Friday, April 11, 2014

On the frustration of trying to educate IDiots

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Mutation

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-mutation types
-mutation rates
-phylogeny
-controversies
The Intelligent Design Creationists are remarkably ignorant about evolution so, over the past two decades, we have tried to explain a little bit about modern concepts of evolution. My latest attempt was to describe how modern evolutionary theory (and evidence) is consistent with the differences in DNA sequence between humans and chimpanzees. This required a brief explanation of Neutral Theory, population genetics, and random genetic drift, along with a description of mutation rates.

It didn't work. Creationists like Vincent Torley and Sal Cordova came up with all kinds of reasons why they couldn't believe the explanation. They were joined by Branko Kozulic, a biochemist who decided to help Vincent Torley come up with criticisms that used the right words.

Their latest attempt is at: Branko Kozulic responds to Professor Moran.
This is a continuation of an earlier post, A short post on fixation, to which Professor Moran replied here. He has asked Dr. Kozulic to contact him directly; Dr. Kozulic is now answering that request as co-author of the present post. We asked Professor Moran to answer three questions relating to the fixation of neutral mutations. But before dealing with his answers, let’s confirm that both sides agree that the key point at issue here is the fixation of neutral mutations in the human lineage, subsequent to its divergence from the lineage leading to chimpanzees.
Yes, that's the key point.

There's a lot of gibberish in that post—Nick Matzke calls it the worst post ever on Uncommon Descent—but I'll try and answer the questions.

Here at the first two questions ....
The crux of our dispute with Professor Moran, as agreed by both sides (see above) is the feasibility of 22 million neutral mutations being fixed in the human population, over a period of five million years. These mutations are nucleotide mutations. Professor Moran is kindly asked to answer the following two questions.

First, since we are talking about nucleotide mutations here, why doesn’t he apply the value for the mutation rate per nucleotide in his calculation?
I've described the human mutation rate in a series of posts from last year.

What Is a Mutation?
Estimating the Human Mutation Rate: Biochemical Method
Estimating the Human Mutation Rate: Phylogenetic Method
Estimating the Human Mutation Rate: Direct Method

There are several different ways of expressing the mutation rate. The typical population genetics definition is the number of mutations per nucleotide per generation. In humans, this value is about 2 × 10-8 mutations per nucleotide per generation. It's easier to convert this to the actual number of mutations in order to simplify teaching.

Thus, the number of mutations is 2 × 10-8 mutations per base pair times the size of the diploid human genome (2 × 3.2 × 109 bp). This equals about 128 mutations per generation. (I calculated 130 mutations per generation in Estimating the Human Mutation Rate: Biochemical Method).

This value is called μ (mu) in population genetics calculations. It doesn't matter whether you use the per nucleotide mutation rate or the overall mutation rate as long as you keep the units correct.
Our second, related question is: since the dispute between us is not about the fixation rate of individual genomes(?), then why does he use the value for the mutation rate per individual genome?
The definition of mutation rate refers to a single generation. If you want to know the total number of mutations in the population then you have to multiply by the effective population size (Ne). Torley and Kozulic do this quite frequently in their posts, so I don't know why they are confused. If the population size is 10,000 then the total number of new mutations in the population every generation is Neμ or 130 × 10,000 = 1.3 million. [Most textbooks treat μ as the mutations rate per haploid genome so the total number of mutations is 2Neμ, It doesn't matter, as long as you keep the units straight.)

This is the key to understanding why the rate of fixation of neutral alleles in a population is equal to the mutation rate since if all of the mutations are neutral (a fair assumption in the case of the human and chimp genomes) then the probability of fixation for each mutation is 1/Ne (diploid). The rate of substitution (fixation) of neutral alleles is then Neμ × 1/Ne = μ.

That's the whole point of the discussion. The population size is not relevant. You can't do the calculation unless μ is the mutation rate per generation per individual.

The third question is a bit complicated because it seems to be based on an even more serious misunderstanding of population genetics. Recall that the probability of fixation of a neutral allele is 1/Ne (diploid). What that means is that the vast majority of neutral alleles are lost before they ever become fixed. It also means that the time to fixation is very long (about 4Ne generations for diploid calculations). For an evolving population of 10,000 individuals (effective population size) this means that when a neutral allele is fixed it will take about 40,000 generations, or over one million years for humans and chimpanzees.

During that time, the populations will contain a great deal of variation as alleles are being fixed and lost. In fact, it was the discovery of this enormous amount of variation that led to the development of Neutral Theory [The Cause of Variation in a Population].

Here's the third question from Torely and Kozulic.
Let us now consider two hypothetical models:
  1. In every human generation there was just a single couple that left descendants (effective population size 2Ne = 2), while all others were infertile or killed, so all new 100 mutations that appeared (scattered across some 3,000,000,000 possible sites in the genome) were fixed in the descendants.
  2. In all individuals of one generation (2Ne can have any value), all the new mutations were of the same type and happened at the same sites, so regardless of which individuals mated, all descendants acquired the same mutations. This same process continued for thousands of generations, with various mutations.
The first model would require continual inbreeding, and the second, continual miracles. Neither model appears credible to us; nor do we believe Professor Moran would espouse either of these models. It is important to note, however, that that both models have one thing in common, which is why they both work: all of the mutations fix without having to pass through the polymorphic state. We suspect that Professor Moran’s back-of-the-envelope-calculations which he referred to (see the footnote below), share this same feature. We would therefore kindly ask Professor Moran to provide a numerical value for Ne that does the job, for a model that’s capable of delivering what he needs, which is: 100 new mutations being fixed in each human generation over a period of 5,000,000 years.
I certainly do not think that the fixation of neutral alleles avoids the situation where the alleles persist in polymorphic states for long periods of time. That would be totally contrary to the evidence. All populations contain enormous amounts of variation that cannot be explained by natural selection.

In my calculation, values of Ne are irrelevant so any value will work equally well as long as you realize that you start with an ancestral population containing existing variation. I'm not sure why Torley and Kozulic are so confused by this since they've read some population biology textbooks. Perhaps they are imagining a situation where the ancestral population consists entirely of clones (homogeneous) and no new alleles are fixed for the first million years of evolution?

There are more questions but they don't have anything to do with teaching about why the human and chimps genomes differ. Let them grasp that point before we move on to other questions.


57 comments :

  1. I repeat (said it in a previous thread here), fixation is not the issue. It is the number of differences between the human and chimp reference sequences. For that, the estimates of mutation rate, and of the time involved, and the judgement that most of these mutations are neutral, suffices. We need not get all tangled up in the subject of fixation. We don't know for sure that all of the 22 million differences are fixed in each apecies.

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  2. I believe the reason they think you're afraid of polymorphism is that at one point they quoted Gillespie to the effect that a population of 10,000 can be expected to have little polymorphism. From this I conclude that they don't see the connection among standing polymorphism (proportional to Ne), time to fixation (inversely proportional to Ne), and fixations per generation (not proportional to Ne).

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  3. Seriously. Anyone know what's wrong with BA77? Has he ever actually replied to a comment? And by reply, I mean, has he ever written anything relevant to the argument presented? Everything he fucking writes is completely off-topic

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    1. What's amusing is whan (and it's often) ba77 makes a comment that is specifically labelled as "OT:".

      As opposed to what?

      ba77's massive OT commenting is tolerated there because ba77 is on their side, and without ba77 they'd lose half their bandwidth.

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    2. Recall what Hitler said about Julius Streicher (to paraphrase): if you want a revolution, you have to work with the mentally unstable.

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    3. I guess God made kairosfocus out of the same mold as BA77. Holy fuck.

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  4. I do have to give Torley some credit for admitting error. This may be an ID first. The cracks are now being papered over by gpuccio and others - it was never about neutral variation anyway. Functional sequence is on 'islands' and never changes except neutrally-or-worse. And genomes are deteriorating by the accumulation of the slightly deleterious.

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    1. ... and 'singleton' genes are the latest fad. Their origin is not always clear (by their very nature since, of course, they stand out from phylogenetically-linkable genes), so that's one possible way in for a Designer. He's been particularly busy in E Coli strains. Shigella dysenteriae is the record holder in the study, with 416 unique ORFans (provisional, of course, on relatives remaining undiscovered). Cheers! Mysterious ways, and all that.

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    2. In other words, modern evolutionary theory successfully accounts for the differences between chimps and humans, but... look over there!

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    3. ... but the Darwinists can't explain the origin of the Universe. Gotcha!

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    4. Me:Shigella dysenteriae is the record holder in the study

      Bleh! "The study" ... what study, I hear you ask. This study.

      There was an anchor link in there originally, but I copy-pasted and lost it. Remove my posting rights; I am a buffoon!

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  5. "Perhaps they are imagining a situation where the ancestral population consists entirely of clones (homogeneous) and no new alleles are fixed for the first million years of evolution?"

    OK ... I *might* be able to solve this mystery. I think, I may be wrong, that they're picturing there was a 'first man'. That when we say 'the human and chimpanzee lines diverged' that what they think happened was that a chimp gave birth to a man. That all the other apes went off to be chimps, leaving behind a man. And, one assumes, a woman.

    I've just had a conversation along these lines on Mark Shea's Patheos blog with Michael O'Flynn ('Ye Olde Statistician'), who knows his Aquinas but not his elementary school science. So this is the state of 'intelligent' theology when it comes to human evolution, an article held up by people as squaring the circle. This is what 'smart' looks like in theological discussions of human origins:

    http://www.strangenotions.com/adam-and-eve-and-ted-and-alice/

    His whole argument is based on this: "at some point an ape that was not quite a man gave birth to a man that was no longer quite an ape. He was H. sapiens"

    In discussion, when I said there couldn't have been a 'first man', because speciation works over populations, so there wasn't just one fixed moment where a parent who wasn't a human gave birth to a human, he took it to mean I was saying that 10,000 men had been born in one generation to parents who weren't human. After extensive discussion he just could not get his head around the idea that there wasn't a 'now this creature is a human being' moment.

    If they are following that model, then, yes, 'the human story' starts with one breeding pair of identifiably human humans at a fixed point in time.

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    1. I think, I may be wrong, that they're picturing there was a 'first man'. That when we say 'the human and chimpanzee lines diverged' that what they think happened was that a chimp gave birth to a man. That all the other apes went off to be chimps, leaving behind a man. And, one assumes, a woman.

      Jem - Right, there were two children in England, born to couples speaking Shakespearean English, who spoke more modern English as soon as they could talk. And so on through the generations until it resulted in the English we speak and write today. Of course with the pace of new technology words today, the "mutation rate" for children born with the ability to speak more modern English will have to pick up.

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    2. For anyone puzzled about the somewhat cryptic comment above, what I did was satirize the thinking that evolution occurs in individuals rather than populations by drawing a parallel with the evolution of language. Languages evolve in populations; if they evolved in individuals, as some IDiots picture biological evolution taking place, you'd have individual children being born with "evolved" language abilities, e.g., speaking a new form of English (or Latin speakers giving birth to children whose first words were in French or Italian).

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    3. It's OK, I got it!

      At one point in discussion, this person - a published authority, held up as being one of the smartest theological minds out there - claimed that the 'first man' was the only one to have language. Which, as I pointed out, was a bit like inventing the first telephone, but not the second.

      We shouldn't be wasting our time with the low hanging fruit, the swamp dwellers who want to build an Ark. We should be exposing the intellectual frauds that are the university theology departments. We wouldn't tolerate departments of Astrology, so why should the so-called 'field of study' of theology be treated seriously?

      Here's the end of every theological argument: 'la la la, I'm not listening, you just can't understand this unless you have faith'. Genuinely smart theologians, like Aquinas, had the honesty to admit that. Theology isn't an intellectual discipline, it's something that apes the form of one.

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  6. That third question means that they think that for both the mutation rate and the fixation rate to be the same there has to be only one individual in the population. (!!!)

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    1. (So that all the mutations in that individual get fixed in the population.)

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  7. If the individual is diploid, half an individual.

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  8. I would like to understand some things:

    "For an evolving population of 10,000 individuals (effective population size) this means that when a neutral allele is fixed it will take about 40,000 generations, or over one million years for humans and chimpanzees."

    If the first 130 alleles took 40000 generations to get fixed shouldn't we count only 180000-40000 generations of mutations fixed till today?

    Why the Ne is 10000 ? Is it constant? what if was 20000? That would mean only 100000 generations of alleles fixed till today(13000000).

    Is the 98% precise , what if the similarity is 96% ?

    http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosome
    Jeffrey P. Tomkins a genetisist says the similarity is only 70%, why is he wrong?

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    1. Why the Ne is 10000 ? Is it constant? what if was 20000? That would mean only 100000 generations of alleles fixed till today(13000000).

      John didn't mention this, but if it was bigger there would simply be more mutations. Back-calculated Ne is the size of an idealised population with the amount of variation your 'real' population has.

      Each one takes 4Ne generations to become fixed, so mutations are arriving at fixation (in a steady state theoretical population) at the rate they were being poured in 4Ne generations ago. A mutation in a population twice the size takes twice as long to fix, but there are twice as many of them.

      Real populations are not steady state, of course. There are more complex treatments dealing with that, but they all reduce real messiness to this 'idealised' state, where the Ne represents a theoretical 'ideal' population that would give the parameters displayed by your real one, as if it were eternally steady-state and maximally outbreeding.

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    2. http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosome

      I have looked through this and I confess that I don't quite understand what Tomkins did. Can anyone tell me what "optimally aligned" means? Since his measure of similarity is "percentage of optimally aligned DNA", that's an important question.

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    3. That's not the reference Torley used to support his claim that the similarity could be as small as 70%, is it?

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    4. Tomkins is wrong, in large part, because of the way he set up his BLASTn search. He wrote a script to constrain search returns to only those sequences that matched 100% on I think it was word lengths of 19. In other words, if a human sequence 19 bases long was compared to a chimp sequence 19 bases long, he told the program to only return matches if they were 100% identical. It is easy to see how he managed ot get such a low figure by engaging in that hood winkery.

      Also of note is that none of these creationists seem to consider how their criteria would affect pairs of creatures they clam are intra-kind variants. Are they afraid to do so?

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    5. I thought it was "niwrad" (not Torley) who showed that similarity was 65% instead of 98.77% -- by requiring perfect matches of blocks of 30 bases.

      At the time, I wrote a response to that on Panda's Thumb.

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    6. Sam: Where do you get the information about Tomkins' methodology?

      Joe: It's Tomkins we're talking about here, not Torley or niwrad. If Sam is right, Tomkins and niwrad used similar methods. But I'm not sure he's right. It all depends on what "percentage of optimally aligned DNA" means, and I can't myself figure it out.

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    7. That would appear to be the article I just cited above. Why would you imagine that citing it back to me would remedy my confusion?

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    8. Sorry for being so late to the party, but Tomkins is wrong about his 70% because of a bug in the BLAST software. See my paper (Tomkins-BLAST.pdf and Figures.pdf):

      https://www.dropbox.com/sh/dm2lgg0l93sjayv/AAATnWSJdER53EYEYZvcgiwma?dl=0

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  9. What do you mean "till today"? Starting when? You understand that our lineage goes back several billion years, and that mutations have been happening, some of which eventually become fixed, all through that time. There is no "first 130 alleles". Given a constant population size of 10,000, mutations fixed today happened on average 40,000 generations ago, mutations fixed 40,000 generations ago happened on average 80,000 generations ago.

    10,000 is someone's estimate of the average Ne in the human lineage for the past several million years.

    No, the 98% is not precise. The actual figure is 98.77% according to the chimp genome paper. (That's average percent identity of alignable sites.) One can of course measure similarity in a great many ways, some of them more sensible than others.

    Tomkins is a geneticist? Are you sure about that? He isn't wrong, precisely. He's just chosen a rather odd way of measuring similarity that has nothing to do with mutation rates and so isn't a good number to use in Larry's calculations.

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  10. If a mutation to get fixed takes 40000 generations doesn't that mean that the last 40000 generations are not fixed yet? So for the number of fixed mutations since the last common ancestor shouldn't the calculation be (180000-40000)* 121? If the population size is 20000 then the number would be (180000-80000)*121.

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    1. Lots of (nearly) neutral mutations that had occurred long before the most recent common ancestor were still on their way towards fixation in either lineage after their separation. The common ancestor was a species, not an individual or a collection of identical clones. Variation within that species -- the heritage of its earlier history -- cannot be ignored when you calculate differences fixed by random drift.

      John said it above, by the way.

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    2. doesn't that mean that the last 40000 generations are not fixed yet?

      It doesn't particularly matter. If there is a difference between the reference chimp and the reference human (both single individuals), that counts towards the total. If there isn't, it doesn't. At the extreme, about 130 mutations in each reference individual will be unique to those respective individuals.

      This pair of individuals differs by that number of sites. The expectation is that this is representative of the differences we would find if we took any other pair and counted. Fixed sites would form a subset of the total variation counted, with the same difference in every pair we looked at.

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  11. "The actual figure is 98.77% according to the chimp genome paper. (That's average percent identity of alignable sites.) One can of course measure similarity in a great many ways, some of them more sensible than others."

    Why only the alignable sites count? If it's not alignable doesn't that mean that is different? Why don't count what is different in a similarity comparison?

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    1. If you're trying to estimate mutation rate, you have to determine how many mutations have happened. regions that aren't alignable probably got that way from a very few mutations (and most likely just one) each. For example, if a single deletion mutation removes 50,000 bases from the chimp genome, the human genome is left with 50,000 bases that aren't alignable with the chimp. Calling that 50,000 mutations would, I hope you can agree, be silly: it's one mutation, and not even one in the human lineage.

      Now of course one can make different sorts of comparisons for different purposes. The one we're using here is an attempt to determine the expected number of mutations. The one Tomkins came up with had a quite different purpose and so is not appropriate for the present discussion. (I believe Tomkins' purpose was to find a measure that made humans and chimps as different as he possibly could, because he really wants them that way. Not really relevant to biology at all.)

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  12. I repeat (said above, and in two other places), fixation is not the issue.

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    1. Joe, you are the expert. I am not.

      Could you explain what you mean in more detail. From what I read in population genetics textbooks (e.g. Li, 1997), substitution is defined as fixation. In other words, when you talk about substitution you are talking about an allele becoming fixed in a population.

      The probability of fixing a new, single, (nearly) neutral allele is approximately 1/(2N) in diploid species, according to everything I've read. The number of new mutations in a population is 2Nμ where μ is the rate per haploid genome. According to my understanding of population genetics this leads to the conclusion that "for neutral mutations, the rate of substitution is equal to the rate of mutation" (Li, 1997). In this case substitution = fixation.

      What am I missing? Are you making the point that if we were to compare the genomes of any randomly chosen human and a randomly chosen chimpanzee, some of the differences would not be fixed in the population? This would certainly be true of the many sites that were heterozygous.

      What percentage of the 22 million (approximately) sites in the chimpanzee genome that differ from the common ancestor do you think are not fixed in the chimpanzee population? Why does this number correspond approximately to the predicted number of substitutions (fixations) if fixation is not the issue?

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    2. Larry, the observations you are trying to explain are the differences between the human and chimpanzee reference sequences. Each position in the human reference sequence comes from a parent, and that copy from its parent, and so on back to the common ancestor of humans and chimps, about 200,000 generations ago. Similarly the ancestry of the corresponding position in chimps goes back along such a chain of ancestry.

      Once they are both back in the ancestor population, they then continue back until they have a common ancestor. How long that will be depends on the common ancestor's population size.

      If we have neutral mutations occurring at a known rate, we can then calculate what is the probabilitiy that the present-day chimp and human sequences differ at that site. You have done such a calculation and shown that there is a pretty good fit between the inferred mutation rates and the inferred times and generation lengths.

      But note what you don't need to do for this calculation. You don't need to see whether the new bases on either lineage are fixed in the human population or fixed in the chimp population. Anyway, we don't yet have big enough samples from either species to be able to directly look at whether a change is actually fixed. But that's OK, because you have shown that the mutation rates are the right size to explain the observed differences between the reference sequences.

      A couple of footnotes: (1) The coalescence time, the time for two copies in the chimp/human ancestor to come from a single copy, could be another 2N generations, which would be a long time, maybe even another 200,000 generations back. But as you were trying to see whether there was enough time for enough mutation, that just gives you even more time.
      (2) I can do some rough calculations and show that almost all of the differences between the reference sequences are in fact most probably fixed in both populations. But the point is that we never really needed to ask that question in asking whether there was enough mutation to explain the difference in reference sequences.

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    3. I should make clear that the "chain of ancestry" I described is a chain of single copies of the gene (or piece of DNA). So a copy in me comes from my mother, and before that from (say) her father, and from his father, and from his mother, and so on. Until we get back to one particular copy in the common ancestor of chimps and humans. Likewise the copy of that piece of genome in Cheetah the Chimp comes from his father, the father's mother, and so on back, until we find it in a particular copy in the human/chimp common ancestor. Most likely a different copy than the one that is ancestral to my copy of that part of the genome.

      Before that there is more time back until they both come from the same individual copy of that gene (or that piece of the genome).

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    4. Thanks Joe. I thought that's what you might mean.

      It's a different calculation than the one I made. I was referring to the evolution of populations and not the lineage of individuals. I wanted to show the creationists that most of the fixed differences between chimps and humans were neutral.

      I wanted to teach them that alleles can be fixed in a population by mechanisms other than natural selection. So, in my calculation, fixation is important and it's important in the population genetics textbooks that describe this calculation.

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    5. I wanted to show the creationists that most of the fixed differences between chimps and humans were neutral.

      But in doing so, you'd have to distinguish fixed sites, not a composite set from single individuals - data that isn't (AIUI) available.

      Joe: I can do some rough calculations and show that almost all of the differences between the reference sequences are in fact most probably fixed in both populations.

      My own rough calculation using 27.5 years as a generation and Ne as 10,000 gives the expectation that such a population would only now be fixing neutral mutations generated 1.1 million years ago, which leaves quite a significant proportion polymorphic - especially given population growth. I may well be missing something.

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    6. Allan, why did you choose 27.5 years as a generation? Humans and chimps reach puberty at about the same age (10-14, with some exceptions on either side of that range), and I can't think of any reason why the common ancestor wouldn't have been sexually mature at the same age or even younger. Plus, the further back in time, the fewer 'rules/laws' there would have been. A hundred thousand, a million, 5 million, 10 million years ago nobody was telling anyone how old they had to be before having sex and babies. Even now, with lots of rules/laws, early teenage girls and boys and some even younger are not only having sex but many girls are having babies too. I have always been mystified as to why mid 20s are chosen as generation times.

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    7. Allan, why did you choose 27.5 years as a generation?

      To be honest, it was a half-remembered factoid. I'd agree, it seems a bit on the long side. Bear in mind we need an average, however, and I was talking only of the last 40,000 generations, and only on the human side. Halve it if you like - the point remains that a significant portion of the 5 million years since the split is covered by a period which is not long enough for mutations arising within it to (on the average) fix.

      Time's not really the issue. I chose 40,000 generations because that is the 'expected' time to fixation for a new mutation in a population with Ne 10,000. Therefore most mutations in the last 40,000 generations will not be fixed (some will, of course - it's a distribution).

      An individual has 130 new mutations of its own, plus 65 from each of its 2 parents, plus 32.5 from each of its 4 grandparents, and so on. Ultimately ancestry coalesces - we don't double individuals as we double ancestral nodes - but the overall result is the same, 130 mutations from each generation -> 130*40,000 = 5.2 million in the average time it takes a single fixed mutation to get from origin to fixation. That's a significant chunk of 22.4 million. (Of course there are forces which confound this naive analysis).

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    8. The average generation time for humans is closer to 30 years and for chimps it's 25 years. I used the average (27.5) in order to make the calculations easier to understand. Remember, I was explainig this to creationists.

      It's important to remember that the generation time represents the average time between generations and not the time when boys and girls are first able to have babies. It doesn't even mean the time when parents have their first child.

      This value for humans (30 years) comes from genealogical studies as I explained in earlier posts. It's almost exactly the average in my own family tree dating back 1000 years.

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    9. Allan and Larry, thanks for your responses.

      Allan, which "forces" do you mean?

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    10. One issue that seems to get lost in this - yes, the current human generation time may be 30 and chimps 25, but 5 million years ago there were neither chimps nor humans. It seems likely to me that the species that initially resulted from that split were more similar to larger monkeys than to either modern humans or modern chimps, and such creatures tend to have shorter generation times, closer to 12-15 years.

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    11. It seems likely to me that the species that initially resulted from that split were more similar to larger monkeys than to either modern humans or modern chimps...

      That seems extremely unlikely to me. They were almost certainly more similar to humans and chimps than to anything else, and any characteristics shared by humans and chimps are most likely to have been present in their common ancestor.

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  13. By the way, it seems Dr Torley no longer acts as spokesman and interpreter for Dr Kozulić. The latter got himself a professional solicitor, Barry Arrington, Attorney at Law.

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  14. I just came across this: http://www.sciencedaily.com/releases/2014/04/140414091917.htm

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    1. I don't know why there are large spaces between my words above.

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    2. Screenshot:

      http://postimg.org/image/xsfpds6q7/

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  15. John Harshman:
    "If you're trying to estimate mutation rate, you have to determine how many mutations have happened. regions that aren't alignable probably got that way from a very few mutations (and most likely just one) each. For example, if a single deletion mutation removes 50,000 bases from the chimp genome, the human genome is left with 50,000 bases that aren't alignable with the chimp. Calling that 50,000 mutations would, I hope you can agree, be silly: it's one mutation, and not even one in the human lineage."

    How do you know the 50000 bases left in the human genome didn't mutate 1000 times before the deletion from chimp genome and 1000 times after the deletion? How do you know what's in plus in human genome isn't what makes us truly different from chimps?

    Again why the main differences are not counted in a similarity comparison? How can you say is 98.9 similar when you left out a great deal of differences?

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  16. How do I know the 50,000 bases didn't mutate? I don't. Why is that relevant?

    How do I know what's in plus in the human genome isn't what makes us truly different from chimps? I don't even know what that question meant. But recall that the original question was about whether 22 million is a good number for the number of mutations in the human lineage. Any mutations not taken into account by that number must be a very small proportion of the total and can be ignored. Remember, all we care about at the moment is the quantity, not what, specifically, those mutations actually do.

    The main differences aren't counted because we aren't interested just in some measure of similarity. We're interested in estimating how many mutations have happened in the human lineage. If one mutation causes 50,000 differences, it's still just one mutation.

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  17. Until someone can produce a working model for unguided evolution, there isn't anything to teach.

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