Tag Archives: biochemistry

Oops: taxonomy #fail

My journey from bench scientist to bioinformatician began with archaeal genomes. So I was somewhat startled to read The catalytic mechanism for aerobic formation of methane by bacteria, in which we learn about the “ocean-dwelling bacterium Nitrosopumilus maritimus“.

So was Jonathan Eisen of course and you should go and read why. Every top hit in a Web search for that organism tells us that Nitrosopumilus maritimus is an archaeon.

Looking forward to a rapid correction and apology from Nature.

Title edited from “phylogeny” to “taxonomy” at the insistence of @BioinfoTools ;)

Finding the truth is a waste of time, scientists say

Before bioinformatics, I worked in both biochemistry and microbiology labs, including a stint in the field of extremophile biology. So like many other people, I’ve been following the “arsenic life” story with great interest.
It seems that far more has been written about the publication, the manner of its announcement, the ensuing online debate and the personalities involved than about the principal scientific question: can arsenate substitute for phosphate in biological molecules? My opinion, for what it’s worth, is that the Science paper presented no compelling evidence for covalently-bound As in DNA and that the editors should have asked the authors either to do better experiments or tone it down.

Now, Nature News reports that the criticisms are in, the authors have responded and as part of their response, they are willing to share samples of the bacterium with other researchers for further analysis. Good on them – that’s the right thing to do. What’s bewildering and saddening are some of the responses to the offer. They include (paraphrased): “I wouldn’t waste my time because I don’t believe it”, “if there is no arsenate in the DNA, how could I publish in a high-impact journal and get a job?” and “I have the technology to do it but I have better things to do.”

Is this what biological science has become? The single-minded, career-oriented selfish pursuit of the high-impact publication to the exclusion of everything else – including the truth? I’m afraid that the answer is “yes” and I suspect this attitude is what got the authors of this Science paper into trouble in the first place.

This is what those who imagine some glorious future open-science utopia are up against. All I can say is: be thankful for Rosie Redfield and her lab.

Conservative (with a small “c”) research

This is really interesting. I’m reading it at work so I can’t tell you if it’s behind the paywall, but I sincerely hope not; it deserves to be read widely:

Edwards, A.M. et al. (2011)
Too many roads not taken.
Nature 470: 163–165
doi:10.1038/470163a

Most protein research focuses on those known before the human genome was mapped. Work on the slew discovered since, urge Aled M. Edwards and his colleagues.

The article includes some nicely-done bibliometric analysis. I’ve lifted a few quotes that illustrate some of the key points.

  • More than 75% of protein research still focuses on the 10% of proteins that were known before the genome was mapped
  • Around 65% of the 20,000 kinase papers published in 2009 focused on the 50 proteins that were the ‘hottest’ in the early 1990s
  • Similarly, 75% of the research activity on nuclear hormone receptors in 2009 focused on the 6 (of 48) receptors that were most studied in the mid 1990s
  • A common assumption is that previous research efforts have preferentially identified the most important proteins – the evidence doesn’t support this
  • Why the reluctance to work on the unknown? [...] scientists are wont to “fondle their problems”
  • Funding and peer-review systems are risk-averse
  • The availability of chemical probes for a given receptor dictates the level of research interest in it; the development of these tools is not driven by the importance of the protein

I love the phrase “fondle their problems.”

I’ve long felt that academic research has increasingly little to do with “advancing knowledge” and is more concerned with churning out “more of the same” to consolidate individual careers. However, that’s just me being opinionated and anecdotal. What do you think?