LUCA latest: Shapiro redux (Introduction)

by David Turell , Thursday, July 13, 2023, 01:59 (289 days ago) @ David Turell

Larry Moran's criticism of Shapiro's book, Evolution:

https://sandwalk.blogspot.com/2012/12/james-shapiro-responds-to-my-review-of.html

"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.

***

"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” 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.

"I discussed all those topics, except CRISPRs, in my big biochemistry textbook twenty years ago. 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.

"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 ...

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.
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. I think RNCSE readers will agree that these certainly constituted major events in animal evolution.

***

"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.

***

"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."

Comment: we know the answer. Shapiro was a president of his Temple. Moran is a devoted Darwinist/Atheist who denies the ENCODE removal of junk DNA in his own new book.