Our understanding of genetics is changing
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  1. #1
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    Default Our understanding of genetics is changing

    Hi all

    Genetics is mentioned frequently in online discussions, especially in the context of bee breeding. Many writers have only a hazy understanding of genetics, based on what they learned decades ago. Here's a good place to start to learn about how our view of genetics has changed:

    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.
    http://www.amazon.com/Evolution-Four.../dp/0262600692

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    Default Re: Our understanding of genetics is changing

    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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    Default Re: Our understanding of genetics is changing

    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.
    Last edited by peterloringborst; 07-29-2014 at 12:58 PM. Reason: clarity

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    Default Re: Our understanding of genetics is changing

    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.o...ge=1&view=FitH

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    Default Re: Our understanding of genetics is changing

    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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    Default Re: Our understanding of genetics is changing

    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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    Default Re: Our understanding of genetics is changing

    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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    Default Re: Our understanding of genetics is changing

    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.
    Last edited by peterloringborst; 07-29-2014 at 11:35 AM.

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    Default Re: Our understanding of genetics is changing

    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/com...CKLw340jkBX.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
    Last edited by peterloringborst; 07-29-2014 at 03:28 PM. Reason: expanded

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    Default Re: Our understanding of genetics is changing

    Deleted by author, off topic
    Last edited by peterloringborst; 07-29-2014 at 04:43 PM.

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    Default Re: Our understanding of genetics is changing

    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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    Default Re: Our understanding of genetics is changing

    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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    Default Re: Our understanding of genetics is changing

    Quote Originally Posted by Michael Johnston View Post
    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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    Default Re: Our understanding of genetics is changing

    Genes discredited:

    Except in a small number of cases, the notion of genes, however they are defined, coding for an organismís 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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    Default Re: Our understanding of genetics is changing

    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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    Default Re: Our understanding of genetics is changing

    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.
    Last edited by peterloringborst; 07-30-2014 at 08:53 AM. Reason: expanded

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    Default Re: Our understanding of genetics is changing

    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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    Default Re: Our understanding of genetics is changing

    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.
    It is not true that you cannot teach an old dog new tricks.
    They can learn them, they just can't do them.

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    Default Re: Our understanding of genetics is changing

    Quote Originally Posted by Michael Johnston View Post
    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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    Default Re: Our understanding of genetics is changing

    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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