Cooper: Assumptions in mutation rate

As you note, the time period matters a lot. We do have “heliocentric certainty” when it comes to an absence of a 2 person bottleneck 3,000 years ago. As we go back in time we can reach a point where we can’t distinguish between a population of 1 million or a population of just 2. Certainty in this context is a function of time.

What we have evidence for is mutation rates comparable to what we observe in modern human populations. We don’t have evidence for mutation rates 10x higher than what we observe. In fact, I doubt you could find any mammal or vertebrate species that has a mutation rate 10x that of modern humans. If the only reason you are proposing a 10x higher mutation rate is to protect a preferred conclusion, then that is a bad way to do science.

A different way to look at it is to ask if there is any positive evidence for a bottleneck of 2 people in the human population, and have that same evidence rule out a population of 10,000. I haven’t seen anything approaching this type of evidence.

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Would seem that population bottleneck studies would want to run the models through sensitivity analysis to see what adjusting the assumptions to upper and lower bounds would do to those bottleneck sizes within time frames.

Just makes the data more trustworthy in my mind. “Ok, these researchers are not just cherry picking and coming to the conclusion they want to show. They at least put their assumptions through the wringer and show a sensitivity analysis to show how likely other scenarios might be.”

I’ll just assume by “you” you mean scientists in general and not me personally as I’ve not proposed a 10x mutation rate, I’ve merely been asking questions about assumptions used and what sensitivity has been done on those.

In fact, I’m saying what you are saying… If you aren’t presenting your assumptions clearly, and/or have not done sensitivity analysis to show the likelihood of other outcomes and/or you aren’t willing to admit any weaknesses is your argument, a skeptic on the other side could also say you are just working to “protect a preferred conclusion” which, in this case, could have been to show that it’s impossible to have had a population less than 10,000 according to several studies.

But, at the same time, I’ve not questioned their motives (though others do). I’m only questioning the assumptions used and sensitivity analysis presented on those assumptions.

By questioning these things, my own motives have been questioned on this board, which seems like a double-standard and also isn’t cool. What if my motives are to help shore up the @swamidass GAE model against similar objections in the future?

Honestly, the only motive I have is for me to personally understand this stuff better. I’m a work in progress, so thank you for your patience in bearing with me. =)

I’ve not been asking about a population of 2.

If one were to accept 14 billion yo universe, reject complete and/or literal genealogies in the Bible and is flexible with “image of God,” why would 20k, 100k, 400k be that much different?

That’s correct. I was using the impersonal “you”.

The mutation rate was determined independently of the population studies. That’s the difference. No one is choosing a mutation rate based on the answers it gives about past population sizes. To emphasize this once again, we can directly measure the mutation rate in humans. We also have known and historic human population movements that allow us to derive a mutation rate. On top of that, we have ancient human DNA that we can look at. This is how the mutation rate was derived.

It is interesting that you only seem to be arguing for a higher mutation rate and not a lower one. If we are talking about the problems with making assumptions, then a higher and lower mutation should be considered equally.

It does move us into questions about brain function and intelligence levels. If we go back a few million years we are talking about Australopithecines with a brain only a bit larger than the brain of chimps. Homo erectus has a brain a bit smaller than modern humans, and it also has structural differences.

But this ancient evidence is spotty prior to 15k yo, yes? And even with spotty evidence and perhaps the chimp study, it shows a higher mutation rate in the past, yes? So I agree with your challenge to show “much higher” in the past. A good challenge.

I’m questioning the 10,000 range of minimums and how that was calculated. Sure, it could be higher than 10,000, yes, but that’s not what seems to be presented. And the evidence seems to show higher mutation rates in the past. Sure, the bottleneck population could be higher than 10,000 and mutation rate could be lower in the past, but that’s not what any of these studies show, do they? If so, please share, thanks.

But you seem to be referring to brain sizes, not brain functions. Yes, a whole different conversation. 2m years, yes, that seems to be significant. Not sure that we know the differences between 50k and 500k well do we?

We have DNA prior to that:

The 10,000 population size is the estimate you get when using the mutation rate we have evidence for.

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Wow, one sample? Ok, you got me. =) Yes, I was aware of that one sample but still doesn’t change my classification as “spotty.”

10,000 ever? is that really an “estimate” or is it a “heliocentric certain” number? What is the range of estimates and confidence levels and assumptions used and sensitivity of those assumptions. We’re back to the beginning of this thread.

Yes, I saw that he liked your answers, I didn’t see that he conceded that he was certain that there was no min. population of 2 prior to 500k. But may have missed it, where did he say/admit that?

On his site, I see this:

“To my mind, the question has now moved on from “Is an ‘Adam and Eve’ bottleneck inconsistent with human genetic diversity data?” to “At what timescale could an ‘Adam and Eve’ bottleneck be consistent with human genetic diversity data?” It would be good to see the AFS and TMR4L approaches followed up with published analyses, and I would be very glad to know of other approaches that could be used to test or date the hypothesis.”

So he’s still looking for AE and seems convinced it’s there, but just not sure what time they existed. But perhaps he agreed it is “certain” that they did not exist prior to 500k yo, maybe I missed that?

Yes, that’s the only explanation that I can see. In the context you gave them, they still look like allele frequencies, not mutation rates.

I haven’t written anything of the sort. I have asked you to please stop conflating mutation rates and allele frequencies; if you can’t, you’re not going to be able to learn anything.

“still look like”? Um, I directly said they are mutation rates. If you think that still looks like something other than what I specified them as, OK, well, then, not much more I can do to help there.

He agreed that was the case. He wants the analysis published. I agree.

OK, in writing somewhere?

20 kya fits in some YEC time lines, and might even be close enough to link with civilizations rise in some ways.

50 kya is connected by some to behaviorally modern humans.

The farther back you go, the more different they are then us. 2mya is pretty different. In the range 700 kya - 400 kya, I do not see any distinctions. We have to include more than Homo sapiens as “human,” and we are far removed from the rest of the narrative details.

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How many samples do we have for higher mutation rates?

From what I understand, that is the estimate. The “heliocentric certainty” that Venema spoke of pertains to probability of that estimate being off by 3 orders of magnitude. However, I think @swamidass is correct when he says Venema’s calculations are not entirely accurate. @swamidass can probably speak to the statistical significance of these calculations better than I can, so I hope he sees these posts and has the time to dig up the numbers.

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He confused average with minimum. For a given period of time, the average can remain high, with high certainty, while the minimum can dip much lower. He was using apples to argue for oranges.

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Yes, I know that is what you said.

You could help by specifying the units of those rates.

I’m trying to help in good faith, Brad. Let’s go back to what you quoted to support your equivocation between allele frequencies and mutation rates:

Do you understand that the journalist you quoted was incorrectly referring to an allele frequency as a mutation rate? That’s the point I’ve been trying to get across.

Yes, this is the challenge.

And pretty sure we won’t be able to figure this out on our own, at least as far as what God considers to be in His image. We do need to call on Him to guide us with this most imporant task, we should not rely on our own understanding.

Scientists will say that’s not very scientific, but this is where confessing Christians who are scientists/ethicists need to speak up.