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Distributed Computing and the Human Genome Project
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.
Are they really worth the effort? RC5 and SETI are both successful, but both of them require a permanent connection to the net (in essence) in order to get the best updates etc. (if ya get what i mean). As this was a UK-based thing, why not send the whole lot around on a CD?
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
More importantly - will there be money on offer?
:)
It's just as if the first man who took a photograph had said :
Now this is MY moon. You can't anymore take photographs of this.
But I wonder in which countries such patents could be valid. For instance in Europe we are having a discussion about the possiblity to patent algorithms, that was not possible in the EU until now. I hope ONLY you americans are allowing companies to patent a thing like our genome.
Fetchez la vache !
I find the idea that someone can patent human Dna knowledge sickening. That someone can control the use of my own DNA is horrible. Patents have gone mad, this is just sad.
I would like to see another distrubuted project on this. If it gets the same publictiy as the Seti Program it could have wonderful results. The only problem I could see is that the community's distrubuted-willing resources are already streched to the bone. I would say this does take presedence, eh? I don't want no stinkin' coperation owning my genes!
:)
Another thing, you don't need a permenant connection to run distuibuted. I run seti at home on a computer with a dialup that goes on about once a week. It works wonders! Cheers
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?
-- r . m o s q u i t o --
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 ... ;-)
EagerEyes.org: Visualization and Visual Communication
How on earth would you justify patenting a gene?
./ Password :)
It has been around for a _very_ long time. You may as well patent some newly discovered subatomar particle and charge everyone who uses it. Or maybe an even better comparison would be a patent to a microscope vs. patenting everything you can see through it. This is insane.
Ciao, Peter (still without
Patents are a sore point in molecular biology if the companies choose to prosecute those that appear to infringe them. The classic case is the patenting of PCR by Cetus/Perkin Elmer/Roche as the companies made open threats against academic institutions. This was especially sad as the PCR patent was extremely shaky as there is clear evidence of prior art.
Even if we did have a distributed effort and made advances, someone would still have to patent the discovery.
As we have seen with Y2K fixes and other things, making a discovery does not stop someone else patenting the idea.
An open source body would have to be setup to patent the discoveries just so that nobody else could patent them.
This body can declare thier patent open for use.
There is a lot of legal issues here - if you opne your patent too much could you lose it.
Patent law is also a case of boiler plating your patent - you have to ensure that every option is covered and also included on the patent.
This sort of thing is costly, and this is why a lot of companies patent thier ideas. Once they have the patent they recoup thier investment, and then some.
If an open source patent body is set up there will have to a lot of time spent considering patent administration and the costs involved.
I live in Iceland, and here there is the company DeCode genetics. They are building a huge database with the medical histry of every Icelander in it, to be able to trace "bad genes".
the funny thing is, they're a privatly owned company and still they are entitled to go through all your medical records at their own will and put it in a database
sure, they say it'll be secure but what if they start selling info on you to insurance companies?
imagine this:
you: Hi, I'm (some name) and I'd like a life insurance.
insurance rep.:well... I'm sorry... it's gonna cost you (insert obscene amount here) because your family has a record of heart failiurs.
these are just my thoughts... check it out for yourself, I think this has made it to most news medias in Europe and America, also check out www.ie.is
---
---
Killroy Woz Here
I was priveleged enough to actually speak with one of the NIH (National Inistitute of Heatlth) scientists working on the project earlier this year. He came to speak in our school Medical Society. Being the geek that I am, I made sure to inquire as to the Y2K compliancy of the computers used for analysis and data storage; alas, he wasn't involved in that aspect. ;-) He said he "thought they were", though.
/.! ;-)
If I remember correctly, and there have been no delays, it's supposed to be finished before 2002.
I tried to tape the whole question and answer session with my microcassette recorder, to put on my webpage (in RealAudio format), but he was against it. Oh well. (I would have tried to sneak it anyway from the back of the room, but my recorder has a crappy mic, so I wouldn't have gotten much by doing so.)
The whole concept is very cool... imagine being able to prevent disease on a genetic level...
Does anyone have any information on the computing systems being used? Come on, there have to be a few NIHers reading
This is slightly off-topic, but has anyone else heard about this "Soul Catcher" project, which I think is based mainly in the UK? (Based on the concept of recording an entire human consciousness to a traditional physical medium, if I remember correctly.)
--
I like to watch.
You heard it here first -- intellectual-property idealists will revive a grand tradition by copying their genes without a patent license. Someone will print "Information wants to be free love" on a black T-shirt, and all around the world, geeks will go out into the streets and protest WIPO and the genome barons by having sex. With themselves, mostly, but hey -- it's the thought that counts.
Since when did they start allowing software patents here ?
If they are indeed allowing them then they are restricting my freedom of expression. My programs are my art (I don't and won't write them for money). Patenting software is like patenting the golden ratio in paintings.
I don't know if you've ever really considered this, but not all software is about money; in my case it's mostly about creativity and art (all non-profit, well, except intellectual profit). In case you want to know, I mostly write sound synthesis and processing software and the field is very heavily patented. What artist makes paintings and doesn't share them with other people ? Imagine if you couldn't show a painting to other people if you painted it with a certain brush unless you pay license fees. This is what software patents are to me and probably many others. They need to be stopped now (or at least make non-profit use legal) !
ACI submitted an idea like this to slashdot just a few days ago. Completley my idea.
- ensembl is an open source genome project designed to get as much data and software into the public domain as possible
- EMBOSS
- bioperl
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.
The whole genome sequencing patent race has me mightily pissed off. But as someone mentioned a couple of weeks ago- maybe it's going to take something as rediculious as this to bring the entire patent-granting operation to its knees.
I think the metaphor used was of a guy walking into a forest and patenting every different type of tree he came up upon. Another favorite is the Amazon.com "one-click" patent. That's like Henry Ford whipping up a nice car and patenting the tires!
-not responsible for spelling errors-
That's what I love about them high-school girls. I get older, they stay the same age... yes they do.
--Wooderson 1976
-- jimmycarter
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, 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
I have no idea as to how much IO these DNA-strand caluculations need, but I would be more than happy to ditch d.net and donate my spare CPU time to this project if it is feasible.
Didn't Levis get there first?
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 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 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?
Common successful distributed projects in cryptography rely on the fact that all you need on a client is the algorithm and a few keys to try. Therefore, clients are really cheap (resourcewise) to distribute and use.
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
--
Reality or nothing.
Does anyone want to write it? If so - I have alot of CPU hungry algorithms to run.
I believe that the bottleneck is somewhere else - namely, getting the DNA, running PCR on it to amplify it, then cleving the DNA into chunks, and then running the chunks thru gel plates, and then getting the data on the chunks ...
From what I remember and understand about gene sequencing, the process is:
Running a PCR reaction. This induces DNA reproduction. You run this (mostly) by cycling the temperature the DNA is at in a special medium. And the DNA chains cleves and reproduces exponentially (1-2, 2->4, 4->8, etc).
Cleving at certain sequences. This breaks the DNA chains into chunks. The chunks are then analysised by some gell chromatography. IN the movies when you see people hold up 2 film with bands in it, that's what they are doing - the chunks are of a certain size and migrate thru the gell at a certain speed - and when the lines match up in intensity and location that means the same concentration of a particular block is present in both the standard and the unknown.
Repeating the process, cleving at different sites, until you have enough information about the "chunks" to reconstruct the sequences.
For a computer to match the chunks up, it's not that difficult. It's just like sorting arrays - not that much processor power is required. Storage, maybe, but not processor power.
The most time consuming part is running the reactions, spottingthe plates, running the plates, blah, blah...
-=- SiKnight
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.
I'll do it for cheesy poofs.
I declare myself prior art....use me as you will.
People who bite the hand that feeds them usually lick the boot that kicks them
Does that surprise you?
//rdj
No one can understand the truth until he drinks of coffee's frothy goodness.
--Sheikh Abd-Al-Kadir, 1587
All the various distributed computing efforts have something in common: while they all require extensive processing resources, they all need very little data to work on.
Basically they just need to synchronize: in the case of the famous distributed.net RC5-64 contest, they just need to decide who will try a given set of blocks.
Sequencing the DNA seems (I don't have the title to claim otherwise) to be not that much a matter of computing power, but of an immense dataset to work on.
It wouldn't be possible to distribute that much information in terms reasonable enough to make the effort worthwile.
They aren't inventing DNA at all; DNA technology
has been around forever. They are just
reverse-engineering something that already exists;
therefore shouldn't be allowed to get a patent.
I'm surprised that the US in particular hasn't done anything to reduce the most glaring anti-competitive aspects of patenting. Doesn't the free market lobby have anything to say on the topic?
Patents have always been intended to reduce competition for a limited period, so that inventors have an opportunity to bring their research to market during a sort of protected honeymoon period, but in practice that no longer works very well in the modern world. It's all to do with timescales: in the computer age and with instant global communications, timescales for everything are shrinking, and in some areas an advantage period for the patent holder of more than say just a couple of years is starting to become inappropriate, a restraint on progress, development and trade. Although it's impossible to tell what might have been, who knows which entire market sectors might have developed if their pivotal idea hadn't been tied down by patents.
Be that as it may, it's rare for a week to pass without totally ridiculous patents being highlighted here, and the analogy with icebergs definitely applies -- there's vastly more out there that we don't see on Slashdot. The whole area is clearly in utter shambles and needs urgent review.
A "fix" doesn't have to be complicated. As far as I can see, just three things are needed: a ban on patenting algorithms (as enforced elsewhere); a short, strict and non-extensible time limit (possibly related to the field, eg. default 2-3 years but longer in the nuclear power arena, for instance); and an informal "public review" system not unlike Slashdot, run by the patent office and used both to supply niche information and also to weed out the type of nonsense that translates into "how to breathe air".
But of course, something that simple could never come about, because otherwise patent lawyers would be out of a job. Oh well.
"The question of whether machines can think is no more interesting than [] whether submarines can swim" - Dijkstra
When I first read of this, I thought to myself "What exactly is the use in patenting the results of this research?" From the posts I've seen, it seems that companies intend to patent the information they discover about the human genome, which can then be used to create cures for diseases. However, if standard medical law prevails, there's no way they can deny a person access to the information necessary to save that person's life or to prevent his/her disease if that person cannot afford to pay for the information. Basically, just like an emergency room can't turn away people who can't pay, how could a company that patented a human genome withold that information from people who can't afford to pay?
Jeremy
Looking for a Python IRC bot?
ac.uk
I do not think such a huge computing power is going to be neccessary. Human brain-power will be far more important IMHO.
Depending on the sequencing methodology used, there are different approaches to assembling the sequence. As far as I remember the human genome has ben cloned into YACs, which may hold some 1,000,000 base pairs. If these are sequenced with a "shotgun like" method, they would generate some 20000 fragments, around 500 base pairs each. The whole sequence would be assembled by means of mathcnig 'overhangs'. If sufficient fragments are sequenced this should not be any problem at all, sth any desk computer could perform.
Once all YACs are sequenced, they would be assembled into the 23 (+1?) chromosomes. This does not seem to be too difficult too.
I see two big problems:
1. Debugging. If they use standard sequencing methods, the error rate may be as high as 0,1%. How are they going to cope with this?
2. Sequencing telomers or regions composed of repeats. This is going to be tricky.
My conclusion is: No distributed computing project is neccessary to accomplish the task.
Unfortunately I have never participated in an coordinated sequencing project, and all of the above are just my personal views.
I would dump my rc5 client and try to get this client running on every box I could. Companies have gone too far, first they want our souls and now they are going for our bodies. Over the past few years I have grown to hate the economic system that exists in most countries today, even my own. Everyone wants to make a buck and some will do anything to get it. It is bad enough knowing that in a few short years I will be working full time someplace and expected to do anything and everything for a corporation to the extent of sacrificing my personal life. Money doesn't make one a better person or truly better off. My father is sucessful and makes a decent buck, and I see what he goes through to make his money. To be honest its not worth it, it changed him, more work, more money, the more it destroyed his life at home. Until he realized that the way he was acting was driving everyone insane and further away from him, all he would ever talk about is how much he is making. He still does talk about how much he makes but not as much anymore. For I it is a good thing that he makes a decent wage. The thing is I am not willing to corrupt myself, I like doing what I do, if I make a heck of alot of money that is fine with me. Sure I will be happy and maybe brag a little but I know not to brag too much. At this current time I must put up with capitalism, but it doesn't mean I have to like it. I prefer to have a society where we can all get what we want and need. I am not talking about everyone having a viper,the bigget house, etc. , nor am I talking about communism, I may be, but never as it was implemented. But then capitalism was never implemented correctly. What ever happened to "Doing it for the good of everyone"? It seems everyone wants themselves to get up, while having everyone else fall over, now tell me, Do you see something wrong with this picture?? I DO!! This has been a rant by The Reverend Helix
isn't the whole point of insurance that ti costs you money but WHEN something happens you're covered. You're paying for security. If you move more and more to charging people whit a family history (of heart failure for example) that defeats the purpose of insurance - you are charging people for the services they require not "insurance"
Neutrino
the light at the end of the tunnel is the headlight of the oncoming train.
I can't even remember what it was I came here to get away from - Bob Dylan
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).
But then capitalism was never implemented correctly.
that should be:
But then comunism was never implemented correctly.
Well, if you do decide to hold such classes then be sure to let us know. If it's anywhere near Cambridge then that means a 2-hour commute for me, but it would be well worth it -- this is an extremely important area.
I sure hope that what you have in mind is evening classes though, as otherwise you'll get just the unemployed to attend, which would be limiting.
Sounds like an excellent project!
"The question of whether machines can think is no more interesting than [] whether submarines can swim" - Dijkstra
The problem is not that patents are short lived, they are too long lived.
Now how about defining the time in internet years? Anybody in favour of defining the time based on the technological rate of change?
I can throw myself at the ground, and miss.
Never knew there was a race to decode gene sequences using computers. There is a race for low paid women to load the sequencers but the "decoding" of the sequence is not the limiting factor. You've got to be damn good to get into those labs. Harvard PhD quality.
This depends a lot on how long it takes to make a profit from a patent. Drugs are in general patented for 20 years. Since you need 12 years of research and development before putting a new drug on the market, you are left with 5 to 8 years to make the money you spent in 12 years of R&D + the money spent in marketing and distribution. If your patent lasts only, say, 5 years, noone will make new drugs, which is bad for everyone.
Now how about defining the time in internet years? Anybody in favour of defining the time based on the technological rate of change?
Real life works differently! Chemicals are still designed by human beings. Yes, a lot of robots are used, but just for dumb things.
I'll do it for cheesy poofs.
The whole area of concern about clients being compromised to return incorrect results stems from the meme-setting effect of dedicated clients like rc5des, seti@home and (it seems) all others currently in existence. Their susceptibility to being cracked and reworked is entirely due to the dedicated nature of their task, as it gives nasty-minded people a visible target.
The problem would not arise if distributed clients were generic, ie. if they would do arbitrary computations on arbitrary data received from arbitrary sources. In other words, if a global distributed computing system accepted numerous different computational tasks from the public and distributed interleaved fragments of them arbitrarily to an undifferentiated pool of clients, it would no longer be possible for clients to be compromised meaningfully. (Clients would really just be maths engines, and you'd be detected pretty quick if your client made 2+2=5.)
Would there be interest in creating such a global computing system as a free software / open source project?
[Note that pretty single-task stats displays would still be available from the task sponsers' site, but that's a completely separate issue to the one of data distribution and computation.]
"The question of whether machines can think is no more interesting than [] whether submarines can swim" - Dijkstra
Someone in Japan has applied to patent curry, of all things. If successful, the guy gets a royalty every time the Brits dig in.
And with the WTO, all other countries will have to recognize and comply with the patent.
Can you believe it? Curry, of all things. Wonder what the folks in India think of this. We've lost our minds.
It's on today's London Times.
I believe that what is meant by patenting, they probably mean their own version of the data. Like someone mentioned in a previous slashdot article (I forget the name) like a surveyors maps, if you put a copy of that map in your report, you should at least acknowledge the source, and even inform them that you're using the maps. Information from the HGC, would be free, that information could not be copywrited or patented by someone else because HGC got the information themselves.
Stupid is as stupid dies.
AFAIK, once you publish an idea or invention in the public domain it becomes un-patentable. This is what the Human Genome Project is doing. every gene is published within 48 hours of discovery.
Correct me if I'm wrong but I've seen this mentioned in other YRO and AS articles.
Remove the NOSPAM to spam me...
I worked for a bit as a CO-OP student in this area last summer, which is not to say I know anything about this, but.. :]
While distributed computing would probably benifti the HGP, there are a couple of points to take into consideration.
1) How secure is distributed computing? SETI and RC5 arent really all that concerned with the the integrity of the data they are getting back. They can just re-check a data block if it is a sure sign of ET or whatever. Here there will need to be a guarantee that data has not been tampered with.
2) It seemed to me that some of the tools used could do with some open source style improvement by the hacking(coding) community before throwing lots of computing power at them.
As for the patent stuff... bah!. Let the lawyers mess around with that, everyone else can concentrate on the advancement of the human race.. or something like that.
links:
Genome database
The Sanger Centre
The NCBI
For open source and distributed computing to showcase itself and what it exists for!
You may be wrong. Several companies in the US have *already* tried to patent raw sequences. It is unclear as to wether they will be granted patents, but unless you're a patent lawyer who has information unavailable to everyone else, you're really overstating your case.
I think it has just as much potential as patening the DNA sequence - just think - the way your lungs force air to pass over your lips may just infringe on patents related to airflow caused by jet engines and wings. Anyone ready for a cease-and-desist-breathing order? :)
The idea of using DNA sequences as predictors of diseases/cancer/... has already been thought of. The idea of introducing geenes with speciffic mutations has already been thought of. EVERY technique that can be used to put this data to use has already been thought of. Therefore, any patent that covers any part of the genome must run into prior art. The Human Genome Project was the first of these projects, correct? If that is correct, then we know that they were trying to sequence this so that drugs could be made, and/or genes developed to counteract what they found there, or to enhance something that is found in the genes. Would that not immediately set prescedent for prior art?
Like the title says this is just an observation here but how is it that any company could patent a application from the infomation they decern is decoding our DNA?
It seems only obvious that no one should be able to patent the DNA sequences or chromosomes themselves, but what about applications arising from said decoding?
If any of these applications are medical in nature ( i.e. the treatment of disease, gene based therapies, etc ) are they not banned from being patented given the first section of the patent law which excludes Medical Therapeutics, Surgeries and diagnostic processes?
It seems that many of the currently patented medical "applications" should be lose their patents since they have been approved by claiming to only be patenting "mechanisms" which in effect allows patent holder to "patent" a therapuetic application.
That being said... is not the patenting of drugs by pharmeceutical companies a similar thing? Are medicines not therapeutic remedies?
Just some thoughts
Jeff
Unless someone has the time and money to distribute microarrays and bench time at a local hospital with a good clinical lab, the clients would be worthless. Venter's efforts are succeeding because of Celera's partnership with Perkin-Elmer.
However, Celera appears to be less than picky about the quality of data they are producing. So the same approach as theirs (multiple shotgun sequencing runs for each block of base pairs) with parity checking and/or some means of verifying data would be fine.
Celera's operation is effectively a distributed effort already, it just happens to be in one building. The government will most likely step in and appropriate the sequences for a reasonable fee if it turns out that Venter et al. have reneged on their promises to distribute the sequences freely.
Remember that what's inside of you doesn't matter because nobody can see it.
i just set up a genome mailing list on HERT (we might rename it Human Emergency Response Team), so we can continue this discussion there and maybe find a way to do something. i can offer web space and cvs space and eventually i can buy 30 gig of hd if we need that too. and btw HERT is non profit.
Hell I got 6 servers and about 150 workstations available. I would be more than willing to put this on a small chunk of my network. It would be better than Setti
root@localbrain root>ps ax |grep thoughtd
It's crazy what they'll grant a patent on. Does anyone remember the patent Compton's multimedia had? The one something like "Information stored and indexed on a CD-ROM"? They actually had that patented, but kept it pretty underground until CD-ROM encylopedias really took off, then announced it as some sort of trump card and implied they were going to start charging royalties to every CD-ROM manufacturer. Seems there's a whole bunch of really silly, generic patents these days. I wonder if I, as an individual can patent some fun ideas. Like "sneaking out the backdoor using yardwork as an excuse to avoid your mother-in-law." Or maybe "accessing informational databases over a computer network." Wouldn't that be wonderful?
The real fix is for the US to stop issuing these crazy patents, however as I recall the courts have done some good when it comes to sanity checking. I think Compton never tried anything because their lawyers decided no judge would let it fly in court. It makes for a nice second line of defense.
So, to carry it over to genetics, the underlying genes (law) cannot be copyrighted (and this is ambiguous still: is it code (copyright) or algorithm (patent)?), but the indices and commentaries on the sequences can be copyrighted, and the search/combination techniques and/or machinery can be patented.
So, we need to make clear and loud the mandate that:
We need to define the problem fairly and completely, then fight strenuously to make sure that bad precedent is not set.
Your Working Boy,
People have this stupid idea that it is the corporations VS. the human genome project and if we help the HGP then our genes (aka souls to some) will be saved. Well here is a shocker...you will be helping the government to patent our genes. If you go look you will notice that the HGP has many many patents. Also the government has been known to approach these genomic companies to work as consultants. This is not a government conspiracy theory. I am merely trying to inform you that this is not Microsoft vs. Open source.
Well, if the packets were tunneled through SSH (built into the client), there wouldn't be much of an issue of data theft now would there?
The huge processor time needed to assemble the Calera sequence is Calera's problem. It comes about because of how the Co. decided to sequence, by cutting all the human DNA (3e9 base pairs, or bps) into tiny bits and sequencing ~500-1000 bps of each bit. Calera owns all this sequence, and no doubt has the computing resources to do at least a poor assembly of the mass of sequence data they'll generate. A more sensible approach to sequencing is being used by the Human Genome Project. DNA clones 10e5 bps in size are cut in small bits and 500-1000 bps are sequenced from each piece. Thus the assembly is of a 10e5 bp clone. Overlapping clones are sequenced to generate larger segments of sequence. Calera is skimming the human genome. They'll generate a bunch of raw sequence, assemble what they can, patent everything that looks appealing, and then with 40-70% done, declare the sequencing complete, and close up shop. The Human Genome Project will be years finishing things up. Jim Lund
You want to put Linux and Unix in general in the public eye? Stuff like this is the ticket. We map the human genome and publish it, it becomes a VERY public positive pro-open source example. You gotta remeber that this issue is very hot at the moment, cuz mom and pop Kettle don't understand what Microsoft's buggy internal code has to do with them, but they SURELY understand what a corporation patenting their flesh and blood does. I heard a debate on NPR recently in St. Louis where I actually listened to a biotech lawyer try to convince people that this was a good thing because of so-called subsidization of said firm's investment capital for research jsutified further research to 'help us find cures' (hehe it's always for the children ain't it?). They're trying to patent anything they can because the higher prices they can demand for cures and treatments affecting patented genes and cell structures (and perhaps even organs in the future) have led Insurance companies to deny treatments and even falsly mislead patients to belive that the treatments are ineffective or do not exist. This is downright WRONG. So is the concept that a company can patent an IDEA about a cure or treatment even though it doesn't exist except in theory in order to justify capitolizing research. People understand personal health issues, and making a public statement agaist this type of thing in the name of the geek community at large could have much milage towards common acceptance... I mean CNN is a GREAT place to win the love of the common man IMHO. -Wanrat
The sentiment expressed on the above post ("you can't patent sequences") is alarmingly common on /.
Of course, it always gets a lot of attention because:
a) we like to hear it, and
b) its grounded in truth.
But "grounded in truth" does not equate to "true."
Yes, its true that you can't strictly patent a gene sequence. So what? You _can_ patent a gene's applications, current or future, discovered or undiscovered. Period. And you don't even need the whole gene sequence to do it.
So....unless your only use for a gene sequence is to make a pretty picture out of it, this means that gene sequences are de facto patentable. You simply can't use them for anything once they're patented (besides, perhaps, abstract art).
Let's try not to let fact interfere with our speculation here, OK?
One word- nanolawyers.
I remember the good 'ol days when all we had to worry about was death by nuclear fire...
I think just about every biologist out there would agree that assembly and alignment are not the limiting steps in this, but getting the sequence out of the sequencers is. But the intractable problem, that I have seen very little progress on is going from the flat, genomic data to the folded three dimensional structure of the protein. This might be a place where a massively distributed energy minimization application might actually work; grabbing known x-ray structures and flat sequence data postulate hypothetical structures for unknown protein coding open reading frames. So far however none of the models I have heard of have even come close to predicting the structure of a modest size protein. Its as I understand it, a hellishly complicated multiple body problem.
Companies specializing in DNA sequencing have applied for patents on hundreds of thousands of sequences, including genes and gene fragments. PTO examines all sequence applications for fulfillment of four major patenting criteria: novelty, nonobviousness, usefulness, and enablement (i.e., detailed enough to enable one skilled in the field to use it for the stated purpose).
/.ers have misunderstood the purpose of patenting gene sequences--A patent on a sequence itself is possible only if the researchers can prove some distinguishing characteristic or application that sets it apart from other sequences. Given that 99.9% of the human genome is identical from one person to the next, it would prove very unlikely that the gene for a trait could be isolated; since many factors contribute to heredity and one sequence can affect a large number of biological variables, patenting the use of any one sequence would be useless in application.
Human Genome News, July-September 1996; 8:(1)
I am a student at Gustavus Adolphus College (St. Peter MN) and recently attended the Nobel Conference held here annually. This year's topic was Genetics--the opening speaker was Dr. J. Craig Venter from the Institute of Genomic Research, Rockville, Md., also the president of Celera, Inc. It would seem that many
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>This is slightly off-topic, but has anyone else >heard about this "Soul Catcher" project, which I >think is based > mainly in the UK? (Based on the concept >of recording an entire human consciousness to a >traditional > physical medium, if I remember >correctly.) Ever seen Max Headroom? I think we're still a long ways from a dynamic system capable of mapping the intricacies of human thought accurately, let alone mapping an entire consciousness. But it could closer than I think. I know I'm not ready for it yet in any case, though I think the idea is feasible. I'm sure this is a sensitive subject for many people-- that we can be broken down into so many pieces. Still, this has been a fundamental task of the sciences since Aristotle, and it of course has real-world consequences. All this concern about the mishandling of genetic knowledge is the latest strain of a reoccuring human condition: people want power. And you thought mustard-gas and anthrax were scary; imagine what it'll be like in another twenty years or so when science has had time to study our genetic makeup in some depth [queue thunder]. And people cringe at cloning. Tis the season for tales of the coming Apocalypse. By comparison, I could give two egg-rolls if companies want to compete over patent rights. - Shrift "It looks like Edison...."
Heeeeelloooo....
The whole idea was to prevent the
capitalistic mega corps in winning this race
and you want money ?
Did you just miss the whole concept here?
And just on a subnote, money is NOT most
importantly...
An Apple G4 with lots of memory and Final Cut Pro, plus a Canon XL with Firewire link thereto should be possible for less than USD8k. That and some talent should do it. Apply to Wellcome for funds?
i think people have gone too far with this one. they dont even know what theyre getting into. i think a lot more needs to be thought about before people start making spare body parts and recreating themselves.
I think the coolthing to do, would be to beat
:-)
them to a whole bunch of major useful
"gene patents", then patent them, and license them
as:
"Any company can freely use this, provided that
the company, all subsidiaries, and all parent
companies, hold no genetic patents".
If you hit really really useful ones, then other
businesses would be able to destroy the ones
that hold other less useful patents.
I think I'll patent this business method,and
call it "The microsloth method of business
negotiation"
I think this would be a great use of spare compute cycles everywhere. I am way up on the distributed.net site, but I would switch everything over to this.
Distributed computing is not very applicable to human genome sequencing while de novo structure prediction could need such power in the future.
It appears that computer professionals have as much clue about DNA sequencing and "gene patenting" as biologists have about DNS services and Open source licensing.
Tim said:
>You _can_ patent a gene's applications, current >or future, discovered or undiscovered. Period...
>You simply can't use them for anything once
>they're patented...
Patent undiscovered applications?! Can you give any examples to support your statements? If you patent a SNP for diagnostic purposes how would that prevent others from, say, marketing anti-sense therapeutics based on the same sequence? Cite a gene-based patent that covers undiscovered future applications - bet you can't.
FUD is bad.
Gene patents protect use of a patented gene product in any manner. Just like you can't use a patented oil formula (or whatever) in your new product without licensing it from the patent holder, you can't use patented gene product without licensing from the patent holder. This isn't unusual.
Taq DNA polymerase is an example, off the top of my head (but not the best example, I'm sure). To have it, you must be a licensed vendor, or you must buy it from a licensed vendor. You can't legally express the stuff, even if you're not doing PCR with it.
I will note, however, that your example is different, because you're talking about patenting a *sequence*, which is not allowed. This is the truth I alluded to in my earlier post. If that sequence codes for a gene, then your patent covers the polypeptide coded by that gene, not the sequence of the gene itself. Thus, I don't believe one would be restricted from marketing an anti-sense therapeutic based on the sequence. The therapeutic does not make use of the gene, so the patent is not violated.
So perhaps I'll be more exact with my wording:
You _can_ patent a gene product, and that patent will apply to all applications, current or future, discovered or undiscovered.
Let's try not to let fact interfere with our speculation here, OK?
Thoughts in my head, dreams I have, and my DNA are things that I own as a individual and it is unlawful for a company to sell information about me without my consent. This may sound like a ultra conservative position, because it is.
Oh my god they wanna patent gnome?
I give this a serious yes vote. Last thing I want to see are my (or my children's) genes patented for Big Pharm. I'll be first in line for a Linux or a Win95/98 client.
I can no longer read Dilbert. It's too depressing, because it is too real. -- Hyperhaplo
So my questions are:
1) is it possible to do some distributed computing on a problem like this?
2) (if it is possible) has anybody informations on something of this kind?
And no, you cannot patent sequences.
[I use many qualifiers in this response, because I can't provide a reference to the original data; it's possible that this information is the product of fevered dreams caused by a late dinner of spicy food. Hopefully some /. reader will be able to point everyone to some concrete data.]
I hope you're aware that the lifetime of patents could change.
As I understand it, patents exist to protect intellectual property. Again, as I understand it, copyrights perform a similar function: they give some entity ownership of the product of their (or someone else's) mind, and that ownership expires after some period.
I seem to recall that in some countries, the lifetime of some (all?) copyrights was extended recently, by many years, and that the change had a grandfather clause: existing copyrighted properties had their copyrights extended. Coincidentally, that extension protects some very lucrative properties, for example the Mickey Mouse cartoon character.
I don't want to sound like a wild-eyed zealot, but if existing copyrights can be extended -- largely for the benefit of large/multi-national corporations -- can we rule out the possibility that patents might be too? If not, then saying "don't worry about them, they'll expire soon enough" is naïve.
I agree that perhaps a distributed system might help, but the time lag in the actual biology of the process allows plenty of time. At Berkeley Labs, there was plenty of time for the computers to crank through the algorithms. The hard part was getting the cells to divide, and to grow, and to cut the DNA at the right length, so the laser readers could analyze the contents. The lasers didn't do the cutting, in actuality, it was enzymes, and there is no real way of speeding those things up. When I left Berkeley, they were implementing robotic procedures for faster throughput, but, once again, the limiting factor wasn't the analysis, but the biology.
The suggestion that corporate interests are "only" patenting the sequences and not the genes is sophistry. The vast majority of genes will have only one or two "uses" detection, alteration and countermeasures. Under the current patent system he who sequences, for all intents and purposes "owns" that gene. Nobody else can use any detection, alteration or counter system system using the gene or protein sequence patented without paying royalties.
For the vast majority of disease causing genes, any kind of gene therapy or other cure is decades away. Meanwhile, we are stuck with the ability to predict without the power to do anything. The genetic information about people which is being collected is by far the most intimate and dangerous information about individual humans that has ever been collected.
Then you die. It's a process called natural selection, and it's quite natural. It happens to animals all the time, yet with people, everyone MUST be guarnteed(sic) a good life. Perhaps it's time to stop diluting the gene pool, allowing those who probably should die to live and pro-create. Who knows? Maybe the downfall of the human race will be caused by our incessent need to tamper with life.....
This is not flamebait, nor a troll. Don't bother commenting on my spelling/grammar... it has nothing to do with my arguement....