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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.
Now you can mod me offtopic, and I can wait for the comments, to try and glean what the article says...
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.
Just register ya morons.
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.
These guys just spread FUD to discredit Celera Genomics.
The DNA is not from Dr. Venter.
The DNA is from his dog.
Owner of a Mensa membership card.
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.
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 current moderator, I would like to know why there isn't a "Karma Whoring" selection? ;-)
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!
I'm a pretty serious economist (frequently mistaken for a capitalist), and I believe that non-monopoly commercial enterprises (or more specifically, any enterprise which is incapable of altering the free market) should not be constrained by ethics. Our laws should be the clear-cut guide that companies can follow without having to worry about what one board member or another feels is "right".
:)
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
Stop-Prism.org: Opt Out of Surveillance
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.
yes, you do
find a login generator at http://www.rds-clan.be/hermes/nyt.html
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.
It would be a further boon and gift to the world for him to bequeath his body to the Visible Man project once he heads off to that great bit bucket in the sky; in order to provide for a more complete data set. This would preclude dissection, which is kind of wierd to think about having done to you anyhow. [Not that going through a band saw 30,000 times while frozen isn't]
(think scanned sliced cadaver, put back together in 3D on computer; you can play Descent in the veins etc..)
~.~
I'm a peripheral visionary.
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.
Just use the Random NY Times Registration Generator.
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).
The conclusion of your syllogism, I said lightly, is fallacious, being based on licensed premises
Here is the deep dark secret (well, not to anyone in the field) about mapping the genome: The Internatioal Human Genome Project used a technique that allowed them to trace back their sequence to the specific region of the chromosome. Celera used a technique that sequenced random clones. They would then find overlaps and create the complete sequence map. Every corporate elitist , e.g. Rush Limbaugh, said it proved that private industry beat the US gov't (forgetting all the other countries involved). What they didn't mention is that every night, the minions of Celera would download the public sequence to help construct the Celera map because they were flying blind. In words that slashdotters could understand, they took open source to construct their product. In a recent paper in the Proceedings of the National Academy of Science, authors showed how it was unlikely that Celera would have failed without using the public data. In my opinion, Celera was a failure. In fact, the joke amongst geneticists is that Celera was founded to force everyone else to by the High Throughput sequencers being sold by their corporate parent.
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.
So does this mean that they will be able to isolate the Ego gene?
eg05 - predisposes to hypertrophy of ego
b1dy27 - gene which predisposes one to have a big shiny head
ch1n2 - predisposed to have two chins
Try this Yahoo link
Even if Dr. Venter had a remote chance of winning the Nobel Prize someday, I think this flagrant, and egotistical action will not go well with his fellow scientists.
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.
as a developer who works for a major research lab that's sequencing and annotating the human genome, I predict that I will have a very amusing Monday morning.
Zero tolerance equals zero intelligence
Jeez, the best point on the whole board and its blithely ignored.
BrokenHalo is right. Celeras entire genome assembly is currently in question. Recently published papers have shown that their genome assembly could NOT have been done as they claim, and they deliberately biased there integration of public genome data so that when shredded, it could be reassembled in the same order - therefore enabling them to fix their own flawed assembly, and in fact invalidating their claims of a shotgun assembly approach.
Now their idiotic CEO has invalidated their DNA selection process as well. What the fuck *have* Celera done right? Let me see - charging us $11,000 dollars a YEAR just to look at their shoddy data? Anyone who has used that system for data mining already knows how bad it is, and how its deliberately crippled to stop bulk data retreival of the sort SERIOUS researchers need to do - which is supported and even encouraged but ENSEMBL, UCSC and NCBI annotations.
I wonder if the commercial licencees of the data but up with the same restrictions.
A very disappointed researcher
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?
We can just bean Venter's genome to Andromeda.
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
Includes interviews with lots of aggravated geneticists.
Oh really? Would you care to point out the interview with even a single "aggravated geneticist"?
For god's sake, the article even says, right up front in the second paragraph: "Reactions among scientists range from amusement to indifference, most saying that it is unimportant whose genome was sequenced."
Does "aggravation" somehow lie in between "amusement" and "indifference" in some way I am not aware?
This was an interesting article. I'm glad you brought it to my attention. But I absolutely CAN NOT STAND the fact that slashdot editors insist on editorializing each and every story with a comment that is usually sensationalistic, or just plain wrong.
I remember when Rich Stevens died, Cmdr Taco posted the story with some inane comment at the end like "And to think, just last week I was in a bookstore and almost bought one of his books." Guess what, Taco? The world does not revolve around you. I stopped reading slashdot for months after that.
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
Not only has it been rumored for a long time,
some Celera higher ups certainly all but said
it at some scientific conferences.
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.
This is just like Craig Venter to do this sort of thing. First he starts an independent, private project to try to get his foot in the door first, then he blows the whole thing out of proportion to make it sound like the first one to sequence the genome will have reached a major milestone (the point is to record a variety of genomes: one doesn't cut it). Then his unbridled ego comes into play as we see him try to get his name in the history books by submitting his own DNA. The human genome project should encourage cooperation. You can't just manage it like a McDonald's or whatever he did before going into biotech. What do you expect of someone whose biggest asset is that he used to be a professional surfer?
they are probably keeping the option open of doing no good. If you want to track this, sign up using a disposable email address from Sneakemail.com, you can put your password in it too if you ever forget. If they eventually get around to spamming or selling this address you'll know where it came from
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.
In making this announcement, Venter has made it much more possible to create a DNA Bomb with his name on it, and he has also upset the same community which has the most potential to create such a beast. It's funny how the only thing really keeping geneticists from attempting to create a DNA specific pathogen is the system of ethics which Venter violated.
I was under the impression that the major source of genetic sequences came from the public Human Genome Project, not from Celera or Dr. Venter. Celera has admitted that they used the public data in addition to their own to assemble their version of the human genome. It's really unfortunate that one of the major endeavors in science has come to this nonsense. This guy is driven by personal gain, not by any sense of duty to the human race. Thousands of scientists worldwide worked on the Human Genome Project, but this one individual is trying to claim HE finished first, and has the most accurate data. I feel sorry for him. He knows no shame.
Now we can search his DNA for easy ways to kill this asshole.
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.
the bald ugly and double chin genes.
Maybe now he'll volunteer for immediate contribution to the visible human project. Hey, it's only fair.
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
a perfect example of the genes that code for human arrogance. Thanks Dr. Frankens...I mean Venter!
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, seeing anti-semitism in what I said. I said it was the best newspaper in the U.S.
Rank has its privileges.