Saturday, March 21, 2015

How the genome lost its junk according to John Parrington

I really hate it when publishers start to hype a book several months before we can read it, especially when the topic is controversial. In this case, it's Oxford University Press and the book is "The Deeper Genome" Why there is more to the human genome than meets the eye." The author is John Parrington.

The title of the promotion blurb is: How the Genome Lost its Junk on the Canadian version of the Oxford University Press website. It looks like this book is going to be an attack on junk DNA.

We won't know for sure until June or July when the book is published. Until then, the author and the publisher will have free reign to sell their ideas without serious opposition or push back.

Here's the prepublication hype. I'm going to buy this book and read it as soon as it becomes available. Stay tuned for a review.
Over a decade ago, as the Human Genome Project completed its mapping of the entire human genome, hopes ran high that we would rapidly be able to use our knowledge of human genes to tackle many inherited diseases, and understand what makes us unique among animals. But things didn't turn out that way. For a start, we turned out to have far fewer genes than originally thought - just over 20,000, the same sort of number as a fruit fly or worm. What's more, the proportion of DNA consisting of genes coding for proteins was a mere 2%. So, was the rest of the genome accumulated 'junk'?
This does not look promising. For one thing, most knowledgeable scientists were not the least bit surprised to discover that the human genome had about 30,000 genes. (That's the original estimate. Now it's about 25,000 of which 20,000 code for proteins [How many genes do we have and what happened to the orphans?].) Knowledgeable scientists knew about the work on genes and development in the 1980s and were quite used to the idea that all multicellular animals had about the same number of genes. This wasn't a surprise either; it was expected.

For a discussion about the true history of the number of genes see: False History and the Number of Genes and Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome.

It's also pretty ridiculous to claim that it was the human genome project that discovered that less that 2% of our genome was devoted to open reading frames. That has been known for forty years!

These are not good signs. It looks like we might be dealing with an amateur.
Things have changed since those early heady days of the Human Genome Project. But the emerging picture is if anything far more exciting. In this book, John Parrington explains the key features that are coming to light - some, such as the results of the international ENCODE programme, still much debated and controversial in their scope. He gives an outline of the deeper genome, involving layers of regulatory elements controlling and coordinating the switching on and off of genes; the impact of its 3D geometry; the discovery of a variety of new RNAs playing critical roles; the epigenetic changes influenced by the environment and life experiences that can make identical twins different and be passed on to the next generation; and the clues coming out of comparisons with the genomes of Neanderthals as well as that of chimps about the development of our species. We are learning more about ourselves, and about the genetic aspects of many diseases. But in its complexity, flexibility, and ability to respond to environmental cues, the human genome is proving to be far more subtle than we ever imagined.
You can't really tell from that description whether John Parrington is for or against junk DNA. The video below is also pretty noncommittal.

However, there's a clue on the main Oxford University Press website: The Deeper Genome. A single review is posted ...
"This is a brilliant book - a wonderfully entertaining history of molecular biology and the surprises and controversies of a field still very much in flux, from early explorations to the emerging realisation that the human genome may be far more sophisticated than we ever imagined." - John Mattick, Director, Garvan Institute of Medical Research
I think the blogosphere is going to have lots of material in a few months! I don't think John Parrington is going to like the response.

Here's an excerpt from the book: The death of "junk" DNA. It doesn't really tell us whether the author thinks most of our DNA is functional but it hints that this might be the case.

Who is John Parrington? He's a Professor of Pharmacology at Oxford with an impressive set of credentials on science communication [John Parrington].
He also has a diploma with distinction in Science Communication from Birkbeck College, London. He has written articles about science for The Guardian and New Scientist as well as preparing reports about scientific issues for the public for the Wellcome Trust, the Royal Society and the British Council. He presented the Charles Darwin Award Lecture at the BA Festival of Science 2003 at the University of Salford.



12 comments :

  1. This comment has been removed by the author.

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  2. There goes the left-handed DNA on the cover, again.

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    1. well, if that is supposed to be helical DNA, that major groove has far too many teeth in its smile.

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    2. If you're writing a book about DNA, it's probably a good idea to get the structure right on the cover.

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    3. Jibbers Crabst, I'm so used to bad DNA graphics I hardly noticed. The way they draw it, you could fit all the base pairs of a gene in about two turns of the helix.


      (Yes I'm exaggerating.)

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    4. How much influence do authors have over cover illustration? I think Gould discusses how a translated version of one of his books had a "march of progress" type illustrations on the cover in Wonderful life and how much that bugged him (though the translation appeared in a country with droit d'auteur laws, which actually did give him a veto for the cover by law and one he could not contractually waive as well).
      It's my understanding that in the US it's not something authors have any say in.
      Not that I'm trying to preemptively excuse the book, but I don't think the cover should feature prominently in the critique...

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    5. It's pretty unusual for the author of a trade book to have rights to the cover illustration (or the title) build into the contract with the publisher. However, it would be very unusual for the publisher not to vet the cover (and the title) with the author before publication.

      That's when the author would raise s stink about an incorrect drawing of DNA on the cover. it's hard to imagine a publisher that would go ahead and publish a scientifically incorrect cover over the objections of the author.

      In this case the publisher is Oxford University Press. It's safe to conclude that they checked with the author before printing the book.

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    1. But you gotta admit it looks fancy with the blueish glow and all. Almost as if it was... designed.

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    2. He just coppied it from one of the following sites

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    3. Another left-handed DNA pic posted there:

      Exhibit N

      But who can blame a pop science writer when we find such stuff at Nature Education:

      Exhibit N+1
      Exhibit N+2

      The cover image with its electric-blue aura, the wrong chirality, and far too many rungs per ladder twist, may have been inspired by such artwork as this:

      Exhibit N+3

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  4. I'm sure that as a Professor of Pharmacology he can find something to blame his book's shortcomings on. :)

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