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Genetic Stone Soup

jamie posted more than 13 years ago | from the unsung-hero dept.

Programming 175

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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Re:more on human genome project (1)

Anonymous Coward | more than 13 years ago | (#435489)

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!

Ambiguous quote... anti-patent spin. (1)

Anonymous Coward | more than 13 years ago | (#435490)

"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.

Re:Thank god for James Kent (1)

Phil-14 (1277) | more than 13 years ago | (#435493)

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?

Re:Grad Student? (1)

Howie (4244) | more than 13 years ago | (#435494)

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).

self printing code... (1)

kevin lyda (4803) | more than 13 years ago | (#435496)

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...

Re:could a distributed parallel system be useful? (1)

Omnifarious (11933) | more than 13 years ago | (#435499)

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.

Re:Things are not as easy (1)

ethereal (13958) | more than 13 years ago | (#435501)

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.

Re:Can we establish a society to honor these peopl (1)

Fluffy the Cat (29157) | more than 13 years ago | (#435505)

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)

You know 'them'... (1)

ASCIIMan (47627) | more than 13 years ago | (#435507)

...always wanting their genes mapped first.

Oh yeah? Map this!
AGTAATGCATGCATCATCTSATGCATGCAT

Bet his program can't handle that!

Re:Grad Student? (1)

theMAGE (51991) | more than 13 years ago | (#435508)

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...

Re:Grad Student? (1)

lamz (60321) | more than 13 years ago | (#435509)

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

NYT article (1)

st.n. (72557) | more than 13 years ago | (#435511)

Here is the link to the NYT article [nytimes.com] without the need to log in.
- Stephan.
--
Carpe diem!

bubblespeak (1)

Rares Marian (83629) | more than 13 years ago | (#435512)

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.

What makes a good /. story!!?? (1)

gargle (97883) | more than 13 years ago | (#435514)

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???

Re:Things are not as easy (1)

Hinrich (99718) | more than 13 years ago | (#435515)

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-)

RTS (1)

Lozzer (141543) | more than 13 years ago | (#435521)

"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...

open source vs. big corporation? (1)

C-Automaton (143133) | more than 13 years ago | (#435522)

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?

Wow (1)

SupahVee (146778) | more than 13 years ago | (#435524)

That is truly amazing, and hats off to the guy.

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.... :-)

What about the speed at which this happened? (1)

gimple (152864) | more than 13 years ago | (#435525)

So, the genome wants to be free. I probably buy that.

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.

Open source science (1)

Zara2 (160595) | more than 13 years ago | (#435528)

This is great. Open source science at the start of a new dicipline. No catching up with the big boys now. The first gene map as public knowledge without any corperate strings or eula's stamped on your babies ass because you didnt want it born blind. This is the most promising news for the future that I believe I have ever seen. I'll be spending the rest of the day in hope for a better tomorrow for my children.

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.

Re:What about the anti-genetic backlash? (1)

Zara2 (160595) | more than 13 years ago | (#435530)

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.

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. [purefood.org] Also farmers must spend a lot of money on pesticides [purefood.org] 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.

Re:10 KLOCs assembler?! (1)

jayfoo2 (170671) | more than 13 years ago | (#435533)

Read the article again. It's a program that assembles the data, not a program written in assembly language.

Re:Things are not as easy (1)

testpoint (176998) | more than 13 years ago | (#435534)

...the public Human Genome Project had actually finished its work three days before the private effort by Celera Genomics...

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.

What about the quality of assembly? (1)

oingoboingo (179159) | more than 13 years ago | (#435535)

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...

Is it Assembly? (1)

wren337 (182018) | more than 13 years ago | (#435536)

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 just don't understand!? (1)

zipC (194873) | more than 13 years ago | (#435538)

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?

Can we establish a society to honor these people (1)

linzeal (197905) | more than 13 years ago | (#435539)

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

Re:10 KLOCs assembler?! (1)

micromoog (206608) | more than 13 years ago | (#435540)

OK, so maybe that was a little too dry. Lemme try again:

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 ;) ;) ;) ;) ;)?

Real Programmers (1)

PHAEDRU5 (213667) | more than 13 years ago | (#435544)

For some reason, it feels right to post this [pbm.com] .

What is interesting is that .. (1)

RedLaggedTeut (216304) | more than 13 years ago | (#435546)

the fellow found the time and interest in genes to do that.

While we spent 8 hours a day sequencing slashcode

Re:Time to pay up (1)

Linux2Mars (219853) | more than 13 years ago | (#435547)

Hey you! Stop using that nose! I have a patent for it!

Time is DNA...I mean money

Time to pay up (1)

alen (225700) | more than 13 years ago | (#435548)

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.

Re:What about the anti-genetic backlash? (1)

Tr15 (230470) | more than 13 years ago | (#435550)

"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.

Congratulations Hamilton Smith! (1)

selan (234261) | more than 13 years ago | (#435551)

A few years ago, the Baltimore Sun [sunspot.net] 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 [northernlight.com] .

"Stone Soup"? (1)

NineNine (235196) | more than 13 years ago | (#435552)

Does anybody want to explain to me what "stone soup" is...?

Some facts were out of place it seems (1)

ishrat (235467) | more than 13 years ago | (#435554)

"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 [the-hindu.com] than what was believed at the time of gene mapping last year."

Re:the dude in question? (1)

gwizah (236406) | more than 13 years ago | (#435555)

Looks slightly Kazincky-ish does he not?

could a distributed parallel system be useful? (1)

kipple (244681) | more than 13 years ago | (#435559)

"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.

South Park ? (1)

Alistair Graham (254201) | more than 13 years ago | (#435560)

now we can make humans with 5 asses

Re:What about the anti-genetic backlash? (1)

jeff13 (255285) | more than 13 years ago | (#435561)


"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

G vs. E (1)

jeff13 (255285) | more than 13 years ago | (#435562)


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? ;p

______
jeff13

Re:Things are not as easy (1)

chemicalwarfare.org (256864) | more than 13 years ago | (#435564)

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.

Re:Grad Student? (1)

chemicalwarfare.org (256864) | more than 13 years ago | (#435565)

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?

more on human genome project (1)

lou2112 (265869) | more than 13 years ago | (#435569)

for more information on of the nutritionists involved with the human genome project, check out a profile of Jose Ordovas [tufts.edu]

Re:more on human genome project (1)

lou2112 (265869) | more than 13 years ago | (#435570)

crap. messed up the link... try this [tufts.edu]

Re:Grad Student? (1)

togilvie (303940) | more than 13 years ago | (#435572)

No, but it doesn't make it wrong either.

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

Re:Grad Student? (1)

Bobo the Space Chimp (304349) | more than 13 years ago | (#435573)

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.

again cerebral diarrhea (1)

ooze (307871) | more than 13 years ago | (#435574)

Assumed the sequence is known.
Then we have the full .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.
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.

Re:again cerebral diarrhea (1)

ooze (307871) | more than 13 years ago | (#435575)

I just wanted to point out, how hard it is to understand complex systems.
Even though we created it, we are not able to completely understand things like market, traffic dynamics or the American elections. We are only able to give some rules of thumb, which often apply, but regularly fail.
I don't think all influences are already even thought of. Or can the influence of slight changes in the gravitation field of the earth by the rotation of the moon be excluded as a trigger of some genes? And I don't mean as the single trigger for a special gene. Or maybe not a trigger but a increase in likelyhood of a gene being triggered?
When data representation is that complicated, what about code?

Re:Thank god for James Kent (1)

rincefysh (309635) | more than 13 years ago | (#435576)

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!

Re:What about the speed at which this happened? (1)

rincefysh (309635) | more than 13 years ago | (#435577)

I agree - extra funding was supplied to HGP because of Celera.

However a key point to take into account is that it's not yet finished. The actual expected date of "finished" sequence is, as far as I know, not too far off the original estimate. They key thing that has changed has been going from "churn it out in high-quality finished data" mode to "churn out a rough draft and tidy up later" mode. The second strategy was employed mainly to prevent patents.

Re:Grad Student? (1)

Dimensio (311070) | more than 13 years ago | (#435578)

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.

Re:Actually... (1)

Dimensio (311070) | more than 13 years ago | (#435579)

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?"

Re:Grad Student? (1)

whanau (315267) | more than 13 years ago | (#435583)

what does it matter how old he is
obviously got more skills than u

Re:G vs. E (1)

dave1791 (315728) | more than 13 years ago | (#435585)

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.

That does not really matter. Genetic research (or any cutting edge non-theoretical biology work) is expensive, expensive, e... well. Just doing the molecular biology equivalent of "Hello World"; say, adding the Lux Operon from squid to e-coli to make them glow in the dark (I am not kidding, this is in an undergrad molbio textbook) can set you back $500 just in consumables (culture media, custom primers, restriction enzymes, etc.). If Celera does not charge too much, Universities and Firms will liscence their map and use along with the "public" one. Having more than one map is like having more than one search engine.

Re:Actually... (2)

CaseyB (1105) | more than 13 years ago | (#435590)

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.

Grad Student? (2)

sql*kitten (1359) | more than 13 years ago | (#435591)

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.

Re:10 KLOCs assembler?! (2)

Lars Arvestad (5049) | more than 13 years ago | (#435593)

"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
__

This guy's my hero (2)

ch-chuck (9622) | more than 13 years ago | (#435595)

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?

Re:Grad Student? (2)

Pig Hogger (10379) | more than 13 years ago | (#435596)

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.

--

Re:What about the anti-genetic backlash? (2)

Pig Hogger (10379) | more than 13 years ago | (#435597)

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.

--

Re:Grad Student? (2)

geophile (16995) | more than 13 years ago | (#435601)

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.

Reminiscent of something (2)

noims (23711) | more than 13 years ago | (#435605)

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

Re:About patents, useful link (2)

Fluffy the Cat (29157) | more than 13 years ago | (#435606)

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.

Re:again cerebral diarrhea (2)

Fluffy the Cat (29157) | more than 13 years ago | (#435607)

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.

Thank god for James Kent (2)

Barbaq (31353) | more than 13 years ago | (#435608)

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.

Re:Gene Patents value overhyped? (2)

SpinyNorman (33776) | more than 13 years ago | (#435609)

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.

Re:Grad Student? (2)

K8Fan (37875) | more than 13 years ago | (#435611)

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.

Re:Grad Student? (2)

K8Fan (37875) | more than 13 years ago | (#435612)

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.

Re:could a distributed parallel system be useful? (2)

K8Fan (37875) | more than 13 years ago | (#435613)

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.)

And now for some karma whoring... (2)

rweir (96112) | more than 13 years ago | (#435617)

the reg-free link is here [nytimes.com]

Actually... (2)

Steeltoe (98226) | more than 13 years ago | (#435618)

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

Re:Grad Student? (2)

Peter Simpson (112887) | more than 13 years ago | (#435619)

His home page. He certainly looks the part. http://www.cse.ucsc.edu/~kent/

I wonder... (2)

glebite (206150) | more than 13 years ago | (#435629)

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!

10 KLOCs assembler?! (2)

micromoog (206608) | more than 13 years ago | (#435630)

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?

Re:Grad Student? (2)

madro (221107) | more than 13 years ago | (#435631)

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 ...

Re:Jim Kent's Home Page (2)

mojo-raisin (223411) | more than 13 years ago | (#435632)

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.

Jim Kent's Home Page (2)

mojo-raisin (223411) | more than 13 years ago | (#435633)

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.

Software Written by a Single Programmer is Great.. (2)

Schwarzchild (225794) | more than 13 years ago | (#435634)

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."

Re:What about the anti-genetic backlash? (2)

sharkticon (312992) | more than 13 years ago | (#435638)

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.

Re:What about the anti-genetic backlash? (2)

sharkticon (312992) | more than 13 years ago | (#435639)

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.

Re:What about the anti-genetic backlash? (2)

sharkticon (312992) | more than 13 years ago | (#435640)

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...

It's not like going to a shop is it? (2)

sharkticon (312992) | more than 13 years ago | (#435641)

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.

Re:What about the quality of assembly? (3)

Lars Arvestad (5049) | more than 13 years ago | (#435642)

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
__

Re:Grad Student? (3)

Fluffy the Cat (29157) | more than 13 years ago | (#435644)

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.

Re:Grad Student? (3)

K8Fan (37875) | more than 13 years ago | (#435645)

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.

Human Genome Data Assembled on Linux Cluster (3)

tlunde (38528) | more than 13 years ago | (#435646)

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;
}

Re:Things are not as easy (3)

wowbagger (69688) | more than 13 years ago | (#435647)

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.

Re:could a distributed parallel system be useful? (3)

OctaneZ (73357) | more than 13 years ago | (#435648)

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

An assembly program, not assembler code... (3)

thue (121682) | more than 13 years ago | (#435651)

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...

About patents, useful link (3)

Leon Trotski (259231) | more than 13 years ago | (#435653)

"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

How is that fair? (3)

sharkticon (312992) | more than 13 years ago | (#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.

What about the anti-genetic backlash? (3)

sharkticon (312992) | more than 13 years ago | (#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.

Possible Slashdot interview?? (4)

moonboy (2512) | more than 13 years ago | (#435657)



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


His previous animation work (4)

jfoust2 (43840) | more than 13 years ago | (#435658)

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.

Re:Grad Student? (4)

KaRll (136503) | more than 13 years ago | (#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.

Re:What about the anti-genetic backlash? (4)

Zara2 (160595) | more than 13 years ago | (#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

Gene Patents value overhyped? (4)

Alien54 (180860) | more than 13 years ago | (#435661)

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.

Things are not as easy (5)

jw3 (99683) | more than 13 years ago | (#435663)

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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