Bioperl: UCSF Discussion, Public V. Private Genome Efforts

[Andrew Dalke]

(Time for a digression and small tirade :)

David J. States <states@gpc.ibc.wustl.edu> said:
> Having said all of this, the free accessibility of molecular
> sequence data is the exception rather than the rule in science.
> [...]

  The most well known proponent for "Open Source [tm]" is Eric
Raymond.  I don't know who here has read his various writings,
available from:
  http://www.tuxedo.org/~esr/
  http://www.opensource.org/
  
In one of them he describes how (his viewpoint of) the hacker
culture is:
| intimately related to (and may derive directly from) the practices
| of the academic world, especially the scientific research commmunity.
| This research community has similar problems in mining a territory
| of potentially productive ideas,  and exhibits very similar adaptive
| solutions to those problems in the ways it uses peer review and
| reputation.

He neglects to point out just what David States says: the open/free
sharing of software, data, reagents, etc. in the academic world is
quite uncommon.  I sent email to Raymond pointing this out, and
refered him to the article in Science, 279 specifically talking
about X-ray crystal structures.  I never received a reply.

I also met him at last month's Python conference, where he was a
keynote speaker.  I asked him afterwards how he can say the open/free
software philosophy comes from academia when that practice is rare.
He did not believe me and said that if it does occur then those
people are shunned by most other researchers.  He then ceased the
conversation.

Compare that to everyone I've talked to who have done research (in
physics, biology, chemistry and computer science).  When I bring up
Raymond's comparison of hacker traditions to academic practices,
the listeners have invariably been astonished that someone could
propose the association.

Therefore, while I believe his idea of peer recognition being an
important reason for people to do open source software, I find his
reasonings and justifications rather flawed.

						Andrew Dalke
						dalke@bioreason.com
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