Bioperl: Re: Open Source and Bio questions

[Clay Shirky]

> People file a patent on sequences as a reagent to do things with
> sequences, in particular retrieve that sequence from a database, 
> retrieve the physical DNA with PCR or hybridisations. Notice that the
> patent is not on "just the sequence" but on the *use* of the sequence
> to retrieve the gene (either electronically or physically).

Oh, now this is interesting. If a published map of, say, chromosome 22
exists in the public domain, and I use a patented sequence to locate a
certain section of that map, I've violated the patent?

Does this extend to the equivalent proteins? I wonder if IBM's 'Blue
Gene' protein-folding supercomputer will only be able to work on licensed
sequences? 

> As doing virtually anything with the sequence with infringe this patent
> (god knows what happens when people use sequences outside of the sequence
> but on the same gene as the sequence that is patented to retrieve
> something - the mind boggles)

My mind boggles just reading this sentence. Do you mean that if I have
a sequence that codes for, say, something in one of the genes that
affect hemoglobin, but that I can use the same sequence to find other
hemoglobin-affecting genes on the same chromosome, I might or might
not be violating the patent.

> If you find out more stuff, can you post back here? (or at least to me)
> I am sure we would all be interested in how this works out.

Of course, though I should say in advance that I have both an outlook
and a thesis which keeps me from being a dispassionate observer. I've
lived through the Web revolution, and many of the forces at work there
are also at work here: for Moore's Law substitute the speed with which
the number of sequenced base pairs in the worlds databases doubles
(with the attendant change in the $/BP ratio), and for IBM and
Microsoft substitute the Big Pharmas.

What happened in the mid-90s is that the price of computing and the
reach of the Internet reached an inflection point where suddenly a
couple of college kids could create Yahoo, and a loose coalition of
programmers could create Linux, and neither MS nor IBM could either
stop them or get in the game themselves. Now the comparison between
media dn genetics shouldn't be over-extended, so this is just a
starting point, but given the collapsing cost of sequencing, coupled
with the rise of purely virtual ways of dealing with biological
information (viz. Blue Gene), I am wondering if the Big Pharmas are
going to start getting serious competition from small, Yahoo-like
bio-informatics groups.

The single biggest obstacle to such a scenario, of course, is the idea
of patenting a sequence, hence my research.

If anything formal comes out of this, I'll let you know.

-clay

--
Clay Shirky
Professor, New Media
Department of Film & Media
Hunter College
http://www.shirky.com/

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