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Science

Learning (And Harvesting) from Extremophiles 192

Posted by Hemos from the long-term-effects dept.
kudyadi writes "BBC News has an article on the threat posed to extremophiles by anxious prospectors ready to exploit their unique nature. Potential discoveries include glycoprotein, which prevents Antarctic fish from freezing, and an extract from green algae for use in cosmetic skin treatment, and anti-tumour properties in a strain of yeast. This article explains the issue more lucidly, but in the end, one must consider the environmental ramifications of this biological exploitation before moving ahead full scale. So how is Tux in danger? Let me remind you of a thing called the food chain and then read this."
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Learning (And Harvesting) from Extremophiles More

Learning (And Harvesting) from Extremophiles

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  • Oh. (Score:5, Funny)

    by proj_2501 ( 78149 ) <mkb@ele.uri.edu> on Monday February 02, 2004 @12:02PM (#8159103) Journal
    I had to read the article before figuring out that extremophiles were not folks who enjoy things like base jumping on Mars, "water"skiing on the freeway, real-life Crazy Taxi, nude Antarctic beaches, etc. etc.

  • It's not like its strip mining (Score:5, Insightful)

    by Anonymous Coward on Monday February 02, 2004 @12:03PM (#8159106)
    Is some great white hunter scientist with a cotton swab and a sequencer really going to be a threat to Antarctica?

  • Extremophiles (Score:5, Funny)

    by Anonymous Coward on Monday February 02, 2004 @12:04PM (#8159118)
    Is that one of those Audiophiles that buys all the best equipment and scoffs at CD audio in favor of DVD audio?

  • Brilliant. (Score:5, Insightful)

    by musingmelpomene ( 703985 ) on Monday February 02, 2004 @12:06PM (#8159133) Homepage
    Let's just stop ALL science until we're absolutely sure of every ramification of every single thing we do. It's a good thing these people weren't in charge in cavemen times; the first man to create fire would have been stoned to death for creating smoke, and the first one to create the wheel would have been burned at the stake for making something that could roll over grass.

    • Re:Brilliant. (Score:5, Funny)

      by yotto ( 590067 ) on Monday February 02, 2004 @12:11PM (#8159179) Homepage
      the first man to create fire would have been stoned to death for creating smoke, and the first one to create the wheel would have been burned at the stake for making something that could roll over grass.

      Well, at least the cavemen in the parallel universe finally accepted fire...

    • Re:Brilliant. (Score:3, Insightful)

      by Azghoul ( 25786 )
      Your point IS flamebait, so I can't argue the mod, but you bring up a fair point...

      The thing is, no science ever really seems to be stopped by the chicken-littles. They will always be there in the background hand-wringing, and their concerns will usually manage to keep the new science "honest", but they'll never really stop anything.

      • Re:Brilliant. (Score:2, Insightful)

        by I_Want_This_ID ( 678839 )
        It depends on who the chicken-littles are. The religious right (the people in control of the US) for instance would see some of this science as blasphemy and create legislation to criminalize researching it.

        Maybe the US can't stop this type of research everywhere in the world, but maybe those in control will decided that this "subversive" research will someday endanger the US and they need to be "liberated"

      • Re:Brilliant. (Score:5, Insightful)

        by drinkypoo ( 153816 ) <drink@hyperlogos.org> on Monday February 02, 2004 @03:39PM (#8161564) Homepage Journal
        But the use of the science often is stopped by the aforementioned chickens. Nuclear power for example. You can tell an activist that coal puts more radioactive materials into the atmosphere every year than all the nuclear accidents ever, and they'll just come back and tell you that coal is bad too and we should all put up solar panels, twine flowers in our hair, join hands, and dance around the maypole. Well, dance around my maypole, you bastards, because in the meantime the coal plants are running day and night and pumping out all kinds of wonderful toxic crap which will haunt us for generations to come.

        Granted, the hyperactive ecowankers need to exist, they just need to not have quite so much power. The problem is that the court of public opinion weighs emotions and not facts. We tend to agree with people and not points, and the winner is whoever comes off as being more charismatic. It's easy to paint those who develop or utilize scientific advancement for profit as greedy, selfish bastards, because they stand to gain something. Every lie is more powerful when it contains some truth.

        • Re:Brilliant. (Score:5, Insightful)

          by the gnat ( 153162 ) on Monday February 02, 2004 @04:25PM (#8162187)
          Two points:

          - The same complaint can be made about the resistance to GMOs. Many of the bioengineered crops being developed today have the potential to save millions of lives, but there are some environmentalists who would literally rather see the Third World starve than see it utilize genetically engineered corn. (Actually, they'd probably rather see our tax rates go up to 50% so we can feed the Third World - which simply prolongs the problem rather than fixing it.)

          (Side point 1: some of the reading I've done indicates that there's also some anti-Americanism involved, since many of the GMOs come from the USA and are seen as a threat to European farmers. The US's ridiculous agricultural policies don't help. Side point 2: yes, there's some IP issues involved with biotech crops, but this is less of an obstacle to deployment.)

          - Many of the environmentalists do not actually believe in a modern industrial society. This is true of many animal-rights or anti-globalization activists as well. Many of the people protesting globalization have started to advocate a return to subsistence farming, because that's all that the Third World will be left with if we stick to ultra-protectionist policies. Without our modern agricultural system, sophisticated medicine, and advanced economy, however, they'd all be so sick from random (curable) diseases and weak from malnutrition that they wouldn't have time to protest fashionable causes and trash Starbucks franchises.

          I don't call myself an environmentalist, because it now comes with so many negative connotations, but working in the natural sciences and growing up in the western USA has given me good reason to support environmentally friendly policies. I would call myself a "conservationist", because I have no problem with sensible and sustainable exploitation of resources, but I don't want to see them plundered due to lack of regulations or desperation. I'd love to see us coexist perfectly with large amounts of undiluted Nature, and the only way that'll happen is with more technology, not less.

          • Without our modern agricultural system, sophisticated medicine, and advanced economy, however, they'd all be so sick from random (curable) diseases and weak from malnutrition that they wouldn't have time to protest fashionable causes and trash Starbucks franchises.

            This is a thing I find interesting. Below a certain population it is not possible to have certain levels of technology, because you simply do not have enough time. How people can be content with going backwards, let alone not going forwards,

          • More technology? (Score:2, Insightful)

            by FlyingOrca ( 747207 )
            Actually, it's not a question of technology - it's a question of population. Less people, less primary production devoted to feeding people, more undiluted nature.
    • Go back and read the article. The concern is not so much environmental impact but that the spirit of open research will be lost.

    • Re:Brilliant. (Score:4, Funny)

      by nomadic ( 141991 ) <nomadicworld@@@gmail...com> on Monday February 02, 2004 @02:51PM (#8160833) Homepage
      Let's just stop ALL science until we're absolutely sure of every ramification of every single thing we do.

      Yes, I would have concluded the article was suggesting that extreme measure as well, if I were also a simpleton.

    • Re:Brilliant. (Score:5, Insightful)

      by localman ( 111171 ) on Monday February 02, 2004 @03:02PM (#8161044) Homepage
      Actually it's a great thing that we have these extremists worrying about the ramifications of every single thing we do. It nicely balances out the other extremists who are prone to plunge ahead without considering the ramifications at all. If either side was given free reign we'd be in big trouble fast. Thankfully they seem to balance out over time.

      It's the same in many fields. Politics comes to mind. If you find yourself not able to stand the folks on the other end of the spectrum, keep in mind that you have just placed yourself in another extreme group and be thankful for the balance.

      It is balance that keeps us moving forward surely but safely.

      More or less :)

      Cheers.
      • Yeah right. This "balance is good" attitude assumes both sides of a conflict are morally equivalent. In this case, I disagree. I say the burden to provide at least some shred of convincing evidence that significant, lasting harm is possible falls on those who claim it exists.

        I also say that a lot of this hand-wringing is a cover for jealousy toward those who are taking action to collect these discoveries, which some people wish would magically "belong to all mankind" - mostly those who don't have the gu
        • And who decides what's morally equivalent? You? Of course you do; for yourself. And they for themselves. I'm sure they'd appeal to morality for their argument as well. And it's that very balance that keeps us alive.

          Don't worry: if the worriers are truly nuts they wouldn't have the numbers to have a loud enough voice to affect change.

          Anything loud enough to annoy you is nearly always based on some tiny bit of truth. Maybe skewed beyond recognition, but truth nonetheless.

          Isn't it a wonderful world?

          C
        • Perhaps you were never heard these sayings before:
          -Look before you leap
          -Think before you speak/act
          -Measure twice, cut once

          It's always a good idea to try to think through the consequences of something that may be irreversible. If it came down to your personal safety I doubt you'd be reckless, so why be reckless with everyone else's?

    • How do you know they weren't?

  • There is a bad joke here someplace... (Score:5, Funny)

    by Saeed al-Sahaf ( 665390 ) on Monday February 02, 2004 @12:06PM (#8159136) Homepage
    Extremophiles are micro-organisms that grow optimally in some of earth's most hostile environments of temperature

    ...and tend to congregate at Slashdot...

    Sorry, had to be said...

  • Invitrogen (Score:5, Insightful)

    by Ann Coulter ( 614889 ) on Monday February 02, 2004 @12:07PM (#8159142)
    Invitrogen patented the harvesting of the polymerase enzyme from the extremophile bacteria thermophiles aquarticus. It's a shame that one company can overcharge researchers by patenting something nature created!
    • Seek, Rape, Destroy. All in the name of money.

      It's part of capitalism...

      And nobody takes the "hippy" type folk who try to stop this. They seem to keep the relationship between capitalists (oil, other minerals, etc.) somewhat in balance though.

      note: keyword being somewhat

    • Re:Invitrogen (Score:5, Insightful)

      by Azghoul ( 25786 ) on Monday February 02, 2004 @12:18PM (#8159263) Homepage
      The company comes up with one way to GET the "polymerase enzyme". Why should they be forced to just give away their methods?

      That's a fair patent, if you ask me. Sure nature might have created the stuff, but getting at it is another question altogether!

      • Re:Invitrogen (Score:5, Insightful)

        by Lehk228 ( 705449 ) on Monday February 02, 2004 @12:21PM (#8159293) Journal
        did they patent a METHOD for harvesting polymerase enzyme or just the harvesting, if they patented a method then good for them, the invent something and should make money off it, if they patened all forms of extraction then they can burn in hell
        • Fair enough, and if they're trying to prevent anyone else from coming up with a new harvesting method, I agree with you.

          But I don't know that you can patent every possible method of achieving result X. I mean even if they're doing "just the harvesting" as you put it... they must have a method for doing so, mustn't they? :)

    • Re:Invitrogen (Score:3, Informative)

      by cinnamon colbert ( 732724 )
      way off base, in many ways..the bug is Thermus aquaticus; isolation of heat stable DNA polymerase, called Taq, was first described by a russian group, then patented by cetus for use in PCR. Many other companies have patented isolation of similar enzymes from other organisms, eg stratagene has pfu polymerase, from pyroccocus furiosis, there is alos pwo polymerase, vent, etc etc The patenting of a use for a natural product,or a method of obtaining a natural product is an intrinsic part of the patent system. I

    • not invitrogen, not the harvesting (Score:5, Informative)

      by Apogee ( 134480 ) on Monday February 02, 2004 @12:44PM (#8159514)
      If I remember corrently, the original patent for the use of thermostable Thermophilus aquaticus DNA polymerase belongs to Roche. Before I posted this comment, I checked in espacenet [espacenet.com] for any patents by Invitrogen regarding "thermostable" or "thermophilus" or "aquaticus". I couldn't find any hits.

      You are right, however, there are a number of patents regarding Taq polymerase, but they actually patent a method using this enzyme, or a laboratory-made mutation of this enzyme, mostly with the goal of improving fidelity of DNA replication. That is in accordance with established copyright laws (afaik -- ianal), they didn't simply patent something they found, but a method that uses it.

      If you are a researcher at a non-commercial institution, you are if I'm correctly informed, exempt from certain patent laws, and I heard of people who have their own expression vectors for Taq polymerase, and use it to produce polymerase for their lab's use.

      Also, no biotech company would go to the point of "harvesting" the polymerase from Thermophilus aquaticus, when you can have your friendly E.coli make the same protein in a much easier way.
    • Agreed, but how do we as a society stop companies from patenting naturally occuring components? Especially since the U.S. will most likely be leading the charge.

      Keeping people out is infeasible so they'll eventually get the material. We can't keep everyone out of something as big as Anarctica (couldn't even do that for a country the size of Iraq). Standards need created to prevent the patenting or additional provisions need created on what constitutes a patent.

    • Re:Invitrogen (Score:2, Informative)

      by Dr. GeneMachine ( 720233 )
      Well, native Taq polymerase is available from all major suppliers(Invitrogen, Stratagen, QIAGEN, etc), as well as different modified recombinant Taq derivates (NovaTaq, AmpliTaq, MasterTaq) - there's nothing remotely resembling a monopoly here. Of course, several recombinant polymerases are patented (HotStart, AccuPrime System, Platinum Taq) - but these are not as nature made them, but heavily modified and optimized systems.

  • extremophiles?! (Score:2, Insightful)

    by Anonymous Coward
    Extremophiles are micro-organisms that grow optimally in some of earth's most hostile environments of temperature (-2C to 15C and 60C to 115C),

    Uh.. I'll grant you that -2 celsius is damn extreme. But isn't 15 celsius just about 45 degrees farenheit? I'm pretty sure 45 degrees is fairly comfortable for most people in north america - especially during winter. And a lot of us have to deal with temperates of 10 degrees and under (0 to 3 degrees celsius)...

    • -2 to 15?

      Pah, that's a normal autumn/winter around here. And this is a city at 3328' - 7038'. Lots of miles to the south to get colder.

    • Yeah, but we humans survive by wearing an insulating layer (or several) woven from the the fibers of plants and skins of animals, both of which tend to be quite dead for the application... these studies look into how living creatures adjust their bodies to survive these temperatures, they're evolved a non-toxic (to them) anti-freeze...
    • I must be an extra extreme extremophile--as are the approx. 10,000 rabbits that infest my neighbourhood! In the past couple weeks it has gotten as cold as almost -40 Celcius. At -2 we just suck it up and put on a sweater when we have to go outside--fer cryin out loud that's about +30 F for the Metrically challenged out there--that ain't cold at all...
    • 45 degrees fahrenheit is a comfortable temperature for us. As long as that's the temperature of the air surrounding us.

      Replace air with liquid, and you've got a different situation altogether. Figure this, water at 70 degrees fahrenheit literally feels like ice water on human skin. 45 degrees is about the temperature of arctic seawater.
    • Read that again: optimally. As in, their proteins work best in this temperature range and perform poorly or not at all in higher temperatures. (Whereas most bacteria grow best in temperatures around or above room temp - I know the incubation room for my microbi class in university was quite warm.)

      And these are microorganisms in water, not animals with fur or clothes in air or surrounded by thick layers of blubber in water. They might have mixed up the negative sign, I dunno... but a human with a body t

  • You can't have it both ways.... (Score:5, Interesting)

    by RocketScientist ( 15198 ) * on Monday February 02, 2004 @12:12PM (#8159192)
    One of the biggest arguments of the folks who promote biodiversity is that we may find organisms that produce pharmaceuticals that we can use to do important things. That way biodiversity seems more commercially appealing (I'm not saying it is or isn't true, I'm just restating the argument.)

    So now we've got folks complaining because we're trying to exploit some of the organisms to produce pharmaceuticals. The priniciples of biodiversity are playing out as the advocates expected, and now a faction of those advocates are crying foul because somebody's actually exploiting the organisms for commercial gain.

    If you're going to use the biodiversity for exploitation argument, you can't complain when someone actually starts exploiting.

    • Re:You can't have it both ways.... (Score:5, Insightful)

      by DdJ ( 10790 ) on Monday February 02, 2004 @12:36PM (#8159450) Homepage Journal
      If you're going to use the biodiversity for exploitation argument, you can't complain when someone actually starts exploiting.
      Yes, we can. It all depends on how people exploit.

      If the exploitation is done by taking a small sample of the organism and then figuring out what compounds it produces that are so useful, and why they're so useful, and then reproducing those compounds and/or effects via an industrial process, that's a fine thing.

      Even if the exploitation is done by taking a gene sequence from a creature, throwing it on a plasmid, shoving that into a friendly bacterial culture, and growing the shit in a vat, that's a pretty decent thing.

      But if the exploitation is done by harvesting enough of the organism to pose a threat to its continued existence in the wild, then that's something that needs to be stopped (or we may have no more Truffula Trees, for example).
      • That is an excellent point.

        I believe that exploring extremophiles can give us great advances in anything from biomaterials to new drug leads. Put in the most simplest way, by looking at extremophiles, we are asking nature to show us its more uncommon solutions to problems. In these extreme environments, organisms have evolved some fairly impressive tricks just to stay alive (try staying alive in a hot water spring a somewhat over 80C for any length of time, and you'll see what I mean).

        The input we get fro
      • But if the value of its continued existence in the wild is predicated upon its potentially exploitable commercial value (as the argument goes, not as is necessarily the case), then that isn't something that needs to be stopped, except insofar as exterminating bacteria A may cause us to lose our supply of substance B.

        That's the problem with the "what about potential medical discoveries" argument: it devalues the organism in question by identifying its value solely with commercial/social gain. This implicitl

        • But if the value of its continued existence in the wild is predicated upon its potentially exploitable commercial value (as the argument goes, not as is necessarily the case), then that isn't something that needs to be stopped, except insofar as exterminating bacteria A may cause us to lose our supply of substance B.

          Not true, really. Exterminating bacteria A may cause us to never discover substance C to begin with. It may also cause us to lose species D, which prevents us from discovering substance E.

          I

      • No you can't.

        What about the popular "organic" label. There are a whole lof of pesticides, medicines, preservatives and the like which were developed in the way you mentioned. Evidently, some people don't like or understand that.
      • I work for a Biotech company. We make enzymes in 80 m^3 tanks. And we really only need one bacteria to start! Most organisms are genetically modified in order to increase yield anyway. So I don't really get the problem. One of our best selling enzymes was found in an organism less then 50 km from the factory. It doesn't always have to come from the poles.
      • >(or we may have no more Truffula Trees, for
        >example).

        But thneeds are what everyone, everyone, EVERYONE needs.

        -l

        (unless)

  • why not open source science? (Score:5, Interesting)

    by ir0b0t ( 727703 ) * <{gro.aluossimnepo} {ta} {llewejm}> on Monday February 02, 2004 @12:15PM (#8159231) Homepage Journal
    This is the sort of story that illustrates the risk inherent in a proprietary approach to knowledge. The first duty of a proprietary interest is to secure a financial return on investment. There's a built-in incentive to discount other competing interests, like stifling innovative software or, as in this case, damaging the environment.

    • Because science is expensive (Score:2, Insightful)

      by Anonymous Coward
      Real science is not like software. You can't take a bunch of former HTML coders, teach them perl, and let them hack away on a couple of thousand dollars worth of laptops to create "the next big thing." It takes real money to pay for real propellerhead scientists using expensive equipment to make the discoveries upon which your future well-being will depend.

      Most of these discoveries end up producing nothing because the original hypothesis was wrong or the end result ended up not making it through the test

  • Not much bias there, eh? (Score:5, Insightful)

    by Aumaden ( 598628 ) <Devon.C.Miller@nOsPaM.gmail.com> on Monday February 02, 2004 @12:19PM (#8159276) Journal
    This seems like typical overreaction. The concern expressed in the article is that there are no regulations on bio-prospecting. Heck, they even admit, "We're not saying there's much danger of environmental damage."

    And "bio-prospecting" is such a loaded term. "Prospector" evokes images of an old, grizzled prospector wearing filthy clothes, leading an overburdened pack mule and "lookin' fer gold in them thar hills." We don't label physicists "particle-prospectors", after all.

    • Agreed. I might be considered a "prospector", but we use airborne geophysics [state.ak.us], geochemistry, and computer programs such as GIS and for other data processing tasks (modern exploration generates a huge amount of data). Here is an article [alaska-freegold.com] about the role of organisms in bringing metals to the user (you). After all, if we don't mine it, we have to grow it. And I don't see agriculture growing raw materials for computers. Some more info here [alaska-freegold.com]: "Two thousand years ago, the Romans noticed that the runoff from the tail

  • hyperstable macromolecules (Score:3, Funny)

    by torpor ( 458 ) <ibisum.gmail@com> on Monday February 02, 2004 @12:19PM (#8159282) Homepage Journal
    yay, nano-slavery!

    t-minus 5 years and counting to 'grow your own processor' vat kits for teenagers and above ...

  • I support the use of extremophiles. (Score:5, Funny)

    by burgburgburg ( 574866 ) <splisken06NO@SPAMemail.com> on Monday February 02, 2004 @12:23PM (#8159314)
    It's the reason that I personally jam over 15 pounds of antartic fish into my radiator every winter. And while the smell can be a bit noisome (especially when the heater is on), it's obviously environmentally friendly and much cheaper than anti-freeze (except for the cost of shipping all those fish, which, now that I think about it, is really expensive).

    I've changed my mind.

  • For those who have no idea whats this about. (Score:5, Informative)

    by sugar and acid ( 88555 ) on Monday February 02, 2004 @12:28PM (#8159372)
    Extremophiles are organisms that live at the edge of the range of environments life can exist in. Essentially very hot (at boiling water temperatures), to extreme cold temperature (cell contents should be freezing but they don't), to high acidity, alkalinity, or high salt. concentrations.

    They are a literal gold mine for biotech companies. Heat extremophiles are a great source of heat stable enzymes that work in almost boiling water. This makes them good for many industrial processes and also makes them easy to make and purify in a none extremophile organism (you grow it up in the bacteria, smash open the cells and cook the contents till the only thing left active is the heat stable protein).

    Cold tolerant organisms have great antifreeze techniques, as well as a source of enzymes that are able to work efficiently at cold temperatures. Handy for many industrial processes and even as additives in such mundane things as laundry detergent that is designed for use in cold water. The anitfreeze may have applications in crygenic applications (more pratically for freezing tissue samples and organs rather than a whole human).

    The problem with cold extremophiles is the biggest source exist in Antartica, and people are sensitive about what happens in that region of the world. The point I should make is that this research will only require sampling and identification and growth in the lab of these organisms, and is really a pratical outgrowth of the scientific research already carried out in Antartica. These organisms are not going to be "harvested" in Antartica for any commercial purpose, and I can't see further research in this area creating anymore disturbance to the ecosystem than the research already carried out in Antartica since the first explorers. If anything this increases the need to preserve the ecosystem, along the same lines as the saving rainforest for the potential undiscovered medicinal plants.

    • "literal gold mine" (Score:3, Interesting)

      by iota ( 527 ) *
      They are a literal gold mine for biotech companies.

      I don't often pick nits, but this one always bothers me...
      Unless the extremophiles are actually an "excavation in the earth from which gold can be extracted" they are not literally a gold mine. They are figuratively a gold mine.

      Anyway...

      These organisms are not going to be "harvested" in Antartica for any commercial purpose, and I can't see further research in this area creating anymore disturbance to the ecosystem than the research already carried out
      • Point taken on literally, its a bad writing/speaking habit I picked up in my youth, and its very hard to shake. I cranked out this short description at work and was trying to do it quick, hence not editing it properly for that kind of stuff.

        Second they are not going to harvest fish for this kind of thing I don't think, but genetically engineer some organism and culture or farm them.

        Anyway fishing for food is already a major issue at the poles. Big factory ships in international waters scarfing up huge qu
    • Why the Antartic? Has everything in the Artic been killed off already?

  • On the horizon... (Score:5, Funny)

    by MarsCtrl ( 255543 ) on Monday February 02, 2004 @12:30PM (#8159388) Homepage Journal
    Potential discoveries include glycoprotein, which prevents Antarctic fish from freezing
    Scientists expect this reasearch to lead to exciting new research in the field of pre-thawed frozen fish sticks.

  • Alternatives to Exploiting Evolution's Accidents (Score:5, Interesting)

    by G4from128k ( 686170 ) on Monday February 02, 2004 @12:30PM (#8159390)
    Do we really need these extremophiles? Only if we have no other means of obtaining novel biological and pharmcological materials.

    Biological and medical science has come a long way from the "lets eat this herb and see if it does anything" mode of experimentation. Genomics, proteomics, combinatorial chemistry, and high throughput screening are all means for engineering new chemicals rather than waiting to discover some organism that happens to produce some useful compound. Advances in simulation, protein folding, in silico pharmacodynamics & pharmacokinetics mean that scientists and engineers can design new chemical species that do what we need them to do.

    My point is that although these extremophiles do offer an interesting source of innovation, they are not the only means for finding cures for cancer or novel materials. Although we may have much to learn from nature, we approach the day when no longer need this haphazard ancient dataset.

    Soon we will design drugs, rather than find drugs.

    • Re:Alternatives to Exploiting Evolution's Accident (Score:3, Interesting)

      by Anonymous Coward
      Of course we need extremophiles. As of yet, no, or very few drugs been synthesised "de novo". The methods you mention are mainly used to examine compounds found in nature and then to improve these. The only only method with a bit of hope of creating completely new drugs is "Combinatorial Chemistry", but is more of a exhaustive search of several thousand random compounds. As of today, no or very few scientists try to create completely new proteins. Why create new when you can use those which have evovled for

    • Re:Alternatives to Exploiting Evolution's Accident (Score:2, Informative)

      by Anonymous Coward
      Most molecular biology techniques which led to the knowledge you are talking about require enzymes which were discovered in extremophile bacteria.

      The prime example is Taq DNA polymerase, used in almost every Polymerase Chain Reaction experiment ever. It comes from an extremely heat tolerant bacterium. With no PCR, you can't do meaningful DNA sequencing, and the entire science of genomics, and most modern molecular biology, would be dead in the water.

      This even includes protein structure determination. W

    • Re:Alternatives to Exploiting Evolution's Accident (Score:4, Interesting)

      by Anonymous Coward on Monday February 02, 2004 @01:04PM (#8159687)
      Quick tutorial in drug discovery. First of all, that term doesn't describe what your nosy Aunt Mildred does when you're out, but, rather, describes how pharma companies hunt for new products. Essentially, zillions of chemical compounds are tested for biological activity, in a process called ultra high throughput screening. This involves heavy use of automation: robots, image capture and processing, etc. And computers. Lots and lots of computers.

      One of the critical issues is the chemical diversity space of the zillions of screened compounds. The more diverse the chemical space, the more likely you'll fine some promising leads. Broadly, there are two ways that high diversity are generated: 1) by organic synthesis, combining lots of organic chemical groups, in lots of ways (combinatorial chemistry), or, 2) by harvesting natural compounds, which are just plants and animals liquified by a Waring Blender. It turns out that natural compounds tend to represent a larger chemical diversity space, and, therefore, may be more likely to contain novel pharmaceuticals. (The details and reasons are way beyond the scope this post. Take an organic chem course, followed by a biochem course, and you'll understand.)

      Here's [acs.org] a pretty readable article that explains more.

    • Re:Alternatives to Exploiting Evolution's Accident (Score:5, Informative)

      by Apogee ( 134480 ) on Monday February 02, 2004 @01:12PM (#8159744)
      Soon we will design drugs, rather than find drugs.

      I hope that we will one day indeed design rather than blindly search. We're centainly on the road to it. But then again, I heard the same line about designed drugs coming soon when I started studying biology, and that was, hmm, about 10 years ago.

      To be fair, rational design has made some big steps forward, but the number of drugs and drug candidates that were designed completely in silico is really small. Likewise, the combinatorial chemistry approach is useful, but hasn't kept up with the big promises that hyped this approach maybe 5 years ago. But I may be biased there, the idea of blindly throwing together molecules and then letting a high-throughput assay sort out what works and what doesn't has always rubbed me as somewhat contrary to the ideal of science. It's a bit like simply bringing in more and faster monkeys to get that shakespeare play written.

      Combinatorial chemistry and rational drug design can still learn a lot from nature, and in fact the two can be combined. It is impossible (and will stay so even in the future) to examine all possible chemical structures for a desired activity. For instance, there are 10^62 different molecules of a molecular weight below 500, a typical cutoff for drug molecules. If you would synthesize one molecule of each, you'd make a ball of mass that covers the whole solar system. (quoting from a recent seminar by Prof. H. Waldmann [mpi-dortmund.mpg.de]).

      We can't explore the whole chemical diversity, but we may not need to. If you compare a random molecule library to one based on substructures occurring in nature, you'll find that the "natural" library has much higher hit rates than the random one. In a way, nature has worked for us as a filter, selectively enriching substructures that are meaningful in the context of proteins and receptors. Proteins are largely composed of conserved folds, therefore the structures that bind to them are likely to have conserved structures as well. Considering the more creative solutions nature uses to overcome extreme problems will enrich this library of natural structures, and thus be beneficial to rational drug design.
      • Combinatorial chemistry and rational drug design can still learn a lot from nature, and in fact the two can be combined. It is impossible (and will stay so even in the future) to examine all possible chemical structures for a desired activity. For instance, there are 10^62 different molecules of a molecular weight below 500, a typical cutoff for drug molecules. If you would synthesize one molecule of each, you'd make a ball of mass that covers the whole solar system. (quoting from a recent seminar by Prof.
    • Soon we will design drugs, rather than find drugs.

      Nature has been creating new drugs for hundreds of millions of years. Why shouldn't we use this valuable resource?

  • Not accurate (Score:4, Insightful)

    by CXI ( 46706 ) on Monday February 02, 2004 @12:31PM (#8159395) Homepage
    Um, what? Food chain, environmental ramifications???

    If the submitter had RTFA, he would have read the quote from the co-author:

    "We're not saying there's much danger of environmental damage, but it does pose a challenge."

    The challenge is simply one of patents and scientific sharing, not the extremist (ironic no?) view described above.

  • Learning from Extremophiles... (Score:3, Funny)

    by Glowing Fish ( 155236 ) on Monday February 02, 2004 @12:32PM (#8159403) Homepage

    Can I call my browsing of the stranger Y! Member Profiles scientific research now?

  • HOw can one describe a potential discovery ? Perhaps you mean potential uses for already known things, or new versions of already known things. The antifreeze protein thing is OOOOLLLD. Also, there is little danger to these organisms: either they are abundant in their natural habitats, in which case harvesting a few for lab use is no problem, or they are rare in their native habitats, in which case they are species that have already lost the evolution lottery

  • Glycoprotien is more than one. (Score:5, Informative)

    by io333 ( 574963 ) on Monday February 02, 2004 @12:38PM (#8159468)
    You wrote it as though "glycoprotein" is a recent discovery. Actually a glycoprotein is a class of substances, to wit:

    A sugar (usually a ketose or aldose) attached to a protein. There are *many*. They've been known about for ages. Perhaps you mean that they've discovered an *interesting* glycoprotein?

  • You have got to be kidding me! (Score:4, Interesting)

    by genetic_freak ( 673003 ) on Monday February 02, 2004 @12:45PM (#8159534)
    Any one who thinks that taking a shovel and bucket to antartica to collect organisms growing in the ice and snow is an econoically viable option is insane. The pin head sized colony of bacteria that they bring back to start production sized cultures in controlled fermeters will never affect the environment.

  • Hmm (Score:3, Informative)

    by Perianwyr Stormcrow ( 157913 ) on Monday February 02, 2004 @01:01PM (#8159656) Homepage
    Well, if we're being idiots and just sucking up mass quantities straight out of the wild, I could see it being a problem. But these lifeforms do live in weird places, so I can't imagine that it's cheap to do that.

    Better to figure out what makes them tick and go and have much friendlier sorts of bacteria make the things we need in places you don't need an icebreaker or a submarine to get to.

  • Computer Modeling and Synthetics (Score:4, Interesting)

    by Seanasy ( 21730 ) on Monday February 02, 2004 @01:36PM (#8159965)

    You don't harvest extremophiles for these substances. You model the substance and find a synthetic analog [psc.edu]

    .

  • this is not like clearcutting rainforests. (Score:4, Insightful)

    by caino ( 683265 ) on Monday February 02, 2004 @01:59PM (#8160175)
    Harvesting a couple of specimens for characterization will not disrupt the antarctic food chain, particularly with the bacterial species. It will just be a matter of creating the appropriate "extreme" habitat/culture conditions, and these organisms can be studied anywhere. There's no way that pfizer or someone else is going to go set up shop down there. Researchers will take a handful of antarctic specimens and study their function elsewhere.

  • Cool (Score:5, Interesting)

    by Pedrito ( 94783 ) on Monday February 02, 2004 @02:23PM (#8160408)
    Potential discoveries include glycoprotein, which prevents Antarctic fish from freezing...

    I wonder if this sort of thing could ever have application in cryogenics of human beings. Right now, my understanding is that cryogenics is a crock because the freezing process causes the cells in the body to, for lack of a better word, explode. I doubt we'll ever encounter technology to undo that. If you could somehow protect the integrity of the cells during the freezing process however, reanimation should be feasible at some point.

    Of course, I don't know if the whole cryogenics thing is worthwhile as is. But for space travel, even within our own solar system, it could come in quite handy by reducing the need for perishables (food, water, oxygen) as well as being easier to shield the astronauts from radiation by only having to provide serious shielding in a very confined space.

    Anyway, that just seems like a cool possibility some day.

    • Re:Cool (Score:3, Informative)

      by pclminion ( 145572 )
      Right now, my understanding is that cryogenics is a crock because the freezing process causes the cells in the body to, for lack of a better word, explode.

      More like they pop, as in a popping balloon. It isn't the expansion of water inside the cell which bursts it (the membrane is elastic), it is the fact that ice crystallizes and forms very sharp crystal edges which cut through the cell membrane like a knife edge.

      The idea behind cryogenic flash freezing is that by freezing the tissue extremely quickly,

    • Modern cryonics uses a sophisticated combination of chemicals and rapid cooling to achieve vitrification of the brain. This is exactly what it sounds like. Water is cooled rapidly and with inhibitors to get right past the danger range where crystalization occurs and down into the nice safe ranges of a couple of hundred degrees below 0 (centigrade, fahrenheit, whatever, I'm being all approximate anyway).

      They've been getting really good at this, modern methods improving the amount that can be flash-frozen
  • Another extraplanetary analogue is Lake Vostok, a subglacial lake detected seismically 3.6 km below the Antarctic icecap.

    Has the seismic detection already altered the environment? How will we know without further altering the environment?

    This is the cost of exploration. Either we accept and mitigate as best we can. Or deny our inner spirit and lapse into over cautious passivity.

  • Renumeration (Score:2, Insightful)

    by canineK9 ( 688795 )
    When bioprospectors search tropical areas, the more accepted practice is to partner with the indigenous people so they can benefit from any financial rewards made from the bio-findings. Since Antarctica is property held in common (like the Moon: eh, W.?) by the entire human species, shouldn't any profit sharing go to an international body?
  • We ought to be able to genetically engineer stuff that can being terraforming Mars. Full speed ahead!
  • If you do research in a country, it is usual to apply for a patent in that country before you apply for any others. Often it is easier and more cost-effective, and a good way of establishing precedence. Now, Antarctica as an unusual international status, but it has been assigned one of the two letter patent codes, like 'US' for USA.

    Maybe part of the solution to the intellectual property free-for-all from exploiting extremophiles might be to establish an Antarctic patent office to go with the letters.

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