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Venter's DNA Major Source of Celera's Database
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.
Scientist Reveals Genome Secret: It's Him
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."
from what I can remember, the human genome, as is with all other living things, stays constant to the species, with minute mutations occuring here and there as a result of evolution. I really don't see a big deal. Guy got a big head and decided that he would make himself to be one really fat lab-rat, fine by me. Just as long as the research was completed.
Kinda reminds me of that fertility doctor in Florida that artificially inseminated all of his patients with *his own* sperm....
I'm a 2000 man.
It's just another scientist wanting his 15 minutes of fame - that's all.
Video Game cheats, hints a
"Monetary motivation is needed to keep innovation at its current rate" ...
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.
When we all learn it was a big practical joke, and that the genome that was sequenced actually belongs to Bubbles, Michael Jackson's pet chimpanzee. I mean, after all, there is what, less than 1% difference overall?
As a Celera stockholder (and a professional molecular biologist) I must say I am extremely disappotinted that the CTO would allow his own ego to get in the way of creating an unbiased, useful genome map, even taking into account the fact that it's probably irrelavent in the long run (i.e., his genome is probably fairly representative of the human populace in general). What does this say WRT any future projects that Celera might undertake? It seems to me that under Venter's direction such future projects may not utilize what science and ethics dictate.
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.
NO CARRIER
Down with Genome! I'll just use KDE for my desktop!
What?! Ooops! Wrong forum for flaming. Oh well!
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.
Same reason as including Easter Eggs in your software. Down the road, when you don't get paid, you have some proof that it is your code.
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.
~.~
I'm a peripheral visionary.
Um. I never mentioned "people", and I never implied it. I was referring to large institutions. Whatever it is that they have, that continues to "produce innovation" for them, it isn't the monetary motivation. I thought I made this point well, but you obviously smoke crack.
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.
I love ignorant trolls. Sure, you're obnoxious, but you're good for contrasting my intelligent posts.
... well, stupid. I was pointing out that profit as an "innovation motivator" is false. There is a correlation, but the cause of innovation is very rarely greed, if ever.
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.
Given that Celera's methodologies for genetic assay are currently the subject of fairly heated debate, I wonder if it makes any difference whose DNA is used.
As many as I like.
Turn off sigs, for Christ's sake, if it bugs you that much.
(Take off every sig, for great justice?)
Try this Yahoo link
Besides, scientists have always had a history of experimenting on themselves: Newton died of mercury poisoning from his experiments, Kevin Warwick has been having chips implanted in his body, and where do you think Antony van Leeuwenhoek got the sperm he observed under his microscope?
As a forenote, I'm the one who submitted this story.
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.
social sciences can never use experience to verify their statemen
Though the fact that Ventner relied heavily on his own genetic material certainly increases the chances for mistaken conclusions (given its being very limited input), but the results of Celera's "decoding of the genome" represent limited output by design.
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.
Scientists have used the sequenced geonome to find the gene for an overblown ego.
Pay no attention to the man behind the curtain with all your metadata.
Can somebody tell me which gene results in a giantic ego?
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
Send mail here if you want to reach me.
Over a year ago I read an interview with Venter where the journalist asked if his DNA was among that being sequenced. He implied that it was.
Maybe now he'll volunteer for immediate contribution to the visible human project. Hey, it's only fair.
There are many things that motivate things to do the things that people do. A person gets paid a lot if:
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.
Couple years back, when I was taking General Biology I my sophomore year, we saw some video about the Human Genome Project, where Venter said just this. Which makes this old news. Not like this matters, old news is a popular topic on slashdot. :P
Working toward a usable PDA environment in the spirit of Newton OS: Dynapad
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)
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.
Why don't people think, before posting?
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.
Pay attention, I'm not usually in a generous mood. If you have to reply, give it some thought first.
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.
You keep saying that it isn't your religion. Or anyone elses. If so, why are you so quick and adamant to defend it?
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.
Analyze your words carefully. You claim it's not your religion, and yet "I know it's the best system for a society of our size.". Sounds like faith to me, for something which is fundamentally unknowable.
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.