Cooper: Assumptions in mutation rate

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. 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.

Sorry, I’m still not at all clear on what you’re trying to say. How do differences in personality traits, etc., affect mutation rates?

How does acceptance or non-acceptance of gross developmental abnormalities, most of which are not genetic in origin, affect mutation rates?

And quoting this article (I love how timely this one is…):

"Northern Ireland between about 2000 and 1500 B.C.E. Although the DNA showed the skeletons were from different populations, thanks to a dramatic genetic turnover, all four people carried the gene that causes hemochromatosis, an uncommon condition that causes excess iron to build up in the blood.

Today, Ireland has the world’s highest rates of that mutation. Bradley suggests the gene may have some advantage, perhaps helping protect against bacterial diseases or boosting iron retention in environments with poor diet. Understanding why rare conditions pop up in certain places “may help researchers today to better understand this genetic burden,” he says."

@purposenation, I split off your conversation so you didn’t have to be under my “Genetics for Dummies” heading :wink: Hopefully this heading is more to your liking.

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Thank you, although I still reserve the right to admit that I’m a genetics dummy =)

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I think this may be poorly worded, and mean to say that Ireland has the highest prevalence of this mutation present in the population, rather than suggesting this mutant actually spontaneously occurrs more frequently in Irish people.

I don’t think you realise that this has nothing to do with the assumption of fairly constant mutation rates over time though.

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@purposenation he is right. Do you understand why?

No.

Now I see what you are trying to say.

That’s really, really bad writing and it’s not your fault that you misunderstand.

The genetically correct way to write that is, “Today, Ireland has the world’s highest frequency of that mutant allele.

Unfortunately, this misleading shorthand is used far too often by those who don’t do genetics.

The mutation only happened once AFAWK. Mutations are events that create mutant alleles. Alleles are different versions of genes. You are asking about allele frequencies, not mutation rates.

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@swamidass: this is an interesting question. Recent studies show that a good percentage of the human genome consists of “mobile elements”.

Since MEs are not associated with the traditional understanding of mutations (like spot changes), would this impact the calculation of mutations rates/the overall conclusions regarding bottle necks?

Do the assumptions inputed into your calculations account for MEs?

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The mutation rate we uses takes ME into account.

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