Bioperl: Re: Open Source and Bio questions

[Alessandro Guffanti]

> 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.

That's an interesting theory, but remember that both MS and IBM are
quite well and alive.
The point is that big pharmaceutical companies are simply outsorcing
advanced technologies like gene distruction, comparative genomics, DNA
chips to small or medium-sized startup companies because it is too
expensive for them to keep the people trained and the labs well equipped
with all the latest in genetic technologies. They then acquire the
knowledge and use it in-house to generate and test on a large scale new
compounds or, still better, outsorce the generation of compounds and
keep only the clinical testing and marketing phase for them. In this
sense, it is an evolution from a classical chemical giant to a knowledge
container. Although there are exceptions to this (SB and Glaxo-Wellcome
for instance), the rising costs of developing new compounds, together
with the problem of fitting young tech-lovers witht the relatively rigid
framework of corporate culture force in this direction all the big
giants. What happens then is that some new realities flourish (Lion,
Exelixis, Lexicon ..) while tradidional R&D department are downsized. In
this sense, no competition at all - the big fishes simply gobble up or
support the small ones. Smart (or barve) people like W.Hazeltine make
bets on breakthrough products (peptides in its case), get wagons of
startup money from some colossus and then hope they can do it.

As far as I have seen from a brief experience, sequences are proprietary
to whoever produces them (e.g Incyte or HGS) in the sense that you pay a
fee to query the database, a (quite high) fee to get the DNA and
royalties on the compound which eventually comes out from this. I don't
know which are the current politics, but I suppose a bit more relaxed.
The amount of money involved here is usually shocking for us poor laymen
but one should rememeber that the largest income for traditional
pharmaceutical companies generally comes from well-established or
over-the-counter remedies.


The concept of making money from sequence data alone has meaning
probably only if one offers new data. Once these were human ESTs, now
they can be some bacterial strains which are not avilable anywhere. In
this sense, I would say that Celera effort is a bit odd because the data
will be publicly available anyway .. 

Alessandro.
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