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


(Peaceful Science) #731

It may not be possible to know from data with out some serious luck.


(Peaceful Science) #732

A beautiful example of an apologetic statement for your position!

Sounds more like @agauger is trying to find a position consistent with her deeply held belief and what the evidence shows.


(Peaceful Science) #733

Very good point.


(Peaceful Science) #734

@DennisVenema has been and is an important part of the conversation. I’ve also very much benefitted from his work and hope to see more from him.

However, we have not been misreading him, but going off how he has clarified what he meant. A key point is that he thought the bottleneck hypothesis was tested, and that psmc could detect these sorts of things very anciently. On both counts he was wrong, and he recently explain it wasn’t even on his mind as an option. He would rewrite that portion of the book now based on how weve all clarified things together here (hopefully citing those that have brought this to his attention).

That is all good and respectable. We expect to make errors when doing scientific work. We respect scientists that retract there errors and oversights, as @DennisVenema has here.


(Dennis Venema) #735

On the second count I was wrong, yes, though it’s not a major point for AatG. The point of AatG is that when anatomically modern humans arise, we do so as a population, and that all the methods we’ve used to date agree on a population of thousands, not a pair (regardless of what time we use). The first point still stands, though. There are papers in the literature that claim to exclude a bottleneck weaker than the one @RichardBuggs is proposing, and I’ve referenced them way up there ^^ somewhere early on in this conversation.


(Dennis Venema) #736

Remember that Adam and the Genome is a popular book for a lay audience. Most lay people think “human” means us. As I’ve mentioned before, I used it in AatG as shorthand for “anatomically modern human.”

If you want an example of a paleoanthropologist using the same way of speaking, Tim White would be one (when speaking to popular audiences). For example, in this lecture he uses “human” the same way as I do in the book.

But of course, another key point in the book is that species designations are attempts to draw lines of demarcation on a continuous gradient. So whatever term one uses, it will have blur around the edges.

Edit: here’s some of the transcript of the lecture that makes the point:


A.Suarez's Treatment on a Pope's Formulation for Original Sin's Transmission!
A.Suarez's Treatment on a Pope's Formulation for Original Sin's Transmission!
(Jon) #737

It’s nothing to do with my position.

That’s apologetics. In contrast, science is determining what the evidence shows, and then arriving at beliefs.


(Peaceful Science) #738

I supposed you are entitled to your opinion, but I disagree. The bottleneck hypothesis of which Buggs was asking about was not tested in the literature. And the only ones in the literature I have seen are stronger along the timing dimension, not weaker. Moreover, observing if a bottleneck is detected is a distinct activity from testing a hypothesis.


(Albert Leo) #739

I’m sure you understand my position, Jay, (since I’ve repeated it often on these posts) but for any new readers I want to be clear that I reject any “biological saltation” that would claim to explain the Great Leap Forward or the sudden appearance of Theory of Mind. If real, the GLF must have be a fortuitous but rare confluence of ‘ordinary’ biology (a larynx capable of sounds needed for language) and perhaps an epigenetic change in brain ‘wiring’ that promoted EWM (enhanced working memory) and expression of sophisticated thoughts through language.

In respect to the recent efforts (see @AMWolfe; @T.j_Runyon) to render the term ‘behavioral modernity’ as unscientific in reference to humankind’s origins, I would suggest that depends on how one plans to use it. Paleo-anthropologists may prefer some statistical method of treating 'behavior variance’ as more reproducible and therefore more comparable between research teams. However in explaining how Christian Faith can be seen as compatible with evolutionary science, it is quite acceptable to use layman’s terms to emphasize humankind’s uniqueness as the theological foundation for the Biblical term "In God’s Image’.
Al Leo


(Jon Garvey) #740

“The fallacious belief that we can quantify the unquantifiable… is responsible for scientism.” (William Briggs)


(Ann Gauger) #741

@Swamidass, you are correct that I am trying to understand how the genetics, population genetics, and paleoanthropology evidence fit together best if we start from the assumption of a first pair. This is, after all, a position that hasn’t been tested, but needs to be. There are a lot of people invested in it.

In order to insure that later lineages (Neanderthals, Denisovans and H Sapiens: N, D, and H) that show signs of having interbred, and knowing that N and D are believed to share common ancestry with H erectus _and that_H erectus migrated into Asia very rapidly and very early on (about 1.8 mya? I don’t know current estimates

), I chose to view H. erectus as the original pair. @Swamidass is right, though, my goal is to find the best explanation for all the data. The date 700 kya fits much of it, but I don’t think it does for the (easily forgotten) Denisovans.

I really don’t like the idea of interbreeding between N and H or D and H if they are far distant on the tree, and do not share the same nature (I mean that in a theological sense). I do not want any people now to have more or less share of the genetics of the first pair, where ever that first pair was in time. Sole progenitorship? You can call it that. The main concern is to be sure that we all come from the same stock.

2 mya, 1 mya, 7mya, 400 kya, 200 kya or smaller–if it fits the data best, any of those dates are OK. To be explained: time of origin: ancestry and ability to interbreed, morphology, cultural and technological artifacts, dispersal, population size and local origin, population genetics, and genetics, with the assumption of a first pair.

The last two categories of data are most important because they provide a historical record in a way that the others cannot. As anyone can see, the data are in tension with one another. It depends on which factors one emphasizes as to where one comes down on the time line as most likely. Or one can throw up one’s hands and discard a first pair, or find a solution that does not involve sole progenitorship, or some other solution I haven’t thought of.

BTW, my thanks to Buggs, Venema, Swamidass and Schaffner for a fine discussion. I have kept silent most of the time, but have observed. It has been worthwhile.


(Chris Falter) #742

Hi Jon - As always, I enjoy your posts. I do want to push back on your view just a bit. I think it’s legitimate science to define the boundary of what the scientific method can ascertain. To say that the data we possess can neither refute nor confirm a certain kind of population bottleneck is good science, in my completely unauthoritative opinion. :slight_smile:

Best,
Chris Falter


(Dennis Venema) #743

I assume that should be 400kya, unless Adam is back in the Devonian? :slight_smile:


(Ann Gauger) #744

@DennisVenema

Oops.


(T J Runyon) #745

image
The real Adam


(Ann Gauger) #746

:smile:

Now the required verbiage, and :smile: again.


(Jon) #747

I agree. I have not raised any objection to this. What I raise objection to, is pretending that motivations such as this do not exist.

“…you are correct that I am trying to understand how the genetics, population genetics, and paleoanthropology evidence fit together best if we start from the assumption of a first pair. This is, after all, a position that hasn’t been tested, but needs to be. There are a lot of people invested in it.”

I really don’t like the idea of interbreeding between N and H or D and H if they are far distant on the tree, and do not share the same nature (I mean that in a theological sense). I do not want any people now to have more or less share of the genetics of the first pair, where ever that first pair was in time. Sole progenitorship? You can call it that. The main concern is to be sure that we all come from the same stock.”

“To be explained: time of origin: ancestry and ability to interbreed, morphology, cultural and technological artifacts, dispersal, population size and local origin, population genetics, and genetics, with the assumption of a first pair.”


(Ann Gauger) #748

I was asked why I chose an old age for the first pair. The main reason was that 2 mya was the time that might most conform to the criteria I laid out. I chose those criteria as I did, “time of origin: ancestry and ability to interbreed, morphology, cultural and technological artifacts, dispersal, population size and local origin, population genetics, and genetics,” because those are the data we potentially have available, or can test by modeling.

I stated my reasons for wanting sole progenitorship because it is the reason I prefer some models over others, and because Josh asked directly. His model does not support sole progenitorship, and has its own assumptions. I am sure others on this list have preferences also, such as not wanting a first pair to be true.

Third, when you make a model to test something, you have to start with some assumptions. I was on record, along with my coauthors, as wanting to test the possibility of a first pair. Nobody had tested the possibility of a first pair yet, until Richard Buggs’ persistent questioning got Schaffner and Swamidass to make their own models. With the results we have seen.

No one is pretending that motivations do not exist. Dennis had his motivations for writing his book. Josh had motivations for making his model. Richard had is motivations for raising the issue, which he also stated clearly: there are a lot of people invested in this question, and the answer needs to be tested before categorical claims are made. You, I surmise, also have motivations.


(George Brooks) #749

@agauger

So, if a “first pair” actually works brilliantly… if you place the pair at 400 kya … would you then begin work to convince Young Earth Creationists that their Adam & Eve don’t fit in the first 6000 years or even the first 10,000 years … and that they would have to reconcile their view of Genesis to a 400 kya time frame?

George


(Peaceful Science) #750

Of all the most odd ad hominems:

Of course people have motivations for doing research. That is a good thing. I entirely agree, also, that there has been no deception from @agauger, at least as far as I can tell. Or from @RichardBuggs.

The much more important question to ask is if people are honest enough to acknowledge where the evidence deviates from what they might prefer. One way to recognize honest is to see that they are willing adjust their beliefs based on evidence, just as @agauger has done:

That engagement with scientific data is exactly what we should admire. Instead of saying “every detail I’ve imagined in Genesis is equally important, so I am going to stick my fingers in my ears and ignore the data”, @agauger is engaged in a creative and productive exchange to form a new position in the origins debate. That is exactly the right thing to do, whether or not she ends up correct in the end.

I want to add also another recent action by @agauger that increases my trust in her work:

She is not wanting an easy win based on only part of the evidence. Instead she really is trying to figure out what makes sense in light of the whole. It is harder to do this, but it does increase my ability to trust her when she can identify spoilers, and is working to make sense of them.

In particular, for her project, she really does need to include Neanderthal and Denisovan genetic data too. From what I know, they will all likely share a common ancestor about 700 kya, but no one has actually tested that with data. It certainly is not part of the argweaver paper or equivalent. Yet, for her to make that claim, she’d have to deal with it. She is already raising this weak point before we are.

This also distinguishes her effort here from the dishonestly inherent to one-sided polemics.

You are missing the point @gbrooks9. She is not a YEC. She is an OEC, and she will probably be on your side in moving YECs into a different timeline.

I’d just clarify you want sole genetic progenitorship. Sole genealogical progenitorship is still possible recently with a genealogical Adam model.


In the end HONESTY is in short supply, and fundamentally more important than the illusion of inquiry free of motivations. So cut @agauger some slack.