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


(Jon) #791

Yes look at the definition.

Ad hominem (Latin for “to the man” or “to the person”[1]), short for argumentum ad hominem, is a fallacious argumentative strategy whereby AN ARGUMENT IS REBUTTED by attacking the character, motive, or other attribute of the person making the argument, or persons associated with the argument, RATHER THAN ATTACKING THE SUBSTANCE OF THE ARGUMENT ITSELF. https://en.wikipedia.org/wiki/Ad_hominem

I did not make any attacks on Ann’s character, motive, or other attribute, and in particular (and most relevant), I did not use any such comments to try and rebut her argument. I did not say “Ann is motivated by her desire for a historical Adam, so her bottleneck argument is wrong”, or anything like that. My comments were made specifically about your representation of Ann, not about Ann’s argument.

But I did not dismiss her argument based on her motives. I did not dismiss her argument at all. As I have said, I was addressing your representation of Ann, not Ann’s argument.

Yes all of this can be true. But my confidence in the integrity of her approach to scientific data is not improved when she makes comments like this.

  1. “there is not enough evolutionary time for all these coordinated changes to have happened by the mutation/selection process”
  2. “Thus the evidences for common ancestry put forward by various scientists are not as solid as they might seem”
  3. “The more we learn about our human genome, the more it seems to be brilliantly and uniquely designed.”
  4. “I would say that unless somebody figures out how to go back in time, we will never be able to establish for certain that we arose from an evolutionary process”
  5. “I actually believe that we will someday falsify Darwinism, which will be great because then the question arises, “If it didn’t happen by a gradual process, how did it happen?””
  6. “It used to be said that only two to three percent of our genome coded for protein, and the rest was junk, speaking loosely. Well, the ENCODE project is revealing that this is a complete falsehood”
  7. (interview with Ann Gauger) "Regarding a couple of Swawidass’s points, Sarah Chaffee asks at one point, “Are those serious arguments?” “No, they’re not.” “Scary arguments?” You can hear Dr. Gauger suppress a laugh. “No.”

If she is “honestly wrong” in her statements about well known and settled science, then she is unreliable at best, and should be identified as such. If I were to make these statements, especially here on Biologos, I would be called out for scientific ignorance. Given her professional position, and given the influence she has, holding her to at least the same standard of accuracy, is entirely reasonable. Given your aim is to “serve the Church with an honest account of the science, regardless of our personal positions”, surely it is reasonable to expect her to do the same.

You wouldn’t accept that kind of dismissive comment if it were aimed at the concerns of someone who is ID or YEC. The fact is I am not the only person who has expressed concern with your approach. Look at this comment.

It’s clear that you’re coming across as rather one sided (to put it mildly), to more than one person. For example, you called out Dennis, saying he “presented a selective account that fit with his personal theological views”. But you haven’t done the same with Ann.


(Christy Hemphill) #792

@Jonathan_Burke
@Swamidass

Please do not have any further public discussion about what is or is not ad hominem. If you really must further adjudicate this particular instance, do it via PM. Thank you. :slight_smile:


(George Brooks) #793

But here’s the rub, @glipsnort, because you don’t care, and you reject the whole idea of an historical Adam being inserted into the Evolutionary scenario (as per @Swamidass constructions)… you are not likely to populate the “bridge” between some YEC and some BioLogos scenarios.

I had been wondering if Prof @agauger might serve as a bridge… but she tells me that she pretty much rejects the idea of primates as a common ancestor for the base population of humans.

So she’s out of the equation too.


(Peaceful Science) #794

She said she is not sure about common descent yet.

Not so. @glipsnort is important because he has been consistently honest about the data, and not overstated it.


(George Brooks) #795

Hey, @Swamidass, we are all important.

My comments were specifically addressing the service of “bridging”… not “anchoring”.
I don’t think @glipsnort will be bothered by this …


(Peaceful Science) #796

Don’t miss this piece by @agauger.

https://evolutionnews.org/2018/03/is-there-a-first-human-couple-in-our-past-new-evidence-and-arguments/

Overall, I think she did a good job.

Then two new scientists entered the debate with Venema and Buggs. Remarkably, neither is an ID advocate, both affirm evolutionary theory, and both came to similar conclusions by different routes. A population geneticist named Dr. Steve Schaffner of the Broad Institute in Cambridge, Massachusetts, ran a simulation to determine whether a bottleneck of two individuals was possible. He found that, at dates older than 500,000 years ago, a bottleneck could not be ruled out. His analysis of allele frequencies could not distinguish between allele frequencies obtained after a bottleneck of two and those from current genetic data. Dr. Joshua Swamidass, assistant professor in the Department of Pathology and Immunology at Washington University in St. Louis, estimated the time to the most recent four alleles in the genome. An allele is a version of a gene. We all carry two copies of each gene (setting sex chromosomes aside), so a bottleneck of two individuals would have a maximum of four alleles per gene. His analysis likewise showed that the most recent time at which a bottleneck of two individuals, or four alleles, could have occurred was about 500,000 years ago. Both researchers used experimentally validated mutation rates in their models, and the precise details are worth looking at closely.


(Richard Buggs) #797

Hi Steve @glipsnort please could I just doublecheck some details with you? The simulations you ran earlier in this discussion were for:

  1. A constant effective population size of 16,384 and a mutation rate (1.6e-8/bp/generation)
  2. A constant effective population size of 16,384 then a bottleneck of two 100,000 years ago, with population doubling each generation for 14 generations (350 years) until it reaches a population size of 16,384 after which the population has constant size (mutation rate 1.6e-8/bp/generation)
  3. A constant effective population size of 16,384 then a bottleneck of two 250,000 years ago, with population doubling each generation for 14 generations (350 years) until it reaches a population size of 16,384 after which the population has constant size. (mutation rate 1.6e-8/bp/generation)
  4. A constant effective population size of 16,384 then a bottleneck of two 500,000 years ago, with population doubling each generation for 14 generations (350 years) until it reaches a population size of 16,384 after which the population has constant size. (mutation rate 1.6e-8/bp/generation)
  5. A constant effective population size of 16,384 then a bottleneck of two 1,000,000 years ago, with population doubling each generation for 14 generations (350 years) until it reaches a population size of 16,384 after which the population has constant size. (mutation rate 1.6e-8/bp/generation)
  6. A constant effective population size of 16,384 then a bottleneck of two 250,000 years ago, with population doubling each generation for 14 generations (350 years) until it reaches a population size of 16,384 after which the population has constant size. (mutation rate 2.0 x 10^-8)
  7. A rapidly expanding effective population size prior to the bottleneck rising to 1.4 million then a bottleneck of two 250,000 years ago, with population doubling each generation for 14 generations (350 years) until it reaches a population size of 16,384 after which the population has constant size (mutation rate 1.6e-8/bp/generation)
    I think that is what you did, but just wanted to double check with you.
    many thanks
    Richard

(Christy Hemphill) #798

Except when you throw in sentences like:

I guarantee a certain percentage of the readership hears "If you don’t have atheist evolutionist assumptions about millions and billions of years, it’s totally plausible that Adam and Eve could have existed 6,000 years ago. Maybe not totally Ann Gauger’s fault, but still unfortunate.

Also, how many of the readers understand that the “we” in this sentence is not homo sapiens?


(Jon) #799

Exactly. That has been the entire aim all along.

Yep. And note “supposedly split from chimps”, intended to communicate clear denial of common descent.


(Christy Hemphill) #800

Also:

“The claim that our population was never smaller than thousands is wrong.”

So, “our population” is hominins who lived more than 500,000 years ago? I wonder how many people would agree that counts as “our population”? Plus, is it wrong, or just unprovable? It is true to say there is no evidence that our population was smaller than thousands, correct? Even using that very generous and not intuitive definition of “our population”?


(George Brooks) #801

@Christy and @Jonathan_Burke

As the narrative is formulated above, as conveyed to us by @Swamidass, it seems pretty emphatic that the studies being discussed permit no Single-Pair Bottleneck at any time within half a million years of the present!

This statement seems rather immune to any obfuscating influences caused by pre-human hybridization or any related consideration. No matter what you throw at this paragraph, regardless of the theoretical possibilities, the very best case is no Single-Pair Bottleneck, regardless of any possible extra-sapiens inter-breeding, can be detected any time sooner than 500kya.

This can be stated emphatically, because we are not projecting forward from some kind of sober estimate of what these proto- or quasi-humans genomes might have been like. No. We are taking the modern human genome as it is right now … and casting backwards - - looking for soonest time a Single-Pair bottleneck of all Humanity could have existed - - that would have left some unmistakable signs on our genome.

Don’t I have that right? Isn’t this a pretty strong conclusion for unhinging the Young Earth Creationists from their fetish for literal interpretations of Genesis.

@Swamidass, thoughts?


(Peaceful Science) #802

I think that @agauger has made some ambiguous statements, but has also made some clear statements. I would take @gbrooks9’s view, that the clear statements are not negated by the ambiguous ones. She is certainly not hiding her position.

Yes on @agauger, but there is no problem with a literal interpretation of Genesis per se. A lot of Christians read the Bible literally and do not believe it teaches a young earth.


(Peaceful Science) #803

Brief update for the curious, that I hope @RichardBuggs and @DennisVenema will fill in more completely.

  1. Another line of evidence appears to be Neanderthal and Denisovan DNA, which are different enough that they do not look like Homo sapien DNA. But if Adam is ancestor of them, we need to have enough time for his lineage to produce the diversity we see in them too.
  2. It appears that probably pushes the plausible CA date back from 500 kya to 700 kya. This is hardly something new, as we have made reference to this a few times. At this point, the error bars are going to range from about 800 kya to 500 kya, and would meaning identifying “human” with more than just Homo sapiens.
  3. I posit that an Adam at about 700 kya introduces no more theological questions, and probably less scientific problems, than one at 400 kya. I’m not sure the theological difference between 400 kya vs 700 kya vs 2mya are important; they are broadly very similar.
  4. I think the conclusion (which I hope @RichardBuggs and @DennisVenema will develop) is that it is seems like scientifically solid ground to wonder about an Adam at 700 kya.
  5. To those intent on disapproving a bottleneck, we do not expect this to be overturned without a total revolution of our understanding of HLA sequences and trans-species variation (not likely happening soon).
  6. To those intent on proving a bottleneck, it appears that this just places a bottleneck outside our view, beyond the horizon of genetic data. I’m not sure how demonstrating a bottleneck back that far could be possible. Though, you are welcome to try. Even if it were possible, that is still a long way off from unsettling common descent, or from demonstrating that the bottleneck was the Adam and Eve of Scripture. Those claims are likely well beyond science.
  7. So, reaching the limits of the scientific account, it might be good to encourage diversity in our views on Adam.

This still needs to be fleshed out. For those of you who can, we will be covering this all in detail at the ASA conference. I’m doing a workshop on the "Reworking the Science of Adam and Eve", and I hope you can join us. http://network.asa3.org/mpage/ASA2018 Friday, July 27th, 2018, 2pm to 5pm at the ASA Conference in Gordon College, Boston.

At this time, I’d be curious to hear comment from @Paul_Nelson, whom I know is following this conversation closely.


(George Brooks) #804

@Swamidass,

This is one of those areas I do not think you will prosper in. Let someone else carry the water for the Neanderthal and Denisovan. They are clearly on the “non-Adam” side, right?

So let the Neanderthal and Denisovan compete with the attention of the newly evolved and arrived Sapiens … and by the time of Adam’s special creation in 4000 BCE, all the genetic oddities have been played out.

I feel you need to keep your time frame for Adam at 4000 BCE. You will win no friends moving off of that period… and it allows plenty of time to become a Universal Ancestral pair by the time Jesus arrives.

As you can see, from this perspective, Neanderthal and Denisovan as issues will have been completely finished up by 4000 BCE.


(George Brooks) #805

@Swamidass

Okay … who is it that you think is clamoring for the Special Creation of Adam at either 700,000 or 400,000 years ago? It’s not the YECs, right? So who?


(Peaceful Science) #806

I think is @agauger and @RichardBuggs and any other Christian more uncomfortable with people outside the garden then losing the Genesis timeline. Obvious, right?

Personally, I like the diversity but am more drawn to a recent genealogical Adam.


(George Brooks) #807

@Swamidass,

I think anyone who opposes Common Descent and wants you to defend a 400,000 year old Adam is just trying to “sink” the entire work. There’s nothing about a 400,000 year old Special Creation of Adam that makes a lick of sense. It just makes things more difficult all the way around.

If you are going to have a special creation, you might as well have it at 4000 BCE.

Why would a scientist argue that it is more scientific for Special Creation to have happened 400,000 or more years ago? That wouldn’t fit anything. It wouldn’t fit the physical evidence nor the Biblical assertions. it’s pretty much guaranteed to discredit both your science and your biblical interpretation.

Shake that dust off of you, doctor … if someone wants that scenario badly enough, let them make sense of it on their own.


(Peaceful Science) #808

I’m just trying to serve the Church with an accurate account of the science. There is value in this scientifically and theologically. It serves the common good.

If helping them make sense of it is received as a work of peace, this serves the common good too.

Though I do agree with you…

There appear to be problems introduced by a sole-genetic origin from a de novo Adam that a genealogical Adam avoids. @agauger, however, is undecided on common descent. So maybe de novo creation is not critical for her.


(T J Runyon) #809

I’ve been trying to find something to do this summer. Maybe that’s what I’ll do!


(Richard Buggs) #810

Hi all,

Just for completeness I would like to note that Dennis has shared Charles Cole’s new analyses with me, @Swamidass and @glipsnort in a private forum back in February. These analyses do not demonstrate that PSMC could detect a bottleneck of two followed by rapid population growth. Rather, they add evidence that this method could not detect such a bottleneck. I am not sure if Dennis is still intending to share these analyses here on the public forum or not.

My understanding is that @DennisVenema now agrees that PSMC estimates of past effective population sizes could not detect a bottleneck of two followed by rapid population growth.