There are two claims involved in this response:
That’s a good idea, but will require a little work, to explain the model and the options. I’ll try to get to it soonish. (If I haven’t done it in a week, I’ve probably forgotten and should be reminded.) My simulation code is actually in C; only the normalization and plotting is done in R.
I don’t see how any of those processes increase the number of alleles in the relevant range of frequencies. Combining processes doesn’t help when the individual processes don’t go in the right direction. Given enough time, a complicated demographic history can produce all kinds of frequency spectra. In this scenario, though, the core problem is recovering diversity in a short time frame; there isn’t time for complexity introduced by multiple rounds of anything. [quote=“RichardBuggs, post:160, topic:37039”]
Also, I mentioned earlier the issue of mating system. Do you have separate sexes in the model, or hermaphrodites? If the latter, could they self-fertilise? If you did have separate sexes and life-long sexual partners, how would that affect the allele frequencies?
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There is no mating system in my model. The model assumes a pool of 2N genomes consisting of unlinked markers. For allele frequencies averaged over the whole genome, such details should not matter.
For the simulation, I know the ancestral state, of course. For the 1000 Genomes data, I used the state assigned by the project, which is based on the allele in one or more closely related species. (I think they used some combination of chimpanzee and macaque, but I don’t remember off-hand.) The assignment is clearly wrong some of the time.[quote=“RichardBuggs, post:160, topic:37039”]
Just a thought: what if you parameterised the ancestral population with the genetic diversity found in present day chimpanzees?
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That would probably look more like the constant-sized population, but I haven’t seen many studies of chimpanzee diversity (or if I have, I’ve forgotten them).
It would correspond to a spectrum with too many low frequency alleles (relative to a constant-sized population) and some much higher frequency ones, with a relative dearth in between.
No, for several reasons: (1) I don’t think this is currently a viable scientific question, (2) doing publication-worthy demographic inference takes a lot of work, and (3) this isn’t what I’m being paid to do. (And it’s not just a matter of obligation to my employers – I work on what I do because I think it’s important. One of the thing I should be working on is malaria. While I’ve been writing this comment, twenty-some thousand people have contracted malaria and fifty have died of it, most of them young children. That fact exerts a certain amount of moral pressure.)
That’s something I intend to do. [quote=“RichardBuggs, post:160, topic:37039”]
Could I push you a little on this, please, as it seems quite a faint denial.
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My denial was intended to be a polite and fairly neutral way of telling you that your suggestion was both off the mark and presumptuous. I’m doing my own simulations because I want to have a better feel for exactly how long effects of a tight bottleneck persist.[quote=“RichardBuggs, post:160, topic:37039”]
Are you as certain that a bottleneck of two has not happened as you are that the earth rotates around the sun?
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No. Similarly, I am not as certain that Bigfoot doesn’t exist as I am that the earth revolves (not rotates! – I have to look it up myself to be sure) around the sun. That doesn’t mean I think the existence of Bigfoot is an open scientific question worth pursuing.
I don’t find any of them convincing since I haven’t read the book – which is one reason I’ve never commented on Dennis’s arguments. I think a recent bottleneck of size two is a nonstarter as a hypothesis. If a colleague brought it to me as a grant or paper idea – without any supporting evidence or modeling – I would tell them to stop wasting both our time. Because of the existing data on human genetic variation, the overall state of demographic inference, and my own experience with modeling human bottlenecks, my prior on this hypothesis is too low for it to be worth pursuing. Detailed perusal of the existing studies on the subject is kind of beside the point for me.
Wow… you have lots and lots of chutzpah.
When will you learn enough that you can actually run these scenarios yourself, and learn (the Old Fashioned Way) what works and doesnt work?
However, you then ask this:
“Or would you be willing to share the code of your model so others can examine it and perhaps play with more scenarios?”
Assuming that the code is not necessarily proprietary and relevant to @glipsnort being able to sustain a viable living, I would support any population geneticist producing a “Kit” for YEC’s to use and play with … so that serious scientists can get on with their work!
Thanks for making that abundantly clear for all concerned.
Thanks for your response @glipsnort. I will respond as soon as I can. I am teaching a postgraduate module at the moment, and this, together with my PhD students, postdocs and infant son, means I don’t have time for this dialogue this week.
@DennisVenema do you plan to respond to my comments on the Zhao et al paper? I see you have posted another blog that does not seem to mention it. Do you no longer see it as supporting your case?
Richard, it is clear that you are well-familiar with the fact that life can get very busy. Perhaps you should consider that other people may get busy as well and extend the grace to ask questions in a way that does not border on belligerence.
Dr Buggs, I realise you’re incredibly busy and I do not like to trespass on your time. I’d just like to know if it’s convenient or not for you to answer my previously asked question.
Does your understanding of the data support the idea of an Adam and Eve who had no ancestors at all (neither human nor pre-human), as the universal progenitors of every human who has ever lived, with no humans descending from any parallel humans or pre-humans, approximately 6,000 years ago?
If it isn’t convenient, then that’s fine. I can just let it go.
Hi Richard,
Yes, life gets busy. Ditto here.
I’ll be honest that I see this discussion as providing ever-diminishing returns. If you want to see your ideas get traction, it’s time for you to do some modelling. You also need to deal with the strongest evidence available, not simply pick at what you see as lesser evidence. For example, there are regions of the human genome that do have haplotypes that could fit into two people. Those are not the areas you need to deal with (!). The most variable ones are the issue.
For that reason it’s unclear to me why you want to continue picking at Zhao when there is stronger evidence to deal with, such as the other papers I’ve pointed you to. For example, the Alu paper, that paper with the haplotype blocks on chromosome 21, and so on. Even if you could shoehorn the data into 4 blocks for Zhao - and even that is not reasonable, as I will discuss briefly below - you just can’t shoehorn the variation on chromosome 21 into four blocks.
If you were my colleague approaching me with this as a hypothesis to be tested, I would immediately point you to the challenges - i.e. the haplotype diversity we see across the genome - and tell you that unless you have a reasonable explanation / mechanism for producing that diversity in the timeframe you propose that this is a waste of time. So would any other geneticist.
I’ll include a brief discussion of the issues here for the benefit of others, since this sort of thing also applies to any other part of the genome, including those haplotype blocks on chromosome 21.
For Zhao, you have in your second haplotype grouping more variation than reasonably can be attributed to one starting haplotype. For example, three individuals (3, 4 and 5) that share an “A” at the position in column six, and a “C” at the position in column nineteen. That looks like another haplotype to me. At position 15, you have about half in group 2 with either allele (A orT). Again, it would be more reasonable to have these as separate types. Ditto for that same column in your group 3. These are all types that have several people in the data set - these are common types.
If you try to start with four ancestral types and then produce the variant types within each of your groupings, you’ll see that you need to invoke too many rare events. For example, in order to produce individuals 3, 4, and 5 in group 2 from one of the other types, here’s what would have to happen:
We would need a mutation to an A at position six, followed by drift to make this variant more frequent. Then, one of the variants later would have to mutate to a C at position nineteen, and once again drift would have to occur to make the new variant more common. These two events could be reversed, of course - mutation to C19, drift, and then mutation to 6A, and drift. Once we establish the 6A / C19 variant, we need either (a) a third mutation at 15 to give 15T for some of the 6A / C19 descendants, or (b) a double crossover event in this region to pick up 15T from another type. This would be needed to explain the fifth individual in your group 2. Then, after these events, you would again have to have drift occur to make these new combinations reasonably frequent such that they would be picked up in Zhao’s sample size. That’s a large number of very rare events, and at least three instances where drift has time to work to take new variants to a reasonable frequency.
You don’t have enough time in your model to make this work. Rare events take a long time to appear, and then drift has to act between each rare event, and that takes a long time too. Multiple rare events interspersed with long times for drift = too much time.
It’s this sort of thing that would be even more of a problem for the chromosome 21 paper, to say nothing of looking at the scope of haplotype blocks across the entire genome as catalogued by the 1000 genomes database.
It’s just not going to squeeze into 4 (or two, which is what it should really be, if Eve was a clone of Adam). If you disagree, feel free to model it and present it for peer review - even the informal peer review that would result from discussing your model here.
I do apologise to anyone who felt hurt by the brevity of my previous post. I had meant to spend longer on it but was interrupted by a PhD student with an urgent request. Once I had spoken to him I had to rush off to lead a class, and decided to sent the post in the minute of my lunch time that I had remaining. Perhaps it was a mistake to send it in such a brief form, but I did want to keep the conversation going. I will respond at greater length to Dennis and Steve soon. It is 9pm my time now, and I have to read three papers for a class tomorrow morning. Apologies.
No worries - I for one did not take it negatively.
This may have been raised before, but I’d like to mention the issue of Noah’s family, which is another putative bottleneck (down to eight people). I think any case for an Adam and Eve bottleneck of two people should also address whether or not a bottleneck of eight people occurred not too long after.
I thought it was perfectly reasonable, not a problem at all.
Well, since someone already did the whole “Since Eve was pulled from Adam’s rib, isn’t it a bottleneck of ONE?” argument, I’ll have fun picking at your “bottleneck of 8”… Wouldn’t it be rather a bottleneck of five genetically speaking? It’s Noah & his wife’s genes that were merely recombined in Shem, Ham & Japheth (assuming Noah was monogamous, and the text gives no evidence otherwise), plus three daughters-in-law.
FIrst, I want to emphasize the critical importance of taking the questions of the Church seriously. Few have done so, and so that is why there is high value in this conversation.
Though not relevant to this conversation, which is merely about bottlenecks, and not special creation.
Keep in mind that some creationists have proposed that Adam and Eve were genetic mosaics, with different genomes in each of their sperm/eggs. If this is the case, there certainly could have been a bottleneck of two. From a 100% genetic point of view (ignoring archeology), it could have even been a recent bottleneck.
That does not solve the problem of the subsequent 5 genome bottleneck of Noah. And it would also give Adam and Eve a very different sort of biology than us. It would also leave us with an “Appearance of Evolution” problem, because God did not make it clear we did not descend from Apes. It also raises theological problems in inferring incest in the first family. However, it would fit the evidence.
To be clear, however, @RichardBuggs been very clear about several things. Also, it appears @agauger has taken a similar view.
This is not to defend his skepticism, but to make sure he is correctly represented. @RichardBuggs, as I read him, is asking a reasonable scientific question. I would instead point out that we are actually starting to engage the limits of science. Some of the discussion here seems to circle around trying to prove “what happened without a shadow of doubt.” This is not a reasonable hurdle for human inquiry. Moreover, there are some very subtle and interesting questions about the statistics involved here about rare outliers. However, these details cannot usually be resolved in public debate.
Instead, I emphasizes what @RichardBuggs appears to have already conceded, and what seems to be our common ground. Regardless of what happened, it really appears as if our ancestors never dip down to a single couple. Whether or not it is ultimately true, the evidence very strongly seems to show that, at least within the last 500,000 years, that our ancestors never dipped down to two.
While some have taken exception to their skepticism and questions, I must disagree. It is the essence of science to ask questions, even of settled answers. @RichardBuggs also is not a polemicist, but a practicing scientist who has earned the right to ask probing questions, even if he is ultimately wrong. I am not skeptical as is he, as I agree with that…
This is the type of inquiry where verbal exchanges have do begin to have limited value. Population genetics in particular is notoriously non-intuitive. Rigorous modeling of the data is the only way forward. Which brings me to what I think is another point of common ground.
While @RichardBuggs has an interesting hypothesis, that is not enough.
At the moment, the only mathematical models that fit the full range of data we currently know about are those that show we arise in a population, that never dips down to 2.
The only way to change that is to present a new model, that shows otherwise.
Even if a model can be presented that fits the data, it may remain most likely that we arise in a population, not a couple. Consistency with the data is not the same as most likely.
As has been known for a long time, I am a frequent critique of ID. In this case, however, I think @agauger and others are taking the right path forward. They are not presuming divine action (directly or indirectly) and they proposing models of their own. They are doing the hard work of building them and plan to test them on data. That is a new and promising development in ID, even though this has nothing to do with recognizing design in nature.
Of course some of us have different beliefs about what the simulations will show. It is my hypothesis that they will end up confirming the consensus. If they do confirm the BioLogos position, and are honest about it, that will do great good for the Church, bringing them into an honest confession of the evidence. If they end up showing a new way forward, that has value on a purely scientific level. I commend them for it. I think the first option (confirming the BioLogos position) is much more likely. They might disagree.
Who cares. Let’s see what the data shows. Give them time.
Though I agree, in the meantime…
C was actually my first programming language, so I would be happy to see the code whenever you have the time to post it.
Blessings,
Chris
I’m a little uneasy with how you expressing the target conclusion: “… it really appears as if our ancestors never dip down to a single couple.”
Now that you have inserted the “sperm and eggs as a mosaic”, we probably should add an additional clause, because all the results discussed so far has actually been more than limited to “a couple, yes or no”.
The conclusion that @RichardBuggs should agree on is not just regarding two (2):
“it appears as if our ancestors never dip down to either a single couple, or even fewer than 1000.”
And, further, the good doctor would immediately win support and credibility if he started telling the YEC audience that they have to drop the 6000 year time frame, because none of the evidence supports it.
I’m still waiting for someone in the I.D. crowd to step up and start pointing that out… while being a promoter of I.D.
For a while, I thought Dr. Gauger was going to be that person – and what does she do? She writes multiple chapters where she couldn’t bring herself to say anything like that… and instead buried her reputation even deeper into the YEC camp.
As you note, making such a statement would alienate YEC supporters, and there seems to be an unspoken rule that you’re not allowed to say anything which might do that.
They are? Where can I get a summary of their model or models?
What I see is a continued (and baseless) attack on Evolutionary models, with not a wit of or trace of any replacement models.
If you have influence on them in respect to this particular issue, please continue to press them for replacement scenarios… so we can all join in the fun of figuring out what is workable and what is not workable.
Ann has mentioned here and in the “Everything Wrong With TE” book that work on a model is underway and the results will be available RSN.
From Chapter 16 annotation:
Not unspoken. They come right out and say it.
There is nothing like ignoring the elephant in the room.
“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6
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