James Shapiro doesn't like junk DNA

Shapiro doubles down on his claim that junk DNA doesn't exist.

It's been a while since we've heard from James Shaprio. You might recall that James A. Shapiro is a biochemistry/microbiology professor at the University of Chicago and the author of a book promoting natural genetic engineering. I reviewed his book and didn't like it very much—Shapiro didn't like my review [James Shapiro Never Learns] [James Shapiro Responds to My Review of His Book].

Shapiro has allied himself with Denis Noble and other founders of The Third Way—a group that challenges the modern view of evolution while distancing themselves from Young Earth Creationists [The Third Fourth? Way]. The only thing that unites this group is their opposition to a particular (mostly false) view of evolutionary theory. Shapiro claims credit for predicting that most of the human genome would be found to be functional and he was delighted when ENCODE seemed to vindicate his claim back in 2012 [James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle"]. His article in the Huffington Post was titled Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin' and it began with a quote from Bob Dylan, (WARNING! Turn off your irony meters.)

And don't criticize
What you can't understand

In 2021 Shapiro resurfaced with an article in the journal Biosemiotics where he and Denis Noble promoted their bizarre views on evolution. The two authors then combined to publish an article in Progress in Biophysics & Molecular Biology where they wondered why evolutionary biologists were not teaching the "truth" about genome evolution [More illusions/delusions of James Shapiro and Denis Noble]. His latest venture into windmill jousting is an article in aeon, Evolution without accidents, where he makes the case that there's more to evolution than just random mutations and natural selection (duh!).

The important part for me is the fact that he continues to dismiss junk DNA.

The ‘central dogma of molecular biology’, first enunciated by Francis Crick in 1958 and restated in 1970, assigned to RNA molecules the primary task of serving as intermediates carrying coding sequence data from the DNA to the ribosomes, where that data is translated into the sequence of amino acids in protein chains. According to this explanation, adaptation took place only through encoded proteins, and it became a puzzle to evolutionary biologists why the protein-coding sequences of the most complex organisms make up such a small fraction of their genomes. In our own genomes, for example, more than 50 per cent of the DNA does not code proteins (our genomes contain only about 1.5-2 per cent protein-coding DNA). This gave rise to notions that genomes contained large amounts of ‘junk’ DNA, which was simply reproducing itself in the name of its own ‘selfish’ survival, as popularised by Dawkins’s The Selfish Gene.

There are many things wrong with this paragraph but the most astonishing is Shapiro's continuing misrepresentation of the central dogma. He has been told repeatedly that this is NOT what Crick said in 1958 and 1970 but that hasn't sunk in [The illusions of James Shapiro]. It's interesting that he criticizes something that he can't understand. :-)

He's also confused about the difference between selfish DNA and Dawkins' view of the selfish gene [Selfish genes and transposons] but that's not surprising since history and accuracy are not Shapiro's strong points.

Notwithstanding the central dogma that proteins execute all the business of living cells, research in molecular genomics has revealed that all cells contain many noncoding RNA molecules (ncRNAs) and, by the late 2010s, the global Encyclopedia of DNA Elements project (ENCODE) found that human cells regulated expression of ncRNAs in the same ways as protein-coding mRNAs. In other words, ncRNAs are controlled and, presumably, biologically functional. They are not ‘junk’.

The ENCODE discoveries and subsequent research on ncRNAs have revolutionised our understanding of genome coding in two important ways. Firstly, many of the copies of TEs and other repeated DNA elements found in large complex genomes contribute transcription templates for the so-called ‘noncoding’ ncRNAs, which carry out a wide variety of cellular and developmental regulatory functions. Thus, there is no ‘selfish’ or ‘junk’ repetitive DNA in genomes; all regions of the human genome code for biologically significant molecules. Secondly, while the importance of ncRNAs was completely unexpected, it turns out that they influence all levels of organismal activity. These range from scaffolding the formation of multimolecular complexes in the cytoplasm, facilitating the formation of three-dimensional genome complexes in the nucleus, to stimulating the reprogramming of terminally differentiated tissue cells with limited growth potential into pluripotent stem cells. New functionalities for ncRNAs emerge daily, telling us that this class of molecules has enormous structural and functional diversity.

As Sandwalk readers know, there was never a time when knowledgeable scientists said that all noncoding was junk and never a time when the original proponents of junk DNA were unaware of noncoding genes. Thus, the discovery of ncRNAs is not new and does not refute junk.

Presumably what Shapiro really means to say is that 90% of our genome (including introns) consists of functional genes that specify ncRNAs. This is the revolution that he's talking about but it's a ridiculous claim. There is zero evidence to support such a claim.

I wonder if Shapiro has heard of the Onion Test?

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