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Is Evolution Biased?

PLoS Biology has an article out today entitled: “Hotspots of Biased Nucleotide Substitutions in Human Genes”. I’ve mentioned this ‘biased’ substitution pattern before. What the authors see, they tell us, is a definite W->S substitution pattern in human genes (Weak to Strong = A:T->C:G) against an overall pattern of S->W; for the entire human genome. This is part of their summary:

Our findings are consistent with a model of recombination-driven biased gene conversion. This leads to the provocative hypothesis that many of the genetic changes leading to human-specific characters may have been prompted by fixation of deleterious mutations.

What the authors report is a non-random shifting within genes, and the introduction of “deleterious” mutations. Neither of these is consistent with Darwin. Darwin said that if it could be shown that any change in an organism was harmful, then his theory would be overturned.

I’ll let you reach your own conclusions. Here’s the link.

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25 Responses to Is Evolution Biased?

  1. I found this video extremely interesting:

    Mathematically Defining Functional Information In Biology – Kirk Durston

    http://www.godtube.com/view_vi.....afb2a1c58a

  2. Bornagain77,

    I watched the video you linked during my school break and was amazed! If that’s accurate, then it becomes as certain as you can about anything, that life was the result of an intelligent agent!

    Do you know if he applied natural selection to the algorithm? I wasn’t sure after I watched it the first time.

  3. The equation is universal as far as I know, I will load the entire lecture later on today and supply a link here on UD this evening sometime.

    ps.
    though I haven’t pondered the equation that deeply I find that log is utilized is interesting. Also the papers’ site is linked/listed in the description on the video.

  4. “Do you know if he applied natural selection to the algorithm? I wasn’t sure after I watched it the first time.”

    He is assuming no selection. The speaker is assuming that genes are put together at random and then calculates the odds against that happening. The odds of course turn out to be astronomical so he concludes that evolution is impossible. When your conclusion is the same as your assumption you are committing a logical fallacy known as a “tautology.”

  5. Darwin didn’t know anything about genes (because the electron microscope hadn’t been invented yet) so it’s hard for me to see how this paper overthrows Darwin.

  6. Slight edit for above: X-ray diffraction, not electron microscopy, was used to first “see” DNA. Sorry about that.

  7. #5: What about neo-Darwinian theory, that includes the notion of genes, does evolution per NDT advance through the “fixation of deleterious mutations”?

    And is that “fixation” non-random?

    Is that how “evolution” is supposed to happen?
    Should we assume ‘all is well’ in the land of Darwinian theory?

  8. PaV, I’m sorry, but you have your facts all wrong.

    What the authors report is a non-random shifting within genes…

    Neo-Darwinian evolutionary theory only supposes that mutations are ADAPTIVELY random. We have long known that there are mutation ‘hotspots’ and that G-C and A-T pairs are biochemically different, which can lead to biased results during gene conversion.

    …and the introduction of “deleterious” mutations.

    You mean “fixation” of deleterious mutations? Big difference, although both are easily explained.

    First, evolutionary theory readily grants the “introduction” of deleterious mutations. That’s what we mean when we say that mutations are “adaptively neutral”. Deleterious mutations happen.

    Second, the “fixation” of deleterious alleles can occur due to:
    a) genetic drift (but only when the selection coefficient is much less than four times the effective population size)

    b) selection (e.g. while the deleterious allele is in linkage disequilibrium with another beneficial allele that conveys net benefits)

    Darwin said that if it could be shown that any change in an organism was harmful, then his theory would be overturned.

    No. What Darwin said was:

    If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection.

    This is not even anything like what the paper has suggested.

    The paper is completely consistent with the gene-centric view of evolution.

  9. PaV:

    My impression, without extensive knowledge of this particular issue, is that the bias is slight. It’s an issue but not that big a deal. But for the sake of argument let’s say that the bias is actually quite serious. Furthermore let’s assume that life on this planet comes from an intelligent designer. If that’s true then the designer in question is using a medium for transmitting genetic information which is inadequate because it requires constant maintenance to undo the bias. What kind of design is that? Wouldn’t an “intelligent” designer use a more reliable method of carrying genetic info? Perhaps on our wayward planet we were unlucky enough to be stuck with a designer who was not exactly the top of his class.

  10. Sorry, I meant to say “adaptively random”, not “adaptively neutral”.

    And I should have said “when the selection coefficient is much less than the inverse of four times the effective population size”.

  11. OK guys here is part 1 of 2 of the lecture:

    Mathematically Defining Functional Information In Biology – Kirk Durston – Full Lecture – Part 1 of 2

    http://www.godtube.com/view_vi.....361e91801f

  12. OK here Durston’s entire lecture: you can skip to the halfway mark if you have seen part 1 already:

    http://www.seraphmedia.org.uk/ID.xml

    as well he deals with natural selection at about the halfway point;

    as well this following video may be very interesting for you guys:

    Does God Exist? – Part 2 of 3 – Kirk Durston – Argument from Design

    http://www.godtube.com/view_vi.....f41ff42adc

  13. Darwin didn’t know anything about genes (because the electron microscope hadn’t been invented yet)

    Mendel and Morgan et al. didn’t have such equipment either.

  14. There is a long exchange between Kirk Durston and Jeffrey Shallit on Shallit’s website

    http://recursed.blogspot.com/2.....ntist.html

    It’s in the comments section. Search for Kirk and you will find a series of comment between Durston and others.

    Apparently Durston just debated PZ Myers also but it was about religion.

  15. Well, after watching the video, he does appear to assume natural selection. Granted, I don’t fully understand all of it, he does bring up natural selection several times and tells the audience not to worry that he is forgetting natural selection.

    So, it does appear, according to his calculations, that ID is the most likely candidate for life on earth, at this time. In fact, 10^80,000 more likely. :-)

  16. “Wouldn’t an “intelligent” designer use a more reliable method of carrying genetic info? Perhaps on our wayward planet we were unlucky enough to be stuck with a designer who was not exactly the top of his class.”

    New here? From this site, arguments that have been refuted a thousand times. Obviously you did not read this:

    “By pointing out imperfections in living things it is somehow made apparent that there can’t be an intelligent agency behind it. This is really odd as it is basically a religious argument being made against Intelligent Design. The proponent of this argument is making a faith based assertion that God is perfect and hence incapable of bad design. ID makes no claim that the source of complexity is a perfect God incapable of imperfection. Write that down.”

    Vivid

  17. If mutations are effectively “biased” by nature then either mutations are destined to be harmful by nature, or some kind of front-loading may be in effect by allowing only “good” changes to happen.

  18. Jerry, thanks for the link at 11. Kirk Durston was quite impressive.

  19. “ID makes no claim that the source of complexity is a perfect God incapable of imperfection. Write that down.”

    This would not be a matter of merely imperfect design but downright faulty design. Imagine designing and building aircraft that need to be constantly repaired while in flight. The buildup of deleterious mutations would not just be a problem for species evolving but species being able to perpetuate themselves.

  20. B L Harville,

    I believe the explanation toward what your example assumes is well known as genetic entropy. What we perceive as “faulty design” now could have been in much better shape prior to generation upon generation of these deleterious mutations. Somewhat like taking a pristine copy of an original cd and subsequently making copies of that copy, followed by copies of those copies, so on and so forth. Yes, this infers the deleterious mutations add up for an overall negative effect, which if proven would infer that the exact opposite of evolution is actually occuring.

  21. PaulN,

    Based on all the data regarding mutations I think someone would be hard pressed to find any information-gaining mutation. I myself cannot think of a single example. Thus, as far as evidence is concerned, there may be no such thing as an information-gaining mutation. Even if there were, on a very, very rare occasion, a beneficial-information-gaining mutation, it would soon be wiped out by all the near-neutral and deleterious mutations.

    John Sanford, author of Genetic Entropy and the Mystery of the Genome, sites studies that suggest that information-gaining mutations to deleterious/near-neutral mutations ratio is anywhere between 1 in 10,000 or 1 in 1,000,000. I’ve heard these studies may be a bit on the extreme, but even granted that, there’s no way that the positive mutations could overcome the negative.

    Another interesting point that John Sanford makes is: even if there was a potentially beneficial mutation (in the sense that it was a step in the right direction), say in a protein, natural selection can only select at the macro level. So, let’s say, being generous, that in one mutation in an organism a protein mutated 1/3rd towards a better, functional protein. But because it is not all the way complete, it has no immediate benefit and so would be invisible to natural selection. Thus, it could easily be wiped out. Of course, the organism may actually still reproduce, but this still doesn’t promise that the 1/3rd better protein will be passed on.

  22. In addition, the simple fact that cells do have machinery in place to correct mistakes and make repairs autonomously infers a great deal of design in the first place; a level of design that we still have yet to achieve in mechanics and engineering, many people dismiss this fact and take it for granted.

    In fact I do believe it’s been recently discovered that the ribosome actually actively ejects and discards invalid amino acid chains entirely, and at a rate 10,000 times faster than it would if it were a sucessful chain.

  23. This is semi-off topic but it’s something I’ve always wondered….

    Why is it that homo sapian is so far advanced from all other members of the animal kingdom? What were the selective pressures that would allow us to become the intelligent, art-loving, space-traveling philosophical creatures that we are? If the Darwinian mechanisms are so powerful, why haven’t we seen further evidence in more than a century of research?

    I can’t get a straight answer from any Darwinists, so I’m hoping I can get one here. Thanks in advance and long-live I.D.!

  24. Jlewis,

    Obviously all of our advances were a survival advantage (or, if that doesn’t work, a bi-product of a survival advantage). :P

    You know, I’m assuming I could substitute “magic” in for all of neo-Darwinists just-so stories and I’d be just as close to accurate as they are. After all, they can’t go into the past to test their theory, and present-evidence is absolutely no help. But rather suggests genetic entropy (that is, near-neutral mutations and deleterious mutations cause species to go instinct, rather than evolve).

  25. jamirokwhy: [8]

    Neo-Darwinian evolutionary theory only supposes that mutations are ADAPTIVELY random. We have long known that there are mutation ‘hotspots’ and that G-C and A-T pairs are biochemically different, which can lead to biased results during gene conversion.

    You’ve stated that I have my facts all wrong. But what ‘facts’ have I presented, other than those of the authors themselves?

    Isn’t the difference between ID and Darwinism not so much about what the facts are as much as how to interpret those facts?

    You’ve stated that it has been long known that there is a bias in mutations. Well, isn’t that problematic for Neo-Darwinism? It seems like it should be. And to say something is “ADAPTIVELY” random seems to contradict what we normally hear from people like Dawkins who tells us that evolution simply “appears” to be random.

    Isn’t the point of the paper the fact that they found a bias going in one direction for the entire genome while in certain areas the bias was in the opposite direction? To me this indicates that the ‘bias’ is not of a biochemical origin. It would appear, then, that these ‘hotspots’ are themselves non-random. So maybe there’s such a thing as ‘directed’ mutations, which, then presupposes some directing agency, which, to my mind, further erodes confidence in the RM+NS scenario.

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