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Friday, April 22, 2016

Templeton gives $8 million to prove that there's more to evolution than natural selection

The Templeton Foundation will fund a group of researchers who promote something called "The Extended Evolutionary Synthesis" (EES). The grant is for $8 million (US). The project is headed by Kevin N, Laland of the University of St. Andrews (Scotland, UK) and Tobias Uller of Lund University in Sweden. You can read all about it at: Putting the Extended Evolutionary Synthesis to the Test.

There are two problems with this funding. The first is the source of the funds. I agree with Jerry Coyne and many others that Templeton Fund money is tainted because the clear purpose of the fund is to lend credence to religion [Templeton keeps up the woo]. Templeton will only fund projects that advance that objective.

The second problem is the science. The advocates of EES promote things like "developmental plasticity," "niche construction," "evo-devo," and "epigenetics"—all of these phenomena are supposed to play a major role in evolutionary theory, a role that is not covered by the Modern Synthesis.

I think that all of these processes may play a role in explaining the history of life on Earth1 but so do plate tectonics, asteroid impacts, and endosymbiosis. The problem is that there's a difference between explaining the events behind the history of life and evolutionary theory. They are not the same thing.

The real question is whether any of these things need to be incorporated into modern evolutionary theory and whether they extend the Modern Synthesis. Personally, I don't think any of them make a significant contribution to evolutionary theory.

But my real beef is with the outdated view of evolution held by EES proponents. To a large extent they are fighting a strawman version of evolution. They think that the "Modern Synthesis" or "Neo-Darwinism" is the current view of evolutionary theory. They are attacking the old-fashioned view of evolutionary theory that was common in the 1960s but was greatly modified by the incorporation of Neutral Theory and increased emphasis on random genetic drift. The EES proponents all seem to have been asleep when the real revolution occurred.

When you listen to them, you get the distinct impression they have never read The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. I have no confidence in biologists who want to overthrow a view of evolutionary theory that's already been dead for half a century. I have no confidence in biologists who aren't at ease talking about non-adaptive evolution. This is the 21st century.2

Elizabeth Pennisi is all over this. She wrote an article for the April 22 (2016) edition of Science: Templeton grant funds evolution rethink. The opening sentence is very revealing ....
For many evolutionary biologists, nothing gets their dander up faster than proposing that evolution is anything other than the process of natural selection, acting on random mutations.
Damn right! I'm not an evolutionary biologist but my dander gets up whenever scientists make such a ridiculous claim.

Help is one the way, according to Elizabeth Pennisi because the Templeton Foundation is funding research to show that there's more to evolution than natural selection. Unfortunately, the "extended" version doesn't include random genetic drift and modern population genetics.
No wonder some evolutionary biologists are uneasy with an $8.7 million grant to U.K., Swedish, and U.S. researchers for experimental and theoretical work intended to put a revisionist view of evolution, the so-called extended evolutionary synthesis, on a sounder footing. Using a variety of plants, animals, and microbes, the researchers will study the possibility that organisms can influence their own evolution and that inheritance can take place through routes other than the genetic material.
I don't object to work on those subjects. My beef is with the idea that they pose a problem for our current understanding of evolutionary theory. More importantly, my main complaint is that the biologists who will spend all this money missed the real revolution that took place 50 years ago.

Here's how Pennisi describes the extended evolutionary synthesis. Her description is pretty accurate.
The extended evolutionary synthesis is a term coined in 2007 to imply that the preeminent current evolutionary theory, the so-called modern synthesis, needed to broaden its focus because it concentrated too much on the role of genes in evolution and lacked adequate incorporation of new insights from development and other areas of biology. The idea has gradually gathered momentum since its advocates first met in Germany in 2008 (Science, 11 July 2008, p. 196). Later, Kevin Laland, an evolutionary biologist at the University of St. Andrews in the United Kingdom, and several colleagues took up the cause, arranging for a point-counterpoint discussion in Nature in 2014 and a comprehensive review last year in the Proceedings of the Royal Society B's annual Darwin Review.

Advocates stress that animals, plants, and even microbes modify their environments, exhibit plasticity in their physical traits, and behave differently depending on the conditions they face. Chemical modifications of the DNA that affect gene activity—so-called epigenetic changes—seem to explain some of this flexibility. These and other factors suggest to some biologists that an organism's development is not simply programmed by the genetic sequences it inherits. For them, such plasticity implies that parents can influence offspring not just through their DNA but by passing on the microorganisms they host or by transmitting epigenetic marks to subsequent generations. “Innovation may be a developmental response that becomes stabilized through genetic changes,” explains Armin Moczek, an evolutionary developmental biologist at Indiana University, Bloomington.

Nor is evolution controlled only by natural selection, the winnowing process by which the fittest survive and reproduce, Laland and others argue. Organisms, by transforming their environments and responding to environmental factors, help control its course, they contend. As such, the extended synthesis “represents a nascent alternative conceptual framework for evolutionary biology,” Laland and dozens of colleagues wrote in a funding proposal to the Templeton Foundation last year.
This is a profoundly adaptationist view of evolutionary theory. The "extended" version merely adds a few more mechanisms that might improve adaptation.

Most of the EES proponents are working on animals, many are physiologists. They share an evo-devo view of evolution that emphasizes the role of natural selection. I share Michael Lynch's view that we live in a post-Darwinian world and nothing in evolution makes sense except in the light of population genetics. I agree with him that most scientists think of evolution as a soft science and that includes many biologists. It includes most of the EES proponents who probably couldn't tell you anything about population genetics beyond the fact that it's too mathematical. That doesn't stop them from criticizing modern evolutionary theory.

Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.

Michael Lynch
Here's a quote from Michael Lynch's book The Origins of Genome Architecture. In my view, it describes the group who were awarded $8 million to overthrow modern evolutionary theory.
Despite the tremendous theoretical and physical resources now available, the field of evolutionary biology continues to be widely perceived as a soft science. Here I am referring not to the problems associated with those pushing the view that life was created by an intelligent designer, but to a more significant internal issue: a subset of academics who consider themselves strong advocates of evolution but who see no compelling reason to probe the substantial knowledge base of the field. Although this is a heavy charge, it is easy to document. For example, in his 2001 presidential address to the Society for the Study of Evolution, Nick Barton presented a survey that demonstrated that about half of the recent literature devoted to evolutionary issues is far removed from mainstream evolutionary biology.

With the possible exception of behavior, evolutionary biology is treated unlike any other science. Philosophers, sociologists, and ethicists expound on the central role of evolutionary theory in understanding our place in the world. Physicists excited about biocomplexity and computer scientists enamored with genetic algorithms promise a bold new understanding of evolution, and similar claims are made in the emerging field of evolutionary psychology (and its derivatives in political science, economics, and even the humanities). Numerous popularizers of evolution, some with careers focused on defending the teaching of evolution in public schools, are entirely satisfied that a blind adherence to the Darwinian concept of natural selection is a license for such activities. A commonality among all these groups is the near-absence of an appreciation of the most fundamental principles of evolution. Unfortunately, this list extends deep within the life sciences.
The real revolution was the incorporation of nonadaptive mechanisms into evolutionary theory and the overthrow of adaptationism. That revolution is not complete. There are still thousands of biologists who remain strict Darwinists even as they try to promote different ways of achieving adaptation. Those biologists still dominate the popular press (e.g. Elizabeth Pennisi) and they are largely responsible for skepticism about junk DNA. That has to change. Evo-devo types need to listen to Michael Lynch when he says ...
Unfortunately, the emerging field of evolutionary developmental biology is based almost entirely on a paradigm of natural selection, and the near-absence of the concept of nonadaptive processes from the lexicon of those concerned with cellular and developmental evolution does not follow from any formal demonstration of the negligible contribution of such mechanisms but simply reflects the failure to consider them. [my emphasis ... LAM] There is no fundamental reason why cellular and developmental features should be uniquely immune to nonadaptive evolutionary forces. One could even argue that the stringency of natural selection is reduced in complex organisms with behavioral and/or growth from flexibilities that allow individuals to match their phenotypic capabilities to the local environment.

1. Some of them are trivial and some are ineffective but that's been debated many times. I want to emphasize the fact that EES proponents don't understand modern evolutionary theory.

2. To be fair, some of these proponents do pay lip-service to non-adaptive evolution from time to time but it's clear that they don't really get it.


Faizal Ali said...

How do you see this furthering the Templeton agenda? I can see this providing encouragement to the creationists, but I don't see how it supports accommodationism.

Faizal Ali said...

To be clear, I don't doubt your opinion regarding the Templeton Foundation's motivations. I'm just unclear on this furthers their agenda. Unless they think that anything that weakens "Darwinism" also weakens atheism.

S Johnson said...

The "straw man version" is the pop science version. Natural selection =adaptationism, and adaptationism=natural selection. Rejecting junk DNA is simply rejection natural selection of the gene, but natural selection still ensures the extended phenotype is adaptive. Gould's essays remain but he is increasingly disreputable. Eldredge is increasingly obscure. And Lewontin is now a fallacy. In pop science, the spandrels of San Marco are at best a dead end. At worst they border on criminal misrepresentation...which is what Gould is supposed to have done in The Mismeasure of Man. In a pop science context, the ferocious condemnation of dissent is affirmation of adaptationism.

"The problem is that there's a difference between explaining the events behind the history of life and evolutionary theory. They are not the same thing." That sounds a little like saying galaxy formation and cosmological theory, or plate tectonics and geological theory, aren't the same thing. Wouldn't it make just as much sense to say that a history isn't the same thing as history?

OgreMkV said...

That's mostly it. If they can drive a wedge in and say "look evolution is wrong"... then conveniently forget to mention that they are talking about outdated versions of evolution or modified versions of evolution, then they can reignite ID or creationism.

Faizal Ali said...

I don't think the Templeton Foundation supports creationism, including the ID variant. Rather, it promotes the idea that religion is compatible with mainstream science.

Unknown said...

Evolutionary theory is necessary, but not sufficient, to explain the history of life because a full explanation also requires plate tectonics/ continental drift, meteor strikes, climate change (some with abiotic causes, some with biotic but non-anthropogenic causes), etc.

As for the EES, if a phenomenon doesn't extend across generations (i.e. is not heritable), then it doesn't involve evolution, no matter how biologically important it is.


judmarc said...

I thought I recognized Pennisi's name (I get a newsletter with thumbnail summaries of recent articles in Science.

Bjørn Østman said...

To me the whole thing is a non-issue. but that may be because I have only been doing evolutionary theory for a little over a decade. I simply don't have all the baggage of the modern synthesis, but wholly embrace evo-devo, evolvability, plasticity, and stochasticity (how we should properly think of drift vs. selection, in my opinion), etc. I suspect that this is true for the recent and coming generations of biologists who actually learn about evolutionary theory, rather than those who just create phylogenies from molecular data, for example.

Bjørn Østman said...

So basically, "$8 million to prove that there's more to evolution than natural selection" sounds like a complete joke. It's already proven, and any serious evolutionary biologists knows this well. Those who don't won't influence the field anyway.

Larry Moran said...

The history of the formation of our particular solar system and gravitational theory are not the same thing.

SRM said...

No, it wouldn't be that they hope to disprove evolution, the goal is more subtle.

It is basically an attempt to show that "science doesn't know everything" at any given time (big surprise, eh). This opens the door to the notion that, just maybe, other ways of knowing things should not be discarded too hastily, since science is evidently not an immediate and direct pathway to absolute truth. Ridiculous of course, since no scientist would ever make such claims anyway.

At the same time, if new discoveries can be made in what is (they think) settled science, this opens the door to the idea that maybe there are mysterious and numinous aspects of life that escape conventional science.

It is basically a soft-sell version of anti-science by people who a) don't understand the scientific process and b) cannot accept that the scientific process, whatever its limitations, is the only reliable pathway to knowledge for humans.

Robert Byers said...

Do these biologists not know and keep up with current ideas in evolution? I understand they have new ideas to improve evolutionary claims and now some money. Public taxpayers pay for evolutionist research and no creationist stuff.
this group might have a religious agenda and not support ID/YEC.
why not support free money to researchers in these things?
Everybody these days thinks the old evolution ideas don't work. so this is another group looking for reform as opposed to revolution.
However iD/YEC is the revolution.

S Johnson said...

I see. There's mere history and there's real science. The real science is predictive, experimental, laboratory tested and the other is just stories.

In pop science, adaptationists fetishize natural selection as the fundamental law of nature, superior to historical stuff like random genetic drift. In pop science, it's why sexual selection is all about fitness markers, i.e., adaptationist. It's why Jerry Coyne's recent pop science discussion of zebras can dismiss the notion that the stripes are not adaptive. Natural selection is the fundamental law, like gravitational theory.

PS Modern gravitational theory, aka general relativity, plays little or no role in studies on the history of our solar system. Orbital mechanics does, but it's still Newtonian. The development of orbital mechanics was based on astronomical observations, not laboratory experiments nor theoretical models. Doesn't affect your point, of course, just compulsive neatness on my part.

Faizal Ali said...

Do these biologists not know and keep up with current ideas in evolution?

It would appear not.

Tim Tyler said...

What about their "extended inheritance" section? Evolutionary theory failed to get to grips with cultural evolution until fairly recently. That's pretty big, important and is fairly directly to do with evolutionary theory.

Larry Moran said...

There are more than 10 million species. How many have been significantly affected by cultural evolution in the past one thousand years?

Unknown said...

Evolutionary theory has to do with biology and genetic inheritance. Cultural evolution, not so much.


Jmac said...

I've always thought that the objective of scientific research and experimentation was and still is to reveal the truth and not to support preconceived ideas...

If Larry, Coyne and many others believe the above, why would they fear other scientists trying to prove what they already know to be the truth? Unless...

Tim Tyler said...

What has that got to do with anything? Cultural evolution is critical to the evolution of our own species. If you are trying to make out that cultural evolution is somehow not important, you are sorely mistaken.

Unknown said...

And again with the misrepresentation of Gould... The Spandrels paper does mention some problems with adaptionism, but the main focus of the paper is the particular problem with adaptionism that arises from Evo-Devo. As G&L look at Weismanns view that natural selection is omnipotent, their key objection is that this misses constraints imposed by development, which do lead to a general non-independence of "traits" (which they identify as usually not taking into account organismal development). In later work Gould gave the use of the umbilicus as a brooding chamber in some snail species as an example for exaptation of a spandrel. It's worth noting here that the shell morphospace introduced by Raup was based on growth patterns in mollusks (also see Erwin, DH (2007) "Disparity: Morphological pattern and developmental context for a more recent view). Raup uses a 3D-Morphospace, which nevertheless recovers most shell morphologies. This means that most of the "traits" one could identify when looking at mollusk shell morphology are not independent from each other. And relevantly, umbilici arise in a substantial fraction of the morphospace (and doe show up in s substantial number of taxa as well). It's worth noting that most theoretical morphospaces are based on developmental pathways (so you get branching patterns for plants from their growth patterns for instance). Hence pointing out that umbilici are not a trait, but a byproduct of the way shells are produced by organisms during their development given a sizable subset of parameters makes the argument that they are adaptations to current utilizations incorrect.

You can not make the claim that evo-devo does not make a significant contribution to evolutionary theory and then cite the Spandrels paper in support, because it is vehemently arguing the opposite.

Jon Fleming said...

GR reduces to NM for low speeds and gravitational effects. Therefore orbital mechanics is GR, just not the hard version.

Larry Moran said...

I did not say that the Spandrels paper was only about random genetic drift and neutral theory. I mentioned it because it is a famous paper that promotes nonadaptive mechanisms and those mechanisms were not a part of the Modern Synthesis.

They cover several alternatives to adaptationism and #1 is "no adaptation and no selection at all." In that section they mention fixation of alleles by random genetic drift, fixation of deleterious alleles in small populations, and the inefficiently of natural selection when the selection coefficient is small (because the probability of fixation is approximately 2s).

They do discuss constraints, of course, but it's not a "misrepresentation" of Gould & Lewontin to say that they were also aware of random genetic drift and neutral alleles.

There are two kinds of constraints; phyletic constraints and developmental constraints. Both of these ideas come from studying whole organisms and their development. It's the concepts of constraints—limitations on the power of natural selection—that are important and these concepts were around long before the modern "evo-devo" fad got going.

If the only contribution of "evo-devo" is the idea of constraints then we clearly don't need to "extend" the Modern Synthesis based on recent discoveries in the field of evo-devo since Gould (and others) already new about that over 35 years ago. In fact, Gould wrote an entire book about the subject in 1977.

daedalus2u said...

The "problem" humans have with evolutionary theory is that it is humans that are trying to study it using human cognition.

Humans cognition evolved. Unfortunately during that evolutionary process, sensory systems became strongly biased to detect "agency", even when it is not there. This is understandable, because ancestors that had many false-positive detections of predators have many more descendants than the non-ancestors with too many (as in one too many) false-negative non-detection of a predator (who are non-ancestors because they were eaten by that single false-negative).

Human hyperactive agency detection compels human cognition to try and find “the agent” that is “causing” the “thing that needs explanation”. The Templeton organization feels that this necessary “agent” is God. For a while it was thought that life required a mythic “vital agent” as in Vitalism. That has pretty much been abandoned for the concept of “homeostasis”, a not-quite mythic “agent” that sort-of does the same thing; keep everything in a living organism “alive”.

Many researchers now, are trying to find “the agent” in the “genome”, or in “development”, or in “junk DNA”, or in “something”. This is the same problem that those trying to find the “agent” of consciousness are having, and so they are looking for it in quantum woo-woo. There isn't an “agent” of consciousness. Consciousness is an emergent property of an assembly of matter. There is no “top-down agent” of consciousness.

An “agent” is a top-down causal agent. The problem with looking for a top-down “cause” of development is that before development happens, there is no “top”. With no “top”, there can be no “top-down development”. There is no homunculus that is the “agent” of consciousness, or the “agent” of the cell, or the “agent” of the genome, or the “agent” of evolution.

judmarc said...

In pop science, adaptationists fetishize natural selection as the fundamental law of nature, superior to historical stuff like random genetic drift.


PS Modern gravitational theory, aka general relativity, plays little or no role in studies on the history of our solar system. Orbital mechanics does, but it's still Newtonian. The development of orbital mechanics was based on astronomical observations, not laboratory experiments nor theoretical models. Doesn't affect your point, of course, just compulsive neatness on my part.

What a load of ignorant bollocks. Drift and selection emerge from the same population genetics equations, and both explain the historical evolutionary record. There is no division between law and history such as you are trying to conjure.

As for orbital mechanics being based on historical observation rather than experimentation or theoretical models, is your education so impoverished you really think Galileo did no experiments, nor Newton any theoretical models?

judmarc said...

The fact that biological evolution and cultural evolution share a word does not mean they share a great deal that is important about the science of biological evolution.

Unknown said...

They do discuss constraints, of course, but it's not a "misrepresentation" of Gould & Lewontin to say that they were also aware of random genetic drift and neutral alleles.

It is a misrepresentation to claim that that was their main point, I cringe when I read their #1, precisely because stating that the probability of fixation is 2s is usually wrong (sometimes by a lot) and the way you stated this in your post (and they did as well) implies that 2s is reasonable for small populations (when it is a limit for infinitely large populations - and small s, but they still need to be somewhat larger than 1/N and well out of near-neutral range, in fact it's the tail end of the distribution for selection coefficients - for mitochondiral genes in Primates you can estimate that 1 in 40 million mutations has a positive selection coefficient that large. Here's how not to make an argument for the importance of "no selection at all": Use an approximation that is only valid when there is rather strong positive selection. Anything for which 2s is a reasonable probability of fixation is certainly adaptive).

It's the concepts of constraints—limitations on the power of natural selection—that are important and these concepts were around long before the modern "evo-devo" fad got going.

Well, the "fad" got going with Goulds Phylogeny and Ontogeny. Evo-devo is certainly not limited to understanding that there are constraints, but one of the key question revolves around how developmental and phyletic constraints are linked.

Tim Tyler said...

There's now a substantial literature on Darwinian cultural evolution. Cultural evolution and organic evolution share lot more than just the word 'evolution'. The general theory of evolution covers them both. If you don't think there's much overlap, you have some literature to catch up on.

judmarc said...

I've used historical development of language as an analogy here, so I'm aware of some parallelism. To suggest that it is a failure of biological evolutionary theory to spend more time on cultural evolution is not a valid conclusion from the fact of that parallelism and its occasional usefulness.

Larry Moran said...

I cringe when I read their #1, precisely because stating that the probability of fixation is 2s is usually wrong (sometimes by a lot) ...

This is called nitpicking ...

Larry Moran said...

Well, the "fad" got going with Goulds Phylogeny and Ontogeny.

No, it didn't. The "fad" part is only about 20-25 years old. Before then, were no calls for revising fundamental evolutionary theory based on evo-devo.

Gould's book, and subsequent discoveries, are mostly concerned with the history of life on Earth. Developmental biology helps us make sense of the particular paths that modern lineages took to get where they are today.

But let's say you are correct. Let's assume that our understanding of developmental biology has been incorporated into modern evolutionary theory beginning with Gould. If that's true, then why all the fuss in 2016 about expanding the Modern Synthesis by adding evo-devo?

The EES proponents want to add "evolvability" to evolutionary theory. That's something that Gould rejects on good solid grounds based on modern evolutionary theory. That debate is fifteen years old and evo-devo lost.

Unknown said...

It really isn't. I shows that G&L did not have a firm grasp of neutral theory, Gould was too far removed from population genetics and Lewontin thought that the high degree of polymorphism was likely due to balancing selection rather than a high number of neutral alleles at the time.

Dk said...

SRM - I have no clue who or what this organisation is, but going by your comment, I can't see what your objection and/or complaint is. They say:

1) Don't want to disprove evolution (You agree)
2) Science doesn't know everything (You agree)
3) There are other ways of knowing things (You agree)
4) We should not just impulsively disregard those other ways (You agree)
5) Science is (evidently) not an immediate and direct pathway to "absolute truth" (You agree)
6) No Scientist would contradict (or say the opposite) to the above. (You agree)

None of this can hardly be considered "soft-sell version of anti-science". So perhaps it's something else?

Your third paragraph wasn't altogether clear, but i'll try to interpret it the best I can.

7) *If* the scientific method can discover some numinous and mysterious qualities exist in nature, or make some discoveries that were not anticipated by strictly scientific predictions, accounts or conventions this tends to support a limitation on science (or is positive for religion). (You agree, that science has some limitations in your last sentence, so I'll go with "religion", as the 'anti-science' element that you think this last statement implies).

So given that it is after this comment, you make a comment about them being anti-science, I am guessing this is the correlation or connection.

But surely (7) is not "anti" Science, if it merely points out that scientific inquiry has limitations, even you seem to grant that. But perhaps you think this because you are a person who thinks that, whatever scientific limitations exist, that science remains to be seen as: "the only reliable pathway to knowledge of human beings", which is just a soft form of a dressed up, reincarnated Scientism.

It is not that surprising that an adherent of such a view-point would consider such mild commentary to be "softly anti-science". But pointing out science has restrictions, or that Science could run into phenomena that were not predicted that vindicate some luminous quality to reality, nature, the universe or our existence, is perhaps the softest way or form of actually saying of testing the parameters of scientific knowledge, in other words if it is found true, we can *confirm* even in an indirect *scientific manner* that some things are outside of scientific comprehension. That is literally the simplest "test", one could construe of in order to test the scope of the scientific paradigm. Again it's totally neutral in principle (even if a religious organisation says it). And you yourself are inclined to admit these limitations (however minimal) do exist. So that can hardly be anti-science.

I suppose that one consequence of that, is that it may corroborate a religious notion. But this is hardly exclusively a religious claim. There are many Atheists and Theist alike who think that life has an ultimate paradoxical or mysterious element. And there are countless irreligious people (among them materialists, agnostics and atheists)who think that science can't explain a whole bunch of stuff, e.g. consciousness phenomenology, even (in that case) including Sam Harris.

So it seems from what I've read, I haven't seen anything even "subtly" scientific. But I do see a kind of "anti-religion" sentiment here, which seems to be the driving force of this conclusion that doesn't follow any of it's premises.