Epigenetics Genetics

Bee genome changes dramatically through life

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Pollinating BeeRemember 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!

202 Replies to “Bee genome changes dramatically through life

  1. 1
    R J Sawyer says:

    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.

  2. 2
    Origenes says:

    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.

  3. 3
    Amblyrhynchus says:

    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.

  4. 4
    R J Sawyer says:

    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.

  5. 5
    Origenes says:

    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.

  6. 6
    R J Sawyer says:

    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.

  7. 7
    Amblyrhynchus says:

    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).

  8. 8
    bornagain77 says:

    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/2.....93851.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-c.....nesis.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-q.....godel.html

  9. 9
    ET says:

    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.

  10. 10
    Origenes says:

    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.

  11. 11
    Amblyrhynchus says:

    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).

  12. 12
    ET says:

    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.

  13. 13
    Origenes says:

    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.

  14. 14
    goodusername says:

    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”.

  15. 15
    Amblyrhynchus says:

    “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?

  16. 16
    OLV says:

    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.

  17. 17
    R J Sawyer says:

    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.

  18. 18
    Amblyrhynchus says:

    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…

  19. 19
    OLV says:

    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.

  20. 20

    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.

  21. 21
    R J Sawyer says:

    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.

  22. 22
    jawa says:

    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?

  23. 23
  24. 24
    OLV says:

    UB @20:

    Good point. Thanks.

  25. 25
    OLV says:

    Peter,

    thanks for providing the link to the paper.

    Here’s the PDF.

  26. 26
    R J Sawyer says:

    Jawa

    Can you explain that inconsistency?

    What’s inconsistent? On GP’s thread I posted an admittedly off topic suggestions that GP and I went back and forth a couple times and I left so as not to drag the thread off on a tangent. I had no desire to comment on the content of the OP.

    On this thread my comments (except the last two) have been on topic.

  27. 27
    jawa says:

    R J Sawyer @26:

    Maybe inconsistence is not the right term in this case. Please help me to understand:

    Apparently you found problems in the title of the current OP but didn’t find any problem in the title of gpuccio’s OP.

    Apparently you strongly disagree with the title of the current “bee genome” OP, but do you agree with the title of gpuccio’s OP?

    If that is not inconsistence, then what is it?

  28. 28
    PeterA says:

    jawa,

    can you leave that guy alone and focus in on the material to discuss? We have a fascinating topic to dig in but you are spending time in a court-style cross-examination that seems irrelevant.

  29. 29
    OLV says:

    jawa,

    I agree with Peter.
    Who cares about what those guys said or didn’t say?
    Let’s move on.

  30. 30
  31. 31
    gpuccio says:

    Amblyrynchus at #18:

    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…

    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.

  32. 32
    R J Sawyer says:

    Just to sate Jawa’s curiosity at 27, I didn’t have a problem with GP’s title because it may be accurate. The title of this OP is just factually wrong and misleading.

  33. 33
    ET says:

    R J Sawyer:

    The title of the OP is misleading. The DNA sequences do not change.

    As you have been told no one said they do

    Ambly:

    Histones are not part of the genome

    Where do you think they are coded? What do you think they do?

  34. 34
    News says:

    I hadn’t supposed that the sequence changed. If a genome is, in some sense, a language, it could change dramatically via small substitutions, without the sequence changing, couldn’t it?

    Suppose we changed “John shoved a cap right in my face!”

    to

    “John shoved a cop, right in my face!”

    The substitution was small. Now, assuming John survives the encounter (natural selection? 😉 ), the outcome for John will likely be different…

  35. 35
    R J Sawyer says:

    Ambly

    Histones are not part of the genome.

    ET

    Where do you think they are coded? What do you think they do?

    As with all proteins, they are coded in the genome. They are not part of the genome.

  36. 36
    jawa says:

    R J Sawyer @32:

    Ok, are you saying that you don’t have a problem with the scandalously “heretic” statement that gpuccio chose for the title of his excellent OP?
    Are you saying that you agree with that statement which explicitly implies that the transcription regulation process was intelligent designed?
    Is that right?

  37. 37
    R J Sawyer says:

    Jawa

    Are you saying that you agree with that statement which explicitly implies that the transcription regulation process was intelligent designed?
    Is that right?

    No. I don’t agree with it. But we are on UD, a site that advocates for design. I would expect OP titles to reflect this. But there is a difference between an OP title that is biased towards a view that cannot be proven or disproven and one that is demonstrably counter-factual.

  38. 38

    one that is demonstrably counter-factual.

    Life requires a symbol system, just as it was predicted, prior to experimental confirmation. The only other example of this physical system is human language. So, wrapping up, we have a confirmed prediction and the universal experience of all research and observation. Which theory is “demonstrably counter-factual”, the theory that says the gene system is an inference to an intelligent act, or the one that says it’s an inference to an unguided physical process?

  39. 39
    jawa says:

    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.

  40. 40
    Amblyrhynchus says:

    This thread just stranger and stranger…

    All Origines or News had to do was say, “quite right, the genome hasn’t change here” and move on. Perhaps they could hve then thought about whether gene-environment interactions of the sort described here are a problem for evolutionary biology, but that may be too much to hope for.

    Instead, Origenes decided to google up some links and parade their ignorance of this topic. News and ET offer some lame excuse to claim (against the plain meaning of the word) that histones are part of the genome. And Jawa has launched into some spammy amateur detective routine to, I can only assume, distract from his fellow-travellers embarrassment.

    Why is so hard for any of you to simply admit this mistake and move on?

  41. 41
    jawa says:

    Amblyrhynchus @40:

    Please, read my comment @22, where I stated this:

    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”,

    I don’t have any problem with pointing at possible errors regardless of their source.

    You avoided the serious discussions with gpuccio but didn’t hesitate to discuss here about an error in the title ?

  42. 42
    Amblyrhynchus says:

    Yeah, that’s good (though I don’t thin “genome-effect” is a term that adds much to the world). I just don’t why you have since gone into this crazy interrogation of which treads people comment on. What has compelled you to do this?

  43. 43
    jawa says:

    Amblyrhynchus,

    What exactly you don’t like about it?
    What exactly bothers you?

  44. 44
    gpuccio says:

    Amblyrhynchus at #40:

    I can agree with you that this thread is strange.

    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?

    That could be more interesting than debating how appropriate a title is. Whatever the title, the issue presented in New’s OP is certainly important and interesting.

    Moreover, as at #40 you also mention the “gene-environment interactions” problem, that is certainly pertinent to this discussion, and has also been raised by R J Sawyer at comment #1, I invite you to join the discussion about that too, and to read my next comment to R J Sawyer about that point.

  45. 45
    gpuccio says:

    R J Sawyer:

    Your comment #1, and some statements by Amblyrhynchus, are IMO a good point to start a serious discussion about the issue mentioned in the OP, rather than continuing a sterile debate about the title or individual “errors” or “intentions”.

    So, let’s start a discussion about what Amblyrhynchus calls “gene-environment interactions”. I would call it differently:

    “Functional information – environment interaction”

    because, as you may know having been a very kind and appreciated guest at my thread about transcription regulation:

    https://uncommondescent.com/intelligent-design/transcription-regulation-a-miracle-of-engineering/

    I think that functional information is always in the form of a dynamic state involving both the genome abd everything else in the cell (let’s say the epigenome), and that’s the entity which interacts with environment or with anything else.

    That said, I think I have partially covered an important aspect of the interaction between the functional program and environment in the final part of my comment #200 in that thread, that I quote here for your convenience:

    Each program written in the dynamic cell is a specific selection of information that can guide that specific cell in that specific state to some new specific state. And so on.

    Of course, much of that must be written in the DNA sequence: protein genes and promoters and enhancers and non coding genes are all written there. But they can only work in the appropriate dynamic context, and nowhere else.

    The complexity of that all is overwhelming. Add to that that many factors come from outside the cell, from the “environment”.

    But that environment is, of course, part of the program, part of the engineering.

    It includes signals from other cells, or even signals from environmental niches. But those signals are functional, not random. They have been engineered, too.

    The program, with its complexity, could never work if the signal from the environment were random. That’s why the embryo requires a very protected and controlled environment.

    Of course, random noise can always happen: it does happen, and often it can destroy or deform the program. As we well know.

    But, in general, the program works very well. Because the procedures are robust. And the general control is robust.

    There is a lot of very, very good engineering there. A lot of extremely good Intelligent Design.

    I will try to develop better that point in my next post, with some more specific reference to bees, and of course both you and Amblyrhynchus are cordially invited to the discussion. 🙂

  46. 46
    PeterA says:

    Amblyrhynchus and R J Sawyer:

    gpuccio has written excellent comments addressed to both of you.

    Now is your turn tu show how serious is your participation in this website.

  47. 47
    gpuccio says:

    To all:

    Now, first of all let’s read the abstract of the paper mentioned in the OP:

    Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval development

    https://genome.cshlp.org/content/early/2018/08/20/gr.236497.118.abstract?sid=83ce03cc-d346-433d-b882-675433a8bbec

    Abstract:

    The capacity of the honey bee to produce three phenotypically distinct organisms (two female castes; queens and sterile workers, and haploid male drones) from one genotype represents one of the most remarkable examples of developmental plasticity in any phylum. The queen–worker morphological and reproductive divide is environmentally controlled during post-embryonic development by differential feeding. Previous studies implicated metabolic flux acting via epigenetic regulation, in particular DNA methylation and microRNAs, in establishing distinct patterns of gene expression underlying caste-specific developmental trajectories. We produce the first genome-wide maps of chromatin structure in the honey bee at a key larval stage in which developmental canalization into queen or worker is virtually irreversible. We find extensive genome-wide differences in H3K4me3, H3K27ac, and H3K36me3, many of which correlate with caste-specific transcription. Furthermore, we identify H3K27ac as a key chromatin modification, with caste-specific regions of intronic H3K27ac directing the worker caste. These regions may harbor the first examples of caste-specific enhancer elements in the honey bee. Our results demonstrate a key role for chromatin modifications in the establishment and maintenance of caste-specific transcriptional programs in the honey bee. We show that at 96 h of larval growth, the queen-specific chromatin pattern is already established, whereas the worker determination is not, thus providing experimental support for the perceived timing of this critical point in developmental heterochrony in two types of honey bee females. In a broader context, our study provides novel data on environmentally regulated organismal plasticity and the molecular foundation of the evolutionary origins of eusociality.

    OK, so he paper is about epigenetic patterns that contribute to establish the two types of honey bee females that, together with the male drone, are the foundation fro the complex “eusociality” of bees, IOW a complex hereditary social structure that is established in bees.

    That said, I will reason about the meaning of all that. In next post.

  48. 48
    PeterA says:

    gpuccio:

    Excellent comments 44 and 45.
    Hopefully they help to take this discussion in the right direction (finally!).
    The main topic of this OP seems very related to your latest thread on transcription regulation and to the previous discussion thread on chromatin topology and functionality. Both discussions became rich sources of serious reference material for future discussions.

    Thanks!

  49. 49
    PeterA says:

    gpuccio @47:

    I appreciate you have started to dig deep into the tremendously rich topic of this OP.

    Thanks!

  50. 50
    PeterA says:

    jawa,

    I see you kind of led Amblyrhynchus and R J Sawyer to this point.

    Now it’s time for you to take a break and then come back ready to join the serious discussion gpuccio has just sparked starting at 44.

  51. 51
    OLV says:

    gpuccio:

    I’m glad to see you have started to lead this thread in the right direction.

    Thanks.

  52. 52
    gpuccio says:

    To all:

    Now, please consider again the reasoning I quote (from my transcription regulation thread) at #45 here.

    I will try to put it even more cleraly, and to extend it to bees’ eusociality, and to other similar examples in animal life.

    So, let’s start again, conventionally, from the zygote in a muòticellular organism, such as humans.

    a) The zygote is a special information program, with the ability to develop into a whole organism.

    b) That information is not only in the genome (sequence of nucleotides), but also in the specific reading of genomic information available in the zygote, IOWs the sum total of its genetic and epigenetic information.

    c) The dynamic program expressed in the zygote starts a developmental process that will, in the end, generate the multicellular organism.

    d) That is done, primarily, by a highly ordered and functional process of cell differentiation, so that many different specific programs are generated in different cell types, by specific new genetic and epigenetic compbinations of functional information, so that the zygote may generate all the different cell types that are needed.

    e) But, of course, that is not enough. Cells must differentiate in spatial and temporal order, to generate tissues and organs and, in the end, the whole organism.

    f) To do that, the developing zygote generates, according to a well defined and hereditary program, already present in the total information content of the zygote itself, different and dynamic “environments”, highly controlled by the program itself, defined by different components, such as the cellular content, the cell to cell interactions, and the structural components of the developing organism. Examples of such environments are the blastula, gastrula, the three germ layers, and so on. And the maternal components too. But also, for example, the bone marrow niches where blood cell production from hematopoietic stem cells takes place throughout life.

    g) All those components are of course “environment” to each individual cell, but they are an integral part of the developing program, and they are under the strict control of the program itself.

    h) But, of course, there is another kind of “environment”, that is not under the control of the program. Let’s call it “the random environment”. IOWs, all those conditions that are contingent. Maybe contingent differences in the uterine environment, or just the way the embryo is implanted, or differences in outer stimuli (temperature, stress conditions, radiations, infections, and so on). We know that such influences, in certain cases, can even compromise the successful development of the organism.

    i) One thing is certain: these differences, because of their random (contingent) nature in relation to the developing organism, are not part of the program. They may generate individual differences in the organisms, good or bad, in the same way that environmental conditions will influence post-natal life. But they are not part of the program that defines the organism as a species. Indeed, the program itself must be able to cope with them, so that it can be successful in generating the organism in spite of contingent influences.

    j) In that sense, the ability of the program to generate a living and functional organism even in the presence of uncontrolled environmental contingencies is a triumph of its functional information.

    OK, now let’s see how that applies to bees and to their eusociality.

    My point is that eusociality, in the measure that it is based on the hereditary program of bees (and it is, because it develops in a controlled way, and not out of contingent conditions) is a process similar to cell differentiation.

    So, as individual cells differentiate to perform different roles in the organism, in the same way individual organisms differentiate to perform different roles in the eusocial structure.

    And that happens under the control of the general program, and in spite of contingent factors.

    Because the organism differentiation, like the cell differentiation, is controlled by the hereditary program and its functional information: the same program that is present in the zygote, and its exclusive combination of genetic and epigenetic functional information.

    So, the functional information in eusocial animals has one added layer of functionality: the control of the specific phenotypic development of different organism types, and of their roles and behaviours in a well organized social structure that is hereditary and functional.

  53. 53
    gpuccio says:

    PeterA at #48:

    “The main topic of this OP seems very related to your latest thread on transcription regulation and to the previous discussion thread on chromatin topology and functionality.”

    Yes, it is. Definitely!

  54. 54
    R J Sawyer says:

    Jawa

    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 why invent a new term when an existing term (phenotype) means exactly the same thing?

  55. 55
    R J Sawyer says:

    GP

    Whatever the title, the issue presented in New’s OP is certainly important and interesting.

    I agree that the referenced paper is very interesting. I have slowly been working my way through it but, frankly, it is well beyond by area of expertise to comment on it other than in a general sense; as I am sure is also the case for most here.

    We have known for a very long time that the phenotype is the result of an interaction of environment and our genes. Please keep in mind that “environment” does not only refer to the environment outside our bodies, although that also plays a part. We have known for a very long time that the same female bee larva can develop into a queen or a worker depending on how it is fed (and I am sure there are other factors as well). But, at the end of the day, whether it is a worker or a queen it’s genome does not change during development. If you mapped the genome of the larva and the adult it develops into, they would bee (tee her) the same. I initially commented on the title as a simple corrective. Others, for whatever reason, decided to take it further.

    As far as I can tell, this paper, although very comprehensive, still boils down to providing a detailed mechanism underpinning what we already know. The phenotype is greatly affected by the environment.

  56. 56
    gpuccio says:

    R J Sawyer:

    Thank you for your very civil contribution.

    Have you read my #52?

    The interesting point here is that we are not talking of a generic phenotype, but of specific different phenotypes in the context of the hereditary eusocial structure. In that sense, epigenetic patterns are the controllers of the specific phenotypes.

    It’s different from differences in phenotype that arise from environmental differences, for example in identical twins.

    Here, the differences are part of the program.

  57. 57
    Amblyrhynchus says:

    At this risk of disappointing Peter A., I can’t say I have anything to say about any of these comments.

  58. 58
    jawa says:

    54 R J Sawyer

    Wrong! genome effect covers a much wider area than phenotype.

    The genome may affect different intra-cellular or inter-cellular processes that may not necessarily get directly reflected in the phenotype. For example, cell fate determination.

  59. 59
    jawa says:

    R J Sawyer,

    Did you miss my question @39?

  60. 60
    jawa says:

    R J Sawyer:

    You’re wrong in 54 and 55.

    And you missed -perhaps intentionally- the comment with question addressed to you @39.

    Now let’s see how you respond to gpuccio’s comment @56.

    Most probably you’ll fail it too, though I would prefer that you do it right this time.

    Something seems wrong with you buddy. Could it be your attitude?

    One doesn’t have to be a rocket scientist in order to understand what gpuccio is explaining here.

  61. 61
    jawa says:

    Amblyrhynchus @57:

    Are you referring to Peter’s comment @46 addressed to you?

    Well, your poor response confirms what was obvious from the beginning: that you are not a serious discussant here.

  62. 62
    ET says:

    R J-

    If histones are coded by the DNA then obviously they were part of the genome. Seeing that they help package the DNA into chromosomes it is clear they are part of the genome as it wouldn’t exist as it is without them.

  63. 63
    ET says:

    Ambly:

    Why is so hard for any of you to simply admit this mistake and move on?

    Said the person whose entire position is a mistake, can’t admit it and move on.

  64. 64
    R J Sawyer says:

    jawa

    Wrong! genome effect covers a much wider area than phenotype.

    The genome may affect different intra-cellular or inter-cellular processes that may not necessarily get directly reflected in the phenotype. For example, cell fate determination.

    Phenotype: “the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.”

    I think that you will find that the vast majority of biologists would disagree with you. The phenotype is not restricted to shape and form. It also includes all of the cellular processes, cell types, etc.

    Something seems wrong with you buddy. Could it be your attitude?

    If by attitude you mean that I don’t insult are demean others, then I guess I have attitude.

  65. 65
    R J Sawyer says:

    ET

    If histones are coded by the DNA then obviously they were part of the genome.
    I don’t follow your logic. Insulin is also coded by your DNA. As is every protein in your body. Does than mean that all of the proteins in your body are part of the genome? I don’t think that is what you are wanting to say.

  66. 66
    R J Sawyer says:

    GP

    The interesting point here is that we are not talking of a generic phenotype, but of specific different phenotypes in the context of the hereditary eusocial structure. In that sense, epigenetic patterns are the controllers of the specific phenotypes.

    It’s different from differences in phenotype that arise from environmental differences, for example in identical twins.

    I think that we are agreeing more than we are disagreeing. I think where we differ is that you are distinguishing epigenetic effects such as we see with the bees from environmental effects on the phenotype, whereas I think that they are one and the same. The major difference being the magnitude of the impact.

    Epigenetics is the study of heritable changes in gene expression (active versus inactive genes) that do not involve changes to the underlying DNA sequence — a change in phenotype without a change in genotype — which in turn affects how cells read the genes. Epigenetic change is a regular and natural occurrence but can also be influenced by several factors including age, the environment/lifestyle, and disease state.
    https://www.whatisepigenetics.com/fundamentals/

    Here [the bees], the differences are part of the program.

    All epigenetic effects are part of the “program”. Whether or not turtles are male or female depends on the epigenetic affects of temperature during incubation. Some breast cancers are triggered by epigenetic effects. A queen develops when she is fed “royal honey” (greatly simplified). In all of these cases, these are “programmed” into the DNA. You can’t have epigenetic effects with out the underlying genetics.

  67. 67
    gpuccio says:

    To all:

    It seems that everybody is only interested in discussing meaningless details. Just to be fair, I will say explicitly that the use of the word “genome” in the title is not accurate.

    For the last time, R J Sawyer, have you read my comments at #52 and #56? Do you agree that the differentiation of social organisms in the case of bees is controlled by the genome/epigenome, even if it uses controlled environmental stimuli? After all, the human genome/epigenome does not control, in some ordered and hereditary way, our differentiation into doctors, engineers, soldiers, and so on. Animal eusociality is a complex hereditary pattern, controlled by the information in the species.

    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.

  68. 68
    R J Sawyer says:

    GP,

    Do you agree that the differentiation of social organisms in the case of bees is controlled by the genome/epigenome, even if it uses controlled environmental stimuli?

    Yes. I thought that I was clear on that. I apologize if I was not.

    After all, the human genome/epigenome does not control, in some ordered and hereditary way, our differentiation into doctors, engineers, soldiers, and so on.

    This is true.

    Animal eusociality is a complex hereditary pattern, controlled by the information in the species.

    In some species this is more so than in others. For example, all clown fish are born male. In a social group, only the largest and most aggressive will become female. I don’t know if the specific mechanism behind this has been worked out in as great a detail as this paper has done for bees, but they are similar in nature.

    Although the fact that the phenotype is affected by both genetics and environment has been known for a very long time, an understanding of the specific mechanisms involved is in its infancy. These are interesting times.

  69. 69
    ET says:

    R J Sawyer- If you are going to selectively quote what I post why even bother responding? Your “objection” was answered in the part that you failed to quote.

    If histones are coded by the DNA then obviously they were part of the genome. Seeing that they help package the DNA into chromosomes it is clear they are part of the genome as it wouldn’t exist as it is without them.

  70. 70
    ET says:

    R J:

    Phenotype: “the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.”

    That is the untestable claim, anyway.

    The fact is no one knows what makes a bee a bee or a human a human. No one knows what determines what form will develop.

  71. 71
    gpuccio says:

    R J Sawyer:

    When I wrote #67 I had not read your #66. I apologize. Thank you for your commnts. 🙂

  72. 72
    R J Sawyer says:

    GP When I wrote #67 I had not read your #66. I apologize. Thank you for your commnts.
    I figured that is what happened. That is why I added my second response. Hopefully to clarify my opinion a bit.

  73. 73
    jawa says:

    R J Sawyer @64:

    The genome effect is not only associated with the environment but also programmed. Also it’s not only associated with observable characteristics as the definition you quoted states. The genome along with the epigenome and other factors are part of the functional complexity that gpuccio keeps pointing at, which affects many biological intracellular and intercellular processes.

  74. 74
    PeterA says:

    gpuccio @67:

    “It seems that everybody is only interested in discussing meaningless details.”

    Did you include me in that group too?

  75. 75
    PeterA says:

    gpuccio,

    How are the epigenetic markers spatiotemporally setup ?

  76. 76
    OLV says:

    gpuccio (67):

    Am I included in the “everybody” too?

    Please see 23, 25, 28, 29, 30.

    Thanks.

  77. 77
    jawa says:

    Peter @75:

    You may want to ask RJ Sawyer.
    He can give you a better explanation.
    🙂

  78. 78
    jawa says:

    Peter,

    Amblyrhynchus could reveal it to you faster than RJ Sawyer will. 🙂

  79. 79
    OLV says:

    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.

  80. 80
    jawa says:

    OLV,

    You may want to ask R J Sawyer too. He could provide a more precise explanation.
    🙂

  81. 81
    R J Sawyer says:

    jawa

    The genome effect is not only associated with the environment but also programmed. Also it’s not only associated with observable characteristics as the definition you quoted states. The genome along with the epigenome and other factors are part of the functional complexity that gpuccio keeps pointing at, which affects many biological intracellular and intercellular processes.

    I don’t mean to be pedantic but how do you know that its not only associated with observable characteristics if you can’t observe these unobservable characteristics? What I am getting at is that phenotype is not restricted to how the animal looks. The phenotype also includes all biological intracellular and intercellular processes.

    In bees, the workers feed a few larvae different than all others and this triggers the epigenetic changes that result in the development of a queen. The basic genome has the potential to be either a worker or a queen, the deciding factor is the impact of diet on how the genes are expressed. In GP’s example, the phenotype is environmentally triggered but with the added complexity of having a social context. I am not disagreeing with this. This is even further complicated by the triggers that result in the workers “knowing” that a new queen is needed and altering the feeding for a few larvae. As mentioned, this is similar to clownfish, in which the change from male to female is triggered, somehow, by social behavior triggering changes to how genes are expressed. Turtles demonstrate a different “strategy”. Genetically, there is no difference between male and female, as is also the case with clown fish, but different than mammals. Sex is determined during incubation by genes being expressed differently depending on the temperature of incubation. However, with turtles, there does not appear to be the “social” link that we see with clown fish and bees.

  82. 82
    Amblyrhynchus says:

    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.

  83. 83
    jawa says:

    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?

  84. 84
  85. 85
    jawa says:

    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-n909791

  86. 86
    jawa says:

    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?

  87. 87
    Amblyrhynchus says:

    Yes. I guess it’s serious enough, but there’s just not very much to any of this.

  88. 88
    PeterA says:

    jawa,
    Don’t you want to take a break, buddy?
    Aren’t you tired?

  89. 89
    PeterA says:

    Amblyrhynchus @87:

    Can you elaborate on the meaning of what you just wrote?
    Thanks.

  90. 90
    PeterA says:

    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.

  91. 91
    Amblyrhynchus says:

    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.

  92. 92
    OLV says:

    Amblyrhynchus,

    You’re missing so much!

    What can I tell you?

    Wake up and smell the coffee!

    ????

  93. 93
    Amblyrhynchus says:

    Probably looking for something a bit more specific…

  94. 94
    OLV says:

    Amblyrhynchus,

    Here’s more specific:

    All that functional complexity in biology was intelligently designed.

    Can’t make it more specific than that.

    🙂

  95. 95
    R J Sawyer says:

    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?

  96. 96
    gpuccio says:

    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.

  97. 97
    gpuccio says:

    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.

  98. 98
    R J Sawyer says:

    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”.

  99. 99
    gpuccio says:

    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.

  100. 100
    gpuccio says:

    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.

  101. 101
    R J Sawyer says:

    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.

  102. 102
    Amblyrhynchus says:

    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.

  103. 103
    OLV says:

    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.

  104. 104
    R J Sawyer says:

    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.

  105. 105
    PaoloV says:

    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.

  106. 106
    Amblyrhynchus says:

    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.

  107. 107
    R J Sawyer says:

    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.

  108. 108
    gpuccio says:

    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.

  109. 109
    jawa says:

    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.

  110. 110
    gpuccio says:

    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.

  111. 111
    gpuccio says:

    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.

  112. 112
    gpuccio says:

    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.

  113. 113
    gpuccio says:

    To all:

    OK, good night for today! 🙂

  114. 114
    jawa says:

    gpuccio:

    Thank you for commenting on those fascinating issues.

    Good night.

  115. 115
    Amblyrhynchus says:

    But the point is hat such “contingency” cannot ever generate complex functional information, unless it is guided and arranged into functional configurations.

    Why not?

  116. 116
    PeterA says:

    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.

  117. 117
    OLV says:

    Peter,

    I would be thrilled too. Wouldn’t you?

    🙂

  118. 118
    PeterA says:

    OLV,

    Yes, I would too.

    But I won’t hold my breath while waiting for such a marvelous revelation.

    🙂

  119. 119
    Amblyrhynchus says:

    You’ll have to define “complex functionally specified information”, but if it’s like Dembski’s csi then natural selection will do the trick.

  120. 120
    OLV says:

    Amblyrhynchus,

    Did you see jawa’s comment @109?

    Would you mind answering the questions in that post ?

    Thanks.

  121. 121
    Amblyrhynchus says:

    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.

  122. 122
    PeterA says:

    Amblyrhynchus,

    Was that your response to jawa 9109?

    Really?

  123. 123
    PeterA says:

    Sorry, I meant jawa @109.

  124. 124
    PeterA says:

    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.

  125. 125
    PeterA says:

    Amblyrhynchus @121:

    No textbook contains the answers to those questions.

    Not even close.

    Please, try again.

    Thanks

  126. 126
    PeterA says:

    Perhaps I could rephrase the question @75:

    What spatiotemporal mechanisms determine the type, location and timing of the epigenetic marks?

  127. 127
    Amblyrhynchus says:

    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?

  128. 128
  129. 129
    gpuccio says:

    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.

  130. 130
    gpuccio says:

    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! 🙂

  131. 131
    OLV says:

    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 mine

  132. 132
    ET says:

    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.

  133. 133
    ET says:

    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.

  134. 134
    gpuccio says:

    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.

  135. 135
    OLV says:

    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).

  136. 136
    OLV says:

    gpuccio @129:

    Excellent!

  137. 137
    Amblyrhynchus says:

    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?

  138. 138
    OLV says:

    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. 🙂

  139. 139
    gpuccio says:

    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.

  140. 140
    Amblyrhynchus says:

    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.

  141. 141
    OLV says:

    Amblyrhynchus,

    Now that you’ve arrived to such a brilliant conclusion, let’s get back to work.

    🙂

  142. 142
    gpuccio says:

    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).

  143. 143
    OLV says:

    The following thread contains interesting comments by gpuccio, though he did not write the OP:

    Breaking: A “junk DNA” jumping gene is critical for embryo cell development

  144. 144
    gpuccio says:

    OLV:

    Yes, we had some interesting discussion about lncRNAs there! 🙂

  145. 145
    jawa says:

    This is interesting:

    after an elaborate conspiracy theory with a thick plot that could be a bestseller in fiction books, we look back and see this:

    #18 Amblyrhynchus September 14, 2018 at 6:52 pm

    “I hadn’t seen the thread. I actually have a paper focusing on chromatin state in review just now.”

    [was he referring to the highly interesting “Chromatin topology” discussion thread started by News?]
    #106 Amblyrhynchus September 17, 2018 at 4:20 pm

    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.

    [was he referring to the paper he mentioned @18 ?]

    #137  Amblyrhynchus September 18, 2018 at 2:37 pm

    “I’ll let you know if I have time to look in more detail.”

    [was he referring to gpuccio’s comment @129 ?]

    Here’s a sample of Amblyrhynchus’ contributions in this website:
    May
    AmblyrhynchusMay 28, 2018 at 2:30 pm

    AmblyrhynchusMay 29, 2018 at 12:30 am

    AmblyrhynchusMay 29, 2018 at 12:38 am

    AmblyrhynchusMay 29, 2018 at 3:27 pm

    AmblyrhynchusMay 29, 2018 at 3:36 pm

    AmblyrhynchusMay 29, 2018 at 3:42 pm

    AmblyrhynchusMay 29, 2018 at 8:01 pm

    AmblyrhynchusMay 29, 2018 at 8:45 pm

    AmblyrhynchusMay 29, 2018 at 10:08 pm

    AmblyrhynchusMay 29, 2018 at 10:32 pm

    AmblyrhynchusMay 29, 2018 at 10:45 pm

    AmblyrhynchusMay 29, 2018 at 11:47 pm

    AmblyrhynchusMay 30, 2018 at 12:29 am

    AmblyrhynchusMay 30, 2018 at 1:04 am

    AmblyrhynchusMay 30, 2018 at 1:59 am

    AmblyrhynchusMay 30, 2018 at 2:32 am

    AmblyrhynchusMay 30, 2018 at 3:44 am

    AmblyrhynchusMay 30, 2018 at 5:21 am

    AmblyrhynchusMay 30, 2018 at 1:51 pm

    AmblyrhynchusMay 30, 2018 at 2:05 pm

    AmblyrhynchusMay 30, 2018 at 4:39 pm

    AmblyrhynchusMay 30, 2018 at 4:40 pm
    June
    AmblyrhynchusJune 4, 2018 at 3:15 pm

    AmblyrhynchusJune 5, 2018 at 8:39 pm

    AmblyrhynchusJune 6, 2018 at 9:24 pm

    AmblyrhynchusJune 22, 2018 at 11:02 pm

    AmblyrhynchusJune 23, 2018 at 3:07 am

    AmblyrhynchusJune 23, 2018 at 5:28 pm

    AmblyrhynchusJune 24, 2018 at 6:28 am

    AmblyrhynchusJune 24, 2018 at 2:57 pm

    AmblyrhynchusJune 20, 2018 at 2:12 pm

    AmblyrhynchusJune 20, 2018 at 2:47 pm

    AmblyrhynchusJune 20, 2018 at 3:30 pm

    AmblyrhynchusJune 20, 2018 at 3:30 pm

    AmblyrhynchusJune 20, 2018 at 3:55 pm

    AmblyrhynchusJune 20, 2018 at 4:27 pm

    AmblyrhynchusJune 20, 2018 at 5:29 pm

    AmblyrhynchusJune 21, 2018 at 3:50 pm
    July
    AmblyrhynchusJuly 18, 2018 at 8:14 pm

    AmblyrhynchusJuly 18, 2018 at 9:50 pm

    AmblyrhynchusJuly 19, 2018 at 5:10 pm

    **************************************************************
    Chromatin Topology: the New (and Latest) Functional Complexity

    Posted July 23, 2018, has been visited 3,271 times, has 241 comments posted

    Was for quite some time at the top 5 popular posts.
    Last comment posted Sep 11.

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    August
    AmblyrhynchusAugust 4, 2018 at 6:45 pm

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    September:
    AmblyrhynchusSeptember 10, 2018 at 8:34 pm

    AmblyrhynchusSeptember 13, 2018 at 6:30 pm

    AmblyrhynchusSeptember 13, 2018 at 9:42 pm

    AmblyrhynchusSeptember 14, 2018 at 1:31 pm

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    AmblyrhynchusSeptember 15, 2018 at 7:47 pm

    AmblyrhynchusSeptember 15, 2018 at 9:12 pm

    AmblyrhynchusSeptember 16, 2018 at 7:29 pm

    AmblyrhynchusSeptember 17, 2018 at 1:21 pm

    AmblyrhynchusSeptember 17, 2018 at 1:42 pm

    AmblyrhynchusSeptember 17, 2018 at 2:04 pm

    AmblyrhynchusSeptember 17, 2018 at 2:28 pm

    AmblyrhynchusSeptember 17, 2018 at 4:03 pm

    AmblyrhynchusSeptember 17, 2018 at 4:20 pm

    AmblyrhynchusSeptember 17, 2018 at 5:19 pm

    AmblyrhynchusSeptember 17, 2018 at 5:42 pm

    AmblyrhynchusSeptember 17, 2018 at 6:22 pm

    AmblyrhynchusSeptember 18, 2018 at 2:41 am

    AmblyrhynchusSeptember 18, 2018 at 2:37 pm

    AmblyrhynchusSeptember 18, 2018 at 4:09 pm

     

  146. 146
    Amblyrhynchus says:

    Now that you’ve arrived to such a brilliant conclusion, let’s get back to work.

    Sorry, I’m not going to engage with you or any of your accounts. Partly because they way you have behaved is very rude, but also because it suggests a less-than-healthy obsession with this site. Not something I want to encourage.

  147. 147
    random.dent says:

    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.

    Most of the ID blogs I used to read, like Telic Thoughts, have shut down. Uncommon Descent is about the only one left. Sadly we have very limited options.

  148. 148
    goodusername says:

    Amblyrhynchus,

    Well, I had though the PeterA, PaoloV, OLV and Jawa

    I was surprised that no one else had said anything until now. As soon as those four accounts appeared I thought it was rather obvious that they were sock puppets of Dionisio.

  149. 149
    PeterA says:

    jawa @145:

    there you go again with your off-topic comments.

    Chill out, buddy!

    Note gpuccio has posted excellent comments here in this discussion thread, while still maintaining his own very informative discussion on the amazing transcription regulation, which he called a miracle of engineering.

    BTW, both threads are now in the top 5 popular list!

    Time to enjoy and learn from these fascinating discussions.

  150. 150
    OLV says:

    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.

  151. 151
    OLV says:

    The effect of maternal care on gene expression and DNA methylation in a subsocial bee

    Our study offers unique insights into the effects of maternal care on offspring development and explores understudied questions about the role of DNA methylation in transcriptional regulation in invertebrate taxa.

    Further exploration of the candidate genes we identified may help to explain the genetic underpinnings of social behaviors in C. calcarata and provide insight into how these genes are regulated in response to environmental stimuli.

     

  152. 152
    jawa says:

    Peter @149:

    Did you read it well?
    Did you understand it well?

  153. 153
    jawa says:

    Well, most probably you didn’t.
    What else is new?

  154. 154
    jawa says:

    Note a few interesting things:

    The guy seems very active in this site at least since May.
    On September 14 he claimed not having seen the highly interesting chromatin topology discussion which News had started July 23 and stayed in the top 5 popular posts list for a while, attracted over 3K visits and more than 200 comments. Hmm… doesn’t it make you wonder?

  155. 155
    jawa says:

    Actually, to make things more pathetic, the allegedly published book -mentioned at least twice- is on a related topic. Hmm…

  156. 156
    R J Sawyer says:

    jawa, your seem to be obsessed with everything Amblyrhynchus says. Your comment at 145 borders on stalking. If you don’t like the way that Ambly interacts with others may I suggest that you simply ignore him.

  157. 157
    PeterA says:

    R J Sawyer,

    I agree with you on that. I’ve told him that a few times. But the guy seems to ignore my advices. It seems ridiculous to waste so much time on such irrelevant issues as who said what. Who cares?
    Specially in this thread where such a fascinating topic is discussed.
    BTW, I’m glad you engaged in the discussion with gpuccio. I’m learning from what is transpiring from it. Thanks.

  158. 158
    R J Sawyer says:

    Thanks Peter. GP and I often agree on most things but differ on what conclusions can be drawn from them. And he has always been civil about it. I have never understood why some people get so emotional about it, on both sides of the debate. Life is too short to get mad about things like this.

  159. 159
    PeterA says:

    R J Sawyer,
    No doubt that gpuccio is on the winning side of this scientific discussion.
    Every new biology-related discovery just confirms it.
    It’s practically obvious. Complex functional specified information is solely the product of conscious design. gpuccio explains each evidence very clearly. However, many folks don’t see it that way. Which raises an interesting question: why? I don’t know. It’s mysterious. That’s why I like to see how people see it so different.

  160. 160
    R J Sawyer says:

    Petera@159, my problem with the “complex functional specified information is solely the product of conscious design “ argument is that we are drawing this conclusion from a single example, human. It is always dangerous to extrapolate from a single example. I also have difficulties with trying to figure out what is meant by “complex functional specified information”.

    For example, can a water molecule be said to have complex functional specified information? it can be water, steam or ice, depending on temperature and pressure. This ability is clearly specified by its molecular and atomic structure and the forces governing it. And, given the nature of these atomic and subatomic physics, I would argue that it is also complex. It definitely isn’t simple by any stretch of the imagination. I guess the big question is whether or not it is functional. Obviously, if we are just looking at the water molecule in isolation, there is nothing functional about its different states. Just as, in isolation, there is nothing functional about insulin, haemoglobin or a hand. The quality of “function ” is based on how something impacts and interacts with something else.

    Both frozen water (snow) and vaporous water (clouds) reflect solar radiation preventing the overheating of the earth. Clearly functional with respect to the ecosphere. And liquid water is the medium required for all of life to function. Again, clearly functional. Obviously, many would argue that physical laws and atoms are the result of conscious design, but I am pretty sure that is not what GP means when he talks about specified functional complexity.

  161. 161
    OldAndrew says:

    Amblyrhynchus,

    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)

    I’ve seen this perplexing argument used from time to time. Boiled down, it finds fault with drawing conclusions based on observation rather than on imagination. ‘Look at what exists’ as long as it paints the picture we want to see. But when we don’t like where the evidence points, don’t look at what exists. I thought that looking at what exists was the whole point.

    Think about the door you’re opening.

  162. 162
    Origenes says:

    R J Sawyer

    R J Sawyer: I guess the big question is whether or not it is functional. Obviously, if we are just looking at the water molecule in isolation, there is nothing functional about its different states. Just as, in isolation, there is nothing functional about insulin, haemoglobin or a hand. The quality of “function ” is based on how something impacts and interacts with something else.

    The eye has function because it serves the cat. The eye is a subservient part of a whole (the cat). The eye has function because it is functional to the cat.

    However, if everything is just blind particles in motion — if materialism is true — then there are no ‘wholes’ (like e.g. a cat) in any meaningful way. Wouldn’t you agree?
    If so, would you also agree that, under materialism, ‘function’ does not exist?

  163. 163
    PeterA says:

    R J Sawyer,

    Did you look in the information contained in the comments @129 and @142 to see if gpuccio talks about complex functional specified information and other topics you disagree with him on?
    If you haven’t done that yet, I suggest you give it a try. It shouldn’t hurt you.

  164. 164
    PeterA says:

    R J Sawyer @ 160:

    “It is always dangerous to extrapolate from a single example.”

    I agree.

    BTW, do you recall any famous extrapolation that turned out to be very wrong?

    I mean really really famous.

  165. 165
    jawa says:

    PeterA @157:

    “But the guy seems to ignore my advices.”

    Well, you ignored my questions @152. Why? Didn’t see or skipped them intentionally?

    BTW, what you call “advice” is just your personal opinion. I surely respect it, but don’t have to accept it. Do you understand this?

  166. 166
    OldAndrew says:

    R J Sawyer

    Just as, in isolation, there is nothing functional about insulin, haemoglobin or a hand.

    You lost me when you compared the functionality of water molecules to that of a severed hand. When we think of hands, we almost always think of functional hands attached to functional arms. If you can find an isolated hand, I’m certain that at some point it was attached to a body. Something doesn’t add up when you reason by pointing out that isolated hands aren’t functional.

    It’s also a “glass-half-empty” perspective.
    Hands are amazing and functional!
    Yeah, but once they come off they’re useless.

  167. 167
    R J Sawyer says:

    PeterA

    BTW, do you recall any famous extrapolation that turned out to be very wrong?

    Extrapolating from characters in the bible to estimate the age of the earth comes to mind.

  168. 168
    PeterA says:

    R J Sawyer @ 167:

    Where is that extrapolation written in?
    I haven’t seen it. Can you point to it?
    Thanks.

    However, I was interested in another case that is written in famous documents. Can you recall it?
    Thanks.

  169. 169
    ET says:

    R J Sawyer:

    my problem with the “complex functional specified information is solely the product of conscious design “ argument is that we are drawing this conclusion from a single example, human.

    That is a single source and not a single example.

    It is always dangerous to extrapolate from a single example.

    That is your opinion and it isn’t a single example

    I also have difficulties with trying to figure out what is meant by “complex functional specified information”.

    That is your problem and it’s personal. You use CSI every day. An education would cure that.

    For example, can a water molecule be said to have complex functional specified information?

    No, why would it be?

  170. 170
    OldAndrew says:

    I understand the reasoning that the only concrete, “observable” creation of complex function is by humans. Based on that, can we judge things of unknown origin, which were certainly not created by humans, and extrapolate that they were also designed? (It’s actually an inference, but whatever.)

    But if we reject that inference and assume that such apparent complexities must have arisen undirected from chemical reactions, from what are we extrapolating? If there was any indication that such things happen, ever, then I might be right there with you.

    We can go with the inference that (to oversimplify) things that exhibit characteristics of what humans design, except a gazillion times more complicated, are also designed. I can see how that might seem odd. But it’s something, and it’s based on something.

    Or we can extrapolate that things happened by themselves, based on… I don’t know. I’ve never heard or read what this determination is based on.

    There’s door number three, deciding that it’s entirely unknown. But the design inference, for all that it doesn’t explain, is pretty solid and makes a lot more sense than an extrapolation from nothing. Isn’t some observation of something better than no observation of nothing?

  171. 171
    R J Sawyer says:

    PeterA

    Where is that extrapolation written in?
    I haven’t seen it. Can you point to it?

    Archbishop Usher. The Annales of the Old Testament. From the Beginning if the World

    Given the knowledge and beliefs of the day, it was certainly a valiant attempt, involving a huge amount of research. But, ultimately, completely wrong. I’m surprised that you have never heard about it.

  172. 172
    ET says:

    I don’t see anything wrong with using our knowledge of cause and effect relationships to make inferences about whatever is being investigated.

    Even if humans are the only known source of complex specified information, those criticizing ID have a plethora of causes to call upon and yet cannot dial up one to counter ID’s claims.

    Nature doesn’t get a pass just because humans could not have been the intelligent agency that produced the CSI observed in biological organisms.

  173. 173
    PeterA says:

    Archbishop Usher?

    Huh?

    Don’t recall ever hearing that name. I’m replying to you before searching for that name.
    However, my cultural/educational level is rather poor by all standards, so don’t take it as a pattern for comparison.

    In any case, it’s not the Christian Bible, hence it doesn’t count in this case.

    Many things have been said and even written by many people through history, but at the end of the day most of it doesn’t count, because it’s not a faithful interpretation of what is written in the Christian Scriptures. We humans like to make a text say less or more than what it really says, and when we don’t understand exactly what it says, then rather than humbly accept our poor comprehension, we prefer to speculate and make things up.

    However, leaving the momentary digression into obscure history and philosophy/theology, let’s go back to our science-related conversation.

    Please, would you mind commenting on the second part of #168? Thanks.

  174. 174

    For example, can a water molecule

    Can you explain what information does a water molecule contain?

    And would you mind addressing the question I asked you 135 comments ago at #38?

  175. 175
    R J Sawyer says:

    PeterA

    However, I was interested in another case that is written in famous documents. Can you recall it?

    The literature is full of examples of extrapolations, correlations and inferences being shown to be wrong. But obviously you have a famous one in mind. Don’t leave me hanging.

  176. 176
    gpuccio says:

    R J Sawyer at #160:

    Thank you for your thoughts.

    You make two “objections” in your comment, and I would like to answer them both, as they are common objections to ID theory and they deserve a clear answer.

    If I understand well, they are (in a logical order, not in the order you gave them in the comment):

    1) “I have difficulties with trying to figure out what is meant by “complex functional specified information”. And the water molecule example.

    2) “My problem with the “complex functional specified information is solely the product of conscious design “ argument is that we are drawing this conclusion from a single example, human. It is always dangerous to extrapolate from a single example.”

    OK, let’s go with it.

    1) We can argue about possible functions of water, and as you know I am open to all possible definitions of function in my approach to functional complexity. But that is not the problem.

    The problem with water is not the function, but the complexity linked to it.

    Let’s try to clarify. The complexity in “functional complexity” is not a generic notion of complexity: it is very specific and well defined.

    The complexity is the ratio of the configurations of the observed object that implement the function versus all possible configurations of the object.

    And the important point is: those configurations must be similarly possible under the laws of physics.

    IOWs, functional complexity refers to specific configurations of what Abel calls “configurable switches”, configurations that implement a function, while all the other possible configurations do not implement it. The ratio of the target space to the search space is the functional complexity observed in the object, for the defined function.

    Now, the key point, again, is that all the configurations in the search space must be possible under the laws of physics. IOWs, a configurable switch is something that, under physical laws, can assume different configurations (at least two) that are possible under physical laws: IOWs, contingent configurations.

    So, in a nucleic acid each of the four nucleotides can be found at some place, in the absence of some template which already has the information. There is no law of physicis or biochemistry that dictates that, for example, the first nucleotide must be A, the second T, the third A, the fourth G, and so on. IOWs, there are no laws of physicis of chemistry that dictate a specific sequence, in the absence of any template that already has that information.

    The same is true for AAs in a protein.

    Can necessity dictate a sequence in particular cases? Of course it can. Let’s say that in your medium in your lab you only have glycine available. Then you will only have polyglycines. But that is not a complex result: it is the result of necessity, an order easily compressible and easily explainable by the laws of chemistry, considering that only one aminoacid was available. Its Kolmogorov complexity is extremely low. So, even if the polyglycine could have some function (it certainly can), it is not complex.

    But consider insulin. In humans, it is a specific 110 AAs sequence, with a well definable function. Of course, there are many possible sequences that can implement the function of insulin, but their number is however reasonably small if compared to the 20^110 combinations that make the search space. If we can reasonable estimate the target space, then the functional complexity can be computed. However, there can be no doubt that there is a remarkable functional complexity here, and that it is of some relevance. My procedure of blasting the human form against cartilaginous fish gives an estimate of 97.8 bits, 49% identities, 0.889 baas: not much, if compared to other proteins, but still we have almost 100 bits of functional information here.

    Compare that to histone H3, a protein of similar length (136 AAs), which, with the same procedure, gives a result of 272 bits, 99% identities and 2.0 baas.

    Now, what about water? The answer is simple enough. If we accept the laws of physics and chemistry as they are, and the conditions of our planet as they are, the existence and configuration of the water molecule is completely explained by necessity: IOWs, water is like the polyglycin, not like the insulin molecule.

    So, from the point of view of functional complexity, it is not complex at all. No configurable switches show a specific configuration against possible configurations, simply because no other possible configurations exist.

    Can we make an argument for design about water? Yes, we can. But it must be either:

    a) The argument that the laws of our universe are designed (IOWs, a cosmological argument)

    b) The argument that some specific context in our universe is designed: for example, our planet (IOWs, a privileged planet argument)

    Both arguments are possible and, IMO, valid. But they have nothing to do with the configuration of water itself. They have to do with the configuration of our universe vs all possible universes, or with the configuration of our planet vs all possible planets. IOWs, the object we are observing in a) is the whole universe, and the object we are observing in b) is our planet. But if the object we are observing is water, no argument for design based on functional complexity can be made.

    I hope that is clear.

    2) It is true that we are drawing our design inference for biological objects from a single class of observed objects, human artifacts. Not really one example, but certainly one class of examples. It’s the observation of human artifacts that reveals to us the connection between functional complexity and conscious design.

    But the simple truth is: we are not deriving our theory about functional complexity and design from one class of objects because we want to be unduly selective. The reason is completely different.

    The reason is simply that human artifacts are the only class of objects in the universe, whose origin is not controversial, that exhibits complex functional information. In the whole universe as we know it.

    IOWs, there are only three classes of objects in the universe as we know it that have a specific status about functional complexity:

    a) Human artifacts, that exhibit tons of it.

    b) Biological objects, that exhibit tons of it.

    c) All other objects in the universe, that exhibit no functional complexity at all, beyond some very trivial level: IOWs, no complex functional information.

    So, if we accept the very simple notion that biological objects cannot easily be explained by natural laws (as everyone should see), and so we accept the simple notion that their origin is controversial (as the same existence of our debate should easily prove), then our choice of human artifacts as the only reliable source of information about functional information, design and their relationship becomes the only possible choice.

    IOWs, it’s not the fact that we draw our conclusions from the class of human arrtifacts that is important: the important thing is that no other class of physical objects exists, in the whole universe, to draw conclusions about functional complexity, because no such class exists that exhibits complex functional complexity.

    Now, if there were a reliable explanation of how biological objects arise out of physical laws, then things would be different. IOWs, if the RV + NS alogrithm were capable of generating complex functional information, that would falsify ID. As I have always said.

    But the simple fact is that it is not capable of that. There is absolutely no scientific evidence for that strange imaginary theory, except for the blind faith of those who need to believe in it out of a personal commitment to a materialistic worldview in science. And personal commitments have no relevance in true science.

  177. 177
    OLV says:

    I can’t tell exactly why, but I like to read gpuccio’s comments on the topic that is discussed here. There’s always some learning from it.
    I’m sure DATCG, UB and other folks here enjoy it too.

  178. 178
    PaoloV says:

    @176
    “There is absolutely no scientific evidence for that strange imaginary theory, except for the blind faith of those who need to believe in it out of a personal commitment to a materialistic worldview in science. And personal commitments have no relevance in true science.”
    Excellent conclusion to his excellent explanation.

  179. 179
    jawa says:

    PeterA,
    After I addressed new questions to you @165, you continued your friendly chat with RJ Sawyer in this thread and wrote comments @168 and @173 for him, but ignored me. Any reason that justifies your attitude?

  180. 180
    EugeneS says:

    GP 176,

    An excellent comment.

    The only thing that requires further clarification/research IMO is whether human artefacts are indeed a single class of such objects. While animal contraptions, for want of a better word, such as beaver dams and termite hills and bird nests are certainly less complex than the most complex human artefacts, in terms of concrete thteshold values for ID detection they may still qualify.

  181. 181
    jawa says:

    Yes, i agree that gpuccio wrote another insightful explanation, but we’re all used to this here. The guy has set the bar so high that his friendly opponents can’t even see it. It almost looks unfair according to the “politically correct” rules of this world.

  182. 182
    PaoloV says:

    EugeneS @180:

    That’s an interesting point with a persuading argument.

    Thanks.

  183. 183
    gpuccio says:

    EugeneS at #180:

    That is an old an interesting point.

    My point of view is as follows.

    I believe that some animals can generate forms of functional complexity in their individual behaviours. One of my cats, for example, can jump and open doors by grasping the handle. My two other cats cannot do that at all.

    In general, these forms of intelligent behaviour are probably of lower complexity than what we can see in humans, and rarely they reach higher abstraction levels, especially symbolic codes. But of course that is a very interesting field of research.

    Beaver dams and similar examples, however, are probably different from that. I think we are in the field of this OP with those examples: complex and intelligent instinctive behaviour.

    The difference here is that those behaviours are, in great part, hereditary. They are repeated in the species. They are not like my cat opening doors, but rather like my cat purring or licking itself.

    Be they genetic or epigenetic, they seem to be hereditary.

    Therefore, the information that governs those behaviours is probably in the genome, or maybe in the epigenome, or in both.

    IOWs, there is a very good chance that such information is designed, exactly like all other biological information.

    In that case, the designer of that information would not be the indvidual animal (like in the case of my cat opening doors), but rather the biological designer of the species.

    In the end, however, human design remains the best, if not the only, example of conscious design generating high functional complexity. Even if we consider animals capable of that too, in some measure, that ability would again rely on conscious representations (I have no doubts that my cat learned to open the doors because it wanted to do that, and in some way it understood how to do it).

    However, in humans we have a direct window to the connection between conscious representations and design: our own personal consciousness, which allows us to have direct experience of the conscious representations that precede and cause the act of design in ourselves. And to infer the same thing, with the highest reliability, for other humans.

  184. 184
    EugeneS says:

    GP
    Conscious representations. I can see where you are coming from. Yes, I agree, a lit of those behaviours are instinctive and may have been preprogrammed. But surely it is possible for animals to program themselves, consciously or not. The latter would be IMO equivalenttous creating AI. AI is intelligence in its own right by many criteria (except being conscious)…

  185. 185
    EugeneS says:

    GP and all 😉

    Sorry for the typos. Fishy fingers on a London train.

  186. 186
    gpuccio says:

    EugeneS:

    If we create AI (which is not conscious), we do it consciously. AI requires complex functional information to work. And it’s our conscious representations that allow us to generate the complex functional information that works as AI.

    Animals are conscious, IMO, at least higher animals certainly are. But I don’t see how they could “program themselves”, either consciously or not.

    To “program” means to use highly symbolic intelligence to achieve a goal by complex functional configurations. Animals apparently cannot do that.

    What they can do is to use their conscious representations to find solutions and procedures that are not highly symbolic, but are still intelligent: like my cat opening the door.

    How is that done? Again, there is a conscious representation of feeling, a desire. My cat wants the door open.

    Then there are cognitive representations of meaning: what possible actions can open the door. Not highly symbolic cognition, but cognition just the same.

    And there is coordinated action and cognition: attempts, evaluation of results. And, in the end, success.

    Nothing of that could happen without conscious representations, I believe. However, something is still missing: higher symbolic language, higher abstraction, and so on.

    I don’t think an animal can “program”. It can learn, and it does that by conscious representations of feeling and cognition, like us. Just simpler.

    An animal cannot create AI. Indeed, they cannot create even simpler machines, with few minimal exceptions. They usually cannot create complex symbolic language. Again, with some partial exceptions.

    Those behaviours that are very complex and instinctive, and for which we have no evidence that they are the result of individual learning, are reasonably pre-programmed. And they cannot be pre-programmed by the animal itself. I don’think that monarch butterflies have learnt how to migrate. Or beavers how to build dams.

    Regarding AI, I would say that it is an intelligently designed machine. In that sense, it is not different from a watch, just more complex.

    Is a watch intelligent? Or an abacus? Or a computer? All of them are, in a sense. They are intelligently designed machines.

    None of them is, in another sense. None of those objects can have any conscious cognition, any understanding of meaning, any desire. And those are the things that really define intelligence.

    The word “intelligo”, after all, means just that: I understand.

  187. 187
    OLV says:

    The word “intelligo”, after all, means just that: I understand.

    If an “AI” robot can be programmed to say “I understand”

    would it have the same meaning as one of us saying it?

    Who is “I” in each case? A conscious or non-conscious being?

    Isn’t there a big difference in lacking or having consciousness?

    On another, though related topic, are the cats self aware of their own existence? We would have to ask them. 🙂

    Also, how does it feel to be a cat? Let’s ask them too. 🙂

  188. 188

    I see we are not going to hear what information is in a molecule of water.

    Likewise, we are not going to hear if the confirmed prediction of a semantically closed, multi-referent symbol system at the heart of the cell (a language structure, as carefully described in the physics literature) is an inference to an act of intelligence or an unguided dynamic process.

    Too bad.

  189. 189
    DATCG says:

    Gpuccio @176,

    Well done in reference to Abel, Order vs Functional. Configurable Switches.

    I think RJ Sawyer is not recognizing differences between Ordered Sequence Complexity(OSC) – snow, ice, and Functional Sequence Complexity(FSC) – symbolic representation and abstract messaging for a myriad of specified forms.

    Pre-Programmed and prescribed informational content.

    From Trevor and Abel’s paper…

    Ordered Sequence Complexity (OSC)

    A linear string of linked units, the sequencing of which is patterned either by the natural regularities described by physical laws (necessity) or by statistically weighted means (e.g., unequal availability of units), but which is not patterned by deliberate choice contingency (agency).

    Ordered Sequence Complexity is exampled by a dotted line and by polymers such as polysaccharides. OSC in nature is so ruled by redundant cause-and-effect “necessity” that it affords the least complexity of the three types of sequences.(edit: example – ice).

    The mantra-like matrix of OSC has little capacity to retain information.

    OSC would limit so severely information retention that the sequence could not direct the simplest of biochemical pathways, let alone integrated metabolism.

    Appealing to “unknown laws” as life-origin explanations is nothing more than an appeal to cause-and-effect necessity.

    The latter only produces OSC with greater order, less complexity, and less potential for eventual information retention

    (Figs. ?(Figs.11 and ? and 22).

    Another words, liquid water, rain to snow and ice does not create artistic images of design like those at following link on ice sculptures…

    https://www.complex.com/style/2011/12/the-25-most-spectacular-snow-sculptures/3

    Funny, the site name is “complex.com”

    😉

    .

  190. 190
    DATCG says:

    Functional Sequence Complexity(FSC)

    Bioinformation has been selected algorithmically at the covalently-bound sequence level to instruct eventual three-dimensional shape. The shape is specific for a certain structural, catalytic, or regulatory function.

    All of these functions must be integrated into a symphony of metabolic functions. Apart from actually producing function, “information” has little or no value.

    What kind of information produces function? In computer science, we call it a “program.”

    A linear, digital, cybernetic string of symbols representing syntactic, semantic and pragmatic prescription; each successive sign in the string is a representation of a decision-node configurable switch-setting – a specific selection for function.

    FSC is a succession of algorithmic selections leading to function. Selection, specification, or signification of certain “choices” in FSC sequences results only from nonrandom selection.

    These selections at successive decision nodes cannot be forced by deterministic cause-and-effect necessity.

    If they were, nearly all decision-node selections would be the same. They would be highly ordered (OSC)(Edit – Like Snow, Ice.

    And the selections cannot be random (RSC). No sophisticated program has ever been observed to be written by successive coin flips where heads is “1” and tails is “0.”

    Shannon [2,3] was interested in signal space, not in particular messages.
    Shannon mathematics deals only with averaged probabilistic combinatorics.

    FSC requires a specification of the sequence of FSC choices. They cannot be averaged without loss of Prescriptive Information (instructions).

    Bits in a computer program measure only the number of binary choice opportunities.

    Bits do not measure or indicate which specific choices are made. Enumerating the specific choices that work is the very essence of gaining information (in the intuitive sense). When we buy a computer program, we are paying for sequences of integrated specific decision-node choice-commitments that we expect to work for us. The essence of the instruction is the enumeration of the sequence of particular choices. This necessity defines the very goal of genome projects.

    Algorithms are processes or procedures that produce a needed result, whether it is computation or the end-products of biochemical pathways. Such strings of decision-node selections are anything but random.

    And they are not “self-ordered” by redundant cause-and-effect necessity.

    Every successive nucleotide is a quaternary “switch setting.”

    Many nucleotide selections in the string are not critical. But those switch-settings that determine folding, especially, are highly “meaningful.” Functional switch-setting sequences are produced only by uncoerced selection pressure. There is a cybernetic aspect of life processes that is directly analogous to that of computer programming. More attention should be focused on the reality and mechanisms of selection at the decision-node level of biological algorithms.

    Codes of Life, not blind, but guided, not simply ordered, but symbolic, highly organized, functional sequences that have purpose and targets to repair, protect and regenerate trillions of times in our cells each day not blindly, but programmatic steps and instructions, rules and conditions.

    What a marvelous work it is this Code of Life, that ENCODE projects are unraveling evermore these days.

    .

  191. 191
    OLV says:

    DATCG,

    Very interesting comments @189, 190. Thanks.

  192. 192
    EugeneS says:

    GP

    I can agree with almost everything you said in your previous comment. I guess when I said that animals program themselves I was too vague.

    All of this comment is just thinking aloud…

    I do not believe that all instincts are written in stone and have been necessarily front loaded. I think that at least some animals can genuinely learn (work out strategies and correct them based on previous experiences). Of course, these abilities in animals are inferior to their human counterparts.

  193. 193
    gpuccio says:

    EugeneS>

    I agree with you. Animals can certainly learn.

  194. 194
    gpuccio says:

    DATCG:

    Abel has everything perfectly right.

    I would just add that, while folding is certainly a big part of functional specification, there are however a lot of other sequence specificities that are not necessarily related to classical folding. Of course there are active sites that are as important as the general 3D folding, but as we know well there are also many sequences, not corresponding to well folded domains, that have great functional importance: they go, in general, under the name of intrinsically disordered proteins or intrinsically disordered regions, but many different functional mechanisms can be hidden behind that concept.

  195. 195
    gpuccio says:

    DATCG:

    About intrinsically disordered regions in TFs, I have just posted a link to a paper, at comment #287 in the transcription regulation thread. 🙂

  196. 196
    EugeneS says:

    GP

    “I agree with you.”

    Great!

    “Abel has everything perfectly right.”

    I like this author. To be a bit critical and hair-splitting, I would not call what he writes about “the birth of programming” (his own words) but… what he writes and how sets the teeth of the likes of Jeffrey Shallit on edge 🙂

  197. 197
    PeterA says:

    RJ Sawyer @175:

    I apologize for leaving you waiting for a couple of days. I was busy working on important tasks.

    Please, don’t give up so easily. I’m sure you know that famous document. It’s from the second half of the 19th century England.
    Its famous author proposed a then revolutionary idea based on observations of evolutionary adaptations (micro-evolution) but made the enormous mistake of extrapolating those observations up to the level of baramins! Attributed extraordinary powers to the allegedly micro-evolutionary RV+NS and incorrectly proposed that such limited mechanisms could eventually lead to the baramins!
    It took many years for some scientists to wake up from the dumbing effect of such mistaken extrapolation, but fortunately now some scientists even within the materialistic worldview have admitted that the failed extrapolation requires serious revision. They have jumped out of the ship where they sailed for long time and have boarded their own “third way” ship. Some have dared to ask for a complete replacement, but others more cautious have reacted like John Lennon in his song “Revolution”, agreeing with changes while opposing destruction. The peaceful folks have proposed an extension to the original ideas to account for the major gaps in the original RV+NS path.
    I’m sure now you realize what famous document this is about.

  198. 198
    jawa says:

    Peter,

    Your inconsistency has increased almost to the pathetic level of Amblyrhynchus.

    You apologize to TJ Sawyer for leaving him waiting 2 days for your response. However, it has been 4 days since you ignored my questions addressed to you @152, which were reminded @165.
    Can you explain?

  199. 199
    jawa says:

    Peter,

    Bad news for you.

    RJ Sawyer has openly ignored your comment.
    He’s not interested in discussing biology. Apparently more interested in philosophical arguments, as you can see in other discussions.

    I’m glad you’ve been given your own bitter medicine back.
    Good for you. Perhaps that will teach you a lesson. Now you know how rude it’s to quit a conversation without any explanation. You did it to me.

  200. 200
    R J Sawyer says:

    Jawa@198&199, your obsession with the amount of time people attend to your demands, or ignore them, is duly noted. But I don’t think that Peter or I will lose any sleep over your concerns.

  201. 201
    jawa says:

    RJ Sawyer,

    I’m glad to know that Peter and you won’t lose any sleep. Sleep deprivation may be detrimental to health.

    However, I just want to call the anonymous readers’ attention to the fact that some commenters quit discussing unexpectedly and it seems like sometimes that has to do with lacking strong arguments against the other side, though perhaps that’s not really the reason for their apathy.

    Apparently the comment @197 has been ignored by the person to whom it was addressed to. But the author has ignored some comments too.

    That’s all. Y’all may keep sleeping. But don’t sleep in the subway.*
    (*) 1967 Petula Clark

    🙂

  202. 202
    PeterA says:

    jawa,
    Don’t you have more important things to occupy your time in?
    Please, don’t take me wrong, but I think you should get help from counseling. I really feel sad for you.
    Nobody is obligated to respond or comment on other comments here.
    You have to understand that.

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