Good News from Gent

While in Gent I got a chance to meet up with some members of the Department of Philosophy at the University of Gent. Jan Verbeeren (right) is a regular reader of Sandwalk. Stefaan Blanke (below left) and Maarten Boudry (below right) are graduate students who I met at the Darwin conference in Toronto in November.

It was easy to convince Maarten to join Jan and I for a beer because Jan was buying. Unfortunately, Stefaan couldn't make it so I'll have to go back for another visit.

There are at least 500 different beers made in Belgium—or so I'm told [Belgium beers]. I doubt that I'll be able to sample all of them before I leave. The ones I had in Gent were "Delirium Tremens" and "Tripel Karmeliet." They were excellent.


We talked about adaptationism vs. pluralism. It seems to be a difficult controversy to grasp if you haven't been trained as a scientist. I think the problem is that the concept of random genetic drift as a mechanism of evolution is not widely accepted among philosophers.

We also spent an hour or so talking about methodological naturalism and philosophical naturalism. This was the subject of Maarten's talk in Toronto last November and I think he's on to something (with Stefaan). I'll write a separate post on this topic.

The title of this post is from How They Brought the Good News from Ghent to Aix by Robert Browning.

I SPRANG to the stirrup, and Joris, and he;
I gallop’d, Dirck gallop’d, we gallop’d all three;
“Good speed !” cried the watch, as the gate-bolts undrew;
“Speed!” echoed the wall to us galloping through;
Behind shut the postern, the lights sank to rest,
And into the midnight we gallop’d abreast.

...

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Dinner with Bjørn

Bjørn Østman of Pleiotropy and Carnival of Evolution was in town for a visit on Monday, Aug. 8, 2011. We talked about evolution, accommodationism, atheism, PZ, education, visas, politics, carnivals, the USA, adaptationism, blogging, and careers in science.

I think he was happy to learn that I agreed with him on almost everything.

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Adaptationomics

 
Jonathan A. Eisen is an evolutionary biologist with a blog called The Tree of Life. He's also one of the authors of a new textbook on evolution published by Cold Spring Harbor Laboratories [A New Textbook on Evolution]. I'm about to order a copy.

I mention this because Eisen is a pluralist. He's as annoyed by adaptationist just-so so stories as I am. Over on the Dennett on Adaptationism thread I'm encountering commenters who question whether there really are modern scientists who believe in the adaptationist program. I can assure you there are. Eisen has discovered some of them in the field of genomics—he didn't have to look very hard—and he decided to label their approach adaptationomics [Adaptationomics Award #1 - Wolbachia DNA sneaking into host genomes]. This is tongue-in-cheek so don't all you adaptationists get your knickers in a knot.

Here's how Jonathan sets up the issue.

For years I have been fighting against the tide on the tendency for people doing genomics work to resort to silly adaptationist arguments for observations. The argument goes something like this. We sequenced a genome (or did some type of genomics). We made an observation of something weird being present (take your pick - it could be a gene order or a gene expression pattern or whatever). We conclude that this observation MUST have an adaptive explanation. We have come up one such adaptive explanation. Therefore this explanation must be correct.

Gould and Lewontin railed against this type of thing many years ago and others have since. Just because something is there does not mean it is adaptive (e.g., it could be neutral or detrimental). And even if something is adaptive, just because you can think of an adaptive explanation does not mean your explanation is correct.

And this is so common in genomics I have decided to invent a new word - Adaptationomics. And I am giving out my first award in this to Jack Warren and colleagues for their recent press release on their new study of lateral transfer in Wolbachia (plus it lets me plug their new study which is pretty ^$%# cool).

Does this sound familiar?

What did the authors say that makes them adaptationists? In order to understand their statement you have to be familiar with their findings. They discovered that the genome of a parasite (Wolbachia) has been integrated into the geonome of their insect host. There are several reasons why this might have happened. It could just be an accident, since these kind of recombinant events occur frequently and most insects don't carry a full complement of their parasite's genome. In other words, it could be junk.

On the other hand, the parasite genome could possibly confer some (unknown) selective advantage on the host. But here's the rub. When the author of the article, Julie Dunning Hotopp, was interviewed for the the Nature News article here's what she said.

You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."

That's a classic adaptationist statement. The result "must be" explained by natural selection. There are no other options. I agree with Jonathan Eisen, this is a fitting recipient of his new Adaptationomics Award.

Congratulations to Julie Dunning Hotopp.

Junk & Jonathan: Part 4—Chapter 1

I received a copy of the book a few days ago and this is my first posting on its contents. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

This is a very small book. There's only 114 pages of text—it's more like a large pamphlet than a book. If I'd read it from front to back in one sitting it would only have taken an hour or so. But I couldn't read it in one go because nobody can put up with IDiot rhetoric for that long!

Chapter 1 is The Controversy over Darwinian Evolution. It has nothing to do with junk DNA.

Wells begins by telling his readers that evolution is a fact. By that he means "microevolution." Wells doesn't believe in macroevolution or common descent and he even challenges the evidence for speciation. As usual, he supports his claims with selected quotations from scientists.

Sixty year after Dobzansky wrote this, biologists had still not observed the origin of a new species ("speciation") by natural selection. In 1997, evolutionary biologist Keith Stewart Thomson wrote: "A matter of unfinished business for biologists is the identification of evolution's smoking gun," and "the smoking gun of evolution is speciation, not local adaptation and differentiation of populations."

Wells is telling his readers that as long as biologists have not directly observed a new species forming then speciation has not been demonstrated. This rules out all evidence from the fossil record and all evidence from molecular phylogeny. Nice trick.

Problem is, there's lots of lots of evidence for speciation, including some examples where speciation has been caught in the act. Wells, like most IDiots, doesn't understand how evolution works. He seems to think that new species will form overnight and that all biologist have to do is keep their eyes open and record the examples.

I don't know for sure whether Wells intends to emphasize speciation by natural selection when he claims that, "biologists had still not observed the origin of a new species ("speciation") by natural selection." If that's his intent then it's true that there are very few examples of true speciation (biological species concept) that can be attributed directly to natural selection. As Jerry Coyne points out, reproductive isolation is mostly due to accident (random genetic drift) and not natural selection [The Cause of Speciation]. That's in line with modern evolutionary theory and Coyne should know because he's one of the world's leading experts on speciation. [UPDATE: Coyne and some commenters have corrected me. Coyne actually does think that most speciation is due to natural selection. I'll stick with Futuyma as my authority. He's much more open to the idea of speciation by random genetic drift (Evolution 2nd ed. p. 447)]

There are two possibilities here. Either Wells is deliberately misleading his readers by emphasizing that speciation must occur by natural selection or he's ignorant of modern evolutionary theory. Since most IDiots have a concept of evolution that dates back to the nineteenth century, I'll go with the second explanation. However, there's almost certainly an element of deception in his remarks since Jonathan Wells has a long history of deliberately misrepresenting evolution.

Theme

Genomes
& Junk DNASo, Wells is dead wrong about the first point in his book. There's abundant evidence of speciation (and macroevolution) and, furthermore, modern evolutionary theory does not attribute speciation exclusively to adaptation (i.e. there's more to evolution than Darwinism).

The importance of Wells' rejection of macroevolution will become obvious later on in the book when he argues that Intelligent Design Creationism does not rule out common ancestry. He agrees that someone like Michael Behe can believe in common descent and still be a card-carrying IDiot.

By the way, Wells is clever enough to cover his bases in case speciation is ever observed.

Of course, even if scientists eventually observe the origin of a new species by natural selection, the observation would not mean that natural selection can also explain the origin of significantly new organs or body plans. But the fact that scientists have not observed even the first step in macroevolution means that "evolution's smoking gun" is still missing.

The rest of the chapter (three pages) is a re-hash of arguments Wells made in Icons of Evolution and elsewhere.

• The Cambrian Explosion "contradicts Darwin's theory that major differences should arise only after millions of years of evolution ...."
• Molecular evolution isn't accurate: "molecular evidence is plagued with inconsistencies." The rejection of molecular evidence as unreliable is going to cause problems for Wells later on since he relies on it for some of his arguments about junk DNA. As usual, the IDiots want to have their cake and eat it too.
• Homology is a circular argument, according to Wells, so you can't use homology as evidence for evolution. That's correct. Similarity is the evidence and homology is the conclusion. This flaw in Wells' reasoning has been pointed out to him repeatedly over the past decade but he ignores all criticism and continues to use arguments that have been refuted.
• The Haeckel drawings were fakes and, "The truth is that vertebrate embryos start out looking very different from each other, then they converge somewhat in appearance midway through development before diverging as they mature." This has nothing to do with junk DNA so I won't discuss the massive amount of embryological evidence for evolution.

Wells closes with,

So microevolution is a fact, supported by overwhelming evidence, but macroevolution remains an assumption, illustrated with icons that misrepresent the evidence or rely on circular reasoning. The icons are not science, but myth.

This sets the tone for the rest of the book. Even though it is filled with references to the scientific literature there's never any discussion of alternative hypotheses or conflicting data. This is not a book where the author wants to inform his readers about the exciting controversies and conflicts within science. This is a book where the author wants to promote creationism by attacking and misrepresenting evolution using faulty logic and untruths.

The next paragraph is quite interesting. He invokes the beliefs of Americans as support for his claims. Apparently they're much more perceptive that the typical evolutionary biologist. (I wonder what he thinks of Australians and Europeans?)

This may be one reason why—despite the Darwinists' near-monopoly over science education—most Americans still reject the doctrine that human beings evolved from ape-like ancestors by unguided processes such as random variation and survival of the fittest.

I think this means that Wells also rejects common ancestry. If so, it will mean that he can't use it to support any of his arguments later on in the book, right?

Finally, at the very end of the chapter we get to the point,

In the 1950s, neo-Darwinists equated genes with DNA sequences and assumed that their biological significance lay in the proteins the encoded. But when molecular biologists discovered in the 1970s that most of our DNA does not code for proteins, neo-Darwinists called non-protein-coding DNA "junk" and attributed it to molecular accidents that have accumulated in the course of evolution. Like peppered moths, Galapagos finches, Darwin's Tree of Life, homology in vertebrate limbs, and Haeckel's embryos, "junk DNA" has become an icon of evolution. But is it science of myth?

I've discussed Wells' ignorance of history in previous postings but, for the record, here are the facts.

• By the 1970s molecular biologist were well aware of the fact that non-protein coding genes existed (e.g. ribosomal RNA genes, tRNA genes etc.)
• By the 1970s molecular biologists knew of several functions of DNA sequences that weren't genes. Origins of replication and regulatory sequences were well-known but there were others.
• Even in the 1970s no knowledgeable molecular biologist could ever defend the idea that all non-coding DNA was junk. (It's true that there were some stupid scientists who weren't aware of tRNA genes and regulatory sequences and made silly statement because of their ignorance but they don't count.)
• By the 1970s junk DNA was a fact. The scientific controversy was over how much of our genome is junk. Is it the majority or only a small percentage?
• By the 1970s knowledgeable evolutionary biologists were well aware of the fact that most of our genome was mutating and evolving as though most changes were neutral (genetic load arguments). This didn't mean that most of our genome was junk but it did mean that the sequence couldn't be important or we would never be able to tolerate the genetic load. This was not common knowledge among biologists—still isn't.
• By the 1970s most molecular biologists were aware of the so-called "C-value paradox" where very closely related species have very different genome sizes. They correctly interpreted this to mean that the species with the large genomes probably didn't need all that extra DNA. (Up until now, Intelligent Design Creationists have not offered a reasonable answer to The Onion Test. Wells tries on Chapter 8.)
• The proponents of large amounts of junk DNA in our genome would hardly ever have referred to themselves as "Darwinist" or "neo-Darwinists." In fact, they tended to be among those evolutionary biologists who opposed adaptationism and favored Neutral Theory and random genetic drift. Pluralist concepts were much more compatible with the idea of significant amounts of junk DNA than strict "Darwinist" interpretations of genome evolution.

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Sandwalk 2007

 
John Lynch of Stranger Fruit started a trend last year when he posted the first sentence of the first blog of each month for the entire year. He's done it again this year [My year in blogging. I couldn't do it last year for obvious reasons so here's my summary for 2007.

• January: Brits Losing After American Invasion: According to recent reports red squirrels in Britain are facing extinction.


• February: Another Canuck Blogger There's a really good blog called Primordial Blog. As far as I can tell the author (Brian) lives in the Yukon—that's part of Canada (barely) so he must be Canadian.


• March: Evolution Is a Fact DaveScot over at Uncommon Descent writes in "Theory of Evolution as well tested as…"


• April: Public Scientific Debates Sean Carrol has posted an article about pubic debates over the validity of string theory [String Theory is Losing the Public Debate].


• May: My Six Months Are Up! I started Sandwalk six months ago. The goal was to give it six months to see how things worked out.


• June: Matthew Nisbet and Chris Mooney Video on Framing Science Chris Mooney has challenged me to respond to a video (see below the fold) of a talk that he and Matt Nisbet gave on framing. Over on his blog, Chris criticizes PZ Myers who couldn't sit through the whole hour [PZ, You Can Do Better Than This....]. Neither could I, but at least I got to the 50 minute mark which was more than twice as far as PZ.


• July: Visible Mutations and Evolution by Natural Selection A recent posting [Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift] raised the issue of adaptationism. The controversy is over the main mechanism of genetic change in evolving populations.


• August: Heme Groups Monday's Molecule #37 is the heme group found in myoglobin and hemoglobin.


• September: Theories of Speciation In order to understand real evolution you have to understand speciation. This fact usually comes as a great surprise to adaptationists who tend not to think of such things.


• October: Do You Think Iran Will Get the Messsage? Here's a scary report from the New York Daily News [ Bush eyes 'surgical' strikes vs. Iran, sez mag].


• November: Can You Smell Isovaleric Acid? Isovaleric acid [3-Methylbutanoic acid] smells like sweat. It is responsible for some of the odor in a locker room, for example.


• December: Seymour Benzer (1921 - 2007) Seymour Benzer died last Friday. In the 1950's and 1960's Benzer was a prominent member of the 'phage group founded by Max Delbrück and Salvador Luria [The Nobel Prize in Physiology or Medicine 1969.].

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Michael Lynch on modern evolutionary theory

Of the Five Things You Should Know if You Want to Participate in the Junk DNA Debate, the most difficult to explain is "Modern Evolutionary Theory." Most scientists think they understand evolution well enough to engage in the debate about junk DNA. However, sooner or later they will mention that junk DNA should have been deleted by selection if it ever existed. You can see that their worldview leads them to believe that everything in biology has an adaptive function.

It's been a few years since I posted Michael Lynch's scathing comments on panadaptationism and how it applies to understanding genomes [Michael Lynch on Adaptationism and A New View of Evolution]. You're in for a treat today.

Here's what you need to know about evolution in order to discuss junk DNA. The first quotation is from the preface to The Origins of Genome Architecture (pages xiii-xiv). The second quotations are from the last chapter (page 366 and pages 368-369.

Contrary to popular belief, evolution is not driven by natural selection alone. Many aspects of evolutionary change are indeed facilitated by natural selection, but all populations are influenced by nonadaptive forces of mutation, recombination, and random genetic drift. These additional forces are not simple embellishments around a primary axis of selection, but are quite the opposite—they dictate what natural selection can and cannot do. Although this basic principle has been known for a long time, it is quite remarkable that most biologists continue to interpret nearly aspect of biodiversity as an outcome of adaptive processes. This blind acceptance of natural selection as the only force relevant to evolution has led to a lot of sloppy thinking, and is probably the primary reason why evolution is viewed as a soft science by much of society.

A central point to be explained in this book is that most aspects of evolution at the genome level cannot be fully explained in adaptive terms, and moreover, that many features could not have emerged without a near-complete disengagement of the power of natural selection. This contention is supported by a wide array of comparative data, as well as by well-established principles of population genetics. However, even if such support did not exist, there is an important reason for pursuing nonadaptive (neutral) models of evolution. If one wants to confidently invoke a specific adaptive scenario to explain an observed pattern of comparative data, then an ability to reject a hypothesis based entirely on the nonadaptive forces of evolution is critical.

The blind worship of natural selection is not evolutionary biology. It is arguably not even science.

Michael Lynch

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 uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer (without any direct evidence). True, we have actually seen natural selection in action in a number of well-documented cases of phenotypic evolution (Endler 1986; Kingsolver et al. 2001), but it is a leap to assume that selection accounts for all evolutionary change, particularly at the molecular and cellular levels. The blind worship of natural selection is not evolutionary biology. It is arguably not even science. 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.

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.It should be emphasized here that the sins of panselectionism are by no means restricted to developmental biology, but simply follow the tradition embraced by many areas of evolutionary biology itself, including paleontology and evolutionary ecology (as cogently articulated by Gould and Lewontin in 1979). The vast majority of evolutionary biologists studying morphological, physiological, and or behavioral traits almost always interpret the results in terms of adaptive mechanisms, and they are so convinced of the validity of this approach that virtually no attention is given to the null hypothesis of neutral evolution, despite the availability of methods to do so (Lande 1976; Lynch and Hill 1986; Lynch 1994). For example, in a substantial series of books addressed to the general public, Dawkins (e,g., 1976, 1986, 1996, 2004) has deftly explained a bewildering array of observations in terms of hypothetical selection scenarios. Dawkins's effort to spread the gospel of the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, and because more people have probably read Dawkins than Darwin, his words have in some ways been profoundly misleading. To his credit, Gould, who is also widely read by the general public, frequently railed against adaptive storytelling, but it can be difficult to understand what alternative mechanisms of evolution Gould had in mind.

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The Third Fourth? Way

Back in 1997, James Shapiro wrote an article for the Boston Review entitled "A Third Way." It was a very confusing article. His main point seemed to be that conventional neo-Darwinism wasn't a complete picture of modern evolutionary theory.

That part wasn't news since by 1997 the ideas of Neutral Theory and random genetic drift had been around for thirty years. Apparently, Shapiro was three decades behind in his understanding of evolution.

Shapiro doesn't demonstrate that he understands population genetics and random genetic drift. This just one (of many) criticisms that I mentioned in my review of Shapiro's book Evolution: A View from the 21st Century in NCSE Reports [Evolution: A View from the 21st Century]. Shapiro responded to my review at: Reply to Laurence A Moran’s review of Evolution: A View from the 21st Century] and I discussed his response on my blog [James Shapiro Responds to My Review of His Book].

The "third" way, according to Shapiro's 1997 article, is not classic Darwinism and it's not creationism. Instead, it's a new way of looking at evolution.

What significance does an emerging interface between biology and information science hold for thinking about evolution? It opens up the possibility of addressing scientifically rather than ideologically the central issue so hotly contested by fundamentalists on both sides of the Creationist-Darwinist debate: Is there any guiding intelligence at work in the origin of species displaying exquisite adaptations that range from lambda prophage repression and the Krebs cycle through the mitotic apparatus and the eye to the immune system, mimicry, and social organization? Borrowing concepts from information science, new schools of evolutionists can begin to rephrase virtually intractable global questions in terms amenable to computer modelling and experimentation. We can speculate what some of these more manageable questions might be: How can molecular control circuits be combined to direct the expression of novel traits? Do genomes display characteristic system architectures that allow us to predict phenotypic consequences when we rearrange DNA sequence components? Do signal transduction networks contribute functional information as they regulate the action of natural genetic engineering hardware?

Questions like those above will certainly prove to be naive because we are just on the threshold of a new way of thinking about living organisms and their variations. Nonetheless, these questions serve to illustrate the potential for addressing the deep issues of evolution from a radically different scientific perspective. Novel ways of looking at longstanding problems have historically been the chief motors of scientific progress. However, the potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise. This is to be expected from the Creationists, who naturally refuse to recognize science's remarkable record of making more and more seemingly miraculous aspects of our world comprehensible to our understanding and accessible to our technology. But the neo-Darwinian advocates claim to be scientists, and we can legitimately expect of them a more open spirit of inquiry. Instead, they assume a defensive posture of outraged orthodoxy and assert an unassailable claim to truth, which only serves to validate the Creationists' criticism that Darwinism has become more of a faith than a science.

Now Shapiro has joined forces with some other "revolutionaries" and started a new website called "The Third Way." It has grandiose goals ....

The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations.

There's only one problem. I'm familiar with Shapiro's ideas and with the ideas of most of the other people listed on the website and I don't think any of them (except Eugene Koonin) have anything significant to say about evolutionary theory. Futhermore, most of them don't seem to understand that there's already been a revolution and population genetics, Neutral Theory, etc. won the day. They seem to have completely missed that revolution.

They are advocating a fourth way that skips right from adaptationism to something else.

They are like a group of would-be revolutionaries marching up Rue de Lyon in Paris only to discover that the Bastille has been replaced by an open square and an opera house.

Note: There aren't many biologists that are interested in this "Third Way" but the creationists are lapping it up [A Group of Darwin-Skeptical Scientists Seeking a "Third Way" in Biology Have Launched a New Website; Welcome to Them!].

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Tomoko Ohta and Nearly Neutral Theory

There's an interview with Tomoko Ohta in the August 21, 2012 issue of Current Biology: Tomoko Ohta.

You should know who she is but in case you don't, here's part of the brief bio ...

In 1973, she presented her first major paper entitled ‘Slightly deleterious mutant substitutions in evolution’. This theory was an expansion of Kimura's ‘neutral theory’, which Ohta called the ‘nearly neutral theory’ of molecular evolution. Her theory emphasizes the importance of interaction of drift and weak selection, and hence the role of slightly deleterious mutations in molecular evolution. With the accumulation of genome data, some of the predictions of the nearly neutral theory have been verified. The theory also provides a mechanism for the evolution of complex systems. Her other subject is to clarify the mechanisms of evolution and variation of multigene families. She has received several honors, including the foreign membership of the National Academy of Sciences, USA and Person of Cultural Merit, Japan.

It's very important to understand the essence of Nearly Neutral Theory since it explains the relationship between fitness and population size. Everyone needs to understand that Ohta demonstrated how slightly deleterious alleles can be fixed in a population. Her work showed that an allele can become effectively neutral in small populations even though it may actually lower the fitness of an individual. It's a way of explaining the limits of natural selection and of extending the Neutral Theory of Kimura.

She describes what happened when she joined Kimura's group at Tokyo.

At that time, Kimura was thinking of combining the theory of stochastic population genetics, the field he had been working on, with biochemical data on the nature of the genetic material. He proposed his now famous ‘neutral theory of molecular evolution’ in 1968. The ‘neutral theory’ proposed that most evolutionary changes at the molecular level were caused by random genetic drift rather than by natural selection. Note that the neutral theory classifies new mutations as deleterious, neutral, and advantageous. Under this classification, the rate of mutant substitutions in evolution can be formulated by the stochastic theory of population genetics. Kimura's theory was simple and elegant, yet I was not quite satisfied with it, because I thought that natural selection was not as simple as the mutant classification the neutral theory indicated, and that there would be border-line mutations with very small effects between the classes. I thus went ahead and proposed the nearly neutral theory of molecular evolution in 1973. The theory was not simple, and much more complicated, but to me, more realistic, and I have been working on this problem ever since.

This has nothing to do with Darwinism even though it's a fundamental part of modern evolutionary theory. You can't have an intelligent discussion about genome evolution, adaptationism, molecular evolution, or junk DNA without a firm grasp of Nearly Neutral Theory.

It's a shame there's no Nobel Prize for evolution.

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Happy Birthday Sandwalk!

 
Today is the first anniversary of this blog. My first posting on November 4, 2006 was Welcome to My Sandwalk. Since then there have been 1282 other postings for an average of 3.5 per day (whew!). My original goal was to average one science-related article per day and I think I've come close to that average. The others are just for fun.

I was told when I began that you have to attract hundreds of views per day in order to generate interesting comments and discussions. That seems to be about right. When I started I saw this blog as an experiment and I intended to re-evaluate after six months. When the six months was up I had not met many of my goals so it was a time of soul searching [My Six Months Are Up!]. What happened was I avoided making a decision so I just kept going by default. I'm glad I did. There are now lots of interesting discussions going on in the comments sections.

All of us science bloggers have discovered one important feature of science blogging. You hardly ever get comments about science. If you check those articles where I talked about science, there are almost no comments or discussion. On the other hand, as soon as you mention politics, religion, or racism, there are dozens of readers who want to speak up.

It's a puzzling phenomenon. That's not to say it isn't fun to talk about those non-science issues—it clearly is a lot of fun or we wouldn't be doing it. The puzzling thing is why there aren't more comments about the science.

From time-to-time I asked for photographs of readers who have walked the real sandwalk. I'd like to acknowledge those who sent in pictures.

Cody
The God Delusion
T. Ryan Gregory
PZ Myers
John Wilkins

I hope I haven't forgotten anyone. Send photographs if you're not on the list already.

For those of you who are interested in the numbers, here are the statistics for Sandwalk. What they mean is that Sandwalk is on the verge of making the transition from a low popularity blog to a medium popularity blog. For comparison, Pharyngula gets one million views a month or 20X more than Sandwalk. In terms of the Top100Science Sites Bad Astronomy is 468th, Pharyngula ranks 794th, and Sandwalk is 1006th

Sandwalk has a long, long way to go. I think I'll try for quality instead of quantity!

Here are the top five postings in terms of number of comments: [Arguing Against God] [The Evolution Poll of Sandwalk Readers] [Propaganda Techniques: Shift the Burden of Proof] [Genomics Is Dead! Long Live Systems Biology!] [Dennett on Adaptationism].

Sandwalk readers are a diverse group in terms of geography. Yes, it's true that a majority of readers come from USA addresses, but there's still a large number of you from Europe, Asia, and Australia. There are even a handful of readers from South America and Africa. Oops ... I almost forget—there are Canadian readers as well.

On other issues the Sandwalk readers are less diverse. About 70% of you are atheists and almost all of you accept evolution—even though it may be the wrong version of evolution.

Next month's poll is going to ask about education. I suspect that most readers have been to university. This month the poll will be about your political views, e.g. where you position yourself on the left-right spectrum. I'll be surprised if most readers don't lean to the left.

Anyway, thanks for reading so far. And please, keep those comments coming—that's the most fun part of blogging.

P.S. If you have any suggestions for improving the looks or content of Sandwalk this is your chance to mention them.

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Dennett on Adaptationism

I've been trying to avoid the discussion of Dawkins vs Gould until the results of the poll are in (see left-hand margin). Those of you who voted for Dawkins will need some major reorientation to bring you into the 21st century. My task is enormous. (I know who you are!)

But since I brought up Daniel Dennett in reference to the aquatic ape just-so story [Aquatic Ape Speculation], I couldn't resist quoting him from Darwin's Dangerous Idea. After outlining the main points in favor of the speculation Dennett says,

The details—and there are many, many more—are so ingenious, and the whole aquatic-ape theory is so shockingly antiestablishment, that I for one would love to see it vindicated. That does not make it true, of course.

The fact that its principal exponent these days is not only a woman, Elaine Morgan, but an amateur, a science writer without proper official credentials in spite of her substantial researches, makes the prospect of vindication all the more enticing. The establishment has responded quite ferociously to her challenges, mostly treating them as beneath notice, but occasionally subjecting them to withering rebuttal. ... I have often asked them just to tell me, please, exactly why Elaine Morgan must be wrong about the aquatic-ape theory. I haven't yet had a reply worth mentioning, aside from those who admit, with a twinkle in their eyes, that they have often wondered the same thing.

We all love an underdog but this is going too far. The fact that Dennett can't see what's wrong with the aquatic ape speculation suggests that his understanding of evolution and how it works is vastly overrated. He then goes on to prove it.

My point in bringing up the aquatic-ape theory is not to defend it against the establishment view, but to use it as an illustration of a deeper worry. Many biologists would like to say, "A pox on both your houses!" Morgan deftly exposes the hand-waving and wishful thinking that have gone into the establishment tale about how—and why—Homeo sapiens developed bipedalism, sweating, and hairlessness on the savanna, not the seashore. Their stories may not be literally as fishy as hers, but some of them are every bit as speculative, and (I venture to say) no better confirmed. What they have going for them, so far as I can see, is that they occupied the high ground in the textbooks before Hardy and Morgan tried to dislodge them. Both sides are indulging in adaptationist Just So Stories and since some story or other must be true, we must not conclude that we have found the story just because we have come up with a story that seems to fit the facts. To the extent that adaptationists have been less than energetic in seeking further confirmation (or the dreaded disconfirmation) of their stories, this is certainly an excess that deserves criticism. [my emphasis in red—LAM]

This is classic adaptationist thinking. It assumes, without evidence, that there must be an adaptationist explanation for every feature. Hairlessness, for example, must be explained by some sort of just-so story involving running on the savanna or wading by the seashore. All the stories seem silly—including the aquatic ape speculation—but since one of the stories must be true we shouldn't reject it just because it makes no sense. There's no room for a non-adaptationist explanation in such a worldview.

Let's see how a pluralist might approach this problem.

For many reasons, ranging from the probable neutrality of much genetic variation to the nonadaptive nature of many evolutionary trends, this strict construction [adaptationism] is breaking down, and themes of unity are receiving renewed attention. ... One old and promising theme emphasizes the correlated effects of changes n the timing of events in embryonic development. A small change in timing, perhaps the result of a minor genetic modification, may have profound effects on a suite of adult characters if the change occurs early in embryology and its effects accumulate thereafter.

The theory of human neoteny, often discussed in my essays (see my disquisition on Mickey Mouse in The Panda's Thumb), is an expression of this theme. It holds that a slowdown in maturation and rates of development has led to the expression in adult humans of many features generally found in embryos or juvenile stages of other primates. Not all these features need be viewed as direct adaptations built by natural selection. Many, like the "embryonic" distribution of body hair on heads, armpits, and pubic regions, or the preservation of an embryonic membrane, the hymen, through puberty, may be nonadaptive consequences of a basic neoteny that is adaptive for other reasons—the value of slow maturation in a learning animal, for example.

                        Stephen Jay Gould in How the Zebra Gets Its Stripes

If you are a Dawkins/Dennett adaptationist then your explanations are confined to the sorts of adaptationist just-so stories promoted by the likes of Elaine Morgan. If you are a pluralist like Gould, you have more choices. Some of the pluralist nonadaptationist explanations might be right. In this case I think Gould is more likely to be right about the evolution of hairlessness. Unfortunately, Dennet and his ilk can't imagine such explanations because it doesn't fit with their idea of how evolution works.

Suzan Mazur doesn't like Carl Zimmer

There weren't many science writers are the Royal Society meeting in London (UK) [New trends in evolutionary biology: biological, philosophical and social science perspectives]. Carl Zimmer was there and so was Suzan Mazur. Carl was there to learn and do some research. Suzan was there to promote herself as the main publicist of the paradigm shifters.

Carl Zimmer wrote a news article about the meeting for Quanta: Scientists Seek to Update Evolution. The subtitle was "Recent discoveries have led some researchers to argue that the modern evolutionary synthesis needs to be amended." It was a pretty fair article and pretty good reporting on what went on at the meeting. I would have been a bit more harsh about the success of the so-called "paradigm shifters" but Carl did a good job of conveying the skepticism exhibited by many at the meeting. [See Kevin Laland's new view of evolution for my take on these "revolutionaries."]

Richard Dawkins' View of Random Genetic Drift

The Greatest Show on Earth is Richard Dawkins' latest book. It's his eighth book on evolution: the others are The Selfish Gene (1976), The Extended Phenotype (1982), The Blind Watchmaker (1986), River Out of Eden (1995), Climbing Mount Improbable (1996), Unweaving the Rainbow (1998) and The Ancestors Tale (2004).

I'm interested in the evolution of Richard Dawkins' ideas about evolution; in particular, his ideas about random genetic drift and mechanisms of evolution other than natural selection.

In Chapter 1 Dawkins says, "All reputable biologists go on to agree that natural selection is one of its most important driving forces, although—as some biologists insist more than others—not the only one."

This looks promising. Dawkins is saying— in chapter 1—that there are two mechanisms (driving forces) of evolution. He implies that he accepts random genetic drift as a "driving force" of evolution. (Assuming that random genetic drift is what he has in mind.) It's clear that "some biologists" have influenced him, although it's not clear from the sentence whether those biologists are "reputable"!

Since this is a book about the evidence for evolution, I eagerly anticipated his explanation of random genetic drift. Would it be as good as Jerry Coyne's?¹ In fact, I was so eager that I couldn't wait. I jumped to the index to look under "random."

Nothing. Not to worry. The other important mechanism must be here somewhere. Is it indexed under "genetic"? No. What about "drift"? No, not there either.

What gives? How can you write a book about evolution in the 21st century without mentioning random genetic drift as an important mechanism of evolution? Even the other adaptationist, Jerry Coyne, has it in the index to Why Evolution Is True.

Maybe Dawkins uses another term for the second mechanism of evolution. I recalled that he often gets mixed up about the difference between neutral theory and random genetic drift. Let's see if "Neutral Theory" is in the index. Nope.

What about "Kimura"? Success at last! Check out page 332.

Page 332 is in the middle of a section on The Molecular Clock in Chapter 10. It seems a bit late to begin discussing the second mechanism of evolution, but, as I said before, it's promising that Dawkins even concedes that there is one.

Dawkins explains that the reason why there's a molecular clock is because the majority of changes at the genetic level are neutral and these changes are fixed in a regular, clock-like, albeit stochastic, process. He then goes on to say...

When the neutral theory of molecular evolution was first proposed by, among others, the great Japanese geneticist Motoo Kimura, it was controversial. Some version of it is now widely accepted and, without going into the detailed evidence here, I am going to accept it in this book. Since I have a reputation as an arch-"adaptationist" (allegedly obsessed with natural selection as the major or even only driving force of evolution) you can have some confidence that if even I support the neutral theory it is unlikely that many other biologists will oppose it!

I can't think of any serious biologists who would deny that neutral mutations exist. The essence of Neutral Theory, or Nearly Neutral Theory as it is currently called, is undoubtedly correct. The fact that Richard Dawkins accepts it in this book is not remarkable. What's remarkable is that he has to tell us that he accepts it, especially in a book about the evidence for evolution.

Meanwhile, we are still waiting for the explanation of the "other" mechanism of evolution. The one that was mentioned in Chapter 1 when he said that natural selection does not account for all of evolution. He can't have been thinking about "Neutral Theory" since that's not a mechanism of evolution. And he can't just have been thinking about a mechanism for fixing neutral mutations since he surely knows that the "other" mechanism can result in the loss of beneficial alleles and the fixation of detrimental ones.

Still waiting. What we see in Chapter 10 is an explanation of neutral mutations but no mention of random genetic drift—the mechanism responsible for fixing neutral mutations in a population. He does briefly mention on page 335 that neutral mutations can "go to fixation by chance." I get the impression that he goes out of his way to not name the other mechanism of evolution. You know what I'm referring to, it's the mechanism that gets a whole chapter to itself in all the evolutionary biology textbooks [Evolution: Table of Contents].

Dawkins concedes that the vast majority of the human genome consists of sequences that aren't genes. Here's how he puts it ...

It is a remarkable fact that the greater part (95% in the case of humans) of the genome might as well not be there, for all the difference it makes. The neutral theory applies even to many of the genes in the remaining 5%—the genes that are read and used. It applies even to genes that are totally vital for survival. I must be clear here. We are not saying that a gene to which the neutral theory applies has no effect on the body. What we are saying is that a mutant version of the gene has exactly the same effect as the unmutated version.

In other words, the vast majority of the DNA in our genome is junk. Mutations that occur in junk DNA will become fixed in spite of the fact that they are not seen by natural selection. This is what he means when he says that most mutations are neutral and it's equivalent to saying that the dominant mechanism of evolution, in terms of overall frequency, is random genetic drift and not natural selection. I just wish he'd come right out and say it.

It's a shame that Dawkins does not actually mention the mechanism by which those neutral mutations become fixed but instead continuously refers to neutral theory as the alternate mode of evolution. The general public needs to hear about random genetic drift and Dawkins is—like it or not—the most prominent evolutionist on the planet.

Dawkins has not changed his mind about the existence of these neutral mutations and he has not changed his mind about their importance. While they may exist, they are not important as far as evolution is concerned. He makes this very clear—once again—in this book.

As it happens, it is probably true to say that most mutations are neutral. They are undetectable by natural selection, but detectable by molecular geneticists; and that is an ideal combination for an evolutionary clock.

None of this is to downgrade the all-important tip of the iceberg—the minority of mutations that are not neutral. It is they that are selected, positively or negatively, in the evolution of improvements. They are the ones whose effects we actually see—and natural selection "sees" too. They are the ones whose selection gives living things their breathtaking illusion of design. But it is the rest of the iceberg—the neutral mutations which are in the majority—that concerns us when we are talking about the molecular clock.

As geological time goes by, the genome is subjected to a rain of attrition in the form of mutations. In that small portion of the genome where the mutations really matter for survival, natural selection soon gets rid of the bad ones and favors the good ones. The neutral mutations, on the other hand, simply pile up, unpunished and unnoticed—except by molecular geneticists.

This is the way the adaptationist dismisses non-adaptive evolution. It's not really of interest to real biologists. It's only interesting to molecular geneticists. And we all know that those people are not real evolutionary biologists!

Now we come to one of the most interesting sentences in the entire book; at least as far as I'm concerned. As most Sandwalk readers know, we have long debated whether or not visible mutations can be neutral. Once you have an observed phenotype, can you ever attribute it to neutrality? Many adaptationists argue that you can't.

Here's what Richard Dawkins says in his latest book.

It is also possible (although "ultra-Darwinists" like me incline against the idea) that some mutations really do change the body, but in such a way as to have no effect on survival, one way or the other.

This is progress. Back when he wrote The Extended Phenotype, in 1982, Richard Dawkins said.

The adaptationism controversy is quite different. It is concerned with whether, given that we're dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. The biochemist's "neutral mutations" are more than neutral. As far as those of us who look at gross morphology, physiology and behavior are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976) wrote: "I interpret 'rate of evolution' as a rate of adaptive change. In this sense, the substitution of a neutral allele would not constitute evolution ..." If a whole organism biologist sees a genetically determined differences among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.

Finally, in 2009, Richard Dawkins admits that it is "possible" that visible mutations could be neutral. Hallelujah!

I'm looking forward to book #9.

---

1. Jerry Coyne's View of Random Genetic Drift

"Reasons to Believe" in ENCODE

Fazale "Fuz" Rana is a biochemist at Reasons to Believe". He and his colleagues are Christian apologists who try to make their faith compatible with science. Fuz was very excited about the ENCODE results when they were first published [One of the Most Significant Days in the History of Biochemistry]. That's because Christians of his ilk were very unhappy about junk DNA and the ENCODE Consortium showed that all of our genome is functional.¹

Fuz is aware of the fact that some people are skeptical about the ENCODE results. He wrote a series of posts defending ENCODE.

1. Do ENCODE Skeptics Protest Too Much? Part 1 (of 3)
2. Do ENCODE Skeptics Protest Too Much? Part 2 (of 3)
3. Do ENCODE Skeptics Protest Too Much? Part 3 (of 3)

The first post is merely a list of the objections many of us raised.

The Evolution Poll of Sandwalk Readers

 
The poles are closed and the results are in. Richard Dawkins is the clear winner (boo!).

The good news is that 87% (499/573) Sandwalk readers have legitimate scientific views of evolution (Dawkins + Gould + Futuyma). Only a small number of readers are creationists or proponents of theistic evolution.

The bad news is that most readers are split between three different views of evolution. Some people have asked me to explain these three views so here's a brief summary of how I distinguish between Dawkins, Gould, and Futuyma.

Richard Dawkins holds the Charles Simonyi Chair for the Public Understanding of Science at Oxford University (UK). In his first book, The Selfish Gene (1976), he promoted the idea that evolution can be viewed as a competition between genes. This concept was amplified in The Extended Phenotype (1982) where he also answered the main criticism of the selfish gene concept. Dawkins' most popular book was The Blind Watchmaker, first published in 1986. In that book he made the case for design by natural selection and attempted to dismiss, or minimize, all other mechanisms of evolution. The emphasis on the power of natural selection was expanded in Climbing Mt. Improbable (1996).

Dawkins is the leading exponent of adaptationism—or Ultra-Darwinism—the idea that everything interesting in evolution can be explained by adaptation. This is especially true of traits that give rise to visible phenotypes. Dawkins is not very interested in macroevolution and he dismisses punctuated equilibria and species sorting. He believes, along with most adaptationists, that macroevolution is just an extension of natural selection acting on populations. (See RichardDawkins,net for a complete list of books and articles.)

Stephen Jay Gould was Alexander Agassiz Professor of Zoology at Harvard University from 1967 until his death in 2002.

He published Ontogeny and Phylogeny in 1977 where he made the case for a relationship between development and evolution. In The Mismeasure of Man (1981) he criticized biological determinism. Wonderful Life (1989) described the Burgess Shale fossils and explained Gould's ideas about the role of chance and contingency in evolution. In 2002, Gould published The Structure of Evolutionary Theory where he attempts to explain macroevolution, punctuated equilibria, and species sorting. These are part of Gould's hierarchical approach to evolutionary theory. Gould identifies himself as a pluralist—one who recognizes many different mechanisms of evolution that can give rise to important and interesting features. He tends to place much more emphasis on chance and accident in evolution than Dawkins.

Gould, along with Niles Eldredge, is famous for the concept of punctuated equilibrium. This is the idea that much of the change in the characteristics of species is concentrated in brief speciation (by cladogenesis) events.

Gould wrote a regular column for Natural History magazine and many of his articles have been collected in a series of anthologies: Ever Since Darwin, The Panda's Thumb, Hen's Teeth and Horse's Toes, The Flamingo's Smile, Bully for Brontosaurus, Eight Little Piggies, Dinosaur in a Haystack, Leonardo's Mountain of Clams and the Diet of Worms, The Lying Stones of Marrakech, and I Have Landed. Some of his essays and some of his scientific articles are widely cited. (For a complete list see SJG Archive.)


Douglas J. Futuyma is a Professor of Ecology & Evolution at the State University of New York at Stoney Brook. He is best known for his textbooks on evolution; Evolutionary Biology (1998) and Evolution (2005). His major research interests are evolutionary theory [see Hypotheses, Facts, and the Nature of Science] and the interactions of plants and insects [see Insect Pests: Resistance and Management].

Futuyma's view of evolution is different from that of Richard Dawkins because Futuyma is interested in random genetic drift and speciation. Futyuma is much more aware of population genetics than Dawkins or Gould and he (Futuyma) frequently refers to it in his books and papers. Unlike Gould, Futuyma is skeptical of punctuated equilibria and particularly species selection/sorting, although, ironically, he is credited with proposing the best explanation of the connection between cladogenesis and evolution.

You can check out some of Futuyma's ideas in this interview. In response to the question, "Is natural selection the only mechanism of evolution?", Futuyma replies,

No, certainly not. There cannot be evolution without genetic variation in the first place. So there must be mutation and often recombination to generate the different genotypes or the different versions of the genes, known as alleles, which then may or may not make a difference in the ability of an organism to survive and reproduce. You can’t have any evolutionary change whatever without mutation, and perhaps recombination, giving rise to genetic variation. But once you have genetic variation, there are basically two major possibilities:

First, there is simply no difference between the different genotypes or different genes in their impact on survival or reproduction, and in that case, you can have random changes of one versus the other type in a population or a species until eventually one replaces the other. That is an evolutionary change. It happens entirely by chance, by random fluctuations. That is what we call the process of genetic drift.

Genetic drift is very different from possibility number two, natural selection, which is a much more consistent, predictable, dependable change in the proportion of one gene vs. another, one genotype vs. another. Why? Simply because there is some consistent superiority, shall we way, of one genotype vs. another in some feature that affects its survival or some feature affecting its reproductive capabilities.

Neither Gould or Dawkins would respond in this way. Dawkins would admit to random genetic drift but downplay its importance. Gould would focus on higher mechanisms of evolution like species sorting.

Futuyma also thinks about the role of mutation in a different way than either Dawkins or Gould, especially Dawkins. While Dawkins is very much opposed to crediting mutations per se with any substantial influence on evolution, Futuyma is more sympathetic to a limited mutationism point of view. For example, when asked what would happen if the tape of life were re-played he says.

Of course, it wouldn’t be the same, because first of all, random processes are involved in the evolutionary process. For example, the origin of new mutations: a lot of evolution is dependent on particular mutational changes in genes that were very, very rare or unlikely, but that just happened at the right time, in the right species, in the right environment, but it need not happen that way. So, there’s this unpredictability.

This is very unlike Dawkins who is more inclined to think of evolution as design and strongly resists any attempt to sneak randomness into the equation. For the most part, Dawkins believes that all possible mutations will be available for selection so mutations can never determine the direction of evolution. Gould prefers to focus on developmental constraints as possible limits to the effectiveness of natural selection.

Freedom in the Classroom (2007): Balance

 
I'm discussing the Freedom in the Classroom (2007) report from the American Association of University Professors [Freedom in the Classroom (2007].

The first posting covered the issue of indoctrination and made the point that Professors have to allow for debate in the classroom [Freedom in the Classroom (2007): Indoctrination].

But allowing for classroom debate is not sufficient. I'd go one step further, I would insist that Professors actually address the contrary opinions in the classroom and provide references to the writings of other academics who present the other side of the controversy.

The reason for advocating this is to avoid indoctrination by default. If the students are unaware of the controversy—which they often are—then the Professor is guilty of bias by not alerting students to the possibility that they can hold a valid, but different, opinion.

I was recently alerted to this problem when I learned that our second year students had never heard of random genetic drift or punctuated equilibria in their first year biology class Organisms in Their Environment. This course is taught by members of the Dept. of Ecology and Evolutionary Biology and the course description is,

Evolutionary, ecological, and behavioural responses of organisms to their environment at the level of individuals, populations, communities, and ecosystems.

I think my colleagues may be guilty of indoctrination if they're only presenting an adaptationist view of evolution and not alerting our students to other mechanisms of evolution.

The AAUP report covers this issue as well.

Balance

Current charges of pedagogical abuse allege that instruction in institutions of higher education fails to exhibit a proper balance. It is said that instructors introduce political or ideological bias in their courses by neglecting to expose their students to contrary views or by failing to give students a full and fair accounting of competing points of view.

I completely agree with this charge. I think it's criminal if Professors don't bring up contrary views in the classroom. How do universities ensure that Professors present both sides of a controversy?

We note at the outset that in many institutions the contents of courses are subject to collegial and institutional oversight and control; even the text of course descriptions may be subject to approval. Curriculum committees typically supervise course offerings to ensure their fit with programmatic goals and their compatibility with larger educational ends (like course sequencing). Although instructors are ethically obligated to follow approved curricular guidelines, "freedom in the classroom" affords instructors wide latitude to decide how to approach a subject, how best to present and explore the material, and so forth. An instructor in a course in English Romantic poetry is free to assign the poetry of the Harlem Renaissance so long as the course remains focused more on John Keats than on Langston Hughes.

This is how universities and departments are supposed to work. Collectively, they draw up guidelines for courses in order to make sure that all the essential topics are covered. Once the course is under way, there should be some feedback between what's supposed to be taught and what is actually taught in the classroom. Unfortunately, this doesn't always occur. Even more unfortunately, it's not always true that the department as a whole is aware of some controversies.

In the case that I alluded to above, I'm not certain that the Dept. of Ecology and Evolutionary Biology thinks there's a problem with the way our first year course is being taught. Does that absolve them of the charge of indoctrination?

To make a valid charge that instruction lacks balance is essentially to charge that the instructor fails to cover material that, under the pertinent standards of a discipline, is essential. There may be facts, theories, and models, particularly in the sciences, that are so intrinsically intertwined with the current state of a discipline that it would be unprofessional to slight or ignore them. One cannot now teach biology without reference to evolution; one cannot teach physical geology without reference to plate tectonics; one cannot teach particle physics without reference to quantum theory. There is, however, a large universe of facts, theories, and models that are arguably relevant to a subject of instruction but that need not be taught. Assessments of George Eliot's novel Daniel Deronda might be relevant to a course on her Middlemarch, but it is not a dereliction of professional standards to fail to discuss Daniel Deronda in class. What facts, theories, and models an instructor chooses to bring into the classroom depends upon the instructor's sense of pedagogical dynamics and purpose.

Fair enough. One could perhaps argue that random genetic drift and punctuated equilibria, for example, are not essential topics in a first year course on evolution. But you'd have to be a damn fool to make such an argument. I think these are "theories, and models ... that are so intrinsically intertwined with the current state of a discipline that it would be unprofessional to slight or ignore them."

To urge that instruction be "balanced" is to urge that an instructor's discretion about what to teach be restricted. But the nature of this proposed restriction, when carefully considered, is fatally ambiguous. Stated most abstractly, the charge of lack of balance evokes a seeming ideal of neutrality. The notion appears to be that an instructor should impartially engage all potentially relevant points of view. But this ideal is chimerical. No coherent principle of neutrality would require an instructor in a class on constitutional democracy to offer equal time to "competing" visions of communist totalitarianism or Nazi fascism. There is always a potentially infinite number of competing perspectives that can arguably be deemed relevant to an instructor's subject or perspective, whatever that subject or perspective might be. It follows that the very idea of balance and neutrality, stated in the abstract, is close to incoherent.

We concede this point. Nobody is asking an adaptationist Professor, for example, to give equal time to punctuated equilibria and Gould's hierarchical theory of evolution. That would be absurd and it would go against one of the most important principles of good education, namely the idea that students should be exposed to the passionate opinions of experts in the field. I don't like the mamby-pamby, politically correct view that we have to be dispassionate reporters of facts in the classroom.

The ideal of balance makes sense only in light of an instructor's obligation to present all aspects of a subject matter that professional standards would require to be presented. If a professor of molecular biology has an idiosyncratic theory that AIDS is not caused by a retrovirus, professional standards may require that the dominant contrary perspective be presented. Understood in this way, the ideal of balance does not depend on a generic notion of neutrality, but instead on how particular ideas are embedded in specific disciplines. This is a coherent idea of balance, and it suggests that balance is not a principle that can be invoked in the abstract but is instead a standard whose content must be determined within a specific field of relevant disciplinary knowledge.

The authors of this report have clearly thought about these criticisms a great deal. They are to be congratulated on crafting an excellent summary of the important issues in university education. The point here is well-taken. The point about "balance" in the classroom is not to enforce strict bland neutrality. It's to make sure that the opinions of Professors are placed in the appropriate context of the discipline.

There might be a controversy about "appropriate context." Maybe there are many evolutionary biologists who believe that "balancing" adaptationism with silly ideas about pluralism is not required in order to maintain professional standards? How do we resolve that?

This part of the report closes with a succinct statement of a principle that most people don't appreciate.

If scholars must be free to examine and test, they must also be free to explain and defend their results, and they must be free to do so as much before their students as before their colleagues or the public at large. That is the meaning of "freedom in the classroom." To charge that university and college instruction lacks balance when it does more than merely summarize contemporary debates is fundamentally to misconstrue the nature of higher learning, which expects students to engage with the ideas of their professors. Instructors should not dogmatically teach their ideas as truth; they should not indoctrinate. But they can expect their students to respond to their ideas and their research. As students complete different courses taught by different professors, it is to be hoped that they will acquire the desire and capacity for independent thinking.

This puts some of the onus on the students. They have an obligation to engage in their own education and not to just sit there and soak up facts. This is not the normal politically correct view of university education. In that view, students can never be blamed for the problems in the universities.

(BTW, just for the record. There are lots of problems in universities and I think that Professors are to blame for most of them.)

The Evolution of God

 
Robert Wright is a journalist known for founding Bloggingheads.tv. He has written several books, notably The Evolution of God, which was published this year.

His schtick is the compatibility of science and religion. According to him, accommodation will be achieved once believers come to accept natural selection and convert to some form of deism, and once atheists learn to accept that this kind of wishy-washy (not his terminology) religion is compatible with science.

I recently linked to a blogging heads discussion between Wright and Daniel Dennett in which I criticized both of them for misunderstanding evolution. Wright seems to have bought into the Dennett idea of natural selection being the only mechanism of evolution. Wright also believes that natural selection will inevitably lead to sentient beings with a sense of moral purpose.

If this is true then science has to accept the fact that God could have cooked the books so that creatures would eventually evolve to the point where they were willing to worship him and offer sacrifices. And they would do so in spite of the absence of scientific evidence for the existence of such a non-interventionist, deistic, God. All the stories about an interventionist God must be wrong. If you're a deist, there was no deluge, no chosen people, and no divine Jesus.

Under such a scenario, I often wonder how believers would know what kind of God to worship. How do you distinguish between a Satan and Gitche Manitou if the deistic god has gone to such great lengths to be hands off during the evolution of sentient beings?

Robert Wright's latest foray into this debate comes as an op-ed piece in yesterday's New York Times: Direction and Purpose in Evolution. He reiterates the point that both sides of the war between science and religion are wrong. He is a confirmed accommodationist.

There are atheists who go beyond declaring personal disbelief in God and insist that any form of god-talk, any notion of higher purpose, is incompatible with a scientific worldview. And there are religious believers who insist that evolution can't fully account for the creation of human beings.

I don't want to discuss that argument except to say, for the record, that I'm one of those who insist that's there's no evidence of purpose in the evolution of life. Any talk of there being a direction to evolution, where sentient beings are the ultimate goal, founders on a massive lack of evidence in support of such a notion.

However, I'm willing to accept that biological science is more or less compatible with the existence of a supernatural being who created life on Earth and then stepped back to let history play out according to the standard rules of physics and chemistry.

Where I differ from people like Wright and Dennett is that my version of evolution is not restricted to natural selection. In my view of evolution, accident and chance play important roles at both the macro- and micro levels. Mass extinctions are just one example at the macro- level and random genetic drift is the most important example at the micro- level.

Why is this important? It's important because it gets us away from "design" talk. Most believers are committed to talk of design and purpose because otherwise life has no meaning. If they accept evolution then they make science and religion compatible by evoking God as the cause of natural selection. In this accommodationist scenario, God achieves his purpose through the law of natural selection.

Some philosophers and evolutionary biologists also believe that evolution is an algorithmic process, relying (almost) exclusively on natural selection as the driving force. Some, like Daniel Dennett, use metaphors such as building skyscrapers in order to illustrate their view of purposeful evolution. By invoking purpose and design, these philosophers and evolutionary biologists lend support to those believers who also see evidence of design and purpose. Robert Wright is correct to point out that the two groups, atheistic adaptationists and deistic believers, are not that far apart.

I bring good news! These two warring groups have more in common than they realize. And, no, it isn't just that they're both wrong. It's that they're wrong for the same reason. Oddly, an underestimation of natural selection's creative power clouds the vision not just of the intensely religious but also of the militantly atheistic.

If both groups were to truly accept that power, the landscape might look different. Believers could scale back their conception of God's role in creation, and atheists could accept that some notions of "higher purpose" are compatible with scientific materialism. And the two might learn to get along.

This is a little confusing because many of the "militant atheists" he complains about are strong adaptationists who are only too willing to explain everything by natural selection. Those scientists clearly see design and purpose in evolution, but that doesn't make them accommodationists.

Robert Wright evokes evolutionary psychology in defense of accommodationism. Using the "moral law" example, he points out that natural selection can explain morality and believers have to accept this "fact." However, those same believers can take comfort in the idea that God planned this when he created natural selection in the first place, so the evolution of a "moral law" is consistent with belief in a deistic God.

Indeed, this dynamic of reciprocal altruism, as mediated by natural selection, seems to have inclined us toward belief in some fairly abstract principles, notably the idea that good deeds should be rewarded and bad deeds should be punished. This may seem like jarring news for C. S. Lewis fans, who had hoped that God was the one who wrote moral laws into the charter of the universe, after which he directly inserted awareness of them in the human lineage.

But they may not have to stray quite as far from that scenario as they fear. Maybe they can accept this evolutionary account, and be strict Darwinians, yet hang on to notions of divinely imparted moral purpose.

The first step toward this more modern theology is for them to bite the bullet and accept that God did his work remotely — that his role in the creative process ended when he unleashed the algorithm of natural selection (whether by dropping it into the primordial ooze or writing its eventual emergence into the initial conditions of the universe or whatever).

Of course, to say that God trusted natural selection to do the creative work assumes that natural selection, once in motion, would do it; that evolution would yield a species that in essential respects — in spiritually relevant respects, you might say — was like the human species. But this claim, though inherently speculative, turns out to be scientifically plausible.

Wright is mostly directing his arguments at theists in order to convince them that they can accept evolution without abandoning the concepts of a God-given morality and a life with meaning and purpose. He spends less time trying to convince atheistic scientists because he believes that his interpretation of the science is correct. His blogging head conversation with philosopher Daniel Dennett has convinced him that most scientists think this way.

For starters, there are plenty of evolutionary biologists who believe that evolution, given long enough, was likely to create a smart, articulate species — not our species, complete with five fingers, armpits and all the rest — but some social species with roughly our level of intelligence and linguistic complexity.

And what about the chances of a species with a moral sense? Well, a moral sense seems to emerge when you take a smart, articulate species and throw in reciprocal altruism. And evolution has proved creative enough to harness the logic of reciprocal altruism again and again.

This is the part I dispute. I don't believe that the evolution of some sort of sentient species was inevitable. And I don't believe there's a universal moral law that evolved due to natural selection. My version of evolution, involving copious amounts of chance and accident, just happened to produce sentient beings on this planet. I suspect that if we looked at a thousand planets with life we wouldn't see another example.

Furthermore, I think that our sense of proper morality is mostly cultural, not genetic. We didn't "evolve" a hard-wired guilty feeling whenever we treated people unfairly. After all, people in many cultures supported slavery and mistreatment of women for thousands of years without being consumed by the expression of their "guilt" genes. Most of what passes for morality is not due to genes (alleles) for reciprocal altruism. Instead, a great deal of "morality" is an epiphenomenon that follows naturally whenever you have intelligent beings living together in a society that has learned the advantages of co-operation.

Robert Wright's mistake is assuming that adaptationism is the general consensus in biology. His accommodationist argument fails if science doesn't recognize design and purpose as the key paradigms of evolution.

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