You might also recall that he's the scientist who criticized the Central Dogma of Molecular Biology when he clearly didn't understand it [Revisiting the Central Dogma in the 21st Century]. I was shocked to learn that he had published a paper with the title "Revisiting the Central Dogma in the 21st Century" without ever bothering to read the literature to find out how Francis Crick actually defined the Central Dogma. (In fact, Shapiro misrepresented Crick's view.) It goes to show you how silly you look when you criticize something you don't understand.
Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin' and it begins by quoting a couple of lines from the song.
I almost choked when I read that."And don't criticize
What you can't understand"
Shapiro continues by mentioning the ENCODE papers and their conclusion that 80% of our genome has a "biochemical" function. Shapiro then says,
In other words, the old idea of the genome as a string of genes interspersed with unimportant noncoding DNA is no longer tenable. Many eminent scientists had opined that the noncoding DNA, much of it repeated at many different locations, is nothing more than "junk DNA." ENCODE revealed that most (and probably just about all) of this noncoding and repetitive DNA contained essential regulatory information. Moreover, much of it was also copied into RNA with additional but still unknown functions.Oh dear, two major examples of lack of understanding in the same paragraph. First, Shapiro repeats the old myth that there were "eminent scientists" who thought that all noncoding DNA was junk. Second, he takes the claim that 80% of our genome has a "biochemical function" and translates that as "ENCODE revealed that most (and probably just about all) of this noncoding and repetitive DNA contained essential regulatory information."
It's going to be difficult to take James Shapiro seriously after that, but let's try.
I had a longstanding, personal interest in the repetitive part of our genomes (up to as much as two-thirds of all our DNA) because it is composed of mobile genetic elements. I first discovered these elements in bacteria in my thesis research in 1968. I remember being scientifically offended by a 1980 article from Francis Crick and Leslie Orgel describing this DNA as "selfish" and functionless.Shapiro is referring to the sequences that are related to transposons of various sort (LINEs and SINEs) [Junk in Your Genome: SINES ] [Junk in your Genome: LINEs]. Almost all of this is defective or inactive transposons and bits and pieces of transposons. We know from studying the evolutionary history of this DNA that very, very, few of the transposons are active.
My interest in the roles of repetitive and mobile DNA has continued since my thesis more than four decades ago. The initial sequencing of the human genome in 2001 found over 40% to be mobile repeats spread throughout our genomes, thirty times more than protein-coding DNA.
In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled "Why repetitive DNA is essential to genome function."
In the paper with (von) Sternberg he also discusses highly repetitive DNA. The paper reads very much like his book. It consists of dozens of examples of specific cases in various species where little bits of repetitive DNA have been implicated in a biological function. It's the same data that Jonathan Wells uses in his book The Myth of Junk DNA.
These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for "guilt-by-association" claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.Shapiro is famous for promoting a "third way" of looking at biology; a way that's not strictly Intelligent Design Creationist, but also not strictly science. He has published on the main Intelligent Design Creationist blog, Evolution News & Views and is widely quoted and admired by creationists who rightly see his views as supportive of theirs. None of that means, of course, that Shapirio is a full supporter of Intelligent Design Creationism.
The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.Please be careful about how you interpret this statement. On the surface it looks exactly like something the Intelligent Design Creationists would say but James Shapiro insists that he is not one of them. He has a completely different reason for thinking that our entire genome looks like a sophisticated data storage device.
Although we could not predict in detail all the ways repeated DNA would serve genome functions, I think our statements stand up well in light of the recent data. Without knowing the specifics, we were correct in asserting that the genome had to be highly formatted to serve as the marvelous information organelle it is in every living cell and organism.We know what Rick (von) Sternberg's motives were. They weren't the same as James Shapiro's but the result is the same: bad science, lack of understanding, and flawed reasoning.
So, while Rick's choice of evolutionary philosophies is different from mine, I am grateful to him for doing so much work on a paper that remains a source of justified scientific pride. Thinking of the genome informatically and of mobile DNA as a potent force for genome organization are central to the arguments presented on this blog and in my book.
This appears to be an unusual case of someone who looks like a creationist, talks like a creationist, and hangs out with creationists, but isn't a creationist.