Intelligent Design

Fixation: the neutral theory’s Achilles’ heel?

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The neutral theory of evolution appears to have won out over its rival, neo-Darwinian selection theory (see here and here). However, the neutral theory makes a very specific prediction about the rate at which mutations are fixed in a population, which I think warrants more testing and scrutiny. The evidence for this prediction which I’ve seen to date is frankly underwhelming.

What is the neutral theory of evolution?

Let’s begin with a few definitions. What is the neutral theory of evolution? Here’s a short definition given by Professor Terry Speed, formerly of Berkeley University:

The Neutral Theory of Molecular Evolution (Kimura) states, in essence, that most of the variation seen at the molecular level is selectively neutral — that is, there are no important fitness advantages or disadvantages associated with particular alleles — and that genetic drift, rather than natural selection, dominates the dynamics. This does not mean that mutations, when they occur, are all neutral, or that the genes themselves are unimportant. On the contrary, it is thought that most mutations are deleterious to the organism, and thus are unlikely to remain in the population long enough to contribute measurably to the “standing” variation. Only those mutations that do not have a harmful effect have an appreciable chance of sticking around long enough for us to see them. The Neutral Theory hypothesizes that this class of “allowable” mutations is composed entirely of selectively neutral variants. The alternative viewpoint (much simplified) is that advantageous mutations, while perhaps exceedingly rare, do play a major role in evolution, and that polymorphism at the molecular level can best (or, at least, possibly) be explained by natural selection.

The triumph of the neutral theory over neo-Darwinism

Professor PZ Myers recently wrote a very revealing post, titled, The state of modern evolutionary theory may not be what you think it is (February 14, 2014), about how the modern theory of evolution has completely changed from the Darwinian version that most of us were taught at school:

…[M]aybe we should be honest from the very beginning about the complexity of modern evolutionary theory and how it has grown to be very different from what Darwin knew.

First thing you have to know: the revolution is over. Neutral and nearly neutral theory won. The neutral theory states that most of the variation found in evolutionary lineages is a product of random genetic drift. Nearly neutral theory is an expansion of that idea that basically says that even slightly advantageous or deleterious mutations will escape selection — they’ll be overwhelmed by effects dependent on population size. This does not in any way imply that selection is unimportant, but only that most molecular differences will not be a product of adaptive, selective changes.

Professor Larry Moran, in a follow-up post, broadly concurred with Professor PZ Myers’ assessment:

Random genetic drift is a mechanism of evolution that results in fixation or elimination of alleles independently of natural selection. If there was no such thing as neutral mutations then random genetic drift would still be an important mechanism…

Random genetic drift is a mechanism of evolution that was discovered and described over 30 years before Neutral Theory came on the scene.

What Neutral Theory tells us is that a huge number of mutations are neutral and there are far more neutral mutations fixed by random genetic drift that there are beneficial mutations fixed by natural selection. The conclusion is inescapable. Random genetic drift is, by far, the dominant mechanism of evolution.

The revolution is over and strict Darwinism lost. We now know that random genetic drift is an important mechanism of evolution and there’s more to evolution than natural selection. Unfortunately, this blatantly obvious fact is not understood by the vast majority of people and teachers. There are even many scientists who don’t understand evolution.

The neutral theory’s predictions regarding rates of fixation

The neutral theory makes a very specific prediction about the rate at which mutations are fixed within a population. This prediction follows from the fact that the only mutations being considered in the model are neutral mutations, as Professor Terry Speed points out in his course notes. He continues:

Whatever we imagine these mutations look like, however, they are
assumed to occur with mean rate generation (on whatever scale we are assessing mutations– transitions, transversions, third-base mutations, etc·). We want to know the rate at which these mutations that are entering the population become established in the population– the fixation process described above. This is known as substitution (a new type is substituted for an old). Then we can … show that

This simple result, that the rate of substitution equals the rate of mutation, has been instrumental in the study of molecular evolution, for good reason. Population genetics is notorious for its reliance on difficult to measure (and often confounded) parameters such as effective population size, mutation rate, and selection coefficients. Here is a formula which tells us that the data we observe (substitutions) is dependent only on one of these, mutation rate.

The neutral theory’s predictions regarding the time it takes for mutations to get fixed

There’s more. The neutral theory also makes a very specific prediction regarding the time it takes for a neutral mutation to get fixed in a population – that is, assuming it gets fixed:

Most neutral alleles [alternative versions of a gene – VJT] are lost soon after they appear. The average time (in generations) until loss of a neutral allele is 2(Ne/N) ln(2N) where N is the effective population size (the number of individuals contributing to the next generation’s gene pool) and N is the total population size. Only a small percentage of alleles fix. Fixation is the process of an allele increasing to a frequency at or near one. The probability of a neutral allele fixing in a population is equal to its frequency. For a new mutant in a diploid population [where each organism’s cells contain two sets of chromosomes, one from each parent – VJT], this frequency is 1/2N.

If mutations are neutral with respect to fitness, the rate of substitution (k) is equal to the rate of mutation(v). This does not mean every new mutant eventually reaches fixation. Alleles are added to the gene pool by mutation at the same rate they are lost to drift. For neutral alleles that do fix, it takes an average of 4N generations to do so. However, at equilibrium there are multiple alleles segregating in the population. In small populations, few mutations appear each generation. The ones that fix do so quickly relative to large populations. In large populations, more mutants appear over the generations. But, the ones that fix take much longer to do so. Thus, the rate of neutral evolution (in substitutions per generation) is independent of population size.
(Chris Colby, Introduction to Evolutionary Biology, Version 2, January 7, 1996, Talk Origins Archive.)

Actually, the figure of 4N generations is not quite correct: according to Professor David H.A. Fitch, of the Department of Biology at New York University, “the time it takes a particular mutant to achieve fixation from the time it arises is dependent on population size (this time is 4*Ne generations, where Ne is the effective breeding population (N if everybody contributes progeny).” (1997 Course notes, Population Size and Genetic Drift)

The implications for human evolution

What does that mean for human beings? In a post titled, Why are the human and chimpanzee/bonobo genomes so similar? (February 28, 2014), Professor Moran helpfully explains:

The human and chimp genomes are 98.6% identical or 1.4% different. That difference amounts to 44.8 million base pairs distributed throughout the entire genome. If this difference is due to evolution then it means that 22.4 million mutations have become fixed in each lineage (humans and chimp) since they diverged about five million years ago.

The average generation time of chimps and humans is 27.5 years. Thus, there have been 185,200 generations since they last shared a common ancestor if the time of divergence is accurate. (It’s based on the fossil record.) This corresponds to a substitution rate (fixation) of 121 mutations per generation and that’s very close to the mutation rate as predicted by evolutionary theory.

What Professor Moran is saying here is that 121 mutations are being fixed in the human population, in each successive generation. Since 185,200 generations have elapsed since the human and chimpanzee lines diverged, this means that 22.4 million mutations have become fixed in the human lineage since our ancestors diverged from the line leading to chimps. That’s a staggering number.

Professor Moran thinks we shouldn’t be surprised. The rate of fixation is supported by three converging lines of evidence, as he explains, in a post titled, stimating the Human Mutation Rate: Direct Method (February 22, 2013):

There are basically three ways to estimate the mutation rate in the human lineage. I refer to them as the Biochemical Method, the Phylogenetic Method, and the Direct Method.

The Biochemical Method is based on our knowledge of biochemistry and DNA replication as well as estimates of the number of cell divisions between zygote and egg. It gives a value of 130 mutations per generation. The Phylogenetic Method depends on the fact that most mutations are neutral and that the rate of fixation of alleles is equal to the mutation rate. It also relies on a correct phylogeny. The Phylogenetic Method gives values between 112-160 mutations per generation. These two methods are pretty much in agreement.

The Direct Method involves sequencing the entire genomes of related individuals (e.g. mother, father, child) and simply counting the new mutations in the offspring. [Moran then cites a paper by Xue et al. (2009) which estimates the mutation rate at 103 mutations per generation.]

That’s not an observation, Professor Moran!

With the greatest respect to Professor Moran, none of these methods counts as an observation of the rate at which mutations get fixed in the human population. Inferring how many mutations must have taken place from an assumed time at which the human and chimp lineages diverged, is not the same thing as observing the rate at which mutations get fixed in the human line. And observing how many mutations occur in the space of one generation, from parent to child, is not the same thing as observing the rate at which mutations occur in the human population as a whole.

Professor Moran might respond that according to the mathematical assumptions underlying the neutral theory of evolution, the rate at which mutations get passed on from parent to child is the same as the rate at which mutations get fixed in the population as a whole. That may be so; but it does not mean that an observation of the former automatically counts as an observation of the latter. The equation of the two rates only occurs within a particular theory of evolution: the neutral theory. If we are to test this theory properly, then, we need a population in which we can observe mutations getting fixed, and see if the rate accords with the mutation rate from parent to offspring.

Mathematical quibbles with the neutral theory: backwards reasoning

I might add that some of the mathematical arguments supporting the neutral theory seem a little questionable to me. Take this “backwards reasoning” argument from Professor Terry Speed’s course notes, in support of the claim that the probability that a new mutation eventually gets fixed is exactly (1/2N), where N is the population size:

…[A]t time 0, there will be 2N gametes in the population, any of which might or might not leave descendants in the next generation. If they do not, the lineage of that allele copy is extinct in the population. If we follow the population through time, eventually all but one of the 2N original lineages will be extinct, and the remaining one will be fixed in the population. Because all of the original gametes have equal probability of generating the surviving lineage, the fixation probability of any allelic type is simply the frequency of that type.

The argument seems to picture the alleles as if they’re all competing against each other, on an individual basis. But what we need to remember is that the new allele (call it A) may be competing against the entire population, all of whose members have another version (call it B) of that gene. In this situation, does it really sound reasonable to say that “all of the original gametes have equal probability of generating the surviving lineage”? No wonder that Professor Speed himself is a little wary of this argument: he acknowledges that it is “simply a verbal argument,” but one which (he thinks) generates powerful insights.

The implausible claims of the neutral theory, when applies to human evolution

Although I’m happy to be proved wrong, the claim that more than 100 mutations get fixed in the entire human population, in each passing generation, strikes me as implausible. I’m tempted to ask: where are all these mutations that are fixed in the human population in 2014, but were not fixed in the human population one generation ago, in 1987? Has anyone identified them?

The time taken for these mutations to get fixed also seems extraordinary. We are told that for a population of N organisms, it takes (4*Ne) generations for a mutation to get fixed in the population, where Ne is the effective size of the human population. For most of human history, the effective population size appears to have been around 10,000, even though the actual human population size is thought to have been considerably higher (350,000 from the Middle Pleistocene onwards, according to a 2008 article by Professor John Hawks). Four times 10,000 equals 40,000 generations, and if we use Professor Moran’s figure of 27.5 years per generation, that’s equivalent to 1,100,000 years ago.

Let me spell that out: if we take a typical mutation out of the 100-odd mutations which (according to the neutral theory of evolution) got fixed in the human population within the last generation (from 1987 to 2014), we will find that that mutation first appeared in the human lineage some 1,100,000 years ago.

Am I the only one who thinks this figure is absolutely extraordinary? And for that matter, doesn’t the notion of a mutation that takes one million years to fix sound a little suspicious?

Should we trust mathematical estimates of how long it takes mutations to get fixed in the human population, given the enormous environmental upheavals (e.g. Ice Ages, the Toba eruption, and so on) that we’ve faced in the past million years?

And what about this? Anthropologist John Hawks estimates that positive selection in the past 5,000 years has occurred at a rate roughly 100 times higher than any other period of human evolution. He adds: “We are more different genetically from people living 5,000 years ago than they were different from Neanderthals.” All this hyper-evolution has been occurring at a time when the human population has been higher than ever before – which means that it should take much, much longer for mutations to get fixed in the population! So how does that work? Go figure.

Testing the neutral theory

Of course, I realize that testing the predictions of the neutral theory of evolution regarding how many mutations get fixed in the population in each generation, and how long it takes for a new mutation to get fixed, might be rather impractical for a long-lived, slow-reproducing species like Homo sapiens.

So I’d be very interested to hear from any readers with a biology background. How do the predictions of the neutral theory check out when applied to bacteria? What about simple eukaryotes? Have any studies been done for animals? Which ones? Over to you.

UPDATE:

In a post over at the Sandwalk blog, Professor Larry Moran cites a paper by Richard Lenski in support of the claims of the neutral and near-neutral theories of evolution. He writes:

Fortunately for Torley, there are a number of papers that answer his question. The one that I talk about in class is from Richard Lenski’s long-term evolution experiment. Recall that mutation rates are about 10^-10 per generation. If the fixation rates of neutral alleles was equal to the mutation rate then (as predicted by population genetics) then this should be observable in the experiment run by Lenski (now 60,000 generations).

The result is just what you expect. The total number of neutral allele fixations is 35 in the bacterial cultures and this correspond to a mutation rate of 0.9 × 10^-10 or only slightly lower than what is predicted. There are lots of references in the paper and lots of other papers in the literature.

Wielgoss, S., Barrick, J. E., Tenaillon, O., Cruveiller, S., Chane-Woon-Ming, B., Médigue, C., Lenski, R. E. and D. Schneider (2011) Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli. G3: Genes, Genomes, Genetics 1, 183-186. [doi: 10.1534/g3.111.000406]

I think it is fair to conclude that short-term studies, done with microbes, lend support to the neutral and near-neutral theories of evolution.

Professor Moran also points out in his post that “Neutral Theory, per se, does not predict the rate of fixation of neutral alleles. That was what population genetics told us 80 years ago. What Neutral Theory says is that this may be the dominant form of evolution.”

Finally, with regard to anthropologist John Hawks’ claim that evolution is accelerating in modern times, Professor Moran writes: “John Hawks is probably wrong but in any case his argument is irrelevant. He’s talking about the small number of alleles that might be fixed by natural selection and not the vast majority of neutral alleles that are fixed by random genetic drift.”

48 Replies to “Fixation: the neutral theory’s Achilles’ heel?

  1. 1
    tjguy says:

    How does Moran’s ideas of the rate neutral mutations get fixed in the population compare with Dr. John Sanford’s work and/or with the rates that other population geneticists like Lynch give?

    Seems to me like Moran’s estimates are a lot lower than what these guys claim.

  2. 2
    Moose Dr says:

    Larry Moran, “The human and chimp genomes are 98.6% identical or 1.4% different. That difference amounts to 44.8 million base pairs distributed throughout the entire genome.”

    Hmmm. That would be based upon variation found within protein coding genes that are common between the chimp and the human. This, of course, does not count all of the variation between these in the “junk”, “junk” which is often much better conserved than would be accounted for by random chance. This, of course, does not include the approximately 100 orphan genes in the human with an average length around 300bp. (This computes to about 300,000 unbelievably unlikely mutations.) Nor does it include the approximately 100 orphan genes in the chimp, another 300,000 unbelievably unlikely mutations.

    Yup, the only difference between us and chimps is some inconsequential genetic noise. I’m convinced.

  3. 3
    JoeCoder says:

    I’m tempted to ask: where are all these mutations that are fixed in the human population in 2014, but were not fixed in the human population one generation ago, in 1987? Has anyone identified them?

    They become fixed when the last person carrying an “original” variant dies. It would be impossible to know this without sequencing every single human genome. But with 7 billion people and 3 billion bases it doesn’t seem that implausible to me.

  4. 4
    Ian Thompson says:

    A million years for a fix?
    That reminds me of the paper The million-year wait for macroevolutionary bursts. Not sure we are talking about exactly the same thing, however.

  5. 5
    bornagain77 says:

    as to:

    Anthropologist John Hawks estimates that positive selection in the past 5,000 years has occurred at a rate roughly 100 times higher than any other period of human evolution. He adds: “We are more different genetically from people living 5,000 years ago than they were different from Neanderthals.”

    Actually the direction we are going the past few thousand years genetically is not up, but is down:

    Human Genome in Meltdown – January 11, 2013
    Excerpt: According to a study published Jan. 10 in Nature by geneticists from 4 universities including Harvard, “Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.”,,,:
    “We estimate that approximately 73% of all protein-coding SNVs [single-nucleotide variants] and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000 -10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs than other genes.”,,,
    As for advantageous mutations, they provided NO examples,,,
    http://crev.info/2013/01/human-genome-in-meltdown/

    Human Genetic Variation Recent, Varies Among Populations – (Nov. 28, 2012)
    Excerpt: Nearly three-quarters of mutations in genes that code for proteins — the workhorses of the cell — occurred within the past 5,000 to 10,000 years,,,
    “One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,”,,,
    http://www.sciencedaily.com/re.....132259.htm

    “We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.” Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.-

    Even all the supposed beneficial mutations are found to be, in actuality, deleterious:

    Daily thought: blue eyes and other gene mutations, April 25, 2013
    Excerpt: “Research on blue-eyes has led many scientist to further affirm that humans are truly mere variations of the same origin. About 8% of the world’s total population has blue eyes so blue eyes are fairly rare. In fact, blue eyes are actually a gene mutation that scientist have researched and found to have happened when the OCA2 gene “turned off the ability to produce brown eyes.”
    http://www.examiner.com/articl.....-mutations
    Critic ignores reality of Genetic Entropy – Dr John Sanford – 7 March 2013
    Excerpt: Where are the beneficial mutations in man? It is very well documented that there are thousands of deleterious Mendelian mutations accumulating in the human gene pool, even though there is strong selection against such mutations. Yet such easily recognized deleterious mutations are just the tip of the iceberg. The vast majority of deleterious mutations will not display any clear phenotype at all. There is a very high rate of visible birth defects, all of which appear deleterious. Again, this is just the tip of the iceberg. Why are no beneficial birth anomalies being seen? This is not just a matter of identifying positive changes. If there are so many beneficial mutations happening in the human population, selection should very effectively amplify them. They should be popping up virtually everywhere. They should be much more common than genetic pathologies. Where are they? European adult lactose tolerance appears to be due to a broken lactase promoter [see Can’t drink milk? You’re ‘normal’! Ed.].
    African resistance to malaria is due to a broken hemoglobin protein [see Sickle-cell disease. Also, immunity of an estimated 20% of western Europeans to HIV infection is due to a broken chemokine receptor—see CCR5-delta32: a very beneficial mutation. Ed.] Beneficials happen, but generally they are loss-of-function mutations, and even then they are very rare!
    http://creation.com/genetic-entropy

    Recently, supposedly ‘beneficial’ mutations were found in Tibetans that have allowed them to survive in extremely high altitudes with less oxygen. Yet once again, the new ‘beneficial mutations’ are actually found to be ‘slightly detrimental’ instead of truly beneficial because the mutations in fact result in a limit on the red cell blood count for Tibetans:

    Tibetans Developed Genes to Help Them Adapt to Life at High Elevations – May 2010
    Excerpt: “What’s unique about Tibetans is they don’t develop high red blood cells counts,”
    http://www.sciencedaily.com/re.....143453.htm

    Yet high red blood cell counts are found to be a good thing,,

    Extremely fit individuals may have higher values—significantly more red cells in their bodies and significantly more oxygen-carrying capacity—but still maintain normal hematocrit values.
    http://wiki.medpedia.com/Red_B.....w_It_Works

    Even John Hawks himself admits to a recent ‘minor discrepancy’ from anatomy that is unexpected if we were truly evolving upwards as Darwinists imagine us to be:

    If Modern Humans Are So Smart, Why Are Our Brains Shrinking? – January 20, 2011
    Excerpt: John Hawks is in the middle of explaining his research on human evolution when he drops a bombshell. Running down a list of changes that have occurred in our skeleton and skull since the Stone Age, the University of Wisconsin anthropologist nonchalantly adds, “And it’s also clear the brain has been shrinking.”
    “Shrinking?” I ask. “I thought it was getting larger.” The whole ascent-of-man thing.,,,
    He rattles off some dismaying numbers: Over the past 20,000 years, the average volume of the human male brain has decreased from 1,500 cubic centimeters to 1,350 cc, losing a chunk the size of a tennis ball. The female brain has shrunk by about the same proportion. “I’d call that major downsizing in an evolutionary eyeblink,” he says. “This happened in China, Europe, Africa—everywhere we look.”
    http://discovermagazine.com/20.....-shrinking

    Supplemental notes:

    Dr. John Sanford “Genetic Entropy and the Mystery of the Genome” 1/2 – video
    http://www.youtube.com/watch?v=pJ-4umGkgos

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.”
    Doug Axe PhD.
    http://www.evolutionnews.org/2.....62351.html

  6. 6
    Joe says:

    Unfortunately no one has verified the neutral theories fixation equations. And no one knows exactly how genetically different humans are from chimps.

  7. 7
    scordova says:

    The Achilles heel is not the fixation equation but the UN-fixation. If we add 100 mutation per generation, we should be around 2% different from each other, not just chimps! This would be true unless we had a bottle neck of an Adam and Eve.

    To understand the problem, if you scroll down to the end of this discussion of the cartoon with Nachman’s paradox you’ll see it:

    http://www.uncommondescent.com.....e-fittest/

    It was touched on in the Cornell conference. At ICC 2013, I pleaded with Robert Carter and John Sanford to investigate the matter more. And Dr. Carter said it would be good for us to look into it (as if I don’t already have other things to do!).

    It is also a quietly acknowledged problem that deeply conserved sequences (on which the ENCODE project relies) are inconsistent with neutral evolution and the problem of the Poisson distribution that I pointed out. If you watch the cartoon and ponder it, you’ll see that for all the fixation going on, we’re UN-fixing just as many! Watch the cartoon and your mind will be enlightened. 🙂

    With some truncation selection and synergistic epistasis the problem may be alleviated, but not by much, it will be slow deterioration. The way to know the outcome is via computer simulation, and one of the Cornell papers worked it out.

    I’m glad you are pondering these things VJ and that you’re highlighting what was is hidden from public view but quietly discussed by those who actually understand population genetics!

    Btw, I talked to a biology faculty member of a department with 30 bio professors and asked if they offered population genetics. He said they don’t teach it since biologists generally don’t like math. Darwin was horrible in math and his lack of understanding has been the legacy of his adherents.

    For all the well-developed understanding of fixation in neutral theory, study of all the un-fixation going on has been sorely neglected.

    I have defended neutral theory as being true in the present day (absence of selection is a fact except for lethal diseases), but I don’t defend it as an explanation for the structure of the genome.

    The genome’s structure across species is inconsistent with neutral theory. Watch the cartoon and ponder it. Your intuition is correct, but for not exactly the reasons you think.

  8. 8
    JacobyShaddix says:

    So to summarise, an argument from incredulity.

  9. 9
    scordova says:

    Random genetic drift is a mechanism of evolution that results in fixation or elimination of alleles independently of natural selection.

    Not QUITE. You unfix almost as many as you fix. If your fixation rate is mu, you unfixation rate is almost mu!

    It’s like a plumber fixing a leak, for every leak he fixes, another breaks. Evolutionists who live by mutation rate you DIE by mutation rate.

    Neutral theory has won for the present (today, realtime) evolution, it fails to explain the evolution in the deep past.

    It’s not much to say, “hey selection is pretty much absent from the genome, it’s almost a random walk from here on out except for front loaded plasticity (front loaded, moderate evolution)”, it doesn’t and cannot explain irreducible complexity, it doesn’t explain deep conservation, it doesn’t accord with lack of sequence divergence in deeply conserved regions that are now presently neural.

    TESTABLE PREDICTION:

    One I’ve been making for the last 10 years!

    Mutations will accumulate in the deeply conserved regions not subject to strong selection, which is most regions as a matter of principle. Testable, provable, and ID will win this claim.

    I’ve argued for neutralism at UD for almost the last 10 years, but did PZ Myers, did Larry Moran, did TSZ, did Pandas Thumb, did most of my detractors acknowledge I was way ahead of everyone else on neutral theory. Nooooo, a creationist isn’t supposed to understand evolutionary biology and population genetics….:roll:

    Neutral theory is better than Darwinism, it superior in explaining PRESENT DAY evolution, but it fails to explain past evolution.

  10. 10
    Eric Anderson says:

    JoeCoder @3:

    They become fixed when the last person carrying an “original” variant dies. It would be impossible to know this without sequencing every single human genome. But with 7 billion people and 3 billion bases it doesn’t seem that implausible to me.

    Isn’t part of the issue the fact that the neutral calculations are just that — a theoretical calculation. In actual practice, it seems a little harder to go from a hypothetical calculation to what we see happening in the real world.

    Here is what I am not understanding:

    Let’s say we have a population of a billion individuals (Generation X). Let’s say 100 mutations are supposed to fix per generation (per the math). Each individual in Generation X produces one offspring in Generation Y. Yet when Generation Y is born, the offspring of X1 will have certain mutations, the offspring of X2 will have different mutations, and so on across the population.

    Even if every single individual in Generation X has 100 mutations, how can any new mutation get fixed in Generation Y? There is simply no physical way — no physical mechanism — that would cause mutations to spread across the entire population and fix 100 mutations across the population in one generation.

    So the math (which I don’t necessarily disagree with, by the way) is an interesting hypothetical, when viewed over a huge number of generations and large timescales — and without trying to trace any particular mutation. But as we zoom in to look at the details of what happens from generation to generation it seems to break down. Does that mean the idea is completely wrong? Not necessarily. But it should raise a tinge of doubt and cause us to say “Wait a minute. How does this actually work, on the ground, in practice, in the real world?”

    (Also, Sal raises some other important considerations, like unfixing).

  11. 11
    Eric Anderson says:

    Of course, the larger problem with the neutral theory is that it is utterly useless in explaining how functional specified information and structures arise. Its general premise on that front: that neutral stuff accumulates until, poof!, it is suddenly needed and put to use by some vague means, is laughable on its face.

    The real value of the neutral idea (perhaps more from a rhetorical than a scientific standpoint) is just (i) to “explain” why there are so many mutations that haven’t been eliminated by natural selection, and (ii) to provide a workaround to the empirical observation that useful mutations are rare.

    On this latter front the neutral theory gives a laughable answer — “Sure, but unlike useful mutations, neutral mutations are quite common and can build up. Then they’ll get useful later.” Essentially kicking the problem down the road to some obscure magical future, rather than dealing head on with the central problem of how chance mutations can ever produce code, specification, meaning, function.

  12. 12
    Barry Arrington says:

    Jacoby: “So to summarise, an argument from incredulity.”

    When people make claims that stretch credulity, there are two possible responses:
    1.Express incredulity (this is the line taken by critical thinkers).
    2. Gulp the pap with no complaint, because following the party line is so much easier than thinking.

    So depending on which camp you are in you are either complimenting or castigating the OP. I can’t tell. Which camp are you in?

  13. 13
    scordova says:

    To understand the UN-fixing problem, let us hypothetically suppose we are going to artificially increase mutation rates by 1,000,000 using radiation and chemicals.

    Ok, so now according to Kimura’s equation, mu is now 1,000,000 times higher, therefore the fixation rate is now 1,000,000 times higher. Do you think this will speed evolution?

    When we have done this in the lab, we killed the organism. Why? We failed to do proper accounting. For all the “fixing” (as in making part of every population) were doing as much, if not worse, BREAKING!

    “Fixing” means to make a part of the entire population, and this can be dysfunction that becomes a part of every individual, and if so, “fixing” is the wrong word, more like “making dysfunction permanent”. Add to that the sort of breaking caused just by increasing the mutation rate, and one can see neutral theory as an explanation of past evolution is greatly challenged.

    That said, I maintain, neutral theory is great for present day evolution, it accords well with the general deterioration of the genome in the present day, it doesn’t explain the appearance of function since neutral theory is a random walk.

  14. 14
    scordova says:

    Thanks for finding PZ quotes and all the hard work. I have another Achilles heel in mind, the rate of breaking. As a supplement to your discussion:

    Fixation rate, what about breaking rate?

  15. 15
    Sebestyen says:

    Ok, so let me get this straight…

    These guys now believe that mutations accumulate over time by randomly getting fixated in the whole population and that this basically turned our alledged common ancestor into chimps and humans?

    Is this really the case?

    Sebestyen

  16. 16
    bornagain77 says:

    Sebestyen, yep that pretty much nails the theroy as it now stands. Berlinski quipped about this development:

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
    http://www.evolutionnews.org/2.....53171.html

    A few more quotes of interest:

    Here is a Completely Different Way of Doing Science – Cornelius Hunter PhD. – April 2012
    Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon.
    Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding.
    Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place.
    http://darwins-god.blogspot.co.....ay-of.html

    Ann Gauger on genetic drift – August 2012
    Excerpt: The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption — that the vast majority of mutations are neutral and have no effect on an organism’s survival. (For a review go here.) According to this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn’t matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don’t matter.
    http://www.uncommondescent.com.....tic-drift/

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

    A Short History Of the Junk DNA argument:
    https://docs.google.com/document/d/14-TXfGxPu-3YeCHtLmxTmL4UZN90Odt135c59yTIFsw/preview

  17. 17
    JacobyShaddix says:

    Neutral theory has won for the present (today, realtime) evolution, it fails to explain the evolution in the deep past.

    Science will always be pushing the boundaries of what can be explained and creationists will always be on the fringes saying “Ah you may have explained that, but you still can’t explain this” therefore God!!

    Give it time

  18. 18
    Joe says:

    Well when it comes to evolution science can’t explain much of anything. When it comes to origins it can’t explain anything.

    And there isn’t anything discovered so far that allows us to say “therefor materialism!”

  19. 19
    bornagain77 says:

    JacobyShaddix you state:

    “Ah you may have explained that, but you still can’t explain this” therefore God!!

    Contrary to what you may imagine to be true, the truth of the matter is that ‘science’ has relentlessly confirmed Theistic predictions and falsified Materialistic/Naturalistic predictions.

    1. Naturalism/Materialism predicted time-space energy-matter always existed. Whereas Theism predicted time-space energy-matter were created. Big Bang cosmology now strongly indicates that time-space energy-matter had a sudden creation event approximately 14 billion years ago.

    2. Naturalism/Materialism predicted that the universe is a self sustaining system that is not dependent on anything else for its continued existence. Theism predicted that God upholds this universe in its continued existence. Breakthroughs in quantum mechanics reveal that this universe is dependent on a ‘non-local’, beyond space and time, cause for its continued existence.

    3. Naturalism/Materialism predicted that consciousness is a ‘emergent property’ of material reality and thus should have no particularly special position within material reality. Theism predicts consciousness precedes material reality and therefore, on that presupposition, consciousness should have a ‘special’ position within material reality. Quantum Mechanics reveals that consciousness has a special, even a central, position within material reality. –

    4. Naturalism/Materialism predicted the rate at which time passed was constant everywhere in the universe. Theism predicted God is eternal and is outside of time. – Special Relativity has shown that time, as we understand it, is relative and comes to a complete stop at the speed of light. (Psalm 90:4 – 2 Timothy 1:9) –

    5. Naturalism/Materialism predicted the universe did not have life in mind and that life was ultimately an accident of time and chance. Theism predicted this universe was purposely created by God with man in mind. Scientists find the universe is exquisitely fine-tuned for carbon-based life to exist in this universe. –

    6. Naturalism/Materialism predicted complex life in this universe should be fairly common. Theism predicted the earth is extremely unique in this universe. Statistical analysis of the hundreds of required parameters which enable complex organic life to be possible on earth gives strong indication the earth is extremely unique in this universe. –

    7. Naturalism/Materialism predicted it took a very long time for life to develop on earth. Theism predicted life to appear abruptly on earth after water appeared on earth (Genesis 1:10-11). Geo-chemical evidence from the oldest sedimentary rocks ever found on earth indicates that complex photo-synthetic life has existed on earth as long as water has been on the face of earth. –

    8. Naturalism/Materialism predicted the first life to be relatively simple. Theism predicted that God is the source for all life on earth. The simplest life ever found on Earth is far more complex than any machine man has made through concerted effort. (Michael Denton PhD) –

    9. Naturalism/Materialism predicted the gradual unfolding of life would (someday) be self-evident in the fossil record. Theism predicted complex and diverse animal life to appear abruptly in the seas in God’s fifth day of creation. The Cambrian Explosion shows a sudden appearance of many different and completely unique fossils within a very short “geologic resolution time” in the Cambrian seas. –

    10. Naturalism/Materialism predicted there should be numerous transitional fossils found in the fossil record, Theism predicted sudden appearance and rapid diversity within different kinds found in the fossil record. Fossils are consistently characterized by sudden appearance of a group/kind in the fossil record(disparity), then rapid diversity within that group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. –

    11. Naturalism/Materialism predicted animal speciation should happen on a somewhat constant basis on earth. Theism predicted man was the last species created on earth – Man (our genus ‘modern homo’ as distinct from the highly controversial ‘early homo’) is the last generally accepted major fossil form to have suddenly appeared in the fossil record. (Tattersall; Luskin)–

    12. Naturalism/Materialism predicted much of the DNA code was junk. Theism predicted we are fearfully and wonderfully made – ENCODE research into the DNA has revealed a “biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.”. –

    13. Naturalism/Materialism predicted a extremely beneficial and flexible mutation rate for DNA which was ultimately responsible for all the diversity and complexity of life we see on earth. Theism predicted only God created life on earth – The mutation rate to DNA is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial, information building, mutations whatsoever. (M. Behe; JC Sanford) –

    14. Naturalism/Materialism predicted morality is subjective and illusory. Theism predicted morality is objective and real. Morality is found to be deeply embedded in the genetic responses of humans. As well, morality is found to be deeply embedded in the structure of the universe. Embedded to the point of eliciting physiological responses in humans before humans become aware of the morally troubling situation and even prior to the event even happening.

    15. Naturalism/Materialism predicted that we are merely our material bodies with no transcendent component to our being, and that we die when our material bodies die. Theism predicted that we have minds/souls that are transcendent of our bodies that live past the death of our material bodies. Transcendent, and ‘conserved’ (cannot be created or destroyed) ‘non-local’, beyond space-time matter-energy, quantum entanglement/information, which is not reducible to matter-energy space-time, is now found in our material bodies on a massive scale.

    In other words,

    God is not a “God of the gaps”, he is God of the whole show.
    John Lennox

  20. 20
    wd400 says:

    From the OP

    I might add that some of the mathematical arguments supporting the neutral theory seem a little questionable to me. Take this “backwards reasoning” argument from Professor Terry Speed’s course notes, in support of the claim that the probability that a new mutation eventually gets fixed is exactly (1/2N), where N is the population size:

    …[A]t time 0, there will be 2N gametes in the population, any of which might or might not leave descendants in the next generation. If they do not, the lineage of that allele copy is extinct in the population. If we follow the population through time, eventually all but one of the 2N original lineages will be extinct, and the remaining one will be fixed in the population. Because all of the original gametes have equal probability of generating the surviving lineage, the fixation probability of any allelic type is simply the frequency of that type.

    The argument seems to picture the alleles as if they’re all competing against each other, on an individual basis

    No – it says the fixation probability is equal to the frequency. If there are hundreds of “B”s then it’s hundres/2N(e), if there is just one new mutation is 1/2N.

    No wonder that Professor Speed himself is a little wary of this argument: he acknowledges that it is “simply a verbal argument,” but one which (he thinks) generates powerful insights.

    The ‘verbal argument’ just the converging back on an ancestor. The mathmatical argument remains sound.

    Am I the only one who thinks this figure is absolutely extraordinary? And for that matter, doesn’t the notion of a mutation that takes one million years to fix sound a little suspicious?

    Should we trust mathematical estimates of how long it takes mutations to get fixed in the human population, given the enormous environmental upheavals (e.g. Ice Ages, the Toba eruption, and so on) that we’ve faced in the past million years?

    If the variants are neutral then environment has nothing to do with it. Why do you thin these are these number ‘suspicious’ or extraordinary?

    All this hyper-evolution has been occurring at a time when the human population has been higher than ever before – which means that it should take much, much longer for mutations to get fixed in the population!

    … by drift. So not selection so not relevent to the apparent speed-up in evolutionary rate.

    I’m not quite sure you’ve understood what the neutral theory is – it’s not a take it or leave thing. Most variants in the genome are selectively neutral, some are subject to selection. We

  21. 21
    wd400 says:

    Not QUITE. You unfix almost as many as you fix. If your fixation rate is mu, you unfixation rate is almost mu!

    What does this mean?

    The Achilles heel is not the fixation equation but the UN-fixation. If we add 100 mutation per generation, we should be around 2% different from each other, not just chimps!

    No. Expected heterozygosity is 4Ne.mu under neutrality, so much smaller than 2%

  22. 22
    wd400 says:

    Larry Moran, “The human and chimp genomes are 98.6% identical or 1.4% different. That difference amounts to 44.8 million base pairs distributed throughout the entire genome.”

    Hmmm. That would be based upon variation found within protein coding genes

    Nope. This is commonly trotted out, but not the case. The similarity in protein coding genes is indeed greater, but the ~98% includes all directly comprably regions (which are the ones that matter for the per-nuceleotide mutation rate)

  23. 23
    bornagain77 says:

    “I’m not quite sure you’ve understood what the neutral theory is”

    i.e. “You just don’t understand evolution!” 🙂

    dependable as always wd400. Perhaps one of these days you will understand that Darwinian evolution is not even a scientific theory in any reasonable sense!

    “nobody to date has yet found a demarcation criterion according to which Darwin(ism) can be described as scientific”
    – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, quote was as stated in 1973 LSE Scientific Method Lecture

    Darwinian Evolution is a Pseudo-Science – Part II
    https://docs.google.com/document/d/1oaPcK-KCppBztIJmXUBXTvZTZ5lHV4Qg_pnzmvVL2Qw/edit

    “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”
    Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.

    WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Evolution is True – Roger Highfield – January 2014
    Excerpt: If evolutionary biologists are really Seekers of the Truth, they need to focus more on finding the mathematical regularities of biology, following in the giant footsteps of Sewall Wright, JBS Haldane, Ronald Fisher and so on.
    The messiness of biology has made it relatively hard to discern the mathematical fundamentals of evolution. Perhaps the laws of biology are deductive consequences of the laws of physics and chemistry. Perhaps natural selection is not a statistical consequence of physics, but a new and fundamental physical law. Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology.
    Little seems to have changed from a decade ago when the late and great John Maynard Smith wrote a chapter on evolutionary game theory for a book on the most powerful equations of science: his contribution did not include a single equation.
    http://www.edge.org/response-detail/25468

  24. 24
    scordova says:

    WD400:

    What does this mean?

    Thanks for asking and weighing in.

    To un-fix is my figurative phrase for the problem stated by Eyre-Walker-Keightly and Nachman-Crowell based on the Poisson distribution:

    Fixation rate, what about breaking rate

    You wouldn’t have sequence divergence without it, but the question is, how come humans aren’t as diverged from each other as chimps? Or better yet, why aren’t sharks (being living fossils) not diverged from each other as they are from any other species, are they somehow exempt from the problems of molecular clocks just because they are the same species? Something seems wrong about this.

  25. 25
    vjtorley says:

    Hi Sal,

    Thank you very much for your helpful comments. I also found your video very illuminating. For those who haven’t read it yet, Sal’s latest post, “Fixation rate, what about breaking rate” over at http://www.uncommondescent.com.....king-rate/ is a tour de force. Great stuff!

  26. 26
    Matteo says:

    Science will always be pushing the boundaries of what can be explained and creationists will always be on the fringes saying “Ah you may have explained that, but you still can’t explain this” therefore God!!

    Atheists have a very strange idea of how theists think. Particular scientific evidences/theories have precisely zero bearing on why a typical theist believes in God. At least for me, this is based much more on direct experience, philosophical reflection, and participation in the sacramental life of the church. So no, instead, it’s more like:

    You may think you have your explanation, but since you insist on denying God, you can’t see that your explanation sucks, even on its own terms.

  27. 27
    jerry says:

    Some comments.

    I have read this cursorily but for what I have to say there is no need for the details now. This whole debate is a red herring. The real debate lies elsewhere.

    The debate on evolution has always been about the origin of new alleles. But what do we mean by a new allele? We do not mean the modification of a coding-region to produce a new allele. That is a new allele that is very similar to previous alleles and this frequently happens. What we really mean is the origin of something that is completely different from what exists in a gene pool, a completely different allele with no similarity to previous alleles.

    The fixation of an allele by genetic drift is not the origin of a new allele. It is the elimination of alleles. From Wikipedia:

    Genetic drift or allelic drift is the change in the frequency of a gene variant (allele) in a population due to random sampling. The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. A population’s allele frequency is the fraction of the copies of one gene that share a particular form. Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation.

    How is genetic drift driving anything meaningful in evolution if it eliminates population variation. The answer is, it doesn’t. So forget about genetic drift or fixation rates of mutations on coding regions etc. The answer to any meaningful evolution must lie elsewhere in the genome, that is in non coding regions. From what I understand this is the only place meaningful evolution can take place. (One caveat is that the control mechanisms that sit on top of the genome are also a source of new variation but leave that aside for the moment.)

    That is why I asked Allen MacNeill a couple days ago to a dialogue about his 47 mechanisms of change in a genome and how it drives evolution. Because it leads to very testable hypothesis. Which will support either the ID position or the evolutionary biologist position. From some articles that Allen suggested we all read about 6-7 years ago, the real action according to the evolutionary biologists takes place in changes in the non coding part of the genome.

    From the theory proposed, these non-coding regions are free to mutate but they are not selected for since there is no characteristic generated that could affect survival rates of the organism. I guess some areas of these regions could become fixed due to random processes and if one wants to call that genetic drift, so be it but that is not what genetic drift usually means.

    As members of the population reproduce there is a constant change in these non coding regions. And with these changes and mutations, a new coding region according to the theory will eventually arise in some sub-population of the species. Somehow this new coding region will be expressed and if it somehow produces a characteristic that leads to greater survival, a new allele is born and leads to a new population very similar to the original population but one in which can no longer breed with the previous gene pool because it is genetically different.

    Over time according to the theory, this process will produce more and more changes to the organism and will further differentiate it from the original gene pool. Meanwhile over in the population that it separated from, new alleles from different non coding regions will arise further differentiating this population from the other population that also came from the same ancestor.

    Think, Ancestor A leading to Chimps and Humans as one such example. Ancestor A no longer exists but somehow according to the thesis, a sub population broke off because new alleles developed in these formerly non-coding regions that then became coding regions. Another example according to Nick Matzke are horses and rhinos. Supposedly they came from the same population a few million years ago.

    Now comes the part of the theory that is meaningful for testable hypothesis.

    All these changes to the genome caused by the various engines of variation seldom lead to a new coding region. In other words, a new coding region must be very rare. The work of Axe says they are so rare they can never really exist but the evolutionary biology community says they are more common. Either way changes in the non coding regions are fairly common over time and are actually part of the gene pool except that they do not code for anything and do not affect survival. As such they must be passed on to offspring and it is only in a rare sub-population that the non-coding region becomes a coding one.

    But when this happens the same region in the other population must show a very similar genetic sequence but one that does not code for anything. So we have two populations which are very similar but in one there is a coding sequence that is not present in the other but a remnant of these coding sequence must exist in the other population. It just never got to where it could code for anything.

    This is the basis of the testable hypothesis of evolution. These regions either exist or do not exist in similar species. If in fact this process is the basis of the generation of new alleles (there doesn’t seem to be any other process that the evolutionary biologist can conceive of), then the successful and failed coding regions should be visible in related species.

    I just came back from South Africa and one of the highlights of the trip was looking for wild animals. Lions, leopards and rhinos are hard to find but what exist is an unlimited supply of various forms of antelope. By the end of the first day of animal exploration no one was interested in an impala. There were literally thousands of them. A big deal was finding various other species of antelope.

    These antelope would make a great testing ground for just how new variation entered the gene pool. If Allen MacNeill’s 47 engines of variation were at work, then there should be lots of similarities between non coding regions of the various species and unique coding sequences which exist in each species must have non-coding remnants in the other species.

    With today’s technology, this comparison is now possible. The answer will either disprove Axe’s thesis and support the evolutionary biologist’s thesis or support Axe because forensic evidence has to be there for the origin of new alleles. I happen to believe it will support Axe but the proof is in the pudding. And making the pudding is just a matter of time. Maybe we will also be able to answer the question just how much similarity there really is between a human and a chimp. A lot of percentages get thrown around. How much similarity is there between an impala and and an eland? But more importantly how do they differ?

  28. 28
    Eric Anderson says:

    wd400 @20:

    I’m not quite sure you’ve understood what the neutral theory is – it’s not a take it or leave thing. Most variants in the genome are selectively neutral, some are subject to selection.

    This is a good point. I think it is also substantively essentially what PZ Myers said in the OP quote (in which he announces that neutral and near-neutral theory “won”)? Maybe we’re all on the same page, but it just isn’t that big of a news story as PZ is making it out to be? 🙂

    Also, I’m glad you are here, because I am hoping to better understand the fixation-per-generation process. I’m familiar with the basic calculation, but when I try to think through how it actually works — on the ground, in real life, in a given population — it seems harder to pin down what is going on. I don’t know if you have any good examples or scenarios that would help us understand how this fixation actually occurs in a population from generation to generation?

  29. 29
    Eric Anderson says:

    Thanks, jerry, for your thoughtful comments, as always.

    Can you point me to the exchange with Allen MacNeill about the different mechanisms of genomic change. This is something I’ve been thinking about recently, so I would be very interested in seeing his list, if there is such a thing.

    Thanks,

  30. 30
    wd400 says:

    You wouldn’t have sequence divergence without it, but the question is, how come humans aren’t as diverged from each other as chimps? Or better yet, why aren’t sharks (being living fossils) not diverged from each other as they are from any other species, are they somehow exempt from the problems of molecular clocks just because they are the same species? Something seems wrong about this.

    How could fixation (the take over a population by a single allele) cause within species divergence? If two populations are unconnected by gene flow (so represent different species) then fixations within those populations are necessarily divergence, the same can’t be said for within-species fixations.

  31. 31
    jerry says:

    Eric,

    Here is a link to several articles that MacNeill wrote on his blog over the years. They are all on variation:

    http://evolutionlist.blogspot......0variation

    If you go down to the one that has the scarecrow from the Wizard of Oz (about halfway down the list of articles and dated October 25, 2007), you will see an actual list. It is titled “RM & NS: The Creationist and ID Strawman”

    He lists 47 processes. In a more recent publication he said there were more than 50.

    http://www.oneclickaudio.com/c.....UT0000.pdf

    That there are at least fifty different mechanisms that produce genetic and phenotypic variation, of which recombination is only one (and perhaps not the most important one).

  32. 32
    wd400 says:

    This is a good point. I think it is also substantively essentially what PZ Myers said in the OP quote (in which he announces that neutral and near-neutral theory “won”)? Maybe we’re all on the same page, but it just isn’t that big of a news story as PZ is making it out to be?

    Well, it depends what you mean. The public’s (and even many non-specialist scientists’s) perception of evolution is overly-focused on selection, so it’s worth pointing out most variaion in the genome (and most between species difference in genomes) is not the result of selection. And the classic/adapationist/balance school v neutralism was once a genuine debate about what proportion of evolutionary change was down to selecion.

    As to the fixation rate – it’s an inevitable consequence of finite population size an non-zero mutation rates. It’s important to understand the ~100 mutations enetering the population in generation x are not the same mutations fixing in that generation (it’s just the same number of mutations) and in modern humans the ‘minor allele’ will be created again in this generation at least once, since every allowable single nucleotide mutation occurs in each generation in our census (i.e. real) population.

  33. 33
    Joe says:

    wd400- no one knows what the fixation rate is as it was determined by assuming Common Descent and then working backwards.

  34. 34
    Eric Anderson says:

    wd400:

    It’s important to understand the ~100 mutations enetering the population in generation x are not the same mutations fixing in that generation (it’s just the same number of mutations) and in modern humans the ‘minor allele’ will be created again in this generation at least once, since every allowable single nucleotide mutation occurs in each generation in our census (i.e. real) population.

    Thanks. Maybe I wasn’t explaining my question very well.

    I realize the 100 mutations in Generation X aren’t being fixed in Generation X, they’re just arising in some individuals at that point. What I’m trying to get my mind around is what happens in Generation Y and down the road.

    If we start with our Generation X population with a current genetic profile (we could even say it is identical across the population in the first generation for simplicity’s sake), and then introduce a large number of mutations in that generation, how would any of those get fixed in the next generation?

    The fact that the minor allele will be created again at least once in the next generation (due to the large population size) doesn’t mean it will spread across the population.

    Or are you using “fixed” in the sense that it shows up somewhere, in any individual, in the population? I think what the OP was referring to was a more traditional definition in which the mutation gets fixed across the entire population.

  35. 35
    wd400 says:

    So, here’s one way to thnk about it. Think of each realised population as a random (these are neutral variants after all) draw from the very nearly infinite possible populations of that size affored by the huge number of gametes that could come together. Obviously, when you take samples, you expect the smaple frequency to differ from the population frequency by some amount (and the relative difference to be greater in small populations, one of the most important concepts to get about genetic drift). So in your second generaton generation the frequency will change a little up or a little down. Over time this sampling means allele frequencies will talk the classic random walk, with the important addition that if a varaint goes to 0 it’s lost and at 1 it’s fixed, and there is no more walking to do. The so called Drunkard;s Walk (alluded to the fact the walker eventually falls in one or other gutter). In this way the final generation at which fixation occurs is the one in which the realised population doesn’t contain any of the ancestral allele.

    Because mutations by definition start out rare (1 / 2N for diploids) they are more likely to be lost to extinction that pushed to fixation, but the maths shows us the chance is just 1/2N which get’s us back to the population fixation rate being equal to the per-indivual mutation rate.

    The point about the ancestral allele being recreated in every generation is really an aside – just to point ut the massive census population size of modern humans makes “fixation” in the “every individial have an ‘A’ here” sense tricky, becasuse new “T”s and “G”s and “C”s are made in each generation so someone doesn’t have an “A”. It’s largely irrelevent to the question of how genetic differences between humans and chimps arose, since such variants are very rare and each compared genome is unlikely to have any such variants .

  36. 36
    scordova says:

    The fact that the minor allele will be created again at least once in the next generation (due to the large population size) doesn’t mean it will spread across the population.

    Simplified illustration:

    Have 10,000 individuals with a mutation rate of 100 per individual. The total number of mutants in the population is

    10,000 * 100 = 1,000,000

    Each mutant has a 1 in 10,000 chance of getting fixed (I’ll defer the proof of how that happens below, but it is called a Moran process (no relation to Larry) ).

    Thus we can now figure how many mutants will get fixed:

    (Total mutants) * (probability of fixation) =

    1,000,000 * 1/10,000 = 100 alleles fixed

    The easy way to understand the end of the Moran process without getting bogged down in the math is to imagine a population of 4 individuals each with an allele for the same loci.

    The start is:

    Individual #1 : Allele-A
    Individual #2 : Allele-C
    Individual #3 : Allele-T
    Individual #4 : Allele-G

    The end state after infinite number of generations will be (because of random recombination):

    Individual #1 : Allele-A
    Individual #2 : Allele-A
    Individual #3 : Allele-A
    Individual #4 : Allele-A

    or

    Individual #1 : Allele-C
    Individual #2 : Allele-C
    Individual #3 : Allele-C
    Individual #4 : Allele-C

    or

    Individual #1 : Allele-T
    Individual #2 : Allele-T
    Individual #3 : Allele-T
    Individual #4 : Allele-T

    or

    Individual #1 : Allele-G
    Individual #2 : Allele-G
    Individual #3 : Allele-G
    Individual #4 : Allele-G

    Thus each allele can be seen to have a 1/4 chance of fixation. Now just scale that idea up to a population of 10,000 and you see each allele then has a 1 in 10,000 chance of fixation.

    That’s kind of a bastardized way of doing the math without the formalisms. If you want the formalisms, here you go:

    http://en.wikipedia.org/wiki/Moran_process

    Yikes!

  37. 37
    Sebestyen says:

    Sebestyen, yep that pretty much nails the theroy as it now stands.

    Everytime you think that they couldn’t possibly come up with a more idiotic theory, they pull out the next one…

    Sebestyen

  38. 38
    wd400 says:

    The correct answer to 15 is “No. That’s not the case at all.”

    Neutral theory explains most of the genetic changes between humans and chimps, and between most other species for that matter. But acccepting neutral theory doesn’t require you to ditch selection.

    (there are also theories of constructive neutral evolution – but that’s qutie a different topic)

  39. 39
    Sebestyen says:

    Neutral theory explains most of the genetic changes between humans and chimps, and between most other species for that matter. But acccepting neutral theory doesn’t require you to ditch selection.

    The way I see it, “neutral theory” doesn’t explain anything because the very idea that random changes in a code without any guidance whatsoever can result in the genetic differences between humans and chimp is absurd in the highest possible degree.

    Natural selection was more or less the only thing of the whole evolution shebang that actually made some sense and apparently they “ditch” it (more or less):

    Random genetic drift is, by far, the dominant mechanism of evolution.

    Sebestyen

  40. 40
    wd400 says:

    The way I see it, “neutral theory” doesn’t explain anything because the very idea that random changes in a code without any guidance whatsoever can result in the genetic differences between humans and chimp is absurd in the highest possible degree.

    Because you say so?

    As I’ve already streseed, accepting the power of the neutral theory to explain observed genetic dat does not require us to exclude over evolutionary forces, and neutral thoery doesn’t explain all the genetic differences between humans and other apes, just most of them.

  41. 41
    doncarlo says:

    The idea that 100000 generation of random copy errors can generate a human out of a chimp is crazy. Why is even debated?

  42. 42
    Sebestyen says:

    Because you say so?

    Because there is not the slightest bit of convincing proof that this mechanism could actually work.

    The claims made by neutral theory (and any other evolution theory) that complex structures can arise by random effects are extraordinary because they are diametral to everything we experience in everyday life and especially in engineering (which is my area of expertise).

    Therefore it is just and equitable that there also should be extraordinary proof presented by the ones made the claims and this proof is just not there, not even a little bit…

    Sebestyen

  43. 43
    wd400 says:

    The claims made by neutral theory (and any other evolution theory) that complex structures can arise by random effects are extraordinary

    Neutral theory makes no such claim. You should perhaps look into it…

  44. 44
    Eric Anderson says:

    Sal @36:

    The end state after infinite number of generations . . .

    What is the effect after 1 generation or 2?

    It is nice to talk about “infinite generations,” but not really relevant to the real world.

  45. 45
    Sebestyen says:

    Neutral theory makes no such claim. You should perhaps look into it…

    Then maybe Professor Moran and PZ Meyers also don’t know neutral theory?
    Moran states that the difference between humans and chimps exists because 22.4 million mutations have become fixed in each lineage since they diverged about five million years ago. Meyers states that “a huge number of mutations are neutral and there are far more neutral mutations fixed by random genetic drift that there are beneficial mutations fixed by natural selection” and that “random genetic drift is, by far, the dominant mechanism of evolution…”.

    So how is this not a claim that complex structures (i. e. 100 orphan genes with an average length of 300bp in each species) arise by random neutral mutations?

    Sebestyen

  46. 46
    scordova says:

    Eric,

    For generations less than infinity, you need to use something like the Patrick Moran process formula which is non-trivial:

    http://en.wikipedia.org/wiki/Moran_process

    The irony is it’s easier to figure out what happens at infinity than the next generation. I read that entry and realized it sort of glossed over what happens at infinity because by comparison to finite generations, the reasoning is quasi-trivial as illustrated above.

  47. 47
    Eric Anderson says:

    wd400 @35:

    Thanks. Again, I understand the calculation and the random walk. I’m on board with that, as far as it goes.

    From what we’ve been discussing, though, it appears there aren’t in fact 100 mutations (or whatever the estimate was) that get fixed across the population each generation.

    The point about the ancestral allele [is] largely irrelevent to the question of how genetic differences between humans and chimps arose, since such variants are very rare and each compared genome is unlikely to have any such variants .

    Well, I guess that is the question that was being discussed. How did the genetic differences between humans and chimps arise? The OP was following a commonly-asserted path of discussing neutral mutations and the idea that 100 or so would get fixed in each generation. But we still haven’t seen anything in this discussion to confirm that a certain number of mutations in fact get fixed in each generation.

    Anyway, I appreciate you bearing with me. Probably there is some substantive answer out there, so I’ll keep thinking about it some more.

  48. 48
    PaV says:

    wd400:

    Neutral theory explains most of the genetic changes between humans and chimps, and between most other species for that matter. But acccepting neutral theory doesn’t require you to ditch selection.

    History is important when it comes to science.

    The ENTIRE reason that “neutral theory” developed was because Kimura, using gel-phoresis methods found a huge amount of polymorpshisms, so many in fact, that genetic load calculations would not permit them. IOW, if you invoked selective pressure for maintaining all of these polymorphsisms, no organism could possibly survive.

    So Kimura was FORCED to move away from selection.

    Now, when you say that “neutral theory” explains “most of the genetic changes between humans and chimps, and between most other species for that matter,” you’re simply pointing out the whole reason it was formulated to begin with: i.e., to “explain” all of the polymorphisms.

    The “neutral theory” was forced upon evolutionary biologists and population geneticists because of better genetic data. What was at first objected to, is now being touted.

    This might make sense; i.e., population geneticists “need” neutral theory to make sense of what genomic data point out. And to overcome the slowness of NGD, selection must be invoked—I’m sure that’s why you’re saying, ” . . acccepting neutral theory doesn’t require you to ditch selection.” But just because you say that ‘selection’ and ‘NGD’ are ‘evolutionary mechanisms,’ doesn’t mean that you’ve “explained how” evolution happened.

    Among the known data is the fossil record. We KNOW that organismal forms have ‘changed’ over time, just like we KNOW that genomes have a great many ‘polymorphisms.’ But to have a “theory”, you must then say how these two mechansims can EXPLAIN these changes.

    OTOH, we now have evidence of organisms that haven’t changed chromosomally for 180 million years—a huge amount of time where ‘stasis’ is seen, and then, OTOH, be told that a plethora of ‘new forms’ can arise because they became reproductively isolated and changed because of “changed environments.”

    The fossil record tells us: incredible amounts of change, and then stasis; not the other way around.

    IOW, “modern evolutionary biology” is “plausible,” but not likely. OTOH, ID is BOTH ‘plausible’ and ‘likely.’ See Meyer’s Darwin’s Doubt.

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