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Wednesday, April 21, 2021

The illusions of James Shapiro

James A. Shapiro is a professor in the Department of Biochemistry and Molecular Biology at the University of Chicago (Chicago, USA). He made signficant contributions to our understanding if the function and structure of transposons but in later years he has become a vocal opponent of evolution culminating in his 2011 book Evolution: A View from the 21st Century. He is one of the founding members of The Third Way of Evolution.

I wrote a critical review of Evolution: A View from the 21st Century for the National Center for Science Education (NCSE) Reports but the issue is no longer visible on the web. Shapiro didn't like my review so NCSE published his rebutal and that's also unavailable. You can see my response at: James Shapiro Responds to My Review of His Book.

Shapiro promotes a view that he calls "Natural Genetic Engineering"—a view that emphasizes the role of moblie genetic elements in reshaping and reorganizing complex genomes. There's nothing wrong with that unless you try to elevate it to a theory that overthrows the standard view of evolution, which he does. But the most annoying thing about his writing is his consistent erection of strawman aguments that he then shoots down as a way of promoting his bizarre theories. One of them concerns the Central Dogma of Molecular Biology and that's what I want to talk about today.

Here's what I wrote ten years ago when I reviewed his book.

Speaking of strawmen, Shapiro's description of the Central Dogma of Molecular Biology contains errors of fact as well as error of omission. These days, there seems to be a class of evolution critics who are determined to overthrow the Central Dogma as part of their crusade to revolutionize biology. Shapior falls into that group. It's not a group that you really want to be associated with if you value your intellectual reputation because its members almost always misrepresent the correct view of the Central Dogma described by Francis Crick in 1958 and 1970. The correct version of the Central Dogma is that once information is transferred from nucleic acid to protein it can't flow back to nucleic acid. In other words, translation is unidirectional. The Central Dogma has never been overthrown or serioulsy challenged. If critics get that wrong, how can you believe anything they say?

I know that Shapiro read this review because he published a rebuttal. Normally people learn from their mistakes and they take steps to fix them in future writings but this doesn't seem to be a characteristic of people like James Shapiro [James Shapiro Never Learns]. Let's look at his latest article to see if he understands the Central Dogma any better now that several poeple have pointed out where he gets it wrong. I'm referring to the article he wrote in Biosemiotics in praise of Denis Noble's attack of evolution (see: The illusions of Denis Noble).

Shapiro, J.A. (2021) Response to Denis Noble’s Article “The Illusions of the Modern Synthesis,” Biosemiotics. Biosemiotics:1-6. [doi: 10.1007/s12304-021-09409-z]

Abstract:The Modern Synthesis (MS) was based on Darwin’s gradualist view of evolution and early twentieth Century Mendelian and population genetics. Although early results in microbial and molecular genetics seemed to solidify MS views through the Central Dogma of Molecular Biology, accepting their basic concepts as permanent truths blinded MS proponents to the importance of incompatible discoveries in the second half of the 20th and early 21st Centuries. Discoveries based largely on the DNA record have provided a radically different view of genome complexity and biologically-mediated evolutionary change.

Oops! This doen't look promising. Looks like he's still going on about the Central Dogma in spite of the fact that his errors have been pointed out to him. Here's what he writes,

Crick's 1958 paper was the initial statement of what he called "The Central Dogma of Molecular Biology"—DNA directs the synthesis of more DNA as well as messenger RNA that encoded the proteins, which are the molecules that do the basic work to determine the properties of cells and organisms.

That's false and Shapiro should know it. You don't have to take my word for it, you can read the original paper yourself at: On protein synthesis. The DNA --> RNA --> protein scheme is called "The Sequence Hypothesis" and the "Central Dogma" is "... once information has passed to protein it can't get out again." In other words, "... the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible but that transfer from protein to protein or from protein to nucleic acid is impossible."

I'm not just quibbling over a strictly semantic issue. This is really important because Shapiro and his allies are building an entire anti-evolution argument based largely on their interpretation of the Central Dogma. There's no excuse for getting it wrong, especially if you actually quote Crick's 1958 paper and you have been told in the past that you got it wrong. I just don't understand why honorable scientists would do this.

Here's the next few sentences in Shapiro's article.

Although (as Noble points out) Crick later had to revise his scheme to accommodate the discovery that RNA can encode DNA by the action of reverse transcriptase (Temin and Mizutani 1970; Crick 1970) ...

That's also a lie. The whole point of Crick's 1970 Nature paper was to point out that the discovery of reverse transcriptase had nothing to do with the Central Dogma. You can read his paper for yourself at: Central Dogma of Molecular Biology or you can read Mathew Cobb's excellent historical account at: 60 years ago, Francis Crick changed the logic of biology. Here's how Mathew Cobb explains it.

In 1970, following the discovery by Howard Temin and David Baltimore of reverse transcriptase, which enables information to flow in the direction RNA → DNA, Nature published an editorial entitled ‘Central dogma reversed.' Crick wrote a slightly tetchy response, repeating what he had actually stated in 1957, and rightly insisting that he had never argued that RNA → DNA was impossible.

So, not only did Shapiro get the Central Dogma wrong, he blatently lied about Crick's 1970 paper (and so did Denis Noble). What's going on here? Both of these men are capable of reading papers that they reference, aren't they?

We know what Shapiro and his ilk are really upset about because they describe in in their publications. Here's what Shapiro says.

Crick’s use of the term “dogma” was meant quite literally to enshrine this genocentric viewpoint as a fundamental and permanent truth. Evolutionary novelty arose randomly through unavoidable copying errors in DNA replication, leading to gradual cumulative changes in protein structure and function.

Several problems with the reductionist Central Dogma view of genomes as vehicles to reproduce collections of protein-coding genes as basic units of heredity were apparent early on. Among these were the cytogenetical knowledge that chromosomes contained other kinds of functional genomic elements, such as centromeres, telomeres, and nucleolar organizing regions.

What they're upset about is the belief that everything in evolution is due to changes in protein-coding genes. They think that Crick's Central Dogma means that the ONLY pathway of information flow is from DNA to protein. There may be some people who think that's true but to attribute it the Modern Synthesis and Crick is just ridiculous. There are no serious evolutionary biologists who believed that in the 1960s or 1970s or at any time since. It's a strawman.

You can see from the above quote that Shapiro is going to destroy that strawman by pointing out other functional regions of the genome like centromeres and telomeres but why is that relevant? We all knew about noncoding information back in the 1960s.

Shapiro and the other cult members are fighing against the idea that protein-coding genes are the only functional elements in the genome and that mutations in these genes and subsequent selection for favorable alleles is the only way that evolution occurs. They use various labels to identify this belief including the "Modern Synthesis," the "Central Dogma," and "gene-centric evolution." None of the these labels are appropriate and all of the cult members should know this. More importantly, no knowledgeable evolutionary biologists believe such nonsense so Denis Noble, James Shapiro, and all the other members of the cult are tilting at windmills.

Shapiro ends his article by listing four items that caused the "breakdown" of the Modern Synthesis.

  1. "The discovery of mobile genetic "controlling elements" in maize plants by McClintock in the late 1940s and early 1950s."
  2. "The study of how genome expression is regulated."
  3. "The discovery of repetitive and largely non-coding DNA in the genomes of humans and other complex eukaryotes." According to Shapiro, this led Modern Synthesis theoreticians to label them as "junk DNA" but it turns out they are essential elements in evolution.1
  4. "Finally, molecular genomc analysis by the encyclopedia of DNA elements (ENCODE) consortium has documented that the vast majority of the supposed non-coding DNA is transcirbed to produce non-coding ncRNAs with a wide range of functional properties."

This is what we're up against when we try to educate students and practising scientists. I gotta tell you that there are some days when I feel like the task is hopeless and I'm just wasting my time.

1. Scientists who were strong supporters of the Modern Synthesis as described by its supporters in the 1960s tended to be adapationists and they strongly opposed junk DNA. Those who supported junk DNA were part of a new group of evolutionary biologists who understood Neutral Theory, and Nearly-Neutral Theory, and the new approach to evolutionary theory that supplanted the Modern Synthesis. The cult members do not demonstate any understading of modern evolutionary theory.

1 comment :

  1. There are more problems with Shapiro's views. As you note, he believes that organisms have maintained machinery that will accomplish Natural Genetic Engineering. This supposed to come up with the right revision of the genome to cope with any crisis. He never addresses two issues: (1) How does NGE know what is the right change to make? and (2) in the face of mutation that would degrade any such capability, how does the organism maintain such a remarkable capability over the millions of years in between occasional needs for it? And of course there is the biggest puzzle of all. Exactly where in the genome do we find this machinery for NGE? Note that we need to find much more than just sequences that do occasional weird things to the genome.