Bee genome changes dramatically through life

_{Denyse O'Leary

September 13, 2018

Epigenetics, Genetics}

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Pollinating Bee Remember old-fashioned, unalterable DNA? It was interesting stuff. So now this:

“A study of chemical tags on histone proteins hints at how the same genome can yield very different animals:”

The bee genome has a superpower. Not only can the exact same DNA sequence yield three types of insect—worker, drone, and queen—that look and behave very differently, but, in the case of workers, it dictates different sets of behaviors.

A key to the genome’s versatility seems to be epigenetic changes—chemical tags that, when added or removed from DNA, change the activity of a gene. Previous studies had shown distinct patterns of tags known as methyl groups on the genomes of bees performing different roles within their hives.Shawna Williams, “As Bees Specialize, So Does Their DNA Packaging” at The Scientist

One wonders what the tax-funded textbooks are still saying about DNA…

See also: Evolution is evolving? [It had better be.] The conference seems to be dedicated to the extended evolutionary synthesis, which it contrasts with the “modern synthesis”

and

Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

Comments

jawa: Please note that when I say: genetic and epigenetic I mean: genetic = everything that is written in the sequence of 3 billion nucleotides that make the genome (in humans, for example). epigenetic = everything that is transmitted to the zygote (or to every cell of the organism at each specific state) and that uses the genetic information to generate the living result. That is a very huge definition, and it includes everything that we still do not know or understand.gpuccio_{September 17, 2018
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jawa: Of course, it's functional information written into the configuration of the species, its cells, its zygote, and so on. It's genetic and epigenetic information that makes a whole big designed machine. And it's probably even more than that. But it is certainly at least that. A huge, extremely complex, fascinating design.gpuccio_{September 17, 2018
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Amblyrhynchus: Thank you for clarifying. I agree and disagree. "Both these processes are pretty haphazard." So haphazad that, without designed control, they could never generate huge amounts of functional information. That's exactly the point of ID. "If count up unique transcripts from closely related species you find a lot fo species-specific transcription of stuff with no obvious functional ORF." That's well known. They are called non coding RNAs. "Some people get excited about these and call them species-specific lncRNA." I am one of them. And it seems that I am in very good company, increasing by the day. "But in general, knocking these transcripts down has no biological effect." This is not really true as a general rule. Moreover, you certainly understand that knock-out experiments are not necessarily the best way to demonstrate function, especially complex regulatory function. "Instead, it looks very much like this is essentially random transcription," You seem to be rather isolated in believing that, if you look at the daily literature about that issue. I certainly disagree. "with only a very few transcripts later being conserved in other lineages and having a biological function." Only a few? Are you kidding? Have you had a look at some of the papers I quoted in the thread about transcription regulation? "Not an elegant way to go about expressing your DNA or generating new genes." And yet, it seems to work perfectly well. Just look at the results. "Distal enhancers are similar. Long-range interactions between a gene and an enhancer can be the result of a transposable element integrating into a region of chromatin that was already near to the gene in the nucleus." I certainly agree. I don't know how much you have read of what I post here, but I have been supporting the idea that transposons are on of the main tools of design for years. Their role in generating new genes, both coding and non coding, and new regulatory networks is now supported by tons of evidence. "If that interaction has a positive fitness consequence it will be conserved, “locking” that topology in. " So, in the end all you have to say is the usual RV + NS miracle catechism. OK. "This is what I mean by “historical contingency”, the sorts of long-range interactions PaV was talking about can be “frozen accidents’, a random TE insertion locking in an existing chromatin state and conserving it from change." As should be clear, I perfectly agree about the "historical contingency" part. But the point is hat such "contingency" cannot ever generate complex functional information, unless it is guided and arranged into functional configurations. So, it is "historical design, often using historical contingency". OK, I am not criticizing you. I am grateful that you clarified your thoughts. But of course, I had to express my views too. Thanks again.gpuccio_{September 17, 2018
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Amblyrhynchus, I see Peter and OLV posed interesting questions that I would like to hear your educated opinion on: PeterA @75:
gpuccio: How are the epigenetic markers spatiotemporally setup ?
OLV @79:
gpuccio (67): “controlled by the information in the species” How is that controlling information setup in the species? For example in the case of these bees in this thread? Thanks.
Thanks.jawa_{September 17, 2018
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R J Sawyer: #101: Lactose intolerance is not really a disease. In many european countries, including Italy, it's almost the rule in adult age. It's probably just a polymorphism with limited functional consequences. But most genetic diseases, either monogenic or multigenic, are really different. A change in one aminoacid can simply mean a really non functional life. And it does, for many people. Those are of course errors. We can debate the reason and the cause, but errors they remain. The function of a protein, often an important protein, is seriously compromised, Usually by just one aminoacid change. #104: I have no intention to deny the existence of instinct in humans! :) But that kind of instinct that generates ordered collective behaviours that are repeated in the same species in the same way are a very special form of instinct, and they can be seen only in certain types of animals. They are an exception, not the rule. But a very interesting exception. So, I remain fascinated by dam buiding beavers, monarch butterflies, ants, bees, and so on.gpuccio_{September 17, 2018
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Ambly
It’s sort of like someone standing up on a mountain pointing at a landscape and saying how amazing it is, how erosion and plate tectonics have worked together to create a valley and ecological interaction have patterned the forests. True enough,...
I think that the big difference is that both ID proponents and evolution proponents can look at a mountain and conclude that the incremental plate movements that we have directly observed are sufficient to add up over time to create a mountain. Even though this has never been observed to actually have happened. But when we look at the small incremental mutations, selection and fixation in populations, evolution proponents are willing to use the same extrapolation and logic we use to conclude how mountains are formed to conclude that these are responsible for the diversity we see. ID proponents are not. Maybe the ID proponents are right. Maybe they are not.R J Sawyer_{September 17, 2018
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I actually have a paper focusing on chromatin state in review just now. Let’s just say my experience of that project has reaffirmed my view that eukaryotic genomes are messy hacks fill of historical contingency…
Could you just clarify that better for us? Is that request specific enough for you?
This paper has been accepted for publication, so I'm not very keen to provide details that would "out" my real life name. But in general, I was thinking about two things. The origin of genes and the evolution of long-range enhancers. Both these processes are pretty haphazard. If count up unique transcripts from closely related species you find a lot fo species-specific transcription of stuff with no obvious functional ORF. Some people get excited about these and call them species-specific lncRNA. But in general, knocking these transcripts down has no biological effect. Instead, it looks very much like this is essentially random transcription, with only a very few transcripts later being conserved in other lineages and having a biological function. Not an elegant way to go about expressing your DNA or generating new genes. Distal enhancers are similar. Long-range interactions between a gene and an enhancer can be the result of a transposable element integrating into a region of chromatin that was already near to the gene in the nucleus. If that interaction has a positive fitness consequence it will be conserved, "locking" that topology in. This is what I mean by "historical contingency", the sorts of long-range interactions PaV was talking about can be "frozen accidents', a random TE insertion locking in an existing chromatin state and conserving it from change.Amblyrhynchus_{September 17, 2018
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95 R J Sawyer: We live in a accursed world. This is not the way things were supposed to be. The biological systems are exquisitely complex functionally, very delicate and very robust at the same time. However, we have historically messed things up big time. Besides, as gpuccio has stated in several occasions, we still don't know or poorly understand many biological processes, including multiple layers of control. Fortunately science research is moving faster these days, because it builds on previous knowledge and because technological advances allow scientists to dig deeper into the systems, thus shedding more light on the unknown and mysterious. What is coming out of that research is more evidences that confirm the intelligent design paradigm.PaoloV_{September 17, 2018
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GP@100. I agree that instinct vs learned behaviour is a very interesting field. We assume that bird migration is purely instinctual but is it really? Most birds repeat the process throughout their lives so you can’t rule out a learning aspect. But monarch butterflies are obviously a different story. But humans are definitely not devoid of “instinct”. Most of us have a fear of heights to some extent. Even our xenophobic tendencies can be interpreted as an instinct. Thankfully, one which most of us can overcome.R J Sawyer_{September 17, 2018
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Actin proteins assemble to protect the genome
The assembly of polymerized actin with motor proteins at DNA breaks in the nucleus supports the mobility and repair of DNA. This finding reveals a layer of regulation that helps to preserve genome integrity.
OLV_{September 17, 2018
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An increasingly strange thread. Maybe I can try to say this clearly one more time. I don't disagree that the molecular mechanisms underpinning development are very interesting, and this paper is a nice contribution to that field. However, I don't find the increasingly lengthy but still extremely high-level comments about it very interesting. It's sort of like someone standing up on a mountain pointing at a landscape and saying how amazing it is, how erosion and plate tectonics have worked together to create a valley and ecological interaction have patterned the forests. True enough, but I can't say it's something I feel compelled to post on.Amblyrhynchus_{September 17, 2018
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GP
Diseases are of course errors in the program.
I guess that is possible. But are they not just different expressions of the same genes? How many of our current gene expressions would be classified as diseases if conditions were different? For example, western doctors diagnose people with lactose intolerance if they can’t properly digest dairy products. We treat it as a disease. For a significant portion of Asians, this isn’t an issue because dairy does not constitute a significant portion of their diet.R J Sawyer_{September 17, 2018
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R J Sawyer at #98: I can agree, but again I think you are conflating two different aspects. Human behaviour is certainly modified by environmental and historical contingencies. Many of those contingencies are the result of human behaviour itself. But human behaviours are an adaptation of intelligent and relatively free individuals to circumstances that continuosly change. Of course, some aspects of human nature remain the same, and are part of the adaptation. But the example of bees, or of other instinctive collective behaviours in animals, is different. There, the whole collective behaviour remains essentially the same. It is not cause by the environment. Bees are bees now as they were thousands of years ago. their behaviour is not "historical", it is just instinctive. So, when birds migrate in amazing patterns, that us not something they have learned and intentionally transmitted through culture and memes. It's controlled by their heredity as a species. Monarch butterflies migrate in astonishing trans-generational patterns, and nobody can really explain why or how they do that. The animal world is rich of such cases. So, any research that can help us understand how genetic and epigenetic functional information can implement those realities is indeed precious.gpuccio_{September 17, 2018
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Amblyrhynchus: "Probably looking for something a bit more specific…" Excuse me. At #18 you stated:
I hadn’t seen the thread. I actually have a paper focusing on chromatin state in review just now. Let’s just say my experience of that project has reaffirmed my view that eukaryotic genomes are messy hacks fill of historical contingency…
(That refers to the old thread about chromatin states. In the meantime, I have also published a thread about transcription regulation). At #31 I have commented: "Well, messy hacks that seem to work really fine, I would say. I am certainly not denying the “historical contingency”. I am not sure what you mean, but in general I can agree with the idea. But if such complex systems work so well, and generate well differentiated cell types and tissues and organisms of amazing functional complexity in spite of all the possible “historical contingency”, that is even more surprising." You have not commented on that, apparently. At #44, I addressed you again: "But I believe that my comment #31 to you was intended to start a more serious discussion, beginning with a statement you yourself have made at #18. Can you answer my point, and maybe clarify better your point about messy hacks and historical contingency? So that I can maybe clarify my objections?" No answer to that, again. At #67, I insist again (I am a rather obstinate guy): "Amblyrhynchus at #57: I don’t understand. You have nothing to say about any comment here? That means that you have nothing to say about my comment to your #18 (at my #31)? And about my request for some more details about your statements at #18? Of course, you can do as you like. But I cannot understand the reason for that." No answer again. But, at #82 you say:
To put it more bluntly: i see very little “serious” content in any of these comments. if there is something I’m missing then let me know, I guess.
At #86 jawa asks you: "Don’t you see any serious content in gpuccio’s comments?" At #87, apparently answering that, you say:
Yes. I guess it’s serious enough, but there’s just not very much to any of this.
Now, I don't understand. I can accept that you are not interested to comment on my comments, serious or not that they may be. But I asked you to clarify better the statement that you yourself made, at #18, without being forced by anyone, I believe. I paste it here again, for your convenience:
I actually have a paper focusing on chromatin state in review just now. Let’s just say my experience of that project has reaffirmed my view that eukaryotic genomes are messy hacks fill of historical contingency…
Could you just clarify that better for us? Is that request specific enough for you? Thank you in advance.gpuccio_{September 17, 2018
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GP@96
I would like to add that the case of eusociality in bees is not the only amazing example of interorganism control in animals. Let’s remind that the “organism differentiation” does not involve only differences in bodily phenotype, but also differences in behaviour.
And, I suspect, we have seen this as humans changed from a dispersed agrarian society to an urban concentrated society. And this is shown most commonly in “mob mentality”.R J Sawyer_{September 17, 2018
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R J Sawyer at #95: I am not sure I understand your point here. Diseases are of course errors in the program. We always have possible errors in complex structures. Indeed, the greater the functional complexity, the greater the risk of errors. That's why error checking algorithms must be added to very complex structures. As they are added to biological structures, too. But no error control can ever be perfect. Are you arguing that the existence of diseases is an argument against design? I don't undertstand.gpuccio_{September 17, 2018
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To all: It was not my intention to criticize anyone. My only point is that it is not interesting to debate who is right or who is wrong in using words. The OP here presents a very interesting paper and a very interesting problem, and that's what, IMO, we should discuss. Words are not the important thing: ideas are. I maintain that the word "genome" in the title is slightly misleading, and that "epigenome" would have been more precise. Because, usually, everybody uses "genome" to mean the sequence of nucleotides in DNA which, with few exceptions, is essentially the same in all the cells of one organism. While "epigenome" refers, usually, to the different "readings" of the genome that are realized by the many levels of epigenetic modifications. That said, the important point is not whether the word is more or less accurate. The point, IMO, is that the hereditary information that, in bees, guides not only the differentiation of cells and tissue and organs in one individual, but also the social differentiation of individuals, is a remarkable example of multi-layered functional complexity. It is also a type of functional complexity (I mean the "eusocial" part) that has no definite counterpart, for example, in humans. So, the OP here is extremely interesting and appropriate, even if the title is probably misleading. I would like to add that the case of eusociality in bees is not the only amazing example of interorganism control in animals. Let's remind that the "organism differentiation" does not involve only differences in bodily phenotype, but also differences in behaviour. And I believe that how hereditary information can controll collective behaviour, IOWs that form of behaviour where different organisms contribute in different ways to a global pattern, is really a fascinating mystery. Think not only of bees, but also of hunts, migrating birds, probably even bacterial colonies. The subject is vast and extremely fascinating. And we know so little about those issues.gpuccio_{September 17, 2018
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OLV
Here’s more specific: All that functional complexity in biology was intelligently designed. Can’t make it more specific than that.
That is definitely one way to look at it. But then how do you explain the many epigenetic/methylation/histone triggered diseases? Their “programming” also exists in genomes. Is it only designed if it benefits survival?R J Sawyer_{September 17, 2018
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Amblyrhynchus, Here’s more specific: All that functional complexity in biology was intelligently designed. Can’t make it more specific than that. :)OLV_{September 17, 2018
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Probably looking for something a bit more specific...Amblyrhynchus_{September 17, 2018
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Amblyrhynchus, You’re missing so much! What can I tell you? Wake up and smell the coffee! ????OLV_{September 17, 2018
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I mean, I think it's pretty simple isn't it? I don't think there is much meaningful content in these posts. If I'm missing something then let me know.Amblyrhynchus_{September 17, 2018
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Now I see that jawa helped to pull R J Sawyer from the discussion related to the inaccurate OP title and brought them to the real substance discussion with gpuccio. Some credits to jawa for that.PeterA_{September 17, 2018
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Amblyrhynchus @87: Can you elaborate on the meaning of what you just wrote? Thanks.PeterA_{September 17, 2018
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jawa, Don’t you want to take a break, buddy? Aren’t you tired?PeterA_{September 17, 2018
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Yes. I guess it's serious enough, but there's just not very much to any of this.Amblyrhynchus_{September 17, 2018
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Amblyrhynchus @82: Don’t you see any serious content in gpuccio’s comments? Really? I would even accept you don’t see much seriousness in my comments, but gpuccio’s? Are you serious?jawa_{September 17, 2018
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R J Sawyer, You may want to exercise certain caution when relying on old fashioned definitions. Here’s another example of how deeply scientists understand the biology of the human body: https://www.nbcnews.com/health/heart-health/daily-aspirin-may-be-harmful-healthy-older-adults-large-study-n909791jawa_{September 17, 2018
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R J Sawyer: See this: https://www.google.com/search?q=Watch+%E2%80%9CWhat+is+a+Gene%3F+(Denis+Noble)%E2%80%9D+on+Vimeo:+https://vimeo.com/173356410%3Fref=em-share&ie=UTF-8&oe=UTF-8&hl=en-us&client=safari#imgrc=iXluKCUjToaN9M:jawa_{September 17, 2018
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R J Sawyer, Since apparently you missed to respond the comment addressed to you @39, I’ll post it again here for your convenience: R J Sawyer @37: Are you saying that gpuccio chose “an OP title that is biased towards a view that cannot be proven or disproven” ? The evidences we know are sufficient proof for the veracity of the title gpuccio chose for his excellent OP and following comments. Actually, gpuccio himself presents some of those evidences with tremendous clarity. However, it’s an undeniable fact that you aren’t willing to accept the truth and nobody can force you to. Do you agree or disagree with the above comment? Why?jawa_{September 17, 2018
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