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Genetic Stone Soup 175

Posted by jamie
from the unsung-hero dept.
It's the scientific achievment of our generation; what can you say about the mapping of the human genome? But here's a story behind the story. parvati turned us on to this NYT article about James Kent, who wrote the gene assembly program GigAssembler last June. It turns out that, thanks to his code, the public Human Genome Project had actually finished its work three days before the private effort by Celera Genomics -- a feather in their cap and a boon to public science. The head of Celera was "astonished" to learn of this grad student's genius -- ten thousand lines of C in a month, and why? -- "because of his concern that the genome would be locked up by commercial patents if an assembled sequence was not made publicly available for all scientists to work on." (The debate over public vs. private science continues to rage; see this Seattle P-I article, which discusses among other things the ethics of NDA'ing scientific data produced for profit.)

Update: 02/13 02:26 PM by J : Thanks to tlunde for finding the link to GigAssembler and thus clarifying which language it was written in.

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Genetic Stone Soup

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  • by Anonymous Coward
    sorry to mention that, bu you did put up the wrong link:
    for more information on of the nutritionists involved with the human genome project, check out a profile of Jose Ordovas [goatse.cx]
    -- Louis P Bennett // and the geek shall inherit the earth // duh! doh!
  • by Anonymous Coward
    "why? -- 'because of his concern that the genome would be locked up by commercial patents if an assembled sequence was not made publicly available for all scientists to work on.'"

    The above quote by Mr. Kent is offered in the /. article out of context - the ambiguity being that it can be taken to imply that Mr. Kent is opposed to commercial patents, as such. The following links (following the above quote, that is) regarding the debate between public vs. private science add the spin: supporting the implication that Mr. Kent is, in fact, opposed to commercial patents. That is what anyone not choosing to read the NYT article would come away thinking.

    From the article: "'The U.S. Patent Office is, in my mind, very irresponsible in letting people patent a discovery rather than an invention,' he said. 'It's very upsetting. So we wanted to get a public set of genes out as soon as possible.'"

    He, Mr. Kent, has made a statement and taken a stand against the truly ridiculous behaviour of the PTO in handing out patents for discoveries (and by implication, of those who seek such patents) - not a statement and stand against commercial patents, intellectual property rights, or public vs. private science.

    -Syraeth.

  • by Anonymous Coward
    "We need to get back to doing real science, the kind that generates patents!" --Schizmatrix [powells.com] by Bruce Sterling, by maybe it should be J. Craig Ventner
  • by Danse (1026)

    yeah.. i misspelled "breeding." Probably one or two other words too.

  • You're repeating the Party Line, that Celera was patenting the genes themselves rather than specific treatment applications, again. I think if your case were that strong you wouldn't need a straw man. First off, patented information is publically available; the usual alternative to patents won't be neat public disclosure, but more and more "trade secrets." Second, isn't it just plain wierd that everyone says that capitalism can't do long-term research, then talks about how immoral they are for trying?

  • It that case, I think the application was Autodesk Animator - his name also appears on some of the (once Autodesk, then Kinetix, now Discreet) 3DS Max plugins, IIRC (the atmospheric post plugins, I think).
  • I think if your case were that strong you wouldn't need a straw man...Second, isn't it just plain wierd that everyone says that capitalism can't do long-term research, then talks about how immoral they are for trying?

    Oh, capitalism is quite capable of doing long-term research. It's just not all that good at it, since the incentives tend to favor the short term. In the case of biotech, the payoffs are happening right now. It's not as though companies would need to wait 20 years for some sort of return.

    And it's ironic you should complain about straw men. The problem isn't that capitalism is "trying to do long-term research". It's that people are trying to turn the basic components of life, which many people feel should belong to everyone, into intellectual property.

    IOW, nice try, but you need better material.

    Jonathan

    Kythe
    (Remove "x"'s from
  • a fun, yet hard, program to write is one that outputs itself. so let's say there's a divine being out there that created all the life in the universe. it wouldn't be that surprising if that being were a programmer.

    so, maybe we're the first successful such project of this being?

    along those lines perhaps this could be one of those babyl fish type proofs...
  • Is PVM/MPI even available in assembly?

    Remember, this code is meant to run on Beowulf clusters....

    Your Working Boy,
    - Otis (LICQ: 85110864)
  • *sigh* It's a long story.

    At NYIT in the late 70's and early 80's, we had the first big CG production facility. Alex Schure, who ran the place, had gone to the University of Utah in the mid 70's, just as their funding was running out for computer graphics research. Alex brought Ed Catmull and his team from Utah out to NYIT to make CG movies.

    Well, we worked developing tools for a few years, and Lance Williams wrote a script for a movie called The Works. Then we tried to make this movie; thinking along the lines of 'we have a story, we have some tools, we have some computers, let's make a movie!'. Well, it turns out that you need more than that; and between all of us we had exactly zero years of movie making experience; so we ended up basically spinning our wheels for the next couple of years.

    On of those spinning wheels was Dick Lundin. He thought that the best approach to making the movie would be to do a few fully-realized scenes from the film. He took the models that were lying around, made some more, and wrote a bunch of dynamics-based tools for secondary motion, and made a couple of short films -- more or less scenes from The Works.

    Unfortunately, we couldn't find a way to make the rest of the movie at the high level set by Dick Lundin's sequences; and the movie foundered in '82 and '83 -- slowly each of us realizing that it wouldn't happen.

    Ed Catmull, of course, went on to found the Computer Division at Lucasfilm, and then split off to become Pixar, and the rest is history. Lance Williams is now at Disney's Secret Lab. The lab at NYIT eventually collapsed around 1989.

    Alex was very protective of the work done at NYIT, and any video that remains from those days was spirited away in the middle of the night. Somebody went by the lab as it was closing and found all of the old 2" video-tapes stuffed into a dumpster -- but those tapes are all on an obsolete video format so they're probably not readable.

    It was a great place, no question. Paul Heckbert keeps the best archive of NYIT stuff. [cmu.edu] if your curiousity hasn't been satisfied.

    thad

  • It's called 'Folding @ Home' :-) Can't remember the URL just now. It runs a complex and fairly accurate protein folding model on your computer so scientists have better quality guesses as to how a particular protein folds.

  • See, people can keep saying that, but that doesn't make it true without either proof or at least a convincing argument. Just making smarmy remarks about "tenured professors" doesn't prove anything, it just demonstrates that you couldn't take the time to make a convincing argument.

    I'm still waiting to hear why Celera didn't start ten years ago, rather than waiting seven years for the HGP to prove out the science before jumping in for the prize at the last minute. If private industry is so smart and all, why didn't they totally scoop the government-funded project before it was even begun? Maybe because they couldn't have justified the investment without a publicly-funded project to prove it was possible first?

  • Well, it doesn't beat public tax-supported research if you want to do use the information and don't have $10K to pay Celera with. The question is more whether the public good of having an open, freely-available database of this information makes it worth the price the public paid for it. I would agree, on the basis that having a commercial competitor validates the usefulness of the information provided by the HGP. Kudos to the politicians who made this a funding priority 7 years before the business community discovered it.

  • Quite frankly there hasn't been a single conclusive study showing that there is any risk from GM crops.

    Don't you think it might be worth having some conclusive studies showing that there is NOT a risk from GM crops before we start experimenting with the worlds food supplies? A lack of a proof of existence is not the same thing as proof of non-existence. Please read the Ghost Not [reciprocality.org].
  • if using genetic tech can keep people healthy longer, people who are not afraid of receiving the benefits will eventually be favored over people who refuse it.

    f 'em

    -c
  • no, dummy. keep your own hangups off my post.

    though i didn't state it, my assumption was that such tech would be available to everyone the same way pennicillin is available to everyone today.

    some people will accept genetic-tech and some people won't . this is already happening (see europe's reaction to gen-foods). if it turns out that gen-tech offers a survival benefit, those who don't refuse it will be better off.

    -c
  • People that give their talents for humanity instead of profit should be honored accordingly. Do the nobel prizes in sciences require this?

    What, you mean like pretty much everyone engaged in academic research? :) I'm looking at about £6500 for the next 3 years while I do my PhD (assuming I do an 8 hour day 5 days a week, that works out at £3.13 an hour. That's under minimum wage, and in reality I'll be working longer hours than that), and assuming I don't run off into industry or produce work of such brilliance that someone grabs me to set up a lab somewhere I won't be looking at an even semi-decent wage until I'm 40 or so. Alternatively I could chuck it all in now, go into computing and earn substantially more now.

    If I turn down the money and go the research route, do I get anything out of your society? :)

    (What I'm pretty much trying to say is that very few scientists are in it for the money, because there isn't much. People know this before they start. If you want to honour people for putting humanity before profit, you're going to have a very long list of people to honour)
  • true but gigassembler kicked celeras arse back into the middle ages...which is DAMN IMPRESSIVE for a underfunded public project fighting against a huge commercial behemoth with loads of money and a massive alpha supercomputer cluster. and dont forget that gigassembler ran on 100 piiis they bought off the shelf.
  • ...always wanting their genes mapped first.

    Oh yeah? Map this!
    AGTAATGCATGCATCATCTSATGCATGCAT

    Bet his program can't handle that!

  • You obviously don't have a clue what market pressure actually means.

    It is not people in the streets revolting because you did not deliver: is the marketeers...

  • The slashdot blurb says "10000 lines of assembly code," when I don't actually think the article is suggesting he wrote the program in assembly language. The articles says that 10000 lines of code were written for the assembly program--a program which assembles data.


    Mike van Lammeren
  • I notice that a lot of the machines in this cluster are very old.. A couple grad students, and faculty members having been kicking around the idea of a cluster for our work (fluid dynamics research) for a while.. we discussed using recycled pentiums from the undergraduate computer labs, but when you sit down and work out the math, you find that it's much more effective to buy 8 fast AMD boxes, than it is to monkey around with 32 old pentiums.. And that's probably being generous on the ratios.. I'm guessing, you'd need 8 - 10 90-166MHz pentiums (assuming linear scaling) to match each of the 1GHz AMD boxes.. Sure the AMDs cost $600-$800 a pop, but the install is a snap, and we only need a 8-16 port switch, and 8 cables.. The cabling and switches for the machine above must be a pain in the ass..
  • No, the Chinese government should be doing that.

    No, Monsanto should be providing them with accurate information regarding their situation. If Monsanto knows that they're essentially selling snake-oil to chinese farmers, then they should be punished for running that scam. If they stated or implied that it is resistant to a disease, without informing the farmers that it is only resistant to certain strains of that disease, then I believe that is deceptive advertising.

  • First of all, the government MOST CERTAINLY SHOULD mandate the labeling of GM foods as such. Perhaps they should go even further and require more specific information regarding the nature of the manipulation. Without such information, consumers CAN NOT make informed decisions about their purchases. This should be common sense.

    Second, I am very much against the use of GM crops when there is a chance of them cross-breading with other crops. We simply don't have the necessary understanding of the possible consequences of the actions of these corporations. We should not gamble lightly with our food supply.

  • Can't prove a negative like that.

  • Any moderators with a spare point?

  • Of course, you can't get that info from an NYT article.

    Nor can you get the info that he wrote even ONE line of "assembly language" code for this "gene assembly" software.

  • From the article:

    Mr. Kent, who turned 41 last Saturday, is a graduate student in his second career. In his first, which lasted more than 10 years, he ran a computer animation programming business.

    I hate to be a nitpicker, but this chap's hardly a typical twentysomething graduate student (which would have been a genuinely amazing feat) - he's a seasoned professional who's experienced in processing large datasets professionally.

    On another, slightly more disturbing note, I am somewhat concerned about the use of academic funding to compete with commercial enterprises. Just because RMS does it doesn't make it right.

  • And you believe that we should all just live in grass huts and use nuts and berries as medicine, I suppose?

    While it certainly is true that I can not personally afford the very best in health care, I certainly am glad that someone can afford it, because without the research and development that goes into creating new medical techniques many of the procedures that I can afford would be unavailable. Sticking your head in the sand and crying out "not fair" doesn't help.

    I personally agree that everyone should get good healthcare. I spent several years of my life without insurance, and I remember very well how that felt. But I don't have an answer to the question of who should pay for universal healthcare. It's easy to point out that the medical companies are well off, but if they had to subsidize everyone's healthcare they would be bankrupted overnight and their research would disappear. All things considered I like the idea of the rich paying gobs of money for experimental procedures much better than the alternative where the poor receive experimental healthcare for free and the rich pay for the privilege of not being used as a guinea pig.

    I would certainly argue that the Human Genome should be public domain, simply because it is too darn important to have in private hands. Since advances here are a benefit to everyone (well, all humans anyway :) it is easy to justify paying for this research out of public funds.

  • "Assembly" referred without doubt to the actual problem: assembling the many snippets of DNA to larger fragments.

    I don't know what he actually coded in though.


    Lars
    __

  • sql*kitten, you turn morality on its head. Commercial enterprises in biotech are also heavily based on academic funding (most biotech startups are formed by professors taking their NSF- or NIH-funded academic research private). And in this case, if the commercial company wins the race, it gets a government-granted monopoly, where anything the academics generate is open to all: commercial companies can use any of the knowledge gained without paying any patent royalties.

  • cluster of one hundred 800 MhZ Pentium III CPUs running Linux

    that's what we're dying to know.

    Also, in jest, I wonder if they'll every creat a bio-compiler out of gene assembly? Maybe dna reproduction techniques are the key to nanotechnology?
  • Agreed, he likely brought a huge amount of pre-existing skill in matrix math. But 10k lines of assembly language hacking to beat richly funded capitalists with super-computers in four weeks is a truely amazing hack, no matter what their skill level.
    What is amazing is that you are amazed to notice that corporate-funded research wasn't as effective as an underfunded solitary matrix arithmetic geek's endeavours.

    --

  • These people are dangerous, and their actions need to be curbed. No longer should they be able to get away with their lies and violent behaviour, no more than any common thug. They can claim moral superiority, but in truth it seems as though these people are as bigoted as any racist, and just as determined to further their cause.

    We can't allow research to the thwarted because of the voices of a small bunch of extremists. That's not democracy at all.

    Ignore them.

    Having companies such as Monsanto, General Electric or the Royal Dutch Shell Company subvert governments to push their own economic agendas is hardly democracy either. Having governments NOT MANDATE compulsory informative product labelling, to insure that consumers CANNOT make an informed choice whilst shopping in grocery aisles, DESPITE the fact that the public IS ASKING FOR IT is not democracy either.

    At least, with protesting zealots, you have the choice of not listening to them. But corporate behemoths cannot be moved aside nor ignored.

    Democracy CANNOT exist when the people are ignorant; therefore, those who go to great lengths to make sure that the people stay ignorant are hijacking democracy.

    Democracy is ABOUT CHOICE MADE DOWN AT THE INDIVIDUAL LEVEL. If you remove what one needs to do informed choice, THERE IS NO MORE DEMOCRACY.

    This is valid whether the "product" is a box of sugar-hypercharged breakfast cereal or a political platform.

    --

  • How exactly is public funding a roadblock? If the science is so profitable to begin with, surely the commercial sector will jump in at the scent of money as has happened in this case. Public funding sure didn't stop Celera from getting the whole thing done quickly, and may have helped them prove their business case to their investors.

    Contrariwise, many scientific advances would not have been begun without the government funding research in areas that industry has disregarded as unprofitable dead-ends. Where would we be without the public funding of the Internet or the space program? Granted, there's a point when government can stop funding research once it becomes profitable enough for business to carry it forward, which has already occurred for the Internet and some would argue should occur for space flight. But it's hardly an either-or decision - government-supported research is often provided in order to jump-start commercial involvement in the field, for example. The two are complementary.

    I would also point out that if the publicly-funded HGP had the funding (adjusted for inflation as well as improvements in technology and basic knowledge over the past ten years) that Celera has had for the past three, it probably wouldn't have taken the public effort 10 years either. The current situation isn't really an accurate comparison between the two efforts, let alone sufficient evidence to indict publicly-funded science.

  • by grappler (14976)
    If this is the new public image for programmers, I like it.

    If I had an article like that written about me, my ego would probably pop. heh.
  • perhaps there's a differenc in potency?
  • Yes, but:
    • "Processing large datasets" brings to mind a set of well-known techniques. From the NYT article, it looks like he had to invent quite a lot of new stuff.
    • The fact that he is 41 is inspirational to aging geek hackers like myself.
  • 4) Here's a biggie. Science costs a LOT of money--the only two groups that can afford it are governments, and expensive biotech companies. [snip]

    The most reasonable way to read this comment is that Big Science costs Big Money. And that is basically true. And there is no doubt that certain truly Huge projects, like the HGP, cost a lot of money. What is quite interesting about the HGP is the fact that there was surprisingly little disagreement that the project was worth doing, and that a public consortium should do it. And this was yet another big reason why Celera annoyed so many people.

    But even though the HGP was as Big a science as it gets, the thing that really takes your breath away is how Small some of the most crucial ideas were; ideas that ending up speeding the whole enterprise by years. This, for me, is one of things that makes Big Science worthwhile: there is so much Small science waiting to get out. Getting any grant to do anything approved these days is an exercise in masochism. It's much easier to burrow into a nice, warm, big project than do the small stuff by yourself. I think this is why much of the really big stuff ends up getting done either by accident, or by somebody willfully doing something other than what they were supposedly getting paid for.

    Of course, Big Science (whether public or coprorate) doesn't always end up appreciating the nuggets of innovation that pan out from time to time. Shotgunning the genome was something that the HGP didn't really think was going to fly, or at least fly so fast, so when push came to shove, Ventner walked out the door.

    In retrospect, probably a pretty good move.

  • Since our number of genes is so surprisingly close to much much "simpler" (as perceived by the human ego) organisms, then genes can't be where it's at is no doubt going to be a popular conclusion.

    I think this is a bit pessimistic. Yeah, people might not dig the fruit fly comparisons, but I think that the comparisons with mice and other mammals are not as likely to provoke as much ire as they would have in the past. Basically, I don't think that people will see anything too weird about only having a thousand or fewer more genes than some creature that can be viewed as a loving pet.

    Where things might get tricky is when people realize that the human superiority in gene number if one in fact exists is probably mostly soaked up by recipes for how to make:

    1. Like, yet Another Trivial Sub-type of GABA receptor (LATSO-GABA)
    2. Assistant to the Counsel of the Junior Vice-Provost in Charge of Keeping a Lid on Homeobox-containing Genes that would Otherwise Pop Up in the Wrong Places (lots of these...)
    3. Genes that Exists Solely to Become Mutated and Cause Weird Cancers.
    4. Nth Assistant to the Gene that Exists Solely to Become Mutated and Cause Weird Cancers.

    :-)

  • People that give their talents for humanity instead of profit should be honored accordingly. Do the nobel prizes in sciences require this?

    Of course not, and in fact it is not clear to me what the IP status of this work would be. While Jim Kent may himself lay no claim to this, it may well turn out that the board of regents at UCSC may have other ideas.

    In any case the the truth of the matter is that discoveries rating Nobel recognition are generally fundamental enough to benefit humankind widely and deeply, long after any IP rights to the application have expired.

    This year the Nobel in Physics was shared by Jack Kilby, inventor of the IC. While TI no doubt profited handsomely from patent licenses thereone, the impact of his device far transcends this short lived grant.


    MOVE 'ZIG'.
  • Is it just me, or does the fact that the public effort finished just days before the private one look familiar?

    I think someone paid the extra 180 energy units to rush the project when they saw the other faction was about to complete it.

    ... or maybe I've just been playing too much Alpha Centauri.

    Noims
  • The problem is that companies aren't just patenting genes once they've developed a specific treatment - they're finding a gene, coming up with several hundred potential uses for it, and then patenting the lot. This isn't that hard - if you know that a gene is involved in cell-division checkpointing, you can immediatly assume that it'll be involved in some tumours and so come up with a bunch of hypothetical cancer treatments based on it. You'll get your patent. Whether or not it'll stand up is probably another matter, but most companies will be unwilling to fight you on it if you're bigger than them, and if you're smaller than them they'll just buy you out so you win anyway.
  • Pretty much. For evolution, it's usually easier to reuse something that's already there than it is to come up with a novel solution. The vast majority of proteins fall into a relatively small number of families, and the interactions between all of them are complex. Many genes can produce several different (related) products depending on how the RNA intermediate is spliced before translation occurs. The way in which a gene is regulated can depend upon the folding of the DNA surrounding it, which itself can depend on whether another gene nearby is switched on or not. Simulating this thing is going to be a nightmare, but it also looks fun. Look out for more computer simulations of protein and gene systems in the future - this is likely to be one of the next big fields.
  • Give the man the nobel prize for saving the human race's ass, previous thought of having my genes locked up in patents can now be thoroughly quashed.

  • What is also noted is that the combination of these protein interactions is staggeringly more complex. I can imagine that the system interactions may be a million times or more complex.

    While this is undoubtably true, I can't help wonder if pop-science isn't going to use this to shift the focus as to what makes us (sarcasm) so wonderfully human and unlike any other animal.

    Since our number of genes is so surprisingly close to much much "simpler" (as perceived by the human ego) organisms, then genes can't be where it's at is no doubt going to be a popular conclusion.
  • Thad,
    What ever happed to the clip I saw WAY back when at NYIT with the Ants (one and was driving an ant like machine...)
  • Replying to my own posting, it appears that in a previous incarnation, Jim Kent was the author of the FLC/FLI animation format [compuphase.com]. That must be why the named was so familiar.

  • The slashdot blurb says "10000 lines of assembly code," when I don't actually think the article is suggesting he wrote the program in assembly language. The articles says that 10000 lines of code were written for the assembly program--a program which assembles data.

    Possibly, but given the gentleman in questions age and history, the task he was trying to accomplish and the fact that speed was of the essense - I'd be shocked if he wrote anything other than the browser in a higher-level language. I can understand the confusion, but from my reading of the article, I came away with the impression that he wrote the Assembler program in Assembly.

  • I wonder if it would be possible to use a massive parallel processing system (such as SETI) just to *start* things. I know that it isn't the lack of CPU the main issue, but I think it *could* become. Once a good strategy has been found, wouldn't a great amount of cpu power be useful? At least to try things, to experiment, to choose or refine a strategy.

    There already is one: Folding @ Home [stanford.edu]. (As potential contact with aliens seems to be well handled at the moment, I'm going to be moving my spare cycles over to this.)

  • If the public wants GM-free foods then they'll get it thanks to the free market, and indeed there are so-called "organic" products on the market


    I have a friend who is a homesteader, and from talking to her I have learned that isn't necessarily true. It is getting nearly impossible for farmers themselves to grow non-GM food. The problem is that GM food often cross-breeds with non-GM crops in farms miles away. Which is a real problem, since often GM crops are not capable of producing viable offspring. Farmers' crops are failing to reproduce becasue a generation that comes after one that crossbreeds with GM plants cannot reproduce.
    I won't deny that there are plenty of great things that can come from GM food, but we HAVE to take it slow. . we're playing with stuff we barely understand here, and companies such as Monsanto that produce GM foods aren't exactly known for being responsible.

    They can be ignored quite easily, by choosing not to buy their products . In a capitlist society your purchasing power is your weapon, and by denying companies your money you send a clear message to them about their products and actions.


    I happen to live in a town where this is impossible. Most people don't even know what GM food is, let alone care whether or not they are buying it, so all the local markets, even the small ones, sell GM food. I am currently trying to find a farmer in the area who is willing to sell me food, but trying to find non-GM foods is a bit like trying to buy a computer without Windows preinstalled, if you know what I mean.
  • The day before the press announced the upcoming publication of the human genome, I sent this message out to my private mailing list:

    From: Jim Bowery [mailto:jabowery@ricochet.net]

    Sent: Saturday, February 10, 2001 5:24 PM

    Subject: Some Implications of Internet Broadcasts by Dr. William Pierce

    of the National Alliance

    AP wire reports out of Israel are being spiked by US editors. One spiked report: An Israeli man is sentenced to community service and fined for battering an 11 year old Palestinian boy who died from the injuries. See:

    http://www.natall.com/internet-radio/ts/021001.ram

    Although reliable figures are not available on Pierce's listenership, evidence of the extraordinary level of attention to his message is that an ebook about him by a New England professor of sociology was #1 on Barnes and Noble's ebook best seller list (at www.mightywords.com) and remains on the best seller list, to the best of my knowledge, despite being denounced by the ADL. At the height of the controversy, and while his book was still the #1 best seller, Barnes and Noble removed their best seller's list from www.mightywords.com and sent the author of the book notice that his book was being removed from their site because of a "repositioning" of their "market emphasis". After news of this spread on the Internet and a storm of protest resulted, Barnes and Noble retracted the letter of removal it had sent to the author and reinstated the best seller list.

    The Brownshirts rose to prominence as protectors of free speech when National Socialists were being stopped from speaking in public places. Spiking AP wire service reports and attempts at censorship of booksellers combined with pending federal hate speech legislation (now law in all western countries except the US) making speech that "arouses ethnic tension" a criminal offense, is creating a political environment like that in which the Brownshirts rose to prominence in partnership with the National Socialists. Although the ethnic mix in the US may result in the "Brownshirts" winning out over the "National Socialists" this time, either way, western authorities are now almost as ill-adapted to the decentralization of media as was the Roman church when Guttenberg rendered its scribes obsolete.

    If the "Brownshirts" do win, it may produce something more akin to the Protestant Reformation than National Socialism. IMHO I think this is the more likely historic model. An Internet-age "Tyndale Bible" (first English translation created with the assistance of Spanish Jews exiled by the Inquisition in Hamburg) could be the response to an "Inquisition" by "The Church" of JudeoChristian Civilization into the "demon possession" of its critics.

    If so, this work of greater public access to mythic authority may prove the most important exercise of the information age.

    The question that has me hooked, as someone who lives and breaths this revolution is, "Just what form will this 'Tyndale Bible' take and from what sources will it derive its mythic authority?"

  • More like Rand McNally patenting continents and rivers.

  • the reg-free link is here [nytimes.com]
  • If you think about it, ten thousands lines of assembly code isn't that much (compared to 10.000 lines of C) or at all interesting. You may even cut it up nicely into proc's and struct's to make it more understandable. What is interesting is what kinds of optimization he has cranked out to get the algorithm faster than compiled-C. In that light, fewer lines is actually The Good Thing with modern processors. Of course, you can't get that info from an NYT article.

    - Steeltoe
  • His home page. He certainly looks the part. http://www.cse.ucsc.edu/~kent/
  • Academic studies may take longer to complete without market pressures to speed things along, while commercially-funded ones are at risk of cutting corners and reducing accuracy to reduce time-to-market.

    Speed does not make science better, and rushing things along is almost always counterproductive in the world of science (just look to the cold-fusion debacle for a perfect example). The problem with adding commercial competition to scientific research is that the peer-review step gets left out in the name of speed, patents, and profit. Without peer review, you don't have science anymore. Other researchers have trouble repeating the experiments because of IP restrictions and the integrity of the data cannot be verified.

    I would much rather know that the data and interpretation is correct, rather than know that it was generated very quickly.

  • The "less biased" comparison is actually not done using Jim's assembly. The Sanger Centre's comparison does use Jim's assembly. It's unclear to me why the authors of the Nature paper chose to use an "assembly" that's different from the assembly that we used for the public human genome project.

    BTW, the Nature article is free even to nonsubscribers.

  • First of all, for those who aren't in the biotech industry, it should be mentioned that the NIH has an agenda to push ...

    OK, sure, I'll bite. What's our agenda, in your view? I haven't been to the secret meetings lately, maybe I'm not in the loop - but last I checked our "agenda" was to facilitate scientific research, by providing a massively important basic resource to the entire public for free, with no restrictions.

  • http://www.cse.ucsc.edu/~kent/ [ucsc.edu]
    is this one the right one?
  • On another, slightly more disturbing note, I am somewhat concerned about the use of academic funding to compete with commercial enterprises. Just because RMS does it doesn't make it right.

    Personally, I'm not concerned at all. This is something the private sector has no business trying to commercialize; to hell with them.

    So academic institutions should meekly avoid doing anything that might compete with a bunch of venture capitalists? They should restrict their own freedom of speech, thought, and action because making money has some sort of higher purpose than anything they can aspire to? Damn it, money isn't morality.
    --
  • or maybe I've just been playing too much Alpha Centauri.

    There's no such thing as too much Alpha Centauri.

    And could someone mod that post I quoted up? That has to be the funniest thing I've ever read on /. /HTML.
    --
  • Since our number of genes is so surprisingly close to much much "simpler" (as perceived by the human ego) organisms, then genes can't be where it's at is no doubt going to be a popular conclusion.

    Philosophers, religionists, and psychoquacks will each in their own way seek to put their own spin on the matter. For example Social Darwinism, was one attempt to rotely apply the idea of evolution to the society at large. They arrived at the flawed conclusion that "If I win/beat/trample over you, then of course I must be better." This was incorporated into notions of social superiority and imperialisms.

    These philosophical mistakes need to be avoided, since they devolve into zero sum games at best.

    You need also to be aware of politically motivated versions of various sciences and philosophies. Psychiatry is infamous for this sort of thing, providing the political underpinnings for the Nazi state, for example. A more recent version of this was the old Soviet Union, where opposition to the state was classified a mental dis-order, treated with electroshock, brain surgury, etc.

    These are things that we tend to think do not happen any more, until we look at thing like ethic cleansing, and other notions of "purity". We even see a weird mix of paranoia and hypochondria, not the imagining of all sorts of diseases in oneself, but the imagining of all sorts of diseases and defect in others. In a political context, this would be dangerous to have in those with heavy influence in the decision making process.

    Obviously, those with political motivations and agendas will often grab onto anything to push them, especially if they are ethically impaired.

  • "They used every piece of information available," he said. "It was really quite clever, given the quality of their data. So honestly, we are impressed. We were truly amazed because we predicted, based on their raw data, that it would be nonassemblable. So what Haussler did was he came in and saved them. Haussler put it all together."

    Well boys, lets all sell these pricks [yahoo.com] short - and hope to put them all in the poor house - while we all get rich: A deserving fate for one of the most selfish, disgusting attempts of all time...

  • Good post. A few more points to add: I've seen Craig Venter, the head of Celera, talk twice now, and he told an excellent story about how he got where he is. He was running TIGR (the institute for genomic research) which had sequenced a few bacterial genomes. He wanted to apply shotgun sequencing techniques to human DNA, but was getting tons of flak and skepticism about whether or not it was even possible. Then Perkin Elmer came to him and said; "Hey we've got this great new DNA sequencer that's a magnitude or so faster than everything out there today. Want to sequence human? Oh yeah, and we'll give $300 million dollars to set up a company to do it." So, even though he'd been an academic all his life he was getting paid to do something he wanted to do anyway, and not have to deal with the usual academia nonsense. Plus, if you beat the public project, then you get to thumb your nose at all the guys who told you it wouldn't work. Who would say no? He also said that since Celera is a for-profit company the drawback is that he's obligated to the shareholders to try and make some sort of profit. That means some of the more obviously important and potentially profitable genes are going to be patented, but mainly he said it should be a service company. Anybody who ran a BLAST search last a year ago knows that GenBank was mess until they recently cleaned it up. Though I haven't seen it myself, I understand that the Celera database is beautifully easy to navigate. Not sure I agree with Science publishing with restrictions either. But the advantages outweigh the disadvantages, I think: (1)two analyses are better than one. (2)The data is still publicly accessable. (3)It will be irrelevent in another few years when the public project finishes and cleans the sequence. (This is my first post!)
  • If his task would have been easier if he had the BNF definition for the genome - oh wait, that's what we're looking for.

    Pump that puppy through lex and yacc, and there we go - gene assembler!

  • The head of Celera was "astonished" to learn of this grad student's genius -- ten thousand lines of assembly code in a month . . .

    Imagine, in this day and age, some poor grad student still has to build a major project in assembly language. What are they using, a PDP-11?

  • I am somewhat concerned about the use of academic funding to compete with commercial enterprises.

    All in all, I think competition between academic and commercial endeavors is a good thing. Academic ventures are good because our tax dollars can fund discoveries that enter the public domain -- public money for public benefit.

    The downside is that academic ventures can suck capital and effort away from commercial ventures ("Why try and study that to make money from it? There's already a government-funded effort.") Academic studies may take longer to complete without market pressures to speed things along, while commercially-funded ones are at risk of cutting corners and reducing accuracy to reduce time-to-market.

    The genome effort was special in that you had well-funded commercial and government entities chasing after a worthy goal -- the competition sped up the process, but a lot of material is now out in the public domain. Not bad at all ...
  • I take that back. I think http://www.cse.ucsc.edu/~kent/src/jksrc382.zip [ucsc.edu] might have the source within the hg directory. If you decide to download it, be careful when unzipping as it creates about 20 directories in the current directory.
  • I tried to find the source for GigAssembler, but the closest I got was the author's home page: http://www.cse.ucsc.edu/~kent/ [ucsc.edu]. He has posted the code to some previous projects, but I don't think the one for the HGP is here.
  • sometimes. Note the following statement from the NYTimes article. They found it hard to believe that a single programmer could do it. Is it not the case that a single programmer can often create a really good useable program in a short time where a large group might not do it as easily? I seem to recall that visicalc is viewed as one of those great programs written by the sole programmer.

    "...if you had assigned a team to build this whole thing over several months it would have been a very difficult proposition. So what Jim has done is miraculous in many ways. No one expected anyone could come in and put this together in four weeks."

  • ...did he respond to the 'Longest Uninterupted Hacking Binge' poll?

  • 1) The Monsanto grain can reproduce; Monsanto has never added the suicide gene to any of its commercial seed products.

    2) There are competing international producers of seed that the rich farmers in your scenario can turn to if Monsanto raises the price of grain. They would not have to "sell out to a large agricorp".

    3) Most lesser-developed countries have laws restricting foreign ownership of land, so a sellout to a "large agricorp" is very often impossible.

    4) It is in the financial interest of Monsanto to have a wide variety of independent farm producers to sell seed to. A company with a few big customers has its well-being hanging by a much thinner thread -- one dissatisfied customer can lead to a major loss of market share.
  • However, when people start arguing against any legislation that allows the consumer to be informed of what may turn out to be a dangerous product, I start to seriously distrust that person's motives.

    That's right -- non-GM crops should be clearly labled as potentially dangerous. Modern non-GM strains of corn and wheat are crossbreeds descended from random mutants deliberately made by artifical irradiation and mutagenic chemicals, which were never tested for safety, envriomental impact, etc.

    On the other hand, GM crops are carefully engineered for specific effects and reviewed by the EPA, FDA, and USDA for safety, enviromental impact, etc.

    So what's the real motive of people who won't acknowledge that GM foods are by any objective standard safer than traditional crops?
  • Ignore them.

    Easier said than done, when the media has jumped all over the anti-GM bandwagon in order to sell more through selective reporting and outright scare tactics.

    Having companies such as Monsanto, General Electric or the Royal Dutch Shell Company subvert governments to push their own economic agendas is hardly democracy either. Having governments NOT MANDATE compulsory informative product labelling, to insure that consumers CANNOT make an informed choice whilst shopping in grocery aisles, DESPITE the fact that the public IS ASKING FOR IT is not democracy either.

    This is just another example of over-regulation by governments all too willing to impose yet more control on corporations. If the public wants GM-free foods then they'll get it thanks to the free market, and indeed there are so-called "organic" products on the market.

    At least, with protesting zealots, you have the choice of not listening to them. But corporate behemoths cannot be moved aside nor ignored.

    They can be ignored quite easily, by choosing not to buy their products. In a capitlist society your purchasing power is your weapon, and by denying companies your money you send a clear message to them about their products and actions.

    Or is it that fact that people don't really seem to care that's bothering you? After all, despite all the hype and backlash, people still seem to be buying modified foods rather than the organic varieties. They have the choice, and how they exercise it is telling.

    Democracy CANNOT exist when the people are ignorant; therefore, those who go to great lengths to make sure that the people stay ignorant are hijacking democracy.

    Exactly, and this is what the anti-GM zealots are doing by spreading their scare stories and misinformation to the public. The hysteria they are raising does nobody any good, and means that rational debate on the subject is subverted.

  • No they cannot because that would loose them the market share that they have gained. They want those big profits that growing corn at twice the natural rate gives.

    As I said, they did not study the consequences of their actions. Either the company is playing by the rules they impose, in which case the farmers are at fault, or they aren't, in which case Monsanto has no case.

    Special fertilizers must be used (GM food requires more and different fertalizers then are required for "normal" food)Also they do not have any seeds because Mansanto forces them to buy new seeds and they cannot hold their seeds to replant the next year.

    How does your link he help your case? As it says they had a contract for 800 acres but were found with 1261 acres of soya with the Roundup Ready gene. If they are breaking the contract they signed voluntarily, then they should be sued for breach of contract.

    This is just a ridiculous argument. Your trying to tell me that an extremely poor rice farmer in china can decunstruct the patented and trade secreted mansanto golden rice's genome to determine if it will survive in China or not.

    No, the Chinese government should be doing that. Your example of tyres is a perfect case - there are minimum safety standards for this sort of thing imposed by the government. If it's just farmers buying this stuff with no idea then unfortunately it's their problem.

    . If Mansanto (or any company) releases a product that does not work as advertised then that company is responcible.

    If they advertised falsely then yes, it may be their fault. But did they actually advertise it as being resistant to Chinese diseases? If not, then they're not to blame.

  • What happens is they set up one or two of the richest farm owners with thier patented grow twice as fast corn or wheat. These farmers then have a large advantage over all of the family farms that did not get the mansanto handout. The monsanto farmer then buys out the smaller farmers. When the mansanto farmers own most of the farmland mansanto then raises the price of thier grain (which by the way cannot reproduce) and the large farmers are forced to sell out to a large agricorp.

    Why? They could always buy their grain from a different supplier. And if they've managed to get themselves locked in to a contract which allows Monsanto to raise their prices at their whim then that's a foolish move and these farmers are reaping what they have sown.

    Whole crops were wiped out in china because the GE food had disease immunities from the western world. China has a slightly different set of crop diseases and *poof* there goes the rice.

    Another strawman argument. You're blaming the GM food when it's obviously the people buying it who are at fault for not doing their research properly. If they were buying huge amounts of GM crops to replace their normal crops then you would think they would investiate things like disease resistance, which one would assume is why they bought it in the first place...

  • I live in a city where EVERY private Mom&Pop coffee shop has been replaced with a Starbucks... do you not understand this whole "Market" economy thing?

    *sigh* Totally different situation. The farmer can order his grain from suppliers who will then deliver it to him. If coffee shops delivered cups of coffee nationally, then it wouldn't matter if every coffee shop in your town was a Starbucks, would it.

    That's the beauty of a market economy.

    The only thing that could force these people into buying from Monsanto is their own free choice to do so, and any contracts that they have signed of their own free will! If you sign a bad contract, it's your own fault and whining about it won't help anyone.

  • by Lars Arvestad (5049) on Tuesday February 13, 2001 @04:24AM (#435642) Homepage Journal
    There is a biased comparison [sanger.ac.uk] available over at the Sanger Center. Summary: The public assembly is much better even though less data is used.

    They measure things such as the number of fragments (fewer=better) and their lengths (longer=better) and estimated coverage of the genome.

    There is also a less biased comparison [nature.com] over at the Nature website [nature.com]. I don't know if you can get to read it without a paid subscription though. Their findings are less controversial, saying that the statistics are similar for the two assemblies, but that the annotations (i.e. descriptions of what is actually there, comparison: A group photo with note on peoples names and their relationships) are better in the public version.


    Lars
    __

  • by Thagg (9904) <thadbeier@gmail.com> on Tuesday February 13, 2001 @07:27AM (#435643) Journal
    I first met Jim Kent on the stage at the Siggraph Technical Papers in 1992, he presented his 3D morph paper right after my 2D morph paper. [hammerhead.com] Later, we hired him to come work with us at Pacific Data Images, where he worked with us in the R&D group. He's definitely a good guy to work with.

    I left PDI six years ago to start my own company, and I've lost touch with Jim; I had heard vaguely that he'd 'gone back to school', but I had no idea that he was up to something this big. It's great to see an old friend make such a great contribution in a new field. Way to go, Jim!

    Another old friend of mine, Carter Burwell, went the other way, from doing genetics with Crick at his Cold Spring Harbor laboratory, to working on early computer graphics at NYIT in the early 80s, to becoming one of the pioneers in digital music, and is finally now a leading composer for films such as the recent O Brother, Where Art Thou (somehow passed over by the Academy).

    And I'm still just making pictures :) Oh well.

    thad

  • by Fluffy the Cat (29157) on Tuesday February 13, 2001 @04:51AM (#435644) Homepage
    On another, slightly more disturbing note, I am somewhat concerned about the use of academic funding to compete with commercial enterprises. Just because RMS does it doesn't make it right.

    Celera have released their sequence under a license that restricts commercial usage (something vaguely like the Sun open source license thing, whatever it's called), whereas the public effort has released their work into the public domain (pretty BSDish, really). If Celera were the only group releasing this data, academic research into the human genome would not be able to attract the same sort of investment and would proceed significantly more slowly than it otherwise would. Using academic funding in this case secures a future for academic research in a very important field.
  • by K8Fan (37875) on Tuesday February 13, 2001 @04:59AM (#435645) Journal
    I hate to be a nitpicker, but this chap's hardly a typical twentysomething graduate student (which would have been a genuinely amazing feat) - he's a seasoned professional who's experienced in processing large datasets professionally.

    Agreed, he likely brought a huge amount of pre-existing skill in matrix math. But 10k lines of assembly language hacking to beat richly funded capitalists with super-computers in four weeks is a truely amazing hack, no matter what their skill level.

    BTW, his home page doesn't say: anyone know what graphics software worked on before? The name seems familiar - I think he used to hack math for a package called Digital Arts, but I could be wrong.

    On another, slightly more disturbing note, I am somewhat concerned about the use of academic funding to compete with commercial enterprises. Just because RMS does it doesn't make it right.

    What's disturbing is that academic institutions are being forced to compete with commercial enterprises that, frankly, should not exist. The idea of a commercial enterprise doing something as important to the entire human race as the sequencing of the genome with the intention to control distribution of the resulting science is deeply offensive. Just because you can make money doing something doesn't make it right.

  • by tlunde (38528) on Tuesday February 13, 2001 @04:29AM (#435646) Homepage
    From http://genome.ucsc.edu/goldenPath/algo.html:

    Assembly Process Overview
    The assembly proceeds according to the following major steps:

    Decontaminating and repeat masking the sequence.
    Alignment of mRNA, EST, BAC end, and paired plasmid reads against genomic fragments. On a cluster of one hundred 800 MhZ Pentium III CPUs running Linux this takes about three days.
    Creating an input directory structure with using Washington University map and other data. This step takes about an hour on a single computer.
    For each fingerprint clone contig, aligning the fragments within that contig against each other. This takes about three hours on the cluster.
    Using the GigAssembler program within each fingerprint clone contig to merge overlapping fragments and to order and orient the resulting sequence contigs into scaffolds. This takes about two hours on the cluster.
    Combining the contig assemblies into full chromosome assemblies. This takes about twenty minutes on one computer.
    The steps will be described in more detail below.

    [snip]

    The program was NOT written in "assembler". From Appendix B:

    mRNA Scoring Function
    int scoreMrnaPsl(struct psl *ali, boolean isEst)
    /* Return score for one mRNA oriented psl. */
    {
    int milliBad;
    int score;

    milliBad = calcMilliBad(ali, TRUE);
    score = 25*log(1+ali->match) + log(1+ali->repMatch) - 10*milliBad + 10;
    if (ali->match <= 10)
    score -= (10-ali->match)*25;
    if (isEst)
    score -= 25;
    else
    score += 25;
    return score;
    }

  • by wowbagger (69688) on Tuesday February 13, 2001 @04:10AM (#435647) Homepage Journal
    The example I like to use is that the Genome project is like the Periodic Table: it just gives you a framework to hang knowledge on.

    Just as the Periodic table helped scientists to deduce the structure of electron orbitals (by observing the sequence of how chemical similarities went with atomic number) and find new elements ("There's a hole here, and what should fill that hole will have these properties. Now we know what we are looking for and where to look..."), the Genome project will allow us to better determine how genes are controlled, and look for new proteins.
  • While some people are discussing Folding@Home as a response to your question of a "seti-like" processing system; there is actually a much more relevant project, also hosted at Stanford. The Genome@Home Project [stanford.edu] is attmepting "to design new genes that can form working proteins in the cell" from the DNA sequence of non-human organisms. It is a new project, but gaining speed quickly. It is worth taking a look at if you have spare cycles you can give to a good cause.
    -OctaneZ
  • by swordgeek (112599) on Tuesday February 13, 2001 @07:11AM (#435649) Journal
    First of all, for those who aren't in the biotech industry, it should be mentioned that the NIH has an agenda to push just as much as private for-profit industry. Never believe that 'the good of the public' is the only thing driving non-profits, especially when a government (ANY government!) is involved.

    Still, this issue isn't quite as cut and dried as many would like to believe. If it was, then everyone would gang up on one side, and the other side would wither and die. Consider some of the following points:

    1) Celera's efforts most likely DID force the HGP to speed up.
    2) Celera's "whole genome" approach appears to be a bust. Before they did it, we could only guess at how well (or poorly) it might work. In other words, we learned something valuable for future research from Celera!
    3) There is a lot of grumbling about Science imposing a restrictive agreement on access to the Celera data. I agree--this isn't how science works! However, it's like book publishing. They "borrowed" publicly available information (preliminary work from the HGP), added their own stuff, and can impose whatever restrictions they want. Don't like it? Go to the HGP. They (Celera) are entirely within their rights, but I don't think that Science should have agreed to publish with those restrictions.
    4) Here's a biggie. Science costs a LOT of money--the only two groups that can afford it are governments, and expensive biotech companies. The former can't afford to fund all science research, and the latter can't afford to not make a profit. Incidentally, biotech is an area where on the whole, the patent system works quite well.

    At any rate, it's an impasse. Either you cut research by about 60%, or you deal with companies that need to make a profit on their research. Flip a coin and make your choice.

  • by swordgeek (112599) on Tuesday February 13, 2001 @07:57AM (#435650) Journal

    Here's the story [ornl.gov], along with (sigh!) a (pretty cool) BEOWOLF CLUSTER!

    I hate to do it, but it's actually on topic. :-)

  • by thue (121682) on Tuesday February 13, 2001 @03:45AM (#435651) Homepage
    ten thousand lines of assembly code in a month, and why?

    Just for clarity; it doesn't say the language is assember, just that what the program does is assemble genome fracments...

    from the unsung-hero dept.
    Not really...
  • by YU Nicks NE Way (129084) on Tuesday February 13, 2001 @08:48AM (#435652)
    In fact, the Celera assembly is proof positive of the value of the HGP. When HGP started a decade ago, a dedicated scientist with years and years of training might be able to sequence a few tens of base pairs in a day, if he or she did nothing else. Five years later, after the public funded a huge improvement in the basic technology of sequencing, a barely competent technician can be expected to sequence thousands of bases a day without breaking a sweat.

    Two years after that, private industry realized that it could make money exploiting that technology. All hail to Celera for doing a good job -- but if they had seen further, it would only be because they stood on the shoulders of public money.
  • by Leon Trotski (259231) on Tuesday February 13, 2001 @03:38AM (#435653) Homepage
    "because of his concern that the genome would be locked up by commercial patents if an assembled sequence was not made publicly available for all scientists to work on."

    So should genes be patented?

    I believe this question has been at least partially answered by the Patent Office. You can patent a gene based medicine or treatment if it is applicable to a particular illness, or disease, or gene based disability. You cannot just patent genes willy nilly because you know they exist. The Patent Office and people in gene research from the NIH and Celera, the two main players in gene research, pretty much agree that it is beneficial to the public if gene based
    medicines can be patented for specific treatments. A more detailed discussion on patenting is at:

    http://www.ornl.gov/hgmis/elsi/patents.html
  • by sharkticon (312992) on Tuesday February 13, 2001 @04:18AM (#435654)

    They wanted to make seeds that couldn't reproduce, ostensibly to control genetically modified plants and keep them from taking over.

    Well you can't have it both ways can you? Either you want seeds that reproduce, in which case you'd be whining about cross-contamination with other crops, or you have seeds that don't produce, in which case you whine about "holding nations' food supplies hostage". Come on, which way do you want it?

    Quite frankly there hasn't been a single conclusive study showing that there is any risk from GM crops. It's all just scare stories and psuedo-science.

  • by sharkticon (312992) on Tuesday February 13, 2001 @04:12AM (#435655)

    Now that the entire genome is sequenced and work is underway on finding the individual genes and their functions, what advances are we going to see? Well plenty really, from screening and treatments for genetic illnesses, to modified organisms that are better and can survive in more extreme conditions. There's the potential to change almost everything as we begin to work out the sequences of more and more living beings.

    But what concerns me is that the whole backlash against anything with the world "genetic" in it will slow or even stop the flow of scientific advancement. We've already seen how companies like Montesanto can have their research attacked, spoiled and subjected to the worst kind of slanderous publicity, and as we get the capacity to do more, these attacks will likely get worse, fueled by an ever more virulent group of protesters and environmentalists.

    These people are true zealots which make RMS look like an apologist. They think nothing of resorting to intimidation, violance and criminal damage, whilst at the same time engaging in a war of words which admits no logic and no compromise. In some cases, the very lives of researchers who labour to increase our knowledge is at risk, and we cannot afford to let this happen, not with the problems of population growth looming large over humanity.

    These people are dangerous, and their actions need to be curbed. No longer should they be able to get away with their lies and violent behaviour, no more than any common thug. They can claim moral superiority, but in truth it seems as though these people are as bigoted as any racist, and just as determined to further their cause.

    We can't allow research to the thwarted because of the voices of a small bunch of extremists. That's not democracy at all.

  • by rlk (1089) on Tuesday February 13, 2001 @07:06AM (#435656)
    What happens is they set up one or two of the richest farm owners with thier patented grow twice as fast corn or wheat. These farmers then have a large advantage over all of the family farms that did not get the mansanto handout. The monsanto farmer then buys out the smaller farmers. When the mansanto farmers own most of the farmland mansanto then raises the price of thier grain (which by the way cannot reproduce) and the large farmers are forced to sell out to a large agricorp.

    Why? They could always buy their grain from a different supplier. And if they've managed to get themselves locked in to a contract which allows Monsanto to raise their prices at their whim then that's a foolish move and these farmers are reaping what they have sown.

    This reminds me of Pastor Niemoller's words. If Monsanto drives out the local suppliers, then the farmers don't have a choice who to do business with. As for their "foolish moves", I don't think it's either a stretch or unfair to say that farmers in developing countries lack the business acumen and strategic foresight that Monsanto has, and it's not realistic to expect that they can do business on the same playing field as Monsanto. Remember that a "free market" assumes good knowledge on both sides of the transaction; if one side has all the knowledge and the other doesn't understand what's going on, it's not a free market any more, but rather a scam.

    The same applies to Chinese farmers buying GM food. You talk about doing research on issues such as disease resistance. Precisely how, pray tell, are they going to do such research? Assuming they even know about the genetic basis for disease resistance, and that crop diseases in the US differ from those in China, you're assuming that they have the resources to do this kind of investigation.

    It's not only governments that can oppress. Anywhere that there's an excessive concentration of power there can be oppression. It's not a matter of duly constituted laws and sovereign states (most dictatorships have neither; Saddam Hussein rules by personal whim and doesn't have too much respect for borders of neighboring states). If Monsanto's doing this kind of divide and conquer in Latin America, it's no better than if it's a government doing the same thing.

    In Germany they first came for the Communists and I didn't speak up because I wasn't a Communist.

    Then they came for the Jews, and I didn't speak up because I wasn't a Jew.

    Then they came for the trade unionists and I didn't speak up because I wasn't a trade unionist.

    Then they came for the Catholics and I didn't speak up because I was a Protestant.

    Then they came for me and by that time no one was left to speak up.

  • by moonboy (2512) on Tuesday February 13, 2001 @04:54AM (#435657) Homepage


    How about trying to get an interview with this guy? Could be very interesting.


  • by jfoust2 (43840) on Tuesday February 13, 2001 @06:08AM (#435658) Homepage
    Jim Kent was once known in the mid-80s for writing Zoetrope, a 2D path-based animation system for the Atari ST, not unlike today's Flash technology. Zoetrope also became Aegis Animator on the Amiga, and Autodesk's Animator Pro for the PC, which begat the .FLI/.FLC animation format. I believe Kent also worked on the first DOS generations of Autodesk's 3D Studio, too.
  • by KaRll (136503) on Tuesday February 13, 2001 @03:49AM (#435659)
    I am more concerned with this kind of projects being run by commercial enterprises. Just because you can make money out of it doesn't make it right.
  • by Zara2 (160595) on Tuesday February 13, 2001 @04:32AM (#435660)
    Man you chose a really bad company to base your argument on. Mansanto is very well known for a lot of underhanded tricks re: frankenfood. On the surface I am not agianst GM food. Actually I see a lot of good things coming from it. However Mansanto will go down to a small south american country and completly bankrupt it. What happens is they set up one or two of the richest farm owners with thier patented grow twice as fast corn or wheat. These farmers then have a large advantage over all of the family farms that did not get the mansanto handout. The monsanto farmer then buys out the smaller farmers. When the mansanto farmers own most of the farmland mansanto then raises the price of thier grain (which by the way cannot reproduce) and the large farmers are forced to sell out to a large agricorp. Much like the ones mansanto owns a lot of stock in. Now all the local farmers are reduced to basically being wheat pickers.

    Also on top of this GE food has never had to pass any serious tests of it. Whole crops were wiped out in china because the GE food had disease immunities from the western world. China has a slightly different set of crop diseases and *poof* there goes the rice. Please do your research into how things are done and not just hope that people are doing the things that they should be. While this is a "anti frankenfood" site it does have some good info in it. http://www.purefood.org/monlink.htm

  • by Alien54 (180860) on Tuesday February 13, 2001 @04:43AM (#435661) Journal
    On theNewsHour [go.com], PBS had a story [pbs.org] on this the past day or so. They have a large webpage [pbs.org] with many links dedicated to the whole issue. One thing that is interesting is that there are fewer genes than had been first imagined. The end result is that the genes are more often like a multi-purpose module, and that much of the functionality of the system is in the proteins system such as enzymes, etc. As it was noted:

    What's going to happen is we have to go into the protein world to really understand where the genome is taking the next level of biology. That's ten times as complex at least.

    What is also noted is that the combination of these protein interactions is staggeringly more complex. I can imagine that the system interactions may be a million times or more complex.

    So in my mind, patenting a gene might wind up being similar to patenting the management system of a nuclear power plant, and thinking that therefore you understand nuclear physics.

  • by SubtleNuance (184325) on Tuesday February 13, 2001 @08:13AM (#435662) Journal
    Im a Tree-Hugger of the highest order. Although I do know that Monsanto's GMOs are getting a 'bad rap'.. let me assure you: Most people's concerns w/ Monsanto are not only the idea that you have 'Frankenfood'. There is a whole group of ideas about why 'Monsanto' is evil:

    1) Produce GMOs that rely on Monsanto produced chemicals. Further enslaving the Farmer to ecologically unsound farming methods and Monsanto's pocket book. Read: Roundup Resistant Crops.

    2) Being a generally massive producer/marketer of Farming Chemicals. Closely related to Item #1, but worth mentioning in a broad sense.

    3) Actively participating in the 'mono-culture' momentum that will produce the next Irish Potato Famine & contribute to the general degradation the biodiversity of the planets food supply.

    And more generally - Tree Huggers like myself are generally in favour of a broad, local, varied sources of food as apposed to the Monsanto Backed "New Age of Industrial Farming".

    When MadCowDisease reaches The Americas which method will be more likely to preserve our food supply? A) 'Industrial' Farming B)Broad, Scaled, Varied, Local Farming... For many reasons this is a Good Thing(TM). Monsanto is the epitome of the industrialization/commodidizaion of the Planets Food Supply. They operate for the benefit to the Bourgeoisie who own stock - not the good of the planets people (which should be pretty relevant when talking about *FOOD*. Their growing strength represents a general 'problem' with our future (not completely described above).

    I am not a Luddite by any sense, but I do not see the value in a 'for profit' company producing GMOs for the benefit of their pocketbooks... this 'unholy' motivation will *NOT* lead to the benefits most of us understand will come from GMOs... it is a matter of motivation. They are more likely to risk our food supply based on profit returns - its not simply a concept of people scared of GMOs.

    I have no problems with responsible, open, IP free GMO research/production by people with without compromised motivations. That is *NOT* Monsanto.

  • by jw3 (99683) on Tuesday February 13, 2001 @03:50AM (#435663) Homepage
    As many of you probably know, the actual work hasn't started yet. The schedule of a genome project looks like that:

    a) sequencing, that is -- getting the actual sequence. This is almost purely technical work, and definitely not very interesting for a scientist, although you can get a lot of credits for it.

    b) annotating the sequence: finding out where are the genes, what are the similarities between them and between the genes known from another organisms, and what can be suggested about their function based on those similarities. This is pure bioinformatics stuff: first finding the "open reading frames" (ORFs), that is -- anything that can be a gene at all: it has to start with an "ATG" (codon for metionine) and stop with a so-called stop codon. This is only the most basic criterium.

    Whatever comes later is called "postgenomics", and it is probably the most exciting stuff in this whole area of reasearch.

    1) in most of the genome projects which were done until now, as much as half of the proposed genes had not even a rough function assigned to them. (the group I'm working in sequenced a bacterial genome back in 1996, and during that time the situation hasn't changed much). Experimental work and more biocomputing is needed to find out what those genes do. The problem with biocomputing isn't the lack of CPU, but the lack of good strategies / models / theory (or, not lack of "good", but lack of "better" strategies etc.).

    2) knowing what a gene does is, contrary to the common belief, only very little information. You need to know how it is regulated, and this means a lot of tedious and complicated experimental work: two hole areas of postgenomic science deal with that -- transcriptomics (regulation on RNA level) and proteomics (on protein level). You have to understand that each gene is regulated on many levels -- transcription of the gene from DNA to RNA, turnover (that is, the speed of degradation) of the mRNA, speed of translation, amino acid composition of the protein, protein turnover. Moreover, the genes are interconnected into networks rather then pathways. Creating a functioning model of an eukaryotic cell will be probable impossible during the next twenty or so years. That is -- among other things -- my group works with a little bacterium [www.zmbh.de], which has only +- 700 genes. And even though it is a couple of orders of magnitude more simple then the simplest eukaryotic cell, it is very, very, very complicated.

    Take-home lesson: don't be too enthusiastic. This is not the flight to the moon. This is only the first Sputnik.

    Best regards,

    January Weiner

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