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


(Chris Falter) #831

Hi Jon,

I’m not sure why you think the epidemiologist fallacy applies here: There is no inference of causation from correlation. The model we are discussing simply estimates minimum population size at some point in the past based on current DNA data + knowledge about rates of change in DNA. (@RichardBuggs @Swamidass @glipsnort please correct me as needed.)

Consider this analogy, Jon: If a comet passes near the earth with a certain velocity, astronomers might pull out their slide rules and determine that the comet was in the Van Oort cloud 200,000 years ago. (Or maybe, just maybe, they would use computers.) They would say, “we have data about the current state of the comet and about the rate of change; these allow us to build a model that projects backwards in time.”

I would be astonished, simply astonished, if some theologian would enter a discussion about comet trajectories and chastise the astronomers for their overconfidence about the location of the comet 200,000 years ago. And if the theologian would justify his skepticism on the basis of the fact that astronomers are learning more and more about astronomy every year, the astonishment would increase. And if theologian were to further argue that there is a confounding factor of a known God who, according to many following the traditional understanding of the Scriptures, created the earth less than 10,000 years ago, so maybe the comet didn’t even exist 200,000 years ago, what would I think?

I would think about the argument between Galileo and Cardinal Bellarmine. It was Bellarmine, after all, who so adamantly argued that Galileo could say what he wanted about celestial mechanics as long as Galileo declared that the scientific findings were hypothetical.

The analogy between celestial mechanics and population genetics is sufficiently clear, I think, so I will not belabor the point further.

Have a great day on the eastern side of the pond, Jon!

Chris


(Jon) #832

What I would think is that I’m hearing people who believe Ken Ham’s “You weren’t there” argument has some kind of value. Every time I hear “But we can’t know about that stuff in the deep past”, that’s what it sounds like.


(Chris Falter) #833

Hi Jon,

While I was writing a reply to a previous message, you made a very interesting post based on your experience as a medical practitioner. This helps me understand your general skepticism about models. However, I do think that your experience in medicine does not apply to hard sciences like physics and population genetics for 3 reasons:

  1. The medical field is far, far behind the scientific fields with respect to experimental methods and evidence-based decision making. It has come a long way, to be sure, but it still has a long way to go.

  2. Causality is very hard to identify in medicine given the ethical and financial constraints on experimental methods, along with the inherent complexity of human body systems. Of course complexity also exists in population genetics, but the fog is much thinner.

  3. The model of determining causality is far more complex than a model that simply determines location in a space over a period of time.

These differences suggest that there are limits on how strongly you can project your personal experience as a physician into the practice of biology.

Best,
Chris


(Andrew M. Wolfe) #834

I’m glad I let you say that instead of trying my hand at it. I was thinking along similar lines, but I appreciate the clarity of your particular presentation. Seems to me there was a false equivalence here.


(Jon Garvey) #836

Chris. I think you understate the complexity of human origin vis a vis medicine: in both cases we are dealing with multifactorial biological processes, of which we have limited (though increasing) knowledge. Or at the very least, population genetics is a lot closer to medicine than it is to calculating the past orbits of comets (though that itself is surprisingly inexact, if one looks at the actual v predicted times of Halley’s comet’s appearance over the centuries).

The specific factor to which Joshua himself referred was the uncertainty of mutation rates under the different circumstances operating back then - that was a known unknown, I suppose like the perturbations of Halley’s comet’s orbit. Some more known - but currently incalculable - unknowns, which also came up in the discussion, are the interactions between the various possible ancestor groups - sapiens, neanderthalis, erectus, at the projected times of the proposed bottlenecks, before and since. Hybridisation events large or small, or other as yet unknown changes around speciation: All decrease certainty.

In the context of the enquiry, that could either change the time of a small bottleneck, or make it more likely, or blow the idea out of the water altogether. All of those would be matters of indifference to me - but the only way to know whether our current “error bars” were correct is by comparison with the real world, just as in the case of projections for Halley’s comet back in time - to quote the infallible Wikipedia:

Researchers in 1981 attempting to calculate the past orbits of Halley by numerical integration starting from accurate observations in the seventeenth and eighteenth centuries could not produce accurate results further back than 837 due to a close approach to Earth in that year. It was necessary to use ancient Chinese comet observations to constrain their calculations.

Even in that simple case of Newtonian gravity, the model was stymied by reality.

Your interfering theologian is not really relevant to the case: this thread was a discussion of the science, but on a science-faith site, in which the bigger debate that prompted it is with those who say, on biblical grounds rather stronger than the position of an unnamed comet, that the first humans were a specially created pair. They do have a dog in the fight.

But my point was simply the scientific one that models depend on theories which are often modified by reality - and so the models need to be calibrated by the reality in which they are employed.I’m not sure why that raises any hackles.


(Jon) #837

That didn’t raise any hackles. What raised hackles was your unsubstantiated claims about the reliability of specific models, based on nothing more than a version of “You weren’t there”.


(George Brooks) #838

@Jon_Garvey

The example of the comet is a study in the butterfly effect … not an invalidation of the scientific method.

The butterfly effect does not reduce the age of the Earth from 4+ billion years down to 10,000 years… nor does it explain why we have meat from mammoths that is less than 40,000 years old, but not from dinosaurs that are supposed to have drowned 4000 years ago.


(Peaceful Science) #839

@Jon_Garvey I saw your post on this on your blog: http://potiphar.jongarvey.co.uk/2018/03/21/do-not-touch-my-anointed/

The irony here is thick. Both you and @Chris_Falter agree with the overall conclusions that a recent sole-genetic progenitor is not likely. It seems you both agree with the conclusions I’ve drawn from the data. However the debate continues in an unclear way about our epistemological certainty about this.

I think there is some confusion about how science reasoning works in conjunction with modeling in this area.

The way I see the situation, is that there is data we have collected about human variation. There is, at this time, a wide range of models proposed to account for that data. However, there is not a single model proposed that can account for the data with a single couple origin less than 200 kya, without either (1) inferring ongoing miracles, (2) totally different biology for Adam and Eve (e.g. genetic mosaics), or (3) mutation rates an order of magnitude (or more) higher than we have ever observed in humans.

That is why, based on our current knowledge, we are calling this evidence against a recent bottleneck. Until a model with a shorter time frame is put forward and tested, this is what we think the data is showing us. For those that disagree, they are welcome to put forward a model of their own to test, but failing that there is not really much to dispute.

Generically calling the conclusions into question is not helpful. The best way to unseat the conclusions is to produce a model that accounts for the data in a shorter time span.

However, I think I understand @Jon_Garvey’s motivation. We do not want to state these claims with too much certainty, as we have just seen a large shift in our understanding here. I’d point, again, to my invitational epistemology as a solution to this paradox. I’ve already pointed out three ways a more recent bottleneck might be possible:

  1. Adam and Eve had totally different biology than us (e.g. genetic mosaics)
  2. Ongoing miracles that diversify us more than is possible by natural processes alone.
  3. Much higher mutation rates in the distant past than we can imagine or observe in humans (perhaps miraculously?)

All these options require deus ex machina miracles, not attested to in Scripture. So we do not consider them in scientific analysis, even if they could be true. We do however invite all who dispute these findings to propose models of their own to make sense of that data. Until a model is produced that can made sense of the data with a recent bottleneck and no miracles, we are justified in saying: the data just looks like we do not have a single couple bottleneck before about 500 kya.

That is the plain reading of human genomes.

Others can dispute those findings, but they better come with a plausible and alternate model with at least as much mathematical rigour as we have done here. Generically casting doubt on the whole exercise does not move us forward. That is not how our understanding progresses.


#840

I suspect that a significant burst in the human mutation rates might be noticed in other comparative studies of genetic divergence.


(Phil) #841

Thank you for such a clear and concise summary of what is a difficult but interesting post for those of us not that familiar with the methods and issues involved.


(Peaceful Science) #842

I just published an article summarizing the current status of the conversation, that might be of interest too.

Hopefully that is helpful.


(George Brooks) #843

Beautiful summation, @Swamidass !!!


(Peter Wolfe) #844

Link not working for me.


(Peaceful Science) #845

Give it another shot:


#846

Even that debate is a bit silly when we get down to it. Are we really sure, or are we really, really sure? It’s like arguing over the Sun being hot, or really hot, and at the same time trying to deal with another claim that the Sun is actually a ball of ice.

Perhaps the surest conclusion we can make is that there is no scientifically defensible justification for thinking that the data supports the hypothesis of the human lineage winnowing down to two people within the time period covered by the data, models, and tools that we currently have.


(Peter Wolfe) #847

:+1: works now thanks


(Peaceful Science) #848

I do not think that is the case. It would be better say there is no scientifically justifiable interpretation of the data, that we know of, that has a single couple bottleneck. Of course, if such a model is forthcoming, that would change.

There is a meaningful reason why it arises. I think this why @Jon_Garvey is raising the point.

For a long time, people have presented evidence against a bottleneck ever in our lineage as a settled finding of population genetics. However, it is not a settled finding, as we have just unsettled it. However, for a long time, questions have been silenced because of the total certainty of that finding. Yet it was wrong.

So how do we avoid that mistake again? I think that is a valid question. I think @Jon_Garvey is arguing that we should hold model’s loosely, and I agree. The data trumps our conclusions, or at least it should.

I think, however, there is some remaining questions about how constructive dialogue with science could be possible. I’ve been thinking about that too. I do not think the answer is in generic skepticism. Rather, I think we need some constructive ways of enabling dialogue, and even constructive types of resistance to scientific claims, that can push us all to better knowledge.


(Jon Garvey) #849

Joshua

The reason I banged on about maintaining healthy uncertainty about even your excellent work in this thread is mainly this: the Christian has another source of information about human origins, which (to put it coarsely, and of course partisanly) is an authoritative eye-witness account from the Holy Spirit. However, like our scientific data its meaning is underdetermined: how are we to relate its teaching to our physical origins?

Each of us who accepts Scripture’s authority, and the Church, make our best judgement on interpretation, and even believe we have the Holy Spirit’s help. And yet our interpretation must always be held provisionally, with a degree of uncertainty - hoping it will be confirmed or corrected down the line.

If we ignore the uncertainty, and avoid “navel-gazing” by assuming our understanding is the last word, we absolutize our reading of Scripture, and relativize everything else - such as science. That’s bigotry.

But the reverse is also true. It’s easy to say that the science is as good as it will ever be, and therefore we may as well assume it is true - but that move absolutizes our science, and relativizes Scripture. That’s scientism.

So to keep in mind, at all times, that both population genetics and biblical hermeneutics (and whatever other sources of information) are human knowledge, not final truth, we remain open to new insights, which is what I think you are saying in your final sentence.


(Jon) #850

Now where have I heard that before?

The point is, the only way we can know for sure how the universe and life were formed is if an infallible eyewitness revealed to us what happened.

When teaching children, we tell them they should politely ask the question “Were you there?” when talking to someone who believes in millions of years and molecules-to-man evolution. If someone replies by asking the same question, as you have done, we say, “No we weren’t there, but we know Someone who was there, Someone who cannot lie, who knows everything, and has always existed. And this One has revealed to us what happened in the past in His history book called the Bible. Are you interested in reading God’s history book to find out what the Word of One who was there tells us about the true history of the world?”


(George Brooks) #851

@Swamidass,

It was wrong? Aren’t you quibbling a bit here?

As far as I can tell, for “presenting evidence against a bottleneck ever in our lineage as a settled finding” to be wrong, somebody has to show that evidence that there is evidence for a single mating pair bottleneck.

Didn’t we only prove that there could be a bottle neck far enough back that it can’t be detected? And isn’t “far enough back” well beyond the 6000 year range?

So, I would think you should be more “wordy” about what we have proved or not proved. I think we have quite clearly showed that there cannot be a single pair bottleneck within a 10,000 year time frame - - don’t you agree?