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.

3 thoughts on “Willing to learn

  1. Brian Haugen

    A powerful interface does not equal an easy to use interface. Can we expect Joe MolecularBiologist to spend weeks learning to use the command-line and EMBOSS so he can figure out the pI of his protein of interest? The bottom line is that the most scarce and therefore valuable resource for scientists is time. If paying $3000 to a bioinformatics company so a scientist doesn’t have to spend time learning the command line that he/she could spend doing ELISAs or loading gels, then maybe that is a good trade-off. I can see it as paying to collaborate with the company.

    At some point, though, if a scientist is doing so much work on a computer, they need to understand that computers aren’t black boxes that can only do so many things. Scientists need to understand that computers can be bent to our will. True story: I went to a seminar where a professor described having 2 unpaid medical student researchers spend their summers submitting each of 3100 protein sequences to a web-server which predicted immunogenic peptides from protein sequences. I was so shocked, I couldn’t believe the complete waste of time and resources.

  2. nsaunders Post author

    True story:
    Horror story! I’ve been to a few seminars where the PI recounted a similar tale (though not so extreme as your example). “So my student spent 6 weeks editing a genome in Word” or some such thing. Everyone has a bit of a laugh, but it’s almost a respectful laugh. I’m usually the only audience member not laughing. There’s nothing noble or worthy about wasting your time through wilful ignorance.
    I take your point about the time/effort trade-off. Here’s a couple of counter-arguments.

    1. If you take 3 hours to perform a computational task that could take a few seconds, you waste 3 hours every time you do it. If you perform that task frequently or regularly, you sum those 3 wasted hours. I reckon most intelligent people could learn the scripting or command-line tools required to automate a task in a few hours at the very most. In other words, time spent now is time saved many-fold later on.

    2. People doing wetlab work are happy to expend time and effort to get things right. If you want to optimise a PCR or protein expression you research the best system, troubleshoot, try to find the best method. Nobody expects PCR or expression to “just work”. Yet when it comes to computation, these same people expect that things should “just work” – without the time, effort or research. I struggle to see the difference between optimising a lab protocol and optimising a computational analysis.

    So no, I don’t expect Joe MolecularBiologist to spend weeks learning the command line – but I can’t understand why he doesn’t see the benefits.

  3. Brian Haugen

    Points taken and agreed with. Scientists should be willing to see the advantages of working at the command line and in programming languages, but I think they can be afraid of the magic black box of computing.

    Is it because many biologists have courses in physics, chemistry, etc that make it obvious that they can understand and manipulate reaction conditions in a PCR tube? However, the thought of changing how a computer does things doesn’t even occur to them. How many of our colleagues web browsers are still set to the default home page set by Firefox/Microsoft/Apple?

    I think blogs on these topics, as well as resources like Scriptome will make a dent in this fear. But ultimately, I think an important first step would be to require a scripting course for biologists, if only in graduate school. If they are too afraid to be “willing to learn” maybe being thrown in the deep end of the pool will show them there is nothing to be afraid of.

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