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

Amblyrhynchus: I will give you one useful (I hope) hint. At #102 you state: "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." OK, the problem is very simple: The valley, as shaped by plate tectonics, is not an exmaple of complex functional information. It may be beautiful and amazing, but there is no independently defined and specific function that it can implement that requires a specific configuration over all possible configurations and is complex enough (more than 500 bits of specific information). Compare that to a Shakespeare's sonnet, or to ATP synthase (two good examples of similar complex functional information, well above 500 bits), and you will see the difference. For reference, check here: An attempt at computing dFSCI for English language https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/ where I compute the functional information in a Shakepseare's sonnet at at least 800 bits. And here: Four fallacies evolutionists make when arguing about biological function (part 1) https://uncommondescent.com/intelligent-design/four-fallacies-evolutionists-make-when-arguing-about-biological-function-part-1/ Where I show that the alpha and beta chains of ATP synthase have functional complexity well above the 500 bits limit (see the OP and comment 32).gpuccio_{September 19, 2018
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Amblyrhynchus, Now that you’ve arrived to such a brilliant conclusion, let’s get back to work. :)OLV_{September 18, 2018
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Well, I had though the PeterA, PaoloV, OLV and Jawa... but quick look at few threads and maybe DATCG is a candidate too. For anyone (like me) that may have mistaken OLVfor someone asking questions in good faith, you'll find this little collection of accounts often post rapid-fire responses to each other , all with a similar style and often attempting to direct a thread's evolution. At least once, they got mixed up about which name they were using (2 mins after Jawa comments here, PaoloV responds but calls Jawa "PeterA"). So I suspect these are all accounts created with the aim of simulating active discussion on some of the very long posts they tend to appear under. I don't think I'll spend much time engaging with these characters int he future.Amblyrhynchus_{September 18, 2018
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Amblyrhynchus: "I’ll let you know if I have time to look in more detail." Thank you. "looks like the classic creationist tactic of over-specifying the target (by looking at what exists now and presuming it’s the only way a given function could be encoded)" Indeed, in all my analyses about information jumps in protein, I look at what appeared in the transition to vertebrates, and has been conserved for more than 400 million years. That does not sound like the "creationist tactic" that you mention, whatever it is. However, again, thank you for the attention.gpuccio_{September 18, 2018
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Amblyrhynchus, Ok, definitely you must be very clever that you figured it all out. :) Yes, I do contribute from several accounts in UD. :) My favorite is one of the most scientifically educated in serious biology topics in the whole blogosphere. For this I use the name gpuccio. :) Also write quite interesting OPs and/or comments under the pseudonyms Eugene S, DATCG, Upright Biped, News, bornagain77 and Kairosfocus. :) Actually, OLV (initials for Oscar Luis V.) is probably the most boring and unattractive of all my contributions in this website. As you can imagine this keeps me quite busy. :) Now I hope my answer satisfies your curiosity. :)OLV_{September 18, 2018
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GP, Obviously, I'm unlikely to read multiple several-thousand-word posts any time soon. In general, this approach looks like the classic creationist tactic of over-specifying the target (by looking at what exists now and presuming it's the only way a given function could be encoded), but I'll let you know if I have time to look in more detail. Peter/OLV, Are you the same person? And you also running several other accounts on UD?Amblyrhynchus_{September 18, 2018
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gpuccio @129: Excellent!OLV_{September 18, 2018
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Transient reduction of DNA methylation at the onset of meiosis in male mice
Our results suggest that contrary to the prevailing view, chromosomes exhibit dynamic changes in DNA methylation in meiotic prophase I (MPI).
OLV_{September 18, 2018
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R J Sawyer: "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." I appreciate your fair position. But, of course, I do believe that available facts are already more than enough to decide who is right and who is wrong. That's why I try to always rely on facts. And every day the evidence becomes heavier. Exponentially, I would say.gpuccio_{September 18, 2018
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Ambly:
You’ll have to define “complex functionally specified information”, but if it’s like Dembski’s csi then natural selection will do the trick.
That is a lie as natural selection has never produced CSI- NEVER. The only "trick" is the ignorant evos claiming otherwise.ET_{September 18, 2018
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R J Sawyer:
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.
False analogy. Heaping parts of land upon itself to build a heaping pile of land is not the same as saying small changes in a genome can produce an entirely different form of life. Evos are so cluelessly desperate. They don't even have a mechanism capable of producing eukaryotes given starting populations of prokaryotes.ET_{September 18, 2018
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Epigenomic and single-cell profiling of human spermatogonial stem cells
it is possible that DNA methylation is precisely regulated in each stage of human spermatogenesis at specific loci. it would be intriguing to speculate that the gene expression programs are distinct between human and mouse spermatogenesis.
emphasis mineOLV_{September 18, 2018
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Amblyrhynchus: I have written a rather detailed answer to you, but it seems that it is awaiting moderation, probably because there were too many links in it. Just have a little patience! :)gpuccio_{September 18, 2018
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Amblyrhynchus: #115: "Why not?" #119: "You’ll have to define “complex functionally specified information”, but if it’s like Dembski’s csi then natural selection will do the trick." Of course, that's neo-darwinist cathechism again. But let me answer briefly. You are certainly competent about biology issues, so I will just give you the answers about ID basics. First of all, the threads we have been debating in recently: Chromatin Topology: the New (and Latest) Functional Complexity https://uncommondescent.com/intelligent-design/chromatin-topology-the-new-and-latest-functional-complexity/ Transcription regulation: a miracle of engineering (OP mine) https://uncommondescent.com/intelligent-design/transcription-regulation-a-miracle-of-engineering/ and the one we are in now, about bees epigenome, are focused on transcription, chromatin states, regulation networks, epigenetics. From an ID point of view, they have an important purpose: to show that there are a lot of new levels of complex functional information that were only scarcely understood before, and that must be added to the amazing levels of functional information that can be found in protein coding genes and in proteins. They are not intended to discuss the basics of ID theory. At the end of my OP about transcription regulation, I wrote:
Summary and Conclusions So this is the part where I should argue about how all the things discussed in this OP do point to design. Or maybe I should simply keep silent in this case. Because, really, there should be no need to say anything. But I will. Because, you know, I can already hear our friends on the other side argue, debate, or just suggest, that there is nothing in all these things that neo-darwinism can’t explain. They will, they will. Or they will just keep silent. So, I will briefly speak. --- And now, a few considerations: This is just an essential outline: what really happens is much, much more complex As we have seen, the working of all this huge machinery requires a lot of complex and often very specific proteins. First of all the 2000 specific TFs, and then the dozens, maybe hundreds, of proteins that implement the different steps. Many of which are individually huge, often thousands of AAs long. The result of this machinery and of its workings is that thousands of proteins are transcribed and translated smoothly at different times and in different cells. The result is that a stem cell is a stem cell, a hepatocyte a hepatocyte and a lymphocyte a lymphocyte. IOWs, the miracle of differentiation. The result is also that liver cells, renal cells, blood cells, after having differentiated to their “stable” state, still perform new wonders all the time, changing their functional states and adapting to all sorts of necessities. The result is also that tissues and organs are held together, that 10^11 neurons are neatly arranged to perform amazing functions, and so on. All these things rely heavily on a correct, constant control of transcription in each individual cell. This scenario is, of course, irreducibly complex. Sure, many individual components could probably be shown not to be absolutely necessary for some rough definition of function: transcription can probably initiate even in the absence of some regulatory factor, and so on. But the point is that the incredibly fine regulation of the whole process, its management and control, certainly require all or almost all the components that we have described here. Beyond its extraordinary functional complexity, this regulation network also uses at its very core at least one big sub-network based on a symbolic code: the histone code. Therefore, it exhibits a strong and complex semiotic foundation. So, the last question could be: can all this be the result of a neo-darwinian process of RV + NS of simple, gradual steps? That, definitely, I will not answer. I think that everybody already knows what I believe. As for others, everyone can decide for themselves.
OK, now here you repeat the expected "objection" (as George Castillo has already done in the original thread): "there is nothing there that neo-darwinist theory cannot explain". Indeed, you are even more "specific": you say that "natural selection will do the trick". Well, we can start a discussion about the reasons why NS cannot do the trick. Or, more in general, about what functional complexity is, and why it allows us to infer design. I am not sure you are interested, but I am certainly available. But, as a starting point, I can give you a few links to some of my OPs here, where I have already debated those issues in some detail. Both in the OPs and in the interesting, and sometimes very long, discussions in the threads. So, you can find my precise definition of design here: Defining Design https://uncommondescent.com/intelligent-design/defining-design/ And you can find my detailed definition of functional complexity here: Functional information defined https://uncommondescent.com/intelligent-design/functional-information-defined/ You will see that my definition is in very good accord with Dembski's, but there are some important differences too. I have dedicated two whole OPs and discussion threads to a detailed analysis of the limits of the neo-darwinian algorithm and of its two components. Here is the first, about the limits of NS: What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/ I go into details about why NS, definitely, cannot "do the trick". And this is about the limits of RV: What are the limits of Random Variation? A simple evaluation of the probabilistic resources of our biological world https://uncommondescent.com/intelligent-design/what-are-the-limits-of-random-variation-a-simple-evaluation-of-the-probabilistic-resources-of-our-biological-world/ Where I give a gross evaluation of the probabilistic resources in the biological world. I have also dedicated many OPs to my procedure to compute functional information in proteins, and to its application: Homologies, differences and information jumps https://uncommondescent.com/intelligent-design/homologies-differences-and-information-jumps/ Information jumps again: some more facts, and thoughts, about Prickle 1 and taxonomically restricted genes. https://uncommondescent.com/intelligent-design/information-jumps-again-some-more-facts-and-thoughts-about-prickle-1-and-taxonomically-restricted-genes/ The highly engineered transition to vertebrates: an example of functional information analysis https://uncommondescent.com/intelligent-design/the-highly-engineered-transition-to-vertebrates-an-example-of-functional-information-analysis/ The amazing level of engineering in the transition to the vertebrate proteome: a global analysis https://uncommondescent.com/intelligent-design/the-amazing-level-of-engineering-in-the-transition-to-the-vertebrate-proteome-a-global-analysis/ Interesting proteins: DNA-binding proteins SATB1 and SATB2 https://uncommondescent.com/intelligent-design/interesting-proteins-dna-binding-proteins-satb1-and-satb2/ Bioinformatics tools used in my OPs: some basic information. https://uncommondescent.com/intelligent-design/bioinformatics-tools-used-in-my-ops-some-basic-information/ Of course, I don't expect that you will have the time or the will to read all that material. It's just to show that those points have been debated here, and in great and long detail. So, I will just offer here a very simple, and necessarily incomplete, explanation, in a nutshell, of why NS (and RV) cannot "do the trick": a) Complex functions are those that require, say, at least 500 specific bits of information to be implemented. IOWs, the function is not there if at least those 500 specific bits are not there. b) The biological world is repleted with complex functions, starting with individual proteins and reaching to complex regulation networks and networks of network. In my OPs, I have given many examples, in single proteins, in groups of proteins, and in more complex structures, like the spliceosome, the ubiquitin system and, most recently, transcription regulation. c) If a function requires at least 500 specific bits to exist, it is definitely beyond the range of the probabilistic resources of our biological world (which, very generously, can be computed at about 160 bits, see the table at the beginning of my OP about the limits of RV). IOWs, it's practically impossible that even one single new complex function may be found by a random search or a random walk. d) Complex functions cannot be deconstructed into simpler steps, each of them giving greater function than the previous one. If you don't agree, just offer one single counter-example. e) Therefore, as no new complex function can be found by RV in the real world, and as complex functions cannot be decontructed into gradual pathways, it is very clear that NS can have absolutely no role in finding new complex functions. Of course, it can certainly have a (very limited) role in optimizing them, once they are already there (seee my OP about the limits of NS). OK, that's it in a nutshell. Now it's up to you whether to go on with the discussion or not. As said, I am here.gpuccio_{September 18, 2018
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DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell DifferentiationOLV_{September 18, 2018
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The answer is the same, I'm afraid. A good textbook will provide you with some information on this. (Though, of course, there is still a lot more for science to learn). I have to ask though, how many accounts do you have at UD?Amblyrhynchus_{September 18, 2018
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Perhaps I could rephrase the question @75: What spatiotemporal mechanisms determine the type, location and timing of the epigenetic marks?PeterA_{September 18, 2018
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Amblyrhynchus @121: No textbook contains the answers to those questions. Not even close. Please, try again. ThanksPeterA_{September 18, 2018
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Here’s what jawa posted @ 109:
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.
PeterA_{September 18, 2018
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Sorry, I meant jawa @109.PeterA_{September 17, 2018
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Amblyrhynchus, Was that your response to jawa 9109? Really?PeterA_{September 17, 2018
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It's encoded in the genome, especially through proteins that modify bases and histones or drive the transcription of certain genes and the binding sites of those proteins. If you'd like to learn more detail, second-hand biology textbooks are usually easy to find at a reasonable price between the start of semesters.Amblyrhynchus_{September 17, 2018
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Amblyrhynchus, Did you see jawa’s comment @109? Would you mind answering the questions in that post ? Thanks.OLV_{September 17, 2018
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You'll have to define "complex functionally specified information", but if it's like Dembski's csi then natural selection will do the trick.Amblyrhynchus_{September 17, 2018
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OLV, Yes, I would too. But I won't hold my breath while waiting for such a marvelous revelation. :)PeterA_{September 17, 2018
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Peter, I would be thrilled too. Wouldn't you? :)OLV_{September 17, 2018
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Amblyrhynchus: Why not? Simply because the only known source of complex functionally specified information is conscious design. Are you aware of another? Can you present it here? I'm sure gpuccio will be thrilled seeing it. Thanks.PeterA_{September 17, 2018
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But the point is hat such “contingency” cannot ever generate complex functional information, unless it is guided and arranged into functional configurations.
Why not?Amblyrhynchus_{September 17, 2018
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gpuccio: Thank you for commenting on those fascinating issues. Good night.jawa_{September 17, 2018
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To all: OK, good night for today! :)gpuccio_{September 17, 2018
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