Wednesday, December 25, 2019

Why Eurasians Don't Have 1.5% of Their Genes, and Likely None, from Neanderthals

The effort to re-define "human" as any member of a veritable "zoo" of hominin species has been very successful. This is due to endless repetition of claims like "Neanderthals made cave paintings in Spain 66,000 years ago." That particular claim was so outrageous that even a rank amateur like me shredded it here, and I was pleased to see more recently some academic pushback on that particular claim. Too bad none of that matters much. In the public mind, and even that of the scientific community, the damage is done from an unrelenting barrage of such articles touting how similar Neanderthals were to us. This includes the claim that they interbred with us. People who look to science have incorporated these beliefs into their internal category "things that everyone knows", and believe it so much that many bridle or get dismissive at the suggestion that it isn't so because at that point it becomes a threat the validity of their seminal category "things that every knows (are true)."

Into that environment bravely stepped Cambridge zoologist Dr. William Amos. He has a large number of studies that in my mind utterly destroy the idea that modern Eurasians have inherited 1.5% of their genome from Neanderthals. He calls his research page "Neanderthal Introgression: A Case of Smoke and Mirrors?" He shows in his research how almost all of the supposed signal for introgression, all but a rounding error, is explained by the fact that small homozygous populations (like the one that supposedly left Africa), have a lower mutation rate than populations with greater genetic diversity- like the one which was supposed to have stayed behind in Africa. This is true even while any mutations the smaller and more homogeneous group do have will be fixed at a much higher rate than those same mutations in the larger original population. The signal is better explained by the African population evolving further away from Neanderthals than Eurasians, along with Sub-Saharan Africans losing mutations which were once in all three populations.

That is the extreme cliff-notes version, and he has meticulous and convincing answers on back-mutations and many other questions which might cause one to doubt his hypothesis. And if that weren't enough, he has offered a reward of twenty-thousand English Pounds to anyone who can show him where his research is in error.  Of course, that's not enough either. Whether it is part of the sin-nature or just a component of our general ridiculousness, we humans are very slow to see all kinds of truth we don't like, not simply spiritual truth. So we will see how this goes.

Even though he has found an explanation for essentially the whole signal, there are yet other explanations for the appearance of introgression which he does not discuss. With regard to the few such genes which are considered helpful rather than regarded as deleterious, an obvious additional explanation is convergent evolution. Eurasians and Neanderthals were shaped by the same environment and exposed to the same pathogens. Why wouldn't their immune systems respond in the same way? Heck, Mammoth genes and Neanderthal genes responded in the same way, with the same mutations, because of CE. Was that "introgression" too?

Dr. Amos does concede "The finding of hybrid skeletons shows that fertile matings did occur." Notice that this is not a concession that people alive today inherited any of their DNA from Neanderthals. These hybrids could have been genetic dead ends with fertility problems even if they managed a few generations of offspring. Many experts have speculated about such pairings having significant fertility issues. And let's not forget that many of our ancestors are supposed to be "genetic ghosts" anyway. That is, even though they were your ancestor you have zero genes from them because you also had more than 20,000 other ancestors whose DNA is competing for those 20,000 (protein producing) gene slots. Not all of their genes can be represented! I would note that even in the non-protein producing genes, they tend to replicate in segments, so even if you had a million total genes you still wouldn't have room for a million ancestors to be represented. You inherit the DNA in chunks, not necessarily gene by gene and there are way fewer chunks than total genes.

The claim that Neanderthals hybridized with Eurasian ancestors 50,000 years ago runs smack dab against the results of this study which concluded that Neanderthals did not mix with modern humans during their range expansion into Europe. So for some reason Neanderthals were supposed to have mixed with our ancestors 50,000 years ago so thoroughly that we can still see they left us 20% of their genome scattered amongst us, but after that, if we ever mated again the results are so obscure that they are "genetic ghosts."  This even though it is clear that something like us mated with Neanderthals long ago

And all of this is juxtaposed against the incredible claim, based on how low the diversity is in most of our DNA, that within this world of a "hominin zoo", our mainline ancestors spent the vast majority of their 200-300 thousand years of existence on the edge of extinction. This until breaking out in a decent way forty-something thousand years ago and in a huge way about twelve thousand years ago. Our creativity and our ability to make things which are unquestionably art also shows sign of a great leap forward forty-something thousand years ago. From what we can see now, it does so globally and contemporaneously. If any place is first, it's east Asia.

All of this suggests another scenario where hybrids could have been born and yet living people have zero contribution from their DNA. I want to put this out there (it is not the model I advocate in my book) as something which needs to be considered by folks like RTB who believe in a "Middle Adam" time-wise. As the TV Detective "Monk" liked to say.....here's what happened..

Around 50,000 years ago, a unique population of hominins came into existence. Whether this was by a Divine Act, a fortuitous combination of natural evolutionary circumstances, or something in-between is beside the point of this story and something we can argue about another day. What made them so unique wasn't very apparent from their structure. Aside from a somewhat more globular brain shape, they were extremely physically similar to all the other hominins that scientists today classify as (Archaic) Homo Sapiens. That's right, not only are we not descended in part from Neanderthals, but even if evolution is the total explanation for our existence, we also didn't descend from most of those fossils from over 50,000 years ago classified as Archaic Homo Sapiens. Something happened, and somehow there was a population of sapiens which did not fit in with the rest. Not even the rest of the things we would call "Homo Sapiens". They looked similar, but here is how they were different...

They could think and speak with recursive language, they had an ability to possesses true empathy, were imaginative and made and/or enjoyed complex art. They were creative for its own sake, as a part of their nature and not just to solve a problem related to survival. They had a desire to connect socially which went beyond instinct and self-interest even into religion. They were us, including spiritually. We don't just operate within the natural realm, but wonder about, and in most cases yearn to connect with, something beyond it. 

I submit to you that if one group of hominids had all that, and others did not, then there will be significant barriers to reproduction between those groups, even if there are no genetic or physical barriers. The barriers will be social, intellectual, and spiritual, but they will still be real and would strongly discourage hybridization between groups. Even if the Others had the power of speech, we wouldn't have much to say to each other, especially not talk of the sort that makes one human decide they want to take the other as a life-long partner. They would be looked at in the way Medieval Europeans looked at the fantastical "Woodwoses". 

Under this definition, even some of the fossils now classified as "Archaic Homo Sapiens" show no evidence of being "us", never mind Neanderthals, Denisovans and the rest. Those older fossils have none of the artifacts indicative of those above-mentioned traits. Perhaps those things weren't like us, and even some groups that seem closer to us than they do were still different enough to be Others. Since the big media is determined to expand the meaning of "human" to include hominins which are clearly "not us" (like Neanderthals) maybe we need a new term to describe this group. We need a name for the subset of Homo Sapiens who were our actual mainline ancestors. I nominate the term "Adamics" (AH-DAHM-ICKS). The definition of "Adamics" is the same as the traditional definition of human, since that word has been expropriated. It's us. 

This is not quite the same as the man Adam referenced in Genesis. I'm not saying that humanity started as a single couple. They started as a population. That's why the MRCA numbers for various genetic parameters don't matter. They are estimates of how long ago something that never actually occurred happened! This is the "Adamic Race" though, in a two-population scenario for Genesis such as the one in my book on theology. At some point in time, there were people (Adamics) outside the garden and Adam and Eve inside it in fellowship with the LORD God. Adam himself, the representative and arch-type of that race as a figure of Christ who was to come (Rom 5:14), wasn't around until much later, around 11-12 thousand years ago. I don't want to rabbit-trail too much into this aspect of it, but just so readers can track the different groups I am talking about....

1) Archaic Homo Sapiens.... not like us in what makes us truly "human" in the traditional sense of the word. We definitely do not evolve from most of them, and from none of them in the most creationist views. They were just what was around before God announced His intention to "make Man in our own Image."
2) Adamics - the population which has all of those traits I listed above as unique to our kind. They either evolved from some small subset of the Archaics or were created by God anew, or some combination of the two. They quickly supplant whatever hominins were there before them, including Archaic Homo Sapiens
3) At the right time, God progressively reveals Himself to the Adamics in a greater way, and initiates His plan to reconcile us to Himself by forming the man Adam and placing him in the garden. 

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Now I feel sure that Dr. Amos would cringe at all of this, even though I think he is right on the Neanderthal introgression. But maybe he is only "kind of right". If there was introgression into the Adamics, maybe it was from the Archaic Homo Sapiens which were closer in their genome to these other distant hominins, not from these more distant hominins themselves. We may find some of that. Or the Adamics may have been a spread-out population from the beginning (but with the largest group in Africa) with their own regional differences due to introgression. Any introgression happened before they became us, not after.

If it did come after, one prediction I could make is that forty-five thousand years ago there was a pan-Adamic population that was the same- Africans looked like Europeans and what have you. The Hofmeyr skull from South Africa for example, looks like that of a European from the same period, and nothing like the exant Khoi-san of the region. Strange how, if Europeans were freshly admixed with Neanderthals and Africans were not, the skulls looked the same forty-something thousand years ago. It seems like some of our our differences were picked up after that, not before it. I and Amos think that is due to micro-evolutionary changes, but let's play along with the introgression thing some more....

Many of the differences since would be from rare and ancient introgression events via non-Adamic Homo Sapiens. They were so close to us genetically, that for most of their genome we couldn't even tell the difference. But they would have more archaic chunks. And those chunks would stick out and this may be what we are seeing. The chunks would not have to be the same everywhere either. Those in Africa might have one set of genetic distinctives, a population in the Near East would have another, and in the far east there might be a third and a fourth. These last, for example, might be labeled "Denisovan" introgression when in truth they are very derived from the true Denisovan genome we have. What if they really came from something much closer to us, another Archaic Homo Sapien group, some of whose genes only looked more like the Denisovan genome than any other we currently have available to compare it to? The so-called 'Denisovan genes' we have found in living humans are not a very good fit with the ones extracted from the actual Denisovan fossil. Maybe that's why.

 Of course some populations of them may have shared more genes with Neanderthals and others had profiles more like Denisovans. And maybe some of that was because Archaics exchanged genes with them. But we don't carry any genes introgressed into our ancestors from dalliances with these species. At most, another Sapiens line served as an intermediary. In such a case much of what might be considered our normal diversity was from these 'others', it is just so close to us that we can't tell yet that it was really from an out-group. We would have started as a more unitary group, made different not just by mutations over time, but by "other" H. Sapiens mixing occasionally with the special ones.

One can get lost on speculations about where and how any introgression occurred. But again, these alternative explanations are only needed if and to the degree that that of Dr. Amos is found wanting. And so far his looks bulletproof to me. Some of you who think otherwise should contact him and try and claim his large monetary prize for showing him the error of his ways. From my limited correspondence with him I think he'd almost be relieved to be free of the burden of seeing something so contrary to the prevailing view as to draw such sharp criticism. 

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