Intelligent Design

Branko Kozulic responds to Professor Moran, Part II

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I would like to thank Professor Moran for kindly addressing the issues raised in my previous post, “Branko Kozulic responds to Professor Moran”. The answers did help me clarify some points that I was struggling with, in my thinking. In this reply, I am speaking in my own name only. (Note by vjtorley: I have made a few minor corrections to Dr. Kozulic’s English, but the views expressed below are his, not mine. However, since he does not have posting privileges on Uncommon Descent, I have agreed to put up this post at his request, as I’m a firm believer in free speech.)

At the outset, I would like to express my conviction that in matters relating to science, Professor Moran and I probably agree on most things, and not just on findings based strictly on experimental data. For example, I would strongly support his effort to give organic chemistry a prominent role in the teaching of biochemistry. In matters of philosophy, we would probably disagree on some issues; however, this is not at all uncommon, among educated people. But let’s talk about science.

The idea of 100 mutations being fixed in the human population in each generation over a period of 185,000 generations, or 5,000,000 years, has always appeared intuitively unrealistic to me, possibly because I am primarily a practical scientist. My first question was: How many mutations are fixed now, in my generation? I am pretty sure that the answer is zero. Fixation means, we agree, that all individuals in the human population acquire the same mutation in a generation, or, equivalently, that the other allele is completely lost. If so, then the question logically follows: When did this change from 100 to zero fixed mutations per generation take place? Alternatively, is there perhaps something wrong with my initial assumptions?

After wandering around, a solution entered my mind while reading the following sentence in Professor Moran’s reply: “In my calculation, the values of Ne are irrelevant, so any value will work equally well, as long as you realize that you are starting with an ancestral population containing existing variation.” Here, the key phrase is “containing existing variation.” That is the essential assumption. What it means in reality is this: throughout the whole period leading up to the fixation – i.e. in the case we are considering, a population of 10,000 individuals over 40,000 (=4N) generations (which, when multiplied by 20 years/generation, equals 800,000 years) – a group of individuals may split off from the population, but no newcomers are allowed to enter it – that is, the population must remain closed in terms of mating. Here, a newcomer is defined as any individual from a group that had lived separately, say on an adjacent island or across a mountain, for some generations. Whenever a newcomer joins the population, the fixation process is broken, because migrants bring with them new variation that did not exist initially. Migration is a powerful force acting against genetic divergence among sub-populations (Hartl & Clark, Principles of Population Genetics, pp. 295-309).

Herein lies the weak point in Professor Moran’s calculations. Based on our knowledge of human history and behavior, we know that groups of people grow in numbers, split in two and merge, repeatedly. This commonly known fact has to be ruled out, in order to allow for the fixation of 100 mutations per generation. And now we can see that the value of Ne will have a major impact: a large Ne makes it more likely that a newcomer will join the population, and also that a group will split away from it and then re-enter it (in part) later on.

In view of the above, I believe I am entitled to continue rejecting the feasibility of 22,000,000 mutations being fixed in the human population over a period of 5,000,000 years, or 100 mutations each generation. Here it is appropriate to mention a reservation relating to the exact number of fixed differences between the human and chimp genomes that has been expressed by Professor Felsenstein: the actual number might be lower than 22,000,000.

There are two remaining issues, i.e. the pattern of fixation and orphans/singletons found in the sequenced genomes, which have yet to be addressed by Professor Moran. But regardless of whether or not he addresses them in the future, I would like to make it clear that my involvement in the public discussion ends with this post.

11 Replies to “Branko Kozulic responds to Professor Moran, Part II

  1. 1
    scordova says:

    VJ,

    Your intuition is correct for evolution today, whereas Dr. Moran is arguing about another era. And that is part of the complication.

    I don’t believe we are fixing at the rate of 100 mutations today because:

    1. the population is no longer well stirred
    2. it is growing, not in steady state
    3. in extremely large populations, the time to fixation will be prohibitively large and unstirred so geographically isolated populations will probably preclude fixation. You correctly saw that difficulty.

    That is why small inbreeding bottlenecks have been proposed to make Kimura’s formula work! The problem is we are comparing apples to oranges — gigantic unstirred population against tiny well-stirred inbreeding populations. The math idealizations where fixation rate approaches mutation rate work for tiny well-stirred inbreeding populations, they don’t for the population structure of humans today.

    I would bet if we set the stirring parameter in Mendel’s Accountant to “non-stirring” or geographical isolation you’ll see the absence of fixation as your intuition says.

    I have a slightly different but related interest. The ENCODE team has argued the fixation and MAINTENANCE of deeply conserved regions is due to natural selection. I predict these “conserved” aren’t conserved at all and they are getting “unfixed” slowly.

    The reason I cautioned against arguing against Dr. Moran is he can always invoke a teeny tiny population at some point a few hundred thousand years ago. I looked at a pop gen website, and if we’re dealing with 10 individuals, fixation will occur in only about 10 generations, assuming the inbreeding doesn’t kill them!

    There is difficulty extrapolating the behavior of monstrously large unstirred populations with tiny inbreeding populations. That is why the situation may look incongruous to you.

    What I have advocated is looking at all the “unfixing” in deeply conserved regions. In small inbreeding populations, fixing will be rapid and decisive, in gigantic geographically spread out populations, I predict “unfixing” will be more prevalent.

    The problem is, there aren’t enough resources to explore these questions, and the political bias against getting the right answers is suffocating because I expect the right answers are ID friendly.

  2. 2
    Mung says:

    VJY:

    At the outset, I would like to express my conviction that in matters relating to science, Professor Moran and I probably agree on most things, and not just on findings based strictly on experimental data.

    Does this mean you’re an adherent of positivism and/or logical positivism?

    Do you think Prof. Moran is?

    If you are not and he is, how can you agree on so much?

  3. 3
    Mung says:

    oops, forgot that VJT is just passing on something written by someone else. But I guess the question can still stand for VJT.

  4. 4
    vjtorley says:

    Hi Sal,

    Thanks for your comments, but I would just like to point out that the above post in no way reflects my views. I’ve put it up at Dr. Kozulic’s request, as he is not able to put up posts on Uncommon Descent.

    According to the principles of population genetics, as I understand them, the rate of fixation of mutations in the human population is independent of the population size or population growth rate; it depends solely on the mutation rate. Personally, I would say that the degree of mixing (or “stirring”) nowadays is probably greater than in times past, when people traveled less.

    In extremely large populations, the time to fixation will be prohibitively long. However, throughout most of the Paleolithic, the effective human population size is believed to have been about 10,000 – which would mean that the time taken from a mutation’s first appearance in one individual to its fixation in all individuals was 4N = 40,000 generations, or about 1,100,000 years, if we use Professor Moran’s figure of 27.5 years per generation.) I should add that N here refers to the effective population size; the actual size is thought to have been 350,000.) The mutations that are making their first appearance today in the human population will take much, much longer than 1,100,000 years to fix, of course; but at the same time, there will be a lot, lot more of these mutations, so the two effects will cancel out. Overall, the rate of fixation of mutations in the human population should therefore remain the same, at slightly over 100 mutations per generation.

    Before anyone else points it out on this thread, I should like to highlight (without making any further comments) Dr. Kozulic’s definition of fixation: “Fixation means, we agree, that all individuals in the human population acquire the same mutation in a generation, or, equivalently, that the other allele is completely lost.” (The bolding here is mine.)

  5. 5
    vjtorley says:

    Hi Mung,

    In answer to your query: I am certainly not a positivist or logical positivist. See my post, “Why science cannot be the only way of knowing: A reply to Jason Rosenhouse” at http://www.uncommondescent.com.....osenhouse/ . I would presume that Dr. Branko Kozulic is not a logical positivist either. Professor Moran on the other hand believes that science is the only way of knowing, so his position would be pretty close to logical positivism: see http://sandwalk.blogspot.jp/20.....owing.html and Michael Egnor’s comment at http://www.evolutionnews.org/2.....15331.html .

  6. 6
    Mung says:

    Salvador:

    The problem is we are comparing apples to oranges — gigantic unstirred population against tiny well-stirred inbreeding populations. The math idealizations where fixation rate approaches mutation rate work for tiny well-stirred inbreeding populations, they don’t for the population structure of humans today.

    So you disagree with Nick, who says population size doesn’t matter?

    NickMatzke_UD:

    If you actually bothered to get off your lazy butt and think about it for half a second, you would realize that population size cancels out of the process.

    Salvador today:

    I would bet if we set the stirring parameter in Mendel’s Accountant to “non-stirring” or geographical isolation you’ll see the absence of fixation as your intuition says.

    Yet elsewhere you asserted that Mendel’s Accountant validates Nick’s/Moran’s argument. Didn’t you?

    Salvador:

    Dr. Torley,

    I’m sorry I must sympathize with Nick Matzke (puke) and WD400 objections, but I feel some obligation to ask you to at least pause and reconsider.

    The YEC Creationist genetics model, Mendel’s Account agrees to great degree with Larry Moran, Nick Matzke, and WD400.

    Salvador:

    Do I always have to be the one to speak up and be the fall guy to criticize our own side when they say something that other IDists privately disagree with? In this case Mendel’s accountant is more in agreement with Dr. Moran, and that is a publicly available pop gen program prominently featured at the Cornell conference.

    Salvador:

    I’m sorry I didn’t mention Mendel’s accountant enough, but in that post of August 2013, which I believed Dr. Torley read, I thought it was quite evident the Mendel team was is large agreement with Kimura’s forumula, which is the focus of this discussion.

    Yes, you did. Repeatedly.

    In fact, you claimed the papers of the Cornell Conference did likewise. Didn’t you?

    Salvador:

    Perhaps one of the great ironies regarding Nick, is the very papers he worked so hard to suppress (the Cornell papers), the very papers that got him the label, “Nick Matzke book burner”, are the very ones supporting his position in this thread. Well done, Nick.

    I have to give you credit though Sal. You fall off that fence and just keep climbing right back up on it.

  7. 7
    Dionisio says:

    vjtorley @ 4

    I’ve put it up at Dr. Kozulic’s request, as he is not able to put up posts on Uncommon Descent

    Why not?

  8. 8
    vjtorley says:

    Dionisio,

    Only some people have posting privileges. That’s all I know.

  9. 9
    Mung says:

    Salvador, could you please explain why Nick is wrong and Mendel’s Accountant is not?

    Or do they agree?

    I think I asked this before and I apologize if I missed your response, but which papers from the Cornell conference explicitly support Matzke and Moran?

  10. 10
    Mung says:

    Salvador continues to argue that Mendel’s Accountant supports Matzke/Moran contra VJ Torley while also maintaining that it doesn’t.

    Where does Sal stand, really?

  11. 11
    Mung says:

    VJT:

    According to the principles of population genetics, as I understand them, the rate of fixation of mutations in the human population is independent of the population size or population growth rate; it depends solely on the mutation rate.

    According to Matzke/Moran, the rate of fixation of mutations is independent of human populations.

    Salvador:

    The problem is we are comparing apples to oranges — gigantic unstirred population against tiny well-stirred inbreeding populations. The math idealizations where fixation rate approaches mutation rate work for tiny well-stirred inbreeding populations, they don’t for the population structure of humans today.

    The difference appears to not be based upon population size but rather on how well stirred the populations are.

    Whatever that means.

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