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Biotech Science

Voyage To Sequence DNA From the World's Oceans 121

Posted by simoniker from the blub-blub dept.
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."
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Voyage To Sequence DNA From the World's Oceans More

Voyage To Sequence DNA From the World's Oceans

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  • The ultimate goal here is... (Score:5, Funny)

    by darth_MALL ( 657218 ) on Wednesday July 28, 2004 @06:44PM (#9826278)
    Sharks with frickin lasers on their heads.
    • My local LUG actually attached a modified laser pointer [thinkgeek.com] to a small shark's head -- the kind of shark you can keep in a fish tank... I don't recall its species name. We had quite a great time reciting Austin Powers lines for a few hours before we removed the water-proofed pointer from the confused shark's body. Unfortunately the only camera at the event met with an untimely death before the pictures could be recovered.

      If you're in the Baltimore LUG and happened to have a camera at the event, please conta

  • How can we take this scientist seriously? (Score:1, Funny)

    by Anonymous Coward
    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?

  • Yikes (Score:4, Funny)

    by Anonymous Coward on Wednesday July 28, 2004 @06:51PM (#9826328)
    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? ;)

  • Taking a risk? (Score:3, Funny)

    by xCepheus ( 687775 ) <dntn31.yahoo@com> on Wednesday July 28, 2004 @06:51PM (#9826330) Homepage
    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.

    • Re:Taking a risk? (Score:5, Funny)

      by sarah_kerrigan ( 764949 ) on Wednesday July 28, 2004 @06:54PM (#9826351)
      Hello,

      Pretty soon legions of young, nubile, slashdot-reading, geek chix0rz will be flooding his inbox with requests for... well you fill in the blank

      Requests for taking part of the expedition, of course 0:-) (ok, offtopic, come to me...)

      Kisses
      --
      • nubile adj.
        1. Sarah Kerrigan [ttuhsc.edu]
        2. Ready for marriage; of a marriageable age or condition. Used of young women.
        3. Sexually mature and attractive. Used of young women.

        If I wasn't already married, I would have proposed by now ;)

  • Patents? (Score:5, Interesting)

    by mangu ( 126918 ) on Wednesday July 28, 2004 @06:51PM (#9826334)
    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...

    • Amen brother! (Score:1, Informative)

      by Anonymous Coward
      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.

    • Re:Patents? (Score:3, Funny)

      by Ichijo ( 607641 )
      How can one patent what has existed for thousands or millions of years in nature is beyond my comprehension...
      God has some pretty nasty ways of defending his patents. We had better watch where we tread.

    • Re:Patents? (Score:3, Interesting)

      by mmmmmhotpants ( 800341 )
      No one ever patented the human genome. I agree, patenting what exists in nature has no merit.
      Nevertheless, I think gene/DNA sequence patents will be very important and fair. There are a handful of researchers today who engineering new proteins and genes which are better than anything found in nature; others create nano-machines built out of DNA/RNA sequences. After millions/billions of dollars of research, dedication, supercomputing, etc. I think these scientists and engineers have every right to claim a

      • Re:Patents? (Score:3, Insightful)

        by Thing 1 ( 178996 )

        Without gene patents, unless you're Craig Venter or Paul Allen and just have money to play with for the sake of discovery, there is no motivation what-so-ever to create future theraputics and bio-devices.

        I completely disagree. The delivery mechanisms and "bulk" structures can still be patented. But patenting genes themselves is a lot like patenting 1+1=2, or one-click shopping: there is a logical way to reduce it to its absolute minimum effort, so patenting that seems a bit absurd. (I should patent

    • I always thought that patents were for inventions, not discoveries (no matter how many zillions of dollars are spent doing the discovering).
      • > I always thought that patents were for inventions, not discoveries

        I don't know the legal definitions, but IMO inventions really are just advanced discoveries. "I've discovered that these two things together do this, which would be very useful. I should patent it."
        • I have always understood invention to mean something that is created or put together for the first time, whereas a discovery is learning something that existed prior to humans learning about it.

          To discover is to uncover is to learn. To invent is to create something new.

    • Re:Patents? (Score:3, Informative)

      by Tassach ( 137772 )
      Most of Ventner's work is done under the auspices of the National Institute of Health [nih.gov], and is therefore in the public domain. I should know, I maintain several [nih.gov] genomic [nih.gov] databases [nih.gov] at the NIH.

  • What about... (Score:2, Interesting)

    by eieken ( 635333 )
    The worlds oceans are going to be one of the last bastions of untouched life. Shores and beaches are being dug up [npr.org] 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.
    • 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 corpo

  • privateer voyage (Score:5, Insightful)

    by Doc Ruby ( 173196 ) on Wednesday July 28, 2004 @06:54PM (#9826345) Homepage Journal
    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.

    • Re:privateer voyage (Score:5, Informative)

      by Angry Toad ( 314562 ) on Wednesday July 28, 2004 @07:08PM (#9826452)
      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.

      • so he used his own DNA...big deal! He had to use someone's! By using his own, no release forms, no malpractice insurance, cuts costs. I don't see the problem with it. Would you have preferred a "perfect human specimen"? Perhaps Arnold? Or Gates? Or Torvalds? One guy is as good as the next. Who cares if he used his own!

        • Re:privateer voyage (Score:3, Informative)

          by dekeji ( 784080 )
          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 indi
          • his contribution was to do it in a different, faster, and now accepted better way. That doesn't sound like a problem to me. No, he didn't have to do it, but he did at private expense, so he gets to do it any way he wants. The fact that he used his own dna does NOT invalidate the results.

            A scientifically careful approach can now be done quickly and easily thanks to his now proven superior technique and his baseline results, which happen to be his own dna. Again, doesn't sound like a problem to me. Private w
            • No, he didn't have to do it, but he did at private expense, so he gets to do it any way he wants. [...] Private works get to do things the way they see fit.

              You are confusing means and ends. The purpose of a free market is an efficient allocation of resources. But that doesn't mean that just because the market does something, it is efficient--it often fails.

              No, he didn't have to do it, but he did at private expense, so he gets to do it any way he wants. The fact that he used his own dna does NOT invali

    • This has nothing to do with patents (Score:5, Informative)

      by Jonathan ( 5011 ) on Wednesday July 28, 2004 @07:58PM (#9826784) Homepage
      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.

      • Re:This has nothing to do with patents (Score:4, Insightful)

        by the gnat ( 153162 ) on Wednesday July 28, 2004 @08:50PM (#9827159)
        Furthermore, one of the problems with Celera was that the scientists involved were more interested in science than making money. I did some work for one of the former higher-ups who's now back in academia, and while he did very well from his association with the company, he's an academic scientist at heart. There's a good book out called "The Genome War" that goes into this in considerable detail; the corporate masters of Celera were apparently furious that Venter et al. were releasing so much data.

        The impression I got was that Celera was really formed because of huge egos and a conviction that their methods were better (which, in retrospect, they probably were), not because the scientists involved honestly thought this would be a great way to make money.

        As far as Venter's current enterprises go, the guy may be a dickhead, but I wish him the best of luck - he's doing fantastic science and he's consistently innovative. There is no shortage of arrogance among academic biologists, and Venter is by no means the worst case.
      • What will Venter do with the genomes he sequences? Put them in the public domain?
        • What will Venter do with the genomes he sequences? Put them in the public domain?

          Basically -- the data goes in GenBank, a publicly available database. The Sargasso data is already there. Records in Genbank are freely available but aren't "public domain" in a technical sense. Since you are supposed to keep the attribution data, I suppose it's closer to one of the Creative Commons licenses.

          Here's [nih.gov] an example of a GenBank record. For the Sargasso Sea data, there's over 50,000 of them.
      • Craig's institutes, TIGR, IBEA, TCAG are *not busineses* -- they are non profit research institutions. Somehow, this does not ring true with what I know. My information is that TIGR were a front for Institute for Genomics Research, which got six months exclusive rights to all patents of all TIGR's research. To my knowldge Venter owned (owns?) 10% of that stock. Calling TIGR a non profit research institution under this arrangement is a LONG streach. I have been told that Venter later broke his ties with
        • TIGR has *always* been a non-profit institute. I think you are referring to the early TIGR deals with Human Genome Sciences, which funded TIGR in exchange for first access rights to EST sequences. Human Genome Sciences is, yes, a business.

          Much of the money brought in from EST sequencing (which had *nothing* to do with TIGR's main goals as a genomics institute -- we just had spare sequencing capability to rent out, just like some organizations rent out spare computing power) was used to fund the sequencing

          • Much of the money brought in from EST sequencing (which had *nothing* to do with TIGR's main goals as a genomics institute -- we just had spare sequencing capability to rent out, just like some organizations rent out spare computing power)

            I don't think you got what I was pointing out as suspect. TIGR's goals cannot be said to have *nothing* to do with the HGS relationship, if Venter, your boss (then) owns 10% of the company that TIGR does research for. This is what I found suspect. Heavens, I don't min

    • 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.

      Uh, you understand that the organisms in question are microbes and plankton floating around in the middle of the ocean, right? You may want to save this boilerplate rant for when it's at least partially relevant.

      • 1> The Pacific ocean is home to thousands of tribes, for thousands of generations, on thousands of islands.

        2> I made up that rant as I went along, it's not boilerplate.
    • As was pointed out in some replies to my (parent) post, the genomes Venter finds will be available to the public [nih.gov]. 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.

  • Cool (Score:4, Interesting)

    by John Jorsett ( 171560 ) on Wednesday July 28, 2004 @07:07PM (#9826432)
    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.

    • Re:Cool (Score:1, Informative)

      by Anonymous Coward
      There's a bootstrapping issue here. You need a compatible egg cell to host the DNA before you can make entire individuals.
      • There's a bootstrapping issue here. You need a compatible egg cell to host the DNA before you can make entire individuals.

        I leave the petty details to others ...

    • Unless of course all the patents are owned by various people thus forbidding the common person access to them once gene technology becomes commonplace. Personally, I'd like to be able to collect my own samples regardless of the patents out there, screw them I say. But in order for that to happen there needs to be source material available.

    • Yeah, I can't wait until the California Condor hunting season opens.

      • Sorry, no hunting season. The Condors are going to be whacked out of the sky by all the windmills we're going to have to build.

  • Watch out for the Klingons! (Score:4, Funny)

    by RobertB-DC ( 622190 ) * on Wednesday July 28, 2004 @07:09PM (#9826454) Homepage Journal
    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!)

  • possibly dumb question... (Score:4, Interesting)

    by Daniel Ellard ( 799842 ) on Wednesday July 28, 2004 @07:09PM (#9826458)
    If they just grab DNA out of microbes they find floating around in the ocean, how will they know what genes correspond to what? Wouldn't it make more sense to sequence the DNA of things about which we have some knowledge?

    (This isn't a rhetorical question -- I'm simply curious but ignorant.)

    • Re:possibly dumb question... (Score:5, Informative)

      by Angry Toad ( 314562 ) on Wednesday July 28, 2004 @07:22PM (#9826554)
      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.

      • Sorry, I'm still in the dark... How can they tell that a particular gene is related to "metabolism of metals, or peculiar photosynthetic components" unless they observe some organism actually doing it? It seems like what they're going to discover is, at best, that some subset of the zillions of microbes in a given beaker have some ability. We're still don't know which ones.
        • 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.
        • The answer is pertty much what a previous poster was talking about - they compare the sequences to ones from other organisms where they already know what a given gene does.

          There's a huge database called "GenBank" (you can go there via ncbi.nlm.nih.gov ) where you can search (via an algorithm called "blast") your DNA or protein sequence against just about every DNA or protein sequence ever. If you get a result back listing fifty different, for instance, fatty acid synthesis genes at high confidence l
        • One way to tell what a gene does is an association study. Proteins that work closely together in a complex are sometimes found in a genome as a single "super gene" that has both functions.

          So if you sequence one genome, it is hard to tell. But if you get even sketchy sequence from hundreds of genomes, you may see an unknown gene merged up with a gene that has already determined to be an exotic metal metabolizer. And that would give you a clue about the unknown gene's function.
    • Congratulations, you've stumbled upon the reason why this is purely a gimmick.

      They won't know.
      • 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 S
    • in finding genes in microbes that are similar to human genes because it can help understand how the human protein works. It's a little like studying a volkswagen (beetle) engine or a Model T engine to learn how a lexus engine works. Sure there major differences but the older ones are easier to study and might give you a clue about the human protein.

      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

    • that pig and elephant DNA just won't splice

      (south park quote)
  • "In the Sargasso Sea alone, Venter's team discovered at least 1,800 new species"

    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,

    • That's like stopping 500 people on the sidewalks of NYC and declaring there are 500 species

      I have that exact feeling each time I walk downtown NYC...

    • Their criteria for determining species is pretty common for that of asexual organisms. Bacteria, which are prokaryotic, tend to reproduce only by binary fission which (in the absense of meiosis) allows for no genetic variation. Thus, if you see two bacteria that are different, the odds are that they are different species. When people start repoducing by splitting in half though feel free to call them species.
    • OMG! Are suggesting that these people, who undoubtably have far better credentials than the average slashdot reader, somehow neglected to think of this very point or account for it? Wow. You better get in touch them real quick to let them know of the horrible mistake they're making!

  • wanna blast the ocean? (Score:1, Interesting)

    by Anonymous Coward
    NCBI has the "Sargasso Sea" here : BLAST the Environmental Samples data [nih.gov]
  • 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.

  • Karma Whore! (Score:2, Funny)

    by Anonymous Coward
    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.

  • Near-infinite amounts of energy? (Score:4, Funny)

    by sssmashy ( 612587 ) on Wednesday July 28, 2004 @07:34PM (#9826626)

    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?

    • It's depends on how you define the "near" operator(*) for infinity.
      Maybe, they work with a definition that makes the few hundred kJ by burning a lump of algae an "near-infinite" amount :-)

      (*) - Remember the good old altavista.com days? There certainly was such a thing!
    • 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.
  • 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.
  • 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
    • The only real benefit I can see is if one of the sequenced organisms has a very unique DNA makeup. This could change some thoughts about phylogeny/evolutionary trends. It's pretty unlikely though.
    • Exactly. I'm a biochemist, and I can't say that I'm too thrilled with the current attidute of "sequence first, ask questions later". Simply solving the sequence of a gene for a protein is NOT ENOUGH. It's just one peice of information, and does not tell you how the protein acts in vivo. Some of the most useful (and, I might add, more difficult to obtain) info to have are kinetic rate constants for the reaction performed by the protein. You can;t get that from a gene sequence. Sorry, I'm a little annoyed at
    • I'm working on a doctorate right now trying to develop a method to help make what Dr. Venter is proposing feasible. The approach I'm using is a semi-industrial method that can hopefully screen thousands of samples in one experiment, while stopping short of full sequencing. I'm actually working on the analytical portions of the problem, not the sampling part. Lots of computer time for me, looking at binary fingerprints . . .

      Dr. Venter is a pioneer. He annoys many people with his stunts, but he does en

  • First they put phenylphaline in the pool... (Score:4, Funny)

    by DavidBrown ( 177261 ) on Wednesday July 28, 2004 @07:58PM (#9826781) Journal
    ...and now they're goin' to do DNA testing of the ocean. Where the hell can I pee now?

  • 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!"

  • Purchase your personal gene map? (Score:3, Informative)

    by dstone ( 191334 ) on Wednesday July 28, 2004 @08:03PM (#9826823) Homepage
    Craig Venter is the same fellow from this [slashdot.org] 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.
  • So ... did this Vetner guy one day say to himself:

    I'd like to sail around the world in a sexy big yacht and visit some hot, exotic places, how can I get someone else to pay for it?
    I know, I'll get some of the deckhands to dangle buckets over the side and write down what they pull out! But we're going to need a name so it sounds all scientific like
  • Here is another article about Venter's journey:

    Venter Makes Waves -- Again [bio-itworld.com]

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