Gauger on Mitochondria Barcodes and Adam and Eve

[swamidass (S. Joshua Swamidass)]

An excellent article from @Agauger on the mitochondria barcodes story (Mitochondrial Barcodes: An Adam-Eve Bottleneck 200,000 Years Ago?). Great job explaining the complexities here, and I think your conclusion is empathetic and correct:

What to Make of It?

Well, I am unwilling to dismiss the article flat out, but neither can I endorse it. I don’t think the study can claim all the things it does based on the evidence they have. That I take this approach is ironic. I myself am investigating the possibility of our origin from a single human pair, so my opinion is not because I exclude the idea a priori . Yet I must confess I have reservations. Too many unanswered questions.

I am also sympathetic because I have seen tactics used on Stoeckle and Thaler similar to those that have been used on ID proponents. Denigrating the journal the article was published in, and therefore declaring the work is junk, is erroneous as an argument, because controversial papers may not ever see the light of day except in non-conformist journals. Saying they are ignorant or worse, dishonest, without first examining the work on its own terms, is simply unfair, and ad hominem .

Does Barcoding DNA Reveal a Single Human Ancestral Pair? | Evolution News

I agree that focusing in on the Journal is an ad hominem. It is worth noting, but it does not tell us much about the quality of the argument or the nature of the evidence. My only critique with this article is that they have wildly extrapolated to conclusions that the evidence does not support, revealing basic misunderstanding of population genetics. It seems that @Agauger agrees.

Great job @Agauger, your graphic showing how coalescence works is important education for your readers too:

Look at this figure. It traces the lineages of women going back eight generations. At the top is the ancestral generation with eleven individuals. I have colored the arrows for one woman’s lineage red. In the final generation, only her lineage persists. Working from the present backwards, you can follow the pattern as it coalesces into one lineage, that one woman’s on the first line. Note also that mitochondria, because they are passed from mother to daughter, never have an admixture of the paternal and maternal DNA. This speeds up the effects of beneficial gene sweeps.

[John_Harshman]

@swamidass

Denigrating the journal the article was published in, and therefore declaring the work is junk, is erroneous as an argument , because controversial papers may not ever see the light of day except in non-conformist journals.

I have to disagree. Bad journals don’t publish all bad articles, but it’s at least a clue. Shouldn’t be the main focus, but it’s worth noting, as you say. Authors generally want to publish in the best journal they can, and “controversial” isn’t the reason papers are rejected by good journals. So publication in a junk journal should raise eyebrows.

Still, the actual content of the paper is more telling.

[T_aquaticus]

@John_Harshman

I have to disagree. Bad journals don’t publish all bad articles, but it’s at least a clue. Shouldn’t be the main focus, but it’s worth noting, as you say. Authors generally want to publish in the best journal they can, and “controversial” isn’t the reason papers are rejected by good journals. So publication in a junk journal should raise eyebrows.

As an analogy, while some stories in the National Enquirer may be true it isn’t exactly the place to go for reliable journalism.

[Eddie (Edward Robinson)]

Thanks for highlighting Ann’s discussion, Joshua.

I have nothing to add on the technical side, not being a geneticist, but I did come across an older article about mitochondrial barcodes, in which a science journalist interviews one of the (at the time) world leaders in the field, Paul Hebert. I find the interview interesting, because Hebert, apparently not a religious believer, and certainly not a creationist, makes the remark that the results so far were consistent with a creationist view, seems eager to avoid that conclusion, and offers a tentative suggestion on how it might be avoided.

If anyone wants to explain in layman’s terms why Hebert calls the results creationist-friendly, that would be helpful to the non-geneticist readers here. Also comments on whether or not some of the statements of Hebert have now been superseded by later research might be helpful.

See:

http://stephenstrauss.ca/index.php/articles/the-barcode-of-life

[T_aquaticus]

@Eddie

I find the interview interesting, because Hebert, apparently not a religious believer, and certainly not a creationist, makes the remark that the results so far were consistent with a creationist view, seems eager to avoid that conclusion, and offers a tentative suggestion on how it might be avoided.

From the interview:

I think that it can be explained scientifically by there being a scouring mechanism that cleanses mitochondrial genomes of their diversity on a regular basis.

Mitochondrial DNA coalescing within a constant population doesn’t exactly support creationism.

[Eddie (Edward Robinson)]

@T_aquaticus

From the interview:

I think that it can be explained scientifically by there being a scouring mechanism that cleanses mitochondrial genomes of their diversity on a regular basis.

Yes, I know he says that in the interview. But if you read that comment in context, he does not sound very confident about the suggestion, and offers it only as a tentative one.

@T_aquaticus

Mitochondrial DNA coalescing within a constant population doesn’t exactly support creationism.

Maybe not, but then why did he, obviously not well-disposed toward creationism, make statements indicating that he thought it could be read in that way?

Read again what he wrote:

"But am I supposed to believe that every aphid species on the planet, every water flea, every fish went through a similar bottleneck at the same time? That is impossible. Honestly, I sometimes wake up at night and think, “If I was a creationist, this would be my proudest moment.”

And even after he gives the tentative suggestion which you repeat, i.e.:

@T_aquaticus

I think that it can be explained scientifically by there being a scouring mechanism that cleanses mitochondrial genomes of their diversity on a regular basis.

when the reporter asks him:

“But how does natural selection wash away the diversity?”

He replies:

“At this point in time, that is a science mystery.”

In other words, at that point in time, he couldn’t provide a mechanism for his proposed solution. But he wanted that solution to be correct, because otherwise…

I’m not drawing any conclusion from this that creationism is correct. I’m simply noting the fact that one of the early leaders in this field was troubled by what his data seemed to show, i.e., was troubled that the data seemed to support creationism. You can say he was wrong to worry about it, but you can’t say he wasn’t worried about it. His words are printed and the meaning of them is pretty plain.

[evograd (Blogging Graduate Student)]

Hebert’s view of creationism doesn’t match any modern creationist’s. Hebert says that each species having a unique “barcode” could imply creationism because it could imply that each individual species was created rather than being related. That’s not what creationists believe is the case - they accept some amount of limited relatedness between species, so unique barcodes delineating species doesn’t support modern creationism in the slightest.

[Eddie (Edward Robinson)]

@evograd

That’s not what creationists believe is the case - they accept some amount of limited relatedness between species

You are generalizing, as if all creationists hold the same doctrine regarding species. In fact there is a wide range of opinion within creationism. And historically speaking, the adjustment of creationism to allow “limited microevolution” is modern; up until fairly recent times, most people though God created individual species. In Darwin’s day this was a widely held view among lay folks, and maintained by some leading naturalists.

Be that as it may, whether you call it “creationism” or not, Hebert is still indicating that it bothers him that there isn’t a blurrier line between individuals and species, which one would expect in the Darwinian framework, where there is ultimately a continuity between individual variation, new varieties, and new species. Any “clumpiness” or “discreteness” in the data needs to be explained. He also uses the word “typological” – which he clearly sees as in contrast with Darwinian theory, because again it would lead to discontinuities rather than continuities. In other words, whatever you call it – typology, creationism – the mitochondrial data, in his mind, pose a disturbing challenge to evolutionary theory as he understood it.

Whether he would still say that today, I don’t know. That’s what he said in 2006. I’m therefore wondering whether the writers of the new study that Ann Gauger references are making arguments along the lines that Hebert identified, and feared. I haven’t read the study yet, so I don’t know, but it struck me that her discussion touched at one or two points on the subject, so I offered this article for comparison. I leave it to the experts to carefully relate what Hebert is saying to what the new guys are saying.

[Ashwin_s]

@evograd

Hebert’s view of creationism doesn’t match any modern creationist’s. Hebert says that each species having a unique “barcode” could imply creationism because it could imply that each individual species was created rather than being related. That’s not what creationists believe is the case

From what little I know about creationist models, this would align with a global flood and creatures surviving in an ark
However that is not Eddie’s main point.
If coalescence happens for a large no: of species at 100kya, then there must be a reason for it… contingency would be a good answer if it was one or two cases.
That seems to be the concern highlighted in the interview.

[Timothy_Horton]

@Ashwin_s

If coalescence happens for a large no: of species at 100kya, then there must be a reason for it…

You missed the point of AGauger’s article. The data does not support the claim coalescence happens for a large no: of species at 100kya.

[Ashwin_s]

@Timothy_Horton

You missed the point of AGauger’s article. The data does not support the claim coalescence happens for a large no: of species at 100kya.

I understood her point. What she is pointing out is that coalescence to a single person or small population need not indicate a bottleneck in the population. (That’s doesn’t mean there wasn’t any bottleneck either. Only that the mitochondrial evidence cannot give conclusive proof).
However, the time calculated need not be the same for pretty much all animal species.
For example, there is no reason for coalescence to happen for moths and humans at 100kya. Anne doesn’t cover that.

[evograd (Blogging Graduate Student)]

@Ashwin_s

From what little I know about creationist models, this would align with a global flood and creatures surviving in an ark

Not really, (modern) creationists believe “kinds” survived the flood on the ark, and then radiated into the many species we see today after disembarking.

[evograd (Blogging Graduate Student)]

@Eddie

You are generalizing, as if all creationists hold the same doctrine regarding species. In fact there is a wide range of opinion within creationism. And historically speaking, the adjustment of creationism to allow “limited microevolution” is modern; up until fairly recent times, most people though God created individual species. In Darwin’s day this was a widely held view among lay folks, and maintained by some leading naturalists.

Of course not every creationist believes the same thing, but all the major creationist organisations have been pushing for this “modern” version of creationism that certainly allows for speciation. If even leading modern creationists have abandoned the idea of special creation of every individual species, I think it’s safe to say it’s untenable.

@Eddie

Be that as it may, whether you call it “creationism” or not, Hebert is still indicating that it bothers him that there isn’t a blurrier line between individuals and species, which one would expect in the Darwinian framework, where there is ultimately a continuity between individual variation, new varieties, and new species. Any “clumpiness” or “discreteness” in the data needs to be explained. He also uses the word “typological” – which he clearly sees as in contrast with Darwinian theory, because again it would lead to discontinuities rather than continuities. In other words, whatever you call it – typology, creationism – the mitochondrial data, in his mind, pose a disturbing challenge to evolutionary theory as he understood it.

Yes, the data interesting and requires explanation (and I think we have good ones). Even without that, I think there’s good enough evidence that the inter-species differences are the result of evolution, not special creation. Consider this 2012 paper:

https://www.sciencedirect.com/science/article/pii/S1055790311005069

Looking at the locations of mutations in COI between species and within species, you can see that they’re very well correlated, indicating that the process that caused the inter-species differences was the same as the process that caused the intra-species differences - mutations.

[evograd (Blogging Graduate Student)]

If you want a really cool recent “barcoding-type” study, look no further than this paper:

“High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries”
www.nature.com/articles/s41467-018-07641-9

Basically, different bacterial species seem to be about 17% or more diverged relative to one another in orthologous regions, while within each bacterial species, there is only up to 5% divergence.

[Eddie (Edward Robinson)]

@evograd

Of course not every creationist believes the same thing, but all the major creationist organisations have been pushing for this “modern” version of creationism that certainly allows for speciation. If even leading modern creationists have abandoned the idea of special creation of every individual species, I think it’s safe to say it’s untenable.

I agree with you that there has been a tendency of creationists to move in this direction for a while now.

However, it may be that Hebert hadn’t kept up much with developments within modern creationism (he may have had in mind Gish and Morris, for example, and I’m not sure how far they went in conceding new species, as opposed to subspecies or variants); and don’t forget, his comments are now 12 years old, and I think the tendency you are talking about has been steadily accelerating in that time. Anyhow, I think it’s quite likely that in making his comments, he was thinking about the older, narrower contention that God created all the species that we now have. Linnaeus early on held to this view, though apparently he allowed for some modification of species later in life. But his original view was still alive among naturalists in Darwin’s day; otherwise, a large number of passages in Darwin’s On the Origin of Species would seem to be aiming at a strawman, a non-existent target.

I agree with you, however, that ultimately the more interesting question is not what is the definition of “creationism” for Hebert, but what is the problem he saw in the data, whether he was right to be worried about it at the time, and, supposing that he was right to be worried, whether later developments have removed the need for his concern. Maybe it’s time for another interview with him! Is he still working in the field?

[evograd (Blogging Graduate Student)]

Hebert is still an active researcher, although he seems to be focused on the application of DNA barcoding rather than the theory behind it. You’re welcome to contact him and see what his response is though.

[T_aquaticus]

@Eddie

Maybe not, but then why did he, obviously not well-disposed toward creationism, make statements indicating that he thought it could be read in that way?

Because he knows how creationist misinterpret scientific papers.

@Eddie

when the reporter asks him:

“But how does natural selection wash away the diversity?”

He replies:

“At this point in time, that is a science mystery.”

The mechanisms are already known: neutral drift and pedigree collapse.

[John_Harshman]

@T_aquaticus

The mechanisms are already known: neutral drift and pedigree collapse.

And selective sweeps. Somebody should mention that the mitochondrial genome is a single linkage group. One does wonder, though, if all we’re seeing here is a rough inverse relationship between generation time and population size.

[Eddie (Edward Robinson)]

@T_aquaticus

Maybe not, but then why did he, obviously not well-disposed toward creationism, make statements indicating that he thought it could be read in that way?

Because he knows how creationist misinterpret scientific papers.

Your explanation might apply to THIS statement of his, where he may be speaking primarily of how OTHERS might think of the results:

DR. HEBERT: Well, there is a typological ring to barcoding. If it were really and truly the case that each species was indelibly barcoded with an invariant DNA marker, that would have some very drastic consequences for theories of the origin of life. If there was only significant variation between species – and none within species – that could imply creationism.

But your explanation cannot account for THIS statement of his, where he is clearly speaking for HIMSELF:

DR. HEBERT: The explanation, when this lack of mitochondrial diversity showed up in humans, was a population bottleneck – the collapse of our species to perhaps 1,000 individuals about 150,000 years ago in Africa and out of that bottleneck modern humans emerged, stripped of mitochondrial diversity. But am I supposed to believe that every aphid species on the planet, every water flea, every fish went through a similar bottleneck at the same time? That is impossible. Honestly, I sometimes wake up at night and think, “If I was a creationist, this would be my proudest moment.” [emphasis added]

@T_aquaticus

The mechanisms are already known: neutral drift and pedigree collapse.

Possibly so, but back in 2006, when the interview was conducted, Hebert either did not know of these mechanisms, or knew of them but was not sure they provided an adequate explanation. Hence, he speaks of a “scientific mystery.” If he had the confidence you are here displaying, he would not have written in the way that he did.