Burke's Objections to Heliocentric Certainty Thread

(Jonathan Burke) #1

Continuing the discussion from Heliocentric Certainty Against a Bottleneck of Two?:

Do you mean all population size estimates include both homo sapiens and the ancestors of homo sapiens? No population size estimates actually estimate the homo sapiens population from now until around 500kya?

You’re saying a homo sapiens bottleneck at 500kya might be consistent with the evidence? So you think homo sapiens might have emerged at least as early as 500kya?

Comments on "Heliocentric Certainty Against a Bottleneck of Two"?
(S. Joshua Swamidass) #2

Thanks for opening this thread @Jonathan_Burke.

No. I mean estimates include Homo sapiens + those they with whom would eventually interbreed. For example, at 100 kya, the estimate include (for example) Neandertals too.

That means that no studies I know of estimate the size of Homo sapien population, specifically, farther back than 20 kya (when we think there were only Homo sapiens left). It is a novel claim to say that they never dip to a single couple over the last 300 kya to 500 kya.

No. I am saying a bottleneck in our “ancestors” (which would not be Homo sapiens at 500 kya) might be consistent with this evidence (ignoring the rest). The reason this is coming up is that these paper were offered as strong evidence against a recent bottleneck of the “human lineage.” There is evidence that troubles that view, but not in these papers.

I’ll edit that original quote to be more clear. Thanks for pointing it out. Thanks for the questions.

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(S. Joshua Swamidass) #3

Here is how I edited it. Hope that helps.

(Jonathan Burke) #4

So when this study says “Archaic African and Asian lineages in the genetic ancestry of modern humans”, what it really means is “Archaic African and Asian lineages in the genetic ancestry of modern humans and the non-humans with which they would eventually interbreed”?

(S. Joshua Swamidass) #5

Unfortunately, there is not enough info in that question to answer. I think you are referring to a bottleneck of Homo sapiens about 300 kya. In that case, the interbreeding events being discussed in that paper appear to predate this bottleneck. Any variation lost by the Homo sapien bottle could have been reacquired by interbreeding after that point.

If that is not what you meant to ask, you will have to more clearly specify your question.

(Jonathan Burke) #6

I am talking about the studies which say they are testing homo sapiens bottlenecks. You say they are not really testing for homo sapiens bottlenecks, they are only testing data which includes homo sapiens and non-homo sapiens. Is that correct?

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(S. Joshua Swamidass) #7

That study does not test for a bottleneck in Homo sapiens specifically. The range of dates it is looking at is before Homo sapiens arise. And the term “modern humans” is not well defined. Nor is it clear that they corrected for interbreeding. I could be wrong, because I only skimmed that paper. Did you read it and find an indication otherwise?

(Jonathan Burke) #8

That seems to be answering the question I asked. So you’re saying that when these papers use terms like “Genetic variation at most loci examined in human populations indicates that the (effective) population size has been approximately 10(4) (i.e., 10,000) for the past 1 Myr”, they don’t mean “human population”, or do they mean “human population, but we didn’t control for inter-breeding”? And when they say things like “the ancient genetic history of humans indicates no severe bottleneck during the evolution of humans in the last half million years”, it means something else? Or what?

Before you said that humans could have arisen as early as 500kya, or even earlier, “we just really do not know”. If all the “archaic humans” like neanderthalensis, rhodesiensis, heidelbergensis, and antecessor are “humans”, then that pushes “humans” back to 1200ka. If we define “human” sufficiently loosely, I am sure we can push back far enough into deep time to find a bottleneck of something. Is that the idea here?

(S. Joshua Swamidass) #9

Exactly. It means something else.

It is critical to remember that “human” is a totally ambiguous term with no scientific precision. In this context, it just means “our ancestors as a whole”, without parsing out the taxonomy of all these ancestors in the distant past, or their respective population sizes. It just means “our ancestors.” That is it.

Once again, it all depends what we mean by “human.” To enumerate the wide range of potentially relevant possibilities:

  1. Some would say “human” begins with the genus Homo (about 2 mya)

  2. Some would say with the common ancestors of Homo sapiens, Neandertals, and Denisovans (about 500 kya).

  3. Some would say anatomically modern humans (i.e. Homo sapiens, that arise about 200 kya to 350 kya).

  4. Some would say behaviorally modern humans (i.e. Homo sapiens about 50 kya).

  5. Some would say “the descendants of Adam” (which could be anywhere from 6 kya to 2 mya). Of course, this last option is not ever considered in science.

Which of these is “correct”? We just have no idea, and there is no consensus in science. There is no scientific way to determine the line between “human” and “non-human”. We can make statements about many of these scientifically definable groups, to be sure, but there is no agreement about what is truly “human” here.

So depending on what one means by “human,” it is entirely possible that (by that definition) they arise as just 2. Especially when we accept interbreeding (as Dennis does), then really all bets are off. They could have been really recent. That is why we just do not know if Homo sapiens dip down to a single couple. They certainly dip down to zero, so why could they not have arisen as a single couple?

So there are really two issues at play here:

  1. Go back far enough (maybe just 400 kya), and a bottleneck of all our ancestors might be possible.

  2. Accept interbreeding with other lines, and there easily could have been a bottleneck among a subset of our ancestors and essentially any point.

Either way, we certainly do not have heliocentric certainty against a bottleneck. I think Dennis is just wrong here, and this arose from the Ecological Fallacy. The scientists have been discussing offline, trying to give everyone a holiday break. As you can see, @sygarte (a population geneticist) seems convinced. So we are getting somewhere.

(Jonathan Burke) #10

Can we make any statements about Adam and Eve and their physical and mental characteristics?

How would this disprove the statement “Homo sapiens specifically do not dip down to a single couple in 300 kya to the confidence we have in heliocentrism”?

What is the likelihood of a homo sapiens bottleneck followed by interbreeding eliminating all trace of the bottleneck, within the last 300kya?

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(S. Joshua Swamidass) #11

Oh, you are worried about that point? That is already settled a much easier way. Dennis thinks that Homo sapiens arise about 200 kya ago (he does not group the group of finds at ~300 kya as fully Homo sapien). At their origin, with his definition of Homo sapien could have been a single couple, with their offspring interbreeding with other hominids in Africa.

No scientific study I know of estimates the size of Homo sapiens specifically at 200 kya. Frankly, that seems impossible. We just do not know at that point how to (1) define Homo sapien, let alone (2) estimate their numbers. After all, we already know that Homo sapiens go to zero, so it’s not unreasonable to think they go to a single couple along the way to zero.

So, it seems, I have just put forward a (1) plausible hypothesis (2) with zero evidence against it, that (3) entirely contradicts Dennis claims. That seems to pretty much end any notions of heliocentric certainty.

Not very much. There does not appear to be much consensus. In theology, most would say they had “language” and were “like us.” I suppose everyone agrees “human” is at least within the last 3 mya, and after we diverge from chimps.

However, it seems clear that Homo erectus had complex language too, and was “like us” in many ways. Was it complex enough to compare with modern humans? Was it a full theory of mind? There is just a lot of debate in science about that among scientists. One can find a full range of opinions, but precious little evidence demonstrating one way or another. So there will be intractable debate until we figure out how to build a time machine.

It’s not wise to make overly certain claims here given the amount of dispute within science on these questions.

(S. Joshua Swamidass) #12

It all depends how we define Homo sapiens. The likelihood we would detect a bottleneck like this in our genomes is zero. So we are not really dealing with evidence here at all.

If we allow for interbreeding, there is no genetic evidence for or against there being a bottleneck of a single couple of Homo sapiens. Visa versa, there is no genetic evidence for or against them arising as a population. Ultimately, it will all 100% hinge on our definition of Homo sapien in the unobservalbe past.

Surprising right? Chalk this up to another case where the science was not communicated clearly. This is almost as bad an oversight as genealogical science.

(Jonathan Burke) #13

Unless you can calculate the probability of your hypothesis being even possible (let alone probable), I don’t see that the hypothesis has any more weight than saying “Homo sapiens passed through a bottleneck of two people, but God waved a magic wand and changed all the genes to eliminate any evidence of the bottleneck”.

So they may not have actually been anthropologically or even anatomically modern humans, in your view, and we don’t know if they could talk like us or had a conscience, or could reproduce, or anything?

Ok but how is that relevant to understanding what Adam and Eve were like?

What are the different ways of defining Homo sapiens?

The main issue is that I don’t see other scientists saying what you are saying. How should I understand these papers?

One. “Genetic variation at most loci examined in human populations indicates that the (effective) population size has been approximately 10(4) (i.e., 10,000) for the past 1 Myr and that individuals have been genetically united rather tightly. Also suggested is that the population size has never dropped to a few individuals, even in a single generation. These impose important requirements for the hypotheses for the origin of modern humans: a relatively large population size and frequent migration if populations were geographically subdivided. Any hypothesis that assumes a small number of founding individuals throughout the late Pleistocene can be rejected.”

Two. “There is no evidence for an exponential expansion out of a bottlenecked founding population, and an effective population size of approximately 10,000 has been maintained.”

Three. “On the other hand our results also deny the hypothesis that there was a severe hourglass contraction in the number of our ancestors in the late middle and upper Pleistocene. If humans were descended from some small group of survivors of a catastrophic loss of population, then the distribution of ascertained Alu polymorphisms would show a pre-ponderance of high frequency insertions (unpublished simulation results). Instead the suggestion is that our ancestors were not part of a world network of gene flow among archaic human populations but were instead effectively a separate species with effective size of 10,000-20,000 throughout the Pleistocene.”

Four. “Moreover, the ancient genetic history of humans indicates no severe bottleneck during the evolution of humans in the last half million years; otherwise, much of the ancient genetic history would have been lost during a severe bottleneck.”

(S. Joshua Swamidass) #14

We are going cover all this in the main thread. I can tell you briefly…

This is entirely consistent with what I have said here. You will see why shortly.

This is also. I am agreeing that there is no evidence for it.

Once again, nothing I have said disputes this.

Once again I agree with this too.

I understand this might be surprising, but if we make our statements precisely, these scientific statements are 100% consistent with what I have been saying too.

(Jonathan Burke) #15

But I thought no one had ever tried to test the idea of a bottleneck anywhere in the human lineage. You and Dr Buggs kept telling us this was an entirely novel and never tested idea which was a completely open scientific question, and no one knew if there was any evidence for it or not.

(S. Joshua Swamidass) #16

I never said it was an entirely novel idea. All I have said is that its valid to test the actual hypothesis, rather than a strawman version of it. Most studies are not actually testing the hypothesis. They are estimating effective population size; which is something different.

These studies, to be clear, are not testing for a brief bottleneck followed by an exponential expansion. The only paper I know that did this is the Ayala paper on MHC (http://www.pnas.org/content/91/15/6787.abstract). The rest are inferring population sizes in the past, without even testing whether or not they have the statistical power to detect a very brief bottleneck.

I’m not playing gotcha games. I’m instead much more curious about what the evidence shows. This only the beginning of the story. The strongest evidence is elsewhere.

(Jonathan Burke) #17

So when those studies I quoted make conclusions about a bottleneck, which they claim to have tested, what they actually did was just test a strawman?

One of them actually says “There is no evidence for an exponential expansion out of a bottlenecked founding population, and an effective population size of approximately 10,000 has been maintained.”

Well thus far we have no evidence for a bottleneck, even according to your own study. So where is the evidence for the bottleneck? How can we know it took place if there’s no evidence for it?

(S. Joshua Swamidass) #18

They were not considering the type of bottleneck that Buggs is proposing: very brief, very sharp, and followed by rapid exponential expansion.

And I agree. There is no evidence for it. The question, however, is if there is evidence against it. It is possible there is no evidence for or against a bottleneck with exponential expansion.

I’ve never aimed to demonstrate a bottleneck. If what we are uncovering here is valid, such an attempt would be impossible. We would not expected evidence one way or another (except maybe Ayala’s…).

(Jonathan Burke) #19

I thought that’s exactly what was being tested by the paper which said “There is no evidence for an exponential expansion out of a bottlenecked founding population, and an effective population size of approximately 10,000 has been maintained.”

If that is the case then we should not be basing theological arguments on it, but that’s exactly what people are doing.

(S. Joshua Swamidass) #20

Bottleneck in that sentence is a different type of bottleneck than proposed by Buggs. It’s a subtle distinction, which is why I missed it at first. But it could be a valid distinction. That’s what we are hashing out.

That’s a different conversation. Theological concerns don’t change the math. At least they shouldn’t.