Monthly Archives: April 2007

Too many networks

I’ve really warmed to the idea of social networking in recent months. There’s a drawback though – you end up subscribed to a lot of different websites, with (possibly) a lot of usernames and passwords. I suppose OpenID is supposed to alleviate this but this list of OpenID sites includes few that interest me. WordPress users – your blog URL is your OpenID, FAQ here.

I’ve created a new page titled “social networks” at this site (see Pages menu, left). Its main function is to remind me of the places where I maintain “web presence”, but perhaps there’s also something of interest to others there.

The great flagellum debate

Flagellae, the whip-like structures that many microorganisms use for propulsion, have long been a favourite case study for biologists. The search “bacterial flagellum” at PubMed generates 2 684 hits as of today, including 274 review articles. Without getting too deep into the literature, the flagellum is a complex, self-assembling piece of molecular machinery. Many of its proteins seem to be derived from other cellular machines, most notably secretory systems.

Parts of the science blogosphere are currently alight with debate regarding a recent PNAS paper which suggests that the 24 core flagellar proteins are derived from a single ancestral gene. Most of the debate is taking place over at The Panda’s Thumb. It’s been interesting to follow the progression from an opinion piece, through a rather dubious protein structure analysis (an area in which the main protagonist is clearly not an expert) to an attempt to replicate the findings.

That last point is important. There’s been a lot of comment about “trial by blogosphere” in this case. I have no problem with informed scientific debate on the Web – but let’s behave like scientists. If you take issue with someone’s data and findings, your very first action should be to analyse their data; either show that their analysis is wrong or your analysis is better. Otherwise it’s easy to come across as just another angry, opinionated blogger screaming into the void.


Just browsing the website of a life sciences company, I found this at their support page:

The need for information may strike at any time

It made me laugh, then wonder who else would laugh. I often wake screaming in the night with the need for information.
It also made me think about the concept of commercial support (service contracts, passwords, incident reports) versus open-source support (mailing lists, discussion forums, bugzilla). I know which I prefer.

Slideshare and WordPress

Slideshare is an online community for sharing presentations. It came to my attention a few months ago via Pedro’s blog post. There’s a similar service at

Slideshare is excellent: you can upload Powerpoint, OpenOffice or PDF presentations which are converted to a YouTube-like Flash presentation. You can add tags, view slides full-screen and share your slide either at the site or by embedding code in a web page. On that last point – WordPress now has code to embed your slideshow in a blog post.

I tested the service using these slides from a talk that I gave to my school last year, on genomic analysis of cold-adapted microorganisms. You can follow that link or see an embedded version, below.
Slideshare presentations tagged “bioinformatics” are here.
Read the rest. . .

What we don’t know

There’s a general perception that we know in outline how everything works and we’re just filling in the details. It’s good to find out that this is not the case – and often for seemingly simple, everyday processes. For instance, did you know that we know next to nothing about what tells a plant to produce flowers? From the Science summary:

Two new reports, published online by Science this week ( and, have identified the signal that tells plants to flower. Contrary to work reported in 2005 showing that the signal was messenger RNA, the new work fingers the so-called flowering locus T protein. (Read more.)

In Science this week, the authors retract a paper from two years ago which suggested that the flowering signal was a mRNA and publish two new studies implicating instead the protein product of the mRNA. The lead author on the previous paper, who no longer works in the group, “strongly objects to the retraction of the paper and has therefore declined to be an author of the retraction.” Ouch. Where do you stand when your ex-boss retracts your work, I wonder? You’d at least leave it on your CV?

How many protein kinases in the PDB?

I often find that the most satisfying problems in bioinformatics are not related to a specific research project. They arise when someone has a query and you have a neat way to send them an answer, quickly. Take this email that I received yesterday:

I’m compiling a table of serine-threonine protein kinase structures. Can you take a look and see if anything is missing?

Strangely, I don’t carry a list of current PDB accessions for every protein kinase in my head. On the other hand if you ask me “can I extract all structures that are protein kinases from the PDB?”, the answer is yes, you can. So here’s what I did.
Read the rest. . .


Bugger. Someone has tagged me with one of those blog memes. It’s called 5 Blogs That Make Me Think.

I am of course flattered, but now the law of the blogosphere dictates that I respond. My reader currently contains 72 subscriptions – I’ve cut down recently! – and only a small proportion are from blogs. Most of them are news, journal TOCs and software announcements. Let me make it clear that my list of five is just a selection of the top of my head, in no particular order.

  • Public Rambling
    No bioinformatics-related list would be complete without Pedro, whose enthusiasm inspires me to keep going.
  • The Loom
    By far the best of the Seed ScienceBlogs collection and one of only two that I bother to read from there.
  • Open Reading Frame
    It doesn’t update as much as I’d like, but is always a good read when it does.
  • Asymptotia
    Perhaps a little constrained by the Cosmic Variance format, Clifford has carved his own niche with observations on physics, teaching, science, spirituality and everyday life in LA.
    I go here for a fix of well-researched, lucid and rational writing on politics and environmentalism.

Note to self: should make my subscriptions public, somewhere.