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

R J Sawyer, In this discussion: Transcription regulation: a miracle of engineering Posted by gpuccio August 28, 2018 Visited 2,288 times, 258 comments posted. The title of that OP is very politically incorrect because it qualifies a functionally complex biological process as "a miracle of engineering". Your contribution was expressed in 4 off-topic comments. The title of the current OP, which was started Sept 13, is perhaps inaccurate because it could have said "genome effect" instead of just "genome", but you jumped at it right away, posting 5 comments so far, out of a total of 21 comments posted. Can you explain that inconsistency?jawa_{September 14, 2018
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OLV
Well, I have to make a correction to my previous post: R J Sawyer posted some comments in gpuccio’s latest discussion: https://uncommondescent.com/intelligent-design/transcription-regulation-a-miracle-of-engineering/#comment-663758 @ 101, 103, 106, 115, then he went running for the hills. gpuccio graciously responded all his comments. Apparently R J Sawyer didn’t stand the heat. That discussion was too serious.
If you had read my comments on that thread you would have noticed that I prefaced them by saying that they were off topic. GP kindly and graciously responded to my comments and then I left the tread as he had answered my questions.R J Sawyer_{September 14, 2018
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just a side note... It's probably worth remembering that DNA is a medium of information, and like any medium of information, it is literally meaningless without the coordinated constraints that establish it as a medium and specify it referents.Upright BiPed_{September 14, 2018
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Well, I have to make a correction to my previous post: R J Sawyer posted some comments in gpuccio's latest discussion: https://uncommondescent.com/intelligent-design/transcription-regulation-a-miracle-of-engineering/#comment-663758 @ 101, 103, 106, 115, then he went running for the hills. gpuccio graciously responded all his comments. Apparently R J Sawyer didn't stand the heat. That discussion was too serious. I don't recall seeing Amblyrhynchus in that discussion at all.OLV_{September 14, 2018
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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...Amblyrhynchus_{September 14, 2018
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OLV
I don’t recall seeing Amblyrhynchus or R J Sawyer in that discussion at all. Why? Are they afraid of being publicly discredited?
I can’t speak for Ambky, but I wasn’t registered at UD at the time.R J Sawyer_{September 14, 2018
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Very interesting article. You may want to ignore the red herrings thrown here to distract readers' attention from the important matter: the mind-boggling functional complexity revealed by the latest research reports. For example, see this:
Chromatin Topology: the New (and Latest) Functional Complexity https://uncommondescent.com/intelligent-design/chromatin-topology-the-new-and-latest-functional-complexity/#comment-661982 Posted by PaV July 23, 2018 Visited 3,250 times. 241 Responses (posted comments)
I don’t recall seeing Amblyrhynchus or R J Sawyer in that discussion at all. Why? Are they afraid of being publicly discredited? That discussion thread is no joke. They know that. That's why they stay away from those discussions. They don't want to be seen running for the hills, like George Castillo, Larry Moran and Arthur Hunt did before.OLV_{September 14, 2018
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"regulatory elements" are DNA sequences. Histones are not. All you have to say is "whoops,my mistake". Instead you continue to google, misunderstand the results, and double down on your mistakes. My question is why. What is so hard about stunning you were wrong?Amblyrhynchus_{September 14, 2018
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Origenes,
FYI not all regulation stems from DNA
No, but all "regulatory elements" are DNA sequences. There are things that play a role in gene regulation that aren't "regulatory elements".goodusername_{September 14, 2018
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Amblyrhynchus, FYI not all regulation stems from DNA, there is such a thing as epigenetics and epigenetic regulation — e.g. see here — which happens to be the topic of the OP.Origenes_{September 14, 2018
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Ambly- Histones clearly play a role in regulation. Even Wikipedia recognizes that:
In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes.[1][2] They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation.
Also histones are proteins which ultimately originate from the DNA.ET_{September 14, 2018
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Origenes, you truly are an idiot. Regulatory elements are DNA sequences, histones are not. If you had even the slightest background in molecular biology you would know this. Clearly you don't have that background knowledge, so I'm left to wonder why you keep doubling down on a topic you are completely ignorant about (let alone doing it in such a snide fashion).Amblyrhynchus_{September 14, 2018
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R J Sawyer: This paper is talking about epigenetics, which does not change DNA sequences.
Again, no one claims that it does.
R J Sawyer: Methylation at specific sites in the DNA can turn on or off a gene, changing the phenotypic expression.
Indeed. So? Sanger would define a histone as a “regulatory element”, which, under his definition, is part of the genome (see #5).
Amblyrhynchus: Histones are not (…) regulatory elements (…)
You are mistaken, they obviously are — click here - - - - BA77 @8 Very interesting post. Thank you.Origenes_{September 14, 2018
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We don't even know what makes a bee a bee. R J Sawyer:
Even back then we were taught that the phenotype was the result of the DNA and environment.
Except that does not determine if a bee will develop or a fly from the same DNA. All that can do is the minor changes in the bee- worker, drone or queen. We don't know what determines what will develop:
To understand the challenge to the “superwatch” model by the erosion of the gene-centric view of nature, it is necessary to recall August Weismann’s seminal insight more than a century ago regarding the need for genetic determinants to specify organic form. As Weismann saw so clearly, in order to account for the unerring transmission through time with precise reduplication, for each generation of “complex contingent assemblages of matter” (superwatches), it is necessary to propose the existence of stable abstract genetic blueprints or programs in the genes- he called them “determinants”- sequestered safely in the germ plasm, away from the ever varying and destabilizing influences of the extra-genetic environment. Such carefully isolated determinants would theoretically be capable of reliably transmitting contingent order through time and specifying it reliably each generation. Thus, the modern “gene-centric” view of life was born, and with it the heroic twentieth century effort to identify Weismann’s determinants, supposed to be capable of reliably specifying in precise detail all the contingent order of the phenotype. Weismann was correct in this: the contingent view of form and indeed the entire mechanistic conception of life- the superwatch model- is critically dependent on showing that all or at least the vast majority of organic form is specified in precise detail in the genes. Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes as Weismann’s “unambiguous bearers of information” or view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a small fraction of all known genes, such as the developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene- Michael Denton “An Anti-Darwinian Intellectual Journey”, Uncommon Dissent (2004), pages 171-2
Assembly-line workers do not determine what they are making but they sure can control and influence it. The same goes for the parts they are given.ET_{September 14, 2018
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R J Sawyer claims that
When scientists talk about the genome and genes they are talking about the DNA sequences. And these do not change during an organism’s life, other tha(n) mutations.
Yet we find that "Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism."
Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: humans have a "few thousand" different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It's called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) "genomic equivalence" -- the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA -- became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html Contrary to expectations, genes are constantly rearranged by cells - July 7, 2017 Excerpt: Contrary to expectations, this latest study reveals that each gene doesn’t have an ideal location in the cell nucleus. Instead, genes are always on the move. Published in the journal Nature, researchers examined the organisation of genes in stem cells from mice. They revealed that these cells continually remix their genes, changing their positions as they progress through different stages. https://uncommondescent.com/intelligent-design/researchers-contrary-to-expectations-genes-are-constantly-rearranged-by-cells/
James Shapiro weighs in here and states, 'Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs).'
How life changes itself: the Read-Write (RW) genome. - 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611
R J Sawyer also claims
we have long known that phenotype is an interaction between the DNA and the environment.
And yet, the following article notes that 'a brief time-lapse video can teach more about embryonic development than any amount of reading. And further notes that it is hard not to be impressed how a repeatable form reliably emerges despite considerable variation in both genes and environment.'
Criticality in morphogenesis - September 17, 2013 Excerpt: In many regards, a brief time-lapse video can teach more about embryonic development than any amount of reading. It is hard not to be impressed how a repeatable form reliably emerges despite considerable variation in both genes and environment. While it had been hoped that concepts borrowed from statistical mechanics or the ideas of self-organized criticality could help to create some kind of physics-based theory of development, much of what has been done lies only at the level of metaphor. In a paper just released to ArXiv, William Bialek and his colleagues from Princeton University, have taken their search for the signature of criticality in a more specific direction. They looked at a particular set of transcription factors in Drosophila embryos which control spatiotemporal development. By analyzing fluctuations in the expression levels of these so-called gap genes, they found evidence for critical (fine) tuning in this particular network. http://phys.org/news/2013-09-criticality-morphogenesis.html
Bottom line, from evidence such as this, and many more lines of evidence, biological form is now known to be forever beyond the reductive materialistic explanations of Darwinian evolution.
Darwinism vs Biological Form - video https://www.youtube.com/watch?v=JyNzNPgjM4w
And as advances in quantum biology have now shown, Darwinists, with their reductive materialistic framework, are not even on the correct theoretical foundation in the first place in order to properly understand biology.
Darwinian Materialism vs Quantum Biology - video https://www.youtube.com/watch?v=LHdD2Am1g5Y
Of supplemental note, the failure of reductive materialism to be able to explain the basic form of any particular organism occurs at a very low level. Much lower than DNA itself. In the following article entitled 'Quantum physics problem proved unsolvable', which studied the derivation of macroscopic properties from a complete microscopic description, the researchers remark that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, The researchers further commented that their findings challenge the reductionists' point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description."
Quantum physics problem proved unsolvable: Gödel and Turing enter quantum physics - December 9, 2015 Excerpt: A mathematical problem underlying fundamental questions in particle and quantum physics is provably unsolvable,,, It is the first major problem in physics for which such a fundamental limitation could be proven. The findings are important because they show that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, "We knew about the possibility of problems that are undecidable in principle since the works of Turing and Gödel in the 1930s," added Co-author Professor Michael Wolf from Technical University of Munich. "So far, however, this only concerned the very abstract corners of theoretical computer science and mathematical logic. No one had seriously contemplated this as a possibility right in the heart of theoretical physics before. But our results change this picture. From a more philosophical perspective, they also challenge the reductionists' point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description." http://phys.org/news/2015-12-quantum-physics-problem-unsolvable-godel.html
bornagain77_{September 14, 2018
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Ah, Origenes, did you read Sanger's quote?
A genome consists of all the genetic material contained in a cell of an organism and contains all of the information necessary for life. In general, this inherited information is encoded in three types of elements – genes, regulatory elements and maintenance elements.
Histones are not genetic material, nor are they genes, regulatory elements or maintenance elements (or any of the more specific ones later listed).Amblyrhynchus_{September 13, 2018
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Origenes, the definition I posted comes from googling genome. This paper is talking about epigenetics, which does not change DNA sequences. Methylation at specific sites in the DNA can turn on or off a gene, changing the phenotypic expression. But as I said, we have long known that phenotype is an interaction between the DNA and the environment. None of this changes the DNA sequences that are passed on to offspring.R J Sawyer_{September 13, 2018
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R J Sawyer: When scientists talk about the genome and genes they are talking about the DNA sequences.
Nope. Just google "genome", or read this:
Frederick Sanger: Chapter 1 Introduction A genome consists of all the genetic material contained in a cell of an organism and contains all of the information necessary for life. In general, this inherited information is encoded in three types of elements - genes, regulatory elements and maintenance elements. Genes contain information to code for proteins while regulatory elements control the spatial and temporal production of proteins by genes. These regulatory elements include promoters, enhancers, insulators and other elements such as non-coding regulatory RNAs.
Origenes_{September 13, 2018
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Origenes
Your comment is misleading, since no one made the claim that DNA sequences change. The claim in the title is that the Bee genome changes.

Genome: A genome is an organism's complete set of DNA, including all of its genes.
When scientists talk about the genome and genes they are talking about the DNA sequences. And these do not change during an organism’s life, other that mutations.R J Sawyer_{September 13, 2018
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Histones are not part of the genome (whether the authors of a press release know that or not). And it's perfectly clear from News' added commentary that she does think the DNA sequence has changed.Amblyrhynchus_{September 13, 2018
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R J Sawyer: The title of the OP is misleading. The DNA sequences do not change.
Your comment is misleading, since no one made the claim that DNA sequences change. The claim in the title is that the Bee genome changes. From the article:
... the researchers found, the genomes of future workers and queens already had “striking differences” in their patterns of histone modifications, says Robert Lowe, a computational biologist at Queen Mary University of London and one of the paper’s authors. And the locations of the histones that were modified differently in workers and queens corresponded with the sites of genes that have different expression levels between the two populations.
Origenes_{September 13, 2018
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The title of the OP is misleading. The DNA sequences do not change. I went through high school and university in the mid to late 70s. Even back then we were taught that the phenotype was the result of the DNA and environment. If my old brain remembers correctly, we were taught that whether a bee larvae became a queen or a drone depended on what they were fed. Similarly, gender in turtles is dependent on temperature of incubation.R J Sawyer_{September 13, 2018
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