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Epigenetics: Organisms’ diet affects their DNA sequence

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From ScienceDaily:

In a study on two groups of parasites, the team detected differences in DNA sequences that could be attributed to the composition of their food.

‘We found that different levels of nitrogen in a parasite’s diet contributed to changes in its DNA. Specifically, parasites with low-nitrogen, high-sugar diets had DNA sequences that used less nitrogen than parasites with nitrogen-rich, high-protein diets.’

The study involved groups of eukaryotic parasites (Kinetoplastida) and bacterial parasites (Mollicutes) that infect different plant or animal hosts.

The results, based on novel mathematical models developed by the researchers, reveal a previously hidden relationship between cellular metabolism and evolution. They provide new insights into how DNA sequences can be influenced by adaptation to different diets. Paper. (public access) – Emily A. Seward, Steven Kelly. Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms. Genome Biology, 2016; 17 (1) DOI: 10.1186/s13059-016-1087-9More.

MUFFINS
Always have muffins for breakfast.

The team hopes to test the thesis on more complex organisms. Like foodies, for example?

It would be good to have some serious nutrition information for once, instead of all the scams and scares fronted in popular mags.

See also: Epigenetics: Aeon writer says Darwin’s theory is “incomplete”

and

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

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43 Replies to “Epigenetics: Organisms’ diet affects their DNA sequence

  1. 1
    wd400 says:

    “epigenetics…. DNA sequence”

    You have to pick one, I’m afraid.

  2. 2
    PaV says:

    wd400:

    From the abstract:

    Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.

    You have to admit, this isn’t neo-Darwinian evolution.

  3. 3
    wd400 says:

    I do not.

  4. 4
    Dionisio says:

    PaV @2:

    You have to admit, this isn’t neo-Darwinian evolution.

    Of course!
    Isn’t this about flexible/robust built-in adaptation mechanisms, ingeniously embedded within the biological systems?

    From the same paper:

    Specifically, adaptation [how?] to low nitrogen availability results [how?] in reduced nitrogen content in nucleotide sequences.

    Better ask your politely-dissenting interlocutors how* we got those built-in adaptation mechanisms embedded within the biological systems to begin with. Just don’t hold your breath while waiting for a serious answer. We don’t want you to turn blue. 🙂

    http://www.uncommondescent.com.....ent-620748

    (*) we should get back the humble sense of wonder we had as children, which somehow we lost as we grew older.

  5. 5
    Silver Asiatic says:

    PaV

    You have to admit, this isn’t neo-Darwinian evolution.

    Let me guess … wd400 will say, as Aeon writer says: “Darwin’s theory is incomplete”. So, it’s still neo-Darwin evolution, but a ‘more complete’ version of it. 🙂

    Hey, even if some were to admit that it’s not neo-Darwinian, they’ll shift to some other terminology that means unintelligent design did it. But I accept it’s a battle of inches. Maybe the process will cause some to abandon unintelligent design entirely – so it’s worth the effort even just to kill of NDE.

  6. 6
    Silver Asiatic says:

    Always have muffins for breakfast.

    I had just a plain blueberry today, even though I realize the frosted kind with cherry on top is much more ideal.

  7. 7
    PaV says:

    You do not admit that it is NOT neo-Dawinian? Did I get that right?

    If I do have it right, then what is your explanation. Please.

  8. 8
    PaV says:

    Here’s this from Science Daily:

    The results, based on novel mathematical models developed by the researchers, reveal a previously hidden relationship between cellular metabolism and evolution.

    As you know from prior discussions, this was not anything ‘hidden’ to me: only the Darwinists.

  9. 9
    PaV says:

    wd400:

    I just looked at the article itself, and it looks like they’re saying that the composition of the “nucleotides” changes; that there is a higher content of nitrogen found ‘within’ the nucleotides themselves, and the codons by extension.

    My reading of the article is that the actual DNA sequence hasn’t changed. If that’s correct, then my statements above are only marginally correct, at best. This looks more like a change in the construction of the codon backbone, influenced by diet.

  10. 10
    Dionisio says:

    PaV and Silver Asiatic:

    Since you’re in this discussion thread, you may want to take a look at this related paper:

    http://www.uncommondescent.com.....ent-620756

  11. 11
    wd400 says:

    I don’t what you guys think this paper says. But it’s pretty clear it’s about DNA sequences (so not epigenetics) and the result of mutation and selection (so pretty standard evolutionary biology).

  12. 12
    Silver Asiatic says:

    It appeared to me to be looking at the epigenetic effect of nitrogen content on mutational bias – beyond what mutation and selection produce on its own.

  13. 13
    wd400 says:

    Well, that’s not what the paper says. And I’m not really sure how that would be epigenetic, if that word still means anything.

  14. 14
    Silver Asiatic says:

    They’re claiming that the presence of nitrogen in the environment merely contributes some selection pressure so they don’t see it as an epigenetic phenomenon – true. At the same time they have 6% of the total variance unexplained and they hypothesize some factors that can account for it. That’s neither here nor there on the topic at hand though.

    Ok, I wouldn’t call this a study on epigenetic factors as such. Add that to PaV @ #9 and there’s not much of a story here.

  15. 15
    Silver Asiatic says:

    Dionisio @ 10

    I didn’t read the paper but I will guess it’s the same phenomenon in the mutation/selection paradigm. The presence or absence of nutrition shapes the environment and creates niches for various effects of mutation and selection.

    I didn’t see that report as looking into epigenetic factors, similar to the one on this thread.

    But then again, it could be — I only looked at the summary.

  16. 16
    Dionisio says:

    This seems to be about built-in adaptation mechanisms that lead to micro-evolution [not macro-evo] in some biological systems, but not all.

    Apparently these two papers are somehow related regarding the presence of the given built-in adaptation mechanisms in biological systems of certain order and the absence of similar mechanisms in higher-order biological systems.
    Can someone confirm this?
    It would be interesting to read gpuccio’s opinion on this subject.
    http://www.uncommondescent.com.....ent-620748

    http://www.uncommondescent.com.....ent-620756

  17. 17
    Dionisio says:

    PaV @9:

    The OP references a paper that does not seem to deal with “epigenetics” in the technical sense, because it doesn’t seem to be about the DNA molecular switches that affect the way the gene regulatory networks are used by the biological systems to perform transcription. Therefore, WD400’s semantic observation @1 does not seem to be incorrect. That’s why I did not react to it at all.

    However, as you implied @2, the conclusions of the paper referenced in this OP does not appear to support neo-Darwinian theories, because it deals with built-in adaptation mechanisms that lead to micro-evolution, not macro-evo.

    At some point in this short thread it looks as though WD400 and you are talking past each other. WD400 seems fixated in his original semantic observation, while you appear to point at the lack of support for the neo-Darwinian ideas. At least that’s my perception of your brief ‘dialog’.

    Please, correct me if I got the wrong perception. Thank you.

  18. 18
    Dionisio says:

    Silver Asiatic @15:

    What the two papers referenced @16 appear to indicate -as far as I can see- is that the built-in adaptation mechanisms described in the paper referenced in the current OP have not been observed in some higher-order biological systems. Maybe this is related to the antibiotic resistance of bacteria. In either case, this has to do with micro-evo, not macro-evo. It’s just another case of the myriad things associated with the complex complexity that science must continue researching.
    There’s not much here for the neo-Darwinian folks to cheer up. Maybe gpuccio can give us a hand with this and correct any inaccuracy he may notice in my comments.
    Now, back to work.

  19. 19
    Silver Asiatic says:

    Dioniso,
    It’s my guess that support for neo-Darwinian theory (for those who defend it) only requires evidence of micro-evolution. Where there is adaptive change due to mutation and selection, that is claimed as support for the theory. This is then extrapolated as evidence for the evolution of all of the biological diversity found on the planet.

    For my part, I incorrectly thought the paper referenced epigenetic factors when it’s actually just talking about mutation and selection with various nutritional levels causing environmental pressures and evolutionary niches — which is standard NDE.

    We could consider environmental pressures changing mutational biases as some sort of epigenetics, but that’s stretching it.

    As for built-in adaptation mechanisms, we’d have to read that into the paper somehow because it’s not part of the authors’ explanation.

    I think the title of the paper is misleading: “Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms”. They don’t seem to be saying that varying levels of nitrogen actually/directly alters DNA sequences. But rather changes in environment cause changes in mutation and selection.

  20. 20
    Silver Asiatic says:

    Dionisio,

    What the two papers referenced @16 appear to indicate -as far as I can see- is that the built-in adaptation mechanisms described in the paper referenced in the current OP have not been observed in some higher-order biological systems.

    I think it’s true to say that the ‘origin’ of adaptation mechanisms has never been demonstrated in neo-Darwinian terms, even at the micro level (irreducible complexity at work).

    But the paper, like most evolutionary studies, assumes the Darwinian origin of mechanisms and systems, and then just talks about how those systems adapt to different environmental conditions.

    So, I think you’re right to point to this gap in the evolutionary story.

  21. 21
    Dionisio says:

    Silver Asiatic @19:

    They don’t seem to be saying that varying levels of nitrogen actually/directly alters DNA sequences. But rather changes in environment cause* changes in mutation and selection.

    (*) How can that happen? Why can it happen?
    First question should describe the possible mechanism(s), but it should hold water tightly.
    Second question is about the origin of such mechanism(s), their location, etc. That’s the “built-in” part.

    As for built-in adaptation mechanisms, we’d have to read that into the paper somehow because it’s not part of the authors’ explanation.

    Generally authors’s explanations may leave unanswered questions. They don’t have to refer to “built-in” mechanisms for us to say they exist. It’s an implicit conclusion drawn from the paper.

    You’re correct, the second paper is pay walled, we can only see the abstract, but the last line says it all. The referenced adaptation mechanisms were not observed in higher order biological systems.

    BTW, I think adaptation implies micro-evolution, not macro-evolution. Bacteria’s antibiotic resistance is a known example of adaptation/micro-evolution, where bacteria remain bacteria. They just become resistant to the presence of certain antibiotics. They don’t become anything else but bacteria.
    Galapagos finches remain birds. Their beaks change through adaptation mechanisms also influenced by environmental cues.
    We humans adapt to rare air (low oxygen) at high elevations.
    Blood changes take place. But we remain humans, with all our defects and sinful attitude. Humans uniquely created in Imago Dei, which confers dignity to all, including WD400, PaV, you and me.
    Have a good weekend.

  22. 22
    Dionisio says:

    Silver Asiatic @ 20:

    But the paper, like most evolutionary studies, assumes the Darwinian origin of mechanisms and systems, and then just talks about how those systems adapt to different environmental conditions.

    Yes, I think they assume too much and many times wrong assumptions. Maybe that’s why they keep saying things like “surprisingly”, “unexpectedly”, etc. 🙂

  23. 23
    Silver Asiatic says:

    Dionisio

    Second question is about the origin of such mechanism(s), their location, etc. That’s the “built-in” part.

    True. There’s no discussion about the origin of the mechanisms and that’s the more important issue.
    Hope you have a nice weekend also.

  24. 24
    wd400 says:

    The “mechanism”is mutation and selection, I’m not sure you’ve read the paper dionisio?

  25. 25
    bornagain77 says:

    Beyond the DNA: Comprehensive map of the human epigenome completed – November 17, 2016
    Source:
    CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
    Summary:
    Scientists have established comprehensive maps of the human epigenome, shedding light on how the body regulates which genes are active in which cells. Over the last five years, a worldwide consortium of scientists has established epigenetic maps of 2,100 cell types.
    https://www.sciencedaily.com/releases/2016/11/161117150743.htm

    a little background:

    Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin – September 5, 2012
    Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well:
    “And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.””
    ,,, under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted.
    http://www.evolutionnews.org/2.....64001.html

    Why Are Biologists Lashing Out Against Empirically Verified Research Results? – Casey Luskin July 13, 2015
    Excerpt: the “vast majority” of the human genome shows biochemical function: “These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions.”3
    Ewan Birney, ENCODE’s lead analyst, explained in Discover Magazine that since ENCODE studied 147 types of cells, and the human body has a few thousand cell types, “it’s likely that 80 percent will go to 100 percent.”4 Another senior ENCODE researcher noted that “almost every nucleotide is associated with a function.”5 A headline in Science declared, “ENCODE project writes eulogy for junk DNA.”6,,,
    Evolutionists Strike Back
    Darwin defenders weren’t going to take ENCODE’s data sitting down.,,,
    How could they possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm–and by personally attacking, (i.e. ad hominem), those who challenge their position.,,,
    http://www.evolutionnews.org/2.....97561.html

    Toppling Another Evolutionary Icon, ENCODE Suggests Endogenous Retroviruses Are Functional – Casey Luskin – September 7, 2015
    Excerpt: ENCODE didn’t merely study the genome to determine which DNA elements are biochemically active and making RNA. It also studied patterns of biochemical activity, uncovering highly non-random patterns of RNA production–patterns which indicate that these vast quantities of RNA transcripts aren’t junk…. ENCODE’s results suggest that a cell’s type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that “the majority of regulatory DNA regions are highly cell type-selective,” and “the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types” studied increases. Thus, as two pro-ENCODE biochemists explain, “Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue-specific transcription in human cells.”
    http://www.evolutionnews.org/2.....99111.html

  26. 26
    Dionisio says:

    The pop-sci article referenced in this OP has the misleading simplistic title “Scientists uncover genetic evidence that ‘we are what we eat'” which is not even wrong.

  27. 27
    Dionisio says:

    BA77 @25:

    Thank you for posting the link to the recent article on epigenome map.

  28. 28
    PaV says:

    Dionisio:

    However, as you implied @2, the conclusions of the paper referenced in this OP does not appear to support neo-Darwinian theories, because it deals with built-in adaptation mechanisms that lead to micro-evolution, not macro-evo.

    At some point in this short thread it looks as though WD400 and you are talking past each other. WD400 seems fixated in his original semantic observation, while you appear to point at the lack of support for the neo-Darwinian ideas. At least that’s my perception of your brief ‘dialog’.

    Please, correct me if I got the wrong perception. Thank you.

    Dionisio:

    Your summary is fairly accurate. I took a quick look at the paper, and it seemed directly attributable to environmental cues. When I took a later look, I think I misunderstood what they were saying, and didn’t think neo-Darwinism was involved. (The problem these days is that whereas years ago I would spend hours looking into these things, these days I have no such inclination, only because Darwinists have failed to present any convincing argument for evolution, and because every day there are articles that make a mockery out of prevailing theory. So, the whole thing doesn’t interest me any more. I just wait for the day that science catches up with Darwinian incoherence.)

    I then took one last look, and saw that they had the idea, quoting papers from the early 90’s, that what they saw happening was actually the result of NS and mutations. Because of the replicative powers of parasites, this might be possible. One would have to do a calculation as to what the “genetic load” of so many changes might be.

    But let’s simply admit that all of these changes came about via mutations and NS. Well, all these changes: point mutation after point mutation, and, guess what, the ‘parasite’ hasn’t changed hardly a bit.

    So, just think about that: a huge amount of mutations have occured, with a huge amount of selection (since the sequence changes are more or less fixed), and yet, no real phenotypic changes; that is, you have to look at the sequences to know that something has happened.

    Now, compare that, say, to whale evolution. How many changes were needed there—given that so many mutations led to nothing in this instance. And, you don’t have huge effective populations with whales as you do with parasites, nor the replication/generation time.

    So, really, what the paper is showing is that RM+NS is no more than a simple system of “adaptation”; and NO MORE!

    Hope this clarifies.

  29. 29
    Origenes says:

    Bornagain77 #25,

    Oops! More bad news for Neutral Theory.

    From the Sciencedaily article:

    One of the great mysteries in biology is how the many different cell types that make up our bodies are derived from a single cell and from one DNA sequence, or genome.

    Good to read that some scientists are willing to admit that this is “one of the great mysteries”. Indeed, the need for higher level guidance is painfully obvious.

    We have learned a lot from studying the human genome, but have only partially unveiled the processes underlying cell determination.

    If here is said that epigenetics can only be part of the story, then I fully agree.

    The identity of each cell type is largely defined by an instructive layer of molecular annotations on top of the genome — the epigenome — which acts as a blueprint unique to each cell type and developmental stage.

    The follow-up question is obvious: what directs the epigenome?

    Our body produces billions of blood cells every day, which develop from a few thousand stem cells at the top of a complex hierarchy of blood cells. Using the latest sequencing and epigenome mapping technology, Bock’s team now unraveled a blueprint of blood development that is encoded in the DNA methylation patterns of blood stem cells and their differentiating progeny.

    Okay. And what directs the DNA methylation patterns of blood stem cells? How do we explain the different methylation patterns of various types of stem cells starting from one single cell? Epi-epigenome?

  30. 30
    Dionisio says:

    PaV @28:

    Thank you for looking into this with so much interest.

    I like to approach this kind of issues carefully, without rush.

    Let’s start.

    In the comment @26:

    The pop-sci article referenced in this OP has the misleading simplistic title “Scientists uncover genetic evidence that ‘we are what we eat’” which is not even wrong.

    The actual research paper is titled:

    Dietary nitrogen alters* codon bias and genome composition in parasitic microorganisms

    Compare the pop-sci title and the related paper.

    Note that the paper is about microorganisms but the pop-sci title is about us humans. It’s not even wrong.

    Let’s ignore the pop-sci article and let’s focus on the actual research paper.

    First, in the above quoted title, notice the asterisk ‘*’?

    (*) how does the ‘alteration’ occur?

  31. 31
    wd400 says:

    how does the ‘alteration’ occur?

    Mutation. Selection. I don’t know why this is so hard for you.

  32. 32
    Dionisio says:

    PaV @28:

    The problem these days is that whereas years ago I would spend hours looking into these things, these days I have no such inclination, only because Darwinists have failed to present any convincing argument for evolution, and because every day there are articles that make a mockery out of prevailing theory. So, the whole thing doesn’t interest me any more. I just wait for the day that science catches up with Darwinian incoherence.

    Thank you for honestly commenting on how you approach the scientific research papers these days.

    I think I understand what causes your frustration with many scientific publications.

    However, keep in mind that a number of scientific researchers are serious about their work and dedicate much time and effort to investigate the biological systems. Unfortunately many times their papers contain pseudoscientific statements that reveal the sad fact that outdated ideas formalized in the middle of the 19th century have permeated the minds of many people, including scientists.

    Don’t let that bizarre situation discourage you.

    We are told that we should test everything and hold onto what’s good.

    Hence, look at the bright side of the story. Most biology research papers contain valuable information that may shed more light on the complex complexity observed in the biological systems. We should pay attention to that information and discard the hogwash. Basically, filter out (ignore) any irrelevant text and focus in on the serious stuff.

    Now let’s follow up the comments @30, which ended with a question.

    First let’s see what the referenced paper say that could help us to answer that question. Then let’s complement it with what other papers say about the same subject.

    Can we do that? Ok, let’s move on.

    🙂

  33. 33
    bornagain77 says:

    “Mutation. Selection. I don’t know why this is so hard for you.”

    I don’t know why things have to be so hard for mutation/selection either. 🙂 (other than the fact that mutation/selection is ‘not even wrong’)

    “Shared Evolutionary History or Shared Design?” – Ann Gauger – January 1, 2015
    Excerpt: The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    http://www.evolutionnews.org/2.....92291.html

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

    Whale Evolution vs. (The Waiting Time Problem of) Population Genetics – Richard Sternberg and Paul Nelson – (excerpted from ‘Living Waters’ video) (2015)
    https://youtu.be/0csd3M4bc0Q

    The waiting time problem in a model hominin population – 2015 Sep 17
    John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner
    Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,,
    Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information.
    While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man.
    It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years.
    http://www.ncbi.nlm.nih.gov/pm.....MC4573302/

  34. 34
    Dionisio says:

    #30 & #32 follow-up

    Here’s the OP referenced paper background:

    Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism’s environment or built from metabolic precursors.

    The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms.

    Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms
    Emily A. Seward and Steven Kelly
    Genome Biology 17:226
    DOI: 10.1186/s13059-016-1087-9

    Ok, let’s continue reading the paper.

  35. 35
    Origenes says:

    I have to agree with wd400: the paper referenced in the OP is not about epigenetics.

  36. 36
    Dionisio says:

    #34 follow-up

    Here are the OP referenced paper conclusions:

    Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.

    Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms
    Emily A. Seward and Steven Kelly
    Genome Biology 17:226
    DOI: 10.1186/s13059-016-1087-9

    Note this:

    […] how genome sequence evolution can be influenced by adaptation […]

    What can be influenced by what?

    “genome sequence evolution” can be influenced by “adaptation

    What can influence what?

    adaptation” can influence “genome sequence evolution”

    What are the players in this story?

    What is “adaptation” in this case?

    What is “genome sequence evolution” in this case?

    How does that “influence” occur and what triggers it?

  37. 37
    Dionisio says:

    Origenes @35
    Maybe everybody agrees on that.
    See the comment @17:

    The OP references a paper that does not seem to deal with “epigenetics” in the technical sense, because it doesn’t seem to be about the DNA molecular switches that affect the way the gene regulatory networks are used by the biological systems to perform transcription. Therefore, WD400’s semantic observation @1 does not seem to be incorrect.

    BTW, the title of the referenced pop-sci article seems to refer to us humans but the actual paper is about microorganisms.
    The paper referenced in this link:
    http://www.uncommondescent.com.....ent-620756
    seems to make that bizarre title conflict even more awkward, doesn’t it?

  38. 38
    Dionisio says:

    PaV, Silver Asiatic, Origenes

    Would you like to comment on the questions posted @36 before we continue that discussion?

  39. 39
    Dionisio says:

    PaV, Silver Asiatic, Origenes

    #38 follow-up

    Note that the title of the given paper:
    Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms
    seems to indicate that something may affect an existing structure in order to adapt it to particular environmental conditions.

    The system seems created in a way that is conducive to such kind of adaptation to the triggering conditions like abundance or scarcity of certain nutrients.

    BTW, the given microorganisms remain what they are. They don’t become something different than microorganisms.

    Antibiotic-resistant bacteria are still bacteria.

    Galapagos finches with larger or shorter beaks remain being birds.

    Butterflies change the wing colors and shapes but remain being butterflies.

    At high elevations RBC count and Hg change in adaptation to rare air.

    That’s micro-evolution or adaptation.

  40. 40
    Origenes says:

    Dionisio @39:
    Note that the title of the given paper:
    Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms seems to indicate that something may affect an existing structure in order to adapt it to particular environmental conditions.

    The paper proposes that this “something” is mutation and selection.

    Regarding “codon bias”, we know that “synonymous codons” code for the same amino acid. Suppose that codon X and codon Y are synonymous and also suppose that codon X requires more nitrogen than codon Y.
    Further suppose that organism A and organism B descended from the same common ancestor.

    Observation: organism A with a high nitrogen diet contains more codons X and organism B with a low nitrogen diet contains more codons Y — “codon bias”.

    Again, in the paper, the proposed mechanism to explain this state of affairs is mutation & selection:

    ”Differences in genome-wide patterns of synonymous codon use are explained by selection acting on codon nitrogen content”

    This is basically an example of synonymous (silent) substitution, which does not result in the modification of the produced amino acid sequence. IOWs no new information is being produced. In that sense it’s not very interesting for the larger debate.

  41. 41
    PaV says:

    Dionisio:

    Where were you eight years ago when the ‘wars’ were being fought here at UD with the Darwinists?

    I have no interest in the particulars of the article. There are few relevant facts. The authors choose to understand what they see in terms of ‘selection.’ That’s the most significant fact, really. And what’s most significant in reply is that they are suggesting that huge amounts of ‘selection’ account for very little phenotypic change—hardly anything at all. To me, that’ the bottom line. It simply underscores the vacuity of Darwinian thought given what we see of sequence space.

    Now, if you want to suggest that there is some built-in mechanism allowing this change in codons, I agree 100% with you that this is the most likely scenario, and not ‘selection.’

    But, as we found out in the ‘wars,’ there’s nothing you can say to a Darwinist that will convince them otherwise. And, when they give their explanation for anything, all you can do is scratch your head, so inadequate are their explanations.

    That is the state of things right now. Only the advancement of science will change this. As I have written for years now, every day is “a bad day for Darwinism.” Everyday uncovers mounting layers of complexity, making ‘random’ explanations overwhelmingly impossible to sustain. So, at some point, the ‘house of cards’ will collapse.

    Unfortunately, I’ll likely not be around to see it. Alas. But I tip my hat to that day.

    I use my time for more interesting things now, so please excuse me if I don’t care to examine this paper in detail—as once I would have done.

  42. 42
    Silver Asiatic says:

    Dionisio

    I will just agree with what PaV and Origenes already said. The paper is about a trivial difference in the organisms (less than 2% difference in the amount of nitrogen atoms used for coding genes). The supposed mechanism is inferred from statistical correlations so it’s not a result of evolutionary experiments.

    As with just about all evolutionary papers, this contributes nothing very little to the grand claims of evolutionary theory when compared with the sophisticated functional diversity that is amazingly evident throughout the biological universe.

  43. 43
    Dionisio says:

    PaV, Silver Asiatic, Origenes:

    Thank you for your comments. I really appreciate what you wrote and understand your valid points, which compel me to clarify my confusing comments.

    Perhaps my use of the term “mechanism” was not appropriate for the case. The issue here is that any mutation and/or selection requires something to change and/or select from.

    All the alleged mutations and/or selections take place on top of a robust built-in complex functional specified information framework that is conducive to that kind of activity. That framework is not hidden. It’s an undeniable fact. We all know it. Y’all have passionately discussed it here in this site even long before I got in here. It’s extensively documented in the scientific literature, specially in the most recent papers, although many outstanding questions remain unanswered and many new questions keep popping up with every new discovery.

    That complex functional specified information framework includes the genetic code, the codons, synonymous codons, their meaningful sequences, the sense/antisense strands, the gene regulatory networks, the signaling pathways, the fantastic transcriptional and translational mechanisms, the post-transcriptional splicing, the post-translational modifications, the chaperon proteins, the protein folding, the epigenetic switches, the circadian clocks, the feedback and feedforward loops, the biological oscillators, the cell cycle with all its fascinating paraphernalia, and the whole nine yards.

    Taken together, all that marvelous stuff is very conducive to adaptation mechanisms that are observed in biology, which in the given case may include some changes of the codon bias and/or genome composition in response to environmental cues like for example the abundance or scarcity of certain nutrients. All within that built-in framework that we got for free.

    The first comment posted in this thread was an allusion to a semantic error in the OP title. I did not see anything wrong with that comment, hence I did not react to it. However, I did react to your reactions to that first comment.

    The paper referenced in this OP is about adaptation mechanisms that can only operate within the above mentioned framework and apparently only affect microorganisms and bacteria. basically, as you all stated so well, this thread has extended beyond what that paper is worth discussing.

    Perhaps News included the term “epigenetics” in the OP title as an intentional “click-bait” to catch the attention of the politely-dissenting interlocutors? If that was the intention, it did work! 🙂

    One thing that called my attention was the conflict between the pop-sci article title and the corresponding paper title. The former referred to us humans but the latter is about microorganisms. That’s quite a difference for some of us, but not for some folks who believe it’s about the same. 🙂

    As far as I’m concerned, this thread is pretty much overdone.

    As you all stated, let’s use our limited time on more valuable things. 🙂

    Have a good weekend.

    PS. PaV @41:

    Where were you eight years ago when the ‘wars’ were being fought here at UD with the Darwinists?

    That’s a very good question. Thank you for asking it.

    I missed all those heated discussions you all were engaged in back then. But anyway I was not prepared for that kind of discussions. Well, now I don’t think I’m prepared for it either.

    Back then I was busy working on software development for a large engineering design system. At that time I thought we were doing really cool things. The software was the standard tool used in a number of engineering projects and the engineers using our software were quite delighted. But now, looking back from the perspective of all this wonderful molecular and cellular choreographies orchestrated within the biological systems, the stuff I worked on all those years seems like Lego toys for toddlers. 🙂

    In the last few years I have learned more as an autodidact student than all I learned through my younger years in schools and university and later the years working on engineering design software development along with brilliant engineers and software developers.
    However, back then I though I knew a lot, but now I know that I don’t know much. The more I know, the more I have to learn. It’s an unending revelation of the ultimate reality. Very challenging, but fascinating.
    Now I’m working on a project that compels me to study and learn about these wonderful biological systems.

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