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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."
Sharks with frickin lasers on their heads.
Oceans don't have DNA!
Seriously, though, that's going to be a lot of work. A single drop of sea water probably contains dozens of different microbes. They would have to be isolated and purified to make sure there was no cross-contamination. If you try to extract DNA from a culture with multiple species in it, your results are not going to reliable or even worthwhile.
I suspect Venter may finish his quest before this article is ever finished.
He seems to have no regard for the risk of skin cancer. When you walk around naked on the beach all day you should at least wear sunscreen.
That said... can I have his job?
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.
;)
So that's what they're calling it nowadays, eh?
Wow, the submitter is really brave saying that he can be seen in one of the pictures. Pretty soon legions of young, nubile, slashdot-reading, geek chix0rz will be flooding his inbox with requests for... well you fill in the blank.
If you think software patents are bad, then what about gene patents? It seems that a big part of any gene sequencing project these days is an effort to find patentable genes. How can one patent what has existed for thousands or millions of years in nature is beyond my comprehension...
The worlds oceans are going to be one of the last bastions of untouched life. Shores and beaches are being dug up and recreational boating and such already puts alot of pollution into small bodies of water like lakes and streams, not to mention industrial waste. In the middle of the ocean is one of the last places where life can grow unhindered. For the most part.
Meet new people, and kill them.
Venter's genome survey is surely a dream geek voyage. But when he patents those genes, it's only his own dreams that will be coming true. Sure, Venter's entire career is built on public funding of open genomic science, back into which he declines to contribute. But even worse, many of the species he documents, and locks up for his own use, were developed over hundreds, thousands of generations of local people, coevolving and husbanding them into their beneficial condition. But Venter has the upper hand over the traditional genetic "developers", end-running them to capitalize on their innovations, only to license them back at a profit actually earned by his customers. Venter's technology is good, his science is great, but his economics is most foul.
--
make install -not war
Take a moment to familiarize yourself with genetic algorithms and you'll begin to understand this research's potential impact on computing. Institutes like HPL are quickly moving on DNA computing and some fundamental bit-manipulation has already taken place at a chromosomal level at MIT. This is the most exciting area of computing, and just might make AI possible.
+ Donald Gunth
+ Email: dgunth@quicktek.net
"Caffeine is the greatest lubricant ever created." -ESR
It's like Star Trek; we're the humans and they're the Vulcans. Sure, they're a smarter race, but low in numbers. We make a bigger presence (well, noisier, anyways) and like to talk alot about stuff. :)
They will all be sorry when thet stumble upon Cthulhu!
Once we have the genetic codes of all species recorded, we won't need the actual creatures any longer. If we have a future requirement for an actual Green-Tinged Fin Wiggler we can just make one. Goodbye Endangered Species Act.
Better get those DNA samples from the oceans before the Klingons get there. They'll get their sample and fry the place. Bastards.
(What TNG episode was that, anyway? Google is not my friend today!)
Stressed? Me? Of course not. Stress is what a rubber band feels before it breaks, silly.
(This isn't a rhetorical question -- I'm simply curious but ignorant.)
Disclaimer: I work for a company, but I don't speak for them.
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.
NCBI has the "Sargasso Sea" here : BLAST the Environmental Samples data
Hey, they want exotic new microbes? They need look no further than my kitchen sink. I've got several new species popping up every day. I will insist upon splitting the patent royalties, however.
They can't patent the gene; but the can patent a modifcation to the gene.
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.
1. Get my picture taken next to someone famous.
2. ???
3. Profit!
Step 2 must somehow involve Slashdot.
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.
They'll know by similarity to other genes. Genes produce proteins. Proteins have "motifs". A motif might be, for instance, an "intra membrane" segment. Viruses have these for getting through cell membranes. If the sequence has an intra-cellular structure gene and a self transcription structure and an evelope structure together, then it's probably a virus. If it has something very similar to a bacteria membranne, then it's probably a bacteria. They can tell sorts of things about a gene by it's similarity to the structures of known genes.
The great majority of Earth's species are bacteria and other microorganisms. They form the bottom of the food chain and orchestrate the cycling of carbon, nitrogen, and other nutrients through the ecosystem. They are the dark matter of life. They may also hold the key to generating a near-infinite amount of energy, developing powerful pharmaceuticals, and cleaning up the ecological messes our species has made.
Interesting article, despite the breathless hype that is typical of Wired science articles.
How might these organisms hold the key to "generating infinite amounts of energy"? A cluster of H2S-metabolizing worms around a geothermal vent? Or have those deep-sea molluscs discovered the secret to cold fusion?
Does anyone else see a connection between Venter and Captain Nemo from 20,000 leagues under the sea?
Brilliant and very wealthy scientist fed up with the political/corporate world (Celera) flees to live a life in the unexplored ocean. He makes all types of new discoveries where he won't be held back by his fellow human.
can't sleep. clowns will eat me.
I am a microbiologist (IAAM?), and while the notion of sequencing so much random genetic material is interesting, I can't really see much point other than hoping to stumble upon something unexpected. And even then...
Yes, I RTFA, but I still don't get the point. Venter says he wants to create an artificial genome into which DNA could be inserted and tested... so crazy. You can't just stick DNA into a genome and "see what it does", you have to have the entire cellular aparatus to translate the sequence into protein. So, assuming that they somehow come up with an artificial cell (or use an existing organism with genome removed), SO MANY factors can affect the final form of the protein. You cannot assume that the protein will fold properly, unless it is constructed in its native cellular environment.
And even assuming you can get the protein to fold properly... then what? He said he'd use robots to perform a million experiments at once, sure. So you stick the protein into glucose solution, and see what it does... and into fructose solution... and so on. Sure, you could do this with simple substrates, but what if the protein is designed to act on a combination of substrates, or in conjunction with other proteins!?
So, it would seem to me, that the best you could ever hope to achieve with this approach is the discovery of ultra-simple proteins (which will fold correctly in any circumstance) which act upon ultra-simple substrates.
Though, in truth, he states that he's looking for something to possibly break down C02, so perhaps if his focus is narrow enough, the discovery of even a simple protein might get things on the right track...
Anyway, I guess it's not the way I'd go about doing things, but sailing around the globe sounds like a fun way to do research. Good luck, guys!
Visit the Game Programming Wiki!
I always thought that patents were for inventions, not discoveries (no matter how many zillions of dollars are spent doing the discovering).
"When the going gets weird, the weird turn pro" -- HST
...and now they're goin' to do DNA testing of the ocean. Where the hell can I pee now?
144l. ph34r my 133t l3g4l 5k1lz!
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.
Professor: "I'm sorry Fry, but the anchovy has been extinct since the 2200s."
Fry: "What???"
Professor: "Oh my, yes. Fished to death. Just about the time your people arrived on earth, wasn't it, Zoidberg?"
Zoidberg: "I'm not on trial here!"
This sig contains repetition and redundancy.
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.
What about the human genome?
I heard a lot of hype about "mapping" the human genome, but I always got the impression that it was like mapping a highway system. They now have a map of where all the highways go, but they don't where anything is in relation to these highways.
"When the going gets weird, the weird turn pro" -- HST
Hey, don't you know? All life forms have access to unlimited energy. However, if they are human beings, you have to show them some form of virtual reality before they'll let you tap that energy.
This voyage of discovery is not merely "fishing"
for new genomes. It is also not merely a new
"gold rush" for patentable genomes. What it is
is the basis for new bio-weapon research.
We are, after all, talking about the Bush/Cheney
administration. An administration that slashes
the NASA budget in favor of ABM pipedreams, halts
the war on terror in favor of the conquest and
Balkanization of an oil-rich country, and stifles
funding for "After School Lunches" and the "No
Child Left Behind" programs in favor of corporate
welfare.
And from those beasts they will extract species DNA and PATENT it.
For instance the best (=only) high resolution structures of ion channels were solved from genes found in microbes, including one from a deep sea thermal vent.
Now have your web designer look up "web standards" so we can actually read it.
that pig and elephant DNA just won't splice
(south park quote)
more stuff to patent.
"It's so convenient to have a system where everyone is a criminal" - A. Hitler
They know what about 50% of the genes do. They have clues to the rest based on motifs but can't quite plug 'em in to the vast network of protein interactions. Yes, mapping the pathways of the cell is next big challenge in cell research but the map of the genome is a huge clue.
Here is another article about Venter's journey:
Venter Makes Waves -- Again
I thought this was more about him having a nice little sea trip with his secretary, which is why he's splitting with his wife (who put up a lot of the cash for TIGR etc.). I hear the 'science' excuse for the trip is a bit of a private joke at the institute...
Read the original paper, and note that two of the assembled genomes (and therefore two of the the most abundant sampled organisms) are probably contaminants - neither Burkholderia nor Shewanella have been found in earlier 16s rRNA surveys of the Sargasso Sea in significant numbers.
This sort of mistake is not one that a great scientist would allow to waste resources or to be published without pointing out. If Venter would be more careful and critical, or simply have less of an ego, this mis-direction of resources would not occur.
The original paper, only available with a subscription (go to a real-world library if you don't have one). Or read a overview
And yes, IAABEM (I am a bioinformatic environmental microbiologist).
As was pointed out in some replies to my (parent) post, the genomes Venter finds will be available to the public. I was overreacting to Venter's past actions, which are now harder to justify with consistency. But we can all applaud his work on our behalf, harvesting the info from the sea for anyone's use. In fact, it certainly justifies his publicity-seeking career, and might even justify some of his privatizing other genome "discoveries", to fund and promote this purely scientific mission.
--
make install -not war
> Sure, they're a smarter race
Wired... Smarter...? Than Slashdot? Maybe if you include all the trolls, but that's like including the Romulans with the Vulcans. Trolls aren't human.
To discover is to uncover is to learn. To invent is to create something new.
"When the going gets weird, the weird turn pro" -- HST