Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1)

(T J Runyon) #913

For what’s it’s worth I know of some researchers who consider the Dali specimen as a possible Denisovan (it’s brow is also very similar to the Broken Hill Specimen. Though it’s face is different). But of course we can’t know without their DNA. Just thought this could lead to some interesting research for you.

(Dennis Venema) #914

When I debated Georgia Purdom at LeTourneau university back around 2011 (?) she was fine with Homo erectus as human. Interestingly, when I debated Nathaniel Jeanson last year at SEBTS, he was trying to avoid the Neanderthal data. Part of the motivation was that he was trying to say present-day mitochondrial variation can be traced back to three women (the wives of Noah’s sons). If you add Neandertal or Denisovan mtDNA to that mix it of course just doesn’t work, and when I pressed him on that he claimed that Neandertal mtDNA was “too degraded” to be certain of its sequence. That’s wrong, of course.

So, what exactly AiG thinks about erectus, Neandertals and Denisovans is a bit up in the air.

(Ann Gauger) #915

Here are some quotes from the past: : Hössjer O, Gauger A, Reeves C (2016) Genetic modeling of human history part 1: comparison of common descent and unique origin approaches. BIOComplexity
2016 (3):1–15. doi:10.5048/BIO-C.2016.3

Out of Africa replacement
adherents also use various common descent assumptions (such
as the divergence time of humans and chimps) and genetic
diversity estimates between humans and archaic hominins, to
predict a split between them about 500,000 years ago or earlier
[28,75,76,77]. If this is true, it is remarkable that two populations,
after such a long time of separation, were still able to
get fertile offspring [78]. But even if this would be possible,
because of the long separation, it is reasonable to believe that
the offspring had low fitness, since our archaic ancestors had,
most likely, accumulated many alleles which are deleterious for
humans, before the admixture took place.
The large fraction of archaic DNA among present-day
humans seems in view of this more reconcilable with a unique
origin model in which Neanderthals and Denisovans are
descendants of the first founding couple, and hence our fully
human ancestors. Indeed, sequencing of mitochondrial DNA
suggests that the diversity among Neanderthals is much smaller
than among humans [79]. As a possible explanation, they could
have been quite early descendants of the first man and woman.
And the close genetic resemblance between Neanderthals, Denisovans
and people of today suggests that the morphological
differences are mostly explained by changed gene expression
due either to mutations of regulatory DNA or to epigenetic
changes [80].

And from Science and Human Origins (2012) Chapter 13 Casey Luskin does not argue for a first pair, but he does argue for a “Big Bang” origin of the genus Homo.

(Peaceful Science) #916

If that is true, then its all the more important to appropriately qualify scientific conclusions, rather than injecting silent assumptions into them. It leave them open to being overturned, as we have already seen here.

That is false. The motivation for including Homo erectus starts from the fossil record, not genetics. There is strong evidence that they are more human-like than ape-like. YEC’s have, for a long time, incorporated that into their model by saying the whole Homo genus is fully human and easily distinguishable from apes. Whether that is true or not is another question, but it is just flat out wrong to say that they have been constantly changing the bar on this one.

The more likely question is that EC writers fixated on the 6 kya date, and ignored the rest of YECs were saying. They probably just were not listening closely enough.

Not really. He is saying they are human, but we can’t measure the mtDNA correctly.

That’s about right.

It will be really interesting to see how Jeanson handles the TMR4A data. It is identical to his mtDNA analysis, but with far more data and much much better measures of mutation rate. MtDNA mutation rate is nearly impossible to measure directly, in contrast with autosomal DNA, which we can measure and have measured very precisely. That data, however, falsifies his position. I wonder if he will try and respond…

Also, I’ll say that some theologians have really appreciated TMR4A because it is easy to understand, and makes space for their position at an earlier date.

(Dennis Venema) #917

Agreed. It was surprising to me, based on my conversation with Georgia, that Neandertals would even be an issue. I expected that Jeanson would argue that their mtDNA variation would fit within his model, but he went a different direction, saying it was too degraded to use.

Denisovans are even a worse problem for Jeanson, since their mtDNA divergence is even greater.

(Peaceful Science) #918

The same could be said of the differences between human and chimp. =)

(Ann Gauger) #919

Indeed. But more of them between humans and chimps than between humand and Neanderthals.

(Dennis Venema) #920

Ann ( @agauger ) - if I’m reading you correctly, introgression of ancient hominin DNA into Denisovans would then be problematic in your view, unless that unknown hominin population also descended from Adam and Eve?

Or, in the alternative view, if it’s due to ancient population structure, you’d be ok with moving the TMR4A back to match the data? Just curious how this evidence plays into your thinking.

(Dennis Venema) #921

Great question. The short answer is that we can observe ILS even with small numbers of alleles that could be, in theory, transmitted through a bottleneck - or even with single alleles. In other words, even if a really severe bottleneck did happen, we still would expect to observe ILS.

The ILS data gives us an opportunity to “check in” on our lineage at various time points along the way, prior to species divergence. We can use it to estimate the common ancestral population of two present-day species. The human, chimp common ancestral population comes in at around 50,000 or so, as do the (human, chimp, gorilla) and (human, chimp, gorilla, orang-utan) populations. After two lineages diverge, the technique is not informative for ruling out bottlenecks after that time point. For that, we look to other techniques - PSMC, MSMC, ancestral recombination graphs (ARGs), and so as we have been discussing in this thread.

Now, ILS is also fantastic evidence for common ancestry, and it’s a line of evidence I’ve not seen adequately addressed by any anti-evolutionary source. IDers even go so far as to claim it’s an ad-hoc attempt to explain away problems for evolution, but that is just silly for anyone for knows the field. We expect it, and we predicted it in advance before we sequenced chimps, gorillas and orangs.

(Steve Schaffner) #922

This paper reconstructs more than 1 Gb of Neandertal haplotype in modern humans. This one identifies 20% of the Neanderthal genome, but reports simulation results suggesting that 35% - 70% persists in modern humans.

I’m not sure what you’re suggesting. Convergent evolution causes greater similarity, and therefore greater difficulty in detecting introgression? In any case, this is a broad effect across the genome, which is not at all what I would expect from convergent evolution.

(Steve Schaffner) #923

For me, that depends on what question you’re asking and (to some extent) on what your approach is to hypothesis testing. I’m a Bayesian at heart (at least on Tuesdays), so I’m fine with explicitly incorporating background knowledge into one’s prior. In this case, if you are posing a purely scientific question about whether a largish mammal underwent a population collapse to single pair followed by a massive increase in population size, I would place a very small prior probability on that scenario. It would be a very odd situation in which such a crash would not lead to extinction, whereas more or less stable population sizes are quite common. (Note that a small founder population during range expansion is a different scenario, and a more plausible one. But that would not meet the conditions required here.)

(Peaceful Science) #924

I agree. This is just a question about Denisovans, not Neandertals. Denisovans have a much smaller amount of their genomes similar to us.

(Dennis Venema) #925

Not only does it not lead to extinction, the conditions are such that exponential population growth occurs immediately after the crash. I asked earlier for @RichardBuggs to speculate what might have led to these remarkable events, but I didn’t see a reply.

(Peaceful Science) #926

Why is that so hard to believe? Whenever you are below carrying capacity, growth is exponential.

(Dennis Venema) #927

What caused the catastrophic decline prior to the expansion?

(Dennis Venema) #928

What’s your prior for that? :smile:

(Peaceful Science) #929

Natural disaster? Act of God?

There does not need to be a catastrophic decline any ways. Geographic isolation. Cultural isolation. Etc.

(Dennis Venema) #930

If a natural disaster occurred, it was very widespread - Hominins are spread out all over Africa, Asia, Europe… how could an event occur that would wipe out all of them except two? Not seeing it.

Geographical isolation? Permanently? How?

Cultural isolation? Suddenly, with no genetic exchange? Not following you here either.

(Peaceful Science) #931

Imagine a context where this is the first couple with symbolic thought and a theory of mind. It is the first couple with language. That could be enough to keep their kids from interbreeding with those around them, even if they were biologically compatible. They would not be able to see the others as one of them.

Also there is a genetic interference as a possibility too.

Taking theology into account, maybe they are the first with souls and know it. Maybe they see the others around them as non-human, and do not want to interbreed with them. Who knows.

Maybe all hominids die across the globe and God resurrects two of them. Who knows. Not science, but possible and not ruled out by evidence.

Does not have to be global. All it has to be is a natural disaster that locally reduces a population to a single couple. As long as there is enough time to sufficiently differentiated, and they become the only surviving lineage, that would do it.

I’m not arguing that any of these events happened. But there are several scenarios that could be possible.

(Dennis Venema) #932

Ok, but I thought we were asking for scientifically plausible events. Suddenly acquired discontinuous characteristics, first souls, and God resurrecting two hominins don’t fit in that category.

Geographic isolation with no genetic exchange isn’t plausible either. You yourself have modelled this. If Tasmania can be reached, as you’ve argued, there isn’t anywhere on the African or Eurasian continents that we can reasonably expect to stay isolated for any length of time.