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open-source software for bioinformatics (was Re: Unix vs Linux - the movie.)

Sean Eddy eddy at wol.wustl.edu
Mon Aug 7 15:16:06 EST 2000

In article <398ef9cd$1 at news.ucsc.edu> karplus at cse.ucsc.edu (Kevin Karplus) writes:
  >I applaud the programmers who provide open source and am glad to
  >encourge more open source.  But requiring that all scientific code
  >follow a particular philosophy is a sure way to stifle innovation.

Boy, this reminds me of teaching research ethics to grad students.

There was the subset that thought that sharing research resources was
a Good Thing -- but only when it came to other people giving *their*
resources away. They didn't feel like they should have to give
anything away themselves. Science is too competitive for that outdated
altruism crap, you know.

So I tried to point out that it's really hard to skirt this issue,
because if you're an academic scientist, there's ethical, economic,
and legal arguments that should be pressing you into releasing

a. the ethics of academic science demands disclosure and sharing of resources.
b. society funds science from taxes and charities
   with an expectation of getting something back -- namely, accessible
   basic research results. Society in general does not
   expect to pay for research twice.
c. NIH, NSF, and many other agencies have policies *requiring*
   you to share research resources.

Someone then argued that ok, sure, he'd give away his research
resources, but not in a form that another lab would actually be able
to do an experiment -- only in some derisory way that would satisfy
the letter of the law, so that his program officer wouldn't take his
funding away. He was completely serious. Though I was looking at him,
speechless, fully expecting him to defend pedophilia, ritual torture,
and the Republican Convention in his next sentence, he reverted to a
seemingly completely normal demeanour.

So by grad school, people have already formed and rationalized an
ethical code, no matter how horrifying; and I've decided it's pretty
pointless to try to change their views.

For instance, according to my own ethics, scientists who don't share
their source code for their published, publicly funded bioinformatics
work should be buried in a mound of fire ants under syrup-soaked back
issues of CABIOS -- and it's no use trying to change my mind, because
that's the way Mom brought me up.

- Sean

- Sean Eddy
- HHMI/Dept. of Genetics, Washington University in St. Louis
- http://www.genetics.wustl.edu/eddy/

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