation. Increasing evidence suggests that small RNAs help confer genetic robustness by
> reinforcing transcriptional programs.


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## Kosta Zhelev

Once I gave a comment.This is my second attempt.This time will be brief.Everyone talks about the levels of mite colonies.But no mention of other characteristics associated with infestation.Can I Download the levels of mite purely mechanical.The question is the expression of the genetic approach.In my practice I have much choice for sustainability.While I see the combination of different features.Deprive all studied colonies of flying bees.Those who have a high% of infestations do not develop well in time.My attention to them.Others remain in the reproduction.Side factors also influence the outcome.As the age of the queen or the method by which it was produced.Racial origin also.For me, grazing is 60 days.And all my practice during this period.My way of evaluation is after him.Of course everyone is entitled to their own.Most interesting - is this approach that I have the opportunity to choose combinations of characteristics.At the same level of infestation.Bee behavior is not constant.It is variable.For me the most - good to have a common denominator.Thank you.


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## squarepeg

hi kosta,

(i have an uncle with that name from macedonia)

you mentioned not treating for mites, how many years have you kept bees without mite treatments?

how many years now have your longest surviving colonies (without requeening) been going?

are there other beekeepers in your area who are also successful keeping bees without treatments?

what percentage of your colonies do not survive the winter?

do you use artificial feeds or allow only a natural diet for your bees?

do you have bees living feral in the woods in your area?

welcome to beesource!


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## Kosta Zhelev

Hello squarepeg.I'm not your uncle.Let's say 7-8 years without treatment.No professional beekeepers around me without treatment.And have around me wild colonies.% Is a low loss.This past winter I have no losses.We'll see how this would be.I do not use artificial food.But often replace the queen.Bees are not eternal syauarepeg.What matters is whether transmitted resistance in generations.I do not keep old queens.Those who have no potential drop of my choice.That's my approach.I only have one queen before 4 years.There% of colonies for repair.They are subject to a program of instrumental insemination.Greetings.


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## squarepeg

interesting kosta and many thanks for the reply.

congratulations on the low losses.

i also have wild colonies around me and i believe they help by introducing survivor genetics via their drones.

almost all of my colonies replace their queen on their own every year either by swarming or by supercedure, so i do not have to requeen often. if i have a poor queen or a colony that is not performing well i split it up into starter colonies and give them queen cells grafted from a good colony.

most of my losses in the winter appear to be from the queen failing, as evidenced by drone brood in worker cells. i've only had bees for four winters now, but my average loss is less than 15%

i also do not use artificial feeds because the forage here is very good and it's easy to leave some honey. i think maybe this helps with resistance to infections.

are you doing the instrumental insemination, or you introducing these genetics from a professional breeder? so far i have only introduced bees i purchased from someone who has been 18 years treatment free, but now i have enough bees to make my own queens.

ps: yes my uncle is now passed away, but i was able to visit him and my other relatives in the old country some years ago. it was a very interesting experience.


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## Kosta Zhelev

That's not what I meant squarepeg.However, I wish you success with swarms.Nothing will be gained by replacing the queen of good colonies.These queens are not tested.Maybe I'll give an opinion other professionals forum.I think there's enough.Which other features is a combination of mite resistance?Which characteristics most - often evaluated?Does anyone observations on the matter?


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## squarepeg

understood kosta.

i was interested in obtaining mite counts at one time (% percent infestation by alcohol wash), and using this information for choosing queens to breed from, but after having success with most colonies surviving and experiencing low varroasis i now choose to make queens instead from the most productive colonies and the ones that i am able to prevent from swarming.

i am only an amateur but i am interested in your approach, and if you have the time to respond here, what features and characteristics are you evaluating? are all of your queens tested in some way? 

many thanks for your replies.


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## peterloringborst

follow up to talk about RNA and epigenetics



> Many cases of heritable environmental responses have been documented but the underlying mechanisms are largely unknown. Recently, inherited RNA interference has been shown to act as a multigenerational genome surveillance apparatus. We suggest that inheritance of regulatory RNAs is at the root of many other epigenetic phenomena, the trigger that induces other epigenetic mechanisms, such as the depositing of histone modifications and DNA methylation. In addition, we explore the possibility that interacting organisms influence each other's transcriptomes by exchanging heterologous non‐coding RNAs.
> 
> Non‐coding RNAs as the bridge between epigenetic mechanisms, lineages and domains of life
> Mor Sela, Yoel Kloog and Oded Rechavi
> 
> Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 64332, Israel


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## Kosta Zhelev

Hello again Peter.In a purely practical sense changes in the genome can only be done in the laboratory or an appropriate program of production of the queen.Change can come to me with the conditions in which is placed a colony as a diet change in caste composition of the population, the activity that performs according to months of the season.Of course this is only in the horizontal posoka.Vav vertical capabilities are also not less.To be honest here already intervened beekeeper.And any changes occur directly and genetically.Precisely because aligning both directions in the comments become disputes.I count both directions.I have no exact formula of my choice.Greetings.


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## peterloringborst

> In a purely practical sense changes in the genome can only be done in the laboratory or an appropriate program of production of the queen.


Well, no. Using RNA interference as a tool, changes can be made that are passed on to the offspring.



> *RNA inheritance*
> 
> RNA inheritance enables physiologically relevant acquired
> traits to be heritable. We discovered that worms are
> resistant to viruses in part owing to the inheritance of
> anti-viral small RNAs (viRNAs). We demonstrated that
> inherited viRNAs could eliminate a transgene-derived
> virus with amazing efficiency. The underlying genetics
> is non-Mendelian, as the persistence of the anti-viral
> viRNAs is achieved byRdRP-mediated amplification of the
> small RNAs in every adopting generation (Rechavi et al.
> 2011). A recent study by Sterken et al. demonstrates that
> similar RNAi-based inherited immunity serves to control
> infection by the Orsay virus, the sole C. elegans virus that
> is capable of infecting Caenorhabditis in the wild as well
> (Sterken et al. 2014). J Physiol 592.11 (2014) pp 2369–2373





> In this study, we investigated the molecular basis of pathogenesis, transmission and genetic diversity of IAPV in honey bees and evaluated the impacts of IAPV infection on colony losses. We also determined the global transcriptional profiles of honey bee responses to viral infection. Finally, we examined the inhibitory effect of small interfering RNA (siRNA) that targets putative virus-encoded proteins (VSR) on IAPV replication. The replication of single-stranded positive-sense RNA viruses results in the synthesis of complementary negative-stranded RNA, thereby producing dsRNA replicative intermediates that are attractive targets for defenses based on RNA interference. To counteract host RNAi antiviral defense, viruses have evolved strategies to suppress the antiviral effects of RNAi. http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004261





> *Discussion*
> 
> Multicellular organisms are classically viewed as entities
> that develop from a dividing progenitor cell, which gives
> rise to cells with a shared genome. In contrast, the ‘hologenome’
> theory defines a holobiont as being composed
> of different interacting organisms (multicellular and
> microorganisms) whose fitness is determined together by
> natural selection (Zilber-Rosenberg & Rosenberg, 2008).
> Regulatory RNA exchange between different organisms
> could be an important component in the hologenome’s
> genetics, since RNA is a ‘universal language’ which affects
> other epigenetic processes, and in certain cases can become
> heritable. (Sterken et al. 2014). J Physiol 592.11 (2014) pp 2369–2373


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## mike bispham

peterloringborst said:


> Well, no. Using RNA interference as a tool, changes can be made that are passed on to the offspring.


What I'm puzzled by is the question: how is any of this of help to us? How can we as beekeepers make practical use of it?

Mike (UK)


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## Kosta Zhelev

I'm impressed Peter.In a word - colonies or individuals of it are constantly changing conditions which placed their genotype.Eventually, the immune system works well when placed well.And hereditary changes can occur even when replaced bees in a colony.If I'm wrong please repair.


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## peterloringborst

> Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions" in evolution—four inheritance systems that play a role in evolution: genetic, epigenetic (or non-DNA cellular transmission of traits), behavioral, and symbolic (transmission through language and other forms of symbolic communication). These systems, they argue, can all provide variations on which natural selection can act. Evolution in Four Dimensions offers a richer, more complex view of evolution than the gene-based, one-dimensional view held by many today.



Applied to honey bee, we have described the genetics of HB, where traits are passed from mother to drone to other colonies, such as aggressiveness. Epigenetic effects would include things like acquired immunity which can be passed either through markers on the genome affecting gene expression, or from individual to individual, something like a human mother passes on immunity to the unborn through placental blood. Behavioral changes in HB can be passed on, as newborn bees pick up behaviors from the older bees, again: such as aggressiveness, but also grooming behaviors. Finally, the four dimension -- symbols -- I don't know if we can apply this to HB or not. In humans, the bulk of our inheritance is symbolic, passed on through teaching, language, learning and imitation. How much of this occurs in HB, we don't know.


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## peterloringborst

> What I'm puzzled by is the question: how is any of this of help to us? How can we as beekeepers make practical use of it?


First, science increases our understanding. That is a benefit right there, even if it is never applied. But beyond that, RNA interference is already being used to knock down viruses. Viruses are the biggest health problem we face, either in honey bee or human. Being able to silence gene expression in viruses would be a significant breakthrough, equivalent to the breakthrough which came with vaccines. 

But on the home ground, if there is something in the colony which is epigenetic, such as symbiotic bacteria or learned behaviors, this changes the way we would increase our colonies. We have already discussed Charlie Mraz's ideas of breeding from the best colonies -- not by raising queens from them merely -- but by actually dividing these best colonies to propagate the whole of the colony, not just its genes.

Because whatever makes that colony a good one, may or may not be transmitted through the genes of one queen raised from one egg from that hive. I realize this is the opposite of Mike Palmer's ideas, where he uses the weak or failing colonies to make increase (using queens from the best stock). That makes sense in a purely genetic way, but not in an epigenetic way. Granted, as JW Chesnut stated, these ideas are controversial and not necessarily proved beyond doubt.


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## squarepeg

nice explanation plb, many thanks.


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## Phoebee

There is a similar insight to that in post 118 to be found at *The Genome Institute* regarding the _Human Gut Microbiome_

http://genome.wustl.edu/projects/detail/human-gut-microbiome/

"The total number of genes in the various species represented in our internal microbial communities (microbiome) likely exceeds the number of our human genes by _*at least two orders of magnitude.*_ Therefore, it seems appropriate to consider ourselves as a composite of many species - human, bacterial, and archaeal - and our genome as an amalgam of human genes and the genes of our microbial ‘selves’.

"Without understanding the interactions between our human and microbial genomes, it is impossible to obtain a complete picture of our biology. Our microbiome is largely unexplored."

Can it be any less true of bees? And not just in their guts, but the microorganisms they employ to make honey, bee bread, and royal jelly. Their larvae are bathed in nutrients, and undoubtedly grow in the presence of microorganisms which affect their development.

The human genome is perhaps around 1% of the total number of genes in our bodies. To what extent are we shaped by the 99% of foriegn genes living inside us? This cannot be insignificant. It certainly affects my social life if I eat beans. 

Some forum members are dead set against treatment using essential oils. Changing the bees' microbiome is the concern. So yes, this is all relevant.

Even within our cells, we have mitochondria with genes independent of our nuclear DNA. These are essentially commensal bacteria which have been part of eukaryotic cells for a few billion years. Plants can photosynthesize because of chloroplasts, which are also commensal bacteria. There is an entire spectrum of degree of commensalism between bacteria and higher organisms, and we're just starting to understand the impact.


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## peterloringborst

> Some forum members are dead set against treatment using essential oils. Changing the bees' microbiome is the concern. So yes, this is all relevant.


I am not strictly a "treatment free" beekeeper but I try to minimize interventions. I have long thought that additives like HoneyBeeHealthy were at best unnecessary and at worst, they could interfere with a wide range of delicately balanced systems including pheromone communication, and as you say -- microbes.


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## Phoebee

Let me get ahead of an obvious objection to one statement I made above. I'll use a rather "off-the-wall" bit of speculation which is nonetheless thought-provoking.

Objection: microbes used to make honey and bee bread are no more a part of the bee genome than the yeasts we use to make beer and to make bread rise.

Counter: Civilization was established to make beer. Seriously. Artifacts from the earliest gathering places which suggest any governmental authority show that they gathered to celebrate, and making beer was central to the festivities. And making beer seems to have been (according to some researchers) the reason for raising grain. We made beer before we made bread.

The speculative extension is that, before beer, we were happy hunter-gatherers. Only when we started to make beer did we start to make our lives complicated, to attach ourselves to one piece of land, did we allow ourselves to be ruled by iron-fisted kings. Serfdom is a consequence for the common person. Why did we do this? Alcohol.

Why do yeasts produce alcohol? The speculation is, it enables simple yeasts to take over the minds of more complex organisms, and coerce those organisms to make food for, and ideal habitat for, yeasts. This may be hard to prove, but the evolutionary "logic" is quite compelling. Yeasts producing alcohol have a strong selective benefit if higher organisms respond in this manner.

The inspiration for this idea came from zombie ants, taken over by microorganisms to do suicidally bad things for ants, but good things for the microorganisms.

Cheers!


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## Ramona

Thank you for this elegant post!




peterloringborst said:


> First, science increases our understanding. That is a benefit right there, even if it is never applied. But beyond that, RNA interference is already being used to knock down viruses. Viruses are the biggest health problem we face, either in honey bee or human. Being able to silence gene expression in viruses would be a significant breakthrough, equivalent to the breakthrough which came with vaccines.
> 
> But on the home ground, if there is something in the colony which is epigenetic, such as symbiotic bacteria or learned behaviors, this changes the way we would increase our colonies. We have already discussed Charlie Mraz's ideas of breeding from the best colonies -- not by raising queens from them merely -- but by actually dividing these best colonies to propagate the whole of the colony, not just its genes.
> 
> Because whatever makes that colony a good one, may or may not be transmitted through the genes of one queen raised from one egg from that hive. I realize this is the opposite of Mike Palmer's ideas, where he uses the weak or failing colonies to make increase (using queens from the best stock). That makes sense in a purely genetic way, but not in an epigenetic way. Granted, as JW Chesnut stated, these ideas are controversial and not necessarily proved beyond doubt.


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## Ramona

On a similar note...bacteria evolved humans out of themselves to invent better and faster transportation devices that enable the bacteria to move more efficiently around the planet and into the solar system!



Phoebee said:


> Let me get ahead of an obvious objection to one statement I made above. I'll use a rather "off-the-wall" bit of speculation which is nonetheless thought-provoking.
> 
> Objection: microbes used to make honey and bee bread are no more a part of the bee genome than the yeasts we use to make beer and to make bread rise.
> 
> Counter: Civilization was established to make beer. Seriously. Artifacts from the earliest gathering places which suggest any governmental authority show that they gathered to celebrate, and making beer was central to the festivities. And making beer seems to have been (according to some researchers) the reason for raising grain. We made beer before we made bread.
> 
> The speculative extension is that, before beer, we were happy hunter-gatherers. Only when we started to make beer did we start to make our lives complicated, to attach ourselves to one piece of land, did we allow ourselves to be ruled by iron-fisted kings. Serfdom is a consequence for the common person. Why did we do this? Alcohol.
> 
> Why do yeasts produce alcohol? The speculation is, it enables simple yeasts to take over the minds of more complex organisms, and coerce those organisms to make food for, and ideal habitat for, yeasts.
> 
> The inspiration for this idea came from zombie ants, taken over by microorganisms to do suicidally bad things for ants, but good things for the microorganisms.
> 
> Cheers!


----------



## mike bispham

peterloringborst;1148517[... said:


> Behavioral changes in HB can be passed on, as newborn bees pick up behaviors from the older bees, again: such as aggressiveness, but also grooming behaviors.


Slow down there Peter. Is there any scientific evidence that these behaviours are modulated epigenetically, or is this speculation? As far as I understand things hygenic behaviors are associated witn specific gene loci - and that's the full story. The rest is maybe's



peterloringborst said:


> Finally, the four dimension -- symbols -- I don't know if we can apply this to HB or not.


Yes a dance is symbolic of a location. 



peterloringborst said:


> In humans, the bulk of our inheritance is symbolic, passed on through teaching, language, learning and imitation.


I don't think you can quantify things in that way. Our entire bodily existence, together with our faculties for learning etc, is supplied by the genetic blueprint, period. Trying to attribute proportions of our being is rather apples and oranges - you can't compute them. 



peterloringborst;1148517How much of this occurs in HB said:


> Given that learning - acquired knowlege - correlates with brain size in all life form, I'd guess not much.
> 
> Mike (UK)


----------



## mike bispham

peterloringborst said:


> First, science increases our understanding. That is a benefit right there, even if it is never applied. But beyond that, RNA interference is already being used to knock down viruses. Viruses are the biggest health problem we face, either in honey bee or human. Being able to silence gene expression in viruses would be a significant breakthrough, equivalent to the breakthrough which came with vaccines.


The problem with that - and its a very real problem - is that in this open-mating organism any interference in health terms becomes a self-perpetuating need. We've seen this with varroa treatments. Its the reason medical experts the world over are desperately cautioning against overuse of antibiotics. Its the same mechanism that results in the MRSA problems in hospitals.

Discovering viruses, and making treatments against them sounds great - until you consider this implication. then it becomes rapidly nightmarish. 



peterloringborst said:


> But on the home ground, if there is something in the colony which is epigenetic, such as symbiotic bacteria or learned behaviors, this changes the way we would increase our colonies. We have already discussed Charlie Mraz's ideas of breeding from the best colonies -- not by raising queens from them merely -- but by actually dividing these best colonies to propagate the whole of the colony, not just its genes.


That's a fair point. Any such benefits can however be already be discovered empirically. 



peterloringborst said:


> Because whatever makes that colony a good one, may or may not be transmitted through the genes of one queen raised from one egg from that hive. I realize this is the opposite of Mike Palmer's ideas, where he uses the weak or failing colonies to make increase (using queens from the best stock). That makes sense in a purely genetic way, but not in an epigenetic way. Granted, as JW Chesnut stated, these ideas are controversial and not necessarily proved beyond doubt.


I don't think you need to invoke epigenetics. A microbiological environment may be suited to a specific genetic line for a combination of lots of reasons, and none of then need be epigenetic in nature. A symbiotic relation may be very simple. It might not be too of course.

Mike (UK)


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## mike bispham

Phoebee said:


> Let me get ahead of an obvious objection to one statement I made above. I'll use a rather "off-the-wall" bit of speculation which is nonetheless thought-provoking.
> 
> Objection: microbes used to make honey and bee bread are no more a part of the bee genome than the yeasts we use to make beer and to make bread rise.
> 
> Counter: Civilization was established to make beer. Seriously. Artifacts from the earliest gathering places which suggest any governmental authority show that they gathered to celebrate, and making beer was central to the festivities. And making beer seems to have been (according to some researchers) the reason for raising grain. We made beer before we made bread.


That isn't 'established' Pheobe. That's 'posited'. Big difference



Phoebee said:


> Why do yeasts produce alcohol? The speculation is, it enables simple yeasts to take over the minds of more complex organisms, and coerce those organisms to make food for, and ideal habitat for, yeasts. This may be hard to prove, but the evolutionary "logic" is quite compelling. Yeasts producing alcohol have a strong selective benefit if higher organisms respond in this manner.


Sorry that's just nonsense. Yeast have located a chemical pathway that releases energy from sugar. All lifeforms require energy - first and formost. Alcohol, like co2, is a by-product. 

That's not to say that yeasts haven't benefitted from all sorts of symbiotic relationships, including some where the alcohol plays a central role.

Mike (UK)


----------



## Rader Sidetrack

Maybe Mike is having another one of _THOSE _days ... 


mike bispham said:


> Laughter is the best medicine as they say, and [HIGHLIGHT]I have a bit of a hangover! [/HIGHLIGHT]




:gh:


----------



## Phoebee

mike bispham said:


> That isn't 'established' Pheobe. That's 'posited'. Big difference
> 
> 
> 
> Sorry that's just nonsense. Yeast have located a chemical pathway that releases energy from sugar. All lifeforms require energy - first and formost. Alcohol, like co2, is a by-product.
> 
> That's not to say that yeasts haven't benefitted from all sorts of symbiotic relationships, including some where the alcohol plays a central role.
> 
> Mike (UK)


The fact that yeasts use the Embden-Meyerhof pathway to produce ethanol as a waste product hardly negates the argument. They could just as easily produce acetic acid or methane. And the pathway has been around probably since before the atmosphere was dominated by oxygen. But at some point, some animals developed a taste for ethanol. To that point, ethanol was still a waste product. 

But evolution works by species stumbling around until they line up the right mutation with the right habitat. Yeasts stumbled on humans, which not only were a species that liked alcohol and its harmful side effects, but could figure out how to create an ideal habitat for the yeasts to make it. This was a bonanza for yeasts. The benefits or detriments to humans have been debated ever since.

Humans constitute a new niche for yeasts, and this niche has evolved (un-naturally) new forms of yeast that would not exist without that niche. 

But more to our point, yeasts and their waste products are of very high importance to people. They create industry. They affect our food source. They affect if we can think straight. We've been known to fight over them, and we've been known to use them to achieve peace. A not inconsequential number of us owe our existence to alcohol lowering the inhibitions of our parents. These things are of non-trivial importance to human life, and go far beyond the genes necessary to set up the Embden-Meyerhof pathway.


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## Kosta Zhelev

Hey Mike bispham.I see that you are an intelligent man.Is epigenetics or symbiosis or biochemistry when a queen is introduced in another colony it completely changed his behavior.Workers of the same queen also have other behavior.Especially when conducting experiments to change mite resistance.However Queen remains new colony% mite is - lower than that of the first.Of course this is within one season.This also applies to indicators such as production of copper, for example.Is it possible to read your opinion on this issue?Greetings!


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## Phoebee

mike bispham said:


> That isn't 'established' Pheobe. That's 'posited'. Big difference
> 
> Mike (UK)


A *lot* of things are not established. This is a discussion of ideas under development. Science is not a body of facts, it is a _*process*_ for bringing up new ideas, testing them rigorously, and seeing what comes out at the other end after a lot of good minds have applied themselves to the problem.

It is rarely about instant agreement. It is about argument, and demanding proof, but it is also about having an open mind and not treating prior knowledge as incontrovertible doctrine. Science is ultimately a tool for _discovery_, and about "establishing" better and better proven knowledge, not about protecting "established" past truth.

And regarding academic qualifications, science started as a hobby. Mendel was an observant gardener, who noticed particular traits of peas could be inherited according to simple rules. I've seen arguments that he fudged his work a bit, disregarding results that would not fit his ideas, and his work probably would not pass peer review today. Yet this flawed amateur's ideas are now accepted as the basis for genetics.


----------



## mike bispham

Phoebee said:


> ... at some point, some animals developed a taste for ethanol. To that point, ethanol was still a waste product.


I agree, and for those yeasts, yes the'd found a niche, and an advantage, and they have thrived. (I'm not sure that human use accounts for a vast percentage of that, at least in diversity terms - its just that there are now so many of us, and so few of anything else that enjoyed a little tipple) 



Phoebee said:


> Humans constitute a new niche for yeasts, and this niche has evolved (un-naturally) new forms of yeast that would not exist without that niche.


Well yes. New strains anyway. We and (some) yeasts have a symbiotic relationship. We have lots of those, and so do other species. 



Phoebee said:


> But more to our point, yeasts and their waste products are of very high importance to people. They create industry. They affect our food source. They affect if we can think straight. We've been known to fight over them, and we've been known to use them to achieve peace. A not inconsequential number of us owe our existence to alcohol lowering the inhibitions of our parents. These things are of non-trivial importance to human life, and go far beyond the genes necessary to set up the Embden-Meyerhof pathway.


Yes, we've evolved in a mutually beneficial partnership (and with many other species).

Without the genes coding for yeasts, and gut bacteria, and skin bacteria, and dogs, and cows and pigs and runner beans... we wouldn't be the same. Sure. But... so what?

Sure, we're all linked in some way through our evolutionary histories. But its still the case that humans are made from human genes alone. Those human genes also code for relations with other species, some of which are essential to us. 

But we go back, in the final analysis, to our own blueprints alone.

Will you remind me what bearing this has on bees? 

Mike (UK)


----------



## mike bispham

Kosta Zhelev said:


> Hey Mike bispham.I see that you are an intelligent man.Is epigenetics or symbiosis or biochemistry when a queen is introduced in another colony it completely changed his behavior.Workers of the same queen also have other behavior.Especially when conducting experiments to change mite resistance.However Queen remains new colony% mite is - lower than that of the first.Of course this is within one season.This also applies to indicators such as production of copper, for example.Is it possible to read your opinion on this issue?Greetings!


I'm sorry Kosta but I'm unable to understand your question well enough to reply. I don't want to guess at your meanings.

Mike (UK)


----------



## mike bispham

Phoebee said:


> Science is not a body of facts, it is a _*process*_ for bringing up new ideas, testing them rigorously, and seeing what comes out at the other end after a lot of good minds have applied themselves to the problem.


Science uses 'working' facts and close reasoning to re-examine existing understanding in light of empirical evidence to try to discover new 'working' facts'.

Some of the 'working facts' have been around long enough to be considered 'hard facts'. Others haven't.

The important thing is to be clear about the sort of grade of knowledge you are dealing with at any time.



Phoebee said:


> It is rarely about instant agreement. It is about argument, and demanding proof, but it is also about having an open mind and not treating prior knowledge as incontrovertible doctrine.


You are overgeneralising Pheobe. SOME prior knowledge SHOULD be treated as incontravertable. The trick is getting the epistemic valuation right in any particular case.



Phoebee said:


> Science is ultimately a tool for _discovery_, and about "establishing" better and better proven knowledge, not about protecting "established" past truth.


Sure, but you don't go throwing the baby out with the bathwater - not anyway till you're sure you have a better baby. And you definately don't confuse speculation with hard facts.



Phoebee said:


> And regarding academic qualifications, science started as a hobby. Mendel was an observant gardener, who noticed particular traits of peas could be inherited according to simple rules.


Science didn't start with biology, or Mendel. Some historians of (modern) science give that honour to Aristotle, more than 2000 years earlier.



Phoebee said:


> I've seen arguments that he fudged his work a bit, disregarding results that would not fit his ideas, and his work probably would not pass peer review today. Yet this flawed amateur's ideas are now accepted as the basis for genetics.


It doesn't matter how new ideas arise, or who they arise in. A number of massively important insights have come to people in dreams for example. The only important thing is that they can be seen to fit, or improve, or replace existing knowledge and understanding through the process of close expert examination.

Till that has happened they are speculation. And we need to be able to tell the difference. And we need to call it when we see people wrongly characterising speculation as 'established' knowledge. 

Mike (UK)


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## Kosta Zhelev

The truth is always harsh Mike.Take instrumental insemination.I'm not clairvoyant Mike.It is impossible to know what is the recombination of genes.It is necessary to explore.Bee genetics is sufficiently flexible and variable to confuse the most - good beekeeper.We must be very brave to say that things are simple.We started from the inside out.And the more we go out we see the changes inside.It's about the honey bee.If we call speculation labor of the people, it must first look at ourselves.Economic interests there in both directions Mike.Who is the right time?I think in both directions to get to the truth.What information can we be helpful?I would say any information.It depends on us whether we accept it or not.Why not talk about how we apply the lessons learned so far in practical beekeeping?Will speak on this issue?


----------



## mike bispham

Kosta Zhelev said:


> Take instrumental insemination.I'm not clairvoyant Mike.It is impossible to know what is the recombination of genes.It is necessary to explore.Bee genetics is sufficiently flexible and variable to confuse the most - good beekeeper.We must be very brave to say that things are simple.


Some things are simple Kosta and some not. And some things are simple while also being complex.

For example, casinos always win in the long run. That's simple, inveitable, fact.

Each hand at cards, each turn of the roulette wheel is random. That's complex.

No matter how much complexity is involved in the random dealing of hands, the shuffling, the throwing of balls and spinning of wheels...

...the casino always wins in the long run. That's an objective truth, and it can be mathematically analysed and derived.

That is a direct and proper analogy. I don't need to be brave to say it - I just need to be familiar with basic mathematical facts of probability, and the way casinos use them. 

Similarly:

With sexual reproduction, no matter how complex are the facts of meiosis, a deeper set of conditions always holds true:

_Those parents well fitted to their environment will, in the long run, produce more offspring well fitted to their environment than the offspring of parents less well fitted_. 

And the converse is also true: Those offspring of parents poorly fitted to their environment, will, in the long run, be less well suited to the same environment than offspring of better-fitted parents.

That's a long winded way of saying: from the best come, in the long run, the best.

That's fact. _Nothing you can say about complex details of reproduction, or epigenetics, will alter it_.

Substitute at will: 'well fitted', 'healthy', 'resistant' (to x, y, z) 'best', 'strongest', 'most suited to'... 

_The simple fact remains_.



Kosta Zhelev said:


> We started from the inside out.And the more we go out we see the changes inside.It's about the honey bee.If we call speculation labor of the people, it must first look at ourselves.Economic interests there in both directions Mike.


I'm finding this cryptic - I imagine accidentally. But I don't want to guess at your meaning.



Kosta Zhelev said:


> What information can we be helpful?I would say any information.


I would say accurate and reliable information. 



Kosta Zhelev said:


> It depends on us whether we accept it or not.


Accepting speculation with the same force as established fact is foolhardy. 



Kosta Zhelev said:


> Why not talk about how we apply the lessons learned so far in practical beekeeping?Will speak on this issue?


I asked Peter recently (since its his thread) to clarify for me what practical use his adventures in advanced and sometimes speculative genetics might have. He replied and I critiqued his answers. What we really want now is his response to that critique. That's how conversation becomes the constructive tool of dialogue. To and fro, to and fro...

Mike (UK)


----------



## peterloringborst

> Those parents well fitted to their environment will, in the long run, produce more offspring well fitted to their environment than the offspring of parents less well fitted.


Yeah, we all learned about evolution in grade school. A ten year old can get this part. The question is: what does it mean to be fit? It will be something different for each species. Next, breeding has nothing to do with fitness, but_ selection of qualities we want_. Human beings have co-opted the plasticity of certain species to remake them according to our desire. Some responded better than others, like wheat, corn, dogs, beef. The original types of many domesticated species are already extinct, as they were not "fit." Further, extinction does not fall on the unfit alone; some creatures went extinct because people hunted them to extinction. Once again, you are attempting to simplify reality to make it fit into your idea of it. Reality in total will never be understood by people, it is always bigger (and better) than our ideas of it.


----------



## Rader Sidetrack

mike bispham said:


> For example, casinos always win in the long run. That's simple, inveitable, fact.


Not true!  

Casinos sometimes _*lose *_in the long run. For example ....



> ATLANTIC CITY - The _*bankruptcy *_auction of the troubled Revel casino hotel, which had been scheduled for Thursday, has been postponed until next week.Lawyers for the casino said in a court filing Wednesday night that they had received multiple bids for the casino by Monday's deadline and needed additional time to review them.
> 
> Read more at http://www.philly.com/philly/busine...cy_auction_postponed.html#zwGyGM03O60I6vyT.99


Mike seems to see life (at least he tells us that it is) as black and white - but in reality it is a whole spectrum of _*shades of gray*_.

:gh:


... beekeeping included ...


----------



## Michael Bush

"Reality in total will never be understood by people, it is always bigger (and better) than our ideas of it."--Peter Loring Borst

I like that. My version is a little different. I've always said "reality is far more wonderful and far more terrible than we can imagine." This is especially true of anything we have no real experience at. We usually have a very simplified model that misses most of the reality. As we progress we get a better and better model that still misses most of the reality... but takes into account more of it as we go...

But I like yours a lot as well. Do you mind if I quote it and credit you for it from time to time?


----------



## JSL

peterloringborst said:


> Next, breeding has nothing to do with fitness, but_ selection of qualities we want_.


Peter, I am puzzled by this statement. I think you are saying that many breeders select for traits that more beneficial to humans than to the plant or animal. However, fitness does have many implications, and I think it should be an important consideration in selection programs, especially in species that are semi-managed and yet subject to the challenges of environment.


----------



## peterloringborst

> But I like yours a lot as well. Do you mind if I quote it and credit you for it from time to time?


Not at all, Michael. Please feel free to do


----------



## peterloringborst

> Peter, I am puzzled by this statement. I think you are saying that many breeders select for traits that more beneficial to humans than to the plant or animal. However, fitness does have many implications, and I think it should be an important consideration in selection programs, especially in species that are semi-managed and yet subject to the challenges of environment.


Of course. Perhaps it would serve us all better if we selected for fitness, but that is easily done by leaving the bees alone. Selection implies choosing criteria and that's what people do when they breed plants or animals. It is seldom simply fitness we want. For example, if you bred bees for survival alone, you may find that they developed all sorts of_ qualities you wouldn't want. _ 

There are several species of honey bee and the others are not so good for beekeeping at all. The tropical ones like dorsata and laboriosa won't live in hives, sting mercilessly and tend to abscond if things don't go their way. Those traits are the product of selection for fitness only by nature (natural selection). The things that people select for are productivity, being manageable, and disease resistance.

Now, lots of times you hear people say that the European honey bee has been selected for its willingness to live in hives and be manipulated like us (sort of like dogs) but there is absolutely no proof of this. We simply don't know what European bees were like prior to domestication. It's possible that the characteristics they have that we like were already in place 10,000 years ago. 

It could be that 100,000 years of living in hollow trees and caves selected for a bee that is not vicious, does not abscond, etc. So far as the willingness to be manipulated goes, the honey bee basically has no idea that it is being manipulated. It's just making the best of the situation from its own point of view by staying in the hives because they are suitable. In fact, it is us that has adapted to them.


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## mike bispham

JSL said:


> I think you are saying that many breeders select for traits that more beneficial to humans than to the plant or animal.


Can I add to that sentence: ... the plant or animal_ in its natural environment_.

It isn't always true - my bringing in resistance genes is, I think, probably of benefit to my local ferals - they might get some arrows to add to their quiver as it were. But generally speaking the changes made by domestication tend to reduce fitness to the natural environment (while improve 'fitness' in the domestic environment)

The impact of treatments on feral bees is a noteworthy example of what can happen, as you seem to note below: 



JSL said:


> However, fitness does have many implications, and I think it should be an important consideration in selection programs, especially in species that are semi-managed and yet subject to the challenges of environment.


I suspect that for the conversation about bee management - about husbandry and breeding - we might be better off using the term 'vigour' to describe that primary quality we seek. But its a useful exercise to use 'fitness' in its special evolutionay sense, and work through the issues using evolutionary understanding in parallel - especially as we want to be able to speak clearly about what happens in the feral population as well as the managed population.

This is all good stuff.

Mike (UK)


----------



## mike bispham

peterloringborst said:


> Perhaps it would serve us all better if we selected for fitness, but that is easily done by leaving the bees alone. Selection implies choosing criteria and that's what people do when they breed plants or animals. It is seldom simply fitness we want. For example, if you bred bees for survival alone, you may find that they developed all sorts of_ qualities you wouldn't want. _


Again, I think we could improve our ability to speak clearly about these things by using the terms 'vigour' when describing acts of husbandry.

A beekeeper wants, primarily, colonies that are vigourous, strong. Weak colonies don't make lots of honey. That desiderata 'wraps up' broad spectrum resistance to all present predators (practically speaking micro-predators and parasites). And that is most often the primary feature of natural populations of bees - since broad-spectrum resistance/vigour is the quality most necessessary to 'fitness' (proper) in the natural environment. 

I have no argument with the rest of what you say in this post. 

Mike (UK)



peterloringborst said:


> There are several species of honey bee and the others are not so good for beekeeping at all. The tropical ones like dorsata and laboriosa won't live in hives, sting mercilessly and tend to abscond if things don't go their way. Those traits are the product of selection for fitness only by nature (natural selection). The things that people select for are productivity, being manageable, and disease resistance.
> 
> Now, lots of times you hear people say that the European honey bee has been selected for its willingness to live in hives and be manipulated like us (sort of like dogs) but there is absolutely no proof of this. We simply don't know what European bees were like prior to domestication. It's possible that the characteristics they have that we like were already in place 10,000 years ago.
> 
> It could be that 100,000 years of living in hollow trees and caves selected for a bee that is not vicious, does not abscond, etc. So far as the willingness to be manipulated goes, the honey bee basically has no idea that it is being manipulated. It's just making the best of the situation from its own point of view by staying in the hives because they are suitable. In fact, it is us that has adapted to them.


----------



## Kosta Zhelev

Yes Mike, the term "Vitality" is correct.But too summary.There are reasons the colony is so vibrant.The term "Susceptibility" is directly related to Vitality.This is the opposite of resistance.My attention is engaged by these terms.Not with vigor as a whole.Trying to figure out a little more about it.From personal experience I know that the conditions set by me can change the results.In this equation genotype is constant.Same with wild bees.I do not know have domesticated bees.Choice of housing in natural conditions is very different from those on offer.Why our hives decreased vigor?Because we do not know the specifics of bee hollow.For us they are not important.Bee biology is much more comprehensive than we think.Takes into consideration everything.I want to know why the colony lives, while others do not.Why some colonies despite playing field grow and others do not.We can not just say that they are viable.Greetings.


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## peterloringborst

> Choice of housing in natural conditions is very different from those on offer.Why our hives decreased vigor?Because we do not know the specifics of bee hollow.For us they are not important


Interesting. Tom Seeley is currently studying some 40 hives that he has set up as one story units and placed around the area. They receive no manipulation. No supers are added, they are simply checked from time to time to see if they are alive. He claims that a one story Langstroth hive is the same size as they would use in the wild, on average. 

I would like to do or participate in such a study myself, but can't afford to keep bees without getting some return from them. Plus, it would be tough for me to let them swarm and lose all those swarms. In my area there aren't that many swarms that I could restock simply by collecting bees. Would be an interesting experiment, though.


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## squarepeg

peterloringborst said:


> Interesting. Tom Seeley is currently studying some 40 hives that he has set up as one story units and placed around the area. They receive no manipulation. No supers are added, they are simply checked from time to time to see if they are alive.


that makes really good sense to me. if this were done on a 'local' level survivors might emerge with adaptations useful for that area. after proving survivability, grafts could be taken from these and distributed in the area. other information could be gleaned from them as well, such as behavioral traits, pollen and wax composition, ect. but as you have pointed out peter, the development of survival traits may come at a cost that would make them less desirable to the beekeeper, but then maybe not. i had thought about suggesting such a project to our state ag. dept.


----------



## peterloringborst

> i had thought about suggesting such a project to our state ag. dept.


It's an interesting project, no matter what the goal. It would be great to have unmanaged hives around, as long as they aren't reservoirs of disease. They would have to be monitored and not allowed to become sources of American Foul Brood. Other than that, introducing bees to the wild seems like a good idea. There are undoubtedly some folks who would object, since the honey bee is not native to the Americas and might compete with native bees. 

Personally, I don't think the honey bee is harmful but the nativists seem to object to everything that wasn't here before the Europeans came, excepting the European people (themselves). One has to make a clear distinction between non-native and invasive. There are plenty of non-native species that are not invasive and plenty of invasives that are not native. Our native black locust tree (Robinia) is considered invasive, for example.

Almost all of the best bee plants in my area are either non-native, invasive, or both. I was surprised to learn that many of them are actually listed by the New York State Department of Environmental Conservation as "illegal plants." At this point it is illegal to sell, transport, or propagate them. I wonder when they will start telling people they have to dig up the wild roses...


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## mike bispham

Kosta Zhelev said:


> There are reasons the colony is so vibrant. The term "Susceptibility" is directly related to Vitality. This is the opposite of resistance.


I think we are in agreement. These are two sides of the same coin. We have to breed, systematically, _toward_ health and vitality (supplied by resistance to micro predators and parasites), and _away from_ weakness and susceptability to disease. These are different ways of saying much the same thing. 



Kosta Zhelev said:


> My attention is engaged by these terms. Not with vigor as a whole. Trying to figure out a little more about it. From personal experience I know that the conditions set by me can change the results. In this equation genotype is constant.


Of course. You can make different size/shape/damp/dry etc. houses, stimulate with feed, spread brood, treat with xyz or not, and more. Lots of things can make a difference.

That's not to say genotype is irrelevent. Stubby legs will never make olympic runners. 



Kosta Zhelev said:


> Same with wild bees.I do not know have domesticated bees.Choice of housing in natural conditions is very different from those on offer. Why our hives decreased vigor? Because we do not know the specifics of bee hollow. For us they are not important. Bee biology is much more comprehensive than we think.Takes into consideration everything.I want to know why the colony lives, while others do not.Why some colonies despite playing field grow and others do not.We can not just say that they are viable.Greetings.


We can say that _some_ of the difference will lie in the genes, and that being skillfully selective is likely to improve things. 

We can also say that the biology of the bee is, like all organisms, _dependent on_ selection of one sort or another to maintain health, as its predators constantly evolve to take better advantage. Selection is _necessary to health and vigour_; and where positive selection is omitted by the beekeeper, nature picks up the strain by selecting negatively. That will show as low productivity, failure to thrive, susceptability to infection, winter losses. 

Whatever else might be causing low vigour as well, wherever there is poor genetic husbandry (or no genetic husbandry) _that will (all else being equal) be_ one of the factors. It couldn't be otherwise. 

Casinos that don't load the odds don't make money.

Beekeepers who don't load odds don't make honey. 

Roughly speaking.

Mike (UK)


----------



## mike bispham

peterloringborst said:


> Tom Seeley is currently studying some 40 hives that he has set up as one story units and placed around the area. They receive no manipulation. No supers are added, they are simply checked from time to time to see if they are alive. He claims that a one story Langstroth hive is the same size as they would use in the wild, on average.
> 
> 
> 
> It worth noting that in the wild an average is an average, and only a small proportion of real sites will conform to it. Its a very unnatural setting.
> 
> I do much the same thing, but give them space to expand the nest as much as they want. What this means is that those with the go to build big can produce proportionately more drones - which is a) one of nature's ways of making each new generation from the best of the last; b) exactly what I want to shape up my own drone population properly.
> 
> Seeley's experiment will (if his bees can manage varroa on their own) probably tend to swarm often, as they'll get cramped. Still, the fastest up to cramping will tend to make more offspring, and as long as they can find a new home the cream should tend to rise to the top over time.
> 
> I don't know if intergenerational development is part of his study though.
> 
> 
> 
> peterloringborst said:
> 
> 
> 
> I would like to do or participate in such a study myself, but can't afford to keep bees without getting some return from them.
> 
> 
> 
> If you can knock up your own boxes it doens't have to cost much. If you want to be able to look closely at them is costs more (removeble frames)
> 
> 
> 
> peterloringborst said:
> 
> 
> 
> Plus, it would be tough for me to let them swarm and lose all those swarms.
> 
> Click to expand...
> 
> Bait hives, properly done, often catch a good proportion.
> 
> Mike (UK)
> 
> BTW: hunting for eggs to graft is proving very hard just now. My (best) hives have almost completely shut down - only capped brood to be seen. I don't think there'll be any September mite explosions.
> 
> Click to expand...
Click to expand...


----------



## peterloringborst

Blundering Along in Bee Breeding


> Bee breeding has doubtless suffered more than has breeding of other animals from a lack of correct ideas of the laws of inheritance, it is gratifying to note that men of science are giving some attention to this subject but it would be better still if some of them would give us something through the press to take the place of the many ideas which so often suggest or directly teach wrong ideas.
> 
> We know that color and temper are separately inheritable, also size and color, and a little is known concerning a few other characters, but very little about any. Our great need just now is for some information that we can get from no body but the geneticist, whether cytologist or experimental breeder or both. Can’t we have a contribution now and then dealing with inheritance as it occurs in our strange little animals? Every breeder will welcome something really instructive for without some help on our problems we will just keep on blundering along and do but little in a long time.


C. C. Stone, Clarksville, Texas
In “The Beekeepers Item”
June, 1925


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## mike bispham

peterloringborst said:


> Blundering Along in Bee Breeding
> Bee breeding has doubtless suffered more than has breeding of other animals from a lack of correct ideas of the laws of inheritance, it is gratifying to note that men of science are giving some attention to this subject but it would be better still if some of them would give us something through the press to take the place of the many ideas which so often suggest or directly teach wrong ideas.


I don't think there is any other form of farming that suffers so much from ignorance of the basic principles of husbandry (I use that term in its fuller sense, taking in reproduction)

I have a theory as to why that is.

First, with few exceptions, commercial beekeepers (who live or die, as it were, on their skills in bee raising) have never been overkeen on sharing their commercial secrets. Second, most of the literature is written (and always has been) by amateurs. They've a) never needed to have reliable yields, and b) historically been helped out in health matters by the feral population and commercial breeding activity.

For these reasons there has been, historically, very little guidance. There simply isn't a strong tradition in the art of beekeeping that supplies guidance to breeding toward health and productivity. But it is there. Most writers will at least mention that it is sensible to make increase from your best. But there's rarely much discussion of why that is, or of how to go about it systematically.

Things have been made a whole lot worse in recent decades by the advice handed down from on high, and pushed hard by the dealers, that drugs are a satisfactory ongoing answer to health problems. The veterinary model of husbandry was always going to fail in an open mating animal. If there'd been a push early on in the varroa epidemic to educate beekeepers in the merits of selective reproduction that would have balanced things out a bit. But the commercial model was always going to do whatever it took to stay in control in the short term, and the commercials and the 'support industry' have been the representative 'stakeholders' who've most influenced policy. 

I think the attitude of most researchers has been little short of shameful. Anyone with a phd in the life sciences should have instantly and clearly seen what the long term effect of treatments would be, and advised hard against going that route - or at least worked hard to investigate the breeding alternative. With only a handful of honourable exceptions, they turned a blind eye and took the money. 

Mike (UK)


----------



## Rader Sidetrack

mike bispham said:


> I think the attitude of most researchers has been little short of shameful. Anyone with a phd in the life sciences should have instantly and clearly seen what the long term effect of treatments would be, and advised hard against going that route - or at least worked hard to investigate the breeding alternative.


And what of the attitude of some amateur bee breeders, Mike? :scratch:


> It can be seen that modern beekeeping practice is the [HIGHLIGHT] sole cause [/HIGHLIGHT]of the crisis affecting both wild and domestic bees.
> 
> http://www.suttonjoinery.co.uk/CCD/


You continue to falsely claim that "modern beekeeping practice" is the _*sole cause*_ for the decline of 'wild bees' when deep down you know that is not true.

You have earlier posted that landowner applied pesticides play a role in that issue, as well as forage availability. Neither of those issues are under the control of beekeepers.

Isn't it a bit _shameful _to continue to propagate this misstatement when you know its not true?


----------



## peterloringborst

> Anyone with a phd in the life sciences should have instantly and clearly seen what the long term effect of treatments would be, and advised hard against going that route - or at least worked hard to investigate the breeding alternative.


Anyone with a high school understanding of agriculture and economics could tell the effect of NOT treating, you lose the farm


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## Richard Cryberg

The subject of this thread is "Our understanding of genetics is changing." Hardly a thing has been said after 154 posts that actually addresses this subject. I taught myself genetics back when I was in high school oh so many years ago. Back then the topic was pretty simple to understand, even for a high school kid. We did not even have a clue what a gene was.

Today a good starting point for learning genetics is to take a course in calculus. Then you can learn thermodynamics and some organic chemistry. That prepares you for biochemistry. Along the way it would not be a bad idea to learn some stats and symbolic logic. About that time you can understand why the Gibb's free energy difference between the keto and enol forms of adenine are important. If you do not know this you do not know any modern genetics. Yep, it has changed all right. And, it is going to get a lot more complex over the next 20 years. The big new topic you need to learn today is control theory as we are starting to rapidly recognize the interesting stuff is not even what classically has been called genes. The best prep for that might be a degree in electrical engineering. A high school kid can no longer teach himself anything useful about modern genetics. Oh how the world has changed in 60 years. I can not come close to keeping up with progress.

Dick


----------



## Phoebee

Richard,

I'd like to see you expand that a bit.

I won't say I'm very good at calculus, but I've studied it. I don't see much application to genetics. Stats is essential. Digital logic could be helpful, but I would think the applicability of symbolic logic would depend on the context in which it was taught. What I got from set theory and philosophy logic courses would not seem to help an awful lot.

Contrary to your earlier assessment, I have studied thermodynamics, but in the context of engines. A thermodynamics course with an emphasis on bulk gas behavior will not give useful insights into genetics.

Organic and biochemistry: definitely. But start with general chemistry. That's where Gibbs Free Energy will be taught.

I also have a degree in electrical engineering technology. I'd love to hear why you think it applies to genetics. My personal explanation would be that it would help you to understand the operation of, and to maintain, your very own personal DNA equipment. It is NOT out of the question for an individual to own DNA analyzers and synthesizers. I've seen an analyzer for sale on e-bay for under $300 ... the new ones are so good that one a generation or two old is scrap. A friend of mine would like me to help him prove out the technology of a new method if he can get funding. And as I said above, understanding digital logic may help understand the logical switches that have been found in DNA. Systems engineering might also help. Fascinating field.

I would think computer programming and information technology would give insights. The evolution I've seen over the decades tells me that DNA is not a blueprint, it is more like a program filled with inputs and conditionals. Parts of it come into play when conditions warrant. It would appear that the bulk of DNA in a living organism is not genes (coding of specific traits) but rather mechanisms for controlling gene expression. To me, this is the key. Genes (stretches of DNA encoding specific traits such as spots on peas) can never explain what DNA does. It is far more like a highly adaptable computer program than it is like a blueprint or simple script.

I would absolutely recommend an interdisciplinary approach. I mentioned my biology degree earlier, but combining biology with electronics, or better yet a chemistry/biochemistry education with electronics, is a powerful career move.


----------



## Phoebee

I write science fiction now and then, and usually publish in _Analog Science Fiction and Fact_. http://www.analogsf.com/2014_10/index.shtml

One of the very best SF authors is a fellow named David Brin. He has a story in the October 2014 issue (already out, probably still on the shelves as this is written).

David is a physicist, but also a polymath. He knows an awful lot about life. The story he has in the October issue is "Chrysalis". Although the central idea in the story is highly speculative and unproven, you can always depend on David to have done his homework, and to have thought out the story in tremendous detail. You see this in his Uplift Wars series of novels. Genetics comes up in those, an also in some of his other works (_Glory Season_ especially). You can tell he's followed the field closely, and in this particular story you'll see his insights into the genetic processes underlying insect development, which is where the story gets its title.

His extrapolation to human development will leave you with a creepy feeling, hoping he is not right.

The complexity of the switching mechanisms controlling life stage development is the underlying science in the story, and you can tell he has really looked into it. Beekeepers with a scientific interest in their avocation will enjoy it.

I recommend it highly. Possibly the best piece of short fiction to appear in the magazine all year.


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## peterloringborst

Richard Cryberg said:


> The subject of this thread is "Our understanding of genetics is changing." Hardly a thing has been said after 154 posts that actually addresses this subject.


My initial post was this



> Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions" in evolution -- four inheritance systems that play a role in evolution: genetic, epigenetic (or non-DNA cellular transmission of traits), behavioral, and symbolic (transmission through language and other forms of symbolic communication). These systems, they argue, can all provide variations on which natural selection can act. Evolution in Four Dimensions offers a richer, more complex view of evolution than _the gene-based, one-dimensional view held by many today. _


I would have preferred the conversation to stay on this topic by it got sidetracked by people insisting on lecturing. I have no intention of lecturing but examining what is being discovered and how it does or doesn't apply to what we see in the field of honey bee genetics. 

Very few people are taking bee genomics to the next level, which is to use RNA interference to silence or activate genes or pathways in order to understand their function. Also, the role of microbiotic inheritance, and the possibility of cultural inheritance in a eusocial colony. 

It is entirely possible that these colonies are capable of learning things about the environment, etc. and passing these on to the next generation. Also, there is the memory of the immune response, which is passed on by higher animals and probably eusocial colonies as well.


----------



## peterloringborst

> I would think computer programming and information technology would give insights. The evolution I've seen over the decades tells me that DNA is not a blueprint, it is more like a program filled with inputs and conditionals.


Exactly. Some of the best minds are writing programs that can parse and interpret the vast quantities of data that are being generated as genomes, proteomes, etc. are being sequences. One of the amazing things is the fact that so many of these sequences appear in all living organisms, giving plain clear evidence of inheritance over millions, even billions of years. Also, many of these sequences, while conserved, appear to be re-purposed by organisms that inherit them.


----------



## Phoebee

peterloringborst said:


> Exactly. Some of the best minds are writing programs that can parse and interpret the vast quantities of data that are being generated as genomes, proteomes, etc. are being sequences. One of the amazing things is the fact that so many of these sequences appear in all living organisms, giving plain clear evidence of inheritance over millions, even billions of years. Also, many of these sequences, while conserved, appear to be re-purposed by organisms that inherit them.


You, especially, would get a kick out of Brin's "Chrysalis." The quote above is exactly why.


----------



## peterloringborst

> You, especially, would get a kick out of Brin's "Chrysalis." The quote above is exactly why.


I will seek it out, then!


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## peterloringborst

One of the interesting things about genetics is linkage. Traits can be linked in various ways. Here is a discussion of smaller bees:


> Smaller, more Africanized-like genotypes of honey bees, may have more undesirable characteristics for beekeeping practices (high tendency to run, to hang, to fly, and to sting) than larger, more European-like genotypes. However, smaller bees may be more hygienic than larger bees. Thus, smaller bees with some degree of Africanization may be more tolerant to brood diseases and Varroa mites.


Genetic Correlations Among Honey Bee (Hymenoptera: Apidae) Behavioral Characteristics and Wing Length
Annals of the Entomological Society of America, 95(3):402-406. 2002.


----------



## mike bispham

peterloringborst said:


> Anyone with a high school understanding of agriculture and economics could tell the effect of NOT treating, you lose the farm


Not if you go about it properly. 

In the early days that was largely true - but it isn't anymore.

I agree that bare economics will tend to support treating - when it takes a short term view. 

That doesn't mean everyone else has to go along for the ride.

Mike (UK) (Who is happily building a farm without treating)


----------



## mike bispham

Richard Cryberg said:


> Today a good starting point for learning genetics is to take a course in calculus. Then you can learn thermodynamics and some organic chemistry. That prepares you for biochemistry. Along the way it would not be a bad idea to learn some stats and symbolic logic. About that time you can understand why the Gibb's free energy difference between the keto and enol forms of adenine are important. If you do not know this you do not know any modern genetics. Yep, it has changed all right. And, it is going to get a lot more complex over the next 20 years. The big new topic you need to learn today is control theory as we are starting to rapidly recognize the interesting stuff is not even what classically has been called genes. The best prep for that might be a degree in electrical engineering. A high school kid can no longer teach himself anything useful about modern genetics. Oh how the world has changed in 60 years. I can not come close to keeping up with progress.
> 
> Dick


Dick,

Interesting remarks; and, as you note on topic.

However, we should bear in mind: just because we're going to fail to comprehend 99% of the actual mechanisms of modern genetic understanding, not all that much has changed at the level of husbandry.

The basic code is still inherited from the parents, and still supplies the core proteins. 

Making bees from unhealthy bees will tend, all else being equal, to result in unhealthy offspring.

And so on. Selective propagation remains essential, and that is unlikely to change. 

Do you agree?

Mike (UK)


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## mike bispham

peterloringborst said:


> I have no intention of lecturing but examining what is being discovered and how it does or doesn't apply to what we see in the field of honey bee genetics.


I'ts dawning on me that your expression 'field of honey bee genetics' is only marginally concerned with things like population dynamics? Its interested in the mechanisms by which individuals acts as agents for population changes, but regards the dynamics of population changes as outside its scope.

Is that a fair summary? 

BTW if you could learn to be polite there'd be a lot less of the lecturing tone from this end. Rudeness begets rudeness, and a downward spiral is the usual outcome. Tiresome though it is, being polite does include responding to questions.

Apologies for the lecture.

Mike (UK)


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## mike bispham

peterloringborst said:


> One of the interesting things about genetics is linkage. Traits can be linked in various ways. Here is a discussion of smaller bees:
> 
> Genetic Correlations Among Honey Bee (Hymenoptera: Apidae) Behavioral Characteristics and Wing Length
> Annals of the Entomological Society of America, 95(3):402-406. 2002.


This doesn't appear to be restricted to African genetics. I'm seeing more and more smaller bees among my best. 

Mike (UK)


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## Rader Sidetrack

mike bispham said:


> Mike (UK) (Who is happily building a farm without treating)


I expect that 'happily building a farm' takes quite a lot of time out of a successful farmer's day. You seem to be a very dedicated farmer - doing what needs to be done on the farm - and then still having enough hours left in the day to share your thoughts with us. Thank you for your dedication. :thumbsup: :thumbsup:





mike bispham said:


> Tiresome though it is, being polite does include responding to questions.



As busy as you are, Mike, no doubt it was just a simple _oversight _that a polite fellow like you missed my question in post #153. For your convenience, I am asking it again here ....



Rader Sidetrack said:


> Isn't it a bit _shameful _to continue to propagate this misstatement when you know its not true?


The misstatement that I was referring to is on your website, regarding "_modern beekeeping practice_". You can click the blue arrow in the quote box to see the full details if you aren't sure exactly what I'm referring to.


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## Richard Cryberg

"The basic code is still inherited from the parents, and still supplies the core proteins.

Making bees from unhealthy bees will tend, all else being equal, to result in unhealthy offspring.

And so on. Selective propagation remains essential, and that is unlikely to change. "

Simply wrong in practice. Selection has little to do these days with what you call "core proteins." That is the old thinking that prevailed back when we knew so little I could teach myself genetics as a high school kid. Those days are long gone. You fail to understand how unimportant those proteins are and how unimportant minor changes in amino acids incorporated into those "core proteins" are. In general any change in amino acid is going to either do nothing measurable or hurt anything you are selecting for. Such mutations are dead common and you likely could spend a life time and never find one that was useful. What is important is the control and feedback mechanisms that regulate the amount of those proteins produced. Little in classical breeding is of much use at all in selecting for those regulatory functions with any degree of efficiency. We sure did not produce today's Holstein cattle doing classic breeding programs. There is a good reason a modern undergrad intro to genetics course spends about a day on classic Mendelian genetics and considers that fully adequate. And, then you take an entry level grad level course and the prof introduces it the way a very good friend of mine introduces his course. "You think you know something about genetics. Within a week you will realize you entered this course knowing nothing at all about genetics."


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## peterloringborst

> Increased applications of genome-level investigation has helped provide a better understanding of how a variety of factors influence honey bee health. With sequencing of the honey bee genome, broad-scale investigation of the genetic pathways involved in honey bee immune response became more tractable. Among other possibilities, selective pressure on disease prevention has acted predominantly on social behavioral responses to disease (such as hygienic behavior) and not individual innate immune responses.
> 
> Further investigation showed that bacterial immunostimulation of honey bees results in changes in expression of hundreds of genes, many of which are not normally associated with immune response. Changes in some of these, particularly those related to chemical signaling, suggest that changes in expression of non-immune response genes help to orchestrate behavioral changes, such as increased grooming (Wilson-Rich et al. 2009), that mitigate pathogen risks (Richard et al. 2012).
> 
> This hypothesis was further supported through investigation of the effects of Varroa infestation on gene expression. When Varroa infestation occurs, many gene expression changes occur, but bees with naturally higher tolerance to Varroa more highly express genes associated with olfaction and stimulus sensitivity, not immunity.
> 
> Further experimentation showed how genes that are upregulated by pollen consumption, like those involved in protein metabolism, are downregulated due to Varroa infestation (and the accompanying viruses that mites vector). This provides insight into how mites may stress bees nutritionally and thus, supplies clues that may be helpful in preventing some pest or pathogen effects (Alaux et al. 2011).
> 
> Further genomic investigations will also likely identify other players in honey bee social organization. For example, the detection of microRNAs in the honey bee genome has only recently begun to reveal the importance of these small, noncoding regions of RNA that regulate gene expression.


Honey bee sociogenomics: a genome-scale perspective on bee social behavior and health
Apidologie (2014) 45:375–395


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## mike bispham

Richard Cryberg said:


> "The basic code is still inherited from the parents, and still supplies the core proteins.
> 
> Making bees from unhealthy bees will tend, all else being equal, to result in unhealthy offspring.
> 
> And so on. Selective propagation remains essential, and that is unlikely to change. "
> 
> Simply wrong in practice. Selection has little to do these days with what you call "core proteins." That is the old thinking that prevailed back when we knew so little I could teach myself genetics as a high school kid. Those days are long gone. You fail to understand how unimportant those proteins are and how unimportant minor changes in amino acids incorporated into those "core proteins" are.


Richard,

You're going to need to back that up with references for me. I simply don't believe it.

You seem to me to be saying that all individuals of a given species are born equal, and differences thereafter are entirely epigenetic. That the old 'nature or nurture' issues have been resolved in favour of nurture. That you can take any individual and make it a perfect specimen simply by arranging for the right switches to be thrown. That inheritance has been shown to be a fallacy.

Have I got that right?

I'm not disputing that environment makes a difference, nor that there are regulatory/feedback mechanisms.

But individuals will come better and less able to use those mechanism as a result of inherited predispositions. 

Mike (UK)


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## mike bispham

peterloringborst said:


> Honey bee sociogenomics: a genome-scale perspective on bee social behavior and health
> Apidologie (2014) 45:375–395


Thank you Peter, very useful.

I note there is (only) one small reference to the evolutionary aspects of health /defences:

"_Among other possibilities, selective pressure on disease prevention has acted predominantly on social behavioral responses to disease (such as hygienic behavior) and not individual innate immune responses_." 

This statement (properly) acknowledges that these health-maintenance details _are subject to selective pressure_. That statement is accepting of the uncontraversial understanding that natural (and unnatural) selection works to locate and promote heath-supporting mechanisms through the overarching mechanism based on hereditary traits (see this Richard?) 

It also means that, what ever else might be achieved in terms of understanding of details, _any applications will play out according to the same general principles_. 

The general criticism of the medical approach to bee health stands, supported by the implication of this statement. In an open mating organism, artificial support leads directly and inevitably to the need for continuing artificial support, and the spread of that need in the local population.

Mike (UK)


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## peterloringborst

> In an open mating organism, artificial support leads directly and inevitably to the need for continuing artificial support, and the spread of that need in the local population.


You mean, like people? We are open mating, rely on medical support, are living longer than ever before and have fewer contagious diseases.


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## mike bispham

peterloringborst said:


> You mean, like people? We are open mating, rely on medical support, are living longer than ever before and have fewer contagious diseases.


Yes. 

Tell me, what do you thing happens to feral bee populations that interbreed with highly domesticated strains, where 'highly domesticated' means fatally reliant on human help.

Do you think that the input of highly domesticated genes is:

a) beneficial

b) harmful

d) neutral.

Give your reasons.

Mike (UK)


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## Kosta Zhelev

Here's a dream - Create bees clones.Whether you live to see this?They say bees can multiply 4.8 mm cell.Have any studies on the impact of this condition on the genome?We can talk a long time about how to influence and change the genome or the behavior of bees.For me the most - important is what's really going on with my bees.When they show the change of the conditions placed on me is that the regulatory mechanisms are underway.As hereditary unit genes are authentic to each individual.But the mechanisms remain the same.So I see two nurses / Queens / same behavior in terms of laying the hive, but with a different result as a success.Such a correlation can be made and other behavioral effects.Their daughters, however, are not so similar from the same perspective.This indicates that the same control mechanisms are more effective against certain strains.Resistant strains also demonstrate this.If the colony received more than others that means that his legacy will have to follow the same regime?Or vice versa.Direct genetic conventions require, but again the mechanisms work in this case.For me - it is right to recognize the changes in the experimental findings.There will be more such.Greetings.


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## Phoebee

mike bispham said:


> Yes.
> 
> Tell me, what do you thing happens to feral bee populations that interbreed with highly domesticated strains, where 'highly domesticated' means fatally reliant on human help.
> 
> Do you think that the input of highly domesticated genes is:
> 
> a) beneficial
> 
> b) harmful
> 
> d) neutral.
> 
> Give your reasons.
> 
> Mike (UK)


One of my highly domesticated hives returned a mite count of 0 on last weekend's sugar roll. We've done no treatments but a few sugar dustings and feeding them.

I happen to appreciate your thinking on the TF approach, but "highly domesticated" does not have to mean "fatally reliant on human help." That definitely CAN be the outcome, but it turns out that human beings are pretty adaptable, too, including a cultural ability to learn from our own mistakes plus the mistakes of others. We can, in fact, adapt the same skills in husbandry that we use to breed gentleness and high honey production to produce bees with varroa resistant characteristics. I seem to have a couple of queens which are pretty far along in this regard (due to the skill and luck of others).

"Good genes" are part of that, absolutely. But only a part. DNA is more than genes. And the microbes the bees share their lives with count. And the mites themselves are part of the equation, as are the diseases they carry.

One of the more important adaptations in nature is for parasites and disease organisms to "figure out" that it is bad strategy to kill your host.

Mixing feral and domestic bees very likely benefits both. In the feral population, any "bad" domestic inherited traits will not be much of an issue ... won't live. But good ones we've selected for will help. And the DNA goes both ways. Drones are notoriously hard to manage.


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## peterloringborst

> feral bee populations that interbreed with highly domesticated strains,


The honey bee has never been domesticated. Some are easier to manage than others, but this is not the result of breeding. Feral bees are not behaviorally distinct; they are only feral by definition (escaped to the wild). African bees, on the other hand are behaviorally distinct from European bees.


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## mike bispham

peterloringborst said:


> The honey bee has never been domesticated. Some are easier to manage than others, but this is not the result of breeding.


It isn't? Choosing the most gentle to make more bees has no effect on the next generation? Or that isn't 'breeding'?



peterloringborst said:


> Feral bees are not behaviorally distinct; they are only feral by definition (escaped to the wild). African bees, on the other hand are behaviorally distinct from European bees.


There is a growing number of studies that show feral bees are managing mites on their own, through inherited behaviours. You yourself have posted links to and quotes from some of them. What on earth are you on about? Are you saying there is evidnce that these abilities are not rooted in specific behaviours? Can you point us to responding or contradictory papers that support your claim?

Lets focus on the question:

I gave my definition of 'highly domesticated' as follows:

"'highly domesticated' means fatally reliant on human help"

Just to be clear that means if they don't get human help they perish.

As I understand it most commercial bees fall into this category. 

We can argue further about this definition if you like, till we agree a satisfactory description of the dependent nature of commercial bees, and agree a term to use if 'domesticated' is not to your liking. (That's Randy Oliver's term btw) And then we can address the question.

Or, 

The question set will become the Loring Borst Test II; that is, another simple question (like that in post #65) that you cannot answer or fault (without imo, your larger position unravelling).

I'm not surprised btw that you don't want to. You are highly invested in the notion that treating bees, and learning more about them in order to treat them in novel ways, is, overall, beneficial.

Actually, it isn't. Ever. Its a short term fix that's damaging in the long run.

Mike (UK)


----------



## mike bispham

Phoebee said:


> I happen to appreciate your thinking on the TF approach, but "highly domesticated" does not have to mean "fatally reliant on human help." That definitely CAN be the outcome, but it turns out that human beings are pretty adaptable, too, including a cultural ability to learn from our own mistakes plus the mistakes of others. We can, in fact, adapt the same skills in husbandry that we use to breed gentleness and high honey production to produce bees with varroa resistant characteristics.


Thank you Pheobe, my position exactly.

By my question is designed to address the issue of what happens when bees that generally perish when not aided interbreed with bees that generally thrive unaided. If you want to put forward a different term, fine. 



Phoebee said:


> "Good genes" are part of that, absolutely.


There's something about bees that perform hygenic actions that isn't present in bees that don't. That something is a specific molecular presence on their dna. This isn't arguable - the trait locii of several specific critical behaviours are known. 

These are straightforward genetically based traits. They may well have epigentic components. But without the genes those components won't be present. 

Of course there are other influences. However; hygenic (and other mite-management traits) are known to be genetically based - where 'genetically' has the simple old-fashioned inheritable dna present-or-not, can-be-bred-in, can-be-bred-out meaning. There is ample scientific evidence of this. 



Phoebee said:


> And the mites themselves are part of the equation, as are the diseases they carry.


All organisms live in a context, and much adaptation is in fact co-evolution. That's a given.



Phoebee said:


> One of the more important adaptations in nature is for parasites and disease organisms to "figure out" that it is bad strategy to kill your host.


Sure. It turns out that one of the most important mite-management traits involves the (genetically based) ability to suppress more fecund mites in favour of less fecund mites. Bees can 'breed' the kind of mite they can live with.



Phoebee said:


> Mixing feral and domestic bees very likely benefits both. In the feral population, any "bad" domestic inherited traits will not be much of an issue ... won't live. But good ones we've selected for will help. And the DNA goes both ways.


That sort of conclusion might well be true if the injection of domestic bees is a one-off, short term thing. But as you note, in the short term they will tend to pass along genes that will kill the ferals. And, since treatments are systematic and long term, that state of play will tend to continue.

So,

Any new drug fixes will have the same effect. The more we help domestic bees to survive without adapting, the more we undermine the ability to survive of those feral bees they come into contact with. 

I fail to see how this is, overall, helpful to the goal of allowing and helping bees adapt to their number one predator, the disasterous varroa mite.

Mike (UK)


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## Phoebee

There's a repeated pattern in nature, the 95% die-off. I don't think I could possibly count the number of times I've seen it. And I've seen 80% a number of times as well. A new disease crops up and the population is devastated. One of the more tragic was the effect of smallpox and other European diseases on American Indian populations on first contact.

The 5% of survivors seed the eventual recovery of the species, but much diversity is lost. Full recovery may take centuries. Sometimes it never recovers.

If commercial beekeepers accepted losses of that magnitude, agriculture dependent on honeybees would collapse. Economically speaking, treatment free is not an option for large scale commercial operations.

I'm delighted that people are trying it. I expect it to work, in time. It probably would work faster if everybody accepted the losses and did it. But our diets would be pretty sorry for a few decades.

I expect to treat my strongest hive for varroa fairly soon. I'm getting mixed messages on the mite drop rate. I think they MAY be dealing with the problem on their own, but their method for dealing with it may be causing an artificially high drop rate. A dose of formic acid should drop most of the mites and give me a true idea of how many of them are really present, so I can interpret the problem. There's also a grizzly job of counting mites on dronesicles I should do this afternoon. This treatment should in no way change the viability of the colony if they are, in fact, getting the job done on their own, it just temporarily removes a selective pressure if they are not.


----------



## Richard Cryberg

mike bispham said:


> Richard,
> 
> You're going to need to back that up with references for me. I simply don't believe it.
> 
> You seem to me to be saying that all individuals of a given species are born equal, and differences thereafter are entirely epigenetic. That the old 'nature or nurture' issues have been resolved in favour of nurture. That you can take any individual and make it a perfect specimen simply by arranging for the right switches to be thrown. That inheritance has been shown to be a fallacy.
> 
> Have I got that right?
> 
> I'm not disputing that environment makes a difference, nor that there are regulatory/feedback mechanisms.
> 
> But individuals will come better and less able to use those mechanism as a result of inherited predispositions.
> 
> Mike (UK)




Interesting you leap to the conclusion I am talking about epigenetics. In fact my comments had nothing at all to do with epigenetics and I was not thinking about that topic at all. I will say the best queen you ever raise will be the result of epigenetics. But, that is always true.

What I was actually thinking about was things like TATAs and other micro and mini satellites as well as supplemental mutants all of which are all normal DNA but can be and often are non coding for protein. All are dirt common. Even supplementals of supplementals are dirt common. And, frequently recessive to boot. Short of a monogamous breeding situation, thousands of generations and many thousands of offspring you are never going to concentrate those by classic breeding selection. I am not going to supply refs as if you have not studied molecular genetics and do not have all the kinds of advanced course background in some form, even if self taught like I am in many of these areas, you really are not going to be able understand any of them. It would take hundreds of refs to start to do justice to these subjects. These things are so difficult to deal with that even when we know for sure they exist and what they do to phenotypes sorting them out with classic breeding experiments can be near impossible to fully impossible. You simply must have a lot of whole genome DNA sequencing data to sort them out. Including things like SNP maps or the equivalent. 

I am fear that a smattering of genetics knowledge like you get even in a modern introductory undergrad course today is simply far short of the knowledge you need to understand such topics. I doubt if you can even find a low level course book that uses the word supplemental mutant. An excellent book might mention things like micro and mini satellites very briefly in passing. Most will not. But, rest assured they are dirt common and absolutely vital to progress in understanding whole organism phenotypes.

I will define supplemental mutant for you so perhaps you can grasp a little why they are so difficult. A supplemental mutant is simply a situation where wild type is epistatic to some mutant but that mutant can express in the presence of some other enabler mutant. In most recognized cases the supplemental is either codominant or dominant in the presence of the enabler. This is because recessive supplementals are generally impossible to deal with in classic breeding situations. The enabler is generally a recessive which may, or may not have expressivity issues that complicate the situation. A supplemental of a supplemental is simply a supplemental that will not express unless another supplemental is acting as an enabler. The ones I know of are either very weak codominants or recessives.

To sort out such situations in honey bees would require raising a lot of sister queens all II by a single brother drone as well as lots and lots and lots of DNA sequencing on individuals produced along with hive testing for performance. Of course half those queens are going to be useless as they are going to lay 50% diploid drones so you can not hive test them. Those are all culls.

The best anyone can probably ever hope to get by classic breeding programs in varroa tolerant queens is probably already available in VSH and Minnesota Hygienics. I think it highly unlikely anyone will improve on them significantly by classic breeding programs. Given enough time and thousands of queens someone might get lucky with one queen like Oliver did with one cross between VSH and MH. But, propagating her and maintaining her performance is very unlikely due to polyandry in bees. Besides, she was most likely the result of epigentics and not DNA. Does it make practical sense to reinvent the same wheel Harbo and Spivac already invented? I think not personally. We need a genetic breakthru, not more of the same. And classic breeding is not going to give it to us.

What we probably need is some combination of very detailed understanding of varroa at a molecular level plus some GMO to get artificial genes in queens to exploit some molecular weakness of varroa. Something like what was done to make roundup ready soy beans for example. That is unlikely to happen soon. Honey bees simply are too small a market to bother spending the major $ needed for such work today. It might be easy in another 25 or more years. Today it is not easy.

Peter is dead on the money. Our understanding of genetics is changing. What he did not say is it is changing fast and will change even faster in the future. The topic is now at the limit of what self teaching for enjoyment and curiosity can deal with. I am rapidly being left in the dust at an alarming rate. And, I have the advantage of knowing college profs in genetics that are willing to talk to me one on one regularly and help turn jargon into English I can understand. When you are a minor collaborator on their projects they tend to spend some small amount of time with you. Sometime I might even contribute enough to get my name on a publication they write. But, if that does not happen it is ok by me.

Dick


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## Phoebee

40 years ago, when I was studying biology, we were not all that far past Watson and Crick. And nobody had heard of Rosalind Franklin. We knew there were genes in DNA, we knew the chemistry, we understood how it replicated (on at least a basic chemical level). We could more or less tease out the pathways for getting from DNA to RNA to ribosomes to proteins (although tertiary structure was still a huge hurdle). We knew about tRNA and mRNA, but I don't think the regulatory functions were known. We were taught that most of DNA was "junk", which sounded pretty suspicious to me.

39 years ago, people were just starting to talk seriously about genetic engineering. We could laboriously read short sequences of DNA, and we could similarly synthesize short sequences, 29 years ago, they started seriously considering sequencing the human genome. A few years into that project we found out that if you put really clever people on a really tedious job for a long time, they will get bored and invent a machine to do it for you. They did, and promptly finished the job, and started looking around for other things to sequence.

Today you can buy an analyzer that can sequence the human genome in ... I dunno, a day maybe? A friend of mine thinks it might be possible in an hour (down to base pairs), but the data flow is stupendous. We can compare against standards. We can take a sample from a 40,000 year old finger bone and spot differences from modern humans. We can tell that an ancient human was prone to male pattern baldness and had wet ear wax.

And we've found out some of what all that junk does. You don't hear about "junk DNA" any more.

We can make DNA at will, and even understand what the new stuff will do, more or less.

In short, we've gone, in 40 years, from realizing that there IS DNA, to being on the cusp of having godlike power. This is not the same as being God ... there's an awfully big gap in wisdom to cross that gap. We have this tremendous power at our fingertips. We're barely opening our eyes as to just what it does, and realizing the mind-numbing complexity of it. A lot of people are scared spitless of it, and rightly so. But this genie is not going back into the bottle. We now have the power to understand life on the molecular level.

The catch is, while life does have a molecular level, that's not the level where we live, nor the level where bees live. It may be the level at which bacteria live, but life is so much more than that. So even if we could understand the molecular level in exacting detail, to understand life you need to understand the consequences up to the macro level on which we live. Otherwise it is like understanding a computer language in minute detail without understanding the _function_ of what you can build from the language elements. And beyond that function, understanding how people will _use_ the programs. We didn't understand the computer revolution back in the 70's (rather, Grace Hopper did but almost nobody else). We don't understand the impact of this godlike knowledge on our future, either.

In science fiction, good writers learn that no good story is about the gadget. The story is about people, their problems, and how they deal with their problems. The gadget plays a role, and in science fiction the science must be a key, but stories are about people. That's a macro level, not rivets.

Are there genes? Of course. But between genes and bees there is an awful lot of complexity. Is there no life without DNA? Certainly not for the last few billion years, on this planet at least. But there is an awful lot more to life than DNA.

Prions, anyone?


----------



## D Semple

Richard Cryberg said:


> I will define supplemental mutant for you so perhaps you can grasp a little why they are so difficult. A supplemental mutant is simply a situation where wild type is epistatic to some mutant but that mutant can express in the presence of some other enabler mutant. In most recognized cases the supplemental is either codominant or dominant in the presence of the enabler. This is because recessive supplementals are generally impossible to deal with in classic breeding situations. The enabler is generally a recessive which may, or may not have expressivity issues that complicate the situation. A supplemental of a supplemental is simply a supplemental that will not express unless another supplemental is acting as an enabler. The ones I know of are either very weak codominants or recessives.
> 
> Dick


Thanks Dick

That is far and away the most complicated paragraph I have ever read.

Cheers. 


Don


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## mike bispham

Phoebee said:


> The 5% of survivors seed the eventual recovery of the species, but much diversity is lost.


Youll need to put figures on that Pheobe. My understanding is that little diversity is lost except in highly extreme cases, and in the great majority of cases such loss is unimportant. 



Phoebee said:


> Full recovery may take centuries. Sometimes it never recovers.


Again with references. Its my understanding that repopulation is generally rapid and complete. (See my table here showing repopulation assuming annual doubling: http://www.suttonjoinery.co.uk/CCD/thesis.htm) 

This is simply everyday stuff in nature. Populations rise and fall all the time.



Phoebee said:


> If commercial beekeepers accepted losses of that magnitude, agriculture dependent on honeybees would collapse.


You're building on doubtful premises; but yes I accept there would have been great losses, and that at the time nobody knew how long recovery would have taken. But 'agriculture dependent on bees' is a tiny fraction of our food needs. It would have been painful for some, but a drop in the ocean in the larger picture.



Phoebee said:


> Economically speaking, treatment free is not an option for large scale commercial operations.


Some are doing it. Its more the case that that treatment free represents an investment and skilled labour cost that is not quite competitive with short term/veterianary management. The market leads, and screw the damage. 



Phoebee said:


> ...our diets would be pretty sorry for a few decades.


(Accepting your premise just for the sake of argument) try putting actual crops to that statement and see what percentage of food variety actually disappears. In reality our selection of puddings would be lightly impacted. No staples would be affected. 




Phoebee said:


> A dose of formic acid should drop most of the mites and give me a true idea of how many of them are really present, so I can interpret the problem.


It'll give you a reading on the immediate problem, while totally obscuring altogether more useful data - the degree of resistance.

Mike (UK)


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## mike bispham

Richard Cryberg said:


> The best anyone can probably ever hope to get by classic breeding programs in varroa tolerant queens is probably already available in VSH and Minnesota Hygienics. I think it highly unlikely anyone will improve on them significantly by classic breeding programs.


A few question Dick

1) Is this anything more than your own theory?

2) Have you made, and read, any comparative study of the different breeding programs that have been undertaken; evaluated the progress of those studies currently being made, seen evaluations of any of the many private breeding/husbandry operations that are succeeding in keeping bees perfectly well without recourse to treatments or other medical interference?

3) Are you quite sure that normal time tested selective breeding methods can simply be abandoned, now that you are able to tell us that they have, and have never had, any effect whatsoever? 

I don't doubt a super-duper high-tech highly funded GM program could someday turn out a better bee. I'd like to ask, before it's tried, what sort of effect its likely to have on the natural population. 

I'd like to ask whether the super-GM bee will have to be bought at some expense from a specialist supplier on every occasion. 

I'd like to ask whether beekeeping or society at large will actually benefit from such a thing. 

Mike (UK)


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## Oldtimer

Been away from this thread for a while & just got back & opened the last page & started with Phoebees post, wow, what a fascinating post! Certainly threw a whole new light on my 40+ year old schoolboy understanding of genetics. So many things covered there I can hardly begin to fathom it.

Also caught a snippet (just from quotes) of what Richard Cryberg has been saying, awesome stuff! Tomorrow when I am more relaxed I'll read the whole thread. It's one of the things I love about Beesource, there are experts here on just about any topic you need.


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## Lauri

I've _got_ to find a way to get internet in my wall tent at hunting camp. Then I'll have the time to read through threads like _this_.

But at least I my book is due to arrive today. At least I'll have that. I expect some of it will be a bit above my comprehension, but it will certainly give me some new insight and inspire my thoughts for the 2015 season.

Amazon also has these: 

http://www.amazon.com/dp/B001ANVDMA/ref=pe_385040_121528360_TE_dp_1

http://www.amazon.com/dp/B001ANVDMU/ref=pe_385040_121528360_TE_dp_1

I got medium and fine point for possibly double marking queens for both year and specific line.


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## peterloringborst

> it is like understanding a computer language in minute detail without understanding the function of what you can build from the language elements.


Right on. DNA does resemble a language, written in secret code. Cracking the code does not give access to the language, that has to be understood as well. But understanding a language still doesn't give you access to the meaning of the language in all the various contexts: ordinary speech, literature, technical manuals, legal mumbo jumbo, etc. 

Where are we on the road to understanding genetics? Not very far. We can use some of what we have learned about the language, pretty much like I can order a cup of coffee in Slovenia. I can describe beekeeping in Spanish, but probably couldn't answer any questions. I can write poetry in English, but can't understand most of other people's poetry. 

You get the drift: there are many levels of understanding, fluency, expertise. Being able to insert a Bt sequence into a plant doesn't mean you have the tiger by the tail. Creating Roundup Ready corn doesn't mean there will be cattle that are nothing but filet mignon any time soon. However, it may be possible to access important immunity systems in the very near future, both in agriculture and in medicine.


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## Daniel Y

mike bispham said:


> It'll give you a reading on the immediate problem, while totally obscuring altogether more useful data - the degree of resistance.
> 
> Mike (UK)


You can base the degree of resistance on the level of infestation. In fact it would be impossible to measure what they did not have. I do not buy that complete resistance just appears complete in a given colony. So if that is true then how do you progress to breed the best to the best (most resistant to most resistant) If you do not keep it alive? Seems to me the best thing to do with any infested failing colonies is let them die out to the last remaining two. treat and breed from those two colonies. With particular emphasis on producing large numbers of colonies from them to flood the drone population for miles around. Simple principal there is that there are nearly 2 dozen drones mating for every queen. Share the genes where it counts the most.

One problem I see with that is how to manage the over resistant nature of Varroa sensitivity. You go from bees that cannot survive varroa infestation to bees that cannot tolerate there resistance to them. Sucks when nature insists on ignoring your best interests.


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## jim lyon

Oldtimer said:


> Been away from this thread for a while & just got back & opened the last page & started with Phoebees post, wow, what a fascinating post! Certainly threw a whole new light on my 40+ year old schoolboy understanding of genetics. So many things covered there I can hardly begin to fathom it.
> 
> Also caught a snippet (just from quotes) of what Richard Cryberg has been saying, awesome stuff! Tomorrow when I am more relaxed I'll read the whole thread. It's one of the things I love about Beesource, there are experts here on just about any topic you need.


Agreed! There are some subjects here that I prefer to just read and try to learn about while staying away from commenting. Genetics is one. I am pretty sure I can discern the difference between noise and information both of which appear in abundance on this thread.


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## Saltybee

Do not quite buying that letting everything but the last 2 to die is the best course either. You may want some of those traits that you are letting die later; like artificially large hives / unnaturally large winter stores/ highly risky early spring build up.


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## Daniel Y

mike bispham said:


> (3) Are you quite sure that normal time tested selective breeding methods can simply be abandoned, now that you are able to tell us that they have, and have never had, any effect whatsoever?
> 
> (A)I don't doubt a super-duper high-tech highly funded GM program could someday turn out a better bee. I'd like to ask, before it's tried, what sort of effect its likely to have on the natural population.
> 
> (B) I'd like to ask whether the super-GM bee will have to be bought at some expense from a specialist supplier on every occasion.
> 
> (C) I'd like to ask whether beekeeping or society at large will actually benefit from such a thing.
> 
> Mike (UK)


3. Once again, you twist things to support your forgone conclusion. You don't have to know how a car works to drive one. You don't have to know a thing about genetics for the methods of selective breeding to work. What you have to be able to do is recognize the traits that are desirable. So the answer is yes it works when it works for the species that it works for and you never have to understand why. I find your opinions are full of such pointless requirements. If selective breeding only worked for those that understand how it works. how did the first person that used it ever get it to work for them? They first saw the effect and then investigate as to the why. and that investigation continues. That it works is proof that there is a why it works. not the other way around.

(A) who cares. we don't keep animals to enhance nature. We keep animals to emphasis the benefits they have to us. Causing them to be less suitable and less likely to survive without care. the more highly bred bees are the more likely they are to have less impact on natural population simply because they will be more dependent on husbandry. Then of course if they did escape they are at a huge disadvantage against the nature made super bee you argue must exist. We all should know that nature is doing such a much better job of breeding bees that the advantage must be obvious for natural bees, right? I really am not sure why you think nature would need you assistance in breeding bees it's way. If your idea that natural selection will result in a better bee. then wouldn't we just go pluck them out of trees? Oh yeah I do. and about half the time they are crap.

(B) Do you think a person or company should not paid for what they produce? I am beginning to see a trend here. maybe you think you should be given whatever it is you desire. That the very universe should bend to your will. and if what you want is a better honeybee. by gum nature will surely provide it.

(C) results vary.


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## mike bispham

Daniel Y said:


> You can base the degree of resistance on the level of infestation.


You're right Daniel, though the longer you let things play out the better the reading you are likely to get.



Daniel Y said:


> In fact it would be impossible to measure what they did not have. I do not buy that complete resistance just appears complete in a given colony.


It may well. A new queen may well turn things around entirely. 



Daniel Y said:


> So if that is true then how do you progress to breed the best to the best (most resistant to most resistant) If you do not keep it alive?


Have a plan. Make increase; mate sensibly, allow time to show you how things are going, requeen...



Daniel Y said:


> Seems to me the best thing to do with any infested failing colonies is let them die out to the last remaining two. treat and breed from those two colonies. With particular emphasis on producing large numbers of colonies from them to flood the drone population for miles around. Simple principal there is that there are nearly 2 dozen drones mating for every queen. Share the genes where it counts the most.


Its a plan, but I'd want to take more steps than that.



Daniel Y said:


> One problem I see with that is how to manage the over resistant nature of Varroa sensitivity. You go from bees that cannot survive varroa infestation to bees that cannot tolerate there resistance to them. Sucks when nature insists on ignoring your best interests.


Is this something you have heard, and are repeating as gospel? Its not my experience, nor have I heard others sufferring from it? I have heard that too many patrilines expressing hygeinic behaviour is a bad thing, but only in the context of AI. Open mating generally gives a balance - if you are mating someplace with a reasonable chance of picking up genes conferring resistance.

Mike (UK)


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## mike bispham

peterloringborst said:


> Right on. DNA does resemble a language, written in secret code. Cracking the code does not give access to the language, that has to be understood as well. But understanding a language still doesn't give you access to the meaning of the language in all the various contexts: ordinary speech, literature, technical manuals, legal mumbo jumbo, etc.
> 
> Where are we on the road to understanding genetics? Not very far. We can use some of what we have learned about the language, pretty much like I can order a cup of coffee in Slovenia. I can describe beekeeping in Spanish, but probably couldn't answer any questions. I can write poetry in English, but can't understand most of other people's poetry.
> 
> You get the drift: there are many levels of understanding, fluency, expertise. Being able to insert a Bt sequence into a plant doesn't mean you have the tiger by the tail. Creating Roundup Ready corn doesn't mean there will be cattle that are nothing but filet mignon any time soon. However, it may be possible to access important immunity systems in the very near future, both in agriculture and in medicine.


Let's remember John Kefus advice: all you need to know is THAT it works, not HOW it works.

Few of us have much of a clue as to what goes on when we tap these keys to talk to each other. It doesn't matter: we know we can talk. 

None of us knows all that happens in the great complexity of bee life. But we can know how to defend genes that work well.

Some of us (not me) have a glimpse of the true complexity of living things. That doesn't make them better beekeepers. In fact they can be dreadful beekeepers.

Knowing the basics of population dynamics and genetic husbandry is critical to successful beekeeping in the longer term. Understanding the vast complexity of genetics isn't.

Its _ knowing what you need to know_ that matters.

Mike (UK)


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## squarepeg

so far and for lack of any other metric i have been using overall success in terms of colony strength and honey production as my selection criteria. i.e. my splits and grafts have come from my best colonies. each season i have fewer dinks and more strong and productive colonies. it's a simplified approach, but perhaps the proven colony is indicative of having all of the variables lined up in such a way that the job gets done.


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## mike bispham

Daniel Y said:


> 3. Once again, you twist things to support your forgone conclusion. You don't have to know how a car works to drive one. You don't have to know a thing about genetics for the methods of selective breeding to work. What you have to be able to do is recognize the traits that are desirable. So the answer is yes it works when it works for the species that it works for and you never have to understand why.


That's my story Daniel. Good to see you on board. 




Daniel Y said:


> I find your opinions are full of such pointless requirements. If selective breeding only worked for those that understand how it works. how did the first person that used it ever get it to work for them? They first saw the effect and then investigate as to the why. and that investigation continues. That it works is proof that there is a why it works. not the other way around.


Not sure what point you're making here - its pretty much a bunch of straw men. I like to point out that this obvious truth stands in contradiction to some of the statements made by others. 



Daniel Y said:


> (A) who cares. we don't keep animals to enhance nature. We keep animals to emphasis the benefits they have to us. Causing them to be less suitable and less likely to survive without care. the more highly bred bees are the more likely they are to have less impact on natural population simply because they will be more dependent on husbandry.


You have that the wrong way round. The more dependent they are on human help, the more likely they are to damage feral populations, and bees belonging to people who don't treat. that's the point the question is designed to bring home. You missed it.



Daniel Y said:


> Then of course if they did escape they are at a huge disadvantage against the nature made super bee you argue must exist.


It isn't a question of 'escaping' Its a question of the influence of such drones.



Daniel Y said:


> We all should know that nature is doing such a much better job of breeding bees that the advantage must be obvious for natural bees, right? I really am not sure why you think nature would need you assistance in breeding bees it's way. If your idea that natural selection will result in a better bee. then wouldn't we just go pluck them out of trees? Oh yeah I do. and about half the time they are crap.


That might be because they're your own escapees; or the offspring of your drones. 



Daniel Y said:


> (B) Do you think a person or company should not paid for what they produce? I am beginning to see a trend here. maybe you think you should be given whatever it is you desire. That the very universe should bend to your will. and if what you want is a better honeybee. by gum nature will surely provide it.


I don't mind people being paid for what they produce at all. I expect to be paid for what I produce. But I do object to people making things that have an environmental cost. Do you have a problem with that?



Daniel Y said:


> (C) results vary.


Do you object to people having the temerity to question the proported benefits of high-tech innovations?

Mike (UK)


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## mike bispham

squarepeg said:


> so far and for lack of any other metric i have been using overall success in terms of colony strength and honey production as my selection criteria. i.e. my splits and grafts have come from my best colonies. each season i have fewer dinks and more strong and productive colonies. it's a simplified approach, but perhaps the proven colony is indicative of having all of the variables lined up in such a way that the job gets done.


Is that with or without treatments SP?

Mike (UK)


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## squarepeg

all without treatments or artificial feeds.


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## mike bispham

squarepeg said:


> so far and for lack of any other metric i have been using overall success in terms of colony strength and honey production as my selection criteria. i.e. my splits and grafts have come from my best colonies.


So the selection criteria includes 'resistance to varroa and all disease organisms'.

And the result is: 'bees that thrive in the face of varroa all on their own'.

Just to be clear. Not for your sake SP, but so the others here can read it. 

I'm getting fed up with being told that varroa resistant bees are far in the future, and will require well funded high-tech solutions - if they ever arrive. 

You got this Dick? Peter? Daniel? Phoebe? John Chesnut?

Its past time we all started shouting down the plain lie: selection doesn't work. Now matter who says it. If your experience is otherwise, have the balls to call it 

Mike (UK)


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## squarepeg

in fairness mike, i believe the discussion is shifting from 'it's not possible' to 'why do we see it here and not there'. at this point i'm placing the presence of feral survivors as a primary prerequisite.


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## mike bispham

squarepeg said:


> in fairness mike, i believe the discussion is shifting from 'it's not possible' to 'why do we see it here and not there'. at this point i'm placing the presence of feral survivors as a primary prerequisite.


I agree SP - together with a clear understanding of how to go about it. Density of treatment-dependent drones also needs to be factored in.

The how-to-go-about-it concerns knowledge of population husbandry, and doesn't need high level knowledge about the complex mechanisms of internal genetics. These are in most ways separate topics.

I worry about the push for authority based on familiarity with the latter, accompanied by a flimsy grasp of the former. It can look good to the unwary eye, but contains the potential for great harm. 

Mike (UK)


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## squarepeg

perhaps mike. to me just different pieces of the puzzle all of which are required to get the overall picture.

squarepegs are notorious for questioning authority, (as did the little boy who exclaimed 'the emperor has no clothes!' ), and experiencing great harm is most helpful in advancing one up the learning curve.

no need to lose any sleep over any of this, it's just bees.


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## Oldtimer

mike bispham said:


> You got this Dick? Peter? Daniel? Phoebe? John Chesnut?


Ha Ha I didn't make the list LOL.

Must be 1. I'm a hopeless case. 2. I'm in the Mike Bispham club of approved people now. 3. Mike is getting forgetful. 4. None of those.

Re 2, my chances are slim there are very few in that club.


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## Saltybee

Shhh, OT, I think the password is ANTi-


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## peterloringborst

> Posted by mike bispham.
> You got this Dick? Peter? Daniel? Phoebe? John Chesnut?


No, sorry. I stopped reading your posts weeks ago.


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## Barry

mike bispham said:


> husbandry,


Thy charm and wit doth betray me when 'husbandry' so fashionably is championed about. I'm going to settle back in my staddle.


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## Rader Sidetrack

I admit that I wondered if _Barry _was referring to a _saddle_, but then I found that this is a staddle ...








photo credit

In times of yore, staddles were used thusly ...







photo credit


... sorry _Barry_, I can't quite manage the quaint Victorian prose ...


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## Barry

Sure you can. Add this to your signature: Ultracrepidarian
Seems we have some in these threads!


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## Rader Sidetrack

I did the best I could - given the maximum 120 characters allowed for a signature. Since I wouldn't want to slight anyone, here is a more complete definition:

http://dictionary.reference.com/browse/ultracrepidarian









photo credit



:gh:


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## mike bispham

peterloringborst said:


> No, sorry. I stopped reading your posts weeks ago.


Another scientific tool eh - a good pair of blinkers? Do they have special masking plates inside the microscopes in your lab to blind the viewer to things that don't suit their purposes? 

You can learn as much as you please about genetics Peter, it looks fascinating. But unless you catch up on the basic population husbandry that is as relevant as ever you won't understand the causes of the present problem or the solutions on offer. 

Mike (UK)


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## Oldtimer

Mike. Please be aware this is the genetics thread.

Husbandry, which you seem to think is a different thing and something that only you truly understand, should not blind you to the advances in understanding that have been made since you left school.

When you make remarks such as "unless you catch up on the basic population husbandry", to professionals who work in this field, one wonders if the gap between you and them is so wide that perhaps it is you who needs to catch up.

An old proverb comes to mind, "the fool is wise in his own understanding".

Incase you forgot, the thread is titled "Our understanding of genetics is changing". You would appear a lot smarter if you were here to learn not lecture.

Me, I will never understand this stuff at the level of a lot of these guys but none the less find it fascinating. It would be great to be able to follow a thread like this without the advanced members being constantly lambasted by one guy abusively interjecting dogma he formulated in the 1970's that he also says in every other thread, regardless of topic. Let's keep it real.


----------



## peterloringborst

Husbandry is a decidedly old timey word, hardly appropriate in the discussion of modern genetics. A brief sojourn to Oxford reveals:



> 1767 A. Young Farmer's Lett. 128 There is not a more dubious point in agriculture than the difference between the Old and the New husbandry.
> 
> 1803 Gazetteer Scotl. at Yarrow, The chief branch of husbandry is the rearing of sheep.


Interestingly, I have a friend that raises sheep and has a few hives of bees. I sincerely doubt that she would suggest that one resembled the other in any way, shape or form. But back to the definition: note that 250 years ago, the debate was on about the old and the new. No doubt there will be those that always cling to the old and decry the new. 

By the way, I never meant to imply that the changes in our understanding of genetics will lead to significant changes in the manner of breeding bees. In many quarters, bee breeding is going on successfully with almost no understanding of genetics. This has a lot to do with the evolutionary mechanisms in the honey bee that lead away from inbreeding, lead toward genetic diversity, and tend to ensure that the genetic advances -- if any -- are caused by natural selection instead of human selection. A shining example of this is the replacement of the European bee by the African bee throughout most of the Americas. The natural traits of the African bee make them vastly more resilient than the European bee, at least in tropical and semitropical habitats.

Many researchers have already pointed to the African bee as an example of a potential source of healthy, vigorous, genetically diverse bees. Just as many have pointed out that they may be completely unsuitable for beekeeping as it is practiced in the US and Canada, due to their unmanageable nature.


----------



## mike bispham

peterloringborst said:


> Husbandry is a decidedly old timey word, hardly appropriate in the discussion of modern genetics.


Husbandry barely enters the discussion of modern genetics. Its a different topic. That doesn't mean that its unimportant to beekeeping! 

This is precisely the problem. Beekeepers generally have no clue as to the importance of husbandry (in its full, yes, old fashioned sense). In every other sphere of agriculture, hortculture, any organic culture, the critical importance of selective reproduction is understood. Not beekeeping.

The danger I'm identifying here is that researchers working on understanding bee genetics (in the full modern sense) may supply the means to provide treatments (this was your answer to my question of what application remember), without being cognizant of the fact that _treating bees at all is deeply problematic_. They're not like other livestock. 



peterloringborst said:


> A brief sojourn to Oxford reveals:


Your quotes are a) bereft of any context, and b) as they stand, i) an opinion that lacks any information that would able us to judge it, b) a mere opinion by heaven knows who; ii) as a general position, then as now, patent rubbish.



peterloringborst said:


> Interestingly, I have a friend that raises sheep and has a few hives of bees. I sincerely doubt that....


I suggest you ask her before putting words in her mouth. She might surprise you.



peterloringborst said:


> ... she would suggest that one resembled the other in any way, shape or form.


It doesn't surprise me that you say that. It reveals pefrectly the continuing depth of your ignorance on matters of livestock reproduction and health. 



peterloringborst said:


> But back to the definition: note that 250 years ago, the debate was on about the old and the new. No doubt there will be those that always cling to the old and decry the new.


I'm not decrying the new. As I've said it looks like fascinating stuff. But you can't replace selective husbandry with something else. Sure you can augment it. But you can also do great damage with new stuff. 



peterloringborst said:


> By the way, I never meant to imply that the changes in our understanding of genetics will lead to significant changes in the manner of breeding bees. In many quarters, bee breeding is going on successfully with almost no understanding of genetics.


We agree on that much. 



peterloringborst said:


> This has a lot to do with the evolutionary mechanisms in the honey bee that lead away from inbreeding, lead toward genetic diversity, and tend to ensure that the genetic advances -- if any -- are caused by natural selection instead of human selection.


There's an awful lot more breeding of a much more prosaic kind going on. Wherever it isn't happening there's plenty of sickness. There is a whole bunch of reasons why it matters - not just the two you've identified. The most important is: the predatory environment continually evolves. Bees have to evolve to just maintain their defences. Stop that evolution - by failing in husbandry - and nature will do it for you. 

There's also much too much poor 'breeding' going on. I'm thinking of the failure to identify and work toward resistance to varroa - the school of thought that says: 'screw it, we've got treatments for that...'



peterloringborst said:


> A shining example of this is the replacement of the European bee by the African bee throughout most of the Americas. The natural traits of the African bee make them vastly more resilient than the European bee, at least in tropical and semitropical habitats.


Are you talking about natural selection here, or breeding, or both?



peterloringborst said:


> Many researchers have already pointed to the African bee as an example of a potential source of healthy, vigorous, genetically diverse bees. Just as many have pointed out that they may be completely unsuitable for beekeeping as it is practiced in the US and Canada, due to their unmanageable nature.


A number of researchers, and many more (tf) beeekeepers have pointed out similar advantages in other feral populations. Its the feral 'natural breeding' that's supplying health, not African genes. 

Mike (UK)


----------



## Rader Sidetrack

OK, no sheep in this post, but how about a nice bunny ....









photo credit


The Energizer folks obviously have met their match! :gh:


----------



## Oldtimer

I'm wondering if ignoring Bispham would work, in terms of enabling a sensible discussion on various topics. Instead of having every thread, regardless of topic, turned into to the same old "best to best" turned into 2000 word lectures we've been getting over and over.

Plus it offends me to see experts in their fields having their freely offered knowledge disparaged with such disrespect.


----------



## Richard Cryberg

Oldtimer said:


> Plus it offends me to see experts in their fields having their freely offered knowledge disparaged with such disrespect.


Well, I do not know if I am much of an expert. Probably not really. I talk to people all the time that know far more than I know. Yet, Bisfam gave me high praise. He labeled my ideas a theory. Anyone who knows even the rudiments of science knows that a theory is an idea that is accepted by the vast majority of experts in the field as proven beyond reasonable doubt at least until someone finds some contradictory evidence. About the only people who would reject the idea would be far right conservatives and/or far left liberals or people who have little expertise. The extremes turn everything into political arguments instead of sticking to math. Those with no expertise are simply filling space and making noise but are generally harmless and also know no math. In all cases they often are happy to dictate to God how he had to do his job. If you can not measure it and turn it into math it is not science.

Like Peter, I quit reading him. Total waste of my time to feed the troll. It is a shame Barry values trolls so highly. I guess they make him money by swelling the post count. Barry is ok but I have no desire to make him rich with my efforts.

Dick


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## Daniel Y

full Definition of THEORY

1
: the analysis of a set of facts in their relation to one another
2
: abstract thought : speculation
3
: the general or abstract principles of a body of fact, a science, or an art <music theory>
4
a : a belief, policy, or procedure proposed or followed as the basis of action <her method is based on the theory that all children want to learn>
b : an ideal or hypothetical set of facts, principles, or circumstances —often used in the phrase in theory <in theory, we have always advocated freedom for all>
5
: a plausible or scientifically acceptable general principle or body of principles offered to explain phenomena <the wave theory of light>
6
a : a hypothesis assumed for the sake of argument or investigation
b : an unproved assumption : conjecture
c : a body of theorems presenting a concise systematic view of a subject <theory of equations> 

synonyms:	
hypothesis, thesis, conjecture, supposition, speculation, postulation, postulate, proposition, premise, surmise, assumption, presupposition;

I personally do not agree with the list of synonyms as I see it crosses a line. Just as there is a line between assume and assert. An assertion is an assumption with evidence to support it while an assumption does not. An assumption is very likely to be incorrect as it is only one out of thousands that could be made.

I do not agree that hypothesis, conjecture, speculation, or assumption should be included in that list. An hypothesis specifically follows a theory in the chain of reliability. It is a step further from support of acts than a theory.

Fact a fire is burning. Theory a fire was started, A fire is evidence that it in fact started. Hypothesis would then be that various ways a fire was started.

Fact: there is a painting. Theory: there is a painter that painted the painting. 

Fact: there is an earth. Theory: there is a creator of the earth. 

Just goes to show that not even theory is widely accepted.


----------



## Rader Sidetrack

On the other hand, Einstein's [HIGHLIGHT]Theory[/HIGHLIGHT] of Relativity is widely accepted! 



> The [HIGHLIGHT]theory[/HIGHLIGHT] of relativity transformed theoretical physics and astronomy during the 20th century. When first published, relativity superseded a 200-year-old theory of mechanics created primarily by Isaac Newton.
> 
> In the field of physics, relativity improved the science of elementary particles and their fundamental interactions, along with ushering in the nuclear age. With relativity, cosmology and astrophysics predicted extraordinary astronomical phenomena such as neutron stars, black holes, and gravitational waves.
> 
> http://en.wikipedia.org/wiki/Theory_of_relativity



As Richard pointed out, scientific theory can be somewhat different than a _casual _theory or _speculation_, as DY's definition suggested.


----------



## Oldtimer

Rader Sidetrack said:


> On the other hand, Einstein's [HIGHLIGHT]Theory[/HIGHLIGHT] of Relativity is widely accepted!


Well, let's see for how long.

Week or two ago I discovered this interesting video, outlining in language laymen can understand, how some of the old beliefs are changing.

https://www.youtube.com/watch?v=fRzPM3FgF9I

Not directly related to this discussion I know, but is excellent in terms of showing how we must remain open to advances in knowledge, and not even consider the physical laws we thought to be true, inviolable.


----------



## Oldtimer

mike bispham said:


> Husbandry barely enters the discussion of modern genetics. Its a different topic. Mike (UK)


That being your personal belief, no need to keep arguing about it in the genetics thread.


----------



## kilocharlie

Richard Cryberg said:


> ... Anyone who knows even the rudiments of science knows that a theory is an idea that is accepted by the vast majority of experts in the field as proven beyond reasonable doubt at least until someone finds some contradictory evidence. About the only people who would reject the idea would be far right conservatives and/or far left liberals or people who have little expertise. The extremes turn everything into political arguments instead of sticking to math. Those with no expertise are simply filling space and making noise but are generally harmless and also know no math... If you can not measure it and turn it into math it is not science....
> 
> Dick


I was going to avoid commenting in this thread, specifically due to the risk of being ultracrepidarian, but I really like your whole quote. I've edited it some, but so much enjoy the part I've left in - may I have your permission to plagiarize this from time to time? Well stated. Bravo!

Yes or no, thank you either way! 
-kilo


----------



## Richard Cryberg

kilocharlie said:


> I was going to avoid commenting in this thread, specifically due to the risk of being ultracrepidarian, but I really like your whole quote. I've edited it some, but so much enjoy the part I've left in - may I have your permission to plagiarize this from time to time? Well stated. Bravo!
> 
> Yes or no, thank you either way!
> -kilo


Sure, go ahead and use it as you wish. I probably stole it from someone else anyhow. Or at least bits from here and there. I know the part about if you can not turn it into math it is not science is stolen. I think the original went more like "if you can not turn it into math it is art and if you turn it into math it becomes science," or something close to that.

Dick


----------



## kilocharlie

Sounds like Max Schroedinger, or maybe Richard Feynman. Good guys to quote - neither was prone to ultracrepidarian chutzpah nor to Bravo Sierra much, though Feynman could be mischievous.

Sorry, off topic. t:

You, PLB, JimLyon, Barry, Michael B, Michael P, Oldtimer and a bunch of others are certainly in my list of "approved people", and Daniel Y has sure improved over the last 3 years! He's in, too.
Thank you all for another great thread.


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## Dave1958

Ive looked though 3 pages of this Hodge podge ofstuff and it hasn't answered any questions about bee genetics. I want to know what genes male drones into the mix? Do they mix x-y like humans do or are they a,b, c- x, y, z recombinations of somekind. How can I pick drones of improving genetics for AI of honeybees? Can I improve my apairy through opennmating and controlling drone yards in thearea. 

Perhaps with all the quoting of sources I really want information specifically on honeybee genetics. I don't care about esoteric quoting of physics, chemistry, biology or higher mathematics. I have minors in all those subjects from 30 year ago. I have no desire to relearned things I haven't used on any consistsnt basis in 30 years


----------



## peterloringborst

> Can I improve my apairy through opennmating and controlling drone yards in thearea.


That's an important question, particularly if the answer is no. I would say, no. We are dealing with breeding populations here. The only way to control the breeding is through isolation and isolation brings about a different problem set (inbreeding, etc.). The honey bee genetic system appears to work best when the breeding population is large, and significant changes appear to take a very long time. When people attempt to shoe horn the bees into some arbitrary breeding program based on the genetic lessons learned from breeding dogs, they are bound to be disappointed in the results. Actual breeding projects need to be extensive and anything done on a small scale is bound to produce nothing but illusions. This is what this discussion has been about. Knocking down all the wrong ideas. If we don't have anything constructive to replace them with, too bad. That's no reason to cling to outmoded and erroneous notions.


----------



## Daniel Y

Sex determination in the honey bees is determined by over 20 genes. Unlike other animals where it is determined by a combination of two X or Y. XX being female XY being male. Effectively sex in a bee is determined by number of sex genes 1 being male 2 being female. A fertile egg can receive the same sex gene also resulting in a male. These males are destroyed in the cell by nurse bees. So discussion on a general scale is only complicated by introducing it.

So only male we would be concerned about is the product of an unfertilized egg that received it's only sex gene from the queen. 

Sex determination in a more exact description is a matter of same or different. same sex gene or genes is a male. different sex genes results in a female. A single gene is still recognized as same.


----------



## Daniel Y

Can you control genetics by controlling drone populations? mathematically and by law of averages the answer would be yes "if". It is the if that is critical. It is depended on a long list of things that would be difficult if not impossible to achieve.

Cutting right to the chase it woudl require you produce drones in such great numbers that mating with any other drones int eh area would statistically be insignificant. For example a queen may mate with 20 drones on her mating flight. if 19 of those 20 are your drones. then the one does not matter.

The questions then are. 
1. At what point do you have the number of drones that render the others insignificant.
2. what exactly would be required to achieve that.

As far as I can tell nobody knows the answer to either question. Attempts have been made and as far as I know they have failed.

Assume a 2 colony per square mile natural bee population. Your bees forage over a 9 square mile range. I will also say queens typically mate within that range as well. This means you have 18 other colonies in your zone. For a 20 to 1 advantage you would need to have have 360 colonies of your own in that same area.

But wait. what about all the colonies that are 4 miles away. they will travel 2 miles into your zone. So now we have an additional 28 colonies that will send drones into your area so you have to ass another 560 colonies at the fringe of your 9 square mile area.

But oh lord we are not done yet. what about all the drones that come from 2 miles outside your zone? This is another 20 square mile or 40 possible colonies that will send drones into your area by one mile. This requires an additional 800 colonies to keep your 20 to 1 advantage.

So what do we end up with? 1720 colonies managed in a 9 square mile area. And you to can control drone genetics at a 20 to 1 advantage if in fact natural population do not exceed 2 colonies per square mile.

Now that is a 5% chance of an unknown drone mating with your queens. Statistically 10% is considered insignificant so you can probably cut that number in half. Whew aren't we all relieved?

Now the above is actually the good news. Because once you are all done getting that nearly 900 colonies all placed and managed. you are going to run smack into the unique genetic makeup of the Honeybee. and that alone is goign to require that you pretty much provide the exact same thing you are attempting to replace.

At this point I am not sure that even II will result in the bee not being the bee as nature is determined to insure it remains.

Breeding is something like trying to cook with only pre mixed packages of spices. And many of the pre mixed packages are very bad. But a few are really good but maybe lacking a thing or two. the problem is the only thing you can do to try and ad the missing parts is to dump in a whole bad package of spices. The nature of the Honeybee is more like all spies have been put in one huge package and there is not a thing anyone can do about it. Maybe on a temporary basis. But not on a permanent you are developing a different breed level.


----------



## peterloringborst

> The nature of the Honeybee is more like all spices have been put in one huge package and there is not a thing anyone can do about it.


This is a great metaphor (I may steal it). Like, suppose you have this mixture of all the spices, and you just want a certain few? Maybe you could sift it, or shake it, and separate some of those few. But you would get some of the others and maybe not some of the ones you want, so you would have a new mix -- neither better, nor worse, but just a different subset of the original. Thanks for your steady stream of contributions, by the way.


----------



## Saltybee

Controlling the outcome through (do I dare say the word) husbandry may be virtually impossible. Maintaining a pure carni line on the mainland by flooding with carni drones comes to mind. Yet if you are aiming for a carni/itatialn mix it is rather easy.
Changing the lineage of bees is not difficult at all, controlling it is a different matter. AHB lines come to mind. The genetics of bees is changing, man has broken down the land barriers. Locked up genetics is not true. Controllable genetics, also not true (except artificially and temporarily).

If the bus is going to NY anyway, it is very easy to believe that the bus is going there under your direction.

If the bees are going TF anyway, the argument that treating is just stopping the bus has validity.

If you believe breeding for TF is impossible than you must believe that bees are headed for extinction except in the equivalent of zoos. Man's hives and the temporary escapes from those hives.

Impure lines have a better chance of adapting than pure lines. Patchwork patterns of TF success and TF failure is logical, the logical result of mixing lines of bees and lines of mites with their own add on species


----------



## Phoebee

Hah, David Brin has the following link posted on LinkedIn. It scatters to many ideas we've talked about here, but down a ways into the rambling, evidently he's taken up beekeeping recently.

No doubt this forms part of his inspiration for writing "Chrysalis".

http://davidbrin.blogspot.com/2014/08/more-science-microbes-pathogens.html


----------



## peterloringborst

> If you believe breeding for TF is impossible than you must believe that bees are headed for extinction except in the equivalent of zoos. Man's hives and the temporary escapes from those hives.


Nobody, nobody, thinks treatment free is impossible. 90% of the world's honey bees are not treated. Most of these are in Asia, Africa, and South America, however. Keeping bees in a northerly climate poses different problems. 

It isn't a matter of belief, in any case. If I believe it will work, and the bees die, I guess I am mistaken aren't I? 

I learned beekeeping in the 70s and 80s, before varroa. I have tried to not treat for varroa for years. The colonies always die. Otherwise, I would still have them, wouldn't I? 

Started this year with zero again, back up to 14. Checked for mites yesterday, half of them were over the threshold.


----------



## Saltybee

Peter, really had no one specific in mind. I get the dog analogy that a bee equivalent is not going to happen, even that it is more complex than the open breeding problems.
There is more resilience in bee genetics than the dog comparison analogy at times sounds like the bees have available to them. Mites are not the first threat in their history, that one may not be genetically fatal either.


----------



## peterloringborst

> Mites are not the first threat in their history, that one may not be genetically fatal either.


It is a real question whether northern European honey bees can develop the ability to thrive alongside mite infestations. I have never seen it. Most cases of genuine mite resistance is linked either to African traits or isolation. Both of these are not really solutions.


----------



## mike bispham

Daniel Y said:


> Can you control genetics by controlling drone populations? mathematically and by law of averages the answer would be yes "if". It is the if that is critical. It is depended on a long list of things that would be difficult if not impossible to achieve.


Daniel,

Both you and Peter are demanding absolutes that are neither acheivable (without AI - and that has its own drawbackes) nor necessary.

The quesion to ask is not 'is (absolute) control possible', but 'is it possibly to significantly influence drone input.'

And the answer is yes, very much, and, in many places, perfectly adequately. 

"....arrange, as far as possible, in our breeding apiaries, that the drones
flying there shall be produced by queens of the very highest
character, while the young queens with which they are expected to
mate shall be derived from breeder queens of a different strain, but
equally outstanding qualities. In this way, although it is impossible to
be certain that all matings will be as desired, yet it can be managed
that a very large proportion of our young queens will be the product
of the male and female parents from which we wish them to be
derived."

R.O.B. Manley, Honey Farming, page 62 of the pdf, 83 of the book
http://www.biobees.com/library/gener...gROBManley.pdf 

Mike (UK)


----------



## mike bispham

peterloringborst said:


> It is a real question whether northern European honey bees can develop the ability to thrive alongside mite infestations. I have never seen it. Most cases of genuine mite resistance is linked either to African traits or isolation. Both of these are not really solutions.


Have you actually been to Europe?

Give this a once over:

Breeding for resistance to Varroa destructor in Europe*
Sélection d’abeilles résistantes à Varroa destructor en Europe
Auslese auf Widerstandsfähigkeit gegen Varroa destructor in Europa
Ralph Büchler1, Stefan Berg2 and Yves Le Conte3
http://www.apidologie.org/articles/apido/full_html/2010/03/m09147/m09147.html

Mike (UK)


----------



## mike bispham

Saltybee said:


> If you believe breeding for TF is impossible than you must believe that bees are headed for extinction except in the equivalent of zoos. Man's hives and the temporary escapes from those hives.


Except African bees. oh, and my (European) bees. 

Mike


----------



## peterloringborst

> Have you actually been to Europe?


After all these weeks of discussion, _that_ is the question you want to ask me? What possible relevance could it have to this discussion, I wonder?


----------



## mike bispham

peterloringborst said:


> After all these weeks of discussion, _that_ is the question you want to ask me? What possible relevance could it have to this discussion, I wonder?


It was, believe it or not, a rhetorical question; intended to draw attention to the distance between your views of what is happening in Europe and the reported facts, some of which were supplied to you in the same post.

Mike (UK)


----------



## Rader Sidetrack

mike bispham said:


> It was, believe it or not, a rhetorical question; intended to draw attention to the distance between your views of what is happening in Europe and the reported facts, some of which were supplied to you in the same post.


But Mike, you are _not _a reliable reporter of facts, to wit, your _misreporting _of the cause of the "wild bee" crisis .... 


> It can be seen that modern beekeeping practice is the [HIGHLIGHT] sole cause [/HIGHLIGHT] of the crisis affecting both wild and domestic bees. The solution lies in the hands of beekeepers and their regulators.
> 
> http://www.suttonjoinery.co.uk/CCD/


You have previously stated here that landowner applied pesticides and loss of forage are significant contributors to this issue. Neither of those factors are under the control of beekeepers.

How are we to know which of your 'facts' are actually true? :scratch:


:gh:

.


----------



## peterloringborst

> It was, believe it or not, a rhetorical question.


Too bad, I was going to brag about going to Ljubljana in 2003 to see the Carniolan bee in its homeland

Pete


----------



## Oldtimer

You were there? LOL.



mike bispham said:


> It was, believe it or not, a rhetorical question; intended to draw attention to the distance between your views of what is happening in Europe and the reported facts, some of which were supplied to you in the same post.
> 
> Mike (UK)


It would appear then that by your measure Mike, Peters distance to what is happening is very small indeed. 

Your "rhetorical question" was what is termed an "own goal".


----------



## Daniel Y

mike bispham said:


> And the answer is yes, very much, and, in many places, perfectly adequately.
> (UK)


Mike, It is nice to know you think so. But sadly what you think does not carry much weight in my opinion. I know you may find that shocking. What are the numbers required to carry a significant advantage? Where is the evidence it makes any difference? Even if you do get the advantage where is the evidence that you altered what already existed. By the time you gt enough bees to have an advantage I say you simply replace a genetic pool with a similar or even identical genetic pool. You say it has been done. Where? You saying so is not evidence.


----------



## Kosta Zhelev

Hello Mike.I live in Europe.In my country are meeting conditions that allow me to see many reflections of bee behavior.Sorry for bad English.I hope you understand me.I support Peter because he was one of the people who allow me to explain the changes that I see.But I see the logic in your comments.I will not convince you of anything.Here are some facts about me and my bees.Mike has to processes that regulate behavior and response of bees against various harmful circumstances.This season, my attention was caught by a colony exposed to strong invasion.Already two seasons it had not received treatment.Colony literally can not live a normal life.And you know what was the response of bees to the invasion?Queen stopped ovipositor for 7-10 days.Do not you think that this is stopping the growth of dust mites?I have not taken part in this change.Do you think this is not proof that there are regulatory mechanisms triggered by circumstances?I can give you examples of sister "and".Conditions were different to her.The results also.Most important - is that the answer to her is another .The only difference in these two colonies is that at some point caste composition was different.I want to ask if you know the origin of wild colonies.Do not you think that they come from our "cultural" colonies?Tell me why I should not believe Peter or another on understanding the changes?Why should not be used for AI research quickly?What do you think happens in the genome of this colony?Because last season this colony showed other indicators.So far it has received no treatment.Only people like Peter give a reasonable explanation of the changes.How would you comment on that?


----------



## BernhardHeuvel

See: http://www.bijenhouders.nl/files/downloads_werkgroepen/Koninginneteelt/Breeding%20on%20Varroa%20resistance%20Utrecht%20290111%20(3).pdf

Get in contact, Mike: 
http://www2.hu-berlin.de/beebreed/ZWS/
http://aristabeeresearch.org/


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## mike bispham

Daniel Y said:


> What are the numbers required to carry a significant advantage? Where is the evidence it makes any difference?


Whatever Daniel. I'm not going endlessly round and round the same ground with you.

Mike (UK)


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## mike bispham

Kosta Zhelev said:


> So far it has received no treatment.Only people like Peter give a reasonable explanation of the changes.How would you comment on that?


Go with it Kosta. You do what makes sense to you. Good luck with your bees.

Mike (UK)


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## Oldtimer

mike bispham said:


> Husbandrymen copy the process and thus reduce natural wastage and improve yields. It's the most fundamental aspect of farming, its what organic husbandry 'is'.
> 
> That's all. It isn't complicated. Don't blind yourselves with unnecessary science.
> 
> Mike (UK)


Nobody is going blind due to unnecessary science.

The word "husbandryman" is quaint sounding term not used where I live so I don't call myself one. (Unless I wanted to get a few laughs). But if I was to be called a "husbandryman", I would rather be an educated "husbandryman", than an uneducated "husbandryman". I would not avoid a more than schoolboy understanding of the subject for fear I may go blind.

When I was young and had the first few years commercial beekeepers experience under my belt, the boss sent me to a week long queen breeding seminar. This was run by a number of people with long qualifications after their names. As none of them were commercial beekeepers I felt a certain suspicion of what they could teach me, how could they know?

Well I'm so pleased I went to that seminar I learned a whole new respect for education, I learned so much from them and came away with huge respect for their knowledge. As my own formal education stopped at quite a young age I realised I could never attain the level of knowledge of these university educated guys. But just that they are around, is a great thing. These kind of people are often at the cutting edge of new developments, and I also have friends among them I can go to with questions I need answers to.

Education does not cause blindness, but ignorance can.


----------



## peterloringborst

> Nobody is going blind due to unnecessary science.


I can't see that happening :waiting:


----------



## peterloringborst

As I have tried to point out, the success of an individual colony is not simply that it had the right genes, nor can this combination of genes be passed on directly and intact to its offspring. This excerpt expands on that idea:




> Simplistic ideas of how genes ‘cause’ traits are no longer viable: life is an orderly collection of uncertainties
> 
> Perhaps the most important single fact ... is that when numerous genes contribute to a trait, the specific set of contributing variants is different for every individual. This is a many-to-many causal relationship: there are many genetic paths to a single height, blood pressure, triglyceride, or cholesterol level. Equally, a given genotype is consistent with many different trait values. Each genetic variant is a very weak ‘coin flip’ with unstable probabilities, and everyone is flipping a different set of coins. So, even if we identify the genotype of an individual, we can’t as a rule accurately predict its effects, even though this is just what ‘personalised genomic medicine’ has promised to do.
> 
> We should not be at all surprised that, just like most other traits, behaviour is not specifically predictable from genes. The massive web of probabilism makes such prediction weak at best, just as we’ve seen for physical traits. But the reason is that the causation involved is so complex and deeply probabilistic that it is, in effect, unpredictable even if we were to try to enumerate all the contributing factors.
> 
> Human beings don’t like things that are unexplained. We want the comfort and sense of safety that comes from predictability. ... We are made very uneasy by things that are only probabilistic unless, as in coin-flipping, we can sense what’s going on. When we can’t see it, and causation is many-to-many, that is far too much for our minds to deal with easily. Yet that seems to be the reality of the world.
> 
> Things genes can’t do
> by Kenneth Weiss and Anne Buchanan
> http://aeon.co/magazine/science/kenneth-weiss-anne-buchanan-genetics/


----------



## mike bispham

peterloringborst said:


> As I have tried to point out, the success of an individual colony is not simply that it had the right genes, nor can this combination of genes be passed on directly and intact to its offspring.


First part: agreed; both genes and environment affect the outcomes. Nothing new there. 

Second part: of course it can't. That's fundamental. Each new individual is just that - an individual. It unique, a one-off. Its built from a random selection of the two gene-pairs carried by each parent.

But.. that _is_ what its built from. Nothing else. Elephant genes don't appear in rabbits; you can't inherit anything that wasn't already in one of the parents.



peterloringborst said:


> This excerpt expands on that idea: "Simplistic ideas of how genes ‘cause’ traits are no longer viable: life is an orderly collection of uncertainties"


Your extract doesn't say anything fundamentally new, it merely expands upon the complexity of the interaction of genes and environment, reflecting an increasing appreciation of the depth of the causes of that complexity. 

It speaks of 'uncertainties'; and we have to understand that some of the intent of that usage is rooted in the scientific use of probability. 

A great many things in the world are determined probabalistically. That is not the same thing as randomly. 

The success or failure of a hive will be due to a combination of inherited genes and environmental influences.

If we could control, hold, the environmental influences (we can't, completely, but we can, and do to a large degree) what would be exposed would be the genetic influences.

The genetic causes are inherited factors from parents. The suitability of offspring to the environment will be (probabalistically) similar to those of their parents. That is: the more suited to the environment their parents were, the more likely it is that the offspring will thrive; and vice-versa.

This is the mechanism employed by evolution to create separated species, and to maintain, as far as is possible, health in populations; and by breeders and husbandrymen to promote valued traits. 

Nothing new has been learned in modern genetics to unsettle this fact.

If it were not the case that traits could be inherited, and thus offspring tend to follow in suitability their parents, there would be no separated natural species. There would be no domesticated species. We would not be eating the great range of vegetables we enjoy. 

Don't throw the baby out with the bathwater Peter. 

Take careful note of the 'when' in your author's statement: 

"Perhaps the most important single fact ... is that _when_ numerous genes contribute to a trait"

Consider this: when it is the case that a great many factors contribute to a feature - a behaviour perhaps - thus making that feature hard or impossible to predict (probabalistically) - are we really being served well when people describe that feature as a 'trait'. 

In my view your authors could usefully examine their language here. Features are only 'traits' as and when they can be (probabalistically) genetically determined. 

Often that determination _is_ as simple as a single gene loci. In such cases: know the genetics of the parents and you know (probabalistically) the outcome in offspring. Some of the genetic factors leading to 'hygenic' behaviours in bees are known to be of such singular genetic causes. 

Genetic inheritance is certainly complex, and we have to cope with the fact that some outcomes are highly predictable, some very much not; and that environmental factors will influence matters too. However: enough is genetically determined to allow evolution to work, to allow breeding to work, and to allow extremely simple rule of thumb operations in husbandry to have distinct outcomes immediately. 

Again, were this not the reality there could be no species, no vegetables. _The fact that there are species, that (domesticated) vegetables do exist tells you this is undoubtedly right_.

Of you think otherwise, explain to me the origins of vegetables. 

Mike (UK)


----------



## Oldtimer

mike bispham said:


> Often that determination _is_ a simple as a single gene loci.


More often it is many gene loci, especially with bees.



mike bispham said:


> allow extremely simple rule of thumb operations in husbandry to have distinct outcomes quite quickly.


This is not another "husbandry" thread. It is about genetics, and particularly how our understanding of genetics is changing. It is not really about "simple rule of thumb operations in husbandry".



mike bispham said:


> Don't throw the baby out with the bathwater Peter.


I don't think he did, it is you who is attempting to discount anything beyond the most basic of understanding.


----------



## peterloringborst

> Often that determination is a simple as a single gene loci.


Describe even one example of this. (It's locus, by the way)



> In my view your authors could usefully examine their language here. Features are only 'traits' as and when they can be (probabalistically) genetically determined.


That's funny. They wrote a textbook on genetics, not you.



> Before genes were discovered
> and understood, it was difficult to explain inheritance and the evolution of
> organized traits. Genetics has become the central, theoretical organizing principle of biology.
> 
> However, recent work, and ideas that will be considered in this book, raise tempering
> questions about several aspects of the present view of genes. First, the connection
> between genes and traits is in many ways more indirect and subtle than
> most biologists have thought (or than many still seem to think).
> 
> In fact, the inner workings of life are far more complex than had been expected.
> In important ways, we attempt to force classical darwinian-mendelian theory in circumstances
> in which the fit is not so good. This does not mean that inherited traits
> do not involve genes, but genes are not always good predictors of traits, as will be
> seen in Chapters 3 through 5. Put another way, the mendelian inheritance of genes
> does not imply the mendelian inheritance of phenotypes (traits). Phenotypes are
> not inherited; organisms begin life as single cells with genes but not with arms,
> stomachs, or flowers.
> 
> Genetics and the logic of evolution / Kenneth M.Weiss, Anne Buchanan.


----------



## peterloringborst

Again, the idea that there is a gene for this and a gene for that, is plain old fashioned



> Various science concepts should be retired because they are just plain wrong. What I am focusing on is a phrase that is right in the narrow sense, but carries very wrong connotations. This is the idea of "a gene-environment interaction."
> 
> My problem with the concept is with the particularist use of "a" gene-environment interaction, the notion that there can be one. This is
> because, at the most benign, this implies that there can be cases where there aren't gene-environment interactions. Worse, that those cases
> are in the majority. Worst, the notion that lurking out there is something akin to a Platonic ideal as to every gene's actions—that any given
> gene has an idealized effect, that it consistently "does" that, and that circumstances where that does not occur are rare and represent either
> pathological situations or inconsequential specialty acts.
> 
> The problem with "a" gene-environment interaction is that there is no gene that does something. It only has a particular effect in a
> particular environment, and to say that a gene has a consistent effect in every environment is really only to say that it has a consistent effect
> in all the environments in which it has been studied to date. This has become ever more clear in studies of the genetics of behavior, as there
> has been increasing appreciation of environmental regulation of epigenetics, transcription factors, splicing factors, and so on. And this is
> most dramatically pertinent to humans, given the extraordinary range of environments—both natural and culturally constructed—in which we live.
> 
> Robert Sapolsky
> Neuroscientist, Stanford University


----------



## peterloringborst

The establishment of Cause and Effect is an old habit which dies hard:



> We humans are fundamentally storytellers. We like to organize events into chains of causes and effects that explain the consequences of
> our actions. We like to assign credit and blame. This makes sense from an evolutionary standpoint. The ultimate job of our nervous system
> is to make actionable decisions, and predicting the consequences of those decisions is important to our survival.
> 
> It is tempting to believe that our stories of causes and effects are how the world works. Actually, they are just a framework that we use to
> manipulate the world and to construct explanations for the convenience of our own understanding.
> 
> Unfortunately, the cause-and-effect paradigm does not just fail at the quantum scale. It also falls apart when we try to use causation to
> explain complex dynamical systems like the biochemical pathways of a living organism, the transactions of an economy, or the operation
> of the human mind. These systems all have patterns of information flow that defy our tools of storytelling. A gene does not "cause" the trait
> like height, or a disease like cancer. The stock market did not go up "because" the bond market went down. These are just our feeble
> attempts to force a storytelling framework onto systems that do not work like stories. For such complex systems, science will need more
> powerful explanatory tools, and we will learn to accept the limits of our old methods of storytelling. We will come to appreciate that causes
> and effects do not exist in nature, that they are just convenient creations of our own minds.
> 
> W. Daniel Hillis
> Physicist, Computer Scientist


----------



## peterloringborst

This excerpt is from "2014 : WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT?". It is a collection of essays in which each other talks about an idea that has outlived its usefulness. This is the third excerpt I have posted, all relating to the outdated concept of "the gene." By the way, the term "gene" was coined before anyone had any idea there was such a thing as DNA. So, naturally when DNA was discovered, they looked there to find "the genes." Gene itself is an outmoded term in need of retirement.



> Essentialist Views of the Mind
> 
> Essentialist thinking is the belief that familiar categories—dogs and cats, space and time, emotions and thoughts—each have an underlying
> essence that makes them what they are. This belief is a key barrier to scientific understanding and progress. In pre-Darwinian biology, for
> example, scholars believed each species had an underlying essence or physical type, and variation was considered error. Darwin challenged
> this essentialist view, observing that a species is a conceptual category containing a population of varied individuals, not erroneous
> variations on one ideal individual. Even as Darwin's ideas became accepted, essentialism held fast, as biologists declared that genes are the
> essence of all living things, fully accounting for Darwin's variation. Nowadays we know that gene expression is regulated by the
> environment, a discovery that—after much debate—prompted a paradigm shift in biology.
> 
> Ridding science of essentialism is easier said than done. Consider the simplicity of this essentialist statement from the past: "Gene X causes
> cancer." It sounds plausible and takes little effort to understand. Compare this to a more recent explanation: "A given individual in a given
> situation, who interprets that situation as stressful, may experience a change in his sympathetic nervous system that encourages certain
> genes to be expressed, making him vulnerable to cancer." The latter explanation is more complicated, but more realistic. Most natural
> phenomena do not have a single root cause. Sciences that are still steeped in essentialism need a better model of cause and effect, new
> experimental methods, and new statistical procedures to counter essentialist thinking.
> 
> Lisa Barrett
> University Distinguished Professor of Psychology, Northeastern University; Research Scientist and Neuroscientist, Massachusetts General
> Hospital/Harvard Medical School


----------



## mike bispham

peterloringborst said:


> This excerpt is from "2014 : WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT?". It is a collection of essays in which each other talks about an idea that has outlived its usefulness. This is the third excerpt I have posted, all relating to the outdated concept of "the gene." By the way, the term "gene" was coined before anyone had any idea there was such a thing as DNA. So, naturally when DNA was discovered, they looked there to find "the genes." Gene itself is an outmoded term in need of retirement.


This is an interesting conversation, and when I have more time I'll make a fuller reply. Meanwhile, some early thoughts and extracts in response:

Identical (human) twin studies are one of the primary tools by which an understanding of the balance between nature and nurture is sought. Its clear from the fact of identical twins that the inherited component ('genes') supply the form of the body proteins, and this we should note _includes the 'epigenetic' capabilities_.

We can see that this is not the end of the causal story: identical twins go on to develop, and to have diseases and die in different ways. Yet they undoubtedly carry similarities in terms of predispositions to health conditions. 

Some of the material below concerns the views of Richard Dawkins, and an extract from another author from his (Dawkins) website. You don't have to subscribe to or admire all his views, but you do have to admit the fellow knows his stuff when it comes to genetics. 

He talks about breeding in the same sort of simple sense - the sense that you describe as 'simplistic' and outmoded - that I do. The second writer, Jerry Coyne, emphatically makes the same specific point that I've been trying to make here: modern 'epigenitic' understanding may be very interesting and insightful, _but it makes no dent whatsoever on the longstanding view of how natural selection (and breeding) work through the principles of inherited qualities_.

By all means call my understanding 'simplistic' - it is. But despite that, it isn't wrong, or misleading, or inadequate to the needs of beekeepers. Breeding is _necessary_ to husbandry - that italicized term being used in its philosophical and logical sense - ommitted it will guarentee progressive health (and concommittent productivity and profitability) degradation. 

Mike (UK)



> "Twins share the same genes but their environments become more different as they age. This unique aspect of twins makes them an excellent model for understanding how genes and the environment contribute to certain traits, especially complex behaviors and diseases.
> 
> For example, when just one twin gets a disease, researchers can look for elements in the twins' environments that are different. Or when both twins get a disease, researchers can look for genetic elements shared among similar twin pairs. These types of data are especially powerful when collected from large numbers of twins. Such studies can help pinpoint the molecular mechanism of a disease and determine the extent of environmental influence, potentially leading to the prevention and treatment of complex diseases.
> 
> To illustrate, for twins with schizophrenia, 50% identical twins share the disease, while only about 10-15% of fraternal twins do. This difference is evidence for a strong genetic component in susceptibility to schizophrenia. However, the fact that both identical twins in a pair don't develop the disease 100% of the time indicates that other factors are involved.
> "http://learn.genetics.utah.edu/content/epigenetics/twins/"


[Dawkins now]


> “[But] if you can breed cattle for milk yield, horses for running speed, and dogs for herding skill, why on Earth should it be impossible to breed humans for mathematical, musical or athletic ability? Or why it is acceptable to train fast runners and high jumpers but not to breed them,”
> 
> http://edge.org/conversation/afterword-to-dangerous-ideas





> "I now groan audibly when a journalist (usually from continental Europe where they spend too much time learning philosophy rather than science) asks me the now inevitable ‘what about epigenetics?’ question. It is a real disease among science journalists, this unseemly eagerness to find something that enables them to say “Darwin was wrong” (New Scientist under Roger Highfield is a lamentable example). I am heartily sick of the ‘epigenetics’ bandwagon and almost look forward to the next one, whatever it turns out to be.)
> 
> (Reply)"Think of it as "epijournalism" where every new discovery is seen as a scientific revelation comparable to the pronouncements of Galileo. Epijournalists make mountains from molehills."


[Coyne follows)



> Is “epigenetics” a revolution in evolution?
> By JERRY COYNE - WHYEVOLUTIONISTRUE.WORDPRESS.COM
> Added: Sunday, 21 August 2011 at 7:53 PM
> 
> One often hears the suggestion that the neo-Darwinian view of evolution is on the skids, and that that view will be completely changed—if not overturned—by new biological ideas like modularity, genetic assimilation, evolvability, and epigenetics. Epigenetics in particular (I’ll define it in a moment) has been especially touted as a concept that will revolutionize evolutionary biology.
> 
> Call me an old fogey, but I think the idea of epigenetics as a Darwin-destroyer is completely bogus. Although certain discoveries in that area are interesting, and have certainly expanded our notion about how genes work, there is not the slightest evidence that the findings of epigenetics will dispel the main ideas of neo-Darwinism, which include the ideas of evolutionary change via natural selection and genetic drift, the randomness of mutations, the ideas of speciation and common descent, and the gene-centered view of evolution. I’ve explained my views on epigenetics as a revolution in several previous posts, for example here, here, here, and here, but, like the Lernean Hydra, each time you cut off a head of the epigenetic beast, it grows another one.
> 
> The latest head appeared in Friday’s Guardian, in a book review written by Peter Forbes; the book is The Epigenetics Revolution by Nessa Carey, and Forbes sees the book as tremendously important, implying that is part of a scientific revolution and explicitly saying that it’s a book that would “make Darwin swoon.” I haven’t read the book, and although it might make Darwin swoon if the old git were to be resurrected, the discoveries of genetics and the mechanism of inheritance itself would make him swoon far more readily. And I know scientific revolutions; scientific revolutions are friends of mine; and believe me, epigenetics is no scientific revolution.
> 
> So what is epigenetics? The term is actually used in two different ways. When I was younger, it simply meant “developmental genetics,” that is, the study of the way the DNA code of genes is translated into the bodies and physiologies of organisms. That, of course, was a tremendously important and exciting area, and still is. It involves understanding how genes are turned on and off in different tissues and cells, how different genes interact with each other, and how the products of a one-dimensional sequence of information can build a three-dimensional body. This study has segued into the new field of “evo devo,” which tries to understand the evolutionary basis of developmental genetics. “Evo devo” itself has, of course, led to its own important discoveries, like the presence and conservation of homeobox genes, the use of the same genes over and over again in forming similar but non-homologous traits (e.g., PAX6 in the formation of fly eyes and vertebrate eyes), and the linear arrangement of genes in some organisms (e.g., Drosophila) that correspond to the linear arrangement of body parts they affect.
> 
> So developmental genetics, and evo devo, are fascinating areas that produce a stream of surprising discoveries. But they’ve done nothing to alter the going paradigm of neo-Darwinian evolution. It is telling that, for example, Sean Carroll, a famous practitioner of “evo devo” and a popular writer, is a firm adherent to neo-Darwinism.  (Underlining by MB) What we learn from these areas is precisely how evolution has acted to sculpt bodies, but it still does so using randomly-generated genetic variation and good old natural selection (and yes, Larry Moran, genetic drift also plays a role). Gene regulation itself is a phenomenon molded by natural selection, and how genes are turned on and off is itself a phenomenon residing in the genes: in the genes that make the DNA or proteins that regulate other genes, and in the many ways that genes evolve (through, for example, the evolution of regulatory regions), to respond to internal “environmental” influences.
> 
> The second meaning of “epigenetics” is more recent, and involves actual changes in the DNA itself that are not based on mutational changes in nucleotides, but in environmental modifications of nucleotides—things like methylation of nucleotide bases or changes in DNA-associated proteins like histones—that can temporarily modify genes and affect their actions. I say “temporarily,” because such environmental modification of DNA, while it can be adaptive, is not usually passed on from one generation to the next. For example, we get our genes in pairs—one from mom and one from dad—but they can be differentially “marked” (the technical term is “imprinted”) during the formation of sperm and eggs, and so the copy from dad can act differently from the copy coming from mom. This imprinting is probably due to natural selection: scientists like David Haig have argued that the different and conflicting “interests” of paternal versus maternal genes has, through natural selection, molded the way they are imprinted, allowing them to act in different ways in the embryo. But an “imprinted” gene is reset each generation: the imprinting disappears and has to re-form depending on which sex the gene is in.
> 
> As I have argued before, however, imprinting of genes, although a novel and recently-discovered phenomenon, is not a “revolution” in how we view evolution: it is an embellishment that doesn’t overturn the main ideas of neo-Darwinism.
> http://old.richarddawkins.net/articles/642737-is-epigenetics-a-revolution-in-evolution


----------



## Barry

There is a quote function available when posting a message. Use it when quoting other people, even material you've grabbed from somewhere off the net. Please edit your post above as it is very hard to decipher your words from quoted words.


----------



## mike bispham

unneeded


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## Barry

It's clear to you because you posted it. I shouldn't have to be so careful in my reading to figure where your words end and quoted words begin. Very easy now that you fixed it.


----------



## Rader Sidetrack

mike bispham said:


> If you explain how to use the quote function I'll do so.


For those similarly challenged .... 
When you get to the point in your message composition that you want to insert a selection of text copied from another source, click the


> button of the toolbar:
> 
> 
> 
> 
> 
> 
> 
> Its the _right_-most button in this image.
> 
> Then paste your text. With many devices/systems, [right-click] then selecting "Paste" works, and often [Control-V] is an alternative method of pasting from the clipboard.





> The text you paste needs to end up _between _the [QUOTE] and [/QUOTE] tags in your message composition window.
> 
> 
> Your quote process is finished!
> 
> 
> 
> :gh:


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## Kosta Zhelev

: Thumbsup: Both deserve respect.You are the face of the discussion.I can not take sides on the topic.Greetings from me.


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## peterloringborst

> Mike: Often that determination is a simple as a single gene loci.
> 
> Me: Describe even one example of this. (It's locus, by the way)


Still waiting on this.


----------



## peterloringborst

Dawkins:



> Call me an old fogey, but I think the idea of epigenetics as a Darwin-destroyer is completely bogus.


He is an old fogey. Nobody thinks of epigenetics as a "Darwin-destroyer." Epigenetics does not supplant anything, it supplements it. What it says is that heredity is _not just_ DNA. It doesn't say that it's _not DNA._

On the other hand, the idea that gene=trait is nonsense. A trait is produced by many factors, including DNA but developed and shaped by other things.


----------



## Oldtimer

Rader Sidetrack said:


> For those similarly challenged ....


Thanks for pointing that out Rader, I've been caught quite a few times not knowing how to properly quote something from an outside source.


----------



## Oldtimer

peterloringborst said:


> Still waiting on this.


And you will continue to wait a very long time.....

Agree with the comments on Dawkins he's a very clever guy but I've read him plus watched him on the net & he seems a kind of obsessive personality plus very much I am right everyone else is wrong type attitude which is sometimes a warning sign. Most of his writings and speech is full of attacking others and even in the small part Mike quoted he does that. When he was young he was probably considered one of the worlds great minds.


----------



## peterloringborst

> When he was young he was probably considered one of the worlds great minds.


Right. Every generation has ground breakers. Like Picasso, who turned things over and shook things up. But eventually became tedious and formulaic.


----------



## mike bispham

peterloringborst said:


> The establishment of Cause and Effect is an old habit which dies hard:





> Unfortunately, the cause-and-effect paradigm does not just fail at the quantum scale. It also falls apart when we try to use causation to explain complex dynamical systems like the biochemical pathways of a living organism, the transactions of an economy, or the operation of the human mind. These systems all have patterns of information flow that defy our tools of storytelling. A gene does not "cause" the trait like height, or a disease like cancer. The stock market did not go up "because" the bond market went down. These are just our feeble attempts to force a storytelling framework onto systems that do not work like stories. For such complex systems, science will need more powerful explanatory tools, and we will learn to accept the limits of our old methods of storytelling. We will come to appreciate that causes and effects do not exist in nature, that they are just convenient creations of our own minds.


This notion is I think utterly off the wall. The final, absolute, statement is so obvious misconceived that its hard to know where to start - or whether to simply write the whole thing off as lunacy. 

There are simple and complex causes. But unless Hillis can throw out the law of conservation of energy, there are no uncaused events. 

It is impossible to relate the entirety of a web of cause and effect relations in a complex systems. In that sense the more or less precise but simple descriptions - stories, narratives - fail. Often we have to speak in terms of tendencies, probablities. Sometimes we only relate a fraction of the fuller accout. Nevertheless such accounts can be perfectly adequate to our needs. 

In the case of cause-effect relations in genetics, we can appreciate that the molecular arrangements of dna are the primary cause of biological structures. They remain the 'blueprint' from which organisms are constructed. This is already complex enough in practice. But there is additional development arising from external causes from the very start, and feedback systems rapidly create an uncomputable level of complexity. All this however occurs at each stage beCAUSE... something nudged something nudged something else, or because an electro-mechanical relation occurred. Cause-effect remains: there are no uncaused events.

The complexity is, yes, massive; and we can never hope to know of each event. But we can learn more and more about the workings. We can appreciate aspects that supply insights into a hierarchy of causes; deep principles, tendencies, and the grinding insistence of the 'laws' of nature.

And on a spectrum of explanatory completeness, in a vast number of cases we can appreciate singular causes. For example: 

If I take all the honey from my bees and they subsequently starve, the narrative already stated is perfectly adequate.

If I fail to to husband the genes well, and they subsequently fall into poor health, the cause-effect relation is almost as clear. 

In neither case does a deeper narrative of the much more complex physical and biological complexities in play offer any help. That's not to deny their existence. Its to say: my story meets the need for explanation adequately. 

Mike (UK)


----------



## mike bispham

peterloringborst said:


> Dawkins:
> 
> He is an old fogey.


He's one of the most respected evoltionary biologists in the world. He's made direct criticisms of the sort of writers whose extracts you've been posting. Calling him names is good old ad hominem. 



peterloringborst said:


> Nobody thinks of epigenetics as a "Darwin-destroyer." Epigenetics does not supplant anything, it supplements it.


Sure it does. And, as pointed out, but as yet not acknowledged by you - it doesn't take away the fundamental facts about heredity, and the way they play out in natural selection or breeding/husbandry.

It doesn't render the simple statement of those simple principles unworthy of consideration on the grounds of being 'simplistic'. 



peterloringborst said:


> What it says is that heredity is _not just_ DNA. It doesn't say that it's _not DNA._


I'm not at all sure about that. Certainly in a manner of speaking environment and culture are 'inherited', but not in the same sense that genes are inherited. What exactly do you mean when you say


> heredity is _not just_ DNA


EVERYTHING subsequent to meiosis is the playing out of environmental influences on the framework, with all its inherited capacities, supplied by DNA. That's been appreciated for donkey's years. An epigenetically focused approach to understanding the complex of cause-effect realations is magnificently useful. But it doesn't overturn anything except a hopelessly infantile and deterministic viewpoint that no-one has held for 100 years. 

The manner by which organisms develop, and the capacities held by, or subsequently developed, are present or not as a result of the inherited dna. They are present as a result of generations of natural selection. And they'll be present or not in future according to the same - now 'simple' - mechanisms of inheritance.



peterloringborst said:


> On the other hand, the idea that gene=trait is nonsense. A trait is produced by many factors, including DNA but developed and shaped by other things.


There are 'traits' and there are 'traits'. Some are the result of simple molecular arrangements from the inherited DNA, others by more complex factors that result from environmental influences, feedback systems and the like. 

Again, as I've pointed out, should we describe an attribute that is not caused by inherited dna as a 'trait'? To do so alters the meaning of a key term.

More closely, since the capacities to develop 'traits' (epigenetically) are inherited features derived from DNA, we can only ever say of a feature it is not a 'trait' as and when it can be shown to have _no_ inherited causes. 

Another angle (I'm thinking aloud here): the capacity to make an epigenetic change is present, or not, as a result of solid inherited DNA molecules. As such it is itself a 'trait' - if and only if other individuals of the same species do not possess it.

Mike (UK)


----------



## mike bispham

More ad hominem. Make _an argument against his positions_ Peter. 

Till you can do that you're just showing how powerless you are.

Mike (UK)


----------



## mike bispham

peterloringborst said:


> Still waiting on this.


I will get back to you with either an example, or an admission of failure to find one. But it might not be soon. There are more urgent things to do just now, and more interesting things to work at.

In the meantime, a start, for comments:



> Six quantitative trait loci influence task thresholds for hygienic behaviour in honeybees (Apis mellifera).
> Oxley PR1, Spivak M, Oldroyd BP.
> Author information
> Abstract
> Honeybee hygienic behaviour provides colonies with protection from many pathogens and is an important model system of the genetics of a complex behaviour. It is a textbook example of complex behaviour under simple genetic control: hygienic behaviour consists of two components--uncapping a diseased brood cell, followed by removal of the contents--each of which are thought to be modulated independently by a few loci of medium to large effect. A worker's genetic propensity to engage in hygienic tasks affects the intensity of the stimulus required before she initiates the behaviour. Genetic diversity within colonies leads to task specialization among workers, with a minority of workers performing the majority of nest-cleaning tasks. We identify three quantitative trait loci that influence the likelihood that workers will engage in hygienic behaviour and account for up to 30% of the phenotypic variability in hygienic behaviour in our population. Furthermore, we identify two loci that influence the likelihood that a worker will perform uncapping behaviour only, and one locus that influences removal behaviour. We report the first candidate genes associated with engaging in hygienic behaviour, including four genes involved in olfaction, learning and social behaviour, and one gene involved in circadian locomotion. These candidates will allow molecular characterization of this distinctive behavioural mode of disease resistance, as well as providing the opportunity for marker-assisted selection for this commercially significant trait.


It may well be that I've mistaken a statement like: " and one gene involved in circadian locomotion" as implying only one locus is, or needs to be, involved. As you know I'm not familiar with this stuff, and will be grateful to be directed to literature that will help me understand it better.

Thus far I'm standing by my longstanding position: this isn't stuff that will help me become a better beekeeper. Getting good at the arts of (genetic) husbandry on the other hand, very much will.

Mike (UK)


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## peterloringborst

> As genomic tools have become available to
> honey bee researchers, more facets of honey bee
> biology have been investigated using a
> sociogenomic approach. Worker behavioral
> maturation, the transition from nurse to forager,
> has received the most attention. Integration of
> genomic studies with the strong background
> knowledge of this system from behavioral,
> ecological, physiological, and genetic studies
> has provided the most comprehensive characterization
> of any component of honey bee biology
> 
> It is worth noting, however, that most of these studies
> provide _predominantly correlative data _
> (i.e., between transcriptome and phenotype), and as
> such, functional analyses on these _genes and
> pathways are still mostly lacking._
> 
> Further genomic investigations will also likely
> identify other players in honey bee social organization.
> For example, the detection of microRNAs
> in the honey bee genome has only recently begun
> to reveal the_ importance of these small, noncoding
> regions of RNA that regulate gene expression._
> 
> _As genomic tools become more advanced
> and accessible,_ the study of more honey bee
> phenotypes at the genomic level become more
> tractable, providing a clearer vision of honey
> bee behavior, communication, development,
> and health.
> 
> Dolezal, A. G., & Toth, A. L. (2014).
> Honey bee sociogenomics: a genome-scale perspective on
> bee social behavior and health.
> Apidologie, 45(3), 375-395.


comment:

I have italicized some key points. The studies of genome function produce _predominantly correlative data _. This means that direct cause and effect relationships have not been established. Correlation does not equal causation. The causative connection that people naturally look for between _genes and pathways are still mostly lacking._ Further, regulatory systems, albeit based upon the genomic instructions, are controlling vast amounts of gene expression. It is very clear that the genome is a resource that the cells use but the actual work of the cell is done by living systems, not the dna. Many of these systems are initiated by DNA coding but are not constrained by it. 

The genome is a library, which contains some books on construction and a whole lot else. The cell checks out what books it needs for whatever function it is performing. But a book on how to build a house, for example, will not be of any use without a master crew on the job. The crew has the knowledge and the skill to use a blueprint to actually build a house. There are countless challenges in applying the blueprint: assembling the materials, piecing them together, troubleshooting, etc. Decisions have to be made every minute. 

_As genomic tools become more advanced and accessible:_ they are not saying we already know enough to explain bee behavior, we can stop right here. They are saying we are at the beginning of developing an understanding. That's why I prefer to look at the work of young researchers like Amy Toth.



> "I am convinced, that, where men are the most sure and arrogant, they are commonly the most mistaken, and have there given reins to passion, without that proper deliberation and suspense, which can alone secure them from the grossest absurdities." — Hume, David (1711-1776)


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## peterloringborst

Speaking of Dawkins, what would he say?



> If Jablonka manages to convince the scientific community that some sort of complex feedback system of developmental cycles constitutes a true replicator, over and above its DNA content, I would be happy to embrace it. But, for the third time and at the risk of seeming pedantic, I insist on tight discipline. The criterion for recognizing a true replicator for a Darwinian model is a rigorous one. The putative replicators must vary in an open- ended way; the variants must exert phenotypic effects that influence their own survival; the variants must breed true and with high fidelity such that, when natural selection chooses one rather than its alternative, the impact persists through an indefinitely large number of generations (more precisely, survives at a high enough rate to keep pace with mutational degredation). If there is something other than DNA that meets these criteria, let us by all means include it, with enthusiasm, in our Darwinian models.
> 
> Dawkins (2004) Extended Phenotype – But Not Too Extended. A Reply to Laland, Turner and Jablonka


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## mike bispham

peterloringborst said:


> The genome is a library, which contains some books on construction and a whole lot else. The cell checks out what books it needs for whatever function it is performing. But a book on how to build a house, for example, will not be of any use without a master crew on the job.


Using your own analogy (which I think is dodgy - why will become clear):

The crew can only come from within the library. The library contains the instructions for building, maintaining, and instructing the crew to go about their work. Effectiveness of the crew will be maintained, like everything else, by natural selection - for the fittest crew. 



peterloringborst said:


> The crew has the knowledge and the skill to use a blueprint to actually build a house. There are countless challenges in applying the blueprint: assembling the materials, piecing them together, troubleshooting, etc. Decisions have to be made every minute.


You need to ask yourself exactly what you mean by 'decisions'. People make decisions in the fullest sense (after reflection). We also make 'decisions' in a lesser sense by impulse, intuitition, by rolling dice etc.

Computers make 'decisions' (an analogical use) utterly mechanically.

In what sort of sense do you think your 'crew' make decisions? It might be useful if you give us a better idea of what sort of thing you mean by 'crew'.



peterloringborst said:


> _As genomic tools become more advanced and accessible:_ they are not saying we already know enough to explain bee behavior, we can stop right here. They are saying we are at the beginning of developing an understanding. That's why I prefer to look at the work of young researchers like Amy Toth.


That's fine. Its very interesting stuff - not least in terms of philosophy of language - how terms (must) shift in meaning as their contextualising frames alter. But be wary of over-enthusiasm, and keep the baby in the bath. Natural selection is still the primary means by which health is maintained in populations. Husbandrymen still have to follow/cheat her methods. 

Claiming this is 'simplistic' and by implication useless, on the grounds that 'things are more complicated', and/or that new understanding has overturned a now outdated model, as you appear to, is not sustainable.

Mike (UK)


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## mike bispham

peterloringborst said:


> It is very clear that the genome is a resource that the cells use but the actual work of the cell is done by living systems, not the dna.


I'm thinking aloud here.

The blueprints of the cells themselves are within the genome (a complete copy of which is located at the heart of every cell). 

The 'work' is accomplished by the unfolding of natural, spontanious physio-chemical events, using energy. 

To say 'is actual work of the cell is done by living systems' is also circular. The cell is a 'living system'. 



peterloringborst said:


> Many of these systems are initiated by DNA coding but are not constrained by it.


They are 'initiated' in the sense of being constructed in accordance with the blueprint supplied by the genome, but some outside influence always triggers cellbuilding, defining the cell type according to need, as far as I know.

As to whether these systems are 'constained' by the dna that supplied the instructions that resulted in their coming to be: I think that might be a less than simple question. In one sense: of course they are constrained by their nature, which is supplied by the blueprint (parts chosen and initiated by the living systems). In another: of course they are not their blueprint, any more than a house is its architectural plans - they are something else, and are not constratend to be nothing but plans.

I think you have to identify the nature of any putative constraint before deciding how objects are 'constained' by their codes. (The computer parallels might be useful).

One thing is for sure: those systems that work well have a better chance of replicating the parts and arragements of those parts that made them work well (in the next generation) than those systems that don't work well. _All_ parts and compound systems are subject to natural selection for the fittest.

Thanks for the opportunity to think about these things.

Mike (UK)


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## peterloringborst

This was posted on another thread but is more relevant here:

Bispham:


> Just for the record: grafting plants doesn't involve any exchange of genetic material.


Sorry. You haven't kept up with the new discoveries being made in the field of genetics. 



> Tissue grafting includes applications ranging from plant breeding to animal organ transplantation. Donor and recipient are generally believed to maintain their genetic integrity, in that the grafted tissues are joined but their genetic materials do not mix. We grafted tobacco plants from two transgenic lines carrying different marker and reporter genes in different cellular compartments, the nucleus and the plastid. Analysis of the graft sites revealed the frequent occurrence of cells harboring both antibiotic resistances and both fluorescent reporters. Our data demonstrate that plant grafting can result in the exchange of genetic information via either large DNA pieces or entire plastid genomes. This observation of novel combinations of genetic material has implications for grafting techniques and also provides a possible path for horizontal gene transfer.
> 
> Stegemann, S., & Bock, R. (2009). Exchange of genetic material between cells in plant tissue grafts. Science, 324(5927), 649-651.
> 
> We show that upon grafting—a mechanism of plant–plant interaction that is widespread in nature—entire nuclear genomes can be transferred between plant cells. We provide direct evidence for this process resulting in speciation by creating a new allopolyploid plant species from a herbaceous species and a woody species in the nightshade family. The new species is fertile and produces fertile progeny. Our data highlight natural grafting as a potential asexual mechanism of speciation and also provide a method for the generation of novel allopolyploid crop species.
> 
> Fuentes, I., Stegemann, S., Golczyk, H., Karcher, D., & Bock, R. (2014). Horizontal genome transfer as an asexual path to the formation of new species. Nature, 511(7508), 232-235.


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## peterloringborst

> Natural selection is still the primary means by which health is maintained in populations.


This would only be true of populations that are exposed to natural selection. Once a population is protected by another species, or even a protective niche, it is isolated from naturally occurring selective pressures. Unless nature breaks through, which it often does. But human directed selection and niche construction has irreversibly skewed the processes of natural selection and evolution. As mentioned before, Bill McKibben was able to write "The End of Nature" in 1989. Without a viable force of nature, there is no natural selection.


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## marshmasterpat

Well that horse has been beaten so badly we have enough ground bone for all of us to take a wheelbarrow of bone meal back to our yards.


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## peterloringborst

A lot of people worry over the possibility of GMO bees. Actually, a more realistic approach would be to use RNA to control pest, rather than genetically modify the bees. RNA can scramble internal cell functions and can be very closely targeted to the pest. The chief obstacle at this point is cost. That's why Beeologic sold out to Monsanto, they need to be able to mass produce RNA to be able to use it.



> A serious problem for insecticides is that they can kill non-targeted animals. To address this issue, the possibility of using RNAi to kill only the target animals by down-regulating essential gene functions in insects has been recognized for many years (Price & Gatehouse 2008). Bando et al. (unpublished data) screened Gryllus target genes to develop G. bimaculatus-specific dsRNA insecticides
> 
> Turner et al. (2006) demonstrated that in the horticultural pest, Epiphyas postvittana (Lepidoptera: Tortricidae), RNAi could be triggered by the oral delivery of dsRNA to larvae. Meyering-Vos and Müller (2007) found that treatment of the adult cricket, G. bimaculatus, by injection or ingestion of a dsRNA for sulfakinin, a group of brain/gut neuropeptides, led to a stimulation of food intake, indicating that the uptake of dsRNA in the Gryllus occurs in the gut.
> 
> Baum et al. (2007) made transgenic corn plants engineered to express dsRNAs for the western corn rootworm (WCR). The plants showed a significant reduction in WCR feeding damage in a growth chamber assay, suggesting that the RNAi pathway can be exploited to control insect pests via the in planta expression of a dsRNA. Mao et al. (2007) also made Arabidopsis thaliana and Nicotiana tobacum transgenic plants expressing dsRNA specific to a cytochrome P450 gene (CYP6AE14) of the cotton bollworm (Helicoverpa armigera), which permits this herbivore to tolerate the cotton metabolite, gossypol.
> 
> When larvae are fed the transgenic plant, larval growth is retarded due to inhibitory effects of gossypol. Thus, they concluded that feeding insects with plant material expressing dsRNA may be a general strategy for the delivery of RNAi and could find applications in entomological research and field control of insect pests (Gordon & Waterhouse 2007).
> 
> Mito, T., Nakamura, T., Bando, T., Ohuchi, H., & Noji, S. (2011). The advent of RNA interference in entomology. Entomological Science, 14(1), 1-8.
> Eukaryotic parasites that exploit insect organs other than the gut would be susceptible to RNAi only where the insect host displays systemic spread of the RNAi signal. This has been demonstrated for the ectoparasitic mite, Varroa destructor, which feeds on the blood of honey bees (Garbian et al., 2012).
> 
> When bees were fed on dsRNA specific to a panel of Varroa genes, the density of Varroa mites on the bees was reduced by up to 50%, with no apparent deleterious effect on the honey bees. The pattern of spread of the RNAi was tested by allowing honey bees to feed on sucrose solution containing dsRNA-GFP (green fluorescent protein; because the genomes of both the insect and mite lack the GFP gene, the distribution of GFP-RNA could be monitored without interference from sequence of endogenous origin).
> 
> When Varroa-infested bees were fed on the test solution, the GFP-RNA was recovered in the Varroa. Moreover, when these Varroa were subsequently transferred to bees feeding on sugar solution without dsRNA-GFP, the recipient bees acquired the GFP-RNA. These experiments demon- strate that the RNAi can be amplified and spread not only at the level of the individual insect, but also at the colony level in honey bees.
> 
> Further research is required to establish the frequency and dose of RNAi applications required to sustain protection of colonies, and whether this approach offers a cost-effective strategy for the control of Varroa mite, which is of first-order importance in compromising the health of honey bee colonies.
> 
> Scott, J. G., Michel, K., Bartholomay, L. C., Siegfried, B. D., Hunter, W. B., Smagghe, G., ... & Douglas, A. E. (2013). Towards the elements of successful insect RNAi. Journal of insect physiology, 59(12), 1212-1221.


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## mike bispham

peterloringborst said:


> A lot of people worry over the possibility of GMO bees. Actually, a more realistic approach would be to use RNA to control pest, rather than genetically modify the bees. RNA can scramble internal cell functions and can be very closely targeted to the pest. The chief obstacle at this point is cost. That's why Beeologic sold out to Monsanto, they need to be able to mass produce RNA to be able to use it.


Just bear in mind: in an openly mating organism, _any help given tends to result in a need for increased similar help in future generations.
_
Is that really what you want?

Mike (UK)


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## Oldtimer

Too simplistic.

Does not take into account what actually happens in the real world.

A beekeeper is able to choose which queens he breeds from & their genetics is 1/2 the equation. 

So to explain via hypothetical example, a beekeeper may do pollination and need early spring build up, and has to "help" his bees to do that by stimulative feeding. Does that mean he ends up with bees that always need "help"? No. Because he also breeds from stock that build up quickly in spring, and so despite open mating, over a few years he is able to incorporate that trait into most of his bees. That is the kind of thing that happens Mike, but you may have needed to be in the business to experience and understand that.


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## peterloringborst

> A beekeeper is able to choose which queens he breeds from & their genetics is 1/2 the equation.


Not even half. 



> Understanding the molecular basis of how behavioural states are established,
> maintained and altered by environmental cues is an area of considerable and growing interest.
> Epigenetic processes, including methylation of DNA and post-translational modification of
> histones, dynamically modulate activity-dependent gene expression in neurons and can
> therefore have important regulatory roles in shaping behavioural responses to environmental cues.
> 
> Despite the clear role of the environment in regulating
> caste fate and behaviour, the phenotype of an organism
> emerges from the dynamic interplay between environmental
> and genetic factors: behavioural responses depend on
> both nervous system ontogeny and immediate sensory
> perception; interpretation of sensory
> cues depends on the expression of specific receptors,
> such as those involved in olfaction, gustation and vision;
> and long-term memory in neurons depends on proper
> recruitment of chromatin regulators such as CBP94.
> 
> Eusocial insects as emerging models for behavioural epigenetics
> Nature Reviews Genetics, published online 9 September 2014


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## Saltybee

peterloringborst said:


> Not even half.


But those influences are relatively stable within an individual's program. In order for a species to thrive within a fluctuating environment, those influences also must be somewhat self regulating.

But your point is not really about a percentage.


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## mike bispham

peterloringborst said:


> Not even half.


Given a beekeeper can also dominate the drone environment from chosen stocks, considerably more than half the dna going forward can be controlled in a largish and relatively isolated outfit.

Subsequent epigenetic development of the organism doesn't negate these factors. If it did there'd be no evolved behaviours leading to speciation. There'd be no point to competitive mating. Since these things are all but universal we can safely assume that the dna inherited from parents is a critical factor in determining the suitedness of offspring to environment.

As if we really need another reason.

You're trying to chuck the baby out again Peter.

mike (UK)


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## peterloringborst

> Given a beekeeper can also dominate the drone environment from chosen stocks
> Subsequent epigenetic development of the organism doesn't negate these factors.


You don't know what you are talking about. You are living in a fairy tale.


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## mike bispham

peterloringborst said:


> You don't know what you are talking about. You are living in a fairy tale.


An intelligent, well reasoned critique. Not ad hominem or content free at all. Well done, you'll make a scientist yet.


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## Kosta Zhelev

mike bispham said:


> An intelligent, well reasoned critique. Not ad hominem or content free at all.


Mike, if you want to know how well the knowledge of Peter, why do not you ask him?


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## JRG13

Epigenetics is an interesting topic, expecially when referring to the super organism that is a beehive. Problem is, most of us won't ever get a taste of the true genetics of our bees, only phenotypical observations so the whole point of this thread is moot.


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## Kosta Zhelev

JRG13 said:


> Problem is, most of us won't ever get a taste of the true genetics of our bees, only phenotypical observations so the whole point of this thread is moot.



Perhaps JRG13.But some of us deeper into crosses.If you start from one strain, the picture is quite clear.As long as you have knowledge in bee genetics.Epigenetic factors are those that allow changes in the normal distribution of marks.They are not visible.They assess.


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## JRG13

Exactly my point Kosta, all we can do is assess at this point, so I don't see the point of arguing genetics vs epigenetics for 99% of people 'breeding' their own bees. Now if we were talking sequencing and marker selection I'd change my tune.


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## Kosta Zhelev

You're right JRG13."If I decide to come visit you, but the flight of the aircraft is delayed for any reason, the meeting will not take place.If I were you informed by telephone, the meeting will be a fact."Many questions can be asked in the given example.All of them meet Epigenetics and Genetics.And as Peter pointed out - genetics and epigenetics complement and explain processes invisible to us.Sequencing and markers serve experts to track and specify certain events.They are useful in my orientation to what is the nature of epigenetic factors.This, in turn, correlates with the distribution of the marks.Greetings.


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## mike bispham

JRG13 said:


> 99% of people 'breeding' their own bees.


Why the hesitation about 'breeding' JRG13?

Mike (UK)


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## JRG13

I didn't mean much with that mike, just that some people think that unless you have isolated yards and a PhD you should not coin anything you're doing as breeding. I don't agree, so I highlighted it to hint at anyone making their own queens. Khosta, I agree with you, but my point is you can't argue epigenetics very well with a blank sheet of paper on the genetics of the bees you are comparing.


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## Kosta Zhelev

JRG13 said:


> Khosta, I agree with you, but my point is you can't argue epigenetics very well with a blank sheet of paper on the genetics of the bees you are comparing.



List is not empty JRG13.I have documentation of your selection.Excellent know who they are instrumental and naturally fertilized.And what are the parental strains.According bee genetics hereditary changes are made ​​during meiosis."I" by the qualitative composition of the diet of the bee larva.In the second case, the leading role was given to Epigenetics.Genome information is accurate JRG13.Within an individual would not be right to show differences under different conditions.But it is a fact right?What to say when these differences create other differences?For example, within one colony.We can easily gather evidence for epigenetic influence.You only need to be observant.Ceteris paribus - What could influence and create differences?Needless to emphasize that for each genotype influence is different.Greetings.


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## JRG13

Are behaviors solely epigenetic in a beehive? Bees use a lot of communication signalling, genetics aside that can direct hive functions. Then you have super-sister and environmental interactions as well. I understand the philosophy behind the argument, but until you show me your sequencing data showing all loci are fixed for all the genes involved in whatever traits you are looking at and that you even know those genes drive said traits, arguing about genetics and epigenetics on this subject really has no merit. I might even believe it's all epigenetics, but I'm not going to push that philosophy on minimal data. It's why beekeeping seems very locational, but without knowing any marker data, I can't say it's the genetics or epigenetics driving it.


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## Kosta Zhelev

I could be wrong JRG13, but will express my thoughts completely.In my comments no criticism or controversy.You're right about that in providing accurate data.The apiary no scientific laboratory JRG13.My research laboratory is that all these publications written by people / spend time for this / that I've read.Analyzed and consistent with my experience.
"Bees use many communication signals, genetics aside, who can guide hive functions. Then you have great sister and environmental interactions as well."
These are the reasons.The result may be different.My thought is that all of these trigger epigenetic mechanisms changing heredity.If you do not eat a permanent colony starter - grower will not have good results.If the entire amount has been genome, it is variable.If the causes can change it, how it will be expressed in an organism?Are not the epigenetic mechanisms that mediate the causes?One genotype carries a "high breeding" or not.We can change this.If everything is right in the cross, why use other methods?If this is the only philosophy, I am a philosopher, not a beekeeper.Greetings.


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