Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1)

[RichardBuggs]

Hi Dennis, good to hear you have had a nice hunting trip. I trust you are enjoying some venison now.

@DennisVenema

Richard - I see you’re still at me for specific references.

I am indeed. I cannot underline enough how important this issue is. If you are making unsubstantiated or mistaken claims about science in your book, just lines after saying “given the importance of this question for many Christians”, I don’t think it is just me who views that as quite a serious issue. This is why I am so keen to give you every opportunity to substantiate this passage.

For readers struggling to follow all the different threads in this comments stream, let me remind them that this is the passage from Adam and the Genome that we are discussing

@RichardBuggs

[Quoting Adam and the Genome] “scientists have many other methods at their disposal to measure just how large our population has been over time. One simple way is to select a few genes and measure how many alleles of that gene are present in present-day humans. Now that the Human Genome Project has been completed and we have sequenced the DNA of thousands of humans, this sort of study can be done simply using a computer. Taking into account the human mutation rate, and the mathematical probability of new mutations spreading in a population or being lost, these methods indicate an ancestral population size for humans right around that 10,000 figure. In fact, to generate the number of alleles we see in the present day from a starting point of just two individuals, one would have to postulate mutation rates far in excess of what we observe for any animal.”

So far, these are the attempts you have made to substantiate this passage from your book.[quote=“DennisVenema, post:13, topic:37039”]
Some of the citations you’re looking for are just working familiarity with published data sets.
[/quote]

@DennisVenema

I am saying this is my understanding of the published literature and the relevant publically-available databases. Li and Durban would be one paper relevant here; moreover the 1,000 genomes consortium papers, papers that estimate the present-day human mutation rate, and so on.

@DennisVenema

What I’m talking about there is a summary of the field as a whole - and the PSMC analyses in the 1,000 genomes paper is certainly one of the relevant experiments. So are LD studies. So are the Li and Durban PSMC results.

@DennisVenema

it’s a summary of allele methods, including PSMC

@DennisVenema

That passage is a summary statement about allele-based methods. Why would I exclude the 1000 genomes papers (including their PSMC results)? I was primarily thinking about the 1000 genomes work when writing that section.

I have argued that the plain meaning of that passage in your book, backed up by your Part I blog, is that it is not a summary statement and not a reference to PSMC and that to merely refer to datasets without the described analyses is not an adequate citation.

I don’t know how much time you have had to read through all the posts since your hunting trip. To make sure that others would agree with me about the plain meaning of the passage from your book about allele counting methods, I posed three simple questions for others to answer about it.[quote=“RichardBuggs, post:35, topic:37039”]
The questions I ask you are, when you read the extract from Adam and the Genome in bold below, which I show in its context:

Does the passage make you think that it is referring to a scientific study where a few genes have been selected and the number of alleles of those genes in current day human populations have been measured?
Does the passage make you think that someone has done calculations on these genes on a computer that have indicated that the ancestral population size for humans is around 10,000?
Does the passage make you think that this is a different method to the PSMC method?
[/quote]
To which your Biologos colleague Ted Davis answered:

@TedDavis

So, my answer to each of your three questions is, Yes.

And another reader also agrees with my reading of the passage: [quote=“tallen_1, post:38, topic:37039”]
As far as I can tell, Dennis makes three claims most relevant to your point: One, that there is a method to estimate minimum ancestral population sizes based upon measurements of number of alleles across various genes present in a population, and that this method indicates a population of approx. 10,000. Two, that an independent method exists that does not rely upon estimates of past mutation rates, involving “linkage disequilibrium,” that converges upon the same ancestral population size of 10,000. Three, that there has been a more recent method that is similar (not identical) that is not independent of mutation rate but also converges on similar results, namely the PSMC method.

Of these three approaches, Dennis’s support for the first seems to derive mostly from calculations on collected data. Presumably done by himself or others. Of the latter two approaches, that does seem to be something that is published and to which he could (and I think did) direct you. But I’m unclear as to whether the published studies for the latter two methods explicitly state Dennis’s conclusions or if he is drawing as well primarily on their collected data for support. I’m perhaps at a bit of a handicap on this as I’m relying on only excerpts of his book here on this thread. But to your point I do believe he describes three distinct methods. I’m eager to hear more about the sort of calculations conducted in these methods and how they may or may not support Dennis’s argument. That is what I am looking forward to in his remaining parts to this topic.
[/quote]
No one, so far, has defended your reading of the passage. This is making me think that your reading of the passage is what you wish you had written, rather than what you actually wrote.

And now in your latest posts you are saying:

@DennisVenema

The paper that specifically undergirds the “pick a few genes” part of the broad-brush summary statement about allele methods is this one, which like PSMC, is a coalescent-based approach:

http://www.genetics.org/content/genetics/147/4/1977.full.pdf

My first response was to think “Well, thank you, why didn’t you say so before?” But a quick skim of the paper convinces me that, again, this is not an adequate citation to support the passage we are discussing.

1. It was published before the Human Genome Project, and before we had “sequenced the DNA of thousands of humans”
2. Most of the genes (if we may loosely call a retrotransposon a “gene)” in the paper are monomorphic in the human population studied and a handful are dimorphic. Thus the maximum number of alleles at any locus in the study is two. The allele counting method as described in your book, and elaborated upon in your Part I blog, explicitly requires higher numbers of alleles.

So again, I don’t think this is an adequate citation.

Dennis, I have to say the conclusion I am coming to is that you made a mistake in your book. If so, I would have huge respect for you if you were willing to admit it, then we could all move on and discuss the interesting science of the other methods you have written about, and the work that Steven Schaffner is doing. We all make mistakes, and those of us active in research are very used to having them forcibly pointed out to us when we get back peer review comments on our manuscripts and grant proposals. It is never much fun to have them pointed out, but part of being a good scientist is being willing to correct our mistakes and move on.