# Adam and Eve and Jerry and Bryan and Vincent

Bryan College in Dayton, Tennessee has recently added to its statement of faith, to which faculty members must subscribe, a “clarification” that

We believe that all humanity is descended from Adam and Eve. They are historical persons created by God in a special formative act, and not from previously existing life forms.

Jerry Coyne at his Why Evolution Is True blog has pointed at this with alarm here, and he linked back to the Chattanooga Times Free Press story here. Jerry cites studies showing from the amount of variability in human populations, that effective population size of the individuals leaving Africa in the Out-Of-Africa event cannot have been much less than 2250, and the effective population size in Africa cannot have been much less than 10,000.

VJTorley at Uncommon Descent has published a firm response, saying Jerry was “In a pickle about Adam and Eve” and saying that when he said that “2250 is greater than two”

Evidently math is not Professor Coyne’s forte.

Note: 2,500 isn’t the same as 2,250.

Note: 2,250 + 10,000 = 12,250.

The math lesson is over.

He also quotes a paper by Luke Harmon and Stanton Braude, which notes that effective population sizes can be larger than actual population sizes, and says

It’s rather embarrassing when a biology professor makes mistakes in his own field, isn’t it?

Has Jerry gotten himself into a pickle? I have some background in this area — I have worked on coalescent trees of ancestry of genes within a species, I wrote one of the two basic papers on effective population size of populations with overlapping generations, and I even shared a grant with Luke Harmon two years ago.

A few simple points:

1. 10,000 + 2,250 = 12,250 all right, but in fact that number is even greater than 2.

2. Effective population size can be greater than population size. It can get as much as 2 times higher. That still leaves us with a long way to go.

3. The Bryan College administration does not know how to write a Clarification. Their statement says that all humanity are descended from Adam and Eve, but does not make it clear whether there could have been other ancestors too. I suspect they meant that there weren’t any.

4. According to UD’s own statements, Intelligent Design arguments are supposedly not statements about religion, so that ID arguments do not predict anything about Adam and Eve. ID proponents are being slandered when they are called creationists, we are told repeatedly. So why the concern about Adam and Eve at UD?

So was Jerry wrong? About Adam and Eve, no. Though he is wrong when he says that his “website” is not a blog.

This entry was posted in Evolution, Intelligent Design by Joe Felsenstein. Bookmark the permalink.

## About Joe Felsenstein

Been messing about with phylogenies, coalescents, theoretical population genetics, and stomping bad mathematical arguments by creationists for some years.

## 103 Replies to “Adam and Eve and Jerry and Bryan and Vincent”

1. Allan Miller
Ignored
says:

PaV has entered the fray. I started to try and make sense of his additional criticism, but gave up. He does make one easily-dealt-with howler, that an Ne of 28,000 can be reached from 2 individuals within 15 generations because 2^15 ~ 32,000. The diversity of such a population would be substantially less than that of a population with Ne 28,000.

And he declares that the discovery of [some] function in non-genic DNA means that neutral drift is an invalid assumption.

2. Steve Schaffner
Ignored
says:

Allan Miller:
PaV has entered the fray. I started to try and make sense of his additional criticism, but gave up. He does make one easily-dealt-with howler, that an Ne of 28,000 can be reached from 2 individuals within 15 generations because 2^15 ~ 32,000. The diversity of such a population would be substantially less than that of a population with Ne 28,000.

I believe that would give you an effective population size of 15.

And he declares that the discovery of [some] function in non-genic DNA means that neutral drift is an invalid assumption.

If much of the genome is functional, widespread purifying selection would greatly reduce the effective population size compared to the census size. So the actual population would have been much larger than current estimates would suggest.

3. petrushka
Ignored
says:

Steve, there seems to be some difference in the way you interpret the word Polygenism and the way Joe interprets it.

Not to mention the way Gregory interprets it.

I think Joe has made his position clear, but I don’t understand your position or Gregory’s.

4. Steve Schaffner
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says:

petrushka:
Steve, there seems to be some difference in the way you interpret the word Polygenismand the way Joe interprets it.
Not to mention the way Gregory interprets it.

I think Joe has made his position clear, but I don’t understand your position or Gregory’s.

Throughout I have been using Joe’s Polygenism Two. Have I said anything inconsistent with that? (It wouldn’t surprise me if somewhere I’ve typed ‘monogenism’ when I meant ‘polygenism’ or vice versa — these aren’t terms I’m used to using — but I’m not going to bother checking.)

5. petrushka
Ignored
says:

Steve Schaffner: Throughout I have been using Joe’s Polygenism Two. Have I said anything inconsistent with that? (It wouldn’t surprise me if somewhere I’ve typed ‘monogenism’ when I meant ‘polygenism’ or vice versa — these aren’t terms I’m used to using — but I’m not going to bother checking.)

I guess I just needed that made explicit. Gregory was all over you, and with that clarification, his hostility makes no sense.

I have been curious for some time whether he believes humans were specially created. He has hinted at this but never made it explicit.

6. Neil Rickert
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says:

Steve Schaffner: Throughout I have been using Joe’s Polygenism Two. Have I said anything inconsistent with that?

Personally, I have found your posts very clear and very consistent.

petrushka: I have been curious for some time whether he [Gregory] believes humans were specially created.

As best I can tell, he believes that Gregory was specially created.

7. petrushka
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says:

Clear to someone familiar with the terminology used in genetics, but not, alas to me.

Now I wonder if Gregory will return and tell us why he thinks there is a problem.

8. Steve Schaffner
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says:

petrushka: Gregory was all over you, and with that clarification, his hostility makes no sense.

I think he doesn’t like me very much(*). I have on occasion been a little snarky with him, after he’s suggested that pervasive ideological evolutionism was causing grave problems, but never delivered the punchline of what the problems were, or even exactly what evolutionism is.

(*) Which is okay — some days I don’t like me very much either. But my dog still loves me, and that’s all that matters, right?

9. Allan Miller
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says:

Update from vjt:

A final suggestion for Professor Coyne. Coyne claims that the effective population sizes he cites are “based on reasonable estimates of mutation rates.” Coyne is assuming here that the mutations are natural and undirected. If Coyne wants to refute the Adam and Eve hypothesis as entertained by believers in intelligently guided evolution, then the question he really should be asking himself is: what would the effective population size need to be, if the mutations that gave rise to the human line were artificial and directed?

I’d like to see Torley have a stab at modelling his own question, with some clarification on unmentioned process such as selection/drift and recombination.

He’s basically talking of using mass-mutation to retain N=2. He can’t do single mutations and wait for ‘conventional’ fixation (no time), so he’s going to have to amend genomes en masse. The Designer is perhaps capable only of creating 2 individuals from scratch, and the rest are made in the conventional manner (it’s a cost-effective business model!). But they are all more-or-less the same. You need variation because … well, you’ve got variation, and you need to account for it without abandoning N=2. So the Designer has the capability of mass-changing an entire subset of a population at every polymorphic locus, but a different-sized subset each time, in a manner that recovers trees of apparent descent coalescing upon N>2 populations (some of them non-human) when you actually analyse ’em?

I hope I haven’t misrepresented the hypothesis.

10. petrushka
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says:

…what would the effective population size need to be, if the mutations that gave rise to the human line were artificial and directed?

All science so far.

A variation of Last Thursdyism.

11. DNA_Jock
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says:

Allan Miller: He can’t do single mutations and wait for ‘conventional’ fixation (no time), so he’s going to have to amend genomes en masse.

I will admit that I haven’t thought this through (I’m all outta brain bleach) but I imagine VJT’s master mutator is introducing prevalent alleles early in his rapidly expanding population, and rarer alleles later. So he can achieve the observed allele frequencies by judicious choice of how far back he introduces each (set of) polymorphisms into the germline of individual ancestors (who have many living descendants.)
Of course this approach would lead to some very strange linkage disequilibrium results.

12. petrushka
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says:

The Devil did it to deceive us.

13. Steve Schaffner
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says:

DNA_Jock: I will admit that I haven’t thought this through (I’m all outta brain bleach) but I imagine VJT’s master mutator is introducing prevalent alleles early in his rapidly expanding population, and rarer alleles later. So he can achieve the observed allele frequencies by judicious choice of how far back he introduces each (set of) polymorphisms into the germline of individual ancestors (who have many living descendants.)
Of course this approach would lead to some very strange linkage disequilibrium results.

The MM (master mutator) would still have to be mutating multiple genomes, since otherwise you won’t get derived allele frequencies greater than 50%. Unless, of course, they’re not really derived alleles, and the MM carefully chose a set of sites, made them different from chimpanzee at those sites, and then added a bunch of mutations to make it look like there was a smooth derived allele frequency spectrum from zero to one. Being careful at the same time, of course, to choose sets of changes that look exactly like naturally occurring mutations, with the right ratio of transitions to transversions, and the appropriately elevated rate of mutations at CpG sites, with the rates on the sex chromosomes adjusted too. Plus the greatly elevated recombination rate to make LD more or less work out.

Yeah, if you work hard enough (or make your putative MM work hard enough), you may be able to come up with a creationist model that exactly mimics what you expect from evolution. Quite a triumph for the creationist approach.

14. keiths
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says:

…what would the effective population size need to be, if the mutations that gave rise to the human line were artificial and directed?

It’s funny to see these guys trying to do science, then casually tossing in a ‘Poof!’ here and there.

15. petrushka
Ignored
says:

This one’s a big badda poof. The biggest since Last Thursday.

16. llanitedave
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says:

petrushka: I guess I just needed that made explicit. Gregory was all over you, and with that clarification, his hostility makes no sense.

I have been curious for some time whether he believes humans were specially created. He has hinted at this but never made it explicit.

Gregory’s hostility never made sense, except in the light that it’s intrinsic to his persona. As for polygenism two, all of Joe’s and Steve’s comments have been completely consistent with that interpretation, as far as I could read them.

17. Allan Miller
Ignored
says:

I imagine VJT’s master mutator is introducing prevalent alleles early in his rapidly expanding population, and rarer alleles later.

Mmmm, I suppose. Although my ‘no time’ also related to the recombinational issue – you can put a mutation on a chromosome, but you need it recombining out of the background, which takes a few generations of slicing. You can up the recombination rate, though you are still only recombining sites on 2 chromosomes in any one meiosis. And you are ‘upping’ the gene conversion rate at the same time. You need to end up with a mosaic that looks like multiple ancestors when there weren’t.

And if you’re going the ‘conventional’ route, you’d have to make twice as many changes just to get 50% of them through the first meiosis, with similar ongoing requirements. It’d be nice to turn drift off for a while, for the alleles you want to get through (which means turning on artificial selection, and probably deciding who mates with whom down to specific gametes, and where the crossovers go and which recombinant gamete gets the thumbs-up).

I’m not going to tell teh Designer his job, but I’d suggest it’s not enough just to control mutation serially and rely on descent.

18. Gregory
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says:

This has been a helpful thread so far, first, in learning about Steve Schaffner’s views, which he has not shared here before now (at least, as much as I’ve seen him participate) and also in revealing that Joe Felsenstein sadly can’t (or just hasn’t found a way yet to) elevate above biology to speak about human beings on a higher level.

The key question is how Bryan College interprets polygenism, whether they focus only on biological polygenism and if they require their employees to accept theological polygenism. Any attempt by people here to cut off talk of theological monogenism is simply a distraction. But that’s what is mostly happening by TSZers. Any private Christian university, nay, any private university among the Abrahamic faiths *should* require theological monogenism as a foundational principle. Can that be agreed here?

Therefore, first, I’d like to ask Steve another question, if he’ll indulge me. Do you accept theological monogenism or not? You’ve stated you accept biological polygenism and focused your (strictly scientific) posts on that, which is a different question. I’d like to hear you give the more important answer if you reject theological polygenism.

That said, I should now wheel back on one thing I said to Steve, which rolled half a wheel too far:

Steve wrote:

“The genetic evidence strongly supports polygenism for humans.”

I replied:

“Then you are heterodox in the eyes of the RCC & OC, as a Protestant “of no particular flavour.”

Biological polygenism is not necessarily heterodox (as the links provided above show), but theological polygenism is. That’s why the above question to Steve is asked. Admittedly, I provoked him, calling out his courage, because previously all he did was criticise without providing any positive messages of his own. Now the opportunity is open to him – a direct invitation.

Steve doesn’t much like the term ‘BioLogos,’ which is fine, but he does ‘strongly’ support the BioLogos Foundation’s work. That would make him a company of one (and a half – I’ll call myself halfway on-board with BioLogos’ evangelical anti-creationist approach) here at TSZ because the small few IDists here loathe BioLogos and the rest of the TSZ ‘community’ are agnostics or atheists, oftentimes anti-theists; they certainly don’t appreciate BioLogos nor probably know much about it. (e.g. KN could benefit, but his agnosticism seems to restrict him.) Many TSZers likely side with Coyne on the very things Steve pays him no attention; just knowing about fruit flies and speciation is a rather low position on the totem pole in the broader discussion.

“I’ve been quite public elsewhere: I strongly support BioLogos’s campaign. I think both the American evangelical church and science in this country stand to gain from it.” – Steve Schaffner

Well, I’m not familiar with what ‘elsewhere’ you’re referring to, so unless you’d like to link that here, it is irrelevant and unknown.

“Polygenism Two. That’s the one relevant to Adam and Eve.” – Joe Felsenstein

I disagree, that is, *if* the thread is actually interested in Bryan College’s Clarification. I’m not sure that it is, for obvious reasons. If Joe just wants to narrow the discourse to (evolutionary) biology, then it’s a rather boring conversation imo.

To me, Adam and Eve are properly a theme of anthropology, psychology and sociology, and both philosophical anthropology and theological/worldview anthropology (i.e. not just physical or biological anthropology) should be heartily welcomed for their important contributions. Paleontology of course is also involved, but a physical ‘proof’ of A&E is simply far-fetched nonsense.

Were Adam and Eve not human beings, and thus don’t they rise into the anthropic category? If so, then why are you reducing them to ‘only animals,’ Joe (polygenism 2), having just now for the first time looked up in pop dictionaries a rather more complex conversation? You sound like a debutant, Joe, not like a scholar on this topic.

“The Bryan College administration does not know how to write a Clarification. Their statement says that all humanity are descended from Adam and Eve, but does not make it clear whether there could have been other ancestors too.” – Joe

Well, personally I wouldn’t sign the Bryan College ‘Clarification,’ not being a USAmerican fundamentalist or right-wing evangelical. I guess that means they wouldn’t hire me. Accepting theological monogenism, however, is something that all Abrahamic believers should (nay, even eventually *must*) confront, regardless of their position on biological polygenism. Can that be affirmed here? Or are people even ‘skeptical’ of that?

As a social scientist, I see a lot of problems with simple biological polygenism depending on the way one defines it; neo-eugenics, civilisational racism (e.g. those savage Indians!), vilification of ‘others,’ and many other challenges lurk in the shadows of this anti-humanistic genomic idea.

“why the concern about Adam and Eve at UD?” – Joe

First and foremost, because it is one of the greatest stories ever told. Whatever one’s position on it, the Garden, the Fall, the Exile, the relationship between men and women, the reality (or even the possibility) of Sin, the promise of Redemption, of Salvation, of Death and Life, of Evil and Good, etc. – these are *still* relevant themes in human existence. Only cultural, small-minded & small-hearted idiots dismiss the Book of Genesis based on natural scientism. Biology is powerless in the face of these larger humanistic questions and biologist-theists seem clearly to understand this much better than biologist-atheists like Joe Felsenstein, Mike Elzinga (oh, sorry, he’s just a physicist) or Ann Reid.

If the Bryan College ‘Clarification’ is indeed the main topic of this thread (which now seems questionable), then one simply cannot avoid speaking about the orthodox rejection of theological polygenism by Abrahamic believers. Indeed, that view has played a monumental role in ‘western’ ideology, in democracy, freedom, human rights, etc. that mere biology cannot and will not undo. It doesn’t seem though that Joe wants to address these higher themes (he even mocks them, with his faux-capitalisation).

Otoh, Steve Schaffner, a natural scientist, but a theist also, seems to have read the Catholic opinions on this topic that I linked above and recognises the appropriate distinction. Thus, it would be helpful to hear from him about theological monogenism, as a biologist. Is it possible for a biologist today to accept theological monogenism, even if they insist upon biological polygenism? That is probably the most significant question that’s been posed thus far in the history of TSZ.

Steve wrote:

“From your description of the links, they’re all attempts to combine theological monogenism with biological polygenism. They are therefore irrelevant to the OP, which concerned biological monogenism.”

To me, the theological monogenism of Bryan College is a more important component in the OP than any biological monogenist speculations. Of course, they don’t agree, but that’s on them. It is why they formulated their provincial ‘Clarification’ and shows their backwardness on the global scale.

“I am sure few of us can separate our worldview from our views on science.” – Joe Felsenstein

Why can’t a more holistic approach be tried where science, philosophy and theology/worldview are seen as complimentary, where peoples’ faith, reason and hope work together? Is it only nihilists, atheists, skeptics and agnostics who disagree with such a cooperative, integral approach?

19. OMagain
Ignored
says:

Gregory: Why can’t a more holistic approach be tried where science, philosophy and theology/worldview are seen as complimentary, where peoples’ faith, reason and hope work together?

Nobody is stopping you renting a compound and getting like minded folk together to start a new society…..

20. DNA_Jock
Ignored
says:

I quite agree. My comment about linkage disequilibrium was a lame attempt at litotes. To be more specific, I believe that VJT et al have not thought through just how involved this meddling would have to be, and how much of it would have the sole goal of deception. Satan was an industrious fellow, it seems.

21. DNA_Jock
Ignored
says:

Gregory: If Joe just wants to narrow the discourse to (evolutionary) biology, then it’s a rather boring conversation imo.

Well, you are entitled to that opinion, but you should acknowledge the fact that the OP is about biology. You are the one who introduced a pair of precious “isms”, so your claim that

Any attempt by people here to cut off talk of theological monogenism is simply a distraction.

is hilarious.
You still have not even attempted to make your case as to why we should care about your personal views of HPSS. Lame attempts at vituperation seem to be all you have provided so far.
Your comment about TSZers and BioLogos is wrong, too.

22. Gregory
Ignored
says:

Bryan College’s ‘statement of faith’ is not just about biology. Saying “the OP is about biology” is therefore myopic.

23. petrushka
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says:

OMagain: Nobody is stopping you renting a compound and getting like minded folk together to start a new society…..

I would say that flitting from forum to forum and calling everyone else stupid and inadequate puts up a few roadblocks on the road to Utopia.

24. Allan Miller
Ignored
says:

Nobody is stopping you renting a compound and getting like minded folk together to start a new society…..

Complete with doctrinal statement …

25. Neil Rickert
Ignored
says:

Gregory: The key question is how Bryan College interprets polygenism, whether they focus only on biological polygenism and if they require their employees to accept theological polygenism.

No, that’s not a key question at all. The only question for me, and it is hardly important enough to call “key”, is whether I should think of Bryan college as an academic institution or as an indoctrination tank.

Any private Christian university, nay, any private university among the Abrahamic faiths *should* require theological monogenism as a foundational principle. Can that be agreed here?

If they want to be indoctrination tanks, and not real universities, then I guess they can do that.

26. Allan Miller
Ignored
says:

For those disreputable souls not above peanut-gallery commentary, there is an amusing byplay in UD comments as wd400 explains the harmonic mean wrt Ne and a varying succession of census sizes. PaV (“I study quantum physics”) seizes on this to aver that if you take the last 3 generations of a 15-generation doubling from 2 then make it steady for 4 more you get a Ne of 24,000! You just ignore the first 12 generations, and hey presto.

Furthermore:

If a population is steadily increasing, and then reaches some stabalized level, then please explain how you can then speak of a “bottle-neck.” How can something be constrained when it is steadily increasing to some greater level? Should the population shrink to some reduced level at some later time, then, yes, you can talk about a “bottle-neck.”

And drift is a cheat for Darwinists because it’s not Darwinian.

wd400 wisely avoids even acknowledging the goading from BjornAgain77 (Knowing Me, Knowing You thru The Name of the Game) re: the complete destruction of evolutionary modelling as an approach by the one ‘correct’ model, Sanford’s. That I could develop such wisdom.

eta:

Let me correct a number I’m using: I’ve used 1/4Ne as the probability of a mutation spreading via random genetic drift through a population. But this is for diploid populations. Since we’re considering haploid populations […]

We are? Right answer, wrong reason.

27. Joe Felsenstein
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says:

In response to Gregory’s most recent two comments:

The original post was a response to posts at UD and at Why Evolution Is True, and they were about whether the scientific evidence contradicted literalist interpretations of Genesis. VJT at UD had argued that Jerry Coyne’s statements were scientifically wrong. People here have said some interesting things about ways that the UD folks are trying to force the science to fit Genesis.

Bryan College’s “clarification”, mentioned in Coyne’s post and with that part quoted by VJTorley, required adherence of science teachers to a (surprisingly ill-defined) theological position. Discussion of what the Bryan College statement really meant is of course on-topic. And that discussion would be about theology. But discussing that is not compulsory.

28. Allan Miller
Ignored
says:

Eric Anderson asks a couple of questions in comments (though I don’t kid myself he will wander this way to read my answers):

For neutral evolution, population size doesn’t matter, correct? At least not in terms of having a particular change becoming fixed in the population.

For a particular change, it takes longer to fix in a large population. For the generality of neutral changes, they are being fixed at the same rate they are being produced irrespective of population size, because the longer per-mutation time to fixation is cancelled out by the proportional increase in mutations produced.

Dumb question about neutral evolution:

There are three basic types of changes: deleterious, beneficial, and neutral.

1. Deleterious everyone knows what will happen.

2. Beneficial can help the organism and be subject to selection.

3. Neutral is just that — neutral to the organism and invisible to selection.

It is argued by some that most changes/mutations are neutral. Let’s assume for a moment that is true.

Why then are neutral changes sometimes held up as an example of evolution? By very definition, they are neutral — meaning they are, by very definition, not causing any evolution.

This is incorrect. Evolution, defined either as change in allele frequency in a population or as descent with modification, does not depend on Natural Selection. Nor does deleteriousness guarantee elimination.

Indeed, the existence of numerous neutral changes in an organism demonstrates that the organism robust against change. In other words, it is resistant to evolution.

All of this follows rather naturally and, it seems, inexorably from the idea of pervasive neutral changes/mutations.

Thus, at most, neutral changes are just that — neutral — and not relevant for evolution. On the other side, however, one could quite easily argue that neutral changes demonstrate that organisms can undergo significant perturbations in the genome and otherwise, while still not exhibiting any meaningful organismal change, and therefore neutral changes/mutations are actually evidence against the “plasticity” of organisms that is important to evolutionary theory.

Thoughts?

Wrong. Neutral /= no change, certainly in genotype but even in phenotype. It just means no selection (more precisely, no effective selection).

29. Joe Felsenstein
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says:

Of course, neutral evolution can, in principle, cause you to wander into a different part of the genotype/phenotype map, in which further substitutions at the same sites now aren’t neutral.

It looks as if Anderson is trying to argue that natural selection on random mutations is ineffective in increasing fitness. He might spend his time instead on showing that deleterious mutations can’t be eliminated, or that beneficial mutations can’t be fixed. He will be disappointed there. Creationists (and these arguments are creationist arguments, not ID arguments) often cite the fact that most mutations are deleterious. They assume that this must mean that most substitutions are deleterious. They’d be shocked if they actually calculated the fixation probabilities of the two kinds of mutants and saw how strongly selection filters out deleterious mutants.

30. petrushka
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says:

Which is why I think it is not a good idea to say neutral drift is not natural selection. It is neutral selection, or purifying selection, bu neutral mutations are still selected.

They just aren’t favored over the prior sequence.

31. Allan Miller
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says:

Well, purifying selection is definitely non-neutral!

As a more general point, there seems to be a tendency – among ‘anti-adaptationists’, as well as the disciples of Sanford – to regard fixation of mildly deleterious alleles as a challenge to ‘adaptationism’. It sees fixation as the end of the matter, whereas, if a population has moved downhill on the fitness landscape, more mutations are ‘uphill’, increasing the likelihood that the deleterious phenotype will be dislodged. The converse occurs for fixation of beneficial alleles.

The succession of small-number effects grows into a more consistent large-number effect, trending towards adaptation, even for small differences in advantage. It’s a bit like meta-analysis in medical research.

32. petrushka
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says:

Well, purifying selection is definitely non-neutral!

The neutrality refers to the comparative fitness of the variants. They are not neutral when compared to all mutations.

Heads and tails are neutral with respect to each other, but not with respect to the coin’s edge.

I think mainstream biologists (or perhaps it’s mostly journalists and headline writers) like to say provocative things. But neutral drift is still under the thumb of natural selection. It’s just that equally fit variants aren’t favored with respect to each other.

Seeing how someone talks about this — whether they claim it is evidence against evolution — is quite telling.

33. Joe Felsenstein
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says:

As a more general point, there seems to be a tendency – among ‘anti-adaptationists’, as well as the disciples of Sanford – to regard fixation of mildly deleterious alleles as a challenge to ‘adaptationism’. It sees fixation as the end of the matter, whereas, if a population has moved downhill on the fitness landscape, more mutations are ‘uphill’, increasing the likelihood that the deleterious phenotype will be dislodged. The converse occurs for fixation of beneficial alleles.

The succession of small-number effects grows into a more consistent large-number effect, trending towards adaptation, even for small differences in advantage. It’s a bit like meta-analysis in medical research.

Those are interesting points. They need more theoretical work, to know what kind of balance we would reach between mildly-deleterious mutants and beneficial ones. It will depend a lot on how fitness are distributed among neighboring sequences in a sequence space.

Sanford and company argue that they are using a realistic model of population genetics. But last I heard, their Mendel’s Accountant computer program lacked recombination within chromosomes (it calls these “linkage blocks”).

If one has a computer simulation program allowing both beneficial and deleterious mutations (and neutral ones too, presumably), here is how to refute evolution:

1. Make the effective population size as small as possible
2. Make each locus very closely linked to as many other loci as possible
3. Make the rate of occurrence of beneficial mutations as extremely small as possible
4. Make the selection coefficients for the beneficial mutations as small as possible
5. If you can, make the beneficial and deleterious mutants recessive
6. Make there be lots of deleterious mutations, many with small enough effects that they could possibly drift to fixation.
7. Have frequent population bottlenecks

Point 2 is to have as much “background selection” as possible, in which tightly linked deleterious mutations create a Muller’s Ratchet which decreases fitness. This requires very tight linkage. And indeed I think Mendel’s Accountant has “linkage blocks” that have no recombination within them.

34. Allan Miller
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says:

The neutrality refers to the comparative fitness of the variants. They are not neutral when compared to all mutations.

In purifying selection, deleterious mutations are eliminated. Other alleles may be neutral with respect to each other, but not to the allele eliminated – they are advantageous; it is deleterious. Positive and negative selection are yin and yang, and result from a gradient, regardless of the relative frequencies of the types. Neutrality ~ no gradient. One could call it a form of selection, since it is really a net balance of selective effects, but purifying selection isn’t the same.

35. Allan Miller
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says:

When I tried to download Mendel’s Accountant, my firewall enquired if I really wanted to go there! I ended up picking up malware which took a bit of shifting.

36. Mike Elzinga
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says:

Perhaps Joe Felsenstein would know the answer to this.

Has anyone experimented with various populations of, say, e. coli in the same environments except for different temperatures? How does drift vary with temperature?

37. Joe Felsenstein
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says:

When I tried to download Mendel’s Accountant, my firewall enquired if I really wanted to go there! I ended up picking up malware which took a bit of shifting.

Thanks for the warning. I wondered, since although the site I was ultimately sent to was Sourceforge, there were some alarming signs of trouble. When I went to install the program (on Mac OS X) it started by wanting me to type in a password. It wanted to do some system-level install and needed my password for that. I bailed at that point. I was basically looking for documentation, and it didn’t have that anyway.

38. Joe Felsenstein
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says:

Mike Elzinga:
Perhaps Joe Felsenstein would know the answer to this.

Has anyone experimented with various populations of, say, e. coli in the same environments except for different temperatures?How does drift vary with temperature?

It’s hard to do that. The problem is that E. coli populations are so huge in any culture that you should not expect to see any genetic drift unless you wait impractically long. Plus there is little enough recombination that favorable mutants occurring elsewhere in the genome drag allele frequencies up or down a lot (a phenomenon known as “periodic selection”).

I think temperature should affect genetic drift mostly by allowing a larger population (hence less drift) in populations near the temperature optimum of that species.

39. Steve Schaffner
Ignored
says:

Joe Felsenstein:
1. Make the effective population size as small as possible
2. Make each locus very closely linked to as many other loci as possible
3. Make the rate of occurrence of beneficial mutations as extremely small as possible
4. Make the selection coefficients for the beneficial mutations as small as possible
5. If you can, make the beneficial and deleterious mutants recessive
6. Make there be lots of deleterious mutations, many with small enough effects that they could possibly drift to fixation.
7. Have frequent population bottlenecks

All you really need is 6 and some combination of 3 and 4. Sanford’s model is of a large number of very slightly deleterious mutations. How all of those sites came to have the very slightly beneficial allele to start with is never stated, and as far as I know, Sanford still doesn’t understand why this is a problem.

40. vjtorley
Ignored
says:

Hi Professor Felsenstein,

Thank you for dropping by. While you’re here, I hope you don’t mind if I ask you a question. I should mention at the outset that although I wrote my Adam and Eve post in a moment of levity, it had a serious point, which I highlighted in the update to my post: scientists who criticize monogenism (or belief in a literal Adam and Eve) should strive to refute the hypothesis on its own terms. What do I mean by that?

As you may be aware, I believe in an old Earth and the common descent of living things. Even though I have no trouble accepting miracles, I don’t believe in an interpretation of Genesis according to which a flood covered all the Earth’s mountains. Why not? Because in order to uphold that interpretation of Genesis, you not only have to suppose that God worked miracles, but that He worked a very large number of ad hoc miracles, which are not even hinted at (let alone mentioned) in Scripture – e.g. making all the excess heat go away after the Flood, or making millions of layers of varves in the Green River, or dumping a layer of iridium on top of the dinosaurs. To invoke a large number of miracles extraneous to Scripture in order to uphold a single miracle which is alleged to have occurred in Scripture strikes me as faulty exegesis -particularly when Scriupture itself nowhere claims that the Flood was miraculous.

Which brings us to Adam and Eve. I’m asking you, because you of all people would know. Suppose (for argument’s sake) that humanity did begin with an original couple, and suppose that their genes were (to some extent) the product of some intelligent engineering carried out on an ancestral population of hominins. Suppose too that they and their descendants were protected by the Intelligent Engineer from natural calamities for (say) ten or twenty generations, allowing their population to increase extremely rapidly to a level of something like 10,000. The question I would like to put to you is: how much (if any) additional miraculous intervention by said Intelligent Engineer would be required, in order to account for the genetic diversity that we observe in humans today?

By way of example, I’d like you to consider the Multi-Germic hypothesis, which was suggested by one of Professor Jerry Coyne’s readers in a 2011 contest which was intended, as Coyne humorously put it, “to help those confused Christians who want to accept both the Biblical story of Adam and Eve and the known genetic fact that humans could not have descended from a single pair of individuals who lived at the same time.” See his post at http://whyevolutionistrue.wordpress.com/2011/06/11/winners-adam-and-eve-contest/ . The Multi-Germic hypothesis goes as follows:

“Roughly 140,000 years ago God slightly tinkered with the genes of two existing hominin pairs to ensure that the next baby they each had would have brains which were capable of interacting with a soul. These two individuals, one male and one female were Adam and Eve. God then imparted them both with many germ line cells each carrying a different genome, this allowed that each of Adam and Eve’s children would not be genetic siblings so that there would be no loss of fitness due to sibling interbreeding. Each distinct gene set was based roughly on the genomes of various human-like beings that had preceded Adam and Eve, which had evolved through natural processes, but was distinct enough that it allowed for the brains of the offspring also to interact with a soul. One consequence of this modification was that it gave the F1 generation enough genetic diversity to appear as though they sprang up from a large pool of existing ancestors. It may also have been necessary that for a few generations following F1 that the individuals continued to have the variable germ cells to further protect the offspring from inbreeding defects.”

I realize that to you this must sound side-splittingly funny. Laugh if you will. Unlike the commenter, I would personally put the dawn of humanity at around 1 million years ago, with the arrival of Heidelberg man, as I explain in my post “Who was Adam and when did he live? Twelve theses and a caveat” at http://www.uncommondescent.com/intelligent-design/who-was-adam-and-when-did-he-live-twelve-theses-and-a-caveat/ . But never mind that. The question I’d like to ask is: is the Multi-Germic hypothesis feasible, on its own terms? Or would subsequent intervention by the Intelligent Engineer have been required, in Adam’s descendants? If the latter is the case, then that would certainly count against monogenism: it would require not merely a one-off supernatural intervention but numerous subsequent interventions which are not narrated in Scripture, rendering it implausible for the same reasons as belief in a global Deluge that once covered the Earth. Of course, one could attempt to salvage it by supposing (as some modern Catholics have done) that Adam and Eve also inter-bred with other hominins that lacked a rational soul, but that strikes me as pretty ad hoc too. The question I’m asking, then, is whether a one-off “genetic miracle” at the dawn of humanity would have sufficed for an Intelligent Engineer.

Over to you, Professor.

41. davehooke
Ignored
says:

Even one epicycle is too many to describe the precession of the planet Mercury.

42. Joe Felsenstein
Ignored
says:

I’ll get back and answer your detailed comment tomorrow. (Busy: this is end-of-quarter for my phylogeny course, a set of homeworks to grade just arriving, plus one student Ph.D. thesis to make comments on, and other stuff too).

I am not sure why you thanked me for “dropping by”. I comment here at TSZ frequently. Anyway, will respond soon.

43. Allan Miller
Ignored
says:

Those are interesting points. They need more theoretical work, to know what kind of balance we would reach between mildly-deleterious mutants and beneficial ones. It will depend a lot on how fitness are distributed among neighboring sequences in a sequence space.

True – my simplistic starting point was that, at the least, the back-mutation would be fitter than the fixed deleterious version, and that more than one genotype would be expected to be capable of responding to the selection pressure, which does not disappear when an allele favoured by it does. But modelling it could be challenging.

44. OMagain
Ignored
says:

vjtorley: The question I’d like to ask is: is the Multi-Germic hypothesis feasible, on its own terms?

For a hypothesis to be a scientific hypothesis, the scientific method requires that one can test it. Can you test it? If not, is it really a scientific hypothesis?
And if it’s not scientific why is it worth spending any time on?

45. Patrick
Ignored
says:

Allan Miller:
When I tried to download Mendel’s Accountant, my firewall enquired if I really wanted to go there! I ended up picking up malware which took a bit of shifting.

Joe Felsenstein: Thanks for the warning.I wondered, since although the site I was ultimately sent to was Sourceforge, there were some alarming signs of trouble.When I went to install the program (on Mac OS X) it started by wanting me to type in a password. It wanted to do some system-level install and needed my password for that.I bailed at that point.I was basically looking for documentation, and it didn’t have that anyway.

If you go to http://sourceforge.net/projects/mendelsaccount/files/ and follow the link “C Source Distribution (v1.5)” you’ll be able to download mendel_v1.5.0.tgz which has C and Fortran source code (as well as some executables I wouldn’t run on a bet).

I was hoping that the code would make the algorithm clear, but no such luck. The user’s manual is also singularly unhelpful. It’s almost as though the authors are more interested in making claims that support their sectarian beliefs than in subjecting their “experiment” to review and possible criticism.

46. Joe Felsenstein
Ignored
says:

Let me answer your long comment, briefly.

1. Adam and Eve represents a 2-person bottleneck, so at most 4 original haplotypes could have been present.
2. Actually, if Eve was made by cloning cells from Adam’s rib, even fewer haplotypes than that, and it would be hard to avoid having her turn out male.
3. About, what, 200 years later (?) we get another bottleneck of 8 individuals on Noah’s Ark, a boat which was built by issuing junk bonds nominally backed by the local city government. But let’s leave that bottleneck out.
4. For mitochondria you have to start with two (or maybe one) genotype.
5. For Y chromosomes you have to start with one (Adam’s).
6. In both those cases you have to generate the present genetic diversity by mutation during, what, maybe 240 generations (?). I am not clear on whether you mean to accept the YEC time scale for this calculation, as you made clear you aren’t of that persuasion yourself.
7. I don’t think that, short of invoking more miracles, the Y and mitochondrial diversity is going to be explainable this way. Inferences of date of mitochondrial Eve give about 200,000 years. Similarly for Y-chromosome “Adam”.
8. For nuclear genes, the coalescent MRCA (Most Recent Common Ancestor) times are long before the YEC dates. Way longer. That going to be a big problem for assertions of a 2-person bottleneck 240 generations ago. Lots of genes should then show that recent a coalescent MRCA time, though. They don’t.
9. As for the Multi-Germic Hypothesis, if Adam is 1 million years ago and only one male among many, would he still have to be assumed to be the ancestor of all modern males? So would his Y chromosome have to be assumed to ancestral to mine and yours?
10. As it allows vast leeway, the 1-million-year-old version of the MGH might well fit all known data, but it is sure not demanded by those data.

As for the issue of a soul, or intelligence, or morality, or something being introduced into two individuals in a 1-million-year-ago population of Archaic Homo Sapiens (or Homo heidelbergensis) I’m afraid I have to leave that hypothesis uncommented on. Because I have never understood what is the scientific definition of a soul, anyway.

47. Joe Felsenstein
Ignored
says:

Woops. In point 4 of my comment an obvious error. For mitochondria, you have to start with one, because only Eve’s gets inherited.

48. Steve Schaffner
Ignored
says:

vjtorley:
“Roughly 140,000 years ago God slightly tinkered with the genes of two existing hominin pairs to ensure that the next baby they each had would have brains which were capable of interacting with a soul. These two individuals, one male and one female were Adam and Eve. God then imparted them both with many germ line cells each carrying a different genome, this allowed that each of Adam and Eve’s children would not be genetic siblings so that there would be no loss of fitness due to sibling interbreeding. Each distinct gene set was based roughly on the genomes of various human-like beings that had preceded Adam and Eve, which had evolved through natural processes, but was distinct enough that it allowed for the brains of the offspring also to interact with a soul. One consequence of this modification was that it gave the F1 generation enough genetic diversity to appear as though they sprang up from a large pool of existing ancestors. It may also have been necessary that for a few generations following F1 that the individuals continued to have the variable germ cells to further protect the offspring from inbreeding defects.”
[…]
But never mind that. The question I’d like to ask is: is the Multi-Germic hypothesis feasible, on its own terms? Or would subsequent intervention by the Intelligent Engineer have been required, in Adam’s descendants? If the latter is the case, then that would certainly count against monogenism: it would require not merely a one-off supernatural intervention but numerous subsequent interventions which are not narrated in Scripture, rendering it implausible for the same reasons as belief in a global Deluge that once covered the Earth. Of course, one could attempt to salvage it by supposing (as some modern Catholics have done) that Adam and Eve also inter-bred with other hominins that lacked a rational soul, but that strikes me as pretty ad hoc too. The question I’m asking, then, is whether a one-off “genetic miracle” at the dawn of humanity would have sufficed for an Intelligent Engineer.

This isn’t really monogenism, since Adam and Eve’s offspring are all genetically different individuals drawn from an existing population; it doesn’t matter whether exists in the haploid or the diploid stage, it’s still there. In fact, there’s no need for Adam and Eve to be human now, since the new brain/spiritual traits are put directly into their germ cells. (I suspect many miracles are still required in this scenario, since the sperm with non-Adamic DNA either have to be created when needed, or be produced by non-Adamic spermatogonia that have to be shielded from Adam’s immune system.)

What traces this scenario would leave depends on how many children A&E had, i.e. how large a population you want to import miraculously into their family. I just modeled what the allele frequency spectrum would look like if they had twenty offspring (followed by rapid population growth — 50% per generation). The bottleneck produces a distinct (and easily detectable) distortion to the spectrum: results.

49. Richardthughes
Ignored
says:

Good for VJT for making falsifiable predictions.

50. SophistiCat
Ignored
says:

Patrick:
If you go to http://sourceforge.net/projects/mendelsaccount/files/ and follow the link “C Source Distribution (v1.5)” you’ll be able to download mendel_v1.5.0.tgz which has C and Fortran source code (as well as some executables I wouldn’t run on a bet).

I was hoping that the code would make the algorithm clear, but no such luck.The user’s manual is also singularly unhelpful.It’s almost as though the authors are more interested in making claims that support their sectarian beliefs than in subjecting their “experiment” to review and possible criticism.

Unfortunately, poor coding and documentation practices were quite typical when I was in academia, so I would sooner blame incompetence than malice.

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