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No, Virginia, Science hasn't debunked Adam

Disclaimer: I write this post as a layman in the area of biology. If possible, I want to make some of the debate over the alleged impossibility of an historical Adam available at the level of laymen. The scientific issues involved are, of course, highly controversial. If I make cut-and-dried errors of factual statement or terminology, I welcome correction.

I have recently found the book Science and Human Origins to be extremely helpful as a starting place for examining some of these issues. Even more interesting is the Internet debate about the contents of the book. Paul McBride, who at least was at the time an evolutionary biology PhD student in New Zealand, wrote a 2012 series of posts criticizing the book. That series appears in six parts here. (That is part 5. It includes links to parts 1-4.) The authors of the book and other ID advocates have written many responses. Casey Luskin posts a link round-up here. See also here. I will be discussing several of Ann Gauger's responses in this post in more detail. Anyone who is interested in the issue of the alleged overwhelming evidence for undesigned human evolution from ape-like ancestors has no lack of material to study; nor have the advocates of intelligent design theory made a one-sided statement of their case without responding to critics. So if you want to read up, this is the Internet age; go for it.

This post will be about Ann Gauger's work concerning population genetics. Population genetics has become a major Darwinian argument of choice, allegedly putting a nail in the coffin of the historical Adam, and it was chiefly for Gauger's essay that I originally got the book. Now, to business:

Gauger's chapter and Ayala's 1990's argument

For a foil in her book chapter, Ann Gauger chooses an argument made by a scientist named Francisco Ayala from gene called HLA-DRB1. Ayala obtained samples of chimp, human, and macaque DNA from a specific region of HLA-DRB1 and constructed conjectural phylogenetic "trees" using alleles (i.e. variants) of this gene. In essence, one takes alleles of the genes, notes similarities and differences among present-day sequences, and then one constructs a "tree" which is supposed to show how these alleles are related. By using estimated mutation rates and various algorithms of population genetics, one calculates far back into time as to how many alleles are supposed to have existed at some period of interest--say, at an estimated time when, according to evolutionary theory, humans and chimps last shared a common ancestor. This procedure is supposed to give an idea as to how big the initial population of humans must have been.

Ayala went back to a particular estimated time when humans and chips allegedly last shared a common ancestor (Ann Gauger points out that estimates on this vary a good deal, but his was that it was four to six million years ago) and stated that, by his calculations, there must have been a minimum of 4,000 individuals alive at that time in the human ancestry. He also argued that the actual population must have been much larger still.

The idea is that this estimated population size shows the impossibility of an historical Adam and Eve, because our ancestors would have had to carry more genetic diversity than would be found in the genome of merely two people.

I cannot summarize Gauger's whole article. (This post is going to be long enough as it is.) But I will summarize a few of her points which seem to me utterly devastating to Ayala's argument regarding that particular portion of the genome: First, Ayala focused on the exon 2 region of the HLA-DRB1 gene, which was a poor choice. When one uses a different region (introns 1-4) of the gene, one gets a tree that sorts out, sensibly enough, by species. Macaque alleles look like other macaque alleles, human alleles like human alleles, and chimp alleles like chimp alleles. When one uses the exon 2 region one instead gets an incompatible tree in which the alleles are all mixed up. Sometimes human alleles are more similar to macaque alleles or chimp alleles than to other human alleles, macaque alleles are sometimes more like human alleles than like other macaque alleles, and so forth. In other words, using the exon 2 region to make a phylogenetic tree creates, to use technical scientific terminology, an unholy mess.

Let me emphasize that the variants of the exon 2 region do not sort by species right now, meaning that something very weird is going on in exon 2. Presumably there is some cause of hyper-variability in that region. In fact, it appears that exon 2 has a much higher mutation rate than do other parts of the gene. A tree based on exon 2 using a mutation rate that is too low will, understandably enough, give a false picture of the number of variants present in a population millions of years ago.

Ayala did attempt to correct for the fact that natural selection will tend to inflate genetic diversity for exon 2, since people with different versions of exon 2 in their genome will tend to have more surviving offspring. Whether his fudge factor sufficiently corrected for this effect of natural selection or not, he disregarded the apparently much higher mutation rate in exon 2 leading to the failure of sorting by species.

Gauger also notes that a different late 90s population genetics argument based on neighboring DNA sequences (not exon 2) came to a very different conclusion from Ayala's, concluding seven versions of the HLA-DRB1 gene existed four to six million years ago, whereas Ayala had concluded that thirty-two existed. (This was the basis for his population estimate.) Let me be clear: I am not saying, and I'm sure Gauger is not saying, that this study was simply right while Ayala's was wrong. As I shall discuss later, Gauger is questioning the reliability of population genetics altogether for estimates about population sizes long ago. The point I would make here is simply that, when we get conflicting trees from these methods, we are justified in asking why we should accept the reliability of the underlying methodology.

Gauger also points out that Ayala's calculations included other assumptions that would have also led to an overestimate of the number of ancestors needed to carry the relevant information. The larger HLA-DRB1 region does not do a lot of recombining when the DNA is reproduced. This is kind of unusual. Different versions of sections of DNA that tend to be inherited as a unit are sometimes called haplotypes. You can think of a haplotype as a chunk of genes that gets inherited together. Now, if the inheritance of DNA in this region is "chunky" like this, that (in addition to the other considerations) throws all of Ayala's calculations into a cocked hat. Pause here to contemplate how easy it is to throw population genetics estimates into a cocked hat.

To do population genetics, one has to make double handfuls of assumptions about rate constancy, equiprobability, and biological independence in order to make the math workable. Sometimes these assumptions turn out to be wrong, and wrong in ways that cause overestimates.

Gauger points out in the chapter that there are just five basic groups of the HLA haplotype in the human population. She then points out that as many as four haplotypes could be carried even by a perfectly ordinary pair of individuals.

This point seriously calls into question the necessity for a minimal bottleneck of 4,000 to 100,000 in the human lineage.

Paul McBride's response to Gauger's chapter

Interestingly, McBride doesn't bother to defend Ayala's argument (as far as I can see). He seems pretty eager to drop Ayala's entire study down the memory hole and move on as quickly as possible, which I'm guessing means that the problems with Ayala's study are as decisive as they appear to be.

McBride does try to make much play out of the fact that, if we grant that the relevant haplotypes (even if only four) first showed up 4 to 6 million years ago, this was before the appearance of any of the genus Homo, including Homo erectus, and hence before any plausible candidate for the species of human beings. McBride thinks that this means that Gauger's point about four haplotypes and her conjecture that these may have been carried by Adam and Eve makes no sense as a defense of a possible first couple, because the first individuals carrying those lineages couldn't have been human at all. He points out that Casey Luskin's preferred candidate species (in a different chapter of Science and Human Origins) for the first true humans is Homo erectus, which are now thought to have showed up circa two million years ago, not four to six. So, says McBride, even the four haplotypes idea still "rules out" the existence of Adam and Eve as the first humans.

Gauger has clarified here that she was not saying that a first human pair was probably created four to six million years ago. An ordinary first couple could have carried as many as four versions of the gene. A fifth variant could have arisen by natural genetic change after humans came on the scene. (There is a reason why I keep saying "ordinary individuals," but you will have to read to the end to get to the explanation.) Since the discussion is over whether there is too much genetic diversity in mankind now to have arisen from a first couple long ago, this point is relevant.

Gauger also points out in this recent post that even some scientists who accept common descent from an ape-like ancestor estimate that there were four to five lineages of this gene long ago and that much of the genetic diversity in this gene, within lineages, has arisen much more recently--between 350,000 to 500,000 years ago. This is directly contrary to Ayala's conclusions.

Li and Durban's claims and Gauger's response

McBride seems eager to move on to discussing something other than Ayala. His favored population genetics study is one by scientists Li and Durban, using a different method from Ayala's. In particular, Li and Durban used much larger regions of DNA to try to rule out confounding effects specific to a narrow area (part of what tripped up Ayala's study). They concluded that a minimum bottleneck around the time of Homo erectus was about 15,000 individuals.

Gauger responds here fairly briefly and at more length here.

Gauger's initial post refers to problematic assumptions in Li and Durban's type of population genetics study, which is known as coalescent theory. McBride at first complains that she doesn't say what the allegedly problematic assumptions are; in her second post on the subject she goes into this in more detail. Coalescent theory, says Gauger, is based on the assumption that, in populations of the relevant size, "the vast majority of mutations are neutral and have no effect on an organism’s survival."

Let that sink in just for a minute. Can you say "natural selection"? Yes, that's right: Natural selection, a crucial, major driver of neo-Darwinian theory, is treated by coalescent theory in population genetics as having no significant effect upon population sizes over hundreds of thousands and even millions of years.

McBride insists that the assumptions made in population genetics tend to cause underestimates rather than overestimates concerning population size, but it should be fairly clear even to a layman that this is by no means necessarily the case when it comes to literally discounting natural selection as a force influencing population size! For example, as noted above, Ayala himself knew that natural selection would sometimes inflate genetic diversity. And Ayala's biological independence and mutation rate assumptions did not cause an underestimate of past population size.

Perversely, I'm tempted not to make too much of this matter of natural selection and then to sit back at a climactic moment and watch the sociobiologists and evolutionary philosophers squirm. Their goal is to "explain" complex sociological phenomena such as why gentlemen prefer blondes or why human beings are religious in terms of the effects of natural selection throughout human evolutionary history. It would be almost too much fun to wait for one of those folks to cite Li and Durban's study allegedly showing that Adam and Eve couldn't have existed and then to spring on him the unwelcome news that Li and Durban are treating natural selection as irrelevant to human evolution for the past three million years.

But actually, I won't. Because I have to admit that, again, speaking as a layman, it seems pretty implausible that most hominid mutations for the past three million years have been neutral in effect and that we can use that assumption to generate population census estimates regarding our long-ago ancestors. Did I say something above about double handfuls of equiprobability assumptions in population genetics? Yes, I believe I did. Gauger (who isn't a layman) apparently agrees, which is why she highlights the neutral mutation assumption of coalescent theory as problematic.

McBride sometimes gives the impression that the phylogenetic trees generated by population genetics are consistent and mutually confirmatory, at least as regards the claimed impossibility of Adam.

I shall reiterate: the possibility of a two-person, Adam and Eve bottleneck is simply not an open question in science. There cannot have been such a bottleneck.
Taken together, there is a bias in our estimates of actual past population sizes, but it is a bias towards underestimation. So, when we make long-term estimates of the human effective population size that vary by two orders of magnitude but bottom out at around 1,000, this lower estimate (and its corresponding census population size of 10,000) are almost-certain underestimates of the real picture. Even with the variation in different estimates, we are left with no room for a census population size of two--a further four orders of magnitude lower again.
Li and Durban, however, trace effective population sizes (evolutionarily relevant estimates of the adult breeding population size) over our evolutionary history as a species, using comparisons of entire genomes from across a range of ethnic groups. At no point is there anything approaching an Adam and Eve population bottleneck at any point that correlates to the genus Homo. Again, when an earlier chapter has drawn the human/non-human distinction between Homo habilis and Homo erectus (i.e. approximately 2 million years ago) we can be quite well assured that a literal Adam and Eve are unsupported by population genetics.The figure below, from Li and Durban, suggests an effective population size of about 15,000 at the origin of Homo erectus.

From all of these statements one might surmise that perhaps there is significant, detailed mutual support going on among various population genetics studies. McBride gives the impression that we can be quite certain scientifically that no Adam and Eve existed because, wherever else they might disagree, these population genetics estimates agree in not coming up with a two-person bottleneck.

There are several things wrong with such an argument. McBride doesn't seem to see that there are real reasons for questioning these estimates, all of them, altogether--in other words, for questioning whether population genetics (in its various incarnations) is a reliable way of finding out how many individual ancestors lived millions of years ago. That is definitely a major point Gauger is making. She says:

[I]n my opinion it is an open question whether present genetic diversity provides sufficient information from which to draw conclusions about ancient populations. Determining events in deep human history may be beyond the reach of population genetics methods.

From her book chapter (p. 119):

Where ancient genetic history is involved, dogmatic statements are out of place. We understand very little of our own genetic makeup--way too little to make accurate calculations about our distant genetic past.

Why should this not be correct? There is certainly no law that says that we have to have reliable methods of estimating how many of our ancestors were alive two or three million years ago! Indeed, to claim that we can make such reliable estimates would seem to require meeting rather a strong burden of proof.

That these various conjectural methods all "agree" in placing the smallest bottlenecks at a number greater than two has virtually no significance in and of itself as support for the enterprise of population genetics, because the agreement is much too broad. Consider: If you have three entrail readers who all agree that next year will be a prosperous year but all for different reasons, does this give you any good evidence for the reliability of entrail reading as a way of divining the future?

McBride does not even try to claim that Li and Durban's phylogenetic tree agrees in detail with other trees throughout millions of years of history. His entire focus is on their agreement that (thank goodness) there were never fewer than 1,000 human ancestors, and allegedly many more for an effective population size. But Gauger is right to point out that variations for the minimum within several orders of magnitude imply that very different trees that disagree with each other are being constructed.

We already saw this from Gauger's chapter: A tree constructed on the basis of one genetic segment was incompatible with a tree constructed on the basis of the rest of the same gene. They couldn't both be right.

According to Gauger, such problems are pervasive:

[W]e see evidence of tangled trees at all levels of phylogeny.

To my mind, this is the mark of a method characterized by guesswork and instability. That evaluation is also borne out by the points above about unjustified equiprobability assumptions. If we do indeed see conflicting and tangled phylogenetic trees at all levels, this raises a very real question as to why we should even care that various conjectures based on population genetics all "agree" with the broad claim that there was no time in deep history when we had only two ancestors.

Part of my point here, and I assume Gauger's as well, is that there is no known-to-be-reliable, independent way to check any of these phylogenetic trees for the distant past.

This points to the relevance of another complaint that Gauger makes:

In addition, all these calculations depend on assumptions of common descent as the only explanation for our origin.
[M]ore worrying to me are the hidden assumptions in evolutionary models. Population genetics is a theory-laden subject, based entirely on neo-Darwinian assumptions.
Population genetics as a scientific discipline makes use of mathematics and the principles of neo-Darwinism to try to understand how genetic variation spreads through populations and influences their evolution. It does so by assuming that all processes are purely natural and unguided, and that phylogenetic history is mainly the product of common descent, at least in multicellular organisms.

Gauger's point, simply put, is that all of these estimates assume that nothing was going on in the relevant millions of years but inheritance and mutation. No intelligent intervention, no creation, for example. Since these estimates are based on this assumption, and since there is no clear independent way to check that these guesses are right or even to confirm the reliability of the methods by independent means, why should we take the mere existence of these conjectures to be evidence against the intelligent design of man? In this situation, the accusation that the argument against an historical Adam from population genetics is circular has force.

Creation, genetic diversity, and ad hocness

Lurking behind the capitulation of some theistic evolutionists to the "no Adam" conclusion lies, I believe, something like the following thought process. The words are mine, but based upon conversations I'm convinced that something like this is worrying people:

You can't bring up the possibility of miraculous activity as an explanation of genetic diversity, because that would be ad hoc. After all, you can "explain" anything by saying that God set it up that way. We don't want to fall prey, just to save the appearances and keep our creation story, to the picture of a deceptive God who, for reasons unknown, made it look just like there weren't two original parents. If that's the best we can do, we should just conclude, however sadly, that the scientific evidence strongly disconfirms the existence of Adam.

I want to confront this concern and not let it be the elephant in the room.

I've recently been doing some philosophical work on the issue of ad hocness. (You can read the results here if your library has a subscription, or write to me for a scholar-to-scholar share of the e-offprint.)

My conclusion, in very brief terms, is that ad hocness doesn't arise unless the auxiliary hypothesis in question has low probability given the overarching theory in question. There are other necessary conditions as well, but that is one of them. Take a classic example of ad hocness: Junior discovers that "Santa's" handwriting on the Christmas present tags looks just like Mom's and confronts Mom about it. Mom tells Junior that Santa has deliberately made his handwriting look like hers to make things more difficult or to throw people off his (Santa's) trail. Why is this ad hoc? One obvious part of the answer is that, based on the assumption that Santa exists, one would have expected the opposite to be true. One would not have expected Santa to disguise his handwriting but rather to use his own handwriting. All the more so since children are supposed to know about Santa anyway, so evidently he's not trying to hide his existence.

An ad hoc hypothesis could come up in connection with God's activity. Suppose that I say that God created my table five minutes ago. Upon having it pointed out that everyone remembers the existence of my table for many years past, I could argue ad hoc that God created all of those memories in our minds. Again, why would we think that? It has very low probability given the initial hypothesis I was putting forward. On the contrary, we would expect God to show Himself by creating something, not to make it seem as if it existed previously for many years.

Now consider the hypothesis that Adam and Eve were specially created, perhaps even ex nihilo. And consider the auxiliary hypothesis that God gave Adam and Eve extra genetic diversity, more than is presently possessed and passed on via sexual reproduction by ordinary human beings. (This is my discussion of ordinary human beings, promised above.) Is this just something made up to try to rebut disconfirmatory studies of population genetics? Is it like the "Santa imitating Mom's handwriting" hypothesis? Not at all. For one thing, I've already argued that the population genetics studies don't give us anything that needs to be rebutted, because their arguments are poor.

But more: Consider what we already know about genetics, independently: We have reason to believe that close interbreeding causes the accumulation of harmful mutations. Therefore, if God were going to create Adam and Eve as the first couple and have all human beings descend from them (the overall hypothesis we are considering), we have independent reason to believe that God would do something to avoid the possible negative effects of in-breeding. One open possibility to fulfill that functional purpose is that Adam and Eve would be created with extra genetic diversity--that they would be different from modern humans in this respect. Their children might not even be genetic siblings. (V.J. Torley discusses this possibility here, among other places.)

If this were true, and if one analyzed Adam and Eve's genetic potential, there is a sense in which it would "look like" the genetic potential of more than two people. But this would not be God's pointlessly and deceptively making it "look like" we had more than two ancestors, because that design plan is not pointless. It has an important functional purpose for the first couple's offspring. Therefore, unlike an ad hoc hypothesis, it does not have a particularly low probability given an intelligently designed first couple.

Hence, even if we had more reliable methods than we do have for estimating distant past populations, and even if they did not happen to come up with a two-person first couple, this would not be serious evidence against the existence of an original couple.

Notice that since the issue is functional, the amount of extra genetic diversity that would be (to some degree) expected in Adam and Eve beyond what is normally found in two ordinary people will depend upon functional considerations--what range or level of genetic diversity would be valuable for a founding population? This should make it clear that the conjecture concerning extra genetic diversity is not being made to counter some study or studies that "seem to show" a high number as the lowest possible number of human ancestors. (As I have argued, the population genetics science is unconvincing.)

The epistemological point concerning function, creation, and genetic diversity should be borne in mind as a confounding factor if one is attempting to use genetic diversity estimates to argue against the existence of Adam and Eve.

Conclusion

What we're being told is that there is something analogous to a video of the past showing, via highly reliable methods, what appears to be an uninterrupted history of the natural evolution of mankind from non-human ancestors--a history of mankind that could not have begun with two individuals.

This is not true. Given the Scriptural evidence for the existence of an historical Adam and Eve, the first and only parents of mankind, Christians are fully justified in asking for strong counterevidence. It doesn't seem to have been forthcoming, despite all the fanfare. Even from the perspective of common sense, it should take a lot to convince us scientifically that there could not have been a first human couple as long ago as 600,000 to two million years. I have real doubts that any such negative can be proven, even within the weaker sense of "prove" that is appropriate to empirical endeavor.

One thing I am confident of: Population genetics has not given us strong evidence for that negative proposition. No, Virginia, science hasn't debunked Adam and Eve.

Comments (28)


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"Ayala went back to a particular estimated time when humans and chips allegedly last shared a common ancestor (Ann Gauger points out that estimates on this vary a good deal, but his was that it was four to six million years ago) and stated that, by his calculations, there must have been a minimum of 4,000 individuals alive at that time in the human ancestry. He also argued that the actual population must have been much larger still."

When it suits their purpose, DarwinDefenders make much of the alleged similarity of human chromosome 2 to two chimpanzee chromosomes as being proof of the hypothesis that humans *are* apes and descend from "an ape-like ancestor" Darwinistically, which is to say, accidentally and without purpose (and as being disproof of any competing hypotheses) -- while, at the same time, studiously avoiding mention of relevant facts that run contrary to that hypothesis.

For the purpose of commenting on the claim that "there must have been a minimum of 4,000 individuals alive at that time in the human ancestry" understand this --

1) IF we are biologically related to apes (whether Darwinistically or not), then since all apes have 24 chromosome pairs but humans have 23 chromosome pairs, then either:
1a) in the human-specific lineage, two chromosomes were somehow fused to form a single chromosome;
1b) in all the ape lineages, a single chromosome (and the same analoge on all lineages) split to form a two chromosomes;
1c) obviously, option 1a) is more plausible;

2) IF at some point in our lineage two individual chromosomes fused to form the "ancestor" of the present-day human chromosome 2, THEN this fusion was first manifest in a single individual, who/which would have been somewhat analogous to a mule:
2a) that is, this individual would not have had either 48 chromosomes like apes do, nor 46 chromosomes like humans do, but rather would have had 47 chromosomes;
2b) this chromosomal arrangement would resulted in drastically reduced fertility for this individual -- perhaps even total sterility;

3) as at the time of the purported chromosomal fusion there exists only one individual with the chromosomal fusion, the only individuals available for him to mate with are individuals with the heretofore normal karypotype (48 chromosomes);
3a) as individuals with "hybrid" karypotype (47 chromosomes) have reduced fertility (and perhaps even total sterility), crosses between such individuals multiply the fertility reduction; that is, if crossing the "hybrid" karypotype (47 chromosomes) with the heretofore normal karypotype (48 chromosomes) produces on average only half as many live offspring matings between normal individuals, then (all else being equal ... and it isn't) matings between *two* individuals with the "hybrid" karypotype (47 chromosomes) will result, on average, in only one quarer as many live offspring;
3b) IF the individual with "hybrid" karypotype (47 chromosomes) is able to produce live offspring, then mating him (or her) to an individual with the heretofore normal karypotype (48 chromosomes) results in about 1/2 the offspring having the "hybrid" karypotype (47 chromosomes) and about 1/2 having the heretofore normal karypotype (48 chromosomes);

4) the *only* way to get from the ape karypotype (48 chromosomes) to the human karyotype (46 chromosomes) is for *two* individuals having the "hybrid" karypotype (47 chromosomes) to successfully mate and produce live offspring;
4a) as mentioned above, these individuals have some level of reduced level of fertility AND this reduced fertility is multiplied in such a cross;
4b) all else being equal, the live offspring of such a cross can be expected to have karyotypes in these proportions:
* 1/4 should have the heretofore normal ape karypotype (48 chromosomes)
* 1/2 should have the "hybrid" karypotype (47 chromosomes)
* 1/4 should have the *new* human-like karypotype (46 chromosomes)


My point is that even on Darwinistic assumptrions, the initial founding population of the human-specific lineage was *extremely* small.

What exactly would happen after a chromosome fusion event is an interesting question, but presumably any individual with such a mutation could in theory have mated with more than one other member of the species (unless he had moral scruples against doing so). And other members, in turn, could have mated among themselves in some sort of tribal group. So I doubt that the hypothesis of such a fusion event, the effects of which spread throughout the population, would necessarily mean a bottleneck of fewer than 4,000 (for example).

On the purported fusion as alleged evidence of common descent, Casey Luskin has an excellent chapter on that in Science and Human Origins. It's really fascinating to see how little is left of these arguments when one dissects them. I found myself saying things to myself like, "So, the big deal is that we might have been descended from ancestors with 48 chromosomes, and apes also have 48 chromosomes? That's what's supposed to be this wow argument?" It's a very useful book, and now one can also see what attempted answers have been made and follow up on further debate.

I'll try to explain again, in more depth (when I get home this weekend) why a fusion event *would* necessarily mean a severe population bottleneck.

From McBride: The figure below, from Li and Durban, suggests an effective population size of about 15,000 at the origin of Homo erectus.

Does this mean (assuming that the progenitor of Erectus was Habilis) that when the first Erectus was born, approximately 14,000 others were born at the same time?

we have independent reason to believe that God would do something to avoid the possible negative effects of in-breeding. One open possibility to fulfill that functional purpose is that Adam and Eve would be created with extra genetic diversity...

Is it also possible that the deleterious genetic effects of the Fall might have taken several or more generations to emerge in the population? If so, it might mean that Adam and Eve didn't need the extra diversity, if genetic diversity widens with population expansion.

that when the first Erectus was born, approximately 14,000 others were born at the same time?

Good question, and one to which I don't know the answer for sure. If I were to guess, I would assume that their idea is that the species lines are fuzzy and therefore that "at the same time" is fuzzy, but that there were about 14,000 in a population capable of interbreeding at about that time. They needn't have all been Erectus as long as similar enough to interbreed with Erectus.

Is it also possible that the deleterious genetic effects of the Fall might have taken several or more generations to emerge in the population?

That also seems possible, and I would have to know more about exactly how deleterious effects of inbreeding tend to work in order to judge how to think of them as results of the Fall or not results of the Fall. For example, some purebred horses with noses of a distinctive shape tend to be born with congenital deformations of the nose when humans interbreed them too closely. This appears just to be a result of getting too much of whatever-the-gene-is for that distinctive nose shape. And even that way of putting it is probably way too simplistic. But my general point is that the nose shape is not in itself a bad thing but just that inbreeding horses with that nose shape too closely is a bad thing. I've suggested elsewhere that early longevity as reported in Scripture may well have been the result of a sort of delayed effect of the results of the Fall--kind of a "residual Eden effect," the mechanism of which we can only guess at. (Perhaps more perfect cellular reproduction preventing aging and the development of cancers, for example.) But whether such a "leftover Eden effect" would make it _not_ advantageous to have an Adam and Eve with extra genetic diversity is yet another question. The longevity itself, if accompanied by long fertility, would tend to increase genetic diversity by natural means within relatively few generations, which may have lessened the amount of extra diversity needed in Adam and Eve.

I would only suggest that, as we lay down our probability distribution, we have some independent reason to think that Adam and Eve may have had extra genetic diversity. It needn't be an absolute prediction.

but that there were about 14,000 in a population capable of interbreeding at about that time. They needn't have all been Erectus as long as similar enough to interbreed with Erectus.

Then those 14,000 had to have been different in some degree from the original Habilis (assuming Erectus could not interbreed with Habilis). I'm having trouble imagining a mutation expressing itself all at once on such a massive scale. If they weren't all fully Erectus (sorry about that), and yet not fully Habilis, could they interbreed with both? And if so, what's to guarantee that the Erecti genes in time become dominant, such that both Habilis and the intermediate population disappear?

I know these questions are annoying, but whenever I try to imagine these evolutionary scenarios, the pictures dissolve into a sort of fog.

Well, as you know, I'm by no means defending them. I'm guessing they may envisage habilis as being able to interbreed with erectus, and the species boundaries as being pretty fluid, so it's possible to be a little bit of both. In a sense, my understanding is that all gradualist accounts of species evolution require that kind of fluidity and possible interbreeding, or else gradual species differentiation couldn't happen at all, whereas the entire theory depends upon it.

Lydia, thank you for doing all this work. I have been putting off tackling the issue for myself, but I have thought it needed doing. I heard a lecture by a Catholic priest about 2 years ago on some of the details implicit in a "mitochondrial Eve" of 80,000 years ago, but at the time I thought even that was based on a LOT of assumptions, like a knowable or constant mutation rate.

That said, I don't know about one point of yours.

Coalescent theory, says Gauger, is based on the assumption that, in populations of the relevant size, "the vast majority of mutations are neutral and have no effect on an organism’s survival."

Let that sink in just for a minute. Can you say "natural selection"? Yes, that's right: Natural selection, a crucial, major driver of neo-Darwinian theory, is treated by coalescent theory in population genetics as having no significant effect upon population sizes over hundreds of thousands and even millions of years.

I don't think that it is logically equivalent to say "most mutations have little to no effect" and to say "mutation has had little to no effect." If you have had 100,000 mutations, and 99,950 had no long term effect at all, it is still possible that the other 50 had a very great effect indeed. And looking at all the effect, ALL of that effect would come about through mutations.

Out of 24,000 genes, with maybe a couple million amino acid sequences, and a large portion of it being switched off or having cut-offs, back doors, and back-ups, it would be not surprising at all if a mutation at many sites had little to no effect. We can easily think of variation that would have little to no impact on survivability and survival selection: hair color of elderly person being white instead of gray, for example (since it happens after child-bearing years). If most of the changes that happen are like that, that would not discount some few changes still having very strong impact on survival and selection and future species' expression.

Gauger's point, simply put, is that all of these estimates assume that nothing was going on in the relevant millions of years but inheritance and mutation. No intelligent intervention, no creation, for example.

Very good point. For one thing, (especially coming from the notion of "survival of the sexiest"), man himself can have an impact on the passing on of traits based not on survivability itself but on (his own) other selection criteria - and biological science would not be able to factor that in at all.

McBride does not even try to claim that Li and Durban's phylogenetic tree agrees in detail with other trees throughout millions of years of history. His entire focus is on their agreement that (thank goodness) there were never fewer than 1,000 human ancestors, and allegedly many more for an effective population size. But Gauger is right to point out that variations for the minimum within several orders of magnitude imply that very different trees that disagree with each other are being constructed.

I've noticed this effect in other areas:

Woman 1 says to my wife: "Oh, you are carrying high - that means it's a girl."

Woman 2 says to her: "Oh, you are carrying low - that means it's a girl."

Woman 3 says to her: "Oh, you are carrying high - that means it's a boy."

Scientific conclusion: 3 different women identified the sex of the baby in utero by noting how you are carrying. Therefore, women can tell the sex of the child in utero from how you carry the baby.

Re. your first point, Tony, subject to correction, my understanding is that coalescent theory does not contain some kind of correction factor for a few mutations that have major effects. The specific sentence I quoted from Gauger is, to that extent, understated. She says more, indicating that coalescent theory really does treat the effect of natural selection within the population as negligible overall during the time period and sheer random drift as the only factor to be mathematically modeled. Here is a further quotation, this time taken from a different source Gauger quotes:

The coalescence model is simple in the sense that it assumes little or no effect of evolutionary forces such as selection, recombination, and gene flow, instead giving a prominent role to random genetic drift.

Here is another quotation from Gauger:

The theory is that in small populations (smaller than a trillion, say) drift can overwhelm the power of selection. In such a case, organisms do not have sufficient numbers for beneficial mutations to arise and be fixed with any frequency. Most mutations are lost to drift before becoming established, even when they are beneficial. The significance of natural selection is thus greatly reduced in shaping evolutionary history.

We can see ways in which such an assumption could lead to an overestimate of the amount of genetic diversity and the number of ancestors present a long time ago. For example, if there is positive selection for heterozygosity, as there appears to be in parts of the genome related to the immune system, this would tend to increase the genetic diversity within a smaller population, leading to an overestimate in a study based on the amount of genetic diversity coupled with the assumption that there was no significant effect of natural selection upon genetic diversity.

I was thinking about your example concerning women telling your wife whether a baby will be a boy or a girl, Tony, and I had some fun changing and elaborating the example. Here's what it would be like:

Suppose there were a book called How to Foretell Your Baby's Future (hereafter "the Book"). It contains a number of, shall we say, independently unconfirmed methods for foretelling the future of an unborn child. Three women are deeply into the Book and try to apply various methods from it. Woman 1 comes up to your wife and says, "I see you are carrying high. That means that your baby is a girl, that she will have a happy and contented personality, and that she will sleep through the night from the third week."

Woman 2 comes up to your wife and says, "May I see your palm? Ah, I've been studying the Book and learning how to foretell your baby's future. I see from your palm lines that your baby will be a girl, that she will be especially large at birth, and that she will grow up to be an athlete."

Women 3 arrives with a ring on a string, which she dangles over your wife's abdomen. First it rotates a few turns one way, then the other. Woman 3 says, "Based on this rotating ring and the methods I've learned from the Book, your baby will be a girl, she will be petite, she will be colicky and difficult as a newborn, but she will grow up to be bookish and brilliant."

Now, all three agree that the baby is a girl, but that is all they agree upon. This set of reports gives no good reason to think that the Book contains reliable methods for foretelling the baby's future, even though all three practitioners of its arts agree that the baby is a girl. That agreement isn't all that remarkable, and the other details either fail to overlap or outright contradict each other.

Yep, that's about the same.

Have you run across "Mitochondrial Eve" and whether that theory has been touched on by these other population genetics scientists?

In her most recent post, Gauger says that Ayala's work in the 90's was expressly intended to refute mitochondrial Eve. As far as that goes, it certainly looks like he didn't succeed.

My _impression_ is that even taken at face value mitochondrial Eve would not have to be Eve in anything like the biblical sense, since, to put it crudely, she could have slept around. I also gather that there is plenty of controversy as to whether Y-chromosome Adam and mitochondrial Eve could have lived at the same time.

The traditional position on Adam and Eve is more restrictive than the position that all humans are descended from Adam and Eve. Compare: All Jewish people are descended from Abraham and Sarah. However, Isaac didn't marry his sister, and Isaac's descendants took mates who were not descended from Abraham and Sarah. So there is a sense in which it is possible both to say that all Jewish people are descended from Abraham and Sarah and also that there was not a true two-person bottleneck from whom all Jews are descended. That sort of "tribal" solution is not open to anyone who wants to retain the traditional Christian notion of Adam and Eve. So I've never looked for much help from mitochondrial Eve, because I was sure that, at the most, she was supposed to be everybody's ancestress in the sense that Sarah is the matrilineal ancestress of the Jews.

I agree that mitochondrial Eve (plus a male) wouldn't constitute that kind of one-couple bottleneck, and I tend not to think that the Adam and Eve of the Bible lived 80,000 years ago anyway (and the chromosomal Adam is supposed to be pegged at 120,000 BC, so they definitely aren't any biblical Adam and Eve). But no matter how much this mEve slept around, there is no way she bore children to 1,000 men, so a "minimum population" of at least 1,000 is incompatible with a mitochondrial Eve - if the theory is coherent, that is. But it looks to me like there is no particular reason to believe that the minimum population theory is scientifically preferable to the mEve even apart from biblical sources of information.

But no matter how much this mEve slept around, there is no way she bore children to 1,000 men, so a "minimum population" of at least 1,000 is incompatible with a mitochondrial Eve

I'm not certain that it is. What if she had only one mate, but their children and children's children then mated freely within a larger population of 1,000? But I may just be missing something.

I certainly agree with you, though, that there is no particular reason to accept the theories that lead to these minimum population estimates. They are just incredibly shaky.

I was thinking of an analogy the other day when I was contemplating the tetchiness in one of McBride's posts. At one point he says, "Well, one has to make _some_ assumptions." But only if one is committed to making these estimates! Why think that it is possible to make an estimate on which any weight can be placed? I thought that it's a bit like this: Suppose that someone is curious about how many scorpions walked across a particular 12 ft. x 12 ft. portion of the desert within a 12 month period a million years ago. So he makes a boatload of assumptions about constancy of scorpion population and climate similarity, etc., and then he presents you with an estimate. If you point out all of these highly substantive assumptions, any of which could quite easily be false when we're talking about a million years ago, he says, in exasperation, "Well, how else am I going to make an estimate if I don't make _some_ assumptions?" But that's just the point, of course.

Great work Lydia,

I did my best to grasp this post. I will now enroll in a Biology class at the community college and reread it next year.

I am wise enough to see that what is being proposed by the community of scientists on origins lacks consensus when it comes down to the nitty gritty. I am content to sit and let them run themselves in circles.

Actually, I should just read a textbook. I don't need to sit in a class.

Thanks again. You do great work by digesting the material and distilling it down for the rest of us.

Gina, yes, definitely does lack consensus. And also lacks the kind of evidence that should be necessary to bring conviction. They just haven't met any sort of burden of proof. It's surprising to me that Christians feel almost _forced_ to draw the conclusion that, e.g., Adam never existed from such hugely conjectural "arguments." I suspect that it is because Christians feel bullied in a way and have no idea of the real weakness of the case.

Naturalists do not consider biblical evidence as credible toward explaining the natural world, but there is no reason we cannot.

Consider the post-Babel world and how the nations arose. Here we see God directly intervening in the world to create distinct ethno-linguistic groups (nations) as part of His divine plan. Why couldn't some (much) of the genetic diversity in modern-day humans be the result of a purposeful act from a God who commanded humans to "fill the Earth"? Regions with long cold winters in the north require populations with different physical, mental, and social adaptations to thrive in them than warm equatorial regions do; much the same with mountainous vs. sea-level groups, plains vs. jungle tribes or inland vs. seaside peoples. The diversity of the earth's geography demands a diversity of those who take dominion over it. If all of humanity came from two people, there is no reason to think it would look like that today. In language, modern-day English and Hindi appear to be wholly unrelated but in fact they both derive from a common ancestor (PIE).

It should also be added that natural selection itself may drive a need for genetic diversity within smaller populations thus trying to extrapolate a minimum number of human ancestors based on current-day populations genetics is worthless. There is an small island near Antarctica named Haute Island which introduced two sheep of a particular species--male and female--around fifty years ago. Recently, when researchers looked into the genetic diversity of the resultant offspring, they discovered much larger genetic diversity within the sheep population than the models had predicted. This shows two things--that models extrapolating population size backward are only as good as they assumptions they make and that genetic diversity can arise more quickly in smaller populations.

Much of the historical sciences in biology is frankly just speculation based on poor a priori naturalistic assumptions.

Here we see God directly intervening in the world to create distinct ethno-linguistic groups (nations) as part of His divine plan. Why couldn't some (much) of the genetic diversity in modern-day humans be the result of a purposeful act from a God who commanded humans to "fill the Earth"?

It could, though the "when" remains up in the air. I do think there are functional reasons for extra at the outset, whatever came later.

It should also be added that natural selection itself may drive a need for genetic diversity within smaller populations thus trying to extrapolate a minimum number of human ancestors based on current-day populations genetics is worthless.

Quite true that genetic diversity with a small founding population sometimes explodes much faster than predicted. Gauger discusses this in the book as well, though she adds in fairness that such an explosion probably would not produce the number of variants Ayala alleges. However, Ayala's calculations were wrong for independent reasons anyway, as discussed above.

Bonus conjecture: The last post I linked by Gauger includes a link to a paper that argues for a great increase in genetic diversity some time between 600,000 and 1 million years ago. V. J. Torley conjectures (his conjecture being different from Luskin's) that the first true humans may have corresponded to Heidelberg man. That would fall at just about that time.

This is as conjectural as anything else, though. I don't mind admitting that as long as the naturalists admit the speculative nature of their own claims, but they refuse to do that.

>This is as conjectural as anything else, though. I don't mind admitting that as long as the naturalists admit the speculative nature of their own claims, but they refuse to do that.

Maybe that's because their claims don't depend on a prior commitment to a fairy tale from an 2000 year old book. Just a thought.


this is one of the many reasons Christians make poor scholars

That's a pretty lame comment on a several thousand word entry in which I _discussed why_ the naturalists' claims in this sub-field are conjectural. I discussed it in a good deal of detail. Getting insulting? Calling Christianity a fairy tale? That's what you've got? Unimpressive.

this is one of the many reasons Christians make poor scholars

Yes, of course. Including scientists like
Nicolas Copernicus
Isaac Newtwon
Gottfried Leibniz
Thomas Bayes
Leonhard Euler
Daniel Bernoulli
Anton Lavoisier
Joseph Priestly
Allesandro Volta
Andre Ampere
John Dalton
Michael Faraday
Charles Babbage
James Maxwell
Gregor Mendel
Lord Kelvin
Ernest Rutherford
Guglielmo Marconi
Arthur Eddington
Max Planck
Georges Lemaitre
Werner Heisenberg

That's just some of the famous ones in science who, if you have a lick of education, you have probably heard of. There are naturally thousands more non-famous ones, plus the many more scholars who work in areas other than science.

The problem with people without faith, such as Dunsany have is that they are uncomfortable with regarding the Bible as truth - not just truth, but truth outside their purely naturalist concepts. For such people, it is "impossible" for the earth to be covered with water after rain for forty days and forty nights, the placing of the rainbow in the sky, the stopping of the sun in the heavens and other Scripturally described miracles. They completely miss, for example, the point of miraculous rainfall and its subsequent miraculous removal as a demonstration of God's power. They think belief in such Scripturally described events is "superstition"!

Science and human reason are separate categories from faith, and each has its sphere. As far as our limited understanding takes us, science is a progressive approximation to truth, and in that sense, the scientists are generally right (IMO, as I was arguing about AGW in another thread). But the one should not be used to "justify" the other. That's how all the highly intelligent scientists mentioned by Tony (and there are many others) thought, and still think.

Actually, DZ, if you're endorsing some kind of "non-overlapping truths" view of science and Christianity, it would be a stretch to say that all the scientists listed by Tony accepted it. Isaac Newton certainly didn't. Mind you, Newton was an Arian, so a heretic in another way, but he certainly didn't think of science and Christian truth as utterly separate spheres.

Since all truth is God's truth, scientific facts and religious statements of fact are *by definition* compatible. As for justifying one another, sometimes they do. History is an empirical discipline, for example, and historical investigation justifies one's belief in the occurrence of miracles, which in turn justifies religious conclusions. That is just one example.

Lydia, I don't think that faith in the miraculous and science as explanatory are compatible. There is no known naturalistic explanation for events such as the Flood - there simply isn't enough water in the world for a Flood to cover all the known mountains 15 cubits deep. But we know from Scripture that every non-marine life form all over the world was killed in the event, and re-emerged and repopulated the world solely from the genetic pool in the Ark.

There are many other such miracles - the Babel event, for example, where ancient engineering constructed a brick-and-mortar tower to reach the heavens higher than the Great Pyramid does at present, or the Ulm Minster (or the Empire State Building) which cannot be explained by "modern" science. Or the fall of the walls of Jericho to the sound of trumpets. Or the taking up of Elijah in a whirlwind. Or the dropping of manna from the heavens. You brought up the parting of the Red Sea somewhere. We know these events actually happened, although science cannot explain them in any way. All these things happened in the past at a time when they needed to happen to preserve men's faith. It would have been good for faith if miracles continued to happen today, because our present-day atheists use the non-happening of miracles as evidence that miracles are myths. A modern parting of the seas would confound them indeed!

I am not actually committed to the utterly universal nature of the flood of Noah, but I think you are somewhat confused in any event. To say that something does not occur _by_ natural means is not the same thing as saying that its occurrence is _incompatible_ with scientific facts, so that one must actually believe a contradiction to believe in both. If a miracle occurs, then God has _intervened_ in the natural order. That is entirely compatible with the _existence_ of a natural order. Indeed, such a natural order is needed as a backdrop to the miracle. The building of the Tower of Babel, however, occurred by mankind's own efforts. Therefore, an interpretation of the text that makes it physically impossible for man to do (as far as we can tell) is probably an inaccurate interpretation. As a matter of fact, man's building of the Tower wasn't meant to confirm man's faith! It was a purely human architectural feat that evidently (so the text implies) reflected man's hubris and hence was frowned upon by God.

Moreover, once a miracle has occurred, its effects can be detected by ordinary, empirical means according to natural law. Photons bounced off of Jesus' resurrected body and into human eyes, and that is why we have the gospels today.

Lydia, I don't think that faith in the miraculous and science as explanatory are compatible. There is no known naturalistic explanation for events such as the Flood - there simply isn't enough water in the world for a Flood to cover all the known mountains 15 cubits deep.

Dan, I agree with Lydia: that God did something nature could not do, something that could not happen through the ordinary laws of nature operating, isn't a situation where "believing God did this" is incompatible with "believing in science and natural laws." The two can co-exist in the same SANE human mind, because God as the author of nature can suspend the natural operation of its laws for a specific purpose. Believing in science and the natural laws, and accepting that science cannot explain the event, just is the backdrop to believing that God stepped in and did something supernatural instead.

If God created a vast extra quadrillion gallons of water to flood the Earth, and then supported the land masses underneath the extra weight so they didn't get smashed to bits, and then evaporated the extra water over a hundred days or whatever - all through extra-natural means - believing that God did this is not incompatible with believing that there is no natural source for all that water.

Of course it is true that I am not proposing that there is fine natural explanation for an event AND at the same time a perfectly fine reason to call it a miracle - if nature is adequate to causing it, then there is no reason to call it a miracle. Even if God intended to bring it about just at that moment for some superlative good reason, there is no reason He could not cause it through natural means. And if the evidence says it was natural, believing it was a supernatural miracle would be foolish.

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