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Distributed Computing and the Human Genome Project
from the breaking-the-genetic-code-instead-of-rc5 dept.
troc asks: "I was watching a TV programme on UK TV last night about the Human Genome Project and how there was a race to sequence and publish the whole thing before the private companies do it and patent the sequences. Basically lasers are used to break up the strands, these are then read and fed into a computer that tries to match the bits up with other bits like a giant jigsaw puzzle. This requires a lot of computing time.
Is this an opportunity for the open source movement to help decode the sequences and publish the whole thing becore it's patented?
<soapbox>
I, for one, don't like the idea of a private company owning my gene sequences. They will be able to limit the use of these so only really rich pharmaceutical companies will be able to develop drugs etc and then sell them at huge profits, which isn't realy for the benefit of mankind blah blah blah.
</soapbox>"
I agree. I don't see how information like this can be patented. There is nothing truly proprietary about it, and it would do more good in the public where the benefit can truly be felt.
perhaps this will be a wake-up call (Score:5)
However, with the computer age, the speed of (dare I say) innovation has been astounding. This has produced two detrimental effects. First, the patent examiners simply don't have the niche expertise to scrutinize patents. I'm sure most of us have seen some of the idiotic patents out there. Second, the time span of a patent has become too cumbersome. By the time the patent expires, the invention is often useless.
I sincerely hope that this particular project will be placed under a HUGE spotlight when the patent requests inevitably filter in. I have a feeling it won't hold up, and at the very least, not in some countries.
However, keep in mind that this is scientific information about a human being, not software / computer advances. In that regard, a patent will be cumbersome, but not quashing. The patent (if granted) WILL expire someday. And I'm fairly certain that the information will still be very important and valuable when that day arrives.
Of course I'm all for beating the would-be patenters to the punch, if possible.
Best regards,
SEAL
Hold on. The seq's can't be patented. (Score:3)
In a number of countries it's already quite specifically illegal to attempt to put intellectual property restraints on anything involving human genes. US is considering some laws as well, but let's just get all the facts straight before panicing, okay?
This can't be open source! (Score:5)
The only problem I see here that developing a distributed client for this takes a lot of time and effort --- and one, which definitely cannot be open-source!
Two reasons:
So, sorry, folks, but I believe this is one of the few things that open source clearly is not suited for. But it would be kinda cool to have a proggy running on my machine that messed with genes ... ;-)
Re:Hold on. The seq's can't be patented. (Score:4)
Otherwise anyone holding such a patent would be
(AFAIK) entitled to control the reproduction of
the sequences, that is, since we are contantly
reproducing them in our bodies he could charge
us for letting us live...
Now, this would make patent law a satire just too obviously.
Still, (again, AFAIK, correct me, if I'm wrong)
patents on gene sequences (that is, their
applications) have a new quality: They do not
cover applications that the patent holder has
thought of, they cover all applications that
become possible only if you know that gene
sequence.
If I remember it correctly, there are already
cases where companies hold patents on certain
proteins in our bodies (again, not the proteins
themselves but any of their applications) and
you are not allowed to TEST for these substances
without paying them license fees, even if you're
using a completely new testing method you developed on your own.
Re:Distibuted computer projects... OT (Score:3)
All this could be done so much easier. Use applets - people do not have to understand anything at all in order to help out on a project like this. No need to install obscure clients and what have we. I think the only good use of applets is for easy distributed computing.
Re:This can't be open source! (Score:4)
The Human Genome Project is extremely open. They try to make all data public as soon as possible, making patents impossible. So data theft is not an issue here.
False results might be a problem, but I would expect it to be relatively cheap (computationally seen) to check a solution to see if it is valid.
A distributed (open source) effort will probably not happen because a computation like this is more difficult to distribute than trying crypto-keys et.c.
Lars
--
Open Source Genome Projects (Score:5)
- ensembl [ebi.ac.uk] is an open source genome project designed to get as much data and software into the public domain as possible
- EMBOSS [sanger.ac.uk]
- bioperl [perl.org]
All these are well backed, strong open source projects with different strengths. Everytime genome stuff comes up on slashdot I try to point these things out to people, but everything gets lost in the noise about people $%!"'ing on about patents (generally without alot of knowledge!).Anyway - check out these projects for more information about real open source efforts in biology.
TIGR, HUGEP and genomics (Score:5)
First issue: could distributed computing help? My answer is a brief "no". First, the bottleneck is on the experimental side - getting the sequences, and not putting them all together. Second, although you need quite a lot of computing power to do so, much of the job must be revised and checked by humans, i.e. there is a lot of skilled manual work to do - you have to have "an eye" for the sequences. But the first point is more important.
Now, TIGR [tigr.org], the commercial alternative to the Humane Genome Project has sequenced more organisms then any other scientific group in the world. Craigg J. Venter seems to be very efficient and hard working guy. Even if you don't like the idea of making money with patents in this area the scientific community owes him a lot - he was the one to sequence the first organism, to sequence Helicobacter pylori and many, many others. On the other side... you know, when M. pneumoniae sequence was about to be published, it was supposed to be the first Mycoplasma sequence. But Venter was faster with Mycoplasma genitalium - and he kept it quiet, so noone involved in sequencing those organisms actually knew there is a race. Now Venter claimed to be able to complete the human genome with much less effort and much less $$, and considerably faster then the HuGeP. I'm not sure whether he is able to do so or not, because it depends chiefly on the "hardware" side - the new Perkin Elmer automatized sequencers they are supposed to use.
Anyway, the question is, whether it is good or bad if Venter sequences the human genome. In my opinion - it's OK. The Hugep is somewhot different in its purely scientific interest, and I'm convinced that they will produce data of much higher quality. On the other hand, human genome has a considerable variation, so two genomes are better then one. I would not be very concerned about the patent issue, because it will come anyway (because of **!'*%$! american and international patent law) - even if TIGR would not sequence the genome, someone takes the output of the HUGEP project and will patent the same sequences Venter would. Venter just wants to gain a little time for evaluating the sequence before releasing it to the public.
And of course, not the _sequences_ are patented - what is patented, is the usage of modification of a certain sequence for medical purposes, or a certain enzyme as an aim in medical treatment.
Regards,
January
warm and fuzzy (Score:5)
It's good that hackers are well-informed and principled enough to think it matters. This happens to be my area of interest; I'm responsible for Bioinformatics at the Institute of Cancer Research in the UK. A couple of weeks back I went to an excellent talk by a clever guy call Ewan Birney from the Sanger Centre [sanger.ac.uk] near Cambridge, UK. He is writing code to catalogue and annotate the assembled sequences in real time as they come off the mammoth robot sequencing "production line". In one of those rare occasions where the British are leading a "big science" project the Centre has been responsible for the largest fraction of the Human Genome sequenced at any single institute. The code does stuff like figure out which bits of the sequence are real genes and which bits are that 90%+ of so-called "junk DNA" you might have heard of and also attempts to assign provisional functions to the genes by various computational means. Eventually people in white coats will have to confirm such assignments properly, but it's important to beat the drug companies to making good guesses.
Ewan's code and all the data are entirely Open Source. If you've got a good reason and a reasonable Pentium with lots of memory and a 30Gb hard disk you could mirror the human genome and get it updated every night. (I feel strange just typing that sentence and I've been following this story for years). The Wellcome Trust and others (including US and European government agencies) funding the project are keeping everything Open because that's the way science is done and because this will subvert commercial attempts to stake a claim on our species' genetic heritage. (Er, go Wellcome!)
Biochemists often talk about the "rate limiting step" in a reaction---the single point which sets the speed of the whole process---like a bottleneck. As far as I understood Ewan's talk (if you're reading this Ewan, please put me right), the rate-limiting step with the Genome Project isn't the assembly of the sequenced stretches of DNA (or "contigs") as the original poster suggests, but the collection of the data in the first place. At the Sanger they have clusters of PCs and Alphas crunching the contigs---distributing the effort would give us all a warm fuzzy feeling, but wouldn't be essential. Again, I may be wrong about this.
One thing that definitely is a priority is making some sense out of all of this information. What would be great would be if members of the global community of hackers started taking molecular biology and biochemistry classes so they could write code to help people like me make sense of the embarrassment of riches that the project is creating. I'm off to Cambridge in two weeks to the Bioinformatics Open Software Development [mrc.ac.uk] meeting to listen to some project leaders talk and discuss the existing efforts. Personally, I would love to give crash courses in biology to programmers with time on their hands in an effort to harness their collective genius rather than sponsor an effort to write a contig-crunching client to harness their collective spare cycles, but I have no idea how such a thing could be organised. Any ideas?
Difficult to distribute (Score:4)
In the case of the Human Genome Project, the situation is somewhat different. A well known analogy is the following: Take a few copies of a newspaper. Feed it through a shredder. Remove a handful or two of paper. Insert errors. Now, piece together one copy of the original newspaper.
In order to make a useful contribution, a client is going to need a lot of data. This means that it will be difficult to distribute (long downloading times for instance) and that few people will appreciate having the client on the machine because the client will be using a lot of memory and the machine might be a bit unresponsive (your HGP screensaver might flush all your apps to disk for instance).
Lars
--
Re:warm and fuzzy (Score:4)
Great that you were following the talk. I thought I put everyone to sleep
The rate limiting step at the moment is effectively the mapping in fact, then sequencing. The interesting thing about the analysis is that the amount of CPU is unbounded. If we have more CPU we just use more accurate algorithms. We can do something within the CPU bounds on the hinxton campus, but if anyone wants to give me a super computer, then we could get more accurate analysis.
I can always use more juice!
Re:Difficult to distribute (Score:3)
This is only for the assembly and not for the analysis. With analysis you have a better data/cycles ratio. Assembly is done at the genome centres anyway...
Who makes drugs now? (Score:3)
This is an interesting statement. How do you think drugs are made now? Well, they are made by big pharma companies which make (often) a good profit. Drugs are not made for the benefit of mankind. They are made to make money.
When it comes to patenting the use of some genes, we should consider that:
On the subject of open source distributed computing for genome data, I am afraid I agree with other people here. There is simply too much data to download. It's a pity, but it won't work. Maybe in a few years time when the problems in genomics will have changed, other problems might be more suitable to this type of computations.
d.net coders wanted for DNA analysis (Score:3)
It is clear from these postings that people would
like the client to run. If there are people with
experience in writing these sorts of d.net systems
then please drop me a note. We have the problem
for you to work on - it is just a question of
figuring out how to do it.
Drop me a mail (birney@sanger.ac.uk).