Extending evolutionary theory? - Sonia Sultan

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for Sonia Sultan's talk on Developmental plasticity: re-conceiving the genotype.

For several decades, the phenotype of an organism (i.e, its traits and behaviour) has been studied as the outcome of developmental ‘instructions’ coded in its DNA. According to this model, each genotype is expressed as a specific phenotype; individual differences in fitness-related traits are seen to arise from this stably inherited internal information. This simplified view of development provides the foundation for a Modern Synthesis approach to adaptive evolution as a sorting process among genetic variants. As developmental biologists are aware, however, an organism’s phenotype is not strictly pre-determined by its genotype, but rather takes shape through the interplay of genetic factors with the organism’s environmental conditions. By means of this developmental plasticity, a given genotype may express different phenotypes under different environmental conditions. Accordingly, the genotype can be understood as a repertoire of potential developmental outcomes or norm of reaction.

Re-conceiving the genotype as an environmental response repertoire rather than a fixed developmental programme leads to three critical insights, as illustrated by norm of reaction data from Polygonum plants. Plastic responses to specific conditions often comprise functionally appropriate trait adjustments, resulting in an individual-level, developmental mode of adaptive variation. Environmental responses can extend across generations via effects on progeny growth and fitness, a form of inherited yet non-genetic adaptation. Finally, because genotypes are differently expressed depending on the environment, the genetic diversity available to natural selection is itself environmentally contingent.

Here's a possible question ...

Back in the 1960s we learned that transcription of the lac operon in E. coli was regulated by the environment. This regulation, activation or repression, was passed on to daughter cells as the cells divided. Why didn't this discovery lead to a major revision of evolutionary theory?

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Extending evolutionary theory? - Douglas Futuyma

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for Douglas Futuyma's talk on The evolutionary synthesis today: extend or amend?

Evolutionary theory has been extended almost continually since the Evolutionary Synthesis, but the principal tenets of the Synthesis have been strongly supported, the single most important exception being the greater importance accorded genetic drift, especially in molecular evolution. The calls for an extended synthesis today are largely a continuation of this process. Some elements of the EES movement, such as the role of niche construction, are welcome emphases on long recognised but perhaps under-studied processes. The union of population genetic theory with mechanistic understanding of molecular and developmental processes is a potentially productive conjunction of ultimate and proximal causation; but the latter does not replace or invalidate the former. Newly discovered molecular genetic phenomena have been easily accommodated by orthodox evolutionary theory in the past, and this appears to hold also for phenomena such as epigenetic inheritance today. In several of these areas, empirical evidence is needed to evaluate enthusiastic speculation. Evolutionary theory today will continue to be extended, but there is no sign that it requires emendation.

Here are two possible questions for Futuyma.

Why do you think that most participants at this meeting seem to be unaware of random genetic drift and the evolution of structures and phenotypes by nonadaptive processes? Doesn't this strike you as bizarre for a group that's so concerned about evolutionary theory?

As you explain in your textbook, describing the pathways to modern species contributes to the FACT of evolution and the FACT of descent with modification but how those genetic changes actually occur and become fixed is part of evolutionary theory. Do you distinguish between evolutionary theory and the actual history of life?

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Extending evolutionary theory? - Gerd B. Müller

I will be attending the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives. I'll post each of the abstracts and ask for your help in deciding what question to pose to the speakers. Here's the abstract for Gerd B. Müller's talk on The extended evolutionary synthesis.

Since the last major conceptual integration in evolutionary biology – the Modern Synthesis of the 1940s – the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and of multiple inheritance systems, the -omics revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge regarding the mechanisms of evolutionary change. Some of these results are in agreement with the classical Synthetic Theory and others reveal different properties of evolutionary change. A renewed and extended evolutionary synthesis unites pertinent concepts emerging from these novel fields with elements from the standard theory, but it differs from the latter in its core logic and predictive capacities. Whereas the classical theory had concentrated on genes and adaptive variation in populations, the extended framework emphasises the role of constructive processes, environmental induction, and systems dynamics in the evolution of organismal complexity. Single level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, this entails a revised understanding of the role of natural selection in the evolutionary process. The extended evolutionary synthesis complements the traditional gene centric perspective and stimulates research into new areas of evolutionary biology.

There are so many things I could ask. I'm tempted to ask the following question,

Many of us believe that the role of adaptation in evolutionary theory was considerably revised by the development of Neutral Theory and Nearly-Neutral Theory almost 50 years ago. These concepts, and the importance of random genetic drift, have been integrated into the standard textbooks for many decades. Why don't you ever talk about those challenges to the old 1940s version of the Modern Synthesis? Is it because you don't think they were significant additions to the old theory?

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A philosopher's view of random genetic drift

Random genetic drift is a process that alters allele frequencies within a population. The change is due to "random" events. It differs from natural selection where the change is due to selection for alleles that confer selective advantage on the reproductive success of an individual. Here's one description,

If a population is finite in size (as all populations are) and if a given pair of parents have only a small number of offspring, then even in the absence of all selective forces, the frequency of a gene will not be exactly reproduced in the next generation because of sampling error. If in a population of 1000 individuals the frequency of "a" is 0.5 in one generation, then it may by chance be 0.493 or 0.505 in the next generation because of the chance production of a few more or less progeny of each genotype. In the second generation, there is another sampling error based on the new gene frequency, so the frequency of "a" may go from 0.505 to 0.501 or back to 0.498. This process of random fluctuation continues generation after generation, with no force pushing the frequency back to its initial state because the population has no "genetic memory" of its state many generations ago. Each generation is an independent event. The final result of this random change in allele frequency is that the population eventually drifts to p=1 or p=0. After this point, no further change is possible; the population has become homozygous. A different population, isolated from the first, also undergoes this random genetic drift, but it may become homozygous for allele "A", whereas the first population has become homozygous for allele "a". As time goes on, isolated populations diverge from each other, each losing heterozygosity. The variation originally present within populations now appears as variation between populations.

Suzuki, D.T., Griffiths, A.J.F., Miller, J.H. and Lewontin, R.C.
in An Introduction to Genetic Analysis 4th ed. W.H. Freeman (1989 p.704)

Ten adaptationist stories about recent human evolution

Does this video contribute to the general understanding and appreciation of science?

1. Blond hair: PROBABLY FALSE ADAPTATION
2. Lactose tolerance: PROBABLY A TRUE ADAPTATION
3. Eating wheat: PROBABLY FALSE ADAPTATION
4. Losing wisdom teeth: PROBABLY FALSE ADAPTATION
5. Smaller brains: LIKELY FALSE ADAPATION
6. Getting shorter: ALMOST CERTAINLY FALSE
7. Malaria resistance: CERTAINLY TRUE
8. HIV Resistance: TRUE BUT TRIVIAL
9. Male extroverts: PROBABLY FALSE ADAPTATION
10. Having kids earlier: ALMOST CERTAINLY FALSE ADAPTATION

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How many lncRNAs are functional: can sequence comparisons tell us the answer?

A large percentage of the human genome is transcribed at some time or another during development. The vast majority of those transcripts are very rare transcripts that look very much like spurious products of accidental transcription initiation at sequences resembling true promoters. They have been rejected by genome annotators. They do not define genes. They are junk RNA. Pervasive transcription does not mean that most of the genome is functional.

Among the transcripts is a class called long non-coding RNAs or lncRNAs. These are usually defined as capped and polyadenylated transcripts longer than 200 nucleotides. Many of them are processed by splicing. They look a lot like mRNA except they don't encode any polypeptides.¹

We don't know how many of these RNAs exist because different labs use different criteria to describe them. Some databases exclude low abundance lncRNAs and some include non-polyadenylated RNAs. There is general agreement that they number in the tens of thousands. A common number in the scientific literature is 60,000 lncRNAs.

This anti-science creationist could be Vice-President of the United States of America

Thanks to PZ Myers for digging up this speech by Mike Pence in the House of Representatives [Mike Pence, creationist]. I think Pence is trying to make America great again by returning the country to the stone age.

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Paradigm shifting at the Royal Society meeting in November

Suzan Mazur has been making a name for herself by promoting the overthrow of modern evolutionary theory. She began with a lot of hype about the Alternberg 16 back in 2008 and continued with a series of interviews of prominent evolutionary biologists.

Now she's focused on the upcoming meeting in November as another attempt to shift paradigms [see New Trends in Evolutionary Biology: The Program]. She's not entirely wrong. Many of the people involved in those meeting see themselves as paradigm shifters.

New Trends in Evolutionary Biology: The Program

I'm going to London next November to attend The Royal Society conference on New trends in evolutionary biology: biological, philosophical and social science perspectives. This is where all the scientists who want to change evolution will be gathering to spout their claims.

Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution, although the issues involved remain hotly contested. This meeting will present these developments and arguments in a form that will encourage cross-disciplinary discussion and, in particular, involve the humanities and social sciences in order to provide further analytical perspectives and explore the social and philosophical implications.

The program has been published. Here's the list of speakers ...

Gerd B. Müller
The extended evolutionary synthesis

Douglas Futuyma
The evolutionary synthesis today: extend or amend?

Sonia Sultan
Re-conceiving the genotype: developmental plasticity

Russell Lande
Evolution of phenotypic plasticity

Tobias Uller
Heredity and evolutionary theory

John Dupré
The ontology of evolutionary process

Paul Brakefield
Can the way development works bias the path taken by evolution?

Kevin Laland
Niche construction

James Shapiro
Biological action in read-write genome evolution

Paul Griffiths
Genetics/epigenetics in development/evolution

Eva Jablonka
Epigenetic inheritance

Greg Hurst
Symbionts in evolution

Denis Noble
Evolution viewed from medicine and physiology

Andy Gardner
Anthropomorphism in evolutionary biology

Sir Patrick Bateson
The active role of the organism in evolution

Karola Stotz
Developmental niche construction

Tim Lewens
A science of human nature

Agustín Fuentes
Human niche, human behaviour, human nature

Andrew Whiten
The second inheritance system: the extension of biology through culture

Susan Antón
Human evolution, niche construction and plasticity

Melinda Zeder
Domestication as a model system for evolutionary biology

I didn't know that Paul Griffiths and Karola Stotz were going. It's a bit surprising that they would associate with some of these views. I'm glad that Douglas Futuyma will be there to represent the voice of reason. He seems to be one of the few speakers who understands modern evolutionary theory.

There are still a few spots available, according to the organizers. Sign up quickly.

The meeting is at Carlton House Terrace, which is just a few blocks from Trafalger Square and a short walk down The Mall to Buckingham Palace where the Corgis live.

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The Encyclopedia of Evolutionary Biology revisits junk DNA

The Enclyopedia of Evolutionary Biology is a four volume set of articles by leading evolutionary biologists. An online version is available at ScienceDirect. Many universities will have free access.

I was interested in what they had to say about junk DNA and the evolution of large complex genomes. The only article that directly addressed the topic was "Noncoding DNA Evolution: Junk DNA Revisited" by Michael Z. Ludwig of the Department of Ecology and Evolution at the University of Chicago. Ludwig is a Research Associate (Assistant Professor) who works with Martin Kreitman on "Developmental regulation of gene expression and the genetic basis for evolution of regulatory DNA."

As you could guess from the title of the article, Michael Ludwig divides the genome into two fractions; protein-coding genes and noncoding DNA. The fact that organismal complexity doesn't correlate with the number of genes (protein-coding) is a problem that requires an explanation, according to Ludwig. He assumes that the term "junk DNA" was used in the past to account for our lack of knowledge about noncoding DNA.

Eukaryotic genomes mostly consist of DNA that is not translated into protein sequence. However, noncoding DNA (ncDNA) has been little studied relative to proteins. The lack of knowledge about its functional significance has led to hypotheses that much nongenic DNA is useless "junk" (Ohno, 1972) or that it exists only to replicate itself (Doolittle and Sapienza, 1980; Orgel and Crick, 1980).

Ludwig says that we now know some of the functions of non-coding DNA and one of them is regulation of gene expression.

These regulatory sequences are distributed among selfish transposons and middle or short repetitive DNAs. The genome is an extremely complex machine; functionally as well as structurally it is generally not possible to disentangle the regulatory function from the junk selfish activity. The idea of junk DNA needs to be revisited.

Of course we all know about regulatory sequences. We've known about this function of non-coding DNA for half a century. The question that interests us is not whether non-coding DNA has a function but whether a large proportion of noncoding DNA is junk.

Ludwig seems to be arguing that a significant fraction of the mammalian genome is devoted to regulation. He doesn't ever specify what this fraction is but apparently it's large enough to "revisit" junk DNA.

The biggest obstacle to his thesis is the fact that only 8% of the human genome is conserved (Rands et al., 2014). Ludwig says that 1% of the genome is coding DNA and 7% "has a functional regulatory gene expression role" according to the Rands et al. study. This is somewhat misleading since Rands et al. specifically mention that not all of this conserved DNA will be regulatory.

All of this is consistent with a definition of function specifying that it must be under negative selection (i.e. conserved). It leads to the conclusion that about 90% of the human genome is junk. That doesn't require a re-evaluation of junk.

In order to "revisit" junk DNA, the proponents of the "complex machine" view of evolution must come up with plausible reasons why lack of sequence conservation does not rule out function. Ludwig offers up the standard rationales ...

1. Some ultra-conserved sequences don't seem to have a function and this "shows that the extent of sequence conservation is not a good predictor of the functional importance of a sequence."
2. The amount of conserved sequence depends on the alignment and alignment is difficult.
3. About 40%-70% of the noncoding DNA in Drosophila melanogaster is under functional constraint within the species but not between D. melanogaster and D. simulans. Therefore, some large fraction of functional regulatory sequences might only be conserved in the human lineage and it won't show up in comparisons between species. (Does this explain onions?)

The idea here is that there is rapid turnover of functional DNA binding sites required for regulation but the overall fraction of DNA devoted to regulation remains large. This explains why there doesn't seem to be a correlation between the amount of conserved DNA and the amount that can possibly be devoted to regulating gene expression. The argument implies that much more than 7% of the genome is required for regulation. The amount has to be >50% or so in order to justify overthrowing the concept of junk DNA.

That's a ridiculous number, but so is 7%. Imagine that "only" 7% of the genome is functionally involved in regulating expression of the protein-coding genes. That's 224 million base pairs of DNA or approximately 10 thousand base pairs of cis-regulatory elements (CREs) for every protein-coding gene.

There is no evidence whatsoever that even this amount (7%) of DNA is required for regulation but Ludwig would like to think that the actual amount is much greater. The lack of conservation is dismissed by assuming rapid turnover while conserving function and/or stabilizing selection on polymorphic sequences.

The problem here is that Ludwig is constructing a just-so evolutionary story to explain something that doesn't require an explanation. If there's no evidence that a large fraction of the genome is required for regulation then there's no problem that needs explaining. Ludwig does not tell us why he believes that most of our genome is required for regulation. Maybe it's because of ENCODE?

Since this is published in the Encyclopedia of Evolutionary Biolgoy, I assume that this sort of evolutionary argument resonates with many evolutionary biologists. That's sad.

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Rands, C. M., Meader, S., Ponting, C. P., and Lunter, G. (2014) 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage. PLoS Genetics, 10(7), e1004525. [doi: 10.1371/journal.pgen.1004525]

Don't call it "The Theory of Evolution"

By now, we all know that a "theory" in science is much more than idle speculation, a point that has been made repeatedly over the past century. With respect to evolution, the most famous essay is by Stephen Jay Gould: "Evolution as Fact and Theory" and the latest explanation is an article in the New York Times by Carl Zimmer: In Science, It’s Never ‘Just a Theory’.

Unfortunately, it's not that simple and there are many scientists who use "theory" in the sense of hypothesis or speculation [see Facts and theories of evolution according to Dawkins and Coyne]. That's not what I want to talk about today.

What do scientists really mean when they refer to "The Theory of Evolution"? There is no single theory of evolution that covers all the mechanisms of evolution. There's the Theory of Natural Selection, and Neutral Theory, and the Theory of Random Genetic Drift, and a lot of theoretical population genetics. Sometimes you can lump them all together by referring to the Modern Synthesis or Neo-Darwinism. These terms are much more accurate than simply saying "The Theory of Evolution" as long as we all understand what those theories mean.

The problem with "The Theory of Evolution" is not only that it's ambiguous but it's misleading. It implies that there's only one theory to explain evolution. Another problem is that it sounds too much like we're talking about the history of life and saying that it's a "theory" that can be explained by evolution.

Instead of using the phrase "The Theory of Evolution," I think we should be referring to "evolutionary theory," which may come in different flavors. The term "evolutionary theory" encompasses a bunch of different ideas about the mechanisms of evolution and conveys a much more accurate description of the theoretical basis behind evolution. Douglas Futuyma prefers "evolutionary theory" in his textbook Evolution and I think he's right. It allows him to devote individual chapters to "The Theory of Random Genetic Drift" and "The Theory Natural Selection."

Here's how Futuyma explains the concept of theory in his book Evolution 2nd ed. p. 613.

So is evolution a fact or a theory? In light of these definitions, evolution is a scientific fact. That is, descent of all species, with modification, from common ancestors is a hypothesis that in the past 150 years or so has been supported by so much evidence, and so successfully resisted all challenges, that it has become a fact. But this history of evolutionary change is explained by evolutionary theory, the body of statements (about mutation, selection, genetic drift, developmental constraints, and so forth) that together account for the various changes that organisms have undergone. [my emphasis ... LAM]

He makes the same point in the opening pages of his book where he uses both terms when discussing the history of evolutionary theory. (Note that when Darwin used the word "theory" to describe natural selection he was not using it in the same sense as Gould and Zimmer to describe a modern scientific theory. That's why Futuyma uses "hypothesis" in the quote below.)

We now know that Darwin's hypothesis of natural selection on hereditary variation was correct, but we also know that there are more causes of evolution than Darwin realized, and that natural selection and hereditary variation themselves are more complex than he imagined. A body of ideas about the causes of evolution, including mutation, recombination, gene flow, isolation, random genetic drift, the many forms of natural selection, and other factors, constitute our current theory of evolution, or "evolutionary theory." Like all theories in science, it is a work in progress, for we do not yet know the causes of all of evolution, or all the biological phenomena that evolutionary biology will have to explain. Indeed, some details may turn out to be wrong. But the main tenets of the theory, as far as it goes, are so well supported that most biologists confidently accept evolutionary theory as the foundation of the science of life. p. 14 [my emphasis ... LAM]

When you're talking about the mechanisms of evolution, please use "evolutionary theory" instead of "the theory of evolution."

I wish the proponents of the Extended Evolutionary Synthesis would agree that the version of evolutionary theory they wish to extend is the one described by Douglas Futuyma. This would make it easier for them to explain what's wrong with that version and why their proposals are an improvement [see Templeton gives $8 million to prove that there's more to evolution than natural selection].

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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 LynchHere'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.

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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.

When philosophers write about evolution

The latest issue of Evolution: Education and Outreach contains a review of two books about evolution written by philosophers. The author of the review is Egbert Giles Leigh Jr. You can read it for free at: Questions about NeoDarwinism: a review of two books.

The books are,

Mind and Cosmos: Why the Materialist NeoDarwinian Conception of Nature is Almost Certainly False by Thomas Nagel. New York: Oxford University Press, 2012. ISBN 978-0-19-991975-8.

Are You an Illusion? by Mary Midgley. New York, NY: Routledge. 2014. ISBN 978-1-84465-792-6.

Both of these books challenge the idea that random mutation and natural selection can explain the world we see around us today.

The reviewer responds with a defense of natural selection from an adaptationist perspective.

I think Nagel and Midgley are wrong but for different reasons. I think that the history of life is the culmination of many random and accidental events and it could easily have gone in different directions [see Replaying life's tape]. I also think that lots of modern features are epiphenomena and not adaptations. Consciousness, to the extent that it actually exists, is one of them.

Nevertheless, Leigh's review is interesting and informative and I urge you to read it if you are interested in knowing why philosophers attack evolution. It helps us understand, once again, where philosophy is going wrong.

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You need to understand biology if you are going to debate an Intelligent Design Creationist

Last night's debate between Lawrence Krauss, Stephen Meyer, and Denis Lamoureux was very entertaining. I finally got to meet Stephen Meyer in person. (My photographer wasn't very good at focusing.)

There were some interesting exchanges during the debate. I want to talk about one of them.

Krauss tried to hammer Meyer on the "ID is not science" issue using quotes from a judge based on things said by lawyers in the Dover trial.¹ Krauss tried to dismiss ID by saying that it never makes predictions but Meyer countered effectively by pointing out that ID predicts that most of our genome is functional and claiming that the prediction was confirmed by the ENCODE study.

The ID position is that Darwinists predicted that our genome would be full of junk while Intelligent Design Creationists predicted that most of our genome would be functional. ID was correct and Darwinism was wrong, according to this story.

Both Lawrence Krauss and Denis Lamoureux accepted the "fact" that ENCODE was right and most of the DNA in our genome has a function. Krauss was also hampered by his misunderstanding of evolution. It's obvious that he accepts the Richard Dawkins view of evolution so he tried to accommodate the ENCODE results by saying it's what you would expect of natural selection. This is the Richard Dawkins position.

Krauss tried to downplay the issue by saying that ID had not predicted what those functional parts of the genome would be doing but this was a weak rebuttal.

The facts are these ....

• "Darwinists"—those who claim that natural selection is the only game in town—were opposed to the idea that most of our genome is junk. They still are.
• Today, the majority of experts believe that most of our genome is junk in spite of the ENCODE publicity campaign from 2012.
• The ENCODE Consortium has backed off it's original claim and now agrees that they misused the word "function." Some of them blame the media for distorting their position.
• The ID "prediction" has been falsified.

A competent biologist would have known all this and could have challenged Meyer's statement. A biologist would have then demanded that Meyer explain how a genome that is 90% junk fits with Intelligent Design Creationism.

I talked to Denis Lamoureux after the debate to let him know that he was wrong about ENCODE and he was very gracious. I promised to send him more information. A genome full of junk DNA poses no threat to his version of Theistic Evolution.

Lawrence Krauss is an expert on cosmology but he's very weak on biology. I know it's common for physicists to think they are experts in everything but that's just not true. It was demonstrated in last night's debate.

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1. This is a bad strategy. It's better to accept that ID proponents are doing science but just doing it very badly. Meyer ignored the issue of whether ID counted as science. He just presented the scientific case for ID and forced Krauss to respond to his "evidence."

An Intelligent Design Creationist disputes the evolution of citrate utilization in the LTEE ... Lenski responds

Most of you are familiar with the long-term evolution experiment (LTEE) run by Richard Lenski. One of the cultures in that experiment evolved the ability to use citrate as a carbon source. Normally, E. coli cannot use this carbon source under aerobic conditions but the new strain not only utilizes citrate but can grow in cultures where citrate is the only source of organic carbon.

The pathway to this event is complex and requires multiple mutations [see On the unpredictability of evolution and potentiation in Lenski's long-term evolution experiment and Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source].

Darwin's statue

A large statue of Charles Darwin was installed in the main foyer of the London's Natural History Museum in 1885—just a few years after Darwin's death. It was removed in 1927 and replaced by a statue of Richard Owen who was no fan of Darwin.

The museum came to its senses in 2009 and put the statue back in it's original position. (It had been in the cafeteria in the basement.) Read the story at: Moving Darwin.

Owen was the man who founded the museum and he was also known for his support of structuralism—the idea that basic body plans cannot be easily explained by evolution. Structuralism is the new buzzword among Intelligent Design Creationists. They don't understand the concept but they're certain it refutes evolution and supports goddidit.

Michael Denton is upset about the statue [see Conversations with Michael Denton: You Can Move the Statue if You Wish...]. Watch the video ...

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Replaying life's tape

Intelligent Design Creationists are promoting a structuralist view of evolution [What is structuralism?]. The idea is that the history of life as we know it was largely preordained by the initial laws of physics and chemistry. According to this view, once life got under way it was inevitable that it would eventually evolve the way it did resulting in humans or something that closely resembles humans.

Structuralism is based on the idea of intrinsic forms that severely limit evolutionary pathways. These forms are constrained, and defined, by the physics of matter and energy. Some creationists like this idea because they believe that god created the universe and fine-tuned it for life. According to their faith, once the original laws of physics and chemistry were set up it was just a matter of time before humans evolved. These creationists can make their belief in a creator god compatible with evolution as they see it.

(Let's not forget that there are many structuralists who are legitimate scientists and some of them are atheists. Structuralism is not a creationist invention.)

The conflict between structuralists and others is brought into focus by Stephen Jay Gould writing in Wonderful Life.

What is "structuralism"?

The Intelligent Design Creationists are promoting Michael Denton's new book Evolution: Still a Theory in Crisis. The new buzzword is "structuralism" and it's guaranteed to impress the creationist crowd because nobody understands what it means but it sounds very "sciency" and philosophical. Also, it's an attack on "Darwinism" and anything that refutes evolution has to be good.

You can watch Michael Denton explain structuralism ... it only takes a few minutes of your time.

"The Selfish Gene" turns 40

Richard Dawkins published The Selfish Gene 40 years ago and Matt Ridley notes the anniversary in a Nature article published today (Jan. 28, 2016): In retrospect: The selfish gene.

I don't remember when I first read it—probably the following year when the paperback version came out. I found it quite interesting but I was a bit put off by the emphasis on adaptation (taken from George Williams) and the idea of inclusive fitness (from W.D. Hamilton). I also didn't much like the distinction between vehicles and replicators and the idea that it was the gene, not the individual, that was the unit of selection ("selection" not "evolution").

It is finally time to return to the problem with which we started, to the tension between individual organism and gene as rival candidates for the central role in natural selection...One way of sorting this whole matter out is to use the terms ‘replicator’ and ‘vehicle’. The fundamental units of natural selection, the basic things that survive or fail to survive, that form lineages of identical copies with occasional random mutations, are called replicators. DNA molecules are replicators. They generally, for reasons that we shall come to, gang together into large communal survival machines or ‘vehicles’.

Richard Dawkins

Richard Dawkins makes a mistake when describing why gene trees are evidence of evolution

Back in 2010, Richard Dawkins was answering questions on Reddit and one of the questions was "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory."

There are several ways to answer this question. Personally, I would take a minute to explain the difference between the "theory of evolution" and the history of life. I would point out that evolutionary theory includes things like Darwin's natural selection and there is overwhelming evidence proving that natural selection exists and operates today. The entire field of population genetics, which included other mechanisms of evolution such as random genetic drift, is massively supported by thousands of published papers in the scientific literature. There is absolutely no doubt at all that the current basic tenets of evolutionary theory are correct.