The fuzzy thinking of John Parrington: The Central Dogma

My pattern of The Deeper Genome: Why in that place’s more to the human genome than meets the have an ~ on has arrived and I’ve highly wrought reading it. It’s a gigantic disappointment. Parrington makes no attempt to recount what’s in your genome in greater amount of than general hand-waving terms. His majority theme is that the genome is indeed complicated and so are we. Gosh, golly, gee whir! Re-write the textbooks!

You determination look in vain for any rigorously numbers such as the total reckon of genes or the amount of the genome affectionate to centromeres, regulatory sequences etc. etc. [descry What’s in your genome?]. Instead, you decree find a wishy-washy defense of ENCODE results and tributes to the views of John Mattick.

John Parrington is some Associate Professor of Cellular & Molecular Pharmacology at the University of Oxford (Oxford, UK). He works steady the physiology of calcium signalling in mammals. This should esteem him well-qualified to write a part about biochemistry, molecular biology, and genomes. Unfortunately, his document leaves a great deal to subsist desired. He seems to be charge of a younger generation of scientists who were somewhat ill trained as graduate students (he got his Ph.D. in 1992). He exhibits the corresponding; of like kind kind of fuzzy thinking as people of the ENCODE leaders.

Let me give you just one example.

Sandwalk readers elect be familiar with the correct acceptation of the Central Dogma of Molecular Biology. It says …

The central opinion of molecular biology deals with the detailed excess-by-residue transfer of sequential knowledge of facts. It states that such information cannot have ~ing transferred from protein to either protein or nucleic pungent. (F.H.C. Crick, 1970)This is surpassingly clear. It says nothing about the explanation of a gene and nothing approximately whether RNAs can be functional. In circumstance, Crick was no idiot (gasp!) he knew well-nigh tRNA genes and ribosomal RNA genes.

Parrington is individual of those scientists who were none taught the real meaning of the Central Dogma. That’s saturnine but it’s understandable. However, like people other scientists, he writes about his misconceptions on the outside of ever checking the original papers or uniform thinking seriously about what he says. He promotes the exemplar that genes are stretches of DNA that encode proteins (not at all genes for functional RNAs) and that the Central Dogma of Molecular Biology is the ground of this belief.

Thus, the making known of non-protein information (like RNA) is a paradigm shift that requires a new defining of a gene. There’s a purport in which he is correct. Anyone who believes the kind of he believes needs a paradigm devise ways and means. However, that shift in thinking should be delivered of occurred decades ago and it has small matter to do with the human genome brew.

Here’s how John Parrington describes the Central Dogma forward pages 38-39.

The discovery of the genetic collection of laws signalled the primacy of the of the present day discipline of molecular biology. Central to this was Crick’s claim that life is a single-way flow of information from DNA to RNA to protein—the ‘central doctrine of molecular biology.’ …This is not the sort of Crick meant but, apparently, there are a al~ment of scientists who think this means by which anything is reached. This lead to a great collision for them when they discovered functional RNAs (They were capital discovered in the late 1960s and Nobel Prizes were awarded in 1989 conducive to other functional RNAs. Some scientists are a coin behind in their reading.)

John Parrington realized in 2012 that in that place was something wrong. He writes put ~ pages 91-91 …

The [ENCODE] study likewise found that 80 percent of the human genome was generating RNA transcripts. In thread with these transcripts having functional consequence, many were found in specific honey-combed compartments, indicating that they have fixed courtship where they operate. Surely there could severely be a greater divergence from Crick’s central principle than this demonstration that RNAs were produced in remoter greater numbers across the genome thatn could subsist expected if they were simply intermediates betwixt DNA and protein. Indeed, some ENCODE researchers argued that the basic one of inheritance should now be considered in the same proportion that the transcript. So Stamatoyannopoulos claimed that ‘the contrive has splayed an important role in changing our general of a gene.’The ENCODE bulge will, indeed, have done some sterling if it causes people like Parrington and Stamatoyannopoulos to finally get up to date on their general of a gene. But, since the present concept of a gene as “a DNA sequence that is transcribed to produce a functional consequence” includes functional RNAs as well for the re~on that proteins, and since that concept is at in the smallest degree forty years old, one wonders wherefore a practicing scientist would want to announce the fact that they are likewise out-of-date.

And why would they defect to mislead the public?

You may plan I’m being unfair. John Parrington isn’t the merely scientist to misunderstand the Central Dogma. True plenty, but most scientists don’t scrawl books about it and don’t annoyance to read the relevant papers. Recall that the ascertainment of reverse transcriptase raised questions in regard to the Central Dogma back in the slow 1960s. This prompted Crick to compose the Nature paper that corrected some false impressions about refuting the Central Dogma (Crick, 1970). He made it spotless that the flow of information from RNA to DNA had trifle to do with the Central Dogma of Molecular Biology. That was allowed in the creative 1958 version (Crick, 1958).

But to this place’s how John Parrington describes it up~ the body page 118.

The recognition that RNA be able to code for DNA was one of the the pristine challenges to Crick’s central article of faith that the information can only proceed in one direction, via RNA to proteins. We axiom in Chapter 3 how, since proteins are required to replicate and transcribe DNA, it could equally be weighty to see information flowing back to DNA from proteins. Nevertheless, this is knowledge of facts flow in an indirect sense. In contrast, turning an RNA sequence into DNA is a extremely literal challenge to the central article of faith, and this reversal of information requires a definite enzyme—reverse transcriptase.This is fuzzy reflection and it’s just one of multiplied examples in the book. This is why it is such a pain to know fully and it’s why I own no confidence in the conclusions of the author. It’s also why I’m going to be seized of such a hard time discussing Parrington’s views up~ the body junk DNA because those views are colored ~ means of deep misunderstandings of fundamental principles of biochemistry and corpuscular biology. It’s going to take during the time that much effort as discussing Jonathan Wells’ main division [The Myth of Junk DNA by Jonathan Wells]. Maybe I should just have you read those posts from 2011. They comely much cover all the problems with Parrington’s book except for the ENCODE stow.

Crick, F.H.C. (1958) On protein composition. Symp. Soc. Exp. Biol. XII:138-163

Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]

This lifestyle has, significantly, been enabled to it ~ the agency of the dual function.

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