Two more signs

  1. The blogosphere is alight with the announcement from Science Commons of a protocol for implementing open access data. This Technorati search with keywords “science commons open data” throws up 528 posts, many of which are relevant. I suggest that you also follow developments via Deepak’s blog and links therein.

    Now, this is great news for those of us who care about all things open – open access, “open science”, open data; and people who follow developments in web technology. However, we need to make it relevant and accessible to the people who matter: interested research scientists with the question “how can I make my data more accessible”. Those people are unlikely to subscribe to the W3C mailing list. So rise up blogging community – start writing short, clear informative posts in non-specialist language, aimed at explaining to a bench scientist why they should care and what they should know concerning this protocol.

  2. John Hawks has had a busy week following his major publication on accelerated evolution. He writes:

What I most want to point out is that the discussion on blogs is at a very high level — people are reading the paper with much more precision than I have ever experienced in the peer review process

If I could have one wish come true in 2008, it would be for more scientists in academia to realise that so-called “non-traditional” modes of publishing, debate and communication are of equal value (for me personally, higher value) to the old ways that they insist on defending, regardless of the evident flaws in those ways.

Stem cells and science blogs

We all know the Seed Group ScienceBlogs, but there are other, similar collections out there.

Correlations is the WIRED Science blog, featuring articles by several prominent science bloggers. I was interested to see Clifford from Asymptotia turning his hand to biology in a very good article on the much-reported recent breakthrough in stem cell research.

This news is also featured over at Scientific Blogging. I received an email from them recently (rather generic, it referred to my “site(s)” and I imagine my other blogging friends got the same invite), asking if I would be interested in the role of biology feature writer. I don’t really have the time or the inclination to write those longer, essay-style science journalism posts at which others are very good, but check out their site if you’re interested.

From hype to reality, just like that

If you’ve been wondering whether personalised genomics startup 23andMe were for real, the wait is over. Details of their service are now available. Simply pay USD 999, spit in a tube and mail it to them (in the US only so far) and they promise a personal web-based genome browser with information about disease susceptibility, ancestry and (if your relatives join in), genealogy. The technology used is SNP genotyping – basically DNA is amplified from your sample and hybridised to an Illumina array, generating ~ 600 000 data points. All the details are available here.

Some reactions (first 2 articles by people who have trialled the service):

So there you go – we talk about the hype, the technical difficulties, the ethical/legal issues and then someone just goes and does it. I suspect that increasingly, this is how the future will unfold. Shall we lay bets on the year of the first cloned human?

Friday light relief

One of my RSS feeds comes from Improbable Research, the source of many an Ig Nobel award. Yesterday’s item is a real treat:

Recurrent Clostridium difficile colitis: case series involving 18 patients treated with donor stool administered via a nasogastric tube.
Johannes Aas, Charles E. Gessert, and Johan S. Bakken.
Clinical Infectious Diseases, vol. 36, March 2003, pp. 585.
Improbable summary | PDF

Improbable feed

Yes, it is every bit as unpleasant as the title suggests.

Over the brainbow

cover_nature.jpg I’m a big fan of cell imaging – pretty pictures of fluorescent cells always enhance a conference presentation. A Harvard team have taken fluorescent labelling to a new level, using combinatorial fluorescent proteins to image brain tissue in 90 distinct colours. What’s more, they’ve come up with a memorable word in “brainbow”.

Bad reporting

Last week, I am creating artificial life, declares US gene pioneer went into my Google Starred list. “Craig Venter, the controversial DNA researcher, is poised to announce the creation of the first new artificial life form on Earth”, stated the Guardian article.

Maybe the reporter was over-excited, maybe the researchers did a bad job. Either way, “poised to announce” is incorrect. You can trust a professional science writer in the form of Carl Zimmer to clarify the story.

Ig Nobels 2007

Can it really be Ig Nobel time again?

Details of the 2007 ceremony are not yet up at the official site; also check these news sites:

Good to see an Australian contribution:

Literature – Glenda Browne of Blue Mountains, Australia, for her study of the word “the”, and how it can flummox those trying to put things into alphabetical order.

All about J. Craig Venter

The Diploid Genome Sequence of an Individual Human
Levy, S. et al. (2007)
PLoS Biol 5(10): e254

We have generated an independently assembled diploid human genomic DNA sequence from both chromosomes of a single individual (J. Craig Venter).

One man’s genes show DNA is still a mystery:

“You can’t even tell with 100 percent accuracy if I would have blue eyes, looking at my genetic code,” he laughed. “We all thought that would be simple.”

See also the Jimome.

  • Rampant egotism or pioneering demonstrations of the personal genome concept? Both, I guess.
  • How long before anyone can access their own genome?
  • And would you want to? I think I would…

Bioinformaticians, take heart

It’s difficult for bioinformaticians to publish in so-called “high impact” journals at all, never mind as first author. Many of us are not group leaders with tightly-defined research programs; we are the “go to” guys, happy to apply our skills to any dataset that comes our way. In academia at least, we’re caught somewhere between research scientist and IT support. It can be a frustrating life.

So it’s good to see that Nature, a journal not renowned for publishing articles with a strong computational biology component, has seen fit to publish this:

Structure-based activity prediction for an enzyme of unknown function
Hermann, JC et al. (2007)
Nature 448: 775-779.
Abstract | Full text | N & V

It’s a fascinating piece of work. The authors started with an enzyme of unknown activity from Thermotoga maritima, a thermophilic bacterium. Initial structure/sequence analysis suggested a superfamily for the enzyme. They then compiled a list of ~ 4 000 potential substrates, modelled tetrahedral intermediates that could resemble the transition state for each one and performed docking simulations of each model with a model of the enzyme active site. This generated 4 candidate substrates, 3 of which were confirmed by biochemical assay. For a finale, they determined a crystal structure for the enzyme + bound product which agreed closely with the model and identified a new metabolic pathway for orthologues of the enzyme in other genomes.

There are a few criticisms of the approach. This is a case where modelling was a good approximation to reality, but there are plenty of cases where that isn’t true. It also relies on quite a lot of prior knowledge concerning sequence/structure and metabolism, which isn’t available for many uncharacterised proteins. And it’s currently quite computationally expensive, so not exactly high-throughput, although that will change of course. Still, if you enjoy genome-scale bioinformatics and structural biology, it’s almost enough to make you drool.

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Farewell to…

Odile Crick, wife of Francis. Interestingly, the illustrator of the figure depicting the DNA double helix in that Nature paper:

In his memoir, “What Mad Pursuit,” Dr. Crick recalled going home that day and telling his wife of the historic discovery. Only years later, he wrote, had Mrs. Crick told him that she did not believe a word of it, saying, “You were always coming home and saying things like that, so naturally I thought nothing of it.”