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Saturday, December 08, 2012

James Shapiro Responds to My Review of His Book

I reviewed Shapiro's book, Evolution: A View from the 21st Century for NCSE reports. (NCSE = National Center for Science Education.) You can read it here.

James Shapiro has responded to my review in the latest issue of NCSE reports: Reply to Laurence A Moran’s review of Evolution: A View
from the 21st Century

Shapiro seems to be really upset that NCSE would choose someone like me to review his book. He opens his rebuttal with ...
Before I saw Laurence A Moran’s book review (Moran 2012), I wrote the following: “It is a shame that NCSE chose Larry Moran to review my book; not because of anything he said in the review but because he is hostile to new ideas and perspectives.”

A year ago, Moran posted a piece entitled “Physicists and biologists” on his Sandwalk blog [Physicists and Biologists1]. In this post, he ridiculed the enthusiasm I expressed in the book for physicists coming into evolutionary studies and bringing new skills and new ideas.
Meanwhile, I welcome all those physicists who know nothing about evolution, protein structure, genetics, physiology, metabolism and ecology. That’s just what we need in the biological sciences to go along with all the contributions made by equally ignorant creationists.
What a great way to make new friends for evolution science—equating physicists with creationists and calling them “equally ignorant”!
I stand by my criticism of physicists who think that all they have to do is think about biology in order to set the rest of us straight on some important concepts. And I stand by my criticism of biologists who support them.

What I object to is is being characterized as someone who is "hostile to new ideas and perspectives."

I suspect that NCSE agreed to my review because I have a bit of knowledge of biochemistry, molecular biology, and evolution. I'm particularly interested in new ways of looking at evolution from the perspective of randomness and accident. I'm also fairly knowledgeable about the history of recent attacks on modern evolutionary theory.

I can understand Shapiro's frustration because everyone who knows anything about his subject matter thinks he's way off base. On the other hand, Intelligent Design Creationists are big fans of his writing. I suppose he would have preferred it if Casey Luskin had written the review for NCSE Reports. I don't think that was going to happen.

Shapiro continues ...
My argument is that molecular research over the past sixty years on DNA change processes has taught us that virtually all genetic variation results from the action of regulated cell biochemistry, including a wide array of cutting, splicing and polymerizing functions that I summarize under the term “natural genetic engineering”. I assert that this realization represents a fundamental shift from the conventional view that genetic change is a random, accidental process.
Yep, that's true. Shapiro claims that the "old" idea of variation caused mostly by accidental DNA replication errors is wrong. The implication is that of the roughly 100 new mutations in every new born baby, most are due to "natural genetic engineering."

And when we compare the DNA sequences of genes from different species the results don't actually show mostly neutral changes that have been fixed by random genetic drift but, instead, they show that most of this variation is due to "natural genetic engineering." There's no defense of these implications in his book but I suppose that's simply because he thinks they are self-evident.

The history of life represents 3.5 billion years of evolution of tens of millions of species. Shapiro presents several pages of references documenting or speculating that there have been some interesting mutations due to gene rearrangements, transposon insertions, genome duplications, and other such events. I found this stuff boring and uninteresting because it's mostly old stuff from the 1970s and 1980s it doesn't address his claim that this is novel and that it represents "a fundamental shift from the conventional view."

Shapiro says,
In his review, Moran tells us “I have to confess that I skipped most of this chapter [that is, Part II, emphasis added]. I know about genome rearrangements and so does everyone else who has read a textbook in the past forty years” (Moran 2012:9.2). Frankly, I am not aware of textbooks that have routinely covered mutator polymerases, diversity-generating retroelements, retrosplicing group II introns, CRISPRs, SINE elements and many other natural genetic engineering systems over the past 40 years. In fact, one of the reasons for writing the book was that people who had seen my journal articles would often ask, “Is there a book where I can read more about this?”
I discussed all those topics, except CRISPRs, in my big biochemistry textbook twenty years ago (Moran, Scrimgeour, 1992). They have also been covered in the various editions of Genes by Benjamin Lewin, beginning in the mid 1980's. I can't begin to imagine how James Shapiro can claim to be an expert on these things without being aware of what's taught in undergraduate molecular biology classes. He seems to be living in an intellectual vacuum.

One of the main points of my critique was that rare events such as genome duplications do occur but that is fully consistent with the role of chance and accident in evolution. Events occurring on million year time scales do not justify a claim that "virtually all genetic variation" is due to "natural genetic engineering."

Here's how Shapiro responds to that criticism ...
When you find yourself in a hole, stop digging.

Will Rogers
To counter my position, Moran writes,
His main thesis seems to be that such mutations are not random as neo-Darwinism demands. Genome duplication is one example. There may have been two genome duplications in the vertebrate lineage. Both of them occurred in fish. (Moran 2012:9.2)
This is wrong and misleading. There were indeed two genome duplications in the history of teleosts, at key points of phylogenetic diversification, but they were far from unique in vertebrate evolution. I was quite explicitly referring to the pair of duplications that, successively, coincided with the origins of all vertebrates and then of all jawed vertebrates (Nakatani and others 2007). I think RNCSE readers will agree that these certainly constituted major events in animal evolution.
So, Shapiro claims that there were actually FOUR events spread out over 400 million years. That's one every 100 million years. I caution RNCSE readers not to assume that those are random accidents. And please, dear RNCSE readers, understand that this is powerful evidence for a "fundamental shift from the conventional view that genetic change is a random, accidental process."

I raised the same issue with respect to transposon mediated events. Are they common and do they provide evidence for some directed form of evolution ("natural genetic engineering"). Are they evidence against randomness and accident as the main source of variation?

Shapiro thinks my criticism was misguided ...
Moran continues to depict what I had to say about the evolutionary role of natural genetic engineering as exaggerated:
Another example involves transposons. In the hominid lineage there may be evidence of a few transposon-related genome alterations that turned out to be beneficial and subsequently became fixed in the population. That’s a rate of approximately one every million years or so. (Moran 2012:9.2)
This downplaying of the role of transposons (a class of mobile genetic elements) is quite an ironic assertion. The rate with which “transposon-related genome alterations” are being discovered by parsing genome sequences is truly astonishing. At the end of last year, a group of bioinformaticians published a Nature paper examining the human genome as compared to 29 other aligned vertebrate genomes. They said:
We report … 280,000 non-coding elements exapted from mobile elementsand more than 1,000 primate- and human-accelerated elements. (Lindblad-Toh and others 2011:476)
Perhaps Moran would not have made his tendentious error about the rarity of “transposon related genome alterations” if he had not have skipped so much of the core of my book.
What I "skipped" is the litany of references to papers documenting the occasional beneficial mutation events due to transposon insertions in various species.2 The list does nothing to convince readers that this is a common process and it does nothing to convince readers that it is planned ("natural genetic engineering"). It's very much like the approach taken by creationists when they list all the papers critical of evolution or all the papers showing evidence that some little piece of DNA is not junk.

Good science requires much more than just long lists of references that you think support your claim. It also requires putting that work into context, reporting the papers that conflict with your view, and discussing the possible flaws and misinterpretations in the scientific literature. In other words, good science requires healthy skepticism and critical thinking.
Finally, since I spoke of cell sensory mechanisms and cognition, Moran pulled out the “intelligent design” card and made disparaging use of the fact that I published two peer-reviewed papers on the importance of repetitive DNA in 2005 with Richard von Sternberg (Shapiro and Sternberg 2005; Sternberg & Shapiro 2005). Sternberg turned out to become something of an ID cause célèbre the following year.
Shapiro’s views seem to be philosophically similar to those of Richard Sternberg (Richard von Sternberg)—the two of them published several articles together a few years ago. (Moran 2012:9.3)
What Sternberg’s personal views have to do with these papers or the contents of my book, readers can judge for themselves. I am happy to stand by their scientific validity. The fact Moran chose to use a “guilt-by-association” approach to criticize my book speaks volumes about the character of his review.
I thought long and hard about this part of the review. The problem is that Shapiro's thoughts are rejected by the scientific community but enthusiastically endorsed by Intelligent Design Creationists. That requires an explanation because it goes to the heart of what NCSE is all about.

I think it's interesting that Shapiro choose to publish with a well-known creationist and I think it's interesting that he agreed to post an article on the main Discovery Institute blog. I think it's interesting that his style of argument is so similar to that used by the Intelligent Design Creationists.

I once asked James Shapiro whether he believes in god(s) and whether his "discovery" of some form of directed evolution has anything to do with that belief. He declined to answer.

1. I added the link. Here's part of what I said in my post.
Why don't I move to physics and solve their problems? I've got all the proper qualifications, "lacking a formal education," "less prejudicial background," and I haven't been taught to exclude impossible things. I bet I could convince half a dozen of my biologist colleagues to abandon the difficult problems of biology in order to help the physicists. It shouldn't take more than a few years.

We need a name for this discovery, let's call it The Shapiro Conjecture.
2. Shapiro thinks that dozens of pages of lists represent the "core" of his book. I find that very interesting.


john harshman said...

What exactly is "naural genetic engineering"? How is it supposed to sense the needs of evolution? How is it supposed to have arisen originally?

Pépé said...

Gee, I always thought NCSE stood for Nineteenth Century Science Education!

SLC said...

I'm sure that the physicists are waiting with bated breath for Prof. Moran's take on the string hypothesis. End snark.

Unknown said...

Is "natural genetic engineering" just another euphemism for intelligent design or directed evolution and is that what Shapiro is advocating?

Piotr Gąsiorowski said...

... or was it "No Creo Shall Enter"?

Larry Moran said...

Your guess is as good as mine. Shapiro won't answer such questions.

Larry Moran said...

You would think that these questions should be answered in his book. Right?

Have you read it?

Larry Moran said...

I tried to help my daughter with her Ph.D. thesis in astrophysics.

She wasn't impressed.

Argon said...

'Natural genetic engineering' covers all the stuff that Shapiro thinks cannot possibly be covered by 'undirected events'. In other words, it means exactly what Shapiro thinks it should mean... nothing more and nothing less.

chemicalscum said...

My guess it is another failed attempt to reintroduce teleology into biology. This was the great achievement of Darwin finally extirpating teleology from biology.

An example in defence of physicists just thinking about biology, is Schrödinger in spite of his immersion in eastern mysticism. In "What is life?" back in the 1940's he demonstrated purely on quantum mechanical grounds that the genetic material must be molecular rather than a supra-macromolecular assembly as was thought by most biologists at the time. This was published in the same year as Avery et al's paper (1944) demonstrating that DNA was the genetic material.

A counter example is of course Fred Hoyle in his later life. Back in the 80's I read an article in the New Scientist that he and Wickramsinghe wrote on diseases from space. It was so totally ignorant of basic biology that it was pathetic. It made me want to weep. It was sad that a once great scientist had fallen so low. The thing Avery and Hoyle had in common was they both deserved Nobel prizes for their work but were ignored.

Rolf Aalberg said...

Shapiro: "...the concept of cell-guided natural engineering fits well inside the boundary of 21st Century biological science. Despite widespread philosophical prejudices, cells are now reasonably seen to operate teleologically: their goals are survival, growth and reproduction."

The question I have all the time reading Shapiro is: What cells, where and when in the reproductiive cycle are involved in the process of natural genetic engineering?

john harshman said...

Haven't read it, but I presume by the answers that he never actually explains anything.

Anonymous said...

Good Lord! I'm not surprised that the man is intransigent; he hasn't even clarified what me means by "natural genetic engineering," much less how that is supposed to produce complex adaptations. But I AM surprised that the NCSE gave him so much space to reply. It's not, after all, The New York Review of Books.

Your review was fair, and Shapiro, like many people who think themselves unappreciated revolutionaries, is showing a thin and unseemly skin. The best response to a critical review of one's book is to say nothing.

Jerry Coyne

Pedro said...

"Haven't read it, but I presume by the answers that he never actually explains anything."

I've read it...and you're right. He basically lists a lot of processes going on in the genome, and then basically tells you that that's what cells use as tools for "natural genetic enginnering". Of course, he never tells how cells do that. He wants you to believe that cells "direct" those genomic changes using said processes, but he never says how. He doesn't have any model whatsoever for how it all works. He presents a teleologic view of genomic dynamics, in which cells "intentionaly" change their genomes but leaves it at that.

He also makes the same retarded arguments that ID proponents make, mentioning a couple of times the old probability argument, etc. He seems oblivious to neutral theory and genetic drift. More probably, he knows about it but since that defeats the purpose of his ideas he simply ignores them.

I'd like to have the money I've spent on that book back.

Alex SL said...

Ye gods. I am only piling on, but really: if that is "engineering", where does the intelligence reside that does the planning? Do our cells have a brain and foresight?

It is sad enough to see this nonsense promoted by the odd crank in a comment thread, but by somebody like Shapiro...

(Then again, I should not be surprised. There are a few colleagues in every area who won't let go of a position no matter how silly, like those panbiogeographers who categorically reject the possibility of long distance dispersal despite having been made aware of the existence of native plants and animals on Hawaii.)

Anonymous said...

Dear Larry,

I think it would do some good to write a summarized and less technical version of your review on the page for Shapiro's book. Many use the review section in making decisions about which books they will purchase. Perhaps you can dissuade some of them. Here is the link:

Kind Regards,

HMB205 Student

Anonymous said...

Physics could be the real key to understanding evolution-phenomenon. See e.g. University of Helsinki professor Arto Annila`s work

Department of Physics
Department of Biosciences
Institute of Biotechnology

Kaila VRI, Annila A. Natural selection for least action. Proc. R. Soc. A. 2008 464, 3055–3070

and a lot of other publications

Anonymous said...

Please note that the guy in your link has a formal education in biochemistry as well...

Alejandro said...

This post (and the original review) made me think about an article on "Arrogance in physics"...

Lactate said...

Francis Crick and Walter Gilbert were physicists.

Anonymous said...

Crick had to earn his chops, he described it as "being born again", Gilbert also had training in chemistry

Pedro said...

I don't think Moran is implying that physicists have nothing to contribute to Biology. Biophysics is obviously a productive field and protein structure has seen many contributions from physics. It would also not be the first time that another field would be making contributions to the understanding of another field by bringing new insight and perspective.

The question is if just bringing physicists in for the sake of it is going to contribute anything of significance to evolutionary theory. I think Moran made a good point with his example. I think bringing a fresh perspective that has to do with one's different training may bring new insight occasionally but one still has to work closely with those that have a vast know-how of what is being talked about. I fail to see what physics by itself would contribute to e.g. speciation theory or punctuated equilibria, except perhaps in providing some experience with mathematical models that have been applied elsewhere in physics and that physicists may detect some similarities in problems that can be helped by using similar mathematical solutions. But that's not really physics, it's mathematics and one's personal experience in using them, plus working closely with those who understand the nuances of the problem at hand. Either that or the physicist will need to spend quite a long time gaining knowledge and experience in a particular field of biology to be able to contribute continuously and systematically to the field. That means, in effect, becoming also a biologist.

So I don't have a problem with physicists taking a look at things as long as they are working with someone who understands the nitty-gritty at the heart of the problem. The lack of understanding of modern theory of evolution and its nuanced details have already produced quite a lot of nonsense e.g. on the field of Evolutionary Psychology, in which many psychologists have worked from a caricature of genetics and evolutionary theory. Fred Hoyle is a good example of someone who talked a lot of nonsense because of a lack of understanding of biology.

Robert Byers said...

Wrongly but people often think physicists are smarter people in the smarter science.
So they might themselves not be intimidated to get involved quickly.
For sure we creationists think we can do a better job and in physics too for lots of reasons.
Biology is a more complicated subject as we see it right now and ideas about its origin.
Physics is in fact a simpler subject and this is why ting groups of them centuries ago figured it all out.
nothing more to do at any level above the atomic level and so on.

Yet i'm sure Mr Shapiro is sharp enough to be able to see problems with evolution and not be biased by coming out of biological circles that would prejudice new ideas or higher criticisms.

I predict there will more like him, non creationists, to bring better criticisms to evolutionary concepts.
If evolutionism falls down then these people will get the greater intellectual credit for doing better science.
Everyone is on the spot.
Its not your fathers evolution acceptance society , in educated circles, anymore.
Someone is coming into a great defeat.