The "Third Way"/EES and Population Genetics

#1

Hello everyone. I’m thoroughly impressed with the work done on this site. Personally, I am partial to what William Lane Craig calls the “mythological interpretation” of Genesis 1-11 mostly because I accept the conclusions of mainstream biblical critics on this point, and I think Paul’s use of Adam in Romans 5 can be adequately accounted for under this interpretation. Nevertheless, I want to understand the science.

I have recently become convinced that the "Third Way"or Extended Evolutionary Synthesis put forth by people like James A. Shapiro and Denis Noble is the best way to understand how evolution works. But I’ve noticed that both Shapiro and Noble issue certain caveats concerning the viability of population genetics, and/or discovering mutation rates, and I am interested in hearing how Swamidass (or Venema, or Buggs) might reply to the caveats offered by Shapiro and Noble. Here are some quotes from them:

Shapiro- “We have progressed from the Constant Genome, subject only to random, localized changes at a more or less constant mutation rate, to the Fluid Genome, subject to episodic, massive and non-random reorganizations capable of producing new functional architectures. Inevitably, such a profound advance in awareness of genetic capabilities will dramatically alter our understanding of the evolutionary process. Nonetheless, neo-Darwinist writers like Dawkins continue to ignore or trivialize the new knowledge and insist on gradualism as the only path for evolutionary change.”

http://bostonreview.net/archives/BR22.1/shapiro.html

This is a quote from Shapiro from Perry Marshall, which Marshall also quotes in his book Evolution 2.0:

"Last year I attended a lecture at Fermilab by Dr. Shapiro. After his talk, a group of people huddled around him in the cafeteria, peppering him with questions.

One guy suddenly ‘got’ what he’d been saying all night long. ‘You mean the mutations aren’t random?’ he asked. 'No sir. They’re not random at all. “When bacteria are comfortable and well-fed, certain DNA changes occur at a frequency of less than one per billion cells.

But when they’re starving, the mutation rate skyrockets by a factor of 100,000. They develop new adaptations so they can survive.’"

Here is Denis Noble:

“For example, the equations of population genetics, which are based on neo-Darwinist mechanisms, could still be valid as descriptions of the particular conditions and processes they were designed to describe, though we should note that those conditions are highly idealized. A rough analogy is the way in which Newtonian mechanics has been replaced by quantum mechanics. That does not invalidate the use of Newton’s equations in many situations to which they apply well enough. But, as with the move in physics to acknowledge what nature tells us by developing new models, we should move on to new mathematics when it becomes clear that our existing maths is inadequate for the job.” https://thebestschools.org/dialogues/evolution-denis-noble-major-statement/

to be fair, in another place, he says this:

“Of course, that does not mean that the neo-Darwinist mechanism (chance genetic variations followed by natural selection) does not happen. Nor does it mean that all the impressive developments of population genetics using the mathematical ideas developed by neo-Darwinism suddenly become incorrect.”

Dr. Swamidass, your input would be greatly appreciated. Thanks again for what you do here. Eventually, I’m hoping to put the answers I find on this topic into a theological book, and/or scholarly article . I have 2 degrees in theology but I know next to nothing about science, so your work is a great help to me.

Thanks,

-Mark

P.S. Sorry for not being able to link to everything I posted, it said I could only put 2 links in my post.

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The Abuse of Science by Scientists?
(George) #2

@Mark

I think your privileges to include more links will increase as your system-measured experience “metrics” increase. @swamidass, since I’ve never bumped into a message like that, I am assuming that it is part of each person’s evolving status.

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(S. Joshua Swamidass) #3

Welcome to the forums @mark. It is great to have your voice. Don’t take this response too personally though.

I’m not sure if that is the conclusion of mainstream critics. It is the conclusions of mainline critics, who are well outside the mainstream of traditional theology. Most conservative theologians roundly reject a mythological interpretation of Adam, even though they acknowledge parallels and borrowing of mythology from surrounding cultures. With inspiration and inerrancy in the mix, it could have been borrowed myth that became true upon inspired modifications.

Sorry to hear that. The problem with Shapiro and Nobel is not so much that the science is bad, but because their history is wrong. Nothing they are offering is really new. Neo-Darwinism as the dominant mechanism of change was put to rest back in the 1960’s. The term itself “darwinism” is a slur that only atheists like to apply to themselves. A better term is “evolutionary science” or the “modern synthesis” which, to be clear, is already extended.

The scientific findings are interesting, and already part of the modern synthesis, and have been well established by others decades before Shapiro entered the scene. The remained a pseudo-history to cast themselves as heroes of the story. Scientists do not like that behavior, which is why they are generally resisted by most scientists.

This is not an accurate way of understanding randomness. In statistics, “random” does not mean “without purpose” or “without function” or “without pattern.” These are still random mutations. Even though they might have a purpose, function or pattern.

Except that we already moved past neo-Darwinism in the 1960’s with Haldane and Kimura’s work. Why are they tilting against windmills? Why are they labeling populations genetics as neo-Darwinism when that is precisely what they overturned? This would have been a great thing to write in 1960. Not sure what it has to do with our current moment.

It is almost as if they just forgot the last 50 years of research in evolution. Neo-Darwinism (chance genetic variations followed by natural selection) as the dominant mechanism of change was falsified by Haldane and Kimura in the 1960s. A new theory replaced it. Then, several new extensions were made and incorporated into what people call “evolutionary science.”

We do not need a new term design merely to make Shapiro famous. I’m happy with just calling “evolutionary science” and continuing to extend it as we continue to discover key mechanisms.

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(S. Joshua Swamidass) #4

I should add that @sygarte may have a different view of this than I.

#5

Yes. I have corresponded a little with Sy and love what he’s doing.

Ok. Well, if as Shapiro says, it is true that mutation rates can vary depending on environmental stress (I’m assuming you accept the science here), how are we still able to accurately come up with a mutation rate?

Thanks,

Mark

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(George) #6

@Mark

You mean for bacteria? Or for higher-level organisms?

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#7

Specifically, humans. I don’t know how any of this works. My main question here is: if I accept Shapiro’s Natural Genetic Engineering version of evolution, should I put less trust in the conclusions of population genetics? Perry Marshall accepts the results of Venema’s work (and I would assume, by extension, Buggs’s and Swamidass’s), but I’m just trying to fit all of this together in my own mind.

I’m assuming most subscribers to Shapiro’s thinking would say that we could accept most of the conclusions of population geneticists but whenever Venema says something like “copying error,” we might change that phrase to a word like “transposition,” etc.

But I don’t know. That’s why I’m on here! :slight_smile:

(George) #8

@Mark

Evidence is the key, right? Science is complex… but it is even more complex if things are assumed without evidence.

Bacteria are pretty amazing creatures… with little pieces of DNA floating about detached from any nuclear material… and some sort of epigenetic apparatus that has evolved to make a population of bacteria “less precise” in replicating genetic information during times of stress.

Do we have any expectation that multi-cellular animals have the same capacity?

It is certainly easy enough to test: looking for congenital deformation rates among well fed tribal societies vs. subsistence tribal societies for example. I choose tribal cultures to try to reduce the vagaries of toxic environmental factors that may abound more in modern cultures than in others.

The one thing Doctors Venema and Buggs are quick to do is use a different mutation rate as needed.

#9

“It is certainly easy enough to test: looking for congenital deformation rates among well fed tribal societies vs. subsistence tribal societies for example. I choose tribal cultures to try to reduce the vagaries of toxic environmental factors that may abound more in modern cultures than in others.”> Blockquote

I have no idea what you’re talking about. Care to explain?

(S. Joshua Swamidass) #10

Now that is a totally valid question.

This question is valid too, and your answer help us scope this out:

Well, to be clear, population genetics woudl not be the problem if we got the mutation rate wrong. The problem would be with the mutation rate. We can put the new rate in, and it merely scales the results up or down by some proportion.

But first, let’s clear some underbrush…

That would be odd if he accepts what all of us are saying. Buggs and I disagree with Venema’s work. You can’t agree with all of us simultaneously. Venema wildely overstated the findings of population genetics, and did not even make a sound argument against a bottleneck. So I certainly disagree with his work. Venema’s work is in error, and that became clear in our dialogue on this. Heliocentric Certainty Against a Bottleneck of Two?


So, coming back to your question, how do we know the mutation rates? Keep in mind we only need the average mutation rate over time, so it is okay if their is variability. And we have several independent ways of measuring the average rate, and they all produce approximately the same results:

  1. Counting the number of mutation differences between chimpanzees and humans, then dividing by the number of years that separate us.

  2. Directly measuring the number of mutations between parents and children, after sequencing triads of mothers and fathers and their children.

  3. Measuring the amount ancient DNA from our ancestor’s remains differs from modern humans.

All these methods, and more, produce about the same results. We covered this in the dialogue with Buggs. See here:

And yes bacteria can mutate much quicker. Buggs raised the issue of the Lenski experiments. And agreed with this analysis I offered…

Panel C is important. See how the rate of mutation is a bit higher at first, but then it drops down. Because it is just an initial spike, it just isn’t relevant in the long run. It get’s averaged away by the later lower rates. And these are bacteria too. Mutation rates among humans are much more stable than bacteria. Large mammals have, essentially, a “speed limit” to how many mutations they can endure.

Does that help make sense of this?

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#11

Yes, this helps a lot!!

I’ll take a closer look again tomorrow. My basic takeaway is that if there was some sort of mutation rate that sped up, we would notice it because of the multiple methods involved in calculation. Same way that ice core/other methods can double check the calculations of other dating methods. Is that correct?

I just skimmed what you said, I’ll be able to take a closer look tomorrow.

Thanks a lot.

And…to respond to something before, I’m eastern Orthodox, so inerrancy rarely enters the picture.

Most modern eastern orthodox theologians, much like Catholics, accept the conclusions of mainline (yes, maybe that’s a better word) historical criticism, and inerrancy, if it’s discussed at all, is understood in a very different way than what many Evangelicals mean by it. I feel like a lot of theologians would probably be ok with Dennis Lamoureux’s understanding of inerrancy, although most theologians’ understanding of scripture is far more Christocentric and allegorical. Gregory of Nyssa, following Origen always saw a spiritual meaning in scripture, but there didn’t always have to be a historical/literal one.

There is a young earth group in Eastern Orthodoxy, but most well-known Eastern theologians would not describe themselves that way.

Thanks again!

#12

And maybe I missed something, but I thought Venema ended up appreciating your work even if he disgreed with it in the beginning? https://evolutionnews.org/2018/05/discussion-is-over-on-adam-and-the-genome-former-biologos-fellow-backs-down/

That’s what I meant when I said “by extension.” I can’t speak for Marshall though. Based on that article, it sounds like it eventually came down to semantics between Buggs and Venema. Maybe I’m wrong about this.

-Mark

(Sy Garte) #13

My differences with Josh in this matter of the EES is mostly one of emphasis. I agree that the EES is not a new theory, and therefore I think that comparing it to general relativity (vs. Newtonian mechanics) is a bit overblown. But there is no question that the EES has indeed provided novel insights into the mechanisms of variation. First it must be stated that the leaders of the very loose group of the Third Way are entirely disparate and diverse when it comes to their claims and their science. Shapiro, for example, claims that natural engineering replaces natural selection, which I find absurd. OTOH, Laland and his colleagues studying Niche Construction have indeed opened new avenues for exploration of evolutionary mechanisms that go beyond the Modern Synthesis. Laland and Noble (and others, including Margulis) also have in common a stress on rejection of the gene-centric view that Dawkins made a cornerstone of evolutionary theory, and since population genetics is (by definition) the mathematics of allele frequencies and mutation rates, the anti-gene centric view must to some degree appear to side step population genetics. But Noble’s call for a new mathematics that will take into account the physiology of the entire cell in its interaction with the genome betrays the fact that such formulations do not at present exist. I therefore understand why Joshua, a computational biologist, finds a great deal of this rhetoric to be troubling. And I half agree with him. I would love to see a comprehensive mathematical theory of evolution that goes beyond pop genetics, but I have strong doubts that its possible. (anyway, certainly not by me!).

To sum this all up, my view remains that the EES is potentially exciting, but that its very much a work in progress, and its true that some of its adherents (including myself, and perhaps to some extent, Perry) might have been a bit overly enthusiastic about its prospects. I think the work of Andreas Wagner on gene regulatory theory, and the Laland group, as well as Susan Rosenberg on directed (non random) mutations hold the best promise for moving forward. Meanwhile, I echo Josh’s remarks concerning the need to refrain from attacks on basic evolutionary theory and its defenders, but would also add that the vitriol from a few of the latter toward the third way folks is also unwarranted.

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Ann Gauger's Recent Talk at Biola
What is the Extended Evolutionary Synthesis?
(S. Joshua Swamidass) #14

The key point, @sygarte, is whether EES calls into question the population genetics work we did here.

Help @mark out here. I think you are in agreement that it does not reduce confidence in the TMR4A work.

(S. Joshua Swamidass) #15

Dennis ended up realizing he was wrong, but refused to retract his errors clearly. If you look in the long post at BioLogos, you will see him realize when he made errors. However he did not publicly retract his statements on the blog or elsewhere. Instead he came up with an ad-hoc argument to support his position.

So yes, now he agrees that Buggs and I are correct. However, that represents a major change from his original position.

This is what he claimed at the beginning of the conversation.

That turns out to be wildly overstating the evidence. He just failed to read it correctly. At this point, I do not trust his work on human population size and cannot recommend it.

(Sy Garte) #16

Of course it doesn’t. Other than possibly Shapiro nobody questions the conclusions of population genetics, and certainly not when the subject is the genetic, mutational or genealogical history of humanity.

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(Jon Garvey) #17

Sy, I thought of this when reading the paper Paul Nelson recently linked, which closely examined the business of “reference” and how it affects theories - there are an unbelievable number of entities that formed the backbone of theories, which have simply been shown not to exist. The most interesting, to me, were the various thories of aether which not only covered vast areas of science, but were highly successful in prediction, and so on.

It was Maxwell (if I remember right) who was quoted in the article as saying the aether was the best established fact in physics.

So it does raise the question of the current uncertainty about what exactly a “gene” is, or whether the term has any true reference to reality beyond what the luminiferous aether had. If not, then genetics is going to look a slightly orphaned science as time goes by.

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#18

I have not read his evolutionary tome, but I google searched inside Shapiro’s book, and he never discredits population genetics. In one place (I can’t access it at the moment), he says something like “this data helps us make sense of the population genetics studies.” So at least in that section, he was saying that his approach actually helps makes sense (I think it was of a certain gene being so prevelant in a population) of the results of population genetics.

Glad to have seen some answers in this thread. My general feeling is that the fact that population genetics is even POSSIBLE actually points to ORDER in the evolutionary process. Denton actually makes this point in Nature’s Destiny regarding molecular clocks. And I’ve heard Dennis Alexander make a similar point.

See https://www.premierchristianradio.com/Shows/Saturday/Unbelievable/Episodes/Unbelievable-Should-Christians-embrace-or-reject-Theistic-Evolution-Wayne-Rossiter-Denis-Alexander.

The fact that mutations (beneficial or not) occur at a more or less consistent rate (even taking into account stress induced mutation rates) certainly implies that mutations are not ENTIRELY spontaneous.

Thanks everyone for your input. Let me know if anything I just said is incorrect.

-Mark

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(S. Joshua Swamidass) #19

It is not just possible, it is a fact. There is a hidden order in just about everything, and population genetics (specifically neutral theory) uncovers that order in random mutations. That is how science works. It seeks to find those stable patterns that emerge. The patterns we are making use of are very stable. That is why even EES supporters are going to support the conclusions I made…

As you will see much of the debate betwee the “modern synthesis and EES” is just insider baseball, case in point:

Of course Dawkins is wrong in a gene-centric view. The problem I have with Laland and Nobel (not Margulis) is that they claim this is somehow surprised by other scientists, these mythical “Darwinists” that do not even exist any more. Appealing to Dawkin’s representation of the science is akin to complaining about Bill Nye. These guys are not the leaders of the field (or even in the field in the case of Nye). Their claims are already part of the modern synthesis, and in the case of Margulis, widely celebrated and cited.

Regardless, @Mark, what just about everyone informed will agree is that this does not reduce confidence in the population genetics I’ve made use of here.

Which gets to one error you make:

This gets back to a major misconception, similar to one I’ve heard from @johnnyb.

The mutations do appear to be ENTIRELY spontaneous. The fact they take place in a largely constant rate does not make them less random. That just tells us there is a pattern to their randomness. Remember, random does not imply “without pattern.” Just because there is pattern to random mutations does not mean they are magically not random. It just means they are “random with said pattern.”

This is not a matter of opinion, but one of definitions. Nothing in the definition of “random” precludes that mutations follow patterns. In fact, the statistically definition of “random” itself assumes that mutations follow some patterns.

I think you have a false conflict in your mind between RANDOM and ORDER. That needs to be stamped out if you want to make sense of this.

Perry Marshall: What is Random?
(Curtis Henderson) #20

Welcome, @Mark, good to have a new “face”!

I’m displaying my ignorance here, but isn’t the number of years separating humans and chimps based on mutation rate and overall divergence in the first place? Time = “distance”/rate?

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