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Genetic Stone Soup
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.
sorry to mention that, bu you did put up the wrong link: // and the geek shall inherit the earth // duh! doh!
for more information on of the nutritionists involved with the human genome project, check out a profile of Jose Ordovas
-- Louis P Bennett
"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.'"
/. 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.
The above quote by Mr. Kent is offered in the
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.
"We need to get back to doing real science, the kind that generates patents!" --Schizmatrix by Bruce Sterling, by maybe it should be J. Craig Ventner
yeah.. i misspelled "breeding." Probably one or two other words too.
It's not enough to bash in heads, you've got to bash in minds. - Captain Hammer
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?
(currently testing something about signatures here)
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).
"don't fall into the fallacy of believing that Perl can solve social problems. Maybe Perl 6 can, but that's a ways off"
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
Kythe
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...
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Is PVM/MPI even available in assembly?
Remember, this code is meant to run on Beowulf clusters....
Your Working Boy,
- Otis (LICQ: 85110864)
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. if your curiousity hasn't been satisfied.
thad
I love Mondays. On a Monday, anything is possible.
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.
Need a Python, C++, Unix, Linux develop
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?
Your right to not believe: Americans United for Separation of Church and
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.
Your right to not believe: Americans United for Separation of Church and
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.Never trust a man in a blue trench coat, Never drive a car when you're dead
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
I have discovered a truly remarkable proof which this margin is too small to contain.
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
I have discovered a truly remarkable proof which this margin is too small to contain.
People that give their talents for humanity instead of profit should be honored accordingly. Do the nobel prizes in sciences require this?
:) 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.
:)
What, you mean like pretty much everyone engaged in academic research?
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.
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
Mike van Lammeren
It will challenge your head, your brain, and your mind.
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..
Carpe diem!
You really should try harder. First there was nothing about licensing in the article. It's likely owned by the college.
Seconc, classic reversal of ideology set up as trick question. Lame. Try harder.
The message on the other side of this sig is false.
When you mentioned backlash I thought more of religious zealots, not tree huggers. If you look at (recent) history, far more senseless violence has been done in the name of religion than the environment.
It'll be interesting (and vexing) to see how the bible thumpers will try to explain away evolutionary relationships which new technology will make clearer.
I'm surprised that we aren't hearing more outcries against genetic research as some kind of blasphemy. But I guess a California college town isn't exactly the right arena.
I submitted this story a few days back (as I'm sure millions other readers did), but /. didn't see fit to publish it until there was a "computer geek" slant to the story.
For goodness sake, will the Slashdot Editors start being more open minded about what makes a good slashdot news article!! Surely the "achievement of the generation" deserves a passing mention on Slashdot even without the computer geek slant to it???
Hi January!
What a slashdot community! I did my PhD in the same lab as January is in now and I started the transcriptomics part (buss word nowadays is microarrays or DNA chips). Nowadays I work for the pharma industry and I can only support his comments. What we have been struggling with in this little beast is completely peanuts when it comes to humans. And even the investments that the pharma industry can make and makes is in my opinion only a very little fraction. Believe me, these folks want the function of the genes and they would pay you big $$ if it would be as easy as media makes you believe...
So moderate him up!!!
Cheers,
hinrich d8-)
I am supposing that is C code, and there is no documentation apart comments, and no qualification apart programmers self-performed tests.
I'm also supposing that the metric used is '1 LOC = a non-blank non-remark line' [e.g. also lines of a single character counts]'.
The formula is:
10000 LOC / 100 LOC per day * 8 hours per day * 30$ per hour.
Pardon my blatant pragmatism. I'm in better mood when I code.
Ciao
----
FB
It happened in the past, with less critical issues, that 'The Official Scientific Truth' has been dictated not by honest research but by corporate money.
Ciao
----
FB
The original poster's point was that there is no government regulation that forces GM food to be clearly labeled as such. One wonders how sales would do if it were immediately obvious to consumers that what they were buying was GM or not.
Personally, I am not all that against GM foods. 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.
any word on the os of the 100 pc cluster ??
42
It's clear from the article that both projects finished sooner because of the presence of the other. So the question of "which is better" is really not the right question, because both of them together is better than either of them alone. Competition is good.
Still, if it takes nearly ten years longer for the public project to finish and a patent is only good for ten years, it seems like "public availability of the data" is really about the same. And the data is privately available in the interim. All other things being equal, that is, which they never are.
If you must make the public vs. private argument, don't ignore the fact that public projects invariably take longer and private patents invariably expire.
"He had to ice his wrists at night because of the fury with which he created this extraordinarily complex piece of code."
Kudos to Mr Kent, but talk to RMS about what you are doing to your self...
Special Relativity: The person in the other queue thinks yours is moving faster.
I have not read the article, but this seems to lead to an interesting problem:
What is preferrable: Open sourced software which everybody (including 'bad corporations') can use or closed source in order to prevent those bad corporations from taking away some freedom?
This might be rephrased a little less charitably as "Once the public has paid the cost of developing the technology, business steps in to collect the profits." Standard practice in American high-tech industry.
As a system it is, as many here have pointed out, very efficient; an efficient mechanism for transferring money from taxpayers to the owners of large corporations. You pay for developing the technology, then pay a second time to be allowed to use it. It's a highly lucrative little scam, made possible by the system of intellectual property rights originally indended as an incentive to innovation, but now used principally as a licence to print money. A gift from the American people to their owners.
I have one question tho, did he have a social life before he started? because you can bet he didn't have much of one after it.... :-)
"See, we plan ahead! That way, we never have to do anything now."
One thing you must admit, the actual sequencing happened very quickly. Why? Competition.
Before Celera entered the fray, the Genome Project was projected to take years longer than it actually did. In fact, this very posting highlights the benefit of this competition between private industry and public science. Were it not for Kent's fear of Celera finishing first, he would not have undertaken this "miracle" effort.
While you may find private industry's scientific work distasteful, you cannot deny that the efforts of the public scientists were accelorated by Celera's.
I know several people concerned about GM food and noone willing to resort to even the thought of violent behavior or intimidation. Your brush is rather broad in painting an entire cross-section of the populace as violent zealots. You've got your zealots in nearly every ideology, granted. But geez, how dangerous do you think the majority of the organic-buying public is?
Mind you I have other issues with Mansanto other than this but they do not fall under the scope of this discussion.
Pithy, yet ultimately meaningless, phrase expressed with gusto!
And before you ask I am not being sarcastic. This is very good news. The first really major big win agianst corperate powerhouses that I have heard of since the AT&T monopoly breakup.
Pithy, yet ultimately meaningless, phrase expressed with gusto!
Thank-you. you said it better than I could. If I could mod you up I would ;)
Pithy, yet ultimately meaningless, phrase expressed with gusto!
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. Also by the time that mansanto raises the prices they have spent extensive amounts of money setting up thier farms around the GM food. 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. Also farmers must spend a lot of money on pesticides that you can only get from Mansanto or it's affiliate companies. The infrastructure involved makes it extremely difficult for a farmer to just switch over to another crop.
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...
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. By this logic firestone shouldnt be in trouble with it's cars because each individual owner of a firestone tire should have done stress tests on thier tires before ddriving on them. No, I'm sorry. If Mansanto (or any company) releases a product that does not work as advertised then that company is responcible. Not the consumer. This is why snake oil salesmen are not legal.
Pithy, yet ultimately meaningless, phrase expressed with gusto!
I think Slashdot should sponsor an award for people like Kent who code for the public good. Call it the Berners-Lee award or Stallman award. Then make a web site with the winners and their accomplishments, with links to their sites. Let's encourage our fellows to fight the good fight!
The Moore-Murphy Law: The number of things that will go wrong will double every 2 years.
"C: All the power of assembly with the convenience of assembly."
Read the article again. It's a program that assembles the data, not a program written in assembly language.
Whether or not they finished is debatable and certainly the quality of the work is important. The Human Genome Project took 10 years. Celera did the work in 3. Celera's map is more complete and easier to navigate. The proof? People willingly pay $10,000 a year for Celera's work even though the Human Genome Project's map is available for free.
Just another example of how private enterprise can beat government (i.e. tax supported) research any day.
The article doesn't say much about the actual quality of this assembly versus the Celera version. Has anyone seen both data sets to make a comparison?
Not all gene assemblers are created equal...
I don't see any indication that this was written in Assembly language, just that it is a "Gene Assembler" - a program to assemble genetic fragments. I'd be amazed if he wrote the app in Assembly per your headline, more likely the obvious C/C++.
I like my food all natural, thank you.
It's very unlikely that anything you eat on a regular basis is "all natural". All modern crops are the result of hundreds of years of selective breeding and decades of systematic cross-breeding. For as long as agriculture has existed man has noticed mutations that created more robust, more productive or better-tasting crops and encouraged and propagated the better variations. Originally, we had to wait until a stray cosmic ray modified a plant's genome in some useful way. Later, as our sophistication increased we learned how to use crossover (via cross-breeding) to force changes to happen more quickly, although still at random. A few years back people even started deliberately bombarding plants with radioactive particles in order to create more random mutations, with the hope of accidentally creating more useful variants. Finally, we're getting to the stage where instead of relying on random changes with completely unknown effects we can make selective, targeted alterations.
I find it bizarre that people trust strains that are the result of random, unconstrained mutations but balk at strains that are long-trusted plants with some carefully targeted modifications. In fact, when new strains spontaneously appear there is little or no testing done, and none required!
Note to ACs: I usually delete AC replies without reading them. If you want to talk to me, log in.
How is it that someone can patent a map of the genome? They did not create the genome, they created the map -- a representation of what already exists! It seems to me that this is akin to Rand McNalley patenting an atlas.
What am I missing?
Madness is only a state of mind
People that give their talents for humanity instead of profit should be honored accordingly. Do the nobel prizes in sciences require this?
An Education is the Font of All Liberty
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 ;) ;) ;) ;) ;)?
Thanks God it is not easy ! I hope the more you dig in, the more complex and complicated it gets. I don't want a solution to this puzzle. I want it to be a perpetuum mobile-style generator of knew questions, new problems, always - for ever and ever.
Celera... Solaris... Hmmm...
Does reading in the bathroom count as multi-tasking?
For some reason, it feels right to post this.
668: Neighbour of the Beast
We can't allow research to [be] thwarted because of the voices of a small bunch of extremists. That's not democracy at all.
Good point. I guess these "extremists" must have missed that extensive, open public debate we all had to decide how to manage the immense potential societal impact (positive and negative) of the coming biotechnology. And they must not have been paying attention that day we all got the chance to "democratically" decide how we would all be affected by the policies of transnational corporations, which ultimately don't have to be responsible to anyone, as long as governments can be bought (3rd world and/or U.S.). Violence is certainly unacceptable, but is peaceful protest?
I, for one, am excited by the wonderful potential biotechnology has to do good. But what is most important to the progress of society is not what decisions are made, but who is allowed to participate in making them. And posting on Slashdot is no substitute for a ballot. --Scott
"Frederick, is God dead?" --Sojourner Truth
While we spent 8 hours a day sequencing slashcode
I'm still trying to figure out what people mean by 'social skills' here.
Hey you! Stop using that nose! I have a patent for it!
Time is DNA...I mean money
AC is AC
Sold my Celera stock last week. Thinking of buying at back again. If I do then everyone here will start paying me royalties just for living. No royalties, no DNA for you.
The quality of the INPUT data was rather poor... making it an even more amazing feat that he was able to develop a functional algorithm for assembling and decoding it--the Celera data was apparently much better organized and more complete. Nobody is doubting the quality of the actual solution--if anything, it is probably more robust than whatever Celera was designing.
As time goes on, it is likely that his software will be used on better data, an act which likely would otherwise be illegal right now.
/* This post not warrantied for mission critical applications. */
"We've already seen how companies like Montesanto can have their research attacked, spoiled and subjected to the worst kind of slanderous publicity," Unfortunately companies like Monsanto are not entirely blameless. They do deserve some of the bad publicity they get. "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." The problems of population growth can be solved by slowing procreation - although in some areas the growth curve is shallowing. The West need not consume and waste the proportion of resources it uses - and there is so much food produced in the West and not consumed that we end up with food 'mountains'. Furthermore, if governments allow the patenting by corporations of the results of the research some people won't be able to afford the products. This is already happening to some Third World countries with drugs and medicines. But at the end of the day, the protestors believe they are in the right. They are like the religious, who have faith in a God - they 'know' they are right! I disagree with the people who believe there should be no research whatsoever, but I don't like the idea of 'open-field' research. I haven't been convinced that this research is safe. Anyway, a democracy that stamps on the beliefs of a 'small bunch of extremists' is no democracy at all.
A few years ago, the Baltimore Sun did an interesting profile of Hamilton Smith, Celera's chief scientist who came up with their unique "shotgunning" method of sequencing DNA.
The article described how Smith won the Nobel Prize in 1978. He felt that he didn't deserve the prize because it was an achievement that he had stumbled upon by accident and hadn't worked to earn it. This caused him to lose confidence in himself and he went into a professional and personal decline. His relationship with his family deteriorated very badly. According to the article, his work with Celera has given him a chance at personal redemption. He began to piece together his family relationships, while dreaming of sequencing the human genome. He felt that this would be a groundbreaking achievement that he would truly earn the credit for. Looks like he has succeeded. Congratulations Ham!
The article is no longer available at the Sun web site, but those with Northern Light accounts can find the article here.
Does anybody want to explain to me what "stone soup" is...?
"Two teams of British and American scientists have found that there are no more than 30,000 to 40,000 genes - nearly a quarter less than what was believed at the time of gene mapping last year."
There's always sufficient, but not always at the right place nor for the right folks.
Looks slightly Kazincky-ish does he not?
There is no spork.
if they complete the Human Genome Project. I prefer KDE anyway. Oh wait, nevermind....
Why did'nt they just use one of them DNA computers we're always hearing about? They're supposed to be really fast.
Supposedly, psychological studies show that by age 40 one's fluid intelligence/logical analysis skills are decreasing. Well, the greatest math puzzle of modern times, Fermat's Proof, was solved recently by a 40 year old.
The Business School twits who tout this Conventional Wisdom don't realize that temperament is what allows a person to solve these types of problems, not speed. The race goes to the patient tortoises.
Another thing they don't realize is that the people who take part in all these medical and psychological studies are usually students and people who need money. If a 40 year old needs money (usually 50-100 bucks) that badly to have stoop to being a study subject, they are usually retards or druggies/alcoholics. And these people are representing 40+ age groups in intelligence tests. Great!
In reality, the PHBs just use this artifact of the studies (age 40+ morons/alkies representing their entire age group) in order to justify age-discrimination because they are intimidated by the knowledge of the 40+ group, and they think they can better exploit younger people.
Sig:
Navy nuke sub lifestyle?
"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.)."
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.
Just a thought.
-- There are two kind of sysadmins: Paranoids and Losers. (adapted from D. Bach)
now we can make humans with 5 asses
"Why? They could always buy their grain from a different supplier."
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?
It's all about control Grasshopper. Trust me... you have no choice.
P.S. Don't fuck with me about Monsanto. Ever been to Central America bozo? Grow up!!!
______
jeff13
The Genetic Map is the greatest discovery since geometry several thousand years ago. It's nothing less than the paradigm shift in the human journey.
That'll be $1000000 please.
Sure, proof that all humans came out of Africa is nice (knowing we're far more like plants - not as much). Tends to stop short some of the silly racial arguments that have been flying around throughout the last few decades. But the real issue is clear...
The genetic map is publicly available thanks to the great publicly funded research science mentioned in these posts. But there isn't just one... there is another from the company Celera.
Celera claims their map is BETTER than the public one. That's why they charge so much and that's why you will be paying.
Honest! This is from statements from Celera given to the Canadian press this morning.
Kinda sounds like Linux and Windoze don't it?
______
jeff13
IÕm not so sure about that. It would be more accurate to say that this phase is more akin to the discovery of elemental particles. There is no real structural understanding (except linear and groupedÑa very trivial form of nomenclature) offered by this informationÑrather akin to the ÔgroupingÕ capabilities in biology. ItÕs somewhat like discovering the underlying 1s and 0s pattern that underlies an incredibly complex bit of code. However we havenÕt the slightest notion how to read itÑlet alone make any kind of prediction. There remains no real insight into the workings of the code. Nor is there any predictive modeling capacity. From the periodic table, an immense range of predictions are made available including structural understanding of virtually any type of reaction through increasing complexity of interaction. For the most part we have none of the lovely structural analysis and prescriptive/predictive insight made possible through the periodic table. LetÕs not pat ourselves on the back just yet. On the other hand, at least the code is open source. This always seems to lead to greater insight and innovation.
A truly frightening observation. At the risk of sounding like a slobbering pomarx type, lets just say that there are very many types of knowledge/research activities that should not be based in the cultivation of purely economic assessment. Fine Arts/Humanities/Social Sciences/Theoretical Sciences anyoneÑsorry, thatÕs just not profitable inquiryÉ Not to mention the actually cost to business interests if we continue to cultivate (or even allow just to sit in the local library) political radicals and social revolutionaries who insist on being critical and thinking things beyond how to influence people and accrue wealth. The damage is immeasurable in any attempt to mold them in this way. In Montreal, Canada now at a local University there is a newly renamed John Molson School of Business (John Molson was a famous brewer responsible for one of the biggest breweries in CanadaÑrather a good sort of fellow, really). The concise mixture of inebriates with the study of commerce and marketing is actually rather appropriate, wouldnÕt you say?
I understand that you are trying to say that privitazation has its purposes, but obviously you are forgetting one little fact about human nature. Those in power will do anything (and I mean anything, like build doomsday devices like the Soviet Union did) to keep a powerful position. And for abusing others? I will not get angry about it and flame, but it is a disturbing truth of life. You simply cannot trust a corporation, and by that I mean almost every single one. They will work you to death, give you black lung, declare bankruptcy to deny you your benefits... all the while playing golf on the profits. I know because it happened to my mother's little coal town. Everyone was dying and they took all the benefits away from dying people "legally." I also have friends in a county in Indiana that hve the second highest rate of lung cancer in the country. There is one plant in the whole place. It makes GE plastics. Trust me... if they get their hands on the genome, it will be no different, and they should be watched INTIMATELY.. because they will definitely try to lord us with it. We all know this, whether we like to admit it or not.
I appreciate that poster's smugness. He/she assumes that intelligence alone is the determining factor in survival. An intellectual cake-eater looking down on all the stupids. How quaint. Surely the weight of the poster's opinions alone will assure suvival. Send this person money and genetically sound mates... and maybe we can ride the coattails to glory. Unfortunately, because of all technology getting priced at a premium when it arrives, only the wealthy will have access to new life-savig techniues. It could be incorporated into more expensive health care, which we all cannot afford now anyway, so the poor are screwed again. And of course, those "other" people who live in the "dirty and uncivilized" countries wil face the burden of it all because they can be bullied around easier. Sorry guys, here it comes again.
for more information on of the nutritionists involved with the human genome project, check out a profile of Jose Ordovas
that's a great analogy. since i can't mod i just thought i'd tell you that.
Actually, I think it's pretty embarassing that they are excited about beating Celera, when articles all over the net (example on CNN) are suggesting that the quality of their data is really quite poor.
I'm much more concerned about bad data (particularly when it might affect my health) than I am about whether a corporation can patent genes or not.
here
Note further that his decision to give it to the "public" sector allowed the "public" sector to "win".
He could have just as easily given it to a corporation. Then, would it be accurate to recognize how a geek individual totally destroyed a bloated, pulic-sector project?
If profiteering drives scientific development, we're all better off for it. Its high cost is a sign of its success, not of some failure.
I am for the complete Trantorization of Earth.
Assumed the sequence is known. .data section of a program which .text and .bss sections are almost unknown, of a machine which instruction set is almost completely unknown, with very varying and hard to analyse input and very varying and even harder to analyze output.
Then we have the full
And it is very likely, that there are no real sections, but a huge bunch of self modifying code, where it is not clear what share the DNA has.
Guess there was some sort of Mel at work.
Just because I can imagine doing a hippopotamus, doesn't mean I'd like to do it.
I think you overestimate the influence of any single person in the HGP. The nature paper listed nearly 3000 authors (and I don't consider it to be complete either).
The total task of sequencing goes all the way from mapping into sets of BAC clones, preparing the physical samples, the ABI instruments doing the sequencing itself, base calling, vector clipping, assembly, joining, editing, and finally producing consensus sequences for each clone.
GigAssembler comes into play (as far as I know) on assembling the "clones". Each of these is typically 150Kb or so in size and contains many thousands of overlapping separate sequences (each a few hundred base pairs long), which themselves have already been assembled using different algorithms (eg Alewife at the Whitehead Institute, or Phrap at Sanger and St.Louis, and our stuff (at MRC) for incremental additions and "finishing" work).
I'm not knocking GigAssembler - it sounds like a fantastic achievement, but just putting it all into perspective. This is a HUGE project and it's still nowhere near finished. This is just the start!
Er, actually, quoting from the /. commentary:
"The head of Celera was "astonished" to learn of this grad student's genius -- ten thousand lines of C in a month, and why?"
So it looks like it was done in C, which is slightly different than assembly.
STOP MISUSING APOSTROPHES, YOU MORONS!!!
Or you could just look at what was in the original /. article: "The head of Celera was "astonished" to learn of this grad student's genius -- ten thousand lines of C in a month, and why?"
STOP MISUSING APOSTROPHES, YOU MORONS!!!
Sounds like DNA research would be a good target for distributed computing. I've been looking for a worthy sucessor to Seti that isn't as abstract as calculating Pi or huge prime numbers.
Wonder if there are any projects along these lines that wouldn't involve losing control of your system to Juno??
Yes. And kudos to the scientists who proved that a project that a private business can complete in three years, a publicly funded project can take ten years to complete.
It's important to keep proving this point, so that roadblocks to scientific progress like public funding (by meddlesome bureaucrats and bogged down by 'committees'), tenure, and the unionization of academics can be overcome.
First, I'd like to argue with a few of the points in that last post:
Typically public research efforts are underfunded, liable to have their funding cut as a political decision, and staffed by second-rate staff (most of the top-class ones will work in the private sector, where they will be paid more).
That's contingent on the flawed argument that the only reason anyone would research for this or that employer is the money, and that the best researchers are only interested in the almighty dollar. Never mind the increased prestige, academic freedom, etc. that come with government research.
The private sector OTOH, although it will certainly charge for its discoveries, which will cost us money, the overall benefit will be better:
1. they are certain to exploit and develop their intellectual property for all it's worth - something we are not assured of from the government - which means that the advances to medical science will be greater - and this is surely the overriding reason why this is better.
So, again, there is the argument that desire for money will drive commerce to develop discoveries better than government, money apparently being the only thing that drives humans to action. This is nice-and-consistent with the image of the lazy salaried government scientist who need not work. This neglects the general, if not universal, point that the ones who accept less money to work for the government tend to be the do-gooder types, motivated to exploit discoveries for--gasp-- non-monetary reasons.
Yes, they will charge for their discoveries, and not necessarily for the better. You lauded the profit motive that will (supposedly) drive the private sector to exploit discoveries for all they're worth. What about that same proofit motive that will allow some company or other to monopolize some hypothetical discovery that may lead to improved treatment of some genetic disorder? Suddenly this company has a strangle hold on a particular field of medicine, bringing me to:
2. we can afford the cost of private ownership. Affluence is at an all time high.
Who's "we"? You? The upper middle class? Surely you can't mean all of those poor people? The point is that the people who may wind up needing some gene research-derived technology won't be able to afford it. The reports of pharmeceuticals compaines fanning the flames of the AIDS epidemic in Africa (granted, the government has not exactly been saintly in this matter) due to the incredible prices for treatments are all the evidence I need to see how much these companies are working for the greatest overall benefit
Aside from money, we can never, ever, afford the concentration of potentially useful technology in the hands of those who are interested first in its profitability, then in its benefits to society and so on. Entrusting something so potentially important, that can have such widespread a impact on our society, to such an organization, or even a collection of them (with the biggest inevitably swallowing up the small-timers), is morally indefensible
*Give a man a match, and he'll be warm for a minute. Light a man on fire, and he'll be warm for the rest of his life*
what does it matter how old he is
obviously got more skills than u
oohhhh im scared pls. hacker speak is so scary!!!
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.
It's not enough to bash in heads, you've got to bash in minds. - Captain Hammer
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.
It's not enough to bash in heads, you've got to bash in minds. - Captain Hammer
Can't prove a negative like that.
It's not enough to bash in heads, you've got to bash in minds. - Captain Hammer
Any moderators with a spare point?
It's not enough to bash in heads, you've got to bash in minds. - Captain Hammer
Nor can you get the info that he wrote even ONE line of "assembly language" code for this "gene assembly" software.
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.
I don't know what he actually coded in though.
Lars
__
Reality or nothing.
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?
try { do() || do_not(); } catch (JediException err) { yoda(err); }
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.
Your right to not believe: Americans United for Separation of Church and
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.
Vidi, Vici, Veni
perhaps there's a differenc in potency?
Vidi, Vici, Veni
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.
Babar
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:
Babar
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
This is not the greatest sig in the world. This is just a tribute.
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.
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.
Never believe in anything until it has been officially denied. -Otto von Bismarck
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...)
-- 73 de KG2V For the Children - RKBA! "You are what you do when it counts" - the Masso
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.
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.
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?"
Seastead this.
the reg-free link is here
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
http://www.debunkingskeptics.com/
BTW, the Nature article is free even to nonsubscribers.
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/
is this one the right one?
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.
"It is a greater offense to steal men's labor, than their clothes"
"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 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!
I donate all spillover Karma to the charity of my choice... Ada was still a babe despite what people may say...
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 take that back. I think http://www.cse.ucsc.edu/~kent/src/jksrc382.zip 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/. He has posted the code to some previous projects, but I don't think the one for the HGP is here.
"...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."
"sweet dreams are made of this..."
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.
There's no "we" in team, only "me"
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?
There's no "we" in team, only "me"
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.
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
I love Mondays. On a Monday, anything is possible.
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;
}
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.
www.eFax.com are spammers
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.
"People who do stupid things with hazardous materials often die." -- Jim Davidson on alt.folklore.urban
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...
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.
"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
Cui peccare licet peccat minus. -- Ovid, Amores.
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.
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.
How about trying to get an interview with this guy? Could be very interesting.
Co-founder and designer at Music Nearby: http://musicnearby.com
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.
Curator of the Jefferson Computer Museum http://www.threedee.com/jcm
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.
"It is a greater offense to steal men's labor, than their clothes"
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, 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