Thursday, November 19, 2009

The Modern Synthesis is Dead - Long Live the Evolving Synthesis!


It has been almost exactly a century and a half since Darwin's Origin of Species was first published, and half a century since the conference at the University of Chicago where the "triumph" of the "modern evolutionary synthesis" was celebrated. So, isn't it a little odd that some well-respected scientists and historians of science are proclaiming in this celebratory year that the modern evolutionary synthesis is dead?

For example, Eugene Koonin, senior investigator at the National Center for Biotechnology Information, National Library of Medicine, and National Institutes of Health in Bethesda, Maryland, has published two essays on the current status of the "modern evolutionary synthesis":
The Origin at 150: Is a new evolutionary synthesis in sight?
Trends in Genetics, 25(11), November 2009, pp. 473-475.

Abstract: The 200th anniversary of Charles Darwin and the 150th jubilee of the On the Origin of Species could prompt a new look at evolutionary biology. The 1959 Origin centennial was marked by the consolidation of the modern synthesis. The edifice of the modern synthesis has crumbled, apparently, beyond repair. The hallmark of the Darwinian discourse of 2009 is the plurality of evolutionary processes and patterns. Nevertheless, glimpses of a new synthesis might be discernible in emerging universals of evolution.

and
Darwinian evolution in the light of genomics.
Nucleic Acids Research, 37(4), 2009, pp. 1011-1034.

ABSTRACT: Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or 'forest' of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

A big deal, right? Well, not really. Will Provine and I have been saying that “the modern evolutionary synthesis is dead” for years. Indeed, Will Provine coined the phrase “the hardening of the synthesis” to describe the narrowing of focus in evolutionary theory during the first half of the 20th century to concepts entirely reducible to mathematical models, especially theoretical population genetics.

Ironically, Dr. John Sanford and Dr. William Dembski (among others in the ID camp) have not moved beyond this narrow focus on theoretical population genetics, and so have apparently missed the fact that evolutionary biology has evolved far beyond the narrow theoretical focus of the mid-20th century. Some ID supporters have also suggested that Dr. Koonin might be taking a “big career risk” in stating the obvious. I don't think so. On the contrary, what Dr. Koonin has pointed out is that evolutionary biology today is broader, more generally applicable, and less narrowly focused than at any time since the publication of the Origin of Species 150 years ago. Being an evolutionary biologist today is like being a physicist in 1905 — a whole new world of theoretical and practical empirical research is opening up, with new discoveries being made every day.

As just one example, Kyoto-prize-winning evolutionary biologists Peter and Rosemary Grant have reported on something that Darwin could only speculate about: the systematic empirical documentation of the “origin” of a new species (reported here yesterday). Creationists have of course moved the goalposts, arguing that they accepted all along that new species could arise from existing ones, it’s just microevolution, which of course everyone accepts. This, despite the fact that speciation has always been considered to be the first (and perhaps most important) stage in macroevolution, and that less than two decades ago creationists were confidently stating that “true” speciation had not only never been observed, it couldn’t ever be observed because it can’t happen.

Now the leaders of the ID movement — people like Dr. Michael Behe and Dr. William Dembski — publicly state that they fully accept that descent with modification from common ancestors (i.e. evolution) has happened, that microevolution (i.e. natural selection, sexual selection, and genetic drift) are also fully supported by the evidence, and that the “real” focus of disagreement is over the “engines of variation” that produce the raw material upon which the “engines of evolution” operate. They’ve come a long way, but they’ve missed the parade by a couple of decades. So it goes…

I would say that Dr. Koonin's essays on where evolutionary biology is today are quite close to the the mark. The concept of natural selection as the foundation of evolutionary change has been largely superseded, mostly through the work of Motoo Kimura, Tomoko Ohta, and others, who have shown both theoretically and empirically that natural selection has little or no effect on the vast majority of the genomes of most living organisms.

However, ID supporters should find this sea change in evolutionary biology to be cold comfort. The overall effect of the advances in our understanding of how genomes and phenotypes change over time has had the same effect on evolutionary theory that the rise of quantum mechanics had on classical physics. Einstein famously asserted that “God does not play dice”, but a century of physics research has shown him to be more wrong about how the universe works at the quantum level than ever.

The same is true for the “evolving synthesis”. Rather than revert to a neo-Paleyan paradigm (as proposed by Behe, Dembski, and their supporters), evolutionary biology has gone in the opposite direction, the same direction that quantum mechanics has taken. According to the “modern synthesis” of the last century, the genome was “homeostatic”, “organized”, and “regulated” primarily by natural selection. Sure there were purely random processes also going on (such as genetic drift), but most evolutionary change was both adaptive and coherent over time.

Here's what Dr. Koonin writes (see above):
"There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation."

Kimura, Ohta, Jukes, and Crow dropped a monkey wrench into the "engine" at the heart of the modern synthesis — natural selection — and then Gould and Lewontin finished the job with their famous paper on “the spandrels of San Marco and the Panglossian paradigm”. The rise of evo-devo over the past two decades has laid the groundwork for a completely new and empirically testable theory of macroevolution, a theory that is currently facilitating exponential progress in our understanding of how major evolutionary transitions happen. And iconoclasts like Lynn Margulis, Eva Jablonka, Marian Lamb, Mary Jane West-Eberhard, and David Sloan Wilson are rapidly overturning our understanding of how evolutionary change happens at all levels, and how it is inherited.

So, as I have said many times before, when ID supporters set their sights on “neo-Darwinism” as a target for criticism, they set their sights on a model that has been all but abandoned. The carnival has moved on and ID supporters are fighting battles that evolutionary biologists left behind a half century and more ago.

And so, on this 150th anniversary of the publication of Darwin's Origin of Species, evolutionary biologists can raise a frosty glass and say


The modern synthesis is dead — long live the evolving synthesis!


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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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9 Comments:

At 11/20/2009 02:29:00 AM, Blogger NickM said...

Alan,

Isn't there room for more than a little skepticism about this "down with the modern synthesis!" hype? Gould claimed in 1980 that a "new and general theory of evolution" was emerging or about to emerge -- but where is it?

Claims for a new synthesis typically look more like a laundry-list of stuff we've learned about, rather than a new, grander, synthetic theory. It may well be that evolution is just too diverse to have another episode of grand unification on the level of Darwin's synthesis, or the Modern Synthesis.

What has really been going on, in my view, is that several fields other than population genetics have experienced "synthesis" -- mathematization and comprehensive theoretical treatment -- in a way similar to the way that population genetics was synthesized. One good example is phylogenetics & molecular evolution. Another is speciation (in fact, these are all tied together and to the Modern Synthesis -- in many but not all ways, they grew out of the Modern Synthesis, let's give some credit where credit is due!).

Things like evo-devo and macroevolution, while great, still seem to be more at the less systematic data-gathering stage, rather than the systematic grand-unifying-mathematical predictive theory stage.

In sum, saying "the modern synthesis is dead" seems to me to be a lot like saying "solar system astronomy is dead." Back in the 1930s we knew a lot about the solar system and little about the stuff outside. Now we know a lot more about both, but our knowledge gain in the latter seems more dramatic, because we already had the basics of the solar system figured out in 1930.

Or, shorter version:

"[W]hen people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together."

Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm

I say all this as a huge fan of macroevolution and as someone who has had plenty of arguments with population geneticists over scale and extrapolation issues. I just have an instinctive skepticism for, I dunno, things that are possibly hype rather than actual synthetic theory!

 
At 11/20/2009 02:37:00 AM, Blogger NickM said...

PS: Similarly -- neutral theory and spandrels are neat, but neutral theory is just what happens when selection = 0, and is fully integrated (and directly derived from!) the modern synthesis.

Spandrels -- this is indeed a great concept and a great paper, but it's more of an asterisk to evolution producing adaptation by natural selection, rather than a paradigm shift.

PS: Dembski does *not* accept common ancestry. As we tried to publicize in 2007:

"The denial of common ancestry is unsurprising in creation science, but it is a common misconception that ID advocates accept common ancestry and “macroevolution.” In fact, the vast majority of ID proponents deny the common ancestry of humans and apes. Behe is the only significant exception, although he is much-touted by those who wish to portray ID as a moderate position. Even Behe's support is lukewarm; in 2005, he wrote that “my Intelligent Design colleagues who disagree with me on common descent have greater familiarity with the relevant science than I do” (66). Dembski's position is typical, accepting “some change in the course of natural history,” but believing “that this change has occurred within strict limits and that human beings were specially created” (67). This is the standard position of an ID advocate. In May 2005, ID supporters on the Kansas Board of Education held hearings to support ID-friendly science standards. Mainstream scientists boycotted the hearings, but a series of pro-ID witnesses, mostly teachers and academics (but few professional biologists) testified in support of the standards. During cross-examination, only 2 of 19 witnesses accepted the common ancestry of humans and apes. One was an independent scholar who clarified that although he supported the Kansas standards, he was not an ID advocate; and the other was Behe. The rejection of evolution by the vast majority of ID witnesses at the Kansas hearings parallels the rejection of evolution by ID proponents in general."

http://www.pnas.org/content/104/suppl.1/8669.full

 
At 11/20/2009 07:45:00 AM, Blogger Allen MacNeill said...

At another website an ID supporter wrote:

"You’re pointing out that ID proponents are out of date, but if that’s true, all it means is they’re fighting a battle they’ve already won, and simply don’t realize it."

To which I replied:

Then how do you reconcile this with the following quote from Eugene Koonin:

"There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation."

So much for "complex specified information", or any kind of "complexity" for that matter. ID supporters have apparently performed a rather classical quotemine on Dr. Koonin, selecting those bits of the abstracts of his papers that supported a viewpoint that was exactly the opposite of the actual content of his work.

Here's what Dr. Koonin actually wrote:

"Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected."

"There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation."

"Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future."

In other words, the evolving evolutionary synthesis of the 21st century is de-emphasizing adaptation. But, since adaptation is the heart and soul of ID (which is all about how things become purposeful in evolution), then the new discoveries are cutting the heart and soul out of ID. Intelligent Design, like its mirror image "the modern synthesis", has always been relentlessly pan-adaptationist. According to ID, even those things that evolutionary biologists assert do not have a purpose actually do, we're just ignorant of what those purposes might be. The Intelligent Designer® does nothing by accident: "not a sparrow falls but that Thou art mindful of it".

But the emerging picture of the genome (and the phenome for which it is at least partially responsible) is that, rather than being a coherent, homeostatic, apparently "rationally designed" entity, it is a frothing ocean of randomly varying nonsensical and furiously selfish genetic entities, none of which give a tinker's dam about the phenome.

Indeed, rather than producing the exquisitely perfect adaptations of living organisms, it is becoming clear that natural selection may be important only as that process that prevents the accelerating disintegration of the genome in the face of increasing chaos. In other words, evolution isn't a steady climb toward greater and greater complexity nor a process designed to produce perfection. No, it's a process out of which adaptation and complexity arise almost as an afterthought in the "mind" of a universe bent wholly on self-annihilation.

Looks like "biological quantum mechanics" to me...

 
At 11/20/2009 07:51:00 AM, Blogger Allen MacNeill said...

NickM wrote:

"Gould claimed in 1980 that a "new and general theory of evolution" was emerging or about to emerge -- but where is it?"

It's here: that was the point of my post. And of course I give credit to the Modern Synthesis; without it, getting to where we are today would have been much less likely.

But, that said, I agree with Stephen J. Gould, Eugene Koonin, and Will Provine, all of whom assert that the "new synthesis" that is emerging from the fields of comparative genomics, evo-devo, and macroevolutionary studies is so different from what lay at the pan-adaptationist heart of the Modern Synthesis as to qualify as a genuinely new and evolving synthesis.

If you like analogies (obviously I do), it's as if the Modern Synthesis has "speciated" and its offspring — the evolving synthesis — is no longer reproductively compatible with its evolutionary ancestor.

 
At 11/20/2009 07:58:00 AM, Blogger Allen MacNeill said...

As for the neutral theory being "just what happens when selection = 0", I agree, but would go on to point out that more and more of the evidence seems to indicate that this is what is happening almost all of the time.

As for the neutral theory being fully integrated (and directly derived from!) the Modern Synthesis (or, for that matter, the idea that punctuated equilibrium or developmental plasticity or exaptation or any of the other major tenets of the "evolving synthesis"), I've been around long enough to remember how acrimonious the fights were between evolutionary biologists committed to the Modern Synthesis and those willing to entertain these emerging ideas. Motoo Kimura and Steve Gould were excoriated by "mainstream" evolutionary biologists, just as Mary Jane West-Eberhard still often is.

Old paradigms die hard, and as Thomas Kuhn asserted, often die when their adherents do.

 
At 11/20/2009 08:00:00 AM, Blogger Allen MacNeill said...

And thank you for the clarification about Dembski's views on common descent. I've always suspected that he was lying about this, too, and your reference confirms it.

But, after reading The Edge of Evolution I have to think that Michael Behe really does accept common descent, he just thinks it has been guided by the Intelligent Designer. Therefore, it's doubly ironic that he's now a regular contributor to Uncommon Descent. Talk about split personalities...

 
At 11/20/2009 08:14:00 AM, Blogger Allen MacNeill said...

For a much better written version of what I have tried to express here, read this:

http://www.uncommondescent.com/natural-selection/is-nature-really-a-struggle-in-which-natural-selection-is-the-key-factor/comment-page-1/#comment-340528

 
At 8/26/2013 01:59:00 AM, OpenID themayan said...

This is called revisionism. The fact remains, the modern synthesis was up held at Dover as an undisputed axiom. So much so, that (even for a moment putting aside the the book Of Pandas and People) just putting a sticker on a book telling students the theory was not a fact, and that gaps in this same current theory exist, was enough to bring on condemnation from the ACLU and the NCSE.

In fact we are still teaching this outdated obsolete paradigm as an undisputed fact in schools all over the country. It also seems the writer has misinterpreted what Koonin actually said, as Koonin did not say that the theory has broadened. What he actually said was, that "the edifice of the modern synthesis has crumbled beyond repair" As for what the future "might" hold, he also said this, and notice the caveat used above and below, as in the word "might" and as follows........"Nevertheless, glimpses of a new synthesis might be discernible in emerging universals of evolution"

In fact according to Eugenie Scott, the reason why the NCSE will not support the new extended synthesis as proposed at Altenberg in 2008, is because she claims people will confuse self organization with intelligent design. And I can only suspect that it might also be due to the fact that this same proposed extended synthesis, which is based on epigenetic factors, seems to indicate that mutations are not random and seem to be programed into the cell. Besides, many a neo Darwinist like Scott and others have made a lot of money on speaking engagements preaching neo Darwinism for a long time. And they are not about to give up that gravy train any time soon. And they're certainly not going to admit they were wrong, and say oh by the way, here is the new and improved theory.

This thread is exactly the kind of hand waiving Stewart Newman spoke of, and he believes this is why their is so much distrust on the side of the general public. Lets just admit we were wrong, and then maybe we could move ahead. And I include the now debunked junk DNA paradigm, gene centrism and biologies central dogma as well.


The new biology: beyond the Modern Synthesis
Michael R Rose1* and Todd H Oakley2

The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research during that century. The foundations of that "Modernist" biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century.


Soft inheritance: challenging the modern synthesis
Eva JablonkaI; Marion J. LambII

Beyond neo-Darwinism—an epigenetic approach to evolution
M.W. Ho

 
At 1/03/2015 12:04:00 PM, Blogger Tom Robbins said...

They did not even have to mention epigenetics which now has a mountain of evidence and disproves common evo-nut theories by themselves - the reason is it would have to postulate that evolution randomly selected in order to evolved us in such a way that we can evolve via environment (we evolved the ability to evolve which is nonsense scientifically). .There are still many that argue that neo-darwinism is alive, but they are deluding themselves as our entire understanding of the gene has changed. Neo-darwinism (random mutation and fitness) may explain a very limited amount of accidental benefit by random mutation (or selective breeding by breeders), but it is completely false to believe that these small accidents, This is no small thing. Most people get confused by animal breeding and anti-biotic resistance proving darwinism. This is the trick they play, they assume that these mistakes can create entirely new body plans if given enough time, but what it will do if given enough time is kill off the organism - fortunately DNA has the ability to catch mistakes and repair them (another proof against evolution - how can a sophisticated or even unsophisticated self-repair mechanism evolve? If one answers "because it improves fitness" this is the standard answer and the game they play. HOW did it "plan" the most efficient self-repairing mechanism known to man, if it were so, the fossil record would be littered by the hundreds of thousands of failed attempts to get it right, but it is not. In fact, every fossil shows sharp and extremely rapid change, the appearance of almost all major body plans at the very beginning. That is a fact, that is the evidence. Also, the tree of life from genetic studies show more of a web of life, but not at all a tree, especially mRNA studies. Also, we now know that complete reshuffling of DNA, and active splicing of DNA takes place - this is decision making, this is intelligence. I am not concluding God here (although I am a believer), but even if I were an agnostic and bought current evolution theory (as I did in my 20's), I would now reject it. Evolutionists say that the theory is just evolving, like in other sciences, but NO, the main law of the theory is false - it is not a honing of the right theory, neo-darwinsim is not the mechanism fore macro-evolution. I even think that micro evolution is NOT accidental mutations or copying mistakes, as there are parts of the genome that the body uses for mutation that are separated into areas where the "experiment" of the change can be tested and do the least damage. This smokescreen of you are either a creationist or a neo-darwinian is absurd. WWW.THETHIRDWAYOFEVOLUTION.COM proves this fact dramatically.

 

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