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Voyage To Sequence DNA From the World's Oceans
joehoya writes "Wired has an extensive article about an expedition with the goal of discovering new microbial species and new genes in the world's oceans. The expedition is led by J. Craig Venter, who is best known for his involvement in the race to sequence the Human Genome. This is a really fascinating expedition with a pretty high geek quotient. I know, as I set up many of the computer and other electronic systems aboard, and traveled with the expedition as far as the Pacific side of the Panama Canal. In fact, you can see me (ok, the side of my head) in one of the article's pictures, next to the Captain while helping to take a sea water sample."
Venter is a grandstander and a media whore. There, I said it.
He regularly trades off scientific benefit in favour of his own personal ego - to wit, most of the Celera genome is *his own DNA* and, even more egregiously, the dog genome is his own *pet poodle*, by all accounts.
I've heard plenty of criticism of this latest bit of nonsense of his - he's going to grab plenty of attention as the father of "metagenomics" or some such nonsense, but it is going to be left to more rigorous scientists to come in and clean up the field that he has barged into.
Bullwhoey. What's the criteria for determining they're different species? Because it sounds a lot like it's "run it through the genetic analysis machine and if it's different, Bingo! New Species!" Or maybe, "does it look different from anything else we've seen thus far?"
That's like stopping 500 people on the sidewalks of NYC and declaring there are 500 species, simply because they all have differing eye/skin/hair color, they're different heights/builds, they speak different languages with different accents, and they came from different places.
Furthermore, some of the little buggers are SO plentiful and reproduce so fast, they could all be of the same species but have rather varying genetic makeups. They're not necessarily all different species.
Please help metamoderate.
http://www.sfgate.com/cgi-bin/article.cgi?file=/ch ronicle/archive/2000/03/27/MN108096.DTL
This guy is controversial to say the least.
Mapping genes can no longer be called invention. It is the work of a skilled practitioner.
The basic idea is to get a sampling of the "genome content" of a volume of seawater, looking for genes related to, for instance, metabolism of metals, or peculiar photosynthetic components, or whatever. You then have an idea of both organismic and metabolic diversity in an area - do it straight down a water column and you see how this varies across layers of the ocean.
Your point is a valid one all the same - this is a newish field called "metagenomics" and lots of professional scientists have been asking precisely the same question you did. The jury is still very much out on whether this is really going to produce anything useful.
I believe they will isolate DNA from the micro-organism cocktail, and then sequence the DNA.
Using the collection of reads from the sequencer, and a large informatics pipeline, the sequences will be annotated and compared to all the known genes and gene products.
A large spreadsheet will be published, and scientist will debate for years on if this experiment had any real value.
I work for TIGR, and therefore indirectly for Craig Venter (Well, actually I work for Craig's soon to be ex-wife, and so I'm not a big personal fan of Craig).
Craig's institutes, TIGR, IBEA, TCAG are *not busineses* -- they are non profit research institutions. Yes, Craig is egotistical -- but the whole point of the Sargasso Sea is science. There is *no profit* to be made or patents to be issued. Yes, Craig worked for a couple of years at Celera, but that doesn't mean everything he's associated with is commercial, any more than Linus having worked at Transmeta makes Linux commercial.
Craig Venter is the same fellow from this story 2 years ago. He was selling people their own gene maps for USD$621,500. Sounds like a successful way of privately funding research.
Congratulations, you've stumbled upon the reason why this is purely a gimmick.
It's no gimmick -- there's lots of ways to associate genes together. One way, which I myself was partially responsible for in this analysis (I got an acknowledgment in the original paper) is phylogenetic inference -- basically you can make evolutionary trees for each gene predicted, and you can assume that genes that fall into analogous clades across trees are either due to the same or dimilar organisms.
Hey, I admit that the Sargasso Sea analysis was crude, and ten years from now we'll be laughing at it, but the fact is metagenomics is basically the only way to explore biodiversity at a molecular level. We'll be seeing more such studies (in fact we already have).
Most of Ventner's work is done under the auspices of the National Institute of Health, and is therefore in the public domain. I should know, I maintain several genomic databases at the NIH.
Why is it that the proponents of "one nation under God" are so eager to get rid of "liberty and justice for all"?
There's a bootstrapping issue here. You need a compatible egg cell to host the DNA before you can make entire individuals.
Here is another article about Venter's journey:
Venter Makes Waves -- Again
He had to use someone's!
No, he didn't have to use anybody's. He didn't even have to do it at all because he didn't have to sequence the human genome--another project was already well underway. Ventner's contribution was to create a lot of unnecessary problems.
I don't see the problem with it. Would you have preferred a "perfect human specimen"?
A scientifically careful approach to sequencing the human genome wouldn't have used any single individual's DNA--it would have selected the fragments and individuals it uses on a case-by-case basis, as work progressed. In the end, you would have ended up with sequences from many individuals covering many genes.