Cooper: Assumptions in mutation rate

Sorry, I dropped off this thread, but I’m still pretty confused, so I hope you’ll bear with me, but this seems important for a layperson like me to understand.

So mutation rate is really the only assumption used? And is it assumed to be constant, then?

What is the sample size of the verification of mutation rates prior to ~10,000 years ago? Seems like it would be a very small sample size from a limited number of geographic distribution points?

Let me give you an absurd example, and forgive me if this is not the best one… there are probably better examples, but let me try…I’m making this up and realize it’s extreme, but bear with me…

A bottleneck population, Group A, of 100 people exists 20,000 years ago. They have a strict reproductive society, where only a certain, small upper class of people are allowed to reproduce and it is strictly regulated.

After 10,000 years, Group B, a population of 5,000, splits off from A and is isolated. They adopt the extreme opposite of Group A and have a society of “free love,” where everyone has offspring with everyone else.

Perhaps one of these groups, maybe Group B, values diversity, where those who are the most “unique” are more attractive and thus, more likely to reproduce. In Group A, uniformity is more attractive and those with very different features are less likely to reproduce.

In the last 2,500 years, Group A and Group B recombine into Group C, and they adopt the free love society of Group B.

We have genetic samples from Group C and Group B, but none from Group A, so as far as we know, Group A may never have existed?

Edited: Based only on the DNA from samples in Group C and a little from Group B, what bottleneck would we come up with and when?

Again, there are probably better ways to do illustrate my point here, but it seems you could come up with some scenarios like this that would give wildly different bottleneck sizes and ages, based on wildly different genetic mixing rates and mutation rates, right?

Have there been studies that have done this kind of extreme scenario modeling and, if so, what bottleneck sizes and age ranges did those come up with?

Thanks and again, sorry if I’m not explaining this well.

ALSO: Perhaps we can break this off into a new thread, such as “Assumptions used in population bottleneck models.” While I might be a dummy, I guess I object to these questions of mine falling under this heading. =)

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Not exactly. We use a mutation rate that is (at first) assumed to be stable (but not constant). We then can test this, to verify with data if it is stable. It is. So this is not an assumption in the end. The model is established by data, through and through. Perhaps there is another way to explain this data, but I have not yet figured out how to do so. I don’t see anyone else close to figuring it out.

Thousands of genomes at this time. I’m not sure (from memory) how many have been used to calculate mutation rates, but there are several studies. If there are any anomalies, we can be certain they will be discovered soon.

In this scenario (assuming it is not a trick question), the sharpest bottleneck at 20,000 years ago is 100.

We may or may not be able to detect this in DNA. It would depend on the data. This is an imaginary scenario, we just cannot say for sure. Maybe we could detect it. Maybe not. Maybe, if it didn’t happen, we could rule it out. Maybe not.

In the scenario above, we have samples from Group B and C. We still might be able to infer that Group A exists. The inference of ghosts populations like this have been done several times already, and then confirmed later by subsequent studies.

No. I do not think so.

You are no dummy. These are good questions.

Would be interested in seeing what is available here. Again, if the samples come from only limited numbers of populations in a few areas, seems like we might miss the outlier populations (like Group A in my scenario).

Sorry, I should have phrased my question better. I meant to ask what the DNA models would show as the bottleneck size and date. Yes, I provided you with the size and date, but I meant to ask, “What if this wasn’t handed to you and all you had was the current Group C sample and maybe a little from Group B?”

I guess this is my answer:

That doesn’t instill me with a lot of confidence. =)

Why not? I’m still pretty confused.

Yes, I realize Group A might be able to be detected as a ghost, but what if Group A was so small and so much mixing took place for it to be fully homogenized within Group C? Would seem like Group A would be lost at some point and thus you might come up with much earlier and much larger estimates of the bottleneck in that case, right? Maybe the 5,000 people in Group B at 10,000 years ago would be the calculated bottleneck. But that would be wildly off compared with the actual answer of 100 at 20,000 years ago.

Maybe I’m barking up the wrong tree, but with these answers, I really don’t see how anyone can claim “heliocentric certainty” on population bottleneck estimates.

Just not feeling warm and fuzzy about what seems to be a lack of scenario modeling on social/group assumptions to find upper and lower bounds on mutation/mixing rates. And then based on the results of these models, providing confidence levels for ranges of bottlenecks and ages.

Maybe someone in the OEC or ID camps has similar questions and can back me up? Or they could also let me know if this is not an area of concern for them.

Well you are right on that. You cannot claim heliocentric certainty going about 10 million years. Venema was wrong.

We can be that certain going back 10,000 years, going back 100,000 years. At about 500,000 years it starts to get murky. The evidence get’s much weaker.

I’m writing a paper with a student righ tnow.

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The good news is that with the right method, with data in hand you can find out how far back the evidence rules out a bottleneck. The data will tell you.

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In your book (or elsewhere), I really think you will have to explain why this is true, even with the types of scenarios I mentioned above. Otherwise, Group A could very well be Adam & Eve’s clan. You aren’t going to convince me by just saying, “trust me, the data shows this.”

Current book is not about this. My next book may be about this, with WLC.

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OK, but I personally cannot go along for the ride on genealogical Adam until you’ve sufficiently ruled out genetic Adam and Eve. Will you just say, “there’s no genetic Adam and Eve pair going back at least 500,000 years” and just leave it at that?

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@purposenation that is certainly true. I will make that claim. Follow what happens with RTB in the mean time. I am working to help them out this summer. @AJRoberts

As for getting you on the GAE bandwagon specifically, that is not my goal. As long as you are tolerant of the GAE, I’m happy. I’m just doing what I can to help make sense of this to the Church.

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Understood, but my only comment is that I think GAE is more attractive if you first “make sense” of the claim that there is no genetic pair going back at least 500,000 years. Esp. since the genetic pair concept is currently the widely held view of a large part of the Church.

So just saying “trust me” doesn’t seem like a good approach on the up to 500,000 year claim. But I guess I’ll stay tuned on what comes out of the collaboration with RTB. But I still wouldn’t be on board even if they say “just trust us too” (which I don’t think I’ll see anytime soon).

Same goes for the wider public, even beyond the Church. Why should the public just accept this type of claim without an explanation provided in layperson’s terms that helps them to understand it? This seems like a dangerous approach in general with science, putting “mainstream science” in the driver’s seat on the dissemination of truth, and then portraying anyone who questions that science (like me, I guess) look like a quack or an anti-science “denier.”

My book on GAE is currently 80000 words.

Population genetics is complex. It would take another 40000 words to explain it. I will get around to writing it up. I’m not saying “just trust us.” I am also explaining it here. We just have to be patient.

Now, the bigger question for you is not scientific, but textual and Theological. Can you produce any evidence that Scripture and theology requires there to be no one outside the garden? If not, why are you so strongly committed to it?

With all respect, many people on this board recently asked for immediate, detailed answers from Behe and @Agauger on their claims. And when @Agauger pushed back and said “I’ve already explained my position” folks just pressed harder.

But when I ask for information to support the 500,000 year claim and answers as to why it seems like there are some holes in the assumptions used in population bottleneck models, I hear “we have to be patient.”

Seems like a double standard, I’m sorry, but it does.

As for me, I’m not “strongly committed” to any claim one way or another.

But in evaluating the information, as an outsider, I still mostly see more of the same that we’ve seen for decades… each side becoming entrenched in their position, viciously lobbing personal attacks at each other, and not giving an inch.

Second request: Can we move this to a new thread, something like “Assumptions used in population bottleneck studies”?

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Not correct @purposenation. Look here:

  1. Heliocentric Certainty Against a Bottleneck of Two?.
  2. http://peacefulscience.org/three-stories-on-adam/

I’m saying the more complete exposition will take time. Moreover, there are unresolved scientific issues regarding the RTB model (which includes interbreeding).

I request that you carefully reconsider this. Where is the forum where we can ask questions directly of Behe about his book?

Moreover, what I am doing here is revising the consensus. There are many books that proport to explain exactly what you are asking for, for example Adam and the Genome by Venema. If you push too hard, you will lose the end game here. I’m not so concerned with convincing you as convincing my colleagues, who still largely believe it is ruled out going back 6 million years.

So, if you want to see the evidence against a recent bottleneck, read those book and what is already in the consensus literature. I am sure @John_Harshman would be happy to answer questions. If you want space for a bottleneck more ancient, you provisionally have it, and can read the technical discussion elsewhere. The book from me on this, you will have to wait for.

So, with all due respect, this is not a double standard. I request you reconsider this characterization.

(yes we can move to a new thread)

I have. And that’s why I came to ask the question about the specific assumptions used, esp. for cultural/interbreeding/group evolution dynamics differences that may have been used, vs. just mutation rates. Seems to me, if you just use and vary mutation rates, and ignore cultural/group dynamics (which may mostly be present in only humans and to some extent, apes), an assumption that mutation rate is constant for 10k yrs. and/or doesn’t change much over 100,000 years might just be wrong. Likewise, assuming we have solid coverage with our ancient DNA samples might also be wrong, esp. if we are missing samples from groups like Group A.

I simply asked if anyone has seriously explored these types of factors and scenarios and/or has done outer bounds modeling with these factors in mind and I feel like I got a “from authority” type response that the “data says otherwise” but then at the same time also hear “yes, with the Group A scenario, DNA might not find them.” (paraphrasing) So that raises even bigger questions for me.

I was referring to the discussion with @Agauger on this board – but, with Behe it’s been in other venues. With @Agauger, I don’t see that my line of questioning was much different or less valid than the line of questioning presented to her. However, with my line, I felt a little deferred and put off and/or felt like I am being told “we’ve already addressed that here and here” or “you’ll just have to wait.” (again, paraphrasing). I feel like her responses were similar, yet she was pressed hard in those cases for direct responses.

So I’m just pressing too, but was still not getting what I consider to be direct answers to my specific questions, without having to ask them multiple times in multiple ways.

Anyway, if I’m barking up the wrong tree, I’m totally willing to back off (for now), I’ll go do some research into these studies and reach out to Venema and others to see what they say.

@John_Harshman, your thoughts?

I had just hoped I’d be saved the trouble by others on this board who already thought these things through, esp. since I’m not anywhere near an expert and haven’t thought things through as much.

Don’t get me wrong, I love you, this board and everyone on it. But I also don’t think leaving questions like this insufficiently addressed (IMO) helps your case with GAE.

Again, it’s just one guy’s opinion and as always, I reserve the right to be completely wrong. =)

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This is an interesting recent article:

It might be an example of how “defects” might be treated in human populations differently than animal populations, thus impacting what we might expect in survival rates, mutation rates, etc.

Seems like group/social dynamics would be important considerations in any human population bottleneck studies, and I’m simply pointing out that I’m not seeing this.

I’m curious about what you mean by “different mutation rates”. Do you think they might have changed much over the past million years or so?

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Perhaps a better term is “effective mutation rate.”

I’m curious to know what evidence that you have that effective mutation rates are not different and have not changed among various people groups over the past 100,000 years or so?

Wouldn’t the effective mutation rates be very different over time between Group A and B in my scenario? And if you also throw in how mutated people are treated (allowed to reproduce or not, etc., see the recent article above) wouldn’t that further change the effective mutation rate over time?

If you have a culture that kills anyone with deformities and/or that is “different” than the average person, vs one that honors and celebrates it, making people with differences more likely to reproduce, wouldn’t each of those societies have very different effective mutation rates?

At the same time, I’ll also add that it’s unclear if @swamidass varies mutation rates outside of 10k windows, but here’s what he says on that:

" 1. Mutation rate is assumed constant across 10kb windows, but is known to vary on shorter distance scales.
2. Most importantly, we expect mutation rate to be different at times in the past. For this reason, we cannot know it for sure. Especially as we are considering times in the deep past (say 300 kya) but not so deep that we can expect the central limit theorem to save us (say if we are going 5 mya)."

I guess my point/question is that it seems humans are different than most other animals in that we can collectively alter our mutation rates via social group dynamics and reproductive choices.

As a close approximation, I wonder if anyone has looked at the effective mutation rates of chimps vs. bonobos since they have very different social structures?

I don’t understand what that term would mean, so can’t really discuss it.

I also don’t know what you mean by “mutated people”. The X-Men? You should remember that most mutations have no effect on phenotype.

Well I guess I made that term up, but I suppose effective mutation rate = average mutations across specific groups of people… those that carry forward due to reproduction vs. mutations being stilted by a society that doesn’t encourage reproduction.

Or, more broadly, different groups of people might have different mutation rates, and the combination of those two groups provides an overall effective mutation rate for humans.

Either way, I think the question that I raise should be easy enough to follow?

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By this i meant exactly what is covered in the Science article I posted, plus “unseen” differences in personality traits, dietary allergies/preferences, things that do manifest in some way.