A paper was published earlier this week making an extraordinary attack on the integrity of the work of the ENCODE consortium, an international group studying the human genome.\u00a0 Scientists don\u2019t normally go in for this type of public blood letting, making the attack all the more surprising.<\/p>\n
Other disciplines are not so reticent.\u00a0 The literary world even hands out a prize, The Hatchet Job of the Year,<\/a> for the angriest, funniest, most trenchant book review of the past 12 months.\u00a0 This dubious accolade was awarded in February to Camilla Long for her Sunday Times review of Rachel Cusk\u2019s memoir, Aftermath<\/a>, cataloguing the breakup of her marriage.\u00a0 I remember reading extracts from Cusk’s book and having to give up; I felt as though I was intruding on something that should not have been made public.\u00a0 Long\u2019s review is beautifully written and wonderfully and shockingly harsh referring to Cusk as a \u201cbrittle little dominatrix and peerless narcissist<\/i>\u201d. \u00a0Here is a longer extract from the review:<\/p>\n \u201cThe book is crammed with mad, flowery metaphors and hifalutin creative-writing experiments. There are hectic passages on Greek tragedy and the Christian concept of family, as well as fragments of ghost stories, references to the Anglo-Saxon heptarchy, and heavy Freudian symbolism, including a long description of the removal of a molar, \u201ca large tooth,\u201d she writes portentously, \u201cof great\u2026personal significance\u201d. The final chapter is an out-of-body experience \u2014 her situation seen through the eyes of her pill-popping Eastern European au pair\u201d.<\/i><\/p>\n Responses from other reviewers were highly polarised: they were either very positive or very negative.<\/p>\n <\/p>\n The scientific world rarely behaves like this in public.\u00a0 Not that is to say that we don\u2019t judge our colleagues; we do it all the time.\u00a0 It\u2019s just that we don\u2019t write it down publicly in the same way.\u00a0 Scientific meetings are rife with gossip and I\u2019ve heard character assassinations on more than one occasion at Grant Committees. \u00a0There is also some trenchant criticism on the blogosphere, as you would expect.\u00a0 Peer-reviewed papers tend to be much more reserved; if we don\u2019t believe another\u2019s work we will say something discrete like \u201cthe inability to repeat X\u2019s work is most likely due to methodological differences\u201d.\u00a0 Until recently, the strongest criticism I had seen in a scientific paper was that a competitor\u2019s work was \u201cna\u00efve\u201d.<\/p>\n Earlier this week a paper appeared on line in Genome Biology and Evolution <\/a>from Dan Graur and colleagues which rewrites these rules.\u00a0 The paper is a critique of work published by the ENCODE consortium last September.\u00a0 To remind you, the ENCODE consortium set out to study that part of the human genome that did not code for proteins.\u00a0 Their headline conclusion, and here I am quoting from the press release<\/a>, was that 80% of the non coding DNA was functional and comprised millions of switches that regulate the activity of our genes.\u00a0 The press release occasioned many articles in the mainstream media including a silly article by Johnjoe McFadden in the Guardian (Soon science could enable us all to run as fast as Usain Bolt<\/i><\/a>) that spoilt my breakfast one Friday morning.\u00a0 I am not a \u201cDNA\/sequencing\u201d person but I objected to the idea of so many, essentially uncharacterised, gene switches and wrote a blog post <\/a>about this.<\/p>\n At the time, some experts and commentators criticised the ENCODE results in a series of blog posts using strong but polite language. Here are links to Michael Eisen <\/a>and Brendan Maher <\/a>both of whom were uncomfortable with the 80% functional figure<\/p>\n Now we have the Graur et al paper <\/a>with its swingeing critique of ENCODE.\u00a0 Here is the Abstract:<\/p>\n \u201cA recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 \u2212 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these \u201cfunctional\u201d regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used \u201ccausal role\u201d definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as \u201caffirming the consequent,\u201d (3) by failing to appreciate the crucial difference between \u201cjunk DNA\u201d and \u201cgarbage DNA,\u201d (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.\u201d<\/i><\/p>\n <\/p>\n You have to read the text to get the full flavour of the critique but to quote PZ Myers <\/a>on his blog: \u201cGraur and friends haven\u2019t just poked a hole in the balloon, they’ve set it on fire, pissed on the ashes and dumped them in a cesspit\u201d.\u00a0 \u00a0A fuller account of the article and its fall out appears on POPSCI<\/a>.<\/p>\n What are we to make of this?\u00a0 In my opinion, a peer-reviewed paper carries much more weight than a blog post.\u00a0 The paper will be indexed in PubMed and the criticism and language will stand for all to see.\u00a0 Is Graur et al\u2019s criticism of ENCODE justified?\u00a0 I am not an expert but it looks as though it is mostly justified.\u00a0 Is the language of Graur et al justified?\u00a0 Here I am in two minds.\u00a0 On the one hand I enjoy watching a good academic spat and I would expect that, once the anger has cooled, there will be progress in understanding.\u00a0 On the other hand, the derisory and sarcastic language makes me feel uncomfortable and I am very surprised the journal agreed to publish this version of the manuscript.\u00a0 I support the criticism but prefer that this sort of language be left to blogs.\u00a0 More measured language can then be reserved for peer-reviewed papers.<\/p>\n Perhaps we should start a scientific Hatchet Job of the Year award, in which case Graur et al must be favourites to win the 2013 award.<\/p>\n <\/p>\n","protected":false},"excerpt":{"rendered":" A paper was published earlier this week making an extraordinary attack on the integrity of the work of the ENCODE consortium, an international group studying the human genome.\u00a0 Scientists don\u2019t normally go in for this type of public blood letting, … Continue reading