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


(Lynn Munter) #589

If we didn’t descend from a population related to the chimpanzees and other apes, God sure went to a lot of pains to make it look as though we did. The similarities go far beyond anything that would be explained by ‘similar function, similar genes’ and include endogenous retroviruses, which are virus-like bits of DNA that go around inserting themselves randomly into our DNA so they get copied down into perpetuity. Some of these retroviruses we find in our DNA we can match with the same retroviruses inserted into the exact same places in chimpanzee DNA. Coincidence? No. Either we both descend from the same ancient creature in which the original insertion took place, or some One really wanted us to think we did.

But on the bright side, it is not stated in the Bible how many humans God first created, nor does it specify how he created them.

“So God created mankind in his own image; in his own image God created them; he created them male and female.” Genesis 1:27

The later story of Adam is set in an environment where there are already other humans in the land (Gen 4:14–17).

I will let @Swamidass clarify the discussion at hand. I have lost track of which claims he is referring to.


(T J Runyon) #590

Was it answered? The thread has gone way beyond the point I felt like Dennis was trying to make and has just turned into word games. I just want this one question answered and no one seems interested in it but instead wants to play word games.


#591

As I understand the current word game the science says there has been no two person bottleneck in the last 200,000 to 300,000 years to a fair degree of certainty. Now it is possible that there was a couple 10,000 years ago who could be related to everyone alive today but not genetically. Said couple obviously being just one of many from that time period. Think how many grandparents you have if you go back 400 generations.


(Richard Buggs) #592

Absolutely, I think you and I both agree with the need to be as rigorous as possible in our science here, and be open with the Church about what we do and don’t know, and when we change our views in the light of the evidence.

I have been thinking over the ARGweaver paper since you clarified for me what the authors were doing. My initial mis-understanding of the paper made me think that different assumptions about population sizes could be a game-change for your calculations of TMR4A, but now I understand the paper better I don’t think this is the case. Thank you for helping me on that one. This was the most major of my criticisms, and now that this is removed I feel more confident in your conclusions.

As you have said, this is just a first attempt at an estimate of TMR4A, and a more rigorous approach would be possible, but would be a lot of work. As we have also noted, the results could be affected by revisions in the estimation of recombination rates and mutation rates. It could also be that if the phylogenetic trees were built in a way which sought to maximise the number of mutations in the first four diverging lineages, different topologies might emerge (I’m not sure about this, but it would be interesting to examine the possibility). Unexpected factors that we have not accounted for as yet could also come into play, as happened in the Lenski experiment in a very different context. We can never be completely sure, as science is always progressing.

However, despite this, the big picture is that I am very much in agreement with you, and it is probably not profitable at this stage to continue to belabour criticisms of your analysis.

I think at this stage, it would be helpful to the Church if we could come up with a statement that we can all agree on, that summarises where we have come to in this discussion. This has been a long discussion that many will not have the time to wade through, and if you, @DennisVenema and perhaps @glipsnort and I, could come up with a statement that summarises the degree of consensus that we are reaching, then that might be helpful to the Church at large.

From my reading of our discussion, though there are things that we still differ over, here is a statement that I think we could all agree on:

As Christian biologists, we have over the last few months reviewed the population genetic literature, asking if it is possible that all modern humans could descend from a single couple within a theistic evolution (or evolutionary creation) framework. We have assumed that humans share common ancestry with apes, and that God has not intervened with physical miracles. Our task has been difficult because the hypothesis of a bottleneck of two in the human lineage has not been directly addressed in the scientific literature using genome-wide human diversity data. Nonetheless, from those published studies of human diversity that we have reviewed, and based on our understanding of current theory, we have drawn tentative conclusions. We conclude that current human genetic diversity data does not rule out a bottleneck of two individuals in the human lineage between approximately 400,000 and 7,000,000 years ago, but neither do they show that such a bottleneck has happened. Current analyses and models suggest that a two-person bottleneck has not occurred below a threshold of approximately 400,000 years before present. More research is needed in this area, and we are open to new analyses moving this threshold up or down.

If @swamidass @DennisVenema and perhaps @glipsnort agree that this is a consensus we have reached, I suggest that we publicly affirm this. I am very happy to discuss modifications to this statement that would enable all of us to affirm it.


(Jon) #593

Yeah, not to my knowledge. Leaving it ambiguous is to the advantage of YECs and IDers, so I expect this won’t be clarified.


(T J Runyon) #594

Thanks for that clearly written statement, Richard. What I’ve been looking for


(Lynn Munter) #595

Would it be more accurate to say they show no support for such a bottleneck, instead of saying they don’t show it’s happened? It seems to leave quite a lot of wiggle room as is.


(Jon) #596

It’s certainly a lot longer than 300,000 years ago.


(Peaceful Science) #597

@RichardBuggs I think this is an excellent idea. In terms of hashing out details, I suggest we do this on a private thread. I’ll start one for us.

Also, we need to discuss trans-species variation. It should not take too long. Within a couple days (maybe today), I’ll post my analysis of this for comment.

Thanks for your contributions here. Your questions and effort have encouraged real progress in our understanding. I appreciate a great deal the example you have set in (1) being sensitive to the questions of the church, (2) being correctable in an area you are an expert, and (3) being honest with the Church about difficult findings in science. I hope we all can follow that example.


(Peaceful Science) #598

As guide for people just joining the conversation, The key scientific points are condensed here. The bolded links at the bottom were just added today, and might have been missed otherwise. In particular, take a look at how this estimate might be adjusted if the whole genome was included (https://discourse.peacefulscience.org/t/heliocentric-certainty-against-a-bottleneck-of-two/61/14?u=swamidass). If you find any errors, please let me know. Thanks.

Claims of Heliocentric Certainty. What are the scientific claims in question?

The Ecological Fallacy.: Homo sapiens go to zero, so why couldn’t they go to two?

TMRCA or Time to Most Recent 4 Alleles? TMR4A (not TMRCA) puts the bounds on a couple bottleneck.

Estimate with Median or Max? The statistically sound approach is the median.

TMR4A from Genome-Wide TMRCA. An initial estimate of TMR4A.

The ArgWeaver Genome Wide Phylogenies 424 GB of data with genome-wide answers.

Genome-Wide TMR4A. A better estimate of TMR4A.

ArgWeaver Does Not Assume Large Population. The computed TMR4A is biased downwards, not upwards, by the prior.

The Correct Mutation Rate. ArgWeager is using an experimentally confirmed mutation rate.

Correctly Weighting Coalescents. An improve esitmate of TMRCA is about 500 kya.

ArgWeaver works like MAP and MrBayes. Really, no assumptions of population size are made, and this is just a measure of human variation, converted to units of time.

A Estimate Robust to Correction. The TMR4A estimate is exceedingly stable. AJ Roberts from Reasons to Believe would want a correction for the amount of genome that is not yet sequenced.

What about Recombination? The errors we see in ArgWeaver do not effect TMR4A estimates.


(Christy Hemphill) #599

Is anyone taking bets about whether or not Evolution News and Views will promptly publish an article about this part of the thread? :face_with_raised_eyebrow:


(T J Runyon) #600

This whole thread has been quite a learning experience. While it was frustrating at times because I’m at the beginning of my genetics education I still feel like I benefited from this. But areas I do feel more than competent to discuss are paleoanthropology and archaeology. These areas are where the vast majority of my studies have taken place and where I have had the most training. So im wondering if I take the time to write up something about the viability of a non sapiens Adam and Eve and start a new thread to discuss it will people here be interested in doing so? I don’t want to waste my time getting all of my sources together and writing it up if no one is interested in having that discussion. Thanks!


(Christy Hemphill) #601

Do it. People will discuss it.


(Richard Buggs) #602

In the beginning, when we were first debating this at Skeptical Zone, I noted:

“a creationist (in the conventional sense of the word) would not be concerned about this entire topic as it assumes common ancestry and creationism can have genetic diversity front-loaded into Eve’s ova anyway, thereby avoiding the whole issue of genetic diversity. I suspect many Christians, Jews and Muslims would be interested in the idea of a half million year old ancestral bottleneck of two.”

See: http://theskepticalzone.com/wp/adam-and-eve-still-a-possibility/comment-page-3/#comment-198358


(George Brooks) #603

@Swamidass

I think this is the sword upon which you must, of necessity, fall.

I think the sentence you have here is false… and demonstrably so.

The sentence that I thought you were defending would be more like this:

“There is ZERO evidence that God did not create a unique mating pair (Adam & Eve)
to contribute to the larger human population, anywhere between 10,000 years to 6,000
years ago.”

In order to defend your original statement, you would have to specify something that
forces the discussion into a non-YEC context (being silent on the issue does not make
the sentence more valid):

**"There is ZERO evidence that [hominids] did not begin as a single couple, more **
than 300,000 years ago… Zero evidence. So how do we come to heliocentric certainty
about a claim substantiated by zero evidence?"

If you attempt to replace “hominids” with “humans” (i.e., Homo sapiens), then the lack
of any human fossils from 60,000yr to 300,000yr old strata is the evidence that it didn’t happen.

What are your thoughts on this brief analysis, @Swamidass ?


(Steve Schaffner) #604

Okay, I’m about a month late and the thread has moved on, but I said I would comment about these papers, so here I am.

This is an interesting paper from a theoretical perspective, but the practical implications are really only addressed in later papers. The authors conclude that the allele frequency cannot uniquely identify the actual demographic history, but as noted in the third cited paper, the example they give is not biologically plausible.

Note: I know this paper fairly well, since I shared an office with two of the authors (Simon and Nick) at different times, including while they were writing the paper. The third author is a math heavyweight they had to bring in to get past a sticky bit. Nick had some trouble getting the paper published, not because there was anything wrong with it, but because a reviewer sat on the paper on the paper for well over a year. I was at a mathematical genetics meeting in Durham (where I really did not belong), where Nick gave a talk. He ended by pointing out that this paper had been out for review forever, that the reviewer was probably in the audience, and could he please do his job? He got the reviews back a few weeks later.

This paper does indeed consider a population bottleneck followed by exponential increase in size, and concludes that there are fundamental limits on how accurately such a demography can be reconstructed solely from the site frequency spectrum. It is important to note, however, that the difficulty they demonstrate is in reconstructing demographic events prior to the bottleneck, not the existence of the bottleneck itself. This is clear from their discussion section: “Intuitively, as the severity of the bottleneck increases, the population is increasingly likely to find its most recent common ancestor (MRCA) during that time; farther back in time than the MRCA, no information is conveyed concerning the demographic events experienced by the population.” Similarly: “Additionally, an interesting aspect of our work is that our minimax lower bounds do not depend on the number n of sampled individuals; increasing n is not enough to overcome the information barrier imposed by the presence of a bottleneck.”

This is the most interesting of the papers. It shows that the results of the first paper apply approximately for much more realistic demographies, and that tight bottlenecks can be invisible when just looking at the frequency spectrum. Again, though, there’s an important point to note: the bottleneck they simulate is still, compared to what we’ve been talking about, quite old: 2.5 times the usual 2N generations. Certainly well over a million years ago for humans. I have no trouble believing that demographic signals from that era can be erased. What I have always found implausible is that a signal from less than 0.5 x 2N could be erased, since it leaves insufficient time to accumulate new mutations and get them to high frequency.


(Peaceful Science) #605

@glipsnort, always great to see you.

Help me understand this…

As I understand it, 2N is about 2 million years ago (approx genome wide TMRCA, right?). Your SFS studies show no signal for a bottleneck at 0.5 million years ago, which is 0.25x 2N. Though, as I think about it, your studies used smaller population sizes we expect (e.g. constant 10,000 at all times), so perhaps your 2N is a lot lower than 2 million years?

So where is my math wrong here? If possible…

  1. square this with your prior simulations on SFS.
  2. give extrapolate to the real human data for where that cutoff might be.
  3. tell us if you think there is anything here that conflicts with the TMR4A work.

Thanks.


(George Brooks) #606

@Swamidass,

I asked you a question at the end of this posting (located above) … It’s passingly important for me to
understand some of the discussions you are maintaining. I hope you can get to it sometime
in the near future! :smiley:


(Curtis Henderson) #607

Thanks, Christy, I got a pretty good laugh out of that one!


(Peaceful Science) #608

It is not. If “human” = Homo sapien as explained by Venema, there is no evidence that, as you almost say…

“There is ZERO evidence that God did not create a unique mating pair (Adam & Eve) (perhaps the first Homo sapiens) to contribute to the larger hominid population, when Homo sapiens arise.”

In this case, there is no evidence against it, and Homo sapiens (“human” according to Dennis) begin with a single couple.

@gbrooks9, regarding the the 6kya - 10 kya timeline, that is not really what I have put forward. For a genealogical Adam (not necessarily the first Homo sapien), they could arise anytime before 6 kya, not just in that narrow range.