Tuesday, January 05, 2016

Intelligent Design Creationists are very confused about epigenetics

I've been trying to figure out why Intelligent Design Creationists are so excited about epigenetics. They seem to think it's going to overthrow everything we know about evolution (= "Darwinism"). That means, in their minds, that "naturalism" and "materialism" aren't sufficient to explain biology.

The logic escapes me.

Denyse O'Leary has added a new wrinkle in her latest post (as "News") on Uncomon Descent. She reveals a profound misunderstanding of epigenetics [Could epigenetics change perspectives on adoption?].

I'll just quote the relevant part and let you try and figure out whether Denyse represents mainstream Intelligent Design Creationism. 'Cause if she does, the movement is in far worse shape than even I imagined.
I remember one adoptive mother, taunted by a rebellious teenager who wanted to find her “real” mother, taking the girl by the shoulders and saying, “Look, I raised you from when you were seven days old; I supported you, sat with you in emergency rooms and juvenile court, laughed and cried with you, … and got you into a good school in the end. I don’t know who or where your birth mother is. But I do know this: I am the only ‘real mother’ you have ever had or ever will have. Look at me. Get used to it. It doesn’t GET better than this.”

I hope the kid smartened up. Meanwhile what if she discovers, when she has children, that their genome reflects in part traits she acquired growing up in the adoptive home? Maybe that would allay some of the sense of alienation.

Might epigenetics could provide some basis for understanding? Time will tell.

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


151 comments :

  1. Well in fairness to IDCs in general, Denyse is pretty much stuck at the "novice" setting in the apologetics game.

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    1. She is still writing for what is purportedly a science blog, though. Quite aside from the question of why such an unqualified person would be allowed to do so, you'd think someone else at the blog would be making sure she doesn't post something to absurdly misinformed.

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  2. True, so why is she put front and center in charge of the main ID blog?

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    1. Because that's who Dembski chose, and he made that choice because, well, he's Dembski. There are *no* sharp knives in this particular drawer.

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    2. Oh, and I would say that ENV is the "main" ID blog, if there is such a thing. If UD ever was, it stopped being when Dembski bailed -- he at least had a simulacrum of academic cred. A hack journo and an accountant/lawyer? Not so much.

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  3. Genes hard wire your personality evo psych and other genes are everything perspectives, including panselectionism of the selfish gene variety really do have a problem with epigenetics, as well as random genetic drift and neutral/nearly neutral evolution. I suppose the large majority of popular writers on evolution will dutifully swear they accept the minor modifications they say these things make to evolutionary theory. In my reading they always assume natural selection is everything and rarely consider any alternatives. I'm never quite sure whether anyone rabbiting on about epigenetics or genetic accommodation or punctuated equilibrium isn't seizing on anything to defy genetic determinism. It seems possible that even here the woman doesn't really mean to say much more than: Not only is your adoptive home more important than your blood line, even (some of) the gene products in your cells are something that happened there, not the treasured essence you inherited from the "real" parents.

    Or maybe not. I guess how worked up you get over this depends on whether you think its worse for the majority of professionals to give meaningless lip service to things like epigenetics, random genetic drift, etc. Or whether its more important that the de facto panselectionism from natural selection triumph by vociferously insisting that none of these things really changes the picture.

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  4. They haven't noticed (or don't want to notice) that epigenetic modifications of DNA revert after at most a few generations. They seem to think that they make permanent changes.

    Changes which would be a natural process that would explain the evolution of humans from their common ancestor with chimps. Which they don't think happened anyway (cf. their discussions of the extra centromere-derived sequences on Chromosome 2).

    Denyse O'Leary endlessly astonishes me.

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    1. Mr Felsenstein,

      What is a few generations in this context?

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    2. In highly controlled conditions in mice, altered DNA methylation states have been seen as far as the F2 generation away from the causative action in the F0 generation. I'm pretty sure the same has been observed in human studies. I don't think persistence beyond 2 generations has been observed.

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    3. @Beau Stoddard

      It kind of depends on what kind of epigenetic inheritance is being talked about, but something like an environmentally induced expression of protein in the cytosol will only last at most a few cell division before the signal is lost to dilution, if the environmental stimuli is no longer present. Think of it this way: Something happens in the environment that the cell detects and in response it produces some proteins in the cytosol. Then the stimuli disappears, but the cell still has these proteins in the cytosol. It undergoes cell division, basically halving the concentration of these proteins. The daughter cell has "inherited" the expression pattern. The daughter cell divides, halving it's already halved amount of proteins in production of the 3rd generation of cells. Usually by the 5th generation, the concentration has already dropped so low the expression pattern is disabled and the cell no longer produces or contains the originally produced protein. It has in effect reverted to the original state.

      This is for single-celled organisms. For a large multi-cellular organism like a human, or mice, these kinds of expression patterns won't even make it to the next generation, because the number of cell divisions between generations are too many.

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    4. Beau Stoddard:

      Mr Felsenstein,

      What is a few generations in this context?


      In the great scheme of things, it is but a passing fancy, a mere bagatelle.

      Delete
    5. Still, these modifications may play a evolutionary role on modest timescales. The group of Frank Johannes has done some nice research on this topic, by showing that new epigenetic variation (DNA methylation) in Arabidopsis can contribute to the heritability of quantitative traits. They also suggest that new epimutations can actually sustain long-term selection responses.

      http://www.ncbi.nlm.nih.gov/pubmed/24505129
      http://www.ncbi.nlm.nih.gov/pubmed/25964364

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    6. Joe, are you saying that epigenetic effects, modifications, changes, results (or whatever other noun is applicable) are "but a passing fancy, a mere bagatelle" in regard to evolution?

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    7. More or less. But actually I was just giving a frivolous response to Beau Stoddard's excessively-vague question.

      It is true that to make epigenetic changes last longer you need genetic changes to stabilize them. And that if you don't have that, they go away soon. The short-term effect is that they can make relatives more similar, which will be mistaken for evidence of heritable genetic variation.

      Mostly epigenetics is just a club creationists use to beat up on evolutionary biology. If I announced a new cellular phenomenon, "eclectic hyperplastic response" and put out a bunch of press releases saying it was being ignored by orthodox, stuffy, unimaginative biologists, and that it "changed everything", creationists would most likely seize on this to attack contemporary evolutionary biology. Without having a clue as to what, if anything, I was describing.

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    8. Hi Joe
      Have you read this paper?http://www.ncbi.nlm.nih.gov/pubmed/25297727#
      Interested in your thoughts.

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    9. @Bill Cole: According to the abstract, which is all I have time for right now, they are looking at gene expression differences and epigenetic differences between species. What's the issue?

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    10. How do we explain the evolution of these differences which appear to be large in the body of the paper. Wondering if this is where the Creation excitement is coming from.

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    11. @ Joe Felsenstein,

      Bill Cole has comprehension problems. He understands things to mean what he wants them to mean, rather than what they actually mean. When people try to correct his misunderstandings, he misunderstands the corrections as well. See below for examples:

      http://sandwalk.blogspot.ca/2015/10/human-mutation-rates.html

      http://sandwalk.blogspot.ca/2015/11/the-birth-and-death-of-salmon-genes.html

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    12. @Bill Cole: Looks like evo-devo to me. If you would like a better understanding of what statements along the following lines mean - "They have also provided intriguing new clues to the regulatory basis and phenotypic implications of evolutionary gene expression changes" - I would suggest reading one or more of Sean B. Carroll's books.

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    13. Hi Judmarc
      Thanks for the recommendation. What leads you to think this is an ego -devo discussion?

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    14. Here's the first paragraph of the article, Bill Cole, which should have made it abundantly clear that it is about evo-devo.

      A primary goal in biology is to understand the molecular basis of phenotypic evolution, most notably that of humans and other mammals. Two major classes of mutations underlie phenotypic innovation: the first comprises mutations that change the coding sequence and consequently the function of the final gene product (that is, the protein or RNA); the second class comprises mutations in regulatory sequences (for example, in promoter regions) that affect transcription, post-transcriptional processing, translation, or transcript and/or protein degradation. Notably, certain gene product sequence alterations that change the function of the protein (for example, mutations in transcription factors1) may also have consequences for gene regulation. By modifying developmental programmes, both types of mutations may lead to distinct tissue morphologies, laying the foundation for species- or lineage-specific physiology and behaviour. Moreover, mutations may also directly affect adult organ phenotypes.

      I'm not sure why I quoted that, since you've obviously read the article already. Only a complete imbecile would claim this article supports creationism without even having read, never mind having understood it thoroughly. Right?

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    15. Joe Felsenstein said:

      "They haven't noticed (or don't want to notice) that epigenetic modifications of DNA revert after at most a few generations. They seem to think that they make permanent changes.

      Changes which would be a natural process that would explain the evolution of humans from their common ancestor with chimps. Which they don't think happened anyway (cf. their discussions of the extra centromere-derived sequences on Chromosome 2)."

      Beau Stoddard asked:

      "Mr Felsenstein,

      What is a few generations in this context?"

      Joe said:

      "In the great scheme of things, it is but a passing fancy, a mere bagatelle."

      Beau said:

      "Interesting. Thanks"

      I asked:

      "Joe, are you saying that epigenetic effects, modifications, changes, results (or whatever other noun is applicable) are "but a passing fancy, a mere bagatelle" in regard to evolution?"

      Joe said:

      "More or less. But actually I was just giving a frivolous response to Beau Stoddard's excessively-vague question.

      It is true that to make epigenetic changes last longer you need genetic changes to stabilize them. And that if you don't have that, they go away soon. The short-term effect is that they can make relatives more similar, which will be mistaken for evidence of heritable genetic variation.

      Mostly epigenetics is just a club creationists use to beat up on evolutionary biology. If I announced a new cellular phenomenon, "eclectic hyperplastic response" and put out a bunch of press releases saying it was being ignored by orthodox, stuffy, unimaginative biologists, and that it "changed everything", creationists would most likely seize on this to attack contemporary evolutionary biology. Without having a clue as to what, if anything, I was describing."

      ----------------------------------------------------------

      Joe, I don't think that Beau's question was "excessively vague". After all, you said "at most a few generations" and his question was obviously based on that. What can be described as excessively vague is your "More or less.", "last longer", "stabilize", "they will go away soon", and "short-term effect" statements. Can you be more specific?

      To help me understand your position I have more questions for you (and I would appreciate it if others, including Larry, would also respond):

      What is your preferred definition of 'epigenetic' or 'epigenetic effect', and how about 'epigenetic changes'? Are you claiming that epigenetic effects, and changes, can only make relatives more similar or do you also accept that epigenetic effects, and changes, can and often do make relatives less similar, and sometimes radically less similar in some way(s)? Do you deny that epigenetic effects, and epimutations, are stably heritable? And how would you define 'stably heritable'?

      Leaving out asteroid impacts, human caused pollutants and destruction, and other 'disasters', do adaptations, variations, speciations, extirpations, and/or extinctions occur only because of random genetic mutations filtered by drift and/or natural selection, or can and do adaptations, variations, speciations, extirpations, and/or extinctions occur because of epigenetic effects and epimutations?

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  5. I've been trying to figure out why Intelligent Design Creationists are so excited about epigenetics. They seem to think it's going to overthrow everything we know about evolution (= "Darwinism").

    I don't think anybody, at least in the right frame of mind, believes that evolution = Darwinism can be overthrown, no matter how strong the evidence against it, as long as the Darwinian bullies are in charge of so called science around this. Tyrannies come and go and we have prove for that if we look back just 100 years.


    That means, in their minds, that "naturalism" and "materialism" aren't sufficient to explain biology.

    For this fact to change you and others need to present experimental evidence and not delusions as some scientific facts. I fear this will not change. I accept it. For now.

    The logic escapes me.

    Well, now you know how I feel.



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    1. Please explain how epigenetics means you did not evolve from a common ancestor with the chimpanzee.

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    2. The group of Frank Johannes has done some nice research on this topic, by showing that new epigenetic variation (DNA methylation) in Arabidopsis can contribute to the heritability of quantitative traits. They also suggest that new epimutations can actually sustain long-term selection responses.

      http://www.ncbi.nlm.nih.gov/pubmed/24505129
      http://www.ncbi.nlm.nih.gov/pubmed/25964364


      For this fact to change you and others need to present experimental evidence and not delusions as some scientific facts.

      Eric, do you see the difference between a discussion of specifics, with citations to real experimental work, as Corneel has done, and your generalized, vague complaining? If you had specifics with real experimental evidence to cite, that would be a whole different matter than what you've done so far, which is vague rhetoric.

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    3. Please explain how epigenetics means you did not evolve from a common ancestor with the chimpanzee.

      I thought that the burden for proof was on Darwinists that it did?

      I will do it after you've proven experimentally that epigenetics was not designed and evolved and by what mechanism.

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    4. judmarc,

      I'm sorry to disappoint you but this is not serious experimental work. You think it is, but this is just the beginning of a new era of Darwinists finally embracing epigenetics.

      My personal opinion is that J. Coyne has recently retired after he had seriously committed himself to epigenetics "as not taking a part in evolution". I know it for a fact, that his assumptions have been proven wrong, very wrong, so Coyne is taking a rest. Not for long though. We are about to enter a new era. J. Coyne is a coward. Banned me more than once.
      I will repay him here, if Larry allows of course.

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    5. Eric, I'm trying to see why you think the epigenetic work on the plant Arabidopsis to be "not serious experimental work."

      The work is experimental. It took a lot of work and time and money. Perhaps you dismiss it because many of the co-authors appear to be foreign? Or because it's on plants? (Oh, please not that! I say as a botanist.)

      The research suggests that epigenetics may have more of an influence on evolution than Coyne seems to believe, so I thought you would have liked the conclusions.

      So, why are these articles not serious experimental work?

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    6. @eric - "I will repay him here..." Yeah, well, he's a cat person, so having his pant-cuff gnawed on by a toothless lap dog probably isn't going to engage his (or anyone else's) interest much.

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    7. > Well, now you know how I feel.

      You feel confused?

      We get it, you find the science difficult to follow.. but that's no reason to chose to go with the small minority who reassure you by telling you what you want to believe (see confirmation bias).

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    8. "I thought that the burden for proof was on Darwinists that it did?"

      That burden has already been carried. Obviously you reject that, which is fine. But now ID comes along and says epigenetics is somehow further evidence that evolution is wrong, so what I'd like to see from an ID proponent is an explanation, using a concrete example (the evolution of humans and chimps from their common ancestor), how epigenetics is a falsification of that.

      Do it!

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    9. "
      I will do it after you've proven experimentally that epigenetics was not designed and evolved and by what mechanism.
      "

      This makes no sense. Do you even know what epigenetics is? Why do you think it is designed in the first place? Explain to me what quality of epigenetics says it is designed?

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    10. I know it for a fact, that his assumptions have been proven wrong, very wrong

      Cool. You've got the citations to peer-reviewed journal publications of experimental work, then? (And we know, since publications in Science, one of the most prestigious peer-reviewed journals, are not "serious" to you, that these experiments that provide slam-dunk proof have got to be in some much more prestigious journal, if that even exists, and peer-reviewed by experts in the field five ways from Sunday.) I eagerly await the citations.

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    11. I have a general question to you ALL (the last 6 comments) before I begin to answer your questions:

      According to the "current scientific knowledge" (no comment) has the science been proven scientifically to be more intelligent than random accidents in nature? How about statistics in this field compering the work of accidental accomplishments vs the intelligent ones? How do you do in this field? I'm aware but the rest is up to...

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    12. Recently I've met a man at a conference who would like to sponsor something that proves that there is no God.

      Because he is a really nice guy and seems really sincere about his beliefs, I thought that he should join this blog but so far, I don't see his presence.

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    13. According to the "current scientific knowledge" (no comment) has the science been proven scientifically to be more intelligent than random accidents in nature? How about statistics in this field compering the work of accidental accomplishments vs the intelligent ones? How do you do in this field? I'm aware but the rest is up to...

      It's a shame you are so insensible.

      Recently I've met a man at a conference who would like to sponsor something that proves that there is no God.

      Which probably isn't actually true, but if it is, then the person is a fool, isn't a scientist, and what the hell, isn't it just high time that you go away now?

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    14. Eric asked, "has the science been proven scientifically to be more intelligent than random accidents in nature?"

      This makes about as much sense as asking which is smarter, basalt or the sky? Or to put it at a level Eric might understand, "random acts in nature" don't take intelligence tests, so we can't make the comparison.

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    15. According to the "current scientific knowledge" (no comment) has the science been proven scientifically to be more intelligent than random accidents in nature?

      I don't think I ever thought of a question so silly and incoherent even in drunken BS sessions in college dorm rooms.

      Here's a more coherent question (though no less silly), if teleology is what you're after: How does a Thermos know when to keep its contents hot and when to keep them cold?

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    16. Perhaps Eric is asking whether, when inventing a new technology, deliberate design is more effective than blind, dumb luck. As it turns out, the answer may be "blind, dumb luck."

      https://en.wikipedia.org/wiki/Evolved_antenna

      The problem is that using evolutionary design processes is much more time and resource intensive. It's just not practical to create millions of randomly varied prototypes, test how they work, further randomly "mutate" the most effective variations, and continue the process for several thousand generations of prototypes until you arrive at the best design. Or it has been so far. Computer simulations may soon be able to more widely mimic this process, as was done with the NASA antenna design.

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    17. Unless what is being designed is a computer algorithm. A good friend worked on the US anti-missile defense system for a while (a/k/a "Star Wars"). Human-coded aiming software could not possibly take on the task of maintaining "lock" on a missile through the varying conditions of Earth's atmosphere. Therefore, starting from an original aiming algorithm, millions of generations of algorithms were "evolved" by introducing random code variations, determining which variation performed best at maintaining lock, introducing random variations in this algorithm, and iterating.

      The result performed extremely well, far better than the original human-coded algorithm.

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    18. There you go, Eric. You got you answer. Now, as you promised, it's time for you to give yours.

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    19. Cool! Evolved antennas and computer programs. I hadn't heard of them before.

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    20. So, what you are ALL saying is that randomness is more intelligent that the intelligence that randomness had "created?
      What are the options?

      Don't feed me the Darwinian shit. I get nauseous each time I read their shit. I can't take it anymore.

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    21. So, what you are ALL saying is that randomness is more intelligent that the intelligence that randomness had "created?
      No, Eric, no one is saying that.

      What are the options?
      1) 150 years of scientific research by some of the best minds in the world is wrong.
      2) Some random internet clown with a penchant for asking nonsensical questions is wrong.
      Gosh, such a hard choice....

      Don't feed me the Darwinian shit. I get nauseous each time I read their shit. I can't take it anymore.
      Perhaps your digestion would be improved if you stopped reading Sandwalk?

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    22. Eric wrote:
      "Don't feed me the Darwinian shit. I get nauseous each time I read their shit. I can't take it anymore."

      Poor, poor Eric. Is this some kind of trial you set for yourself? Do you think your 'suffering' in enduring 'Darwinian shit' will make your 'suffering' comparable to baby Jezus?
      Do you think your 'suffering' on earth will make your chances of reaching heaven more likely?
      Why Eric, do you think you need to 'endure this suffering'? Why?

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    23. So, what you are ALL saying is that randomness is more intelligent that the intelligence that randomness had "created?
      What are the options?


      Yes, what are the options Eric?

      If it is nonsensical for intelligence to be created by something more intelligent than itself, and if God created human beings, then God is less intelligent than the stupidest person on earth. In fact, under your creationist belief system, God is even dumber than a slug.

      Nice job of shooting yourself in the foot, Eric.

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    24. Eric,

      What Darwinists are actually admitting is that they are much, much dumber than random, accidental processes or dumb luck in nature and that is why they can't recreate life or make themselves or any other life kinds to evolve into other kinds...

      This is a Darwinian-materialism driven "fact" about life.
      Unfortunately, everything else contradicts their beliefs.
      Computers are not assembled by random processes and neither are other much, much simpler creations. Once created, they can't even "evolve themselves" to inprove unless intelligence is involved. They just deteriorate...

      Darwinists don't have one experimental proof that random processes can even make lifeless matter to make one leap towards anything resembling life...

      It's bogus they have no choice but to believe in ...

      BTW: If random processes are smarter than Darwinists, let all of them return all the Nobel Prizes and awards and let them be given to the dumb luck!!! Why should they receive all the praises and rewords that for the creative works of dumb and dumber? Lol


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    25. "Don't feed me the Darwinian shit. I get nauseous each time I read their shit. I can't take it anymore."

      I don't want to answer your requests in the traditional sense so much as I want to recommend you seek help from mental health professional .

      Delete
    26. If ALL Darwinists admit that dumb and dumber random processes are more intelligent than them, let them experimentally prove how what was first? The chicken or the egg?- paradoxes were resolved by dumb and dumber random processes.

      Inside even the simplest of cells, what was first chicken or the egg paradox (if only that were a problem for dumb and dumber) are clearly seen.

      Here are some examples:

      How did dumb and dumber random processes resolve the issue of enzyme-ATP mutual reliance as enzymes are essential to make energy (ATP) but energy from ATP is essential to produce enzymes?

      How did dumb and dumber random processes resolve the issue of DNA-enzyme mutual reliance as DNA is essential to make enzymes, but enzymes can't be made without DNA?

      Since these molecules break down and can’t function outside of the cell-membrane, how did dumb and dumber random processes resolve this issue as a cell membrane can’t be made without DNA and proteins and DNA can only be made by a cell?

      I’m positive that ALL Darwinists have proof that explains how all those essential molecules appeared not only at the same time, but more so how did dumb and dumber random processes convinced them to interact with each other overcoming the interdependence of each other to be formed in the first place…

      Darwinists must believe that dumb and dumber random processes can perform magic and poofed those molecules into existence while making the cell membrane around them from scratch out of dust at the same time hypocritically accusing creationist of believing in the same thing…lol

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    27. Velhovsky,

      You have some important misconceptions about what "darwinists" "believe." This make it very hard to decide how to approach your "problems." For one, well, I'm no "darwinist." I doubt that many here would call themselves "darwinists," and the few who would, well, they would not mean it the way you do. See? We don't hold to some credo like you do. We don't worship some person (let alone Darwin). We just accept that something like evolution happens, and that we share ancestry at the very least with a lot of other species, if not with all of them. Why so? Not because we worship some guy (like Darwin), not because we follow some credo (like you do), but because we understand the evidence for those things. That doesn't mean that we know everything. That doesn't mean that we think that we know everything. That just means that we accept things because the evidence shows it so, even if that won't give us a complete picture of the universe.

      What I'm trying to say is that we do not go around thinking "what should we put here instead of Velhovsky's god?" Most of us don't even think of a god when something puzzles us. We just think "wow, some nice problem to figure out!" Some of the problems might have been solved (like our common ancestry with many other life forms, if not all). Some haven't (like whether it's with all of them, or not, or how exactly did life originate in our little planet). That there's open questions, to us, means that there's open questions. You think that open questions means that your god did it. We don't even imagine gods there because no convincing evidence for gods can be found out there (but quite convincing evidence that we imagine gods out of ignorance and indoctrination). Chicken/egg dilemmas might sound convincing for you ("God" did it!), but for us they're either no brainers (the egg, of course, by millions and millions of years), or just open questions.

      Now, to approach your chicken/egg-like problems, you have to think about them more carefully. Not just imagine that they must be unsolvable. How hard is it for you to think that maybe a situation that looks chicken/egg-like today, wasn't chicken/egg-like eons ago?

      If you were a bit more serious, instead of imagining that you're presenting us with problems that will turn us into idiots like yourself, you might notice that your questions are far from getting anybody on their knees. Before ridiculing yourself again, I suggest you to imagine how we think. We think of actual problems as things to figure out, not as rhetorical bullshit. To do that, to figure out solutions to those problems, you have to think about whether all those assumptions you put on top are real. For example, you see to think that only proteins can catalyze reactions (enzymes are proteins that catalyze reactions), and that somehow they do so by magic. Yet, what they do is quite a natural phenomenon (no magic involved), and other molecules, biological and non-biological, can catalyze reactions. Not only that some molecules can both carry genetic information (like DNA) and also catalyze reactions (like enzymes). So maybe when things started there was no DNA that required enzymes that required DNA, and the current chicken/egg-dna/enzyme situation is not the way things started. Anyway, what I'm saying is that there's avenues towards understanding how those chicken/egg-like situations evolved. I'm also saying that thinking of gods because of open questions is just lame.

      You're welcome!

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    28. The first thing that Eric, Velhovsky, and their ilk should realize about evolution (especially "Darwinism") is that it is not simply a random process. Random variation, then sorting out and keeping the best (in the situation), then random variation, then sorting, then random variation . . . . and so on. The sorting is critical to evolution, whether the natural kind or human applications like the evolution of an antenna or computer program.

      Thinking about random variation AND sorting involves thinking about two complementary things at once. Perhaps these particular thinkers should be congratulated for mastering even one, but it's really impossible to hold a meaningful discussion about evolution with people who don't get that evolution of adaptations involves both processes.

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    29. Supposed paradox: "DNA is essential to make enzymes, but enzymes can't be made without DNA."

      No paradox. Amino acids and nucleotides can form by natural processes. They can link together for form short proteins and RNA, respectively. RNA can catalyze it's own reproduction and can catalyze the production of proteins. Even unselected proteins can influence (catalyze) other chemical reactions. (DNA came later.)

      Delete
    30. Supposed paradox: "a cell membrane can’t be made without DNA and proteins and DNA can only be made by a cell."

      No paradox. Cell membranes are essentially phosopholipid bubbles, enhanced by stabilizing compounds. Phosopholipids can by made by natural processes. When agitated in water (e.g. by waves) they form bubbles. They coat rocks and sand, too, and form little bubbles or compartments there. The simplest phospholipid bubbles are leaky but they do tend to concentrate organic compounds. DNA and proteins aren't needed to form these simple bubbles that can be primitive cell membranes.

      Delete
    31. Ah, Velhovsky....

      How is there rain if you need bodies of water to evaporate, but you don't get bodies of water unless there's rain?

      See, every cyclical phenomenon looks like an impossible puzzle if you're sufficiently ignorant.

      Delete
  6. One thing I don't understand about the IDiots' obsession with epigenetics. Even if it worked as they believe it does, how does that help the ID creationist agenda? It still doesn't demonstrate any room for an intelligent designer, but simply provides an alternative model thru which descent with modification can occur thru purely naturalistic means. Am I missing something?

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    1. I think this is just an example of "The enemy of my enemy is my friend." If epigenetics disproves "Darwinism" then epigenetics is to be embraced.

      Of course epigenetics doesn't disprove evolution, but that's another issue.

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    2. Darwin's Doubt has a chapter on this. But I don't think it answers your question. Basically, Meyer assumes that epigenetic pathways are too complicated to have evolved, therefore Jesus.

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    3. Of course, the old complexity = design canard.

      You know, I wonder how creationists would have responded if it was found that cells were nothing but empty bags of protoplasm, with no elaborate structures and chemicals to explain how they function. Would they take it as evidence there was no god? It seems to me that would the sort of thing to require a supernatural explanation. Did any early biologists expect that, at the microscopic level, organisms would be simple? Why would they?

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    4. Exactly ! An organism moving around, but with no moving parts, now THAT would be magic. And a finely tuned universe with NO TUNE-ABLE PARAMETERS .... THAT would be BIG magic.

      Delete
    5. I don't get what is so complicated about methylation? Obviously multicellular organisms need a way to silence certain genes and activate others depending on the cells environment.

      All epigenetics tells us is that sometimes the effects of this can be inherited and can last a couple of generations. This isn't rocket science. Or am I simplifying things a little too much?

      Delete
    6. One reason a design person might like epigenetics.
      With epigenetics we get that the information coded in the DNA will be implemented differently depending on the environment the organism lives in.
      If the organism were the result of an intelligent design, then a salesman would point to that feature as part of the brilliance of the design.
      If one is looking for reasons to believe the system is designed, that might be seen as a good feature.

      Delete
    7. By that line of reasoning, beneficial mutations would also be an example of "good design". Yet the creationists often insist these do not exist.

      Delete
    8. lutesuite-
      After seeing your reply I read something called ‘the myth of beneficial mutations’. I won’t link to it.
      How bizarre.
      I guess a beneficial mutation isn’t mentioned in the bible, so one can’t happen.
      I have no idea how to argue with that line of reasoning.

      I was thinking along the lines of how some plants can respond when some insects attack by producing nasty tasting chemicals. The plants produce the chemicals when attacked and stop when the attack is over. It seems like this would be a good feature in a GMO.
      I think epigenetic controls could be very useful for producing that sort of behavior in plants.

      Delete
    9. Can you name a couple of the chemicals plants produce to defend against insect predators (there are quite a few well known ones). What do most of them have in common? Why might this be an issue with plants used for food? And what other possible application for GMOs does this open up?

      Delete
    10. Can you name a couple of the chemicals plants produce to defend against insect predators (there are quite a few well known ones). What do most of them have in common?

      That they will shortly be patented by Monsanto? ;-)

      Delete
    11. I'm not sure they aren't already. IIRC they had a patent for β-Carotene in carrots granted to them in the initial dump, because we repeated the mistakes for software patents.
      But I'm sure anybody could easily name 5 and if you polled people for chemicals produced by plants more than half the answers would be defenses against insect predators. I could amend my list of questions with "what is the (adaptionist) explanation", because in this case there is one.

      Delete
    12. With regard to the "myth" of beneficial mutations, the following line of reasoning seems relevant: Imagine a sequence that is functional. Presumably creationists admit that it is possible for a mutation to arise that makes it less functional, say replacing an A by a G at site 139.

      Now imagine that nonfunctional sequence. Is there some cosmic principle that there cannot be a mutation of a G to an A at site 139 ?

      Waiting to hear what that principle is. Something about entropy or information theory, I suppose.

      Delete
    13. Simon-
      I don’t know much. What are the chemicals and what do they have in common?
      My ideas about GMO traits are probably fanciful and wildly off topic.
      At this point I’m thinking the ‘complexity = design’ explains the creationist liking of epigenetics.
      How about you?

      Delete
    14. Well, I think you could have gotten some by guessing. A (by no means exhaustive) list would be: Caffeine, Cocaine, Nicotine, THC, Strychnine, Morphine.
      What they have in common is that they interact with the nervous system of animals and the explanation for this commonality is that plants of course don't have a nervous system and thus enriching their tissues with something that messes with particular pathways in nerve cells doesn't affect the plants function. In general you don't want your foodstuff to contain a lot of psychoactive chemicals - the ancient Egyptians started breeding lettuce to have lower levels of Lactucin for instance. This of course produces some issues for lettuce farmers, who have a lot of problems with pests (both insects and molluscs), but on the upside your average modern lettuce isn't addictive.
      The defenses against insects of other plants are potentially interesting for medical purposes, there's a fair chance that we will find better anesthetics, muscle relaxants, anti-depressants, etc. among them and we might want to use GMO bacteria to produce these in a bioreactor rather than try to farm some plants that may be hard to cultivate.
      It's worth noting that there are currently GMO strains on the market that use Bt toxins, which were derived from a bacterium and do affect insects only (and not through a nervous system). But there are some companies that have announced wanting to use plant defenses and it seems like a really bad idea...
      I think they mainly like that it came with some rather overblown press releases. The same reason they jumped on encode, or on the web of life stuff. If there's something that at least looks like it is a big deal, they want in on it and they usually do it with a "told you so". It's not as if creationists had made any predictions about how much of the genome should be functional before encode, but as soon as that pressrelease hit they had been saying that for years. And when epigenetics made big waves they of course had been saying that for years as well. I don't know what they will latch on next and if you asked them they couldn't tell you. But when it happens, rest assured that they will have been retroactively been talking about nothing else for a decade.

      Delete
    15. Joe Felsenstein:

      With regard to the "myth" of beneficial mutations, the following line of reasoning seems relevant: Imagine a sequence that is functional. Presumably creationists admit that it is possible for a mutation to arise that makes it less functional, say replacing an A by a G at site 139.

      Now imagine that nonfunctional sequence. Is there some cosmic principle that there cannot be a mutation of a G to an A at site 139 ?

      Waiting to hear what that principle is. Something about entropy or information theory, I suppose.

      ------------------------------

      Whilst not a 'cosmic principle' there is Dollo's Law. Not to mention Gould's replaying of the tape.

      If a random mutation occurs twice in the same place, that might suggest design. But I don't think that's your point.

      Instead it seems like you are equating a functional sequence that gets broken, with a non-functional sequence that via some random mutation happened to be functional through good luck. However, the two things are not equal. There are plenty of examples of the former. Very few of the later.

      Waiting to hear why you think that might be. Fortune favours the non-functional I suppose.

      Delete
    16. I don't think you understood Joe's point, BC. He's not proposing an example in which A is replaced by G and then, at a later time, reverts to A. I believe he is saying that, according to the claim that beneficial mutations cannot occur, if an organism started with G and then this was replaced with A, that could happen. But if it started with A, that could never be replaced with G. The creationists need to provide a mechanism that prevents the latter from happening. What is it?

      Delete
    17. Hey, the myth of beneficial mutations? Lessee ... (Google, Google)

      An ape could, theoretically, mutate into a man by changing just one percent of his DNA. While the claim of a one percent DNA difference between man and ape is controversial and highly debatable, one might conclude, if we assume the claim to be true, that evolutionists have a point. One must remember, though, that all mutations have to be in exactly the same order as a human person’s genome. It is estimated that one million mutations are required for every one percent difference. Moreover, all the mutations must occur exactly where the two genomes differ.

      So stick that in your pipes, evolutionists!

      Delete
    18. Moreover, all the mutations must occur exactly where the two genomes differ.

      Because if they happened somewhere else, um, the genomes would still be different, but a different sort of different.

      Honestly, creationists are beyond parody. Nothing you could make up would be stupider than the stuff they write themselves.

      Delete
    19. (BTW, could you provide a source for that quote, Allan?)

      Delete
    20. lutesuite,

      If that really is Joe's point then he's hacking away at a straw-man.

      Most creationists accept that beneficial mutations occur, but argue that harmful mutations are far more likely. And that position is supported by the evidence.

      Delete
    21. But some creationists do argue that beneficial mutations cannot occur (without God's intervention), and Joe is arguing against that specific claim. An example of a creationist institute making just that claim (which seems to be the source that Allan Miller was quoting):

      http://www.creationstudies.org/operationsalt/myth-beneficial-mutations.html

      Anyway, yes: Harmful mutations are more frequent than beneficial ones (and neutral mutations far more common than either). So what's your point?

      Delete
    22. @lutesuite - sorry, yes, that was indeed my source.

      Delete
    23. lutesuite: The creationists need to provide a mechanism that prevents the latter from happening. What is it?

      That's exactly my argument. Their mechanism will turn out to be either some terribly sophisticated argument from information theory and thermodynamics. Or else something about a Logos Gospel saying something about who originates information. Either way, it's got to stop that G from mutating into an A.

      Delete
    24. I realize I'm taking the creationist arguments way more seriously than they deserve, but I notice the CSI article argues that things like antibiotic resistance in bacteria represent a "loss of function" and therefore do not actually qualify as a beneficial mutations. IIRC, Behe made much the same claim when dismissing Lenski's LTEE study. But it seems to me this actually offers a solution to the question that has long vexed Behe, of how detrimental mutations can persist in the population long enough to combine with other mutations to produce a beneficial trait. It demonstrates that "loss of function" mutations can actually be favoured by natural selection in certain environments. How odd that Behe did not notice this himself.

      Delete
  7. Meanwhile, the creationist think tank The Biologic Intitute has just published a new "study" in its homegrown "journal" Bio-Complexity:

    http://www.donotlink.com/htdp

    As is usual for this "journal", the paper was written by members of its editorial board, Doug Axe and Ann Gauger, both of whom will be well known to Sandwalk regulars. It actually appears that Axe has learned from the criticism received by his previous attempt to prove the evolution of functional proteins was impossible, where he essentially argued "If evolution is true, why don't humans give birth to chimpanzees?" So this time he tried something different. However, he and Gauger still have a lot to learn about evolutionary biology. Can anyone see the error they make this time?

    ReplyDelete
    Replies
    1. Perhaps they read the blurb for Wagner's "Arrival of the Fittest" and thought it was a good idea to point out that selection doesn't cause useful mutations.

      Delete
    2. It would seem that all of Doug Axe's work is based on the premise that if a mouse doesn't evolve into a squirrel in the course of a few generations, evolution is rong.

      Delete
    3. By my reading, they are presuming that if Enzyme Y is a modern enzyme with a specific function that evolved from a more promiscuous ancestral protein called Enzyme X, and if you recreated Enzyme X and let it evolve, you should always end up with Enzyme Y again. But they have forgotten about historical contingency. Enzyme X might well evolve, but to produce Enzyme Q,R,S,T or anything else, not necessarily Y.

      In effect they are performing Gould's thought experiment of rewinding the tape of life, but they are assuming that when you replay the tape it always produces the same result. Lenski's experiments have already shown that is not the case.

      Make sense?

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    4. @lutesuite

      That thought did occur to me

      Is it not also a major problem that their fitness function only has one peak? With each new generation, they are only evaluating the fitness of the sequences against a single function whereas in reality there may be other ways that intermediate sequences could interact with things, other local peaks could serve as stepping stones in the ascent of mount improbable.

      Delete
    5. That's how it appears to me. So, in their computer simulation, they pick one particular Chinese character and are unable to reproduce this thru natural selection. However, if they selected their mutants on how closely resembled any Chinese character, not just the one they arbitrarily picked, they'd probably have ended up with a very different result, and not the one they wanted.

      Delete
    6. They seem to assume functions are determined in advance and evolution has to reach fixed, highly specific targets, or else it will fail as "proficient design". A solution will fail not if the organism can't survive and reproduce, but if it doesn't do exactly what Axe & Gauger want it to do.

      Delete
    7. Yes. Which, it strikes me, is actually evidence against design. A designer operates with a specific objective in mind and then tries to realize the means to achieve this. Axe and Gauger have added to the evidence that nature does not operate in this manner. I somehow suspect that is not what they intended to do.

      Delete
    8. sez lutesuite @ Wednesday, January 13, 2016 8:45:00 AMP:
      "A designer operates with a specific objective in mind and then tries to realize the means to achieve this. Axe and Gauger have added to the evidence that nature does not operate in this manner. I somehow suspect that is not what they intended to do."
      Not the first time Gauger has friendly-fired a bullet into ID's foot. As was noted at the Panda's Thumb:

      [Gauger] was then prompted by one of her colleagues to regale us with some new experimental finds. She gave what amounted to a second presentation, during which she discussed “leaky growth,” in microbial colonies at high densities, leading to horizontal transfer of genetic information, and announced that under such conditions she had actually found a novel variant that seemed to lead to enhanced colony growth. Gunther Wagner said, “So, a beneficial mutation happened right in your lab?” at which point the moderator halted questioning. We shuffled off for a coffee break with the admission hanging in the air that natural processes could not only produce new information, they could produce beneficial new information.

      Delete
    9. Yes, she shall forever be a legend for that. That, and the green screen.

      Delete
    10. A solution will fail not if the organism can't survive and reproduce, but if it doesn't do exactly what Axe & Gauger want it to do.

      This is of course what I like to call the "lottery fallacy." It's used by virtually every ID proponent to produce erroneously inflated probabilities against evolution.

      Lottery fallacy: The odds against any *particular individual* winning the PowerBall lottery are ~175 million to 1. But there were three winners just last night. That's because *someone* winning the PowerBall is not an especially rare occurrence. It happens every few weeks throughout the year.

      In exactly the same way, Axe, Gauger, Behe, and the rest of the ID folks always base their math on the chances that a *particular* neutral or beneficial mutation will occur, and just as with the lottery, the chances of a *particular* outcome are utterly minuscule. The occurrence of *some* neutral or beneficial mutation, however, is, as with the lottery, so relatively common as to be completely unremarkable.

      To summarize: ID proponents misuse probability math to make the common appear impossible.

      Delete
    11. judmarc and lutesuite (and others) are correct about how IDiots calculate probabilities. They calculate the probability that a very specific, pre-ordained, event will happen as if it were the only "design" possible. Instead, they should be calculating the probability that SOMETHING will happen including pathways that lead to the same result by a combination of different mutations.

      That's the mistake that Behe makes all the time (e.g. "The Edge of Evolution") and it's the same error that characterizes all the calculations by Axe & Gauger.

      I like the term "lottery fallacy" and I'm going to steal it from judmarc.

      Delete
    12. I like the term "lottery fallacy" and I'm going to steal it from judmarc.

      You can't steal what's freely given. :-)

      Delete
  8. I can't say whether the story about an adoptive mother taunted by a rebellious teenager represents mainstream Intelligent Design Creationism or not. But since there is some truth behind epigenetic changes later having influence at the genetic level I would be interested in knowing how it later turned out between them, whether that helped or not.

    ReplyDelete
  9. How in the hell did unintelligent processes manage the symbiosis boys? They make one cell to swallow another, the swallower cell decides not to digest it-it must be an act of kindness or something- or it must be in good faith of all humanity and Darwinian evolution, because the swallower can't survive without its digestive system???

    This is not all. They (the unintelligent processes) hide some genes needed for the evolution of prokaryotic cells to eukaryiotic. There are some genes that are "ghost genes" and there is no evidence where they came from, why and so on but my guess is as good as yours.

    ReplyDelete
    Replies
    1. No, that isn't the scenario. Hint: the closest relatives of mitochondria are Rickettsiae. Talking about cellular endoparasites.

      Delete
    2. Velhovsky,

      There you go again. Didn't you learn anything yet? Your rhetorical scenarios are nothing but rhetorical scenarios. Think before ridiculing yourself and your beliefs so badly.

      Endosymbiosis was a proposal based on evidence that suggested that mitochondria look like "eroded" bacteria. Lots of mitochondria and bacteria examined later confirmed the hypothesis. more was found that convinced people that endosymbiosis is how mitochondria evolved. We start that way. We don't start by pretending to know every mechanism by which one cell "swallowed" another. We start by noticing that something makes sense given the evidence. We worry about how, of course, but the evidence cannot be denied just because some idiot (aka Velhovsky), posits the "question" within a rhetorical ridiculing scenario.

      So, instead of loading the field with rhetoric we keep investigating, we find more evidence of endosymbiosis, we actually find, for example, organisms where endosymbiosis is happening now! Yes. there's organisms harbouring endosymbionts that can be isolated and grown apart from the host. What I'm saying is that we examine the issue and look for more information. We don't just stop and say "this might be so hard that we rather say that the gods did it."

      Anyway, endoparasites are part of the story (as John said above). But don't get me wrong. We don't know the whole thing, the whole answer is still to be found. But the evidence that mitochondria evolved as endosymbionts is so strong that it takes ignorance to deny it. Take home message: rhetorically ridiculing a hypothesis or a theory doesn't make the evidence disappear. It does, however, make you look like an ignorant fool.

      You're welcome.

      Delete
    3. Velhovsky,
      Asking questions is all right. Without questions there would be no science to talk about. However, asking questions pretending that evolution is false because there might not be an answer is plain stupidity. Lack of answers means lack of answers.

      Delete
    4. How in the hell did unintelligent processes manage the symbiosis boys?

      Your question betrays your inability to divorce yourself from the notions of intent and design. There is no managing and no management. Either some given event can occur in this universe, and eventually it probably will somewhere, or some given event can't happen in this universe, and it therefore never will.

      If endosymbiosis was something that could not occur in this universe, then no human would be here now, nor suffer in the slightest from that alternative reality. But you can't imagine that possibility.

      Furthermore, as others have mentioned, you seem to be unaware that endosymbiosis happens all the time. Not just in some distant past, but right now.

      Delete
  10. Aha! "Noted Nobel nominated evolutionist admits the theory has no anwers!"

    ;-}

    ReplyDelete
  11. Denyse has thrown down the gauntlet for Larry and Joe F. to pick up. This should be fun.

    http://www.uncommondescent.com/intelligent-design/academic-cover-up-can-neutral-evolutionary-processes-rapidly-generate-complex-adaptations/

    ReplyDelete
    Replies
    1. OMG! That post is a laugh riot! Just one excerpt of Torley's inadvertent comedy fest:

      I emailed Lynch a couple of months ago, inviting him to comment on Axe’s paper. To my surprise, he said he hadn’t seen it before.

      BWA HA HA HA HA HA! "To my surprise". Stop it, VJ, your killing me!

      Delete
    2. I'm taken aback to learn that Michael Lynch isn't a regular and dedicated reader of BIO-Complexity, that peer-reviewed scientific journal with a unique goal. For shame!

      Delete
    3. Since all the professional scientists are too busy doing science stuff to provide Doug Axe the peer- review that he is unable to provide himself (what with being the editor of the journal in which he publishes almost all his "research"), maybe an enthusiastic amateur like myself can give it a try.

      All of this with the caveat that I don't pretend to be able to fully understand Lynch and Abegg's paper, with the math in particular going over my head. So I'm just going to take Axe's professed understanding of that paper, as summarized in VJ Torley's blog post, at face value and see how his argument holds up on its own terms.

      First of all, Axe summarizes Lynch's argument, in part, as follows:

      Lynch and Abegg calculate the mean waiting time for arrival of an allele carrying a particular complex adaptation that is destined to be fixed within a diploid population as (1):

      w_seq = [d.u]^(-1) + [(d-1).u]^(-1) + [(d-2).u]^(-1) + … + [2u]^(-1) + [2u. N_e. phi_2]^(-1), (2)

      where d is the number of specific base substitutions needed to produce the complex adaptation, N_e is the effective population size (2), u is the mean rate of specific base substitution (per site per gamete), and phi_2 is the probability that an instance of producing the adaptive allele will result in fixation (given by Equation 1 of reference 6).


      (Incidentally, that exact equation, as written, appears nowhere in Lynch and Abegg's paper. It is supposed to be an equivalent of equation 5a, and I am assuming it is, but it would probably be important for someone to confirm this is actually the case).

      Axe then claims the following:

      (I)f the implications of this equation are as implausible as has been argued (by Axe), then there must be a mistake in the calculation.

      This indeed appears to be the case. Specifically, of all the possible evolutionary paths a population can take, the analysis of Lynch and Abegg considers only those special paths that lead directly to the desired end—the complex adaptation. This is best illustrated with an example. Suppose a population carries an allele that confers no selective benefit in its current state (e.g., a pseudogene or a gene duplicate) but which would confer a benefit if it were to acquire five specific nucleotide changes relative to that initial state, which we will again refer to as stage 0. Lynch and Abegg assign a waiting time of (5u)^(-1) for a stage-1 allele to become fixed in this situation, which is valid only if we can safely assume that the population remains at stage 0 during this wait.

      But this cannot be assumed. A stage-0 allele of kilobase length, for example, would have about 200-fold more correct bases than incorrect ones (with respect to the complex adaptation), which means the rate of degradation (i.e., fixation of changes that make the complex adaptation more remote) would be about 600-fold higher(3) than the rate of progression to stage 1. It is therefore very unlikely in such a case that the population will wait at stage 0 long enough to reach stage 1, and the situation becomes progressively worse as we consider higher stages.


      But wait a minute. It seems to me that Lynch did take this into account. Recall Axe's description of the last element in the Lynch's equation: "phi_2 is the probability that an instance of producing the adaptive allele will result in fixation." That's just what Axe is describing in his criticism. There is a given probability that an allele will go to fixation, and a converse probability that the allele will be lost from the population due, in part, to the possibilities that Axe describes. The equation includes this as a factor. Axe just didn't realize this.

      That would be a really dumb error. But no dumber than the errors Axe has made in all the other articles he has published in Bio-Complexity,

      Does anyone else come to the same conclusion as I do?

      Delete
    4. "I can't stop laughing at this"

      Can you imagine what kind of laugh my 10 year old had when I told them that the science of OOL promotes the idea that the vents did the job for ID. I have a video. Wanna see?

      Delete
    5. On further thought, Axe's error may be even more basic than that. It seems to be the same one he often makes, of confusing the odds of a specific trait evolving with those of any trait evolving. Lynch is not interested in demonstrating that evolution can actually occur. That job was completed long, long ago, no matter how much the creationists refuse to admit this. His paper is concerned, rather, with investigating whether particular models of population genetics can elucidate the particular process by which adaptive traits arise. And the criteria by which he evaluates this is whether the model being tested is consistent with a trait arising over time scales and within population sizes that this has been observed to occur.

      Axe's objections, then, are nothing but red herrings. If the particular set of mutations required for a particular trait did not arise, then some other set of mutations and another trait would have, instead. All that matters, for the present purposes, is the number of mutations and degree of selection these undergo, which are used as parameters for putative models.

      My take, FWIW (Probably not much).

      Delete
    6. @Lutesuite

      Are you reading the "paper" called Model and Laboratory Demonstrations That Evolutionary Optimization Works Well Only If Preceded by Invention—Selection Itself Is Not Inventive?

      If the title is also the conclusion, the paper is so utterly idiotic and a waste of space it beggars belief. Who the fuck ever thought that selection was itself generating variation?

      Delete
    7. That's the one I discuss in another post, up above:

      http://sandwalk.blogspot.ca/2016/01/intelligent-design-creationists-are.html?showComment=1452260274752#c4093738733364733177

      Maybe BIO-Complexity should hire me as a reviewer. Whoever they have doing that for them now is not doing a very good job.

      Delete
    8. Wanna see?

      Sure Eric, right after you provide that slam-dunk proof Coyne is wrong that you said you had.

      Delete
    9. Eric says,

      Can you imagine what kind of laugh my 10 year old had when I told them that the science of OOL promotes the idea that the vents did the job for ID. I have a video. Wanna see?

      I don't want to see the video of your ten year old child laughing at science. It would make me very sad.

      Delete
    10. Sooo much stupid in that Uncommon Descent thread! And me, being banned, I can't do anything about it. My SIWOTI syndrome is kicking in so hard, I fear I might have a seizure or something.

      Here's one example from our own Bill Cole:

      Dr Moran posted Lynch’s 2005 response to Behe and Snoke recently. This model was fixed with 2 adaptive mutations where the Behe Snoke model was variable. (ed: Sorry, what?) The 2005 paper claimed that 2 adaptive mutations could be achieved with 10^8 generations and 10^6 population sizes. Since multicellular evolution especially vertebrate would seem to require thousands of adaptive mutations I am struggling to see how these models do anything but make neutral theory very unlikely. Lynch’s 2010 model appears to improve the numbers but doesnot not seem to even scratch the surface of the number of mutations required for a new specie to evolve.

      Gaaah! Does the think there are variable alleles at only one locus of a population's genome at any time, and every member of a species are otherwise identical clones?

      Delete
    11. Gaaah! Does the think there are variable alleles at only one locus of a population's genome at any time, and every member of a species are otherwise identical clones?

      For the purpose of his rhetoric he surely does. As every creationist. They also assume that only very particular sequences can be functional, and only very particular mutations can be beneficial. When you explain the contrary, and ask them to see around them and note if everybody is a clone, or if they have considered that mutations in many different alleles, might confer a benefit, or if they have considered that each protein doesn't evolve from scratch each time, but rather diverge from ancestral forms, they will refuse to answer (os deform your questions, or pretend that they are red-herrings). Maybe they truly don't understand their own assumptions.

      Delete
    12. It would make me very sad.

      It will make Eric very sad in a few decades when his child couldn't get a decent job due to lack of a good science education in a technological world, and that child's income determines what nursing home Eric winds up living in.

      Delete
    13. "Who the fuck ever thought that selection was itself generating variation?"

      I would answer that with a quote from the Wikipedia entry on Ribosome, in the section on origin:

      "Thus, the driving force for the evolution of the ribosome from an ancient self-replicating machine into its current form as a translational machine may have been the selective pressure to incorporate proteins into the ribosome’s self-replicating mechanisms, so as to increase its capacity for self-replication"

      You could call statements like this several things; canned evolutionary double-talk, appeal to imaginary influence, or just so much horse shit.

      Delete
    14. txpiper, that's an example of bad writing on evolution, but the error isn't the one we were speaking of.

      The passage you quote says absolutely nothing at all about selection generating variation. As we all(?) know, selection acts to *reduce* variation. So when the quoted passage talks about selective pressure generating a particular result, it simply means that single variation was selected from among many - i.e., selection acted to reduce variation, just as we(?) understand.

      The bad writing IMO is the bit about "so as to increase its capacity for self-replication." That's way too close to the obviously incorrect (at least to most of us) view that evolution has a purpose or direction.

      Delete
    15. judmarc,

      The problems with the storyline are much more profound than just the semantics about selection. The same article includes these statements:

      "The ribosome is a complex molecular machine found within all living cells, that serves as the site of biological protein synthesis (translation)."

      "In eukaryotes, the process takes place both in the cell cytoplasm and in the nucleolus, which is a region within the cell nucleus. The assembly process involves the coordinated function of over 200 proteins in the synthesis and processing of the four rRNAs, as well as assembly of those rRNAs with the ribosomal proteins."

      This is a chicken/egg problem the size of a galaxy, and one unrelated to mutations or natural selection.

      Delete
    16. It's OK, txpiper. Just because something is too complicated for your feeble little creationist mind to grasp, doesn't mean it's an unfathomable mystery that can only be solved by appealing to the existence of deities. History is replete with similar questions, the answers to which are now commonplaces.

      Delete
    17. You have faith that far exceeds mine, lutesuite. I think you're gonna have to come to terms with the feebleness of proposed evolutionary mechanisms. You could start by noticing what DNA replication errors actually do, as opposed to what the rules of materialism demand that they do. I'll give you a hint: They screw things up.

      What would you use as an example of a problem of similar scope that was solved? I see this one as being up there with arriving at a complete collection of homochiral amino acids coming from deep sea vents and/or meteorites.

      Delete
    18. What would you use as an example of a problem of similar scope that was solved?

      "What happens to the sun at night?" is the first one that comes to mind.

      Delete
    19. Anyway, it would appear you think that all the proteins involved in RNA processing had to come into existence at once. That's very funny.

      Delete
    20. " "What happens to the sun at night?" is the first one that comes to mind."

      Not quite similar in scope, but I can appreciate your dilemma in finding something that is.

      "you think that all the proteins involved in RNA processing had to come into existence at once"

      And you think they, along with the mechanisms that regulate them, are miraculous, accidental assemblies that just happen to have a specific biological purpose. That's not funny at all.

      Delete
    21. The IDiots at Uncommon Descent are now complaining about "censorship" because journals and websites don't immediately acquiesce to their demands when they want something printed. I'd like to explain to them that editorial oversight is not censorship, but I can't. Because I've been banned from their website.

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    22. Not quite similar in scope, but I can appreciate your dilemma in finding something that is.

      I don't see how you come to the conclusion that it is not similar in scope. The solution to the question seems quite simple now, but that is only because we know it. The question was highly vexatious and defied human understanding until only very recently, as a result of which theological answers were the only ones considered. If this was such a simple question, why did its answer evade all of those supposed great thinkers that you supernaturalists hold in such high esteem? Plato, Aristotle, Aquinas. None of them had the faintest clue what was happening to the sun at night. Today, that knowledge is possessed by the average primary school child.

      And you think they, along with the mechanisms that regulate them, are miraculous, accidental assemblies that just happen to have a specific biological purpose.

      I do? That's news to me.

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    23. “I don't see how you come to the conclusion that it is not similar in scope.”

      Because it was a mechanical problem, with no chicken/egg complications.

      Ribosome assembly “involves the coordinated function of over 200 proteins in the synthesis and processing of the four rRNAs, as well as assembly of those rRNAs with the ribosomal proteins”. And on the other hand, protein synthesis depends on ribosome. See the problem? You could call it hyper-complex interdependence.

      Mutation and natural selection can’t be the mechanisms behind ribosome origins. It is not phenotypically expressed, so there could not have been any kind of advantage to be “selected for”. The only method available is raw, random, accidents. You’ve been taught to think in terms of simpler antecedents (accidentally) occurring and evolving, but there is not a speck of genuine science to support such a sappy notion. Minimal gene sets necessary for life are a baseline reality, and they are anything but simple.

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    24. Yes, txpiper. We know how desperate you creationists are to find a gap that can only be filled with "Goddidit." Unfortunately, scientists keep filling those gaps:

      Origin and Evolution of the Ribosome

      Not to say that model is necessarily correct, but just to point out that solutions to your "chicken/egg" problem exist. Ignorance and intellectual laziness are not the only options.

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    25. "Although the modern translation machinery is very complex, two small RNAs, the PTC RNA fragment and tRNAs are at its core. Both of these are less than 100 nucleotides in length, and their importance supports the notion that the translation machinery was originally a discovery of the RNA world. In fact, the ability to synthesize coded peptides of increasing complexity would eventually terminate the RNA world and create the RNA/protein world."

      This is really, really stupid. You have to appreciate his use of the word 'discovery'. It would have been unsettling to readers like yourself if he’d said "ridiculously implausible accident”. But it would have been honest.

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    26. "You could call statements like this several things; canned evolutionary double-talk, appeal to imaginary influence, or just so much horse shit."

      I'd just stick to pointing out you've failed to understand what the difference between "driving force" and the entirety of the mechanisms of evolution is. The article you quote does not say that the only thing that produced the ribosome is natural selection.

      So you're just plainly wrong. All your issues go away once you acquire the ability to read.

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    27. "This is really, really stupid. You have to appreciate his use of the word 'discovery'. It would have been unsettling to readers like yourself if he’d said "ridiculously implausible accident”. But it would have been honest."

      How improbable? You seem to be claiming you know the state of the origin of the translation system so much you can assign a probability to it. Then do it and tell us how you know.

      Also, merely having a probability of it is meaningless if you don't have a probability for your suggested alternative. How unlikely is the explanation you would replace evolution with? We need two probabilities to compare so we can pick the highest.

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    28. "The article you quote does not say that the only thing that produced the ribosome is natural selection."

      So what would be the other things?
      ---
      "You seem to be claiming you know the state of the origin of the translation system so much you can assign a probability to it."

      No, I'm claiming that accidental origins for things like ribosome are silly.

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    29. "No, I'm claiming that accidental origins for things like ribosome are silly."

      Well then, that's one powerful argument right there. I hope your beliefs serve you well.

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    30. And the mechanisms that produced ribosome were what? My beliefs are partly based on the fact that you can't name any. You just believe it happened.

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    31. I gave you the reference, txpiper. What's the problem? Too many big words for you?

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    32. No, too many gaps filled up with conjecture. Not the kind of thing you would notice.

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    33. He openly states that his model is speculative. The point, which has sailed a mile over your pointy little head, is that his scenario is entirely plausible and relies on nothing more than chemical processes. No gods needed, and your desperately conceived "chicken and egg" problem is thusly blown up to smithereens. My condolences.

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    34. "He openly states that his model is speculative."

      And so it is a poor reference. There is nothing plausible about his model. I showed you what all it is involved in eukaryotic ribosome synthesis:

      "The assembly process involves the coordinated function of over 200 proteins in the synthesis and processing of the four rRNAs, as well as assembly of those rRNAs with the ribosomal proteins."

      You are trivializing that, and "nothing more than chemical processes" demonstrates the difference between science and religious materialism. The former is characterized by intense curiosity and difficult questions. The latter is satisfied by some idiot saying that “the translation machinery was originally a discovery of the RNA world”. Did you even pause when you read that?

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    35. Well, if you think there is "nothing plausible about his model", kindly demonstrate the exact step or steps you believe are inconsistent with what is known about how chemical process operate. Then go publish your finding in a peer-reviewed journal, as this would be valuable information to people working on OOL issues.

      Time to put up or shut up, txpiper. "It's too complicated to have happened" is not a valid scientific argument. You need specifics. Let's hear them.

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    36. This is a chicken/egg problem the size of a galaxy

      And how do galaxies come about, txpiper? These days in the universe you need stars to make galaxies and galaxies to make stars. So God had to invent galaxies? Again, it's an example just like your views on the origin and evolution of life: if you are sufficiently ignorant it all looks like an impossible chicken and egg problem. If you are sufficiently familiar with the science, on the other hand, the surprising thing would have been if life and galaxies had *not* happened. The chemistry that gives rise to life is so common and prosaic that the building blocks of proteins are found in space rocks.

      One recent example of an artificial difficulty created by your lack of knowledge is your statement that there could have been no selection without phenotypic differences. This would be news to my friend who worked on the "Star Wars" anti-missile program (and who last year won the armed services' award for best engineering project), where the aiming algorithm, which worked better than anything directly designed by humans, was "evolved" through a mutation and selection process. Please show me the phenotype of an aiming algorithm.

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    37. “kindly demonstrate the exact step or steps you believe are inconsistent with what is known about how chemical process operate”

      Despite the title of the piece, I don’t recall any exact steps being mentioned. Nor do I recall any proposals for a mechanism to initiate orderly chemical processes. But you seem convinced, so perhaps I overlooked these things. Can you copy and paste the steps, and what caused the reactions to occur?

      “ "It's too complicated to have happened" is not a valid scientific argument. You need specifics.”

      I do? I believe I’m pointing out that you’ve accepted ideas with no specifics at all, and now you want me to critique something you haven’t provided. Fox’s email address is provided in the paper. Why don’t you ask him about some of the exact steps you are curious about?

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    38. judmarc,

      “if you are sufficiently ignorant it all looks like an impossible chicken and egg problem.”

      No, it doesn’t just look like that. It is like that. All proteins are synthesized by ribosomes, and lots of proteins are necessary to synthesize ribosome. There is no place to hide from this. If ignorance is involved, it is just the ability to willfully ignore the problem.


      “the aiming algorithm, which worked better than anything directly designed by humans, was "evolved" through a mutation and selection process.”

      Well, algorithms are instructions and procedures which are directly designed by humans. Your friend was not standing with his hands in his pockets watching an algorithm occur. He was using deliberation and intent, and was trying to achieve a desired result. There is no kind of equivalency between what he was doing and the accidental formation of hyper-complex molecular machines.

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  12. And if Axe had sound reason to point at a flaw in the math, why didn't he submit the response in the same journal that the original article appeared? Instead of in the "journal" that he is the Managing Editor of.

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    1. Exactly, why not submit to a serious journal? Did he think he was so wrong that no serious journal would accept the article?

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  13. lutesuite,

    "they are presuming that if Enzyme Y is a modern enzyme with a specific function that evolved from a more promiscuous ancestral protein called Enzyme X, and if you recreated Enzyme X and let it evolve"

    What do you mean by 'more promiscuous'?

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    Replies
    1. @ txpiper:

      See this:

      http://sandwalk.blogspot.ca/2012/07/the-evolution-of-enzymes-from.html

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