Biologists, software and ELNs

Every few months, my colleagues decide that electronic laboratory notebooks (ELNs) are a good idea. I go through the ritual of searching the web, bookmarking some resources and where possible downloading, installing, configuring and running packages to see how well they work. I know in advance that I’m wasting my time, because I’ve tried them all and there isn’t one free/open-source ELN that works for me.
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Looking for something to read?

I recommend Bio::Blogs edition 11 (or the PDF for offline reading). Bio::Blogs this month features not one but two special editions: bioinformatics tips and tricks and personalised medicine (both PDF links).

I think we’ve really raised the standard this month; all the contributions and the production standards are excellent. Well done to all involved. Next month will be the first anniversary edition, so get working on those posts.

Willing to learn

Via Nodalpoint: Paulo Nuin (Genedrift.org, Blind.Scientist) is running a series of interviews with scientists. I enjoyed Brian Golding’s answer to a question about companies who package and sell freely-available open source bioinformatics software:

If it is important to people to have a package that they need not worry about piecing together then they can pay for it. I am however, surprised to find any people that have paid big bucks for packages that I piece together for free often with a more powerful interface. Difference is, I am willing to spend some time to try to learn.

Selling free software is common practice for the very few biotech startups in Australia and to me, smacks of cashing in on ignorance to make a quick buck, rather than contributing to bioinformatics education. It’s always annoyed me immensely.

Mathematics and biology

There’s a blog meme going around concerning the mathematical education of biologists – interesting discussion here (Keith), here (Deepak) and here (RPM).

In my experience, you pick up the maths that you need during the course of your research. That makes the question “what maths should undergraduate biologists learn?” rather difficult to answer – but I think we’re all agreed that one response is “more than they do now”. Anyway, on to those meme questions and I’m with Deepak – it’s maths, not math:
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Uh-oh, evolution misconceptions alert

If you’re looking for a really poor opinion piece by someone who doesn’t understand biology, followed by a bunch of even less informed comment, try Human evolution has stalled, over at Kuro5hin. You thought I was going to say Slashdot, didn’t you!

Gems include:

  • “runs counter to the purpose of evolution”
  • “evolution itself encourages adaptive traits while weeding out maladaptive traits”
  • “for untold millenia, natural selection has directed the evolution of life on this planet, gradually from simple primordial goo into more complex life forms”

and of course, a complete failure to understand “fitness” in the Darwinian sense.

One of those evolution bloggers needs to go over there and sort them out. You reading this RPM?

Science education

Much of the science blogging world (the Seed magazine crowd at least) is alight over an article in Science on how scientists might better engage with policy makers, press and public. The great irony here, of course, is that this article has ended up in a closed access forum that requires subscription to read. That in itself says a lot about one big problem in science: scientists are encouraged to aim for so-called prestige over wider dissemination.

The gist of the article seems to be that as most people are ill-equipped to understand technical arguments, scientists need to find other ways to argue their case in non-science forums. Sounds reasonable enough. I suspect the point of the article was to ignite a debate and it certainly has. Predictably, a lot of science bloggers suggest that the task of communicating science would be easier in a world that (a) cared about science and (b) was populated by people with a basic science education. I think it’s unfortunate that the article focuses on the problem of debating with those sectors of society that don’t want to listen to reason in the first place. All I really got from the article was that the American Right contains a disproportionately-high number of stupid people – which I knew already.

More interesting to me: If We Taught English the Way We Teach Mathematics, over at Kuro5hin. I’ve rediscovered this site after a long absence and there’s a lot of worthwhile reading.

Sensing a trend

In general, I don’t find the Careers section in Nature very helpful. It often features rather general, obvious advice such as “acquiring new skills is good”, then fails to expand further. Once in a while though, there is a longer more helpful article and these are more popular, judging by the hits. The top two articles for last December are:

Should I stay or should I go?
Gut check time: should you stay in academia, on the bench or even quit science?

Prospect
How to ask yourself questions about major career decisions.

Which says rather a lot, I think.