@Jonathan_Burke, let’s put this in context…
What is written here is an honest gesture of good will coming from a curious scientist in the Church. I have also been clear that I do not think the YEC data fits the data, and am happy to explain why, and have explained why several times. The fact that I am glad to acknowledge when the data does fit their model does not make me suspect. It makes me honest.
Yes I understand that.
Yes, but I am not talking about that. I’m talking about the fact that you want to “find a way for YEC time scale to work with the evidence without abusing” indicates that your motivation for involvement in this subject is apologetic and theological, rather than scientific.
Not true @Jonathan_Burke. Seriously, that is not a valid read. It honestly comes off as an ad hominem. If you have a problme with the data I’ve presented, feel free to point it out.
I’m honestly curious how you are going to square my statements about the evidence with being a YEC apologists. That is totally absurd. Remember, I’ve said:
It is not ad hominem. An ad hominem argument takes the form “Person X has character flaws Y, therefore their argument is false”. I have not said anything like that. I have not said that any of your arguments about the data are false, and I have certainly not said “Swamidass has character flaws X, therefore his arguments about the genetic data are wrong”. Nor have I said “Swamidass is a YEC apologist, therefore his arguments about the genetic data are wrong”. Nor have I called you a YEC apologist, which is a phrase implying you believe in YEC (which you obviously don’t).
As you know, I have not contested the data you have presented.
I have not said you are a YEC apologist. I have said that your statement that you think it would be great to “find a way for YEC time scale to work with the evidence without abusing” indicates that your motivation for involvement in this subject is apologetic and theological, rather than scientific. If your only interest in the topic was scientific, then I don’t understand the need for such a statement. I don’t see why you would say it would be great to “find a way for YEC time scale to work with the evidence without abusing” if that is not actually something you would like to see happen.
I should not need to remind you that this entire topic was raised by Dr Buggs specifically as a Christian apologetic for Christians who believe in a literal Adam and Eve (as in fact I do). This is the post in question.
“Does genomic evidence make it scientifically impossible that the human lineage could have ever passed through a population bottleneck of just two individuals? This is a question I am asked semi-frequently by religious friends.”
“The issue is this. Believers in Abrahamic religions who accept evolution often combine it with belief that all humans have descended from a single couple. Until now, many have assumed that this belief is compatible with evolution and mainstream science.”
“Venema declares that a bottleneck of two is impossible, and this is a fact of comparable scientific certainty to heliocentrism. He gives his Christian readers a stark choice between embracing mainstream science, or sticking with untenable beliefs about an ancestral couple.”
“Whilst this issue may seem trivial to many readers, for large numbers of religious believers in the world, this is a critical issue. Do they really face a binary choice between accepting mainstream science and believing that humans have, at some point in their history, all descended from a single couple?”
Yes I know what you’ve said. You’ve said this.
YECs wouldn’t have an issue with that, since you’ve deliberately said “without either miracles”. Naturally they would be happy with the idea of fixing the data with miracles. You’ve also said this.
I don’t see those as mutually exclusive statements, and clearly you don’t believe you’ve contradicted yourself either.
Jonathan,
It took some digging to find the original quote, but what I gather Josh is getting at is not attacking strawmen. Something I very much agree with as well. There’s enough absurdity within the YEC movement that there’s no need for us to manufacture it. That’s why when Dennis and others started talking about Eve as essentially a clone of Adam, my eyes rolled. Virtually all of my family are YEC, and I don’t know a single one who would ascribe to that view. They’d rather think that God worked some magic genetically to pack in as much diversity as possible into their genomes. Also silly, but let’s talk about the silliness that exists rather than forcing on others that which doesn’t.
Josh also points out that if you can get in the habit of avoiding strawmen, your rebuttals of YEC’s actual arguments will carry much more weight. Again, I completely agree. He also makes clear the aspect of the YEC timeline he’s interested in is Adam. Not all of creation or all of humanity or human ancestors. If “what’s important” to the YEC community is an Adam at 6,000 years ago, well if Josh can give them a sliver of a straw to grasp onto on some technicality, and that works for them, then maybe that might open the doors to a few to accept what we know to be scientific fact about the history of our planet and life on it. I personally think that’s a stretch too far and require, even by YEC standards, too much in the way of mental gymnastics. But that’s where Josh’s head seems to be at. I do think you’re misunderstanding him on this. He seems to be trying to play the role of “missionary” to the YEC community.
I raised no objection to his statement that strawmen should not be attacked. I fully support him on that point. The quotation I provided was on a completely different subject.
In about ten minutes I found and posted two YEC organizations which discussed the idea that Eve was a clone of Adam. One presented it as one of two possible ways God had created Eve, the other said it was the way God had created Eve. Creation Ministries said this.
“There is an intriguing possibility that Eve was a clone of Adam. The science of cloning involves taking DNA from an organism and using it to manufacture an almost perfect copy of the original. Here, God is taking a piece of flesh, with cells, organelles, and, importantly, Adam’s DNA, and using it to manufacture a woman. Of course, she could not be a perfect clone, because she was a girl! But what if God had taken Adam’s genome and used it to manufacture Eve? All he would have had to do was to leave out Adam’s Y chromosome and double his X chromosome and, voilá, instant woman!”
They go on to say this later.
“There are indications, however, that Eve may not have been a clone.”
But they still say the cloning idea is one of two available possibilities. Meanwhile, another YEC organization says this.
“Since Eve was made from one of Adam’s ribs [Genesis 2:21-22], she would have been a clone of Adam and, had there been any genetic mutation in Adam, this would have been reproduced in Eve and expressed in their offspring.”
So there are definitely YECs who argue this.
I agree in part. It’s a nice idea which might work in some cases, but the fact is that most of us avoid strawmen when it comes to YECs and it makes not a scrap of difference whatsoever.
Yes he is definitely trying to offer them a sliver of hope, but I don’t see that his motivation for helping them believe they are right, is to move them to a position where they accept they are wrong. I really don’t see how that is going to work. We’re talking about people who think that the “soft tissues” found by Schweitzer proves that dinosaurs only died out recently. I cannot see how giving them the impression (wittingly or unwittingly), that their views on Adam and Eve and a 6,000 year old earth are not in conflict with science, is going to help them change their minds.
Consequently I can’t see this is as a missionary endeavour. Trying to give them reasons to hold onto their 6,000 year old earth and 6,000 year ago Adam and Eve, isn’t going to lead to them abandoning their 6,000 year old earth and 6,000 year ago Adam and Eve, especially when that 6,000 year timeframe is there precisely as their only bulwark against evolution.
[quote=“tallen_1, post:424, topic:37039”]
I do think you’re misunderstanding him on this. He seems to be trying to play the role of “missionary” to the YEC community.[/quote]
I see him as mediator rather than missionary. If he was playing the role of missionary he would be aiming to change their views, not suggesting people come up with concordist interpretations of the evidence which could agree with what YECs believe.
Jonathan,
I was providing the background context for Josh’s sympathizing with the YEC community. The quote you lifted out of that context can create the wrong impression.
Also, I don’t think what I provided was off topic given you included this in your quote: “And that is exactly the hypothesis that YECs and OECs have been working with over the last decade. Anyone who does [not] know this has just not been listening.” To know what Josh is referring to you have to attend to what he was saying about misrepresentations and straw men, which is what I explained. Maybe you didn’t mean to include that section in your quote, but there it is.
Anyway, Josh does not appear to be facilitating any sort of hope to the YEC community for their 6K year earth or creation de novo of all living species within that time. He’s only extending them that hope for a 6K year old Adam. As their greatest theological hold up always seems to go back to Adam.
Josh - do I have this about right?
Certainly they are combined roles. As fellow Christians, I would not see a YEC adherent as in need of a missionary, but there are many in that mindset who have fallen away from Christ due to the dichotomy presented in that culture ( of course, that is another kettle of fish but AIG seems to agree with that loss from what I have read ) and that becomes a place where a missionary field is present.
Phil,
I was using the term “missionary” metaphorically of course ;). That said, I think the YEC community does an amazing amount of harm. They spread a distrust of science and established scientific fact, and a pernicious tribalism that glorifies everything within their echo chamber while seeding suspicion and dismissal without. So, in the metaphorical sense, I’d value all the missionaries we can send their way.
Yes, you do. There are enough challenges that science brings to theology that we do not need to force them where they do not exist. Certainly some Christians see need for Adam. Many do. Let’s just be honest about the science with them and see how it shakes out from there. Perhaps the will end up just a different type of Christian than us in the end. That is okay, as long as they are in Christ.
I think mediator is a better term than missionary. But I am aiming to change their views so that we all might adopt a more Christ centered faith. With Jesus as the foundation, we adopt a more orthodox faith and these questions are not so concerning.
My biggest problem with scientific YEC creationism is not its scientific problems but its theological emphases. Our faith is not grounded in a specific understanding of creation and the human effort to study nature (creation science or evolutionary science). Rather, our faith is grounded in Jesus, the one who rose from the dead. By Him, we can find a confident faith, unthreatened by evolution.
As for Adam? There are reasons why the common solutions offered by TE / EC Christians are unsatisfying to many Christians. My point is just that we should be empathetic to the questions of the Church, and not force conflict where it need not be. Instead, lets be honest about how the theological values we bring to the table could work in light of mainstream science.
Regarding Adam and Eve as homologous clones.
Yes of course some people thing that. However. that is not what @agauger and @RichardBuggs has argued, nor is it what John Sanford or most knowledgeable YECs I know have argued. If one model of Adam is falsified by the data, does not mean the other is falsified too. If we are going to make strong claims about what the evidence rules out, it behooves us to take seriously the all the alternate hypotheses we can. To the point, for at least 5 years now, most YECs in this area have been trying to work out a model of created diversity. We cannot claim to rule this model out, unless we actually examine it in light of the evidence.
Of course, as should be clear from my prior posts, baring miracles this seems to be ruled out in the recent past. However, in the more distant past, maybe not. It seem false to say we have certainty there was no single couple bottleneck over the last several million years (as has been put forward). The evidence does not seem substantiate that claim. except perhaps in trans-species variation (but we haven’t even discussed that yet).
Replies moved to new post to clean things up a bit, tough to find a good cut off so may have to modify a bit but bear with me: “Reaching out through Adam”
Hi Joshua,
This is just going to be a rather brief holding response as I have only got part way through my first read of the ARGweaver paper, and a series of mini-crises in my lab are taking up much of my time now, so it may be a while before I can give you a fully considered response. I don’t want to leave you waiting for too long, so here is a quick reply, with all the shortcomings that this necessitates.
I agree with you that the ARGweaver results, given the assumptions and simplifications behind its analyses, does appear, on your further analyses of its graphs, to give a reasonable bound of a bottleneck of 420 kya +/- 100 Kya. I don’t say this as someone who has worked through all of the analyses for a second time: I just say this as what you have described seems to me to be reasonable. To be perfectly honest, I am quite surprised at how low this figure is. If you had asked me to guess beforehand I would have probably suggested a higher figure.
Having said that, on my rather shallow reading of the work so far, I would be slightly cautious, in that just having 4 lineages left in a population does not mean that those 4 lineages are all found in just two individuals, as I think you have already pointed out. Demonstrating that only four alleles are left in a population is a necessary pre-requisite of a bottleneck of two, but is not in itself evidence that a bottleneck of two actually occurred. For the four alleles to coalesce to the point of being in the same human bodies may take quite some while and could add a bit to to the timing (This depends on effective population size, of course, as has been frequently noted in the discussion above). I think I would therefore have more confidence in your lower bound than your upper bound.
My point "I do think that the coalescent models used in a test of the bottleneck hypothesis would need to include the effective population size decreasing down to two as we go back in time. " Was a reiteration of a point that I have made several times before in the discussion above when discussing coalescent analyses in the Zhao et al paper.
In the ARGweaver paper, in a footnote to Table 1 the author’s write “Model allows for a separate Ni for each time interval l but all analyses in this paper assume a constant N across time intervals.” It sounds to me as if they use a constant Ne. I have to admit that I find the paper rather confusing on the point of effective population sizes, but you have spent longer than I have working out exactly what they did, so I look to you for enlightenment.
[By the way, I was reflecting on my point “I do think that the coalescent models used in a test of the bottleneck hypothesis would need to include the effective population size decreasing down to two as we go back in time” after I had posted it, and I have a caveat about this. No method of estimating Ne based on genetic diversity (that I am aware of) is capable to identifying a short sharp bottleneck of two as an Ne of two. That is because every method (that I know of) would need the population size to remain constant for at least a few generations before it could estimate an Ne of 2. Thus, I think we can safely say that when effective population size is defined by an equation based on genetic data, a single generation of census size two does not have an Ne of 2, but of a higher number (exactly what I don’t know - I guess it would depend on the size of the pre-population bottleneck and the rate of population expansion afterwards). I have - in effect - made this point before, but have never quite formulated it in my mind in these terms, so thought it might be worth sharing for discussion/correction.]
I think the most important take home message for me from your ARGweaver analyses is that (as far as I can see) you have shown nicely that genome-wide allele counts do not provide evidence that a bottleneck of two has not happened in the human lineage. That is a real step forward in our understanding of this area. Thank you!
No problem. Believe it or not, I have my own fires I’m putting out in my lab this week. I also have 4 public events I’m doing next week, including one with Hugh Ross. So a lot is going on here too.
Take your time in responding, but there is a lot you’ve written here I want to echo.
Thanks for offering your public thoughts on that too, as hopefully that should put some criticism to rest.
I agree. This was surprising for me too. I would have guessed a different number. It is still important to caveat that this is just a subset of the data, and subject to revision to a more ancient data with more evidence. It is hard, however, to imagine it being revised more recent than 300 kya.
In particular, I would point to two pieces of evidence that are not considered here:
Genetic evidence of interbreeding with Neanderthals/Densiovans seems to put a bound on a single couple bottleneck back to the Homo sapien common ancestor with them, perhaps 400 kya to 700 kya ago. This analysis of TMR4A used the median, and would underestimate that date because interbreeding with them only affects the minority of the gnome (it seems).
Interspecies variation will always put an asterix on these results. Though on re-looking at the literature, it is very sparse. In contrast with population genetics estimates of population size, there are only a handful of papers that address this. I have not been able to find definitive evidence of >4 alleles at a single locus with interspecies counterparts. However, that maybe just because no one has looked at enough of the Chimp data (which very sparse). Nonetheless, I’m less convinced now than when I started that this will be (at least in current form) definitive evidence against a couple bottleneck. Still, we have not taken it into account here.
The phrasing here is difficult, but it sounds like you are saying you have more confidence in bound on single-couple bottlenecks of 520 kya than 320 kya. I’d agree with you here too.
That is correct, and I have been working out the math on this, and planning some experiments. It looks like the key variables for Ne is (1) how many generations are at a single couple (just one in our case), (2) the number of offspring they have and degree of exponential growth in the few subsequent generations (which we can assume here is very high), and (3) how distant this is in the past (as the averaging window for Ne increases in the past). Keeping mind that #2 is essential a free parameter, #1 and #3 are such that the farther back we go in time the much less a single couple generation affects Ne. So, therefore, a single couple bottleneck can be entirely consistent with a very high Ne in the distant past (say at 500 kya)
Once again, this is just an informal description, but there are some interesting details in the math. Sufficiently interesting, I’m nearly convinced its worth turning into a publication in its own right. Interesting stuff.
This is an important caveat to emphasize.
This is not evidence for a single couple bottleneck but evidence that population genetics will be unable to detect a bottleneck in the distant past. It is an argument that such a bottleneck would be hidden in the shadows, and not clearly seen in the data.
Moreover, median TMR4A, as you suggest, may be too generous a cutoff. My instinct is that we should probably use a CDF cutoff of about 70 to 80% instead of 50%, which would put TMR4A at about 525 kya. Though, I cannot be certain on instinct. The right way forward is to determine this cutoff from simulations, which I am nearly convinced are worth the effort to embark on. There seems to be good theoretical reason to think that detection power will correspond relatively tightly with some cutoff on the TMR4A CDF. Once I get around to doing those experiments, we’ll have a much better bound.
They are not clear in the paper. But the code itself is clear. The only way they seem to use Ne is to set the prior, and the prior (if anything) pulls TMR4A downwards. However, the influence of the prior on the joint likelihood (just 5%) is very low, so I’m not really concerned about this. There is no plausible reason I see to doubt the results of this study because of their use of the prior. As I have explained, the prior thinks mediant TMR4A is at about 200 kya, but we compute it at about 420 kya. So the data is pulling the estimate upwards, and there is sufficient data to totally overwhelm the prior.
To be clear, I agree that “genome-wide allele counts” alone are not very good evidence. Moreover, their overall diversity do not provide evidence against a single couple bottleneck after about 400 kya_ (subject to revision). They do, however, provide evidence against a more recent bottleneck, as you have already affirmed.
As many people have noted, for most people, this is a fairly disturbing challenge to theology. Perhaps some will find solace in an ancient Adam that was not Homo sapien. At the moment, that seems to be an outlier position, though perhaps it will grow, especially as it seems we are beginning to come to a consensus here.
Hi Joshua,
I am glad we have reached such a level of agreement.
Regarding ARGweaver:
I wonder if the code itself is pointing in a slightly different direction to the paper. Their footnote under table 1 suggest that the code does allow for separate Ne estimates at each time interval, but for all the analyses in the paper itself they assumed that Ne did not vary among time intervals. Perhaps they did this to speed up the analysis as they had such a large dataset? I still have more reading to do of this paper.
I am not sure how much different this would make anyway, as (as we both agree) any method they used to estimate Ne would likely not detect a bottleneck anyway, if one had in fact occurred.
That is brilliant. Do keep me updated!
Interestingly, I believe that this has been the position of @agauger all along.
Hi all,
I have been doing a bit more reading about the theoretical background of some of the methods we have been discussing here. I am not a mathematician, so much of this is outside of my area of expertise. However, I have come across three papers that suggest that seem to suggest that site frequency spectra (as presented earlier in this discussion) have severe limitations as a source of evidence about past population sizes. The second of these papers specifically examines scenarios of a bottleneck followed by exponential population growth.
Simon Myers, Charles Fefferman, Nick Patterson Can one learn history from the allelic spectrum? Theoretical Population Biology, Volume 73, Issue 3, 2008, pp. 342-348
https://www.sciencedirect.com/science/article/pii/S0040580908000038
Abstract: It is well known that the neutral allelic frequency spectrum of a population is affected by the history of population size. A number of authors have used this fact to infer history given observed allele frequency data. We ask whether perfect information concerning the spectrum allows precise recovery of the history, and with an explicit example show that the answer is in the negative. This implies some limitations on how informative allelic spectra can be.
Terhorst, Jonathan, and Yun S. Song. Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum. Proceedings of the National Academy of Sciences 112.25 (2015): 7677-7682.
http://www.pnas.org/content/112/25/7677.short
Abstract: The sample frequency spectrum (SFS) of DNA sequences from a collection of individuals is a summary statistic that is commonly used for parametric inference in population genetics. Despite the popularity of SFS-based inference methods, little is currently known about the information theoretic limit on the estimation accuracy as a function of sample size. Here, we show that using the SFS to estimate the size history of a population has a minimax error of at least O(1/log s), where s is the number of independent segregating sites used in the analysis. This rate is exponentially worse than known convergence rates for many classical estimation problems in statistics. Another surprising aspect of our theoretical bound is that it does not depend on the dimension of the SFS, which is related to the number of sampled individuals. This means that, for a fixed number s of segregating sites considered, using more individuals does not help to reduce the minimax error bound. Our result pertains to populations that have experienced a bottleneck, and we argue that it can be expected to apply to many populations in nature.
Baharian, Soheil, and Simon Gravel. “On the decidability of population size histories from finite allele frequency spectra.” Theoretical population biology (2018).
https://www.sciencedirect.com/science/article/pii/S004058091730148X
Abstract: Understanding the historical events that shaped current genomic diversity has applications in historical, biological, and medical research. However, the amount of historical information that can be inferred from genetic data is finite, which leads to an identifiability problem. For example, different historical processes can lead to identical distribution of allele frequencies. This identifiability issue casts a shadow of uncertainty over the results of any study which uses the frequency spectrum to infer past demography. It has been argued that imposing mild ‘reasonableness’ constraints on demographic histories can enable unique reconstruction, at least in an idealized setting where the length of the genome is nearly infinite. Here, we discuss this problem for finite sample size and genome length. Using the diffusion approximation, we obtain bounds on likelihood differences between similar demographic histories, and use them to construct pairs of very different reasonable histories that produce almost-identical frequency distributions. The finite-genome problem therefore remains poorly determined even among reasonable histories, where fits to few-parameter models produce narrow parameter confidence intervals, large uncertainties lurk hidden by model assumption."
So I think I should add these to the criticism I made earlier of this approach to @glipsnort here:
In addition, I came across this paper which @DennisVenema may find interesting as he writes his blog about the PSMC method
Kim, J., Mossel, E., Rácz, M. Z., & Ross, N. (2015). Can one hear the shape of a population history?. Theoretical population biology, 100, 26-38.
http://www.sciencedirect.com/science/article/pii/S0040580914000987?via%3Dihub
I have also been reading up more on ARGweaver and intend to post again on this soon @Swamidass .
Hello @TedDavis, I hope you are well my friend. Things have come a long substantially since you first posted on this thread, back about 2 months ago. I summarized the scientific highlights of this conversation here.
Surprisingly, at lease to me, @RichardBuggs was on to something. Our certainty about a bottleneck in the distant past (e.g. before 500 kya) may not be as high as we imagined. As I write here…
And the implications for theology…
Now, @TedDavis, I agree with you that a recent genealogical Adam (A Genealogical Rapprochement on Adam?) is probably more significant in the long run that an ancient single-couple bottleneck. This, nonetheless, is a surprising finding. Assuming, of course, that it pans out. We are still early in the game, and might find a mistake. This reminds, many ways, of a similar point we were almost exactly 12 months ago on the genealogical Adam work.
Nonetheless, this really could pan out, and some Christians mich join @agauger in taking this view. At the very least, much of the claims on the science have been overstated if it takes this much effort to disprove an ancient bottleneck, and we have yet to do so.
I’m curious, therefore, your thoughts on a few levels as a historian many of us trust in this conversation:
Thanks for your thoughtfulness here. I’m wondering how your perspective could guide us here. Many of us are doing what we can to serve the Church, and the science of Adam appears to be a place where the ball was fumbled.
Allele frequency spectrums (AFS) do not give a solid view of ancient bottlenecks, but they do of recent population structure. Ironically, very recent bottlenecks are not well ascertained by MSMC and PSMC and LD-Blocks, but they are clear in AFS. This is covered pretty well here:
So yes, in the ancient past you cannot really infer much from AFS, but that has never been @glipsnort’s claim. His claims are consistent with what I showed with argweaver.
@glipsnort has not made any claims of heliocentric certainty.
He would agree that past about 500 kya, we do not expect allele frequency spectrums to detect a bottleneck of a single couple. That is where he places a tentative cutoff. So his results are essentially the same as argweaver, though the evidence form argweaver is much stronger.
His original reason for delving into AFS was to respond to some young earth creationists that claimed the AFS was inconsistent with a large ancient population and required a single couple origin just 6,000 years ago: (Can someone explain like I'm 5 yo, what's wrong with this refutation of Biologos?).
His response to Ola Hossjer (colleague of @agauger) has been very well measured, and entirely correct. (Glipsnort responds to a critical article) Notice that he does not prese a case against ancient bottlenecks, but only for common ancestry with great apes and huamns, and against a recent bottleneck. Both those claims are very well supported by the evidence, and he produces analysis of his own all the time.
I know you are not attacking @glipsnort personally, or even leveling an unfair scientific critique. I do think, however, it is important to clarify that he has been a measured and careful voice. In my opinion, he has not drawn incorrect conclusions from the AFS work, nor has he overstated his certainty of those results.
A couple technical updates:
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.
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