Dr. William Amos of Cambridge Makes Case Against Neanderthal Admixture in Modern Humans

Dr. Amos has a long string of papers casting doubt that modern humans carry any appreciable admixture from Neanderthals. He has an alternative explanation which seems to fit the evidence much better. I have tried to raise these points on another forum and the experts there would not really engage. They just made vague comments about how he was mostly looking at single gene comparisons when the real evidence is in corresponding mutations in gene regions. I asked him about it and he replied with a study which showed that often times genes mutate in linkage to other genes- the study he cited had up to eight genes in a region linked in their mutations. If one mutated a certain way then the others would also mutate in a certain way. This in his mind made a hash of claims that a region containing matching mutations found in a sister species was due to introgression from that species, and I have to say that sounds reasonable. The other site would not engage on that and basically got testy. So I wonder if anyone here would like to take it on?

There seems to be a big push to try and sell Neanderthals as so much like us, I’ve seen evidence stretched to silly lengths to make that case. So papers like this one are not getting the attention that IMHO, they deserve.

I’m not sure of the problem. My Neanderthal part is by far the better looking division of my genes, I think.

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Hi Mark,

I think you have misread Amos. You claim his conclusion was no appreciable admixture, but Amos’ actual claims are far less categorical:

I conclude that, while some inter-breeding probably did occur, an appreciable component of the signal seems better explained by mutation slowdown.

Amos is saying that an appreciable amount of the signal attributed to admixture is actually the result of changes in mutation rate. Nevertheless, Amos concludes that the Neanderthal contribution to non-African DNA is 0.14%.

Other research has shown that the Neanderthal contribution has had effects with regard to susceptibility vs. resistance to certain diseases. To me, this seems like a significant contribution to non-African DNA.

Best,
Chris

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Chris I know it is hard to believe given the barrage of studies and claims and articles we have been subjected to, but he is actually claiming that number, which is less than one-tenth of everyone else’s number, is an UPPER LIMIT.

Since Neanderthal fragments will be appreciably more divergent it is reasonable to assume that upwards of 50% of archaic fragments would be detected. Using the 50% value, the average archaic proportion in non-Africans is 0.14%, about 10 fold lower than currently estimated. Moreover, since divergent sequences but can arise through chance, selection and population mixing, even this figure should be treated as an upper limit.

To give you an example of what he means by “selection” see my musings on a study which found that Neanderthals and Mammoths had some of the same mutations, clearly not a result of introgression but rather convergent genome evolution…

This is the same struggle I have had elsewhere trying to get qualified folks to look into this. It is difficult to grasp what he is saying for them because they have already put significant introgression into their category of “things we know are true from science”.

Regarding that part, that’s the sort of changes which are easiest to see as coming from adaptations rather than introgression. Eurasian genes against infection look different from Sub-Saharan African genes and more like Neanderthal genes simply because they have been exposed to the same pathogens while adaptation has been driving such genes in SSA in a different direction.

I have seen neither of these things in the professional literature. Maybe you are referring to conversations on religious sites.

This isn’t a paper. It’s a preprint, not (yet) subjected to peer review.

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This isn’t a paper. It’s a preprint, not (yet) subjected to peer review.

Yeah, because the reviewers won’t look at it. After a while, that excuse wears pretty thin.

I have seen neither of these things in the professional literature. Maybe you are referring to conversations on religious sites.

Nupe. Examples…

And…

And my reasons that these conclusions are nonsense…

That’s a very serious accusation. You will want to immediately provide evidence or I will flag this for attention of the moderators.

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Go ahead. I think you are the one acting like a jerk. Let’s let them decide.

Dr. Amos has been putting papers out on this subject since 2016. As you yourself noted, this one isn’t peer-reviewed, and none of the others have been either. How long should it take for a Cambridge professor to get his papers peer-reviewed?

https://www.researchgate.net/project/Neanderthal-introgression-a-case-of-smoke-and-mirrors

So, when you make an accusation about peer review, and I ask for evidence, that’s “acting like a jerk?”

I asked for evidence that his work has not been peer reviewed. You just posted a link to the scientist’s ResearchGate site. I read the first entry there. Here’s the second sentence: “I do have a paper late in the review process…”

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So, when you make an accusation about peer review, and I ask for evidence, that’s “acting like a jerk?”

You threatening to flag me my first day back in six months for expressing a contrarian viewpoint is acting like a jerk. It takes no class at all to be nice to people who agree with you. The real test is how you treat people who don’t agree with you. Running off to tell the moderators as a reflex-response for example.

Yes, which means it is not done yet. Which means we still don’t know if anyone is going to do it. And its been four years. And most of those years he’s offered a 10,000 pound reward, I believe it is up to 20,000 now, for anyone who can show him why his work is off. Only 1 guy has even tried, but the method he used would also negate the evidence that introgression ever occurred.

When someone with his credentials has to work that hard and that long to get past the gate keepers, there is a problem. There is a problem with the process. Don’t make me waste my time finding links describing why the peer review process is broken. We both know they are out there, and this is not a problem that will go away if you just tattle to the moderators anytime someone mentions it.

Which is the opposite of what you claimed above. You wrote “the reviewers won’t look at it.”

Now that we know you are making things up, I hope I can spare others the hassle of engaging your posts.

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When they publish, I will stop saying it. What good does it do if they look at it but don’t publish it? If they jerk him around for a year, and then don’t publish and are vague about why they won’t, how does that count as a legitimate look at it? And I happen to know that has happened to him on this issue. If they are only looking to find a reason to disqualify it, and then fail to find one but then withhold publication anyway I don’t consider that a legitimate look at it, because they were never giving it a fair shot. They were just trying to find reasons to avoid publishing a contrarian conclusion.

I am not the only one pointing out these problems. Examples.

and

and

I could find more.

Now that we know you are willing to construe everything I say in the worst possible light, I hope you will spare me the further hassle of engaging me. Instead of discussing the merits of his paper, you sniff that it is not peer reviewed. Then you use my skepticism of the process and lack of action on his requests to continue personally attacking me instead of dealing with the evidence in the paper, which is what I came here to discuss. I sure didn’t come here to argue over peer review. He has very good evidence. Maybe its too good. [content removed by moderator]

I don’t know enough about these subjects sadly to draw a good conclusion. But I am grateful for all the posts because this is something I have been really curious about in the last few months and it use to seem like nothing was talked about it really and now I see it often. Or maybe it’s just I’m paying more attention… unless y’all are all elaborate bots “cookied” into my search history lol jk.

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Please try and keep the discussion here focused on ideas rather than attributing motivations, beliefs, or attitudes to others, whether users here or people who are the subject of a discussion. When things get personal it detracts from what could be a fruitful exchange.

In the case of research in a field that requires much training and experience I trust the results of the peer review process. What other option is there? Laypeople can speculate and argue about some researchers results but I would place no confidence in anything a layperson would say and / or argue for. Yes people can point out problems with the peer review process but until someone comes up with something that produces the same over all high level of the results it is all we have.

There is absolutely no reason qualified people cannot examine and comment on a pre-print paper like the one in the OP. They just won’t. I am of the opinion that many many people in the field use the lack of peer-review as an excuse to avoid grappling with evidence that some belief they have is incorrect. Maybe that doesn’t apply to anyone here, but then why has no one seriously engaged on this paper?

You are attributing motivation to people you do not know which @Laura just cautioned against.

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