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Tuesday, December 17, 2013

Arlin Stoltzfus explains evolutionary theory

A few days ago, I asked the following questions, Is the "Modern Synthesis" effectively dead?, and What do they mean when they say they want to extend the Modern Synthesis?. The point I was trying to make was that there are many different views on evolutionary theory and it's often difficult to figure out which version of evolutionary theory someone is defending.

For example, which version of evolutionary theory is compatible with the "selfish gene" as a metaphor for evolution? Or for adaptation? Which version of the "Modern Synthesis" is being attacked in the book edited by Massimo Pigliucci and Gerd Müller? Is it the version defended by Ernst Mayr? Does it incorporate Neutral Theory and random genetic drift?


I'm not an expert on the history of evolutionary theory as Arlin Stoltzfus pointed out in the comments. He said,
Every scientist with a PhD knows that it takes years of study to be an expert-- you not only have to ingest hundreds of books and papers, you have to digest this information, sifting it and evaluating it, and converting it into knowledge and judgment. Yet evolutionists all think they are automatic experts on the topic of "the Modern Synthesis" or "the history of evolutionary thought" without doing original research on it, or reading hundreds of secondary sources.
He is correct. I hope I didn't try to give the impression that I'm anything more than an informed spectator. In my defense, I think I'm at least aware of the fact that the "Modern Synthesis" isn't as obvious as most people think. Neither is "neo-Darwinism."

Here's the rest of Arlin's lengthy comment ...
Scientists' views of their history are based largely on b***s*** written by other scientists in the Introduction and Conclusion sections of their papers, and books written by old scientists who claim to have authority because they were there. Ernst Mayr, who has been far too influential, was a Lamarckian systematist pondering birds in a dusty museum during the time that the 20th century genetical view of evolution was being built by others-- people conducting genetical experiments, analyzing data using statistics, and developing mathematical models that Mayr understood only secondarily, through the interpretations of others. He wasn't there. Mayr's version of history was basically to tell unflattering stories about how intellectual opponents were misled by prejudices, due to "essentialism" or "typology" etc. Historians have thoroughly discredited Mayr's main ideas. Although Gould actually did read extensively about the topic of history, his magnum opus attributes some kind of psychological problem to every single scientist who comes out against Darwin. Shame on Gould.

To know what the Modern Synthesis means, you actually have to do a research project that takes years. That sucks. In an ideal world, what the "Modern Synthesis" means would be clearer. But it isn't. I could explain it in a few sentences, but you wouldn't believe me because the explanation has to come with a huge justification.

The reason that so much justification is needed is that there are droves of scientists who-- for reasons that I can't fathom-- imagine they are doing the right thing by defending the idea that the Modern Synthesis covers whatever we think today, without bothering to consider that proposition skeptically, as a hypothesis. In fact, the mainstream of evolutionary thinking today includes views that were considered "non-Darwinian" and "anti-Darwinian" a century ago, such as the view that evolution depends frequently on new mutations, or the view that selection is not creative but merely sorts out pre-existing genetic varieties.

To understand history, one must begin by tossing out a false conception of change as a set of continuous shifts along pre-existing dimensions (i.e., Darwinists think history works in the same way they think evolution works). The history of evolutionary thought cannot be described by moving a variety of sliders. For instance, today most of us think that an allele fixation (by selection or drift) is the unit event in evolution, and we tend to think of evolution as a Markov chain of such events. It makes sense in this view to tally up fixations by drift vs. fixations by selection. This is a familiar idea to us. A generation of evolutionists were raised with the idea that the most important question in evolution is what fraction of changes are due to drift vs. selection. However, 70 years ago this question would not have made sense because they just did not think about evolution in this way. The Modern Synthesis was very much a reaction against the idea that evolution can be understood as 2-step origin-fixation process. That was "mutationism". I see no evidence that biologists 70 years ago had a clear concept of fixations by drift as an evolutionary process. So, with apologies to Larry, we cannot understand the history of evolutionary thinking by asking questions like this.
Arlin Soltzfus published a series of articles on Sandwalk a few years ago. It was largely a defense of mutationism—a concept that certainly needs defeinding since almost everyone has a knee-jerk reaction against it. But most of Arlin's posts were devoted to a discussion of evolutionary theory, including the Modern Synthesis.

Anyone who's really interested in becoming an informed spectator, as I was, should read these posts. I've given you the links below.

And if you are really ready for some serious critical thinking on the subject, you should read Arlin's article on Constructive Neutral Evolution. I also suggest you read the interview with Arlin on Kele's Science Blog: Conversation with Arlin Stoltzfus.

Warning, this might be more that the average biologist can handle. ENCODE scientists should stop reading right now.

March 19, 2010
Introduction to "The Curious Disconnect"
Arlin Stoltzfus says,
This way of thinking suggested that mutational-developmental bias in the introduction of variation was a general cause of evolutionary bias or direction. That contradicted two things I knew about evolutionary thinking. First, I knew that the notion of "internal" variational causes of direction, called "orthogenesis", had been rejected as a heresy. Second, I knew that, among contemporary researchers, mutation bias was not seen as a general bias on the course of evolution, but as a special aspect of neutral evolution, incompatible with selection.

The mutationism myth tells the story of how, just over a century ago, the scientific community responded to the discovery of Mendelian genetics by discarding Darwinism, and how Darwinism subsequently was restored.March 30, 2010
The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion
Arlin Stoltzfus says,
Our journey to explore The Curious Disconnect-- the gap between how we think about evolution and how we might think if we were freed from historical baggage-- begins with the Mutationism Myth. In this, the first of four parts, we are not going to confront any tough scientific or conceptual issues. Instead, we are just going to review an odd story about our intellectual history.

April 16, 2012
Theory vs Theory
A theory1 contains a major supposition or unproved conjecture about the world. Kimura's Neutral Theory is the conjecture that most changes at the "molecular level" represent the random fixation of effectively neutral alleles. Darwin proposed, but could not prove, that all large-scale evolutionary changes were built from infinitesimal increments of change that emerged by a process of hereditary "fluctuation". A theory1 takes risks: in Popperian terms, its subject to empirical refutation; in the words of Huxley, a beautiful theory1 can be "killed by an ugly fact."

The relevant standard of validity for theory2 is not verisimilitude (trueness to life), but consistency: the principles derived in the theory are consistent with its assumptions. Importantly, new principles added to a body of theory2 are consistent with previous principles, except in the sense that a body of theory2 may be subdivided into branches that cover non-overlapping universes. If they are not, a logical error has occurred.

May 4, 2010
The Mutationism Myth, II. Revolution
Arlin Stoltfus says,
Our journey to map out the Curious Disconnect— the gap between how we think about evolution and how we might think if we were freed from historical baggage— began with The Mutationism Myth, part 1. Then, in Theory vs Theory, we took a brief detour to distinguish theory1 (grand conjecture) from theory2 (body of abstract principles). Today we are back to the Mutationism Myth and our goal is to probe its claim that the scientific community rejected Darwin's ideas on erroneous grounds.

May 20, 2010
The Mutationism Myth: III Foundations of Evolutionary Genetics
Arlin Stoltfus says,
Today in the Curious Disconnect we continue with our series on the Mutationism Myth. In this oft-told story (see part 1), the discovery of genetics in 1900 leads to rejection of Darwin's theory and the rise of "mutationism", a laughable1 theory that imagines evolution by mutation alone, without selection. "Mutationism" prevails for a generation, until Fisher, Haldane and Wright show that genetics is the missing key to Darwinism. In the conclusion to the story, the world is set right again when the "Modern Synthesis", combining selection with Mendelian genetics, shoulders aside the mutationist heresy, which ends up in the dustbin of history with the other "doomed rivals" of Darwin's great theory.

June 3, 2010
The Mutationism Myth, IV: Mendelian Heterodoxies
Arlin Stoltfus says,
The reader who has been following our story so far may be baffled. As we found out in part 3, the Mendelians understood how to conceptualize a population as a dynamic system of allele and genotype frequencies (the Bateson-Saunders equilibrium), how to see evolutionary change as a probabilistic 2-step process of the introduction and acceptance-or-rejection of mutations, and how to think about selection-driven changes in a quantitative trait.

Why don't the Mendelians get credit for laying the foundations of the 20th-century consensus?

June 22, 2010
The Mutationism Myth, V: The response to Mendelian heterodoxies
This is the seventh in a series of postings by guest blogger, Arlin Stoltzfus.

Deconstructing The Mutationism Myth erodes the conventional wisdom about the early Mendelians, and also exposes the incompatibility with genetics that led the Mendelians to reject Darwin's theory. As we will see today on the Curious Disconnect (credits), unraveling the Mutationism Myth also puts the Modern Synthesis in a new light.

August 31, 2010
The Mutationism Myth, VI: Back to the Future
This is Arlin's last contribution. The entire series has been an excellent introduction to the history of evolutionary theory and the concept of mutationism. There are many ways in which the so-called "Modern" Synthesis has to be revised and extended. One of them is to reinstate the concept of mutationism which was purged from evolutionary theory in the 1940s. If you want to understand why this is important then these articles are the place to start.


Georgi Marinov said...

Warning, this might be more that the average biologist can handle. ENCODE scientists should stop reading right now.

I read both the blog posts from 3 years ago and the CNE article when they came out with great interest.

I've also worked for ENCODE

Which one of those things is it that I should go back and undo?

Unknown said...

Stoltfus says today's mainstream evolutionary theorists think that "selection is not creative but merely sorts out pre-existing genetic varieties." I don't think that is quite right. At a given locus, sure, selection filters pre-existing variation. But this takes place at many different loci simultaneously throughout the population. If not for natural selection, these variants at different loci would be sorted independently, with no chance that they would all appear in the same individual. Natural selection creates novelty by uniting these independent adaptive traits into single individuals.
Lou Jost

anthrosciguy said...

You mean actual study is required before making profound pronouncements? This is gonna put a major kink in science as practiced. :)

Larry Moran said...

The fact that your head didn't explode when you read Arlin's posts indicates that you are not a true ENCODE scientist!

But we already knew that. :-)

Sergio A. Muñoz-Gómez said...

What do you think Larry? Was the Modern Synthesis really all about sorting out preexisting variation in the gene pool?

Pedro A B Pereira said...

Larry, have you already read "Mutation-Driven Evolution" by Matoshi Nei? You promised a review.

Pedro A B Pereira said...

correction: Masatoshi, not Matoshi.

Larry Moran said...

Many biologists think that populations will respond very quickly to changes in the environment. They certainly give the impression that mutation is not a rate-limiting factor. The Blind Watchmaker is full of evolutionary explanations of this sort and It also contains a lengthy attack on mutationism.

rich lawler said...

I agree with the assessment of Mayr. He is very biased and Mayr thinks his version of history is correct, largely because he's written some (otherwise impressive) tomes on the history of Biology. His magisterial "The Growth of Biological Thought" gives short-shrift to population genetics and is pretty biased (so much so that when GG Simpson reviewed it, he titled his review "Auto-Biology"). Mayr further emabarrased himself with his whole "bean bag" genetics paper, which Haldane later demolished.

Larry Moran said...

You and I might agree with this assessment of Ernst Mayr but that's not the point. The point is whether the majority of evolutionary biologists think like Mayr or like Gould, Nei, Stoltzfus, Lynch etc.

I have to break it to you but I'm afraid we might be in the minority.

I was stuck by a passage in one of the articles in The Princeton Guide to Evolution. The authors, Jeffrey Feder, Scott Egan, and Patrik Nosil, are at the University of Notre Dame and the University of Colorado, Boulder. The title of the article is "Speciation and Genome Evolution."

Here's what they say about beanbag genetics.

Our empirical and theoretical understanding of the genetics of speciation has been dominated by what Ernst Mayr described as "beanbag thinking" ...

They go on to say that we are now ready to escape that way of thinking because of advances in technology.

Consequently, the field of evolutionary genomics is moving away from "beanbag" approaches and purely descriptive studies of individual genes and their individual effects toward a more predictive framework that tackles the causes and consequences of genome-wide patterns.

To me, that sounds like someone who is quite sympathetic to Mayr and his biases.