[DMCA-Activists] Aigrain on Sulston: On Embedded Software Patents

[Seth Johnson]

Why software - in particular embedded software - should not be patented 

Submitted by paigrain. on 2004-06-13 02:30 PM. EN 

Analysis of a long - but worth reading - quote from John Sulston and
Georgina Ferry's Common Thread book

The promoters of software patents have often recourse to the case of
embedded software to try to justify them.  Because physical machines that
embed software have both physical and information components, they conclude
that the principles of both should be equally patented. I have produced
various analysis to demonstrate that it is not the case, but none is as
compelling as the example described by John Sulston in the book he wrote
with Georgina Ferry, titled The Common Thread: Science, politics, ethics and
the Human Genome (NAS, Bantam Press, 2002).  John Sulston was the head of
the Sanger Centre, and is a joint winner of the Nobel Prize for Medicine.
Let's first read what he has to say about events that occurred around 1990
when his group was occupied with sequencing the nematode worm's genome:


Once the first fluorescence sequencing machines arrived, it became clear
that we had to take control of the software. The machines worked well, but
ABI wanted to keep control of the data analysis end by forcing their
customers to use their proprietary software. In order to finish a sequence
properly in the way I described above, you must have easy access to the raw
data in order to evaluate their quality from point to point. A good way of
displaying the readout from the gel is as a set of coloured traces on the
screen. ABI's software produced a display, but not in the form that we could
combine flexibly with Rodger Staden's assembly programmes. It was
inconvenient to use and slowed us down. I could not accept that we should be
dependent on a commercial company for the handling and assembly of the data
we were producing. The company even had ambition to take control of the
analysis of the sequence, which was ridiculous. I had a complete obsession
of getting data out - I saw that as the bottleneck. There was an awful lot
of people out there theorizing about genomes, so for the moment I did not
see that as our job. The best way to drive the science was to get the
sequencing machines going, cheaper and faster, and get the data out so that
all the theoretists in the world would work on the interpretation.


So, one hot summer Sunday afternoon, I sat on the lawn at home with
printouts spread all around me and decrypted the ABI file that stored the
trace data. I don't think it was deliberately encrypted; it was just
constructed in a rather Christmas tree fashion, which I needed to track from
one point to another. I came in on Monday morning and said, 'Look, this is
how we get the file data'. Within a very few days, Rodger and his group had
written display software that showed the traces - and there we were. The St
Louis team joined in, and they all went to decrypt more of the ABI files, so
that we had complete freedom to design our own display and analysis systems.
It transformed our productivity. Previously we'd only been able to get the
traces as printouts, which we bound together in fat notebooks, infuriating
to fast workers such as Rick WIlson.


You'd sit down at the computer, and youy'd have to flip through this stupid
notebook, until you found the trace that you wanted. And hopefully it would
be in the right direction. The great idea was to figure out a way to get
this on line, but ABI would not help us out. So sat down and cracked it.
That was a huge advance, really an important development. If we hadn't done
that we'd had have been way, way behind on the worm project.


ABI was not at all happy that we had done this. We had been negotiating
towards the idea that they would sell us a key that would unlock the files,
but it was clear that even then they woudl always have control and they
would take it away again. There remained a real risk that they would
re-encrypt the file in a way we could not get at; so we made sure that their
other customers were aware of what was going on, and they did agree quite
quickly to keep their formats public. We went on to become one of their
biggest customers. I think I was the first to decrypt the files, but I'm not
certain - there were others doing it at about the same time. I certainly
feel that between us we did push ABI back a bit and denied to them complete
control of this downstream software. It was the first experience of the kind
of battle for control of information that I seem to have been fighting with
commercial companies ever since: a foretaste of the much larger battles that
would later surround the human genome. 

I don't want to add much to this quote: it speaks for itself. It tells you
why the vendors of machines with some software embedded in them  want to be
able to patent it, and why they should never get it. It tells you why, in
the context of software and information, the search for interoperability
should always be exempted from being an infringement of patents (even for
hardware patents). It tells you why such exemptions, though necessary, are
are not sufficient if you allow the principles of software and information
to be patented (in which case the machine vendor will always be in a
position to claim infringement by saying writing operating software went
beyond the search for interoperability). And it tells you that after you
refuse this abusive monopoly, the companies will still do OK, but in a
normal realm of control. Finally, it enables you to dream about a world
where the freedom of software and information will be the rule and not the
exception, where futur Nobel prize winners will be able to make advances in
science without having to hack proprietary software. Thanks Mr. Sulston!

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