One more time about the uniqueness of Adam and Eve's genome

This could be a question that has already been asked and explained here. But I want to know exactly what restrictions there are on the possibility that in a GAE model, Adam and Eve’s genomes could be slightly different from their contemporaries. On page 84 of the book, Joshua writes,

It is conceivable that God made Adam and Eve with some important biological differences. Only small changes are needed to produce large changes to an organism. However, these differences would not propagate to each and everyone of their genealogical descendants. Their genealogical lineage would quickly spread across the globe till they were ancestors of everyone in a few thousand years. Their genetic ancestry, however, would dilute and dissipate. If their genetic differences were meant to pass to all of the genealogical descendants, then ongoing miracles are required. Speculative and exotic biological mechanisms (such as gene drives) have been proposed to overcome the need for ongoing miracles. There is no evidence of such mechanisms in human biology.

This question assume no ongoing miracles.

Is it impossible that A&E had special genetic material resulting in certain advantageous traits (e.g. consciousness, additional intelligence, etc.) that were passed on to some, though not all, of their descendants? And that their descendants who happened to inherit these traits simply died out?

The background for my question is that in the popular understanding of evolution, every useful trait I have as a human (which differentiates me from similar animals like chimpanzees) must have originated from some random mutation in an individual living in Africa tens of thousands of years, which conferred tremendous reproductive advantage to that individual and his/her descendants, such that now virtually all humans have it. Is this popular understanding completely wrong, or grossly incomplete? Why can’t it apply to Adam and Eve?

I understand that many of our ancestors are genetic ghosts, but does that mean that all the information in my genome that I have in common with virtually every other human being (e.g. being able to multiply 10 by 10) must have come from an ancestor who is not a genetic ghost and identifiable in my genome?

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Three complaints: 1) not “tens of thousands” but hundreds of thousands and/or millions. 2) The traits you’re thinking of don’t arise all at once by a single mutation but by accumulated changes over a long period. 3) No tremendous reproductive advantage is necessary; a slight one will do, and in fact most mutations that become fixed are neutral.

A question: how recent are A&E in the scenario you’re envisioning? Can’t be younger than H. sapiens, can they?

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Let’s say that there is a set of mutations S = \{x_1, x_2, ..., x_n \} that contribute towards advantageous trait Z, and that each member of the set x_i was acquired by accumulated changes over long periods of time, as you said.

Imagine this scenario: Mutations x_1, x_2, ..., x_{n-1} are all neutral, and were acquired “randomly” and fixed in the species over a long period of time. However, at some point x_n was acquired which in combination with x_1, x_2, ..., x_{n-1} resulted in a much more reproductively advantageous trait Z that also became fixed in the species.

  1. Is this scenario possible? Is it realistic?
  2. If this happened, from our genomes, would we be able to identify the individual who first obtained the x_n mutation, or for that matter, the different individuals who first obtained the x_1, x_2, ..., x_{n-1} mutations?

Why is species the defining line? Shouldn’t there be plenty of slightly advantageous and/or neutral mutations (or set of mutations) within different subsets of the H. sapiens population today which are slowly being accumulated, such that say, 100,000 years from now, there will be more H. sapiens with certain traits than others (e.g. hair color, social inclinations, susceptibility to various diseases, etc.) ?

I’d say yes and no, respectively. We do see such things, but on a much more minor scale than you’re going for here.

No. But what do you mean by “identify”? If the mutation is fixed, there’s no way to trace it to a particular point. Only if it were limited in extent would we have any means of doing anything like that, based on the pattern of distribution.

Because it seems clear from the record that anatomically modern H. sapiens had all the characteristics we associate with “human”. Earlier, it’s a bit less clear. But you didn’t answer my question.

More broadly, where are you trying to go with this?

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I’m not sure, but let’s take two scenarios:

  1. 20,000 - 50,000 years ago
  2. 10,000 years ago or less.

My question was prompted by the insistence of several Christian philosophers and theologians that Adam and Eve just had to have some physical trait that distinguished them from people outside the Garden. Even if the main distinctive trait of A&E was, for example, their unique calling as God’s representatives, some people think there had to be some ontological basis for it.

On the other hand we have Joshua’s reminder that scientifically, things are not that simple. You can’t guarantee that any genetic trait of A&E will be passed on to all of their descendants. And this seems to be linked to the notion of A&E likely being genetic ghosts, although I’m not entirely sure of how that linkage works either.

So I’m looking to see how absolute this restriction is, by trying to understand how neutral or beneficial mutations can arise and become fixed. Specifically, I’m looking into the possibility that there could be some sophisticated genetic tinkering that happened to Adam and Eve that “activated” some advantageous trait that propagated to a large portion (but not necessarily all) of their descendants. It could be something subtle - not “consciousness” or “free will” or “intelligence” or language - but perhaps a slightly heightened tendency towards religious belief, or something like that.

By “identify”, I mean in the sense that would we be able to know whether this mutation initially came from 1 specific individual (e.g. “Adam”), or a bunch of individuals in the same place, or a bunch of individuals scattered in different places.

To further flesh out the scenario using the previous points I talked about:

Let’s imagine that at a certain time t years ago in human history, the vast majority of Homo sapiens (or one of their ancestor species) had the set of neutral mutations S' = \{x_1, x_2, ..., x_{n-1}\}. Then at t, God created a new set of individuals, Adam and Eve, who had all mutations in S', but also had a new mutation x_n. Thus Adam and Eve now have the full set of mutations S = \{x_1, x_2, ..., x_n\} which resulted in them having reproductively advantageous trait Z. This trait was passed on to a large number of their descendants (who interbred with other populations who only had S' and not S) and became gradually fixed in the species.

  1. Since you said that the previous scenario is realistic, the above scenario would also be realistic. Am I correct?
  2. Would we be able to scientifically such a scenario actually happening?
  3. If the answer to 2) is yes, what is approximately the smallest value of t that coheres with our current evidence?

Yes this is possible. @glipsnort recently posted a paper on it. If I recall:

  1. If it was a recessive trait, it would not spread very quickly.
  2. If it was a dominant trait, it would spread quickly but it would not fix easily.
  3. If it was additive beneficial, then it would spread and fix fairly quickly.

Hypothetically an advantageous trait could spread across the globe fairly rapidly, in thousands of years.

The challenge, however, is that if the took place in the the last 10,000 years, we should see evidence in our genomes. At least as I understand it. This would be evidence that I am pretty sure would have been discovered already. That being said, I don’t know for sure we would have detected it, but that is why I’m skeptical.

Now, if AE were more ancient, say 100,000 years ago like @DJensen supposes, in that case it seems it could work. His best bet, I think, is to say it was additive beneficial trait that provided that final bump up to “rational soul.”

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What kind of evidence would it be?

Now I realize that my hypothetical model is similar to @DJensen’s, but I didn’t follow that discussion.

Although that @DJensen thread is very long for me to read in detail, I got the gist that both @swamidass and @John_Harshman think the presence of a set of neutral mutations S' fixed in the genome for many generations before being “activated” by a final mutation (or set of mutations) to create S that results in advantageous trait Z would be a case of ongoing miracles to sustain the presence of S'. But I don’t quite understand this.

First, is it very rare for neutral mutations to become fixed?

Secondly, how would a “naturalist” think something like consciousness and advanced human cognitive capacities evolved anyway? At some point, there has to be a mutation or set of mutations corresponding to it (or some simpler version of it) to arise, right?

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All the evidence is that humans were just like people today that long ago. Unless your extra feature is invisible in material culture, your scenarios are out. Of course you could decide that it’s something that just wouldn’t show in any data. In that case the time wouldn’t matter.

Why would they insist that? What would be the point?

No, if you will look I said it wasn’t realistic. And your new scenario seems identical to your old one.

Say what?

That all depends on how advantageous it was. To reach fixation in a few thousand years you would need a very advantageous one. I think we could actually rule that out, since such a selective sweep would severely reduce population genetic variation around that locus.

I’ll try to explain.

Depends on what you mean by that. Almost all mutations that become fixed are neutral, so in that sense it’s common. Then again, the proportion of neutral mutations that eventually become fixed is tiny; the usual fate is to be lost in one or two generations. However, none of that matters. We aren’t talking about neutral mutations in general, but about a chain of very specific neutral mutations. The probability of even one of those specific mutations becoming fixed is minuscule, and the probability of a whole set of n specific ones being fixed is minuscule to the power of n. So yeah, lots of miracles.

Sure. But gradual evolution over a long time, with the majority of those events being advantageous.

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OK, but it’s primarily archaeological or material evidence, not something you can rule out from just analyzing the human genome. Am I right?

OK, I looked at that again. Sorry I misread you. You said it was possible, but not realistic. Can you explain what you meant by the following:

Why do you think what I’m going for is not “minor”?

I meant scientifically detect. Is there scientific evidence that could support or rule out such a scenario?

I understand that. But to repeat my point, even an atheist would say that although the set of mutations corresponding to the (gradual) evolution of consciousness were each unlikely to become fixed, it did happen, “miracles” or not. Am I correct? As you said:

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Well, one can try to detect strong positive selection because the region around that locus should show reduced nucleotide diversity. One can also try to estimate the age of the selection, but I bet the error bars would be huge.

It’s the number of specific neutral mutations that need to happen and be fixed in the population. Both the number and the specificity are exceedingly unlikely.

No. Your scenario supposes specific neutral mutations being fixed. My scenario supposes advantageous mutations being fixed. The probabilities are much greater. And who knows how many other pathways there could have been? No miracles required, unlike your scenario.

I ask again: Why would anyone require all this? GAE is much simpler.

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OK, I’ll tweak the scenario then. All mutations in the set S are advantageous and were progressively fixed over time through entirely natural means and conferred rudimentary forms of consciousness, but the final mutation x_n or the final set were implanted miraculously by God. This would only require one final miracle, wouldn’t it?

Complicated. Some people believe the image of God has to be substantial or structural. But I’m not interested in debating the details of that here. This is just exploratory theory building. Theoretical physicists do this all the time, for example.

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That’s my understanding too. With ancient DNA we’d be able to precisely identify it too, because no one would have the mutation 15 kya, but everyone would have it now. And the surrounding DNA would lack much variability.

I expect we would have discovered this by now, if it existed, but we have not. Admittedly I haven’t looked specifically for this signature, which is why I am hedging some what. However, it seems like there are several studies of human populations should have stumbled across such a finding if it did exist.

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