Venter's DNA Major Source of Celera's Database 134
dh003i writes "According to this article, Dr. Craig Venter's DNA is the major source of Celera's database of the human genome. Interesting stuff." Includes interviews with lots of aggravated geneticists.
Wow, another NYT story. (Score:1, Troll)
Re:Wow, another NYT story. (Score:1, Insightful)
Re:Wow, another NYT story. (Score:2)
Re:Wow, another NYT story. (Score:1)
Is it that hard to fill out a form with fake information, or even, God forbid, your real name??!
NYT is your friend, and the friend of fnork33qz (Score:1)
For a long time, the login name "password" worked with the password "password".
Just don't give any accurate information. You make $200,000 to 300,000 per year, remember?
Set Mozilla or Opera to throw away cookies on exit.
The quality of the articles is excellent. Probably the best newspaper writing in the United States for any stories that don't involve Jewish interests. Then there is conflict of interest.
You must be Jewish... (Score:1)
You must be Jewish, seeing anti-semitism in what I said. I said it was the best newspaper in the U.S.
Re:Wow, another NYT story. (Score:1)
No worries... (Score:1)
Just use the Random NY Times Registration Generator [majcher.com].
How many people is this really a problem for, anyway? I can understand that college students don't necessarily have the advantage of cookies, but everyone else? I filled out a fake account, ONCE, and I never have to re-enter it here, unless of course I install a new browser (/me hugs Mozilla 1.0).
Re:Wow, another NYT story. (Score:1, Offtopic)
You know you're on to something, when the moderation is so ambiguous. Hehehe...
Doesn't suprise me in the least (Score:1, Insightful)
I'm going to guess these people will be shunned by the rest of the research community, though no light will be shed on these acts. Monetary motivation is needed to keep innovation at its current rate (look at the drug companies for god's sake), but this has to be the best place in the world to point out a case in which the freedom of information sharing is most successful- open source! I believe eventually we will see a splintered scientific community based on the open source premise of sharing, and it will evolve something similar to what we know as the open source movement today.
Re:Doesn't suprise me in the least (Score:3, Interesting)
Huh? How bout your example of drug companies... whatever it is that they need, it isn't money.
Sorry, but in many cases, those who truly love what they do, do it for alot less. There are days, that a $100,000 grant to some unknown researcher in a backwater university, is worth $10 billion in pharmcorp capital.
What the world needs, is fewer greedmongers and profitsluts. This reminds me too much of the current intellectual property fiasco, where the RIAA claims that if they only have $5 billion in sales, instead of $6 billion, they'll starve and no music will ever be recorded again for the next 1000 years.
Re:Doesn't suprise me in the least (Score:1)
What? No. Unlike in the private sector, when a professor is at a university long enough, he/she gets tenure. Just because someone was hired 10 years ago by a certain university doesn't mean their work is still up to the same standard. Or maybe they were hired because they were working in a hot area which has since fizzled. I know of plenty of scientists who are "one-trick ponies" and they've gotten tenure in a short time. Ten years from now I'd put my money elsewhere. Furthermore, smaller universities do not necessarily get the leftovers of larger universities. When a scientist is offered a position from multiple institutions, there are many factors to consider besides the size or prestige of a university. Smaller universities that are trying to grow in a certain area tend to give much larger startup packages than universities with more established programs. Sometimes a professor will move to a smaller university because he is offered a position as a chairman. Or sometimes people factor in location or who their colleagues will be. It's more complicated than you make it out to be.
Re:Doesn't suprise me in the least (Score:2)
Yes, some profitable companies innovate. Some unprofitable ones do too. Some companies don't innovate at all... do you not think that the executives are running around like retarded little millionaires screaming "Innovate for profit!" ? Whatever inspires the genius that does the work, it isn't the big profits that he'll see... likely, he won't see much of that. Profit as an innovation motivator is a lie.
Re:Doesn't suprise me in the least (Score:2)
Using "costs" as a counter-argument to my comment is
But I'm feeling generous. Let's argue what you want to argue. Expense... the thing morons like yourself always fall back on. Money isn't an abstraction of gold, or pearls, or industrial raw materials. It isn't the gameboard tokens of the rich and powerful. In its most honest, and least evil state, it is simply an abstraction of work. I get a paycheck, as a literal translation of the work I performed.
In which case... those thousands of man hours of labor ARE money. So including the word "paid" in there is circular.
Re:Doesn't suprise me in the least (Score:2, Insightful)
1. Their product is in high demand (if you're dying of cancer, you really don't care how much the anti-cancer drug costs).
2. Their product is scarce (how many people are there that have the skills necessary to make that drug?).
3. Their work is distasteful - trash haulers are paid disproportionately in light of the skill necessary, and conversly musicians tend to be underpaid relative to their skills (probably because the work is so enjoyable).
If any or all of the above are the case, the costs of the product will be high to pay the various wages involved. You can try to legislate the cost away, but everyone is at heart a capitalist. People will move to where the capital is. If you take the money out of a job, the most talented and entreupenurial will move elsewhere.
As far as people not being motivated by greed goes - you're mostly right. However, the fact is there are a lot of things I'd like to do with my life, and money is the only reason I'm not doing them. I enjoy the job I do right now, but it also pays well, so if opportunities to do other enjoyable things come up I'll probably turn them down unless they pay equally well. Money isn't the only reason I'm where I am, but it is a strong reason.
And as far as the Marxist proposition that your pay is simply an abstraction of the work you perform goes - that's just silly:
I can sprint around my back yard until I pass out from utter exhaustion. In one sense I may have done more work than I do all week at my job, but nobody is going to pay me for it.
Money is simply a measure of value. If somebody values your labor they will give you money for it. Money forces us to prioritize our buying and our labor. We are free to do whatever we want, but labor spent on tasks of no value to anyone will not be rewarded.
I bought a house, and I value the bank's money, so I give them some of my money over time in exchange for their giving me their money up front. In my opinion, their lump sum up front is worth more to me than the larger sum I forfeit over time, because I have opportunity to use their money now that I would lose if I waited until I could save up the whole sum.
Capitalism is a win-win. If a person pays $50 for a pill, it is because the pill is worth more to the recipient than $50, and the $50 is worth more to the seller than the pill. If you don't think it is worth $50, then don't pay for it - you'll probably still live longer than people did 100 years ago.
Other systems don't work, because they depend on citizens accepting a governmental body's system of values. If you pay everyone the same, you have to then use force to compel them to perform the tasks you want them to. And who gets to be the one who decides what has value? Capitalism requires only freedom to thrive.
Re:Doesn't suprise me in the least (Score:2)
I don't know whether to laugh or cry. Sure, as someone who has sucked on the teat of capitalism all his life, it seems like a neat system. Hell, I'll grant you that it's nice, even in aa reasonably idealized state... something that if it ever existed at any time in history, it was a very brief.
Capitalism isn't win/win. Tell that to the people dying in third world countries, because drug companies have to protect their intellectual property. Capitalism has several advantages, I'll grant you, but needs to be heavily regulated, so that it doesn't squash people whose only crime is being born in the wrong country. Capitalism is completely amoral, and is only tolerable when we leash it with our own morals. I'm tired of retards worshipping it, like you do.
Do you honestly think I like communism? Or any of the other failed economic systems that you can dredge up from history? You must not want something better. You seem to think this is the pinnacle of human endeavor.
Re:Doesn't suprise me in the least (Score:1)
You just insulted him for saying capitalism is good, and insisted the only reason he said that is because he hasn't experienced anything else.
Then you tell *him* to come up with a better system?
If you don't like communism, but capitalism is to blame for all of the world problems, what system *do* you propose we use?
You have yet to give an example of a system better than our current one for giving people a motivation to spend thier time on R&D. So far you have insulted 3 people for being moronic in defending capitalism, and provided nothing but the argument "inovation isn't driven by money", well people are more likley to attempt to inovate (generally a prerequisite for inovation) if they are getting paid, otherwise they would probably spend all thier time doing other things to get paid.
Capitalism is an effective system. If we were a comunist country (or whatever) there would probably still be people dying in 3rd world countries, because thier average person would be worth less than ours, so our 'overpriced drugs' would be used on us first. If you would like to propose a economical and politcal and social system that will solve these glaring problems, I'd love to hear it.
Calling everyone else a troll is an easy option, but I haven't seen you do anything but troll so far.
Re:Doesn't suprise me in the least (Score:2)
Maybe the problem itself, is that everyone feels they have to have a "system". In this context, there is no better system, they are all flawed (maybe in some cases, capitalism less than others). For things to get better, and I honestly believe this, people have to learn that maybe capitalism isn't the greatest, and that they shouldn't defend it for no other reason that it's what they're used to. They have to learn, and this truly is learning, that innovation isn't driven by money. Honest to god, did humans, or did they not, innovate the most before the concept of money was ever invented?
I propose that you abandon capitalism as a religion, and that you only keep it around as a dangerous tool to be distrusted.
Remember, calling it effective means very little. Effective at what? Hitler was effective at exterminating jews, though I don't believe this was a good thing.
Re:Doesn't suprise me in the least (Score:1)
It is effective because it leads to R a socialist society that gave benifits for doing research would be just as effective, but it would be less effective at other things. It leads to companies wanting to inovate, and when companies want to inovate, people want to become inovators so they can get paid. This leads to more people trying to inovate, so it's not just curiosity driven learning (which is highly effective, but it isn't effective as curiosity driven inovation happening at the same time as corperate idea churning).
Capitalism has nothing to do with IP rights, so that shouldn't even be part of this discussion. Capitalism leads to trade secrets, and our scociety leads to IP, but capitalism does not lead to IP.
There is no 'capitalism is god' religion outside of washington, and morons. But most of the morons are also willing to believe anything the media feeds them. Most people (especially here) are well aware of capitalism and its flaws, but at the same time, it is a fact that it *works*, and so far no other system for a country our size has been proposed that would work.
Re:Doesn't suprise me in the least (Score:2)
Sure it works. It works as well as my car does, when I'm driving down the shoulder on a flat, ruining the rim. It's a bumpy ride, it makes me nervous, and it causes damage that just isn't going to be fixable. This level of "but it works" just isn't impressive enough to warrant the kind of devotion people like you have to it.
Oh well. I gotta go try to teach quantum dynamics to chimpanzees now. Much more rewarding, they may actually understand what I'm talking about.
Re:Doesn't suprise me in the least (Score:1)
What is your proposed system of economics? I still haven't heard it. I don't follow capitalism like a religion, but I know it's the best system for a society of our size. If I'm wrong I want to hear why, not "why are you so quick and adamant to defend it".
The fact I defend it is not an argument against it being effective.
Re:Doesn't suprise me in the least (Score:2)
I claim to not know what the best system is, and you accuse me of being religious? All I know, is that it could be alot better, and that it is flawed enough (capitalism that is) that it worries me.
Effective? Effective is a word that is meaningless by itself. As in, you can only be effective AT SOMETHING, not plain EFFECTIVE. What is it that you're trying to imply that you think is so damn obvious? The only thing capitalism is effective at, is indoctrinating fools like you, and making the poor poorer.
Re:Doesn't suprise me in the least (Score:1)
you have the last word...
none the less your still wrong
Re:Doesn't suprise me in the least (Score:2)
Turn off sigs, for Christ's sake, if it bugs you that much.
(Take off every sig, for great justice?)
For those who wish not to register (Score:4, Informative)
By NICHOLAS WADE
When scientists at Celera Genomics announced two years ago that they had decoded the human genome, they said the genetic data came from anonymous donors and presented it as a universal human map. But the scientist who led the effort, Dr. J. Craig Venter, now says that the genome decoded was largely his own.
Dr. Venter also says that he started taking fat-lowering drugs after analyzing his genes.
Reactions among scientists range from amusement to indifference, most saying that it is unimportant whose genome was sequenced. But members of Celera's scientific advisory board expressed disappointment that Dr. Venter subverted the anonymous selection process that they had approved.
Dr. Venter, a pioneer in the use of new DNA sequencing machines, challenged the government-supported effort to decode the human genome and held his academic rivals to a draw in June 2000, despite starting years later in the race.
Both teams said their DNA sequence was based on the DNA of anonymous donors, with Celera's being drawn from a pool of 20 donors from 5 ethnic groups. But in an interview this week, Dr. Venter elaborated on his brief mention on "60 Minutes II" on April 17 that the Celera genome was based principally on his DNA.
In making this known, he has abandoned his genetic privacy in the most thorough way possible, even though for now only subscribers to Celera's genome database can browse through his genetic endowment.
Though the five individuals who contributed to Celera's genome are marked by separate codes, Dr. Venter's is recognizable as the largest contribution. He said he had inherited from one parent the variant gene known as apoE4, which is associated with abnormal fat metabolism and the risk of Alzheimer's, and that he was taking fat-lowering drugs to counteract its effects.
Dr. Venter's reason for having his own genome sequenced, he said in an interview this week, was in part scientific curiosity -- "How could one not want to know about one's own genome?" -- and also a sense of responsibility that because he was asking other people to donate tissues, risking invasion of their genetic privacy, he should be first in line.
He did not make this known at the time, he said, "because I didn't want it to be the issue or the focus."
"Now, after the fact," he said, "I don't think it matters."
As to opening himself to the accusation of egocentricity, he said, "I've been accused of that so many times, I've gotten over it."
The academic consortium expressed no great emotion at the news that their rival had sequenced his own genome.
"That doesn't surprise me; sounds like Craig," said Dr. James D. Watson, the co-discoverer of the structure of DNA. Dr. John Sulston, former director of the Sanger Center in England, said, "It doesn't have any great significance." Dr. Francis Collins, director of genome research at the National Institutes of Health, declined through a spokesman to comment.
But members of Celera's scientific board of advisers expressed regret that the process they had approved for choosing anonymous donors had been subverted.
"I think the original idea, to keep everything anonymous, was not a bad one," said Dr. Richard Roberts, scientific director of New England BioLabs and a board member.
Another member, Dr. Arthur Caplan, a biomedical ethicist at the University of Pennsylvania, said, "Any genome intended to be a landmark should be kept anonymous. It should be a map of all us, not of one, and I am disappointed if it is linked to a person."
The drive to sequence the human genome was an opportunity for personal glory as well as scientific discovery, and Dr. Venter's action emphasized the first motive, Dr. Caplan said.
It seems that Celera's intended process of choosing randomly among anonymous samples must have been overridden at some stage so that Dr. Venter's became the one selected. A Celera spokesman, Robert Bennett, would not confirm or deny Dr. Venter's claim and declined to make available Dr. Sam Broder, the company's vice president for medical affairs, who oversaw the donor selection process.
Dr. Venter, however, said that "I made the selection with a team," and that "only me and two other people" know the codes to Celera's five donors.
Because the human genome decoded by the academic consortium is a mosaic of different individuals, Dr. Venter is at present the only person whose genome has been largely sequenced, and may remain so for many years. In his person, he offers a unique way to connect a human genotype with its phenotype, as biologists refer to a genome and the physical form it specifies.
Is his body now particularly valuable to science? "You mean for dissection?" Dr. Venter said. "I haven't thought that far ahead. You have given my critics a chance to dissect me."
Dr. Norton Zinder of Rockefeller University said he saw some value in less drastic investigations to study the link between Dr. Venter's genotype and phenotype. "You would have to do experiments on him," Dr. Zinder said. "Craig would become an experimental animal. He's certainly made himself liable for that."
But Dr. Kenneth Kendler, a psychiatric geneticist the Virginia Institute for Psychiatric and Behavioral Genetics, said that science was not advanced enough to read off a person's personality from their genome and that, as a sample of one, Dr. Venter and his genome were not of much help to scientific inquiry.
The same verdict came from Dr. Stephen Warren, editor of the American Journal of Human Genetics.
"I think it's of much more interest to him to know his genotype than for other geneticists to know it," Dr. Warren said. But he praised Dr. Venter's drive and ambition for forcing the public consortium to speed its efforts.
As for the idea that Dr. Venter's body should somehow be preserved along with his genome, Dr. Warren said, "That would be his wish, no doubt, to be prominently displayed in the Smithsonian."
Re:Hey Taco (Score:1)
Re:For those who wish not to register (Score:1, Funny)
does this really matter? (Score:2, Insightful)
Re:does this really matter? (Score:1)
Creepy Scientist (Score:3, Insightful)
Kinda reminds me of that fertility doctor in Florida that artificially inseminated all of his patients with *his own* sperm....
Re:Creepy Scientist (Score:1)
I can't wait til 5 years from now... (Score:3, Funny)
Re:I can't wait til 5 years from now... (Score:1)
Re:I can't wait til 5 years from now... (Score:2)
very disappointing (Score:3, Insightful)
On another related semi-off topic note, I am sick of listening to people complain about NYT articles and registration. One of the most influential newspapers in the world is giving you free daily access to their articles and all they require is some bogus registration info. Sheesh, stop whining already.
Re:very disappointing (Score:5, Insightful)
Nonetheless, I can understand the loss of trust some shareholders and collaborators might be feeling. Dr. Venter acted dishonestly and in direct violation of the instructions given him. This does not speak well of his character.
On the other hand, it seems he spearheaded one of the most significant scientific expeditions of our time, and on a very impressive schedule. Maybe a little eccentricity is manageable given the results. Each shareholder and colleague will have to determine for themselves their tolerance for this sort of thing.
As an aside, a few years back I was lucky enough to work with some excellent geneticists, neuroscientists, and neurologists in the field of Parkinson's disease. In order to reach the highest levels of their profession, these folks have had to jump through many hoops related to funding, collaboration, and peer review. Justly or unjustly, they tend to be very proud of their accomplishments with egos to match. I think it's something you have to learn to deal with if you want to play the game at this level.
Re:very disappointing (Score:4, Interesting)
The stakeholders should not complain about from whom the genome came form, but instead that the data generated is uncertain. I mean.. a scientific experiment with only one source, which was until now even not known to the public (or stakeholders).
Re:very disappointing (Score:1, Informative)
They did at least a 6x oversampling of the whole genome and are still in the process of assembling the fragments to contigs. They are also using their mouse genome data (two strains) to assist in the assembly of the human data and vice versa.
The celera effort is as serious as the public one.
Re:very disappointing (Score:1)
In the end there is no gnome map. There is this sciencist map. My family tree has not been included, so any guess of the meaning of this data to my family is nill.
Re:very disappointing (Score:2)
Nope, even the article itself says they used 6 people's DNA to build the genome. Dr. Venter is just the biggest contributor.
Cheers,
-j.
down with genome (Score:2, Funny)
What?! Ooops! Wrong forum for flaming. Oh well!
Ethical Indicator (Score:1, Insightful)
But sequencing the human genome is an inherently research oriented venture. When research opens entirely new areas of human knowledge, the laws cannot possibly contain sufficient information to guide a person or company's actions; as a result, pure commerce orientation is insufficient to produce the optimal outcome. This is why pure scientists and pure science institutions have to be ethical. They have to understand that new science is capable of actions that the market and the law aren't prepared to handle.
Reactions among scientists range from amusement to indifference, most saying that it is unimportant whose genome was sequenced.
The problem I see with Venter's act is not the effect on the information gathered. The problem is that it suggests (at least to me) deep ethical problems. I'm commercially oriented, but I have many friends who are researchers. There is not one of them who would be capable of even forming the concept of using his or her own DNA as the dataset for the project. IMHO, that is a fairly important qualification for being a pure scientist.
Addendum: In previewing this comment I am struck with the impression that pure research and monopolies require ethical inhibitions for the same reason. They are both capable of altering the course of the free market, so the free market cannot be an accurate guide. (too lazy to figure out where this fits into the above
Advisory boards (Score:5, Insightful)
If this revelation leads us a step closer to Federal regulation of just about everything to do with Genetic technology, you can thank this guy.
Why this may be (Score:2, Interesting)
Or perhaps- if you were dedicating several years of your life to a project, wouldn't you want it to be YOU that was the basis for all furtherment of human medical understanding of genetics? (tradition usually uses the wife, but that gets icky in medical related stuff)
That or pure unabashed ego.
He should bequeath his body to the Visible Man (Score:1)
(think scanned sliced cadaver, put back together in 3D on computer; you can play Descent in the veins etc..)
Re:He should bequeath his body to the Visible Man (Score:1)
Hmmm... (Score:2, Interesting)
Another Corp. stealing from Open Source (Score:1)
In fact, I would go so far as to predict that the DNA Craig claimed was his turns out to have been Francis Collins's (Head of National Human Genome Research Institute) DNA.
Re:Another Corp. stealing from Open Source (Score:1)
I agree that a physical map of the genome is helpful, but the purpose of the shotgun method is to bypass this step, which allows for a significantly faster sequencing timeframe. The fact that the random clones overlap is of significant statistical significance. You have A, C, T, and G, and when you have a clone, match up with another clone on the order of 40 or more base pairs, the number you get is astronomically large (4^40). I also find it interesting that the supercomputer that assembled the genome was running on Alpha CPU's, running Tru64 UNIX
Re:Another Corp. stealing from Open Source (Score:2, Interesting)
Well, I don't see any problem with Celera using the public data.
The problem is hypocrisy. When Celera was just gearing up to begin sequencing, I recall that Venter testified in front of Congress, claiming that the entire public effort was a waste of the taxpayer's money, and that the government should let Celera do the job alone, because it would do it much better and much faster.
As it turned out, Celera relied heavily on the existing public sequence to assist in their assembly (this is not an uncommon technique - but in light of that testimony, it smacks of hypocracy).
The analogy with open source software is a good one, in light of the company's attempts to patent gene sequences from their assemblies (see previous slashdot articles on this)
Re:Another Corp. stealing from Open Source (Score:1)
"One method invloves the computational combination of all sequence reads with shredded data from GenBank to generate an independent unbiased view of the genome. The second approach involves clustering all of the fragments to a region of chromosome on the basis of mapping information. The clustered data were then shredded and subjected to computational assembly. Both approaches provided essentially the same reconstruction of assembled DNA sequence with proper order and orientation. The second method provided slightly greater sequence coverage and was the principal sequence used for the analysis phase."
Celera could have done the job alone. If the Whole Genome Shotgun Assembly (WGA) method "failed", how is it that a comparable genome (in terms of size), the Mouse, was assembled without any public data? Furthermore, with the recent announcement of the Rice Genome(s), they too were sequenced and assembled using the WGA method.
Re:Another Corp. stealing from Open Source (Score:1)
Celera could have done the job alone
Believe me, both Venter and his computer hotshots spent plenty of time developing their techiques and expertise with public funding. They just didn't pop up out of a vacuum; their research was extensively funded by NIH, DOE, etc.
Re:Another Corp. stealing from Open Source (Score:2, Insightful)
Oh, I suppose you feel that it was a race, and that since one of those horrible FOR-PROFIT companies was working on the same thing, then everyone EXCEPT them is allowed to see and work with the data.
It shouldn't come down to "for-profit companies vs. publicly funded research". There is a strong symbiotic relationship between business and public research, especially in molecular biology these days. Both need each other, and we all benefit from this relationship.
There are many, many, many examples of business providing products and services for research groups, far more cheaply than those groups could themselves provide (i.e restriction enzymes, oligonucletide synthesis, sequencing machines, etc). Research is thriving now because of these developments. Our standard of living is very high because of these developments, and it continues to improve.
At the same time, its important for businesses to recognize that publicly-funded research is a goose that has laid and continues to lay golden eggs for new business opportunities, and therefore it should not be killed. On the contrary, it should be nourished to keep it thriving. It drives me berserk when some personality makes some short-sighted recommendation to reduce (or even eliminate) public funding for research, and just let for-profit companies do everything, because the economic health of those companines (and therefore, our lifestyle) depends on a vibrant public research program. It drives me beserk because that kind of ignorant short-sightedness threatens our well-being in the long term.
Alternate to registration (Score:2)
Bye bye Nobel Prize... (Score:1)
On his scientific merits alone, I believe he should be in the running for a Nobel Prize at some future date. This admission, however, isn't really going to look all too good on his resume.
Personally, I think I would have liked my genome to be sequenced, but because this was the first time it was done in history, I don't think it would have been beneficial to society if they knew it was *my* genome.
amusing week ahead (Score:1)
It's his work. (Score:3, Informative)
Besides, scientists have always had a history of experimenting on themselves: Newton died of mercury poisoning from his experiments, Kevin Warwick [kevinwarwick.org] has been having chips implanted in his body, and where do you think Antony van Leeuwenhoek [berkeley.edu] got the sperm he observed under his microscope?
Re:It's his work. (Score:3, Interesting)
Re:It's his work. (Score:2)
barnes and noble [barnesandnoble.com] and amazon list it as out of print. most college libraries seem to have a copy :-)
Re:It's his work. (Score:1)
http://www.psychedelic-library.org/child.htm [psychedelic-library.org]
Beam his genome to Andromeda (Score:1, Offtopic)
Then the Andromedans will mix his genome with Andromedan genome and create a being that looks like an Andromedan fashion model but is actually an horrible monster inside
Not the end of days (Score:5, Interesting)
To me, as a undergrad majoring in molecular biology, this is interesting but not a disaster.
All of us are for the most part almost completely identical at the genetic level. More than 99.99% of our DNA is probably the same. Most of the variation in our DNA is likely due to selfish elements and "junk DNA" where variation is irrelevant. When it comes down to what separates you from me from Dr. Venter, you'd be surprised that it might come down to a relatively few locations on the genome, and very subtle changes.
Of course, for those few areas where there is some variation in the human genome, this may be important. But how important? So his genome is *most* of Celera's database, as opposed to the genome of 5 randomly selected people. Having a sample of 5 individual's hardly gives due account to diversity in the genome anyways. Besides, much of our diversity is in things which don't matter from a medical point of view: what makes our eyes and hair different colors, our faces different shapes, and other superficial largely irrelevant differences.
An interesting benefit to Dr. Venter's bypassing Celera's random selection process may be that we may in some cases see how phenotype relates to genotype. For example, what exactly is it in Dr. Venter's genome which gives him that most hideous smile which makes him look like a poster for the movie, "The Clowns"? Seriously, there may be some interesting studies to be done, provided Venter is willing.
I'm not saying he did this for all the right reasons. It was, of courses, a selfish act. I think he did this out of eccentricism and curiousity about himself. Richard Dawkin's book is titled, "The Selfish Gene," not "The Benevolent Gene".
I'm not saying I particularly like Venter, or Celera. Celera indeed leached off of the public project, and could've never accomplished what they did without doing so. Also, the public project was headed by Crick. When Waston and Crick discovered the structure of DNA, they didn't hide it and make the world pay for it; they showed it to the world. That was the attitude of true scientists: Even Rosaline Franklin, who's work was used without her permission to determine the structure of DNA by Watson/Crick, wasn't bitter, and wanted the work to be published. I believe she said something along the lines of, "It doesn't matter. It's beuatiful." The discovery of the structure of DNA was made available to us all -- because that's the attitude of true scientists, and because its something that belongs to us all. Celera and Venter, however, have abandoned that tradition. On the bright side, Celera does offer public access to their database with a free registration. The payed-for access gives you a superior genome browser which allows you to find material much easier.
I believe that the essay in the beginning of Jurassic Park by Michael Crichton about the biotechnology revolution captures the essence of what I'm thinking of.
Re:Not the end of days (Score:2)
This was a bad move on his part purely because it shows him to be untrustworthy, even in a minor way. He should have been upfront with his advisory board. Now, on his next project, it will mean that the sponsors will take a more risk-averse attitude, and this may interfere with good science being done. But as you say, human DNA is human DNA.
Celera and Venter, however, have abandoned that tradition. On the bright side, Celera does offer public access to their database with a free registration. The payed-for access gives you a superior genome browser which allows you to find material much easier.
So what's the problem here? You've already paid for their rival's database through your taxes. Celera are true to the "open source" principle: give away the generic product for free (speech *and* beer), charge for the value-added services. I don't think even RMS could complain about that - and the people footing the bill are Celera's shareholders, not the ordinary taxpayer.
Hilarious (Score:2)
In short, I think this tells us nothing more than we already knew -- that Dr. Ventner has an ego the size of Texas. (And, luckily, the talent to go with it too).
-E
Re:Not the end of days (Score:2)
A final point- from what I've heard about patent coverage, both genome projects will see much of their potential for medicinal applications wasted because most of the genes are already spoken for by biotechs (and some universities, sadly). Now protein structures are being patented too. Makes me wish I'd been a history major.
Re:Not the end of days (Score:2)
The first few genomes give the basic outline - but the real payoff will be when we can easily sequence everybody's genome to be able to use an individual's genomic DNA as a diagnostic tool. This kind of technology is still a ways away and will require a much larger sample size to be interpretable in a meaningful way.
Re:Not the end of days (Score:2)
How can you make the assertion "Besides, much of our diversity is in things which don't matter from a medical point of view: what makes our eyes and hair different colors, our faces different shapes, and other superficial largely irrelevant differences" when the whole point of this exercise is to determine whether or not those "..superficial [and] largely irrelevant differences.." really "..don't matter from a medical point of view..."!!!
Re:Not the end of days (Score:2)
Granted, blue eye color (for example) may be linked with a certain disease because it may be close to that allele; however, to state that such things cause diseases is absurd.
Re:Not the end of days (Score:2)
I'm not saying that there is causality - I am saying that we undertook the project of mapping the genome precisely to find out if there is causality between a particular gene and disease. I don't think we know enough about side-effects of what we assume is an eye-color-only gene. It may have effects in other areas of the body. IIRC many genes regulate the synthesis of proteins that circulate throughout the bloodstream. These proteins may have far-reaching effects aside from the obvious "primary" effect (such as hair color, etc).
Parenthetically, I also find it absurd that 90% of the genome has been declared 'junk', just because we haven't found a purpose for it that we deem 'useful'. It could be there for something as simple as timing during transcription. I'd say waiting is a perfectly good use!
Re:Not the end of days (Score:2)
However, you run afoul in:
Selfish DNA. There's nothing absurd about it. The human genome is very sloppy, and most of our DNA is composed of various selfish elements, such as LTRs, retrotransposons, etc. Selfish elements for the timing of transcription? I assume your getting at the idea that that 90% of non-coding DNA is just there to slow down the cell cycle so it doesn't go too fast? That's laughable; that's like saying that if I'm riding a bike and want to slow down, I stuff a stick in the spokes, rather than press the brakes. There are mechanisms to make sure the cell cycle doesn't go by too quickly, as well as regulatory mechanisms. Its a stretch to think that the approach arrived at by evolution was to jam the replicative machinery by having 90% non-coding DNA.
You have to think about it in terms of selective pressure. Once a selfish element such as an LTR gets into our genome, it has the evolutionary advantage. The selective pressure on it to maintain itself in the genome is great; however, the selective pressure on the host (us) to remove it is minute because it has a marginal effect.
Re:Not the end of days (Score:2)
The timing example is just that, an example. I'm certainly not a geneticist, so naturally any example I think up is liable to be "laughable" and very simplistic.
I think we're violently agreeing! 8-)
Limited Input, Limited Output (Score:4, Informative)
While Celera's accomplishment may have gained *Press Acclaim*, and while it in some ways has validated the so-called "shotgun" sequencing technique (which has been around since before the days of Celera), Ventner and Co. didn't claim to have resolved the full sequences (and their variations between individuals) of the human genome as many are mislead to believe. Rather, Celera claimed to map the loci of human genes to the chromosomes (loci ~= regions that code genes). Further, it claimed to discover regions that are possible or even likely to be loci for genes not yet characterized, based on sequence patterns that are generally considered to be "flags" for gene loci. Given that loci characterize a set of alleles (allele ~= version of a gene, for example, you may have an allele that codes for connected earlobes, or disconnected earlobes, or both [ humans are diploid, meaning they recieve one allele form your father and one from your mother, barring crossing-over events, in which case you can recieve 2 alleles from either your father or mother exclusively]), and given that sequence patterns and homologies between species were mostly used to identify the loci, the fact that Ventner used Ventner's DNA seems an acceptable way to get a rough map of the gene loci, and Celera freely admits that further characterization is necessary to identify alleles, and to refine the definitions of the loci.
If you aim to sketch a rough outline of the gene locations, it really doesn't matter whose DNA you use to start it, because you anticipate that it will be refined with the DNA of others.
All of this has been thoroughly reviewed by genetisists the world over, and none of them to my knowledge are up in arms about this.
A popular misconception is that Celera accomplished in a short time what other bodies have failed to accomplish. Celera used a different approach to get a full rough outline of gene loci completed, whereas other researches have taken a step-wise approach to gain information about regions in greater depth. The rough outline in itself is a useful accomplishment, because it allows researchers to focus on areas of the genome that appear to affect specific genetic phenomena of interest, but it's not the key to the kingdom, and there is much work to be done even to characterize regions that *look* like they code for proteins, much less characterize genetic diversity amongst humans.
The Human Genome Project, which makes up the bulk of Celera's "competitors", uses a more elegant, and painstaking approach to sequencing DNA (relying heavily on a technique known as "primer-walking"). Their approach generally begins with the "shotgun" approach applied to moderately-sized regions to gain an outline, and then uses "primer-walking" down the assemblies to verify that they are correct, and to gain information about gaps in the assembly. In many cases, primer-walking validates shotgun sequence assemblies, but sometimes, it indicates errors. The process of validating sequence using this approach is more expensive, more time consuming, and absolutely necessary to refine the genetic map, and to obtain sequence information for certain "hard to sequence" regions of the chromosome.
If share holders want to worry about their investment in Celera, they should be think about the fact that genetic sequences have been declared "unpatentable" in the U.S., which makes Celera's real goal (making money) much more difficult.
Re:Limited Input, Limited Output (Score:1)
The ubiquitous PHB strikes again (Score:1)
In a related story.... (Score:2, Funny)
which gene? (Score:2, Funny)
Venter putting his neck on the chopping block (Score:1)
Major Source??? (Score:1)
Not exactly a surprise (Score:2)
we can finally isolate (Score:1, Offtopic)
maybe now... (Score:2)
Old news? (Score:2)
At last we finally have... (Score:1)