Comments on What Genetic Science Says About Adam and Eve

This thread is intended for comments on and corrections to the arguments in my article, not in other articles. If you guys want to discuss those other arguments, could you start another thread, please? Thanks.

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I am discussing your article @glipsnort . This an indispensable component of your argument. Several respected scientists argue the evidence going back way farther that rules out a bottleneck, as far back as millions and millions of years. That includes, for example, @John_Harshman, but also material on the website you published your article.

You can’t just ignore those arguments and lines of evidence to make your case. That would be cherry picking.

So how do you respond to those arguments and lines of evidence?

This question is directly related to your article. Just ignoring this question would be cherry picking. Of course, I know you have a response to those arguments. So why not just give it to us?

If he’s supposed to respond to something, shouldn’t you at least cite what he’s supposed to be responding to? And unless this is supposed to be a cryptic private conversation, shouldn’t you let all of us know what that is too?

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OK, moderator hat time, and I’ll do my best to keep this unbiased. This is Steve’s thread, so I will honor his request and make a new thread for the question. It’s not clear if citations to this other material is called for, but I agree it would be helpful for the rest of us. I may have more to say, still considering.

/fnord

edit: or maybe it will just be closed.

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Sure @Dan_Eastwood, but I need to be clear on my position here. If @glipsnort wants to respond, we can reopen.


@glipsnort, I think your article is good in many respects, but it neglects serious arguments against your conclusion. For this reason, I think the article has critical omissions. Neglecting the case against your conclusion is one type of omission. There are others too. But just ignoring arguments against your preferred conclusion is not a valid approach to scientific argumentation.

Great point. Let me give four sources with far more than three arguments:

  1. BioLogos still recommends Adam and the Genome without any caveats. In this book, Dennis puts forward several arguments that appear to conflict strongly with your thesis.

  2. Dennis backed off those arguments of course, in this article: Adam — Once More, With Feeling | Scot McKnight. So perhaps to address #1 you might add a citation and brief sentence addressing this to your article. However, in his article, Dennnis puts forward a whole new set of arguments that he claims stretch back more ancient than 500 kya.

  3. As @John_Harshman keeps chiming in, he is a legitimate scientist who believes his evidence against a bottleneck stretches back 6 million years, at least, if not farther.

  4. This article, recently deleted by BioLogos. Claims to have several lines of evidence stretching back 18 million years. What do you make of the evidence there?

I do not think your article makes a scientifically sound case because it does not address these arguments against your conclusion. I’m honestly puzzled by you unwillingness to engage with Dennis and John’s work. They claim to have evidence against your conclusions. I think you need to address them.

Now, William Lane Craig and I have addressed these arguments head on. It is possible you could cite us. But relying tacitly on our work, without citing us is not really fair. If you would like to add a few sentences that appropriately cite us, I can provide the best citations to you.

For all the real strengths of your article, I think this ends up being a significant shortcoming. This is a scientific oversight. A good scientific article would not have this critical omission.


On a different note, but still relevant to this thread, next week I am presenting a response to your paper at the ASA. This paper will make clear another substantial omission, one that is even more significant than the one I describe here. That will be an academic paper. I will look forward to seeing your response to it @glipsnort .

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You asked the mods to help - I’m helping by freeing you from moderating this thread, removing any appearance of bias. Splitting the thread is a good solution, and it’s what I would do even it you were not involved. In any case, I would not restrict you from presenting your position. :slight_smile:

This thread is now closed until @glipsnort requests it is opened. I happy with that, once my comment is returned to it, and I agree think further discussion should be on this thread.

Okay @Dan_Eastwood , thanks for the private communication about this. I will just put it into a new thread.

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Okay. I accept your decision @Dan_Eastwood .

For those that care to follow the conversation, see here: What Genetic Science Says About Adam and Eve (Omission #1)

I look forward to hearing @glipsnort’s response.

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I could have misread Dr. Schaffner’s article, but the conclusion seemed to be that if there was a 2 person bottleneck then it would have had to have happened at least 500,000 years ago. The “at least” is important here. If someone is arguing that the figure could be as high as 10 or 18 million years ago that doesn’t contradict what Dr. Schaffner is saying.

IMHO, the main point of Dr. Schaffner’s article was to address the possibility of a 2 person bottleneck in the last 10,000 years. The evidence presented in the article clearly shows that this isn’t supported by the data. Again, the data presented puts a lower limit at 500,000 years. I don’t understand why Dr. Schaffner would need to address older estimates that other people have derived from different types of data since it neither contradicts Dr. Schaffner’s conclusions nor does it nullify the main focus of the article.

Am I missing something here?

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Yes you are.

The reason why is the other estimates do contradict his conclusions.

Two scientists, @John_Harshman and Dennis Venema, have come forward making claims that contradict @glipsnort 's article. Though distinct challenges, taken together they claim to have several lines of evidence against his conclusion.

Good scientists deal with criticism like this head on. @glipsnort is a good scientist, so I expect he will respond.

How does “10 million years ago” contradict “at least 500,000 years ago”?

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With respect, you have simply restated your complaint without clarifying it based on @T_aquaticus’ question. I am as confused as he seems to be.

Edit: this whole conversation has the feeling that there are important background details or motivations that are going largely unstated.

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Saying you’ve ruled out a bottleneck more recent than 10 mya contradicts the claim that a bottleneck is possible 700 kya ago. That should be fairly obvious.

Is that clearer?

“At least 500,000 years ago” does not rule out a 10 mya bottleneck. I didn’t read anywhere in Dr. Schaffner’s article where he ruled out time periods older than 700 kya.

At best, he states that using specific data sets he can’t differentiate between a 2 person bottleneck 500,000 years ago and a standard population from that same time period. This is simply resolution vs. noise, not a hard upper limit.

Radiometric dating might be a good analogy. Carbon dating can only get you to 50 kya, at which point 14C is so low that you can’t distinguish between older dates and noise. If someone says that carbon dating dates a sample to at least 50 kya, is that contradicted by someone claiming a 10 mya date using K/Ar dating?

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That is exactly right!

However Dennis Venema and @John_Harshman disagree with @glipsnort . They claim to have evidence that pushes this date back 1 to 2 orders of magnitude from 500,000. That is quite a bit of a contradiction. The way evidence works in this space, their date trumps his, unless he shows why they are wrong. Others have addressed this evidence, but @glipsnort does not, nor does he even acknowledge these challenges or cite any rebuttals.

That is the gap. That is why he fails to make his case.

Unless of course, he agrees with those arguments. In that case, the 500,000 date is misleading cherrypicking. Except he just stated in another thread that he doesn’t agree with the 18 million year date. So he really needs to justify the range he proposes by engaging with these arguments. They are active positions held by many people. He cannot just ignore them.

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They agree with Dr. Schaffner because they also believe that the bottleneck would have to be more than 500 kya.

Let’s look at the actual conclusion:

Here is the graph that goes with it:

Here is the question. Where did Venema et al. look at this same data (number of variants vs. frequency of variants) and come to a different conclusion based just on that data? Where did Dr. Schaffner state anywhere in the article that the upper limit was less than 5-20 mya?

That is a different issue entirely.

Both Dennis Venema and @John_Harshman have brought other lines of evidence to the table, evidence that @glipsnort has not addressed. He cannot just ignore them.

As for the evidence that he presents from the site frequency spectrum (SFS), @glipsnort also omits that this an exceedingly weak line of evidence. There are in fact scientists who claim that SFS does not even rule out a bottleneck at 6 kya. Who is correct? Them or @glipsnort?That is another discussion I look forward to having down the line. I believe we both will benefit greatly from input from @Joe_Felsenstein on that discussion. But I am hitting snooze on that conversation for good reason.

We need to deal with each objection in turn, one at a time. Otherwise everyone will quickly get lost.

Why not? The evidence in Dr. Schaffner’s article was more than enough to show that there is no support for a 2 person bottleneck in the last 10,000 years.

That would at least be more relevant than the articles by Venema et al. which actually agree with the conclusion that there wasn’t a 2 person bottleneck in the last 500,000 years.

As I have said, that is just an aside.

Because of their claims are correct, his claims are not. That’s why.

And, in fact, I’m not convinced SFS is good evidence against a 2 person bottleneck at 10,000. Besides the fact that this isn’t his conclusion, this is a different discussion. Not for now.