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Learning (And Harvesting) from Extremophiles

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."

192 comments

  1. Extremophiles? by Anonymous Coward · · Score: 0, Funny

    Is that like Michael Jackson bungee jumping?

  2. Oh. by proj_2501 · · Score: 5, Funny

    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.

    1. Re:Oh. by NixLuver · · Score: 1

      LOL! Exactly.. for a moment I thought the article was about Linux Zealots and Windows Fanboys, and I was wondering how anyone was going to exploit those aberrations to profit...

    2. Re:Oh. by Anonymous Coward · · Score: 0

      go barefoot skiing on a busy inland lake and you'll feel like your right at home on the highway. then of course, you can't even begin to get up barefoot if there is another boat around.

    3. Re:Oh. by dedalus2000 · · Score: 1

      funny, I read it and thought organ harvisting from unlucky base jumpers.

      --
      My keyboads not woking popely.
    4. Re:Oh. by proj_2501 · · Score: 1, Offtopic

      Barefoot skiing on pavement? YIKES!

    5. Re:Oh. by Anonymous Coward · · Score: 0

      haha, well from my experience slalom skiing is pretty interesting when you have to watch out for thirteen year old jetskiers crossing your wake about fifty feet from you or less. and you tend to point your head downwards during a spinout.

    6. Re:Oh. by andih8u · · Score: 1

      for a moment I thought the article was about Linux Zealots and Windows Fanboys, and I was wondering how anyone was going to exploit those aberrations to profit

      easy, put the two in a room together, generate heat energy from friction

      --


      slashdot, news for crazed liberal socialist zealots
    7. Re:Oh. by Anonymous Coward · · Score: 0

      That's exactly what I was thinking. My mind crashed into the word "glycoprotein" and the most bizzare image came to mind of this fanboy I know hooked up to medical equipment having his glycoprotein extracted.

      I really need to get more sleep...

    8. Re:Oh. by lonb · · Score: 1

      i can empathize... i had to read the article to learn what 'food' is. Someone pass the nachos.

      --
      "Ain't I a stinka..." - Bugs
    9. Re:Oh. by Anonymous Coward · · Score: 0

      LOL! Exactly.. for a moment I thought the article was about Linux Zealots and Windows Fanboys, and I was wondering how anyone was going to exploit those aberrations to profit...

      Simple:
      1. Put Linux Zealot and Windows Fanboy in same room
      2. ???
      3. Profit!

    10. Re:Oh. by Anonymous Coward · · Score: 0

      I had to read the article

      No! Shocking! You actually had to read the article before feeling that you knew enough to post a reply? That's a serious violation of your Slashdotter rights. Sue Slashdot.

    11. Re:Oh. by Anonymous Coward · · Score: 1, Funny

      I thought extremophiles refered to Howard Dean supporters.

  3. It's not like its strip mining by Anonymous Coward · · Score: 5, Insightful

    Is some great white hunter scientist with a cotton swab and a sequencer really going to be a threat to Antarctica?

    1. Re:It's not like its strip mining by kfg · · Score: 5, Funny

      Haven't you ever had a throat culture taken?

      Man, them cotton swabs is deadly weapons, I'm tellin' ya.

      KFG

    2. Re:It's not like its strip mining by kabocox · · Score: 1

      Yeap, cause the microscopic organisms on the scientist might gasp out compet these organisms that have spent their entire lives in this one "extreme" enviromment. Yeah right. They are extreme environments for humans and most known life. I wonder how durable these organisms actually are. Could they actually oh reproduce and live out in the oceans near the surface, on land, or in the air? I bet they would consider us extreme organisms as well.

    3. Re:It's not like its strip mining by Anonymous Coward · · Score: 0

      A pen is not a sword, and yet we think it mighty.

      The research is being done to search for ways to exploit the natural resources in those areas. Cause leeds to effect, and knowledge still serves greed.

    4. Re:It's not like its strip mining by Rupert · · Score: 3, Funny

      They use those cotton swabs in places much more sensitive than your throat. I've had broken bones that hurt less.

      --

      --
      E_NOSIG
    5. Re:It's not like its strip mining by Syrrh · · Score: 1

      Bah! Whippersnappers!

      I had my first throat culture last week, expecting a fistful of steel wool rammed down my throat. It was nothing, and I don't even have a high tolerance for pain. I'm almost to the point where I'm excited to lean how insignificant medical procedures really are after the hype. Blood samples, wisdom teeth extraction, ECG, various shots, tests, pills and medical torture implements... No big deal. Some were even kinda fun, in a twisted way.

      Hell, at this point I'm ready to go for colonoscopy and a root canal, just to see how bad they really aren't...

  4. Extremophiles by Anonymous Coward · · Score: 5, Funny

    Is that one of those Audiophiles that buys all the best equipment and scoffs at CD audio in favor of DVD audio?

    1. Re:Extremophiles by Anonymous Coward · · Score: 0

      DVD audio is inferior to SACD because SACD uses the superior DSD encoding rather than legacy PCM. Thank you.

    2. Re:Extremophiles by Anonymous Coward · · Score: 0

      For the true audiophile it's vinyl all the way baby!!!

      (They are of course hideously wrong.)

    3. Re:Extremophiles by Anonymous Coward · · Score: 0

      Audiophiles? Such silliness! Of course not. That's one a them there extraterrestrials that have sex with our wimmins to cure their acne. You know, like GUBOSH RAH guy. They only do it in Arkansas trailer parks, though, which is why they're called extremophiles.

  5. Brilliant. by musingmelpomene · · Score: 5, Insightful

    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.

    1. Re:Brilliant. by Anonymous Coward · · Score: 0

      i believe he meant exploitation by businesses, not enviromentally concerned researchers / scientists.

    2. Re:Brilliant. by yotto · · Score: 5, Funny

      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...

    3. Re:Brilliant. by Azghoul · · Score: 2, Insightful

      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.

    4. Re:Brilliant. by Anonymous Coward · · Score: 0

      Odds are fire comes first, since it's a naturally created thing. Lightning hits a tree, trees catch fire, etc. A wheel requires a human to invent it. The Mayans made huge cultural leaps without a wheel, although they did have zero.

    5. Re:Brilliant. by CFBMoo1 · · Score: 1

      Well depending on what he burned the whole tribe could have been stoned if it was some ancient canabis plant or something.

      Also probebly the only way the guy who made the wheel got burned was sniffing too lose to the fire. Or he may not have gotten burned at all cause they were too stoned to care.

      --
      ~~ Behold the flying cow with a rail gun! ~~
    6. Re:Brilliant. by I_Want_This_ID · · Score: 2, Insightful

      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"

    7. Re:Brilliant. by cens0r · · Score: 1

      Actually they did have the wheel... but only on toys (if I remember correctly, but I could be confusing them with the aztecs). The research I've read says they probably never made the leap to the wheel because of their lack of draft animals.

      --
      Jack Valenti and Orrin Hatch will be first up against the wall when the revolution comes.
    8. Re:Brilliant. by teromajusa · · Score: 1

      Go back and read the article. The concern is not so much environmental impact but that the spirit of open research will be lost.

    9. Re:Brilliant. by nomadic · · Score: 3, Funny

      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.

    10. Re:Brilliant. by localman · · Score: 4, Insightful

      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.

    11. Re:Brilliant. by drinkypoo · · Score: 4, Insightful
      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.

      --
      "You're right," Fisheye says. "I should have set it on 'whip' or 'chop.'"
    12. Re:Brilliant. by Anonymous Coward · · Score: 0

      At the risk of going even further off topic, I believe you may have the Aztecs and Mayans reversed, since the Mayans did have draft animals. Namely, llamas. They also had roads, but what they didn't have was flat land that a llama-drawn cart could cross.

    13. Re:Brilliant. by the+gnat · · Score: 4, Insightful

      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.

    14. Re:Brilliant. by drinkypoo · · Score: 1

      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, is beyond me. But, the question of carrying capacity is certainly an interesting one. However, as long as technology keeps increasing, so will carrying capacity, if we use it properly.

      --
      "You're right," Fisheye says. "I should have set it on 'whip' or 'chop.'"
    15. Re:Brilliant. by TomRC · · Score: 1

      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 gumption (or haven't bothered to invest in the skills) to join in the 'gold rush'.

      Put ME squarely in that "extreme" camp opposed to those who claim to be fretting over unproven and likely insignificant "problems", when there are so many real problems in the world - some of which may be solved by research into the nature of these creatures.

    16. Re:Brilliant. by localman · · Score: 1

      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?

      Cheers.

    17. Re:Brilliant. by Anonymous Coward · · Score: 0

      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.

      Some shread of evidence is always possible, otherwise only the timecube guy would worry. Convincing is relative, some people may not be convinced until lasting harm is already done and there's nothing else to pin it on. (Even then, how do you know it's "lasting harm"?)

      Basically, you've set your standard so high that it can't be met.

    18. Re:Brilliant. by Azghoul · · Score: 1

      Can't find much wrong with what you're saying here. Facts are, more technology = more food per acre (per "resource" used to create that food) = less overall land used for agriculture. We could feed everyone in the world, have plenty of surplus, and have tons of spare land left over.

      But no, let's starve the Africans lest our EVIL corporations let loose their EVIL GMOs!!!

      Heh.

    19. Re:Brilliant. by Anonymous Coward · · Score: 0

      "At the risk of going even further off topic, I believe you may have the Aztecs and Mayans reversed, since the Mayans did have draft animals. Namely, llamas. They also had roads, but what they didn't have was flat land that a llama-drawn cart could cross"

      Incas are the American Indians in Peru with llamas and no flat land.

      Aztecs are the American Indians in central Mexico with no big animals to pull stuff.

      Mayans are the American Indians south of Mexico, in the south of Mexico and on that peninsula that sticks out creating the southern border to the gulf of Mexico.

      The Mayan civilazation collapsed prior to Columbus while Europeans brought down the other two with advanced weapons and disease.

      None of the three had wheeled vehicles larger than toys at the time of Columbus. All three do now.

      All three have a living language, culture, and continued repression by European blooded peoples living on all the best land stolen from them.

      I'm 1% Iroquois myself. So says grandpa.

    20. Re:Brilliant. by Concerned+Onlooker · · Score: 1
      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?

      --
      http://www.rootstrikers.org/
    21. Re:Brilliant. by Anonymous Coward · · Score: 0

      Thanks for clearing that up so concisely. In exchange for your knowledge of ancient cultures, I offer you a small piece of geographic knowledge: The peninsula you referred to is called the Yucatan Peninsula.

    22. Re:Brilliant. by Anonymous Coward · · Score: 0

      The problem is that the court of public opinion weighs emotions and not facts.

      You just described the whole Democratic party platform.


      +------
      Oops. I must have checked the Anonymous Coward button.

  6. There is a bad joke here someplace... by Saeed+al-Sahaf · · Score: 5, Funny
    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...

    --
    "Who are in control, they are not in control of anything - they don't even control themselves!" - Glen Beck
    1. Re:There is a bad joke here someplace... by kfg · · Score: 5, Funny

      Bunch of posers. Real extremophiles inhabit the alt groups of usenet.

      Stupid git.

      KFG

    2. Re:There is a bad joke here someplace... by Lehk228 · · Score: 3, Funny

      those are pedophiles

      --
      Snowden and Manning are heroes.
    3. Re:There is a bad joke here someplace... by kfg · · Score: 3, Funny

      Why is everybody always picking on cyclists?

      KFG

    4. Re:There is a bad joke here someplace... by Saeed+al-Sahaf · · Score: 1
      Why is everybody always picking on cyclists?

      No, pedophiles are people with foot fetishes.

      --
      "Who are in control, they are not in control of anything - they don't even control themselves!" - Glen Beck
    5. Re:There is a bad joke here someplace... by Anonymous Coward · · Score: 0

      Hey! Read the faq and don't top-post!

    6. Re:There is a bad joke here someplace... by Anonymous Coward · · Score: 0

      umm... wtf?

    7. Re:There is a bad joke here someplace... by kfg · · Score: 1

      Hey asswipe, *Hitler* banned top posting!

      KFG

    8. Re:There is a bad joke here someplace... by qw(name) · · Score: 1

      What about PETAphiles?

      Those are people who believe everything the People for the Ethical Treatment of Animals state as fact.

    9. Re:There is a bad joke here someplace... by Saeed+al-Sahaf · · Score: 1

      No, PETAphiles are those that have an obsession with Middle Eastern food.

      --
      "Who are in control, they are not in control of anything - they don't even control themselves!" - Glen Beck
    10. Re:There is a bad joke here someplace... by JackCroww · · Score: 1

      pItaphiles...

      --
      "Ayn Rand is a bloody socialist compared to me." - Robert A. Heinlein
    11. Re:There is a bad joke here someplace... by Sylver+Dragon · · Score: 1

      And here all this time I though PETA was:
      People for the Eating of Tasty Animals. Who knew?

      --
      Necessity is the mother of invention.
      Laziness is the father.
  7. Invitrogen by Ann+Coulter · · Score: 5, Insightful

    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!

    1. Re:Invitrogen by Beatbyte · · Score: 0

      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

    2. Re:Invitrogen by Azghoul · · Score: 4, Insightful

      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!

    3. Re:Invitrogen by Lehk228 · · Score: 5, Insightful

      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

      --
      Snowden and Manning are heroes.
    4. Re:Invitrogen by Azghoul · · Score: 1

      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? :)

    5. Re:Invitrogen by Anonymous Coward · · Score: 0

      OMG Save the bacteria! Won't anyone please think of the bacteria! Let's go march of washington! "NO BACTERIA FOR OIL!"

    6. Re:Invitrogen by Anonymous Coward · · Score: 1, Funny

      The bacteria which live in fish that keep the food chain going that.... wait for it... keeps you from being DEAD!

      Maybe you went to a school that wasn't allowed to teach science. That's ok, the rapture will come soon enough. Right?

    7. Re:Invitrogen by cinnamon+colbert · · Score: 3, Informative

      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. It may not be fair, or right, but thems are the rules. Actually, the cost of heat stable polymerase is not that great (related to other parts of the proces, such as dNTPS, etc) it is the cost of the license for the process, such as a pcr licence, that is exspensive.

    8. Re:Invitrogen by SummerMan · · Score: 1
      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.

    9. Re:Invitrogen by Anonymous Coward · · Score: 3, Insightful

      Newsflash: No one is deploying 100,000 nazi scientist stormtroopers to Anarctica with syringes to extract bacteria from 1,000,000 fish and kill them off. Research is all about finding ways to artificially synthesize these organisms & their byproducts in a lab.

    10. Re:Invitrogen by kfg · · Score: 1

      Is their method truly an invention, or just the end result of some engineering labor any other expert in the field would duplicate given the same task?

      If I build a game controller the controller itself may or may not be patentable, but the particular values of the resistors and capcitors I use are not. The values are not part of the invention and are, at best, trade secrets, until I file for the patent.

      Yes, I have expended time and labor to determine those values, just as anybody else could. I have also expended time and labor when I fix your car. That doesn't mean I carry any extended rights on your car.

      KFG

    11. Re:Invitrogen by Dr.+GeneMachine · · Score: 2, Informative

      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.

      --
      This comment does not exist.
    12. Re:Invitrogen by Anonymous Coward · · Score: 0
      No more stupid than some government claiming this plant or that plant is illegal. Hell, next thing you know, they'll be outlawing animals. Oh wait, they already did that, and guess what? Wolves almost went extinct in North America because of the government bounties on them.

      No, I'm not saying everyone should be smoking up or collecting magic mushrooms, and I don't use any mind altering substances myself - other than the rare bit of alcohol, but I find it ridiculous that something nature created should be outlawed by mere men.

      I strongly believe that we have to do 2 things: use what nature and our own innovation gives us to IMPROVE ourselves; and take responsibility for our OWN choices. Not to the point of exploitation or making choices for others (hint: You make someone elses choice, they don't want to take the responsibility).

      If something adverse happens in the antarctic because of this research, I highly doubt it would continue past the point of no return - or even to the point of any real distress. Hell, global warming is probably a bigger danger than these scientists.

      Research is how we apply our innovation to learn what nature has given us, and there are bound to be mistakes. If we don't learn, we fail to fulfill #1. If we fail to learn from our mistakes, then we fail in #2.

      I know this is by far the worst flamebait posted in this thread, but that's my story and I'm sticking to it :)
      </rant>
  8. extremophiles?! by Anonymous Coward · · Score: 2, Insightful

    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)...

    1. Re:extremophiles?! by SoTuA · · Score: 1
      -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.

    2. Re:extremophiles?! by Anonymous Coward · · Score: 0

      -2C to 15C damn extreme? That's fucking t-shirt weather up here. (In the winter, anyway.)

    3. Re:extremophiles?! by Orne · · Score: 1

      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...

    4. Re:extremophiles?! by plastik55 · · Score: 1

      I doubt that even north americans could survive long at a body temperature of 15C.

      --

      I have a positive modifier on Troll. When I mod someone Troll their karma should go UP!

    5. Re:extremophiles?! by zerobeat · · Score: 1

      15 celsius might seem warm especially this time of the year in the Northern Hemisphere, but your body is not actually at 15 C. It's at about 37 C. Biology moves slowly at about 15 C, but some organisms can still grow optimally at 15 or less. Human cells are not one of them

      --
      What other people think of me is none of my business
    6. Re:extremophiles?! by canineK9 · · Score: 1

      That is probably a typo and should be -2 to -15 C (+15 C = +59 F).

    7. Re:extremophiles?! by iq+in+binary · · Score: 1

      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.

      --
      Of all the Universal Constants, here's one I know: Nice guys finish last ;)
    8. Re:extremophiles?! by ggvaidya · · Score: 1

      Proteins work best at 37 deg C, so any organism which works best at temperatures far enough away from 37 deg C to be interesting, qualifies as an extremophile.

      Then again, this *does* look like a typo ...

    9. Re:extremophiles?! by Rob+Simpson · · Score: 1
      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 temperature of less then, say 30 degrees will generally have no (or undetectable) pulse, no breathing, no reflexes or responsiveness, and appear to be dead of hypothermia (and will be very shortly unless something is done).

  9. Re:The human race is doomed by Anonymous Coward · · Score: 0

    C'mon, that is a dumb thing to say even by troll standards.

    Everyone knows punch cards where an essential step towards the development of interactive computing.

  10. You can't have it both ways.... by RocketScientist · · Score: 5, Interesting

    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.

    1. Re:You can't have it both ways.... by DdJ · · Score: 5, Insightful
      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).
    2. Re:You can't have it both ways.... by Apogee · · Score: 1

      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 from extremophiles is valuable, because it is tried and proven to work. I see the benefit, however, more in a gain of knowledge than in actually harvesting these creatures. Such a responsible exploration can lead to new interesting molecules without killing off species. Hopefully there's enough financial interest in learning from an extremophile versus harvesting the extremophile organism, since finding/growing/hunting extremophiles tends to be expensive, and if the molecule can be made synthetically or using bacterial/eukaryotic expression systems, this should prove economically more interesting.

    3. Re:You can't have it both ways.... by Control+Group · · Score: 1
      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 implicitly accepts that, given an adequate commercial/social gain, extinction of a species is a legitimate tactic.

      Which is not, actually, what proponents of the argument mean (in my experience, anyway).

      --

      Reality has a conservative bias: it conserves mass, energy, momentum...
    4. Re:You can't have it both ways.... by DdJ · · Score: 1
      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.

      In other words, you can value its continued existence in the wild on an economic basis without tying it to a single known chemical compound, and you would be wise to. You wanna keep that biodiversity up, and study the bejezis out of it.
    5. Re:You can't have it both ways.... by Goldsmith · · Score: 1

      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.

    6. Re:You can't have it both ways.... by spectrokid · · Score: 2, Informative

      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.

      --

      10 ?"Hello World" life was simple then

    7. Re:You can't have it both ways.... by PitaBred · · Score: 1

      You know what's funny? Even people who eat organic food and all that have as high a pesticide levels in their blood as the rest of us "normals"

    8. Re:You can't have it both ways.... by Loligo · · Score: 1

      >(or we may have no more Truffula Trees, for
      >example).

      But thneeds are what everyone, everyone, EVERYONE needs.

      -l

      (unless)

  11. Re:The human race is doomed by kfg · · Score: 3, Insightful

    Yeah. I remember vacuum tube compters. I personally scratch built one. While it's abilities were somewhat limited compared to those of today I'd note that it was functionally superiour to those commonly in use today.

    It didn't do much, but it did what it did.

    Today's computers are still immature, but complicated enough that they fail regularly in ordinary usage.

    In martial arts it isn't the white belt or the black belt who is dangerous. It's the brown belt, who has developed certain skills and possesses real power, but who as yet has no deep understanding or control.

    KFG

  12. why not open source science? by ir0b0t · · Score: 5, Interesting

    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.

    --
    I'm laughing at clouds.
  13. Not much bias there, eh? by Aumaden · · Score: 5, Insightful
    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.

    1. Re:Not much bias there, eh? by core+plexus · · Score: 1
      Agreed. I might be considered a "prospector", but we use airborne geophysics, 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 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: "Two thousand years ago, the Romans noticed that the runoff from the tailings pile of one of their copper mines in Spain was blue with copper salts. They found ways to recover the leached copper without worrying about how the metal entered solution. Forty years ago, someone finally figured that out, and blamed it on bacteria.

      The tiny rod-shaped bacterium known as Thiobacillus ferrooxidans gets energy by oxidizing some inorganic materials such as sulfide-containing minerals. As the bacteria metabolize, they release acid and an oxidizing solution of ferric ions, which can wash metals right out of ore. The copper industry quickly and enthusiastically put this discovery to work.

      Biological heap leaching is an inexpensive way to extract the metal from low-grade ores where copper is bound in a sulfide matrix. As the microbes chew up the ore, which has been treated with sulfuric acid to encourage them, the copper is released and concentrated in a solution that flows into a catch basin. The metal is extracted, and the acid solution is recycled. According to the journal Science, from which I gathered this information, fully 25 percent of the world's copper--worth about $1 billion annually--comes from such bioprocessing.

      Though the busy bacteria may some day help extract copper from Alaskan ores, it's a sure bet they'll first see employment here as gold bugs. Elsewhere, T. ferrooxidans is pretreating gold-bearing ores to the satisfaction of mining companies ... to their considerable profit. Low-grade gold ore often contains the metal bound up with sulfides, and typically requires roasting or pressure oxidation to burn off the sulfides before the gold can be extracted with cyanide. Using bacteria does away with the need for the costly cooking treatments, and in at least one instance has improved the rate of gold recovery from 70 to 95 percent.

      Now, I have to live here, too. I don't want my work area looking like a moonscape, so we actively reclaim the ground as we mine it. As a result, not only do we make a very small impact while we are mining, but we also leave behind habitat for wildlife (example: Moose love shallow ponds, as do migratory birds-they also love the grasses we plant to stabilize the soil). We also reclaim areas left by others. It is unfortunate that the miner has been vilified by the popular press.

  14. hyperstable macromolecules by torpor · · Score: 3, Funny

    yay, nano-slavery!

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

    --
    ; -- the corruption of government starts with its secrets. a truly free people keep no secrets. --
  15. Potential? by Anonymous Coward · · Score: 0

    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.

    Since these are still potential discoveries, I think I'll be the first to discover them:

    I have discovered glycoprotein that helps keep arctic fish from freezing, extract from green algae for cosmetic skin treatment, and anti-tumor properties in strain of yeast.

    Maybe they met discoveries with potential?

    1. Re:Potential? by Anonymous Coward · · Score: 0

      Maybe I meant to say meant instead of met?

  16. I support the use of extremophiles. by burgburgburg · · Score: 4, Funny
    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.

  17. For those who have no idea whats this about. by sugar+and+acid · · Score: 5, Informative

    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.

    1. Re:For those who have no idea whats this about. by Anonymous Coward · · Score: 0

      I suspect that the fear is that there will be harvesting of the extremophiles instead of sampling and cultivating. After all, why spend $100 million to produce the desired biologic compound when it's so much cheaper to spend $10 million to send a dozen people to the antarctic to harvest the stuff, ship it home and refine it.

      Of course it's still possible to claim the $100 million in r&d costs.

  18. looking for answers by NoGuffCheck · · Score: 0, Offtopic

    Extremophiles are micro-organisms that grow optimally in some of earth's most hostile environments of temperature

    have they tried looking at the area between SCO and the truth? or Gatesies fist for that matter??

    --
    serenity now!
  19. On the horizon... by MarsCtrl · · Score: 5, Funny
    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.
    --

    I was going to put a sig here, but I had already submitted the message.
  20. Alternatives to Exploiting Evolution's Accidents by G4from128k · · Score: 4, Interesting

    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.

    --
    Two wrongs don't make a right, but three lefts do.
  21. Not accurate by CXI · · Score: 4, Insightful

    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.

  22. Learning from Extremophiles... by Glowing+Fish · · Score: 2, Funny

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

    --
    Hopefully I didn't put any [] around my words.
  23. is the sky falling yet by iii_rjm · · Score: 0, Redundant
    Regarding your worries over the 'food chain':

    Just a small quote from the article

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

  24. re potential discoveries by cinnamon+colbert · · Score: 2, Insightful

    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

  25. Glycoprotien is more than one. by io333 · · Score: 4, Informative

    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?

  26. not invitrogen, not the harvesting by Apogee · · Score: 5, Informative

    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 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.

  27. "literal gold mine" by iota · · Score: 2, Interesting

    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 in Antartica since the first explorers

    I have to disagree. It's just not cost effective to do so now -- if there was a fish in antartica that could be ground up into an AIDS cure or cancer cure, you can be sure someone would fish it clean, ecosystem be damned.

    1. Re:"literal gold mine" by tornado2258 · · Score: 1

      In normal circumstances it is a toss up whether it is cheaper to farm fish or to catch wild ones. With the added complication of fishing in the antarctic, farming ought to come out cheaper (esp. if you factor in the PR costs to convince people you aren't evil after fishing a species to extinction)

    2. Re:"literal gold mine" by LetterJ · · Score: 1

      I've found that what a lot of folks *mean* when they say "literal" is "veritible", but can't think of that word until they're told. This one and "I could care less" are about the only 2 phrases that raise the hair on the back of my neck.

    3. Re:"literal gold mine" by Anonymous Coward · · Score: 0

      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.

      Amen! Thank you for pointing this out in a much more restrained way than I would have. After I read what amounts to "you can really mine gold nuggets from this organism", it makes no sense to read the rest of the poster's comment.

    4. Re:"literal gold mine" by Anonymous Coward · · Score: 0
      I think the OP was pushing the bounaries of the language a bit, but what I think he was getting at is that some extremophiles can be used to extract gold from solution.

      This would make them literally gold miners, rather than mines, but I think you get the gist.

    5. Re:"literal gold mine" by sugar+and+acid · · Score: 1

      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 quantites of deep sea cold water fish. A good example is the orange roughie, a bland inoffensively tasting fish that freezes well, big in fishstick and that kind of thing, but is a relatively new addition to Humans diets (like the last couple of decades) as it is a deep sea fish that requires big equipment to hual up and big factory ships to process. We actually know very little about the biology of these animals, population densities or anything, yet they now make up a signficant component of the worlds diet of fish. This has come about from a lack regulation for fishing in the remote parts of the worlds international waters, and it is very hard to figure out how to regulate it, or even how it would be policed in such remote localities as these ships operate.

  28. You have got to be kidding me! by genetic_freak · · Score: 4, Interesting

    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.

    --


    Rice University Department of Biochemistry and Cell Biology- "Engineering the freaks of tomorrow"
    1. Re:You have got to be kidding me! by trouser · · Score: 1

      Yeah, small actions can only have a small effect which is completely quantifiable and the whole chaos theory is a lie.

      --
      Now wash your hands.
    2. Re:You have got to be kidding me! by genetic_freak · · Score: 1

      well if that is the argument, then impact of crushing a million micro-organisms and distrupting the natural habitat done by harvesters walking to the point where the collect the microgram of bacteria is much more likely to send us into a spiralling black hole of death. I'll be sure not to sneeze today so that I don't set off a chain reaction that results in a sahran sand storm that kills millions.

      --


      Rice University Department of Biochemistry and Cell Biology- "Engineering the freaks of tomorrow"
    3. Re:You have got to be kidding me! by trouser · · Score: 1

      I appreciate your consideration for others. Thank you.

      --
      Now wash your hands.
  29. Hey, I've read this book! by Anonymous Coward · · Score: 0

    For a perspective of how bad this could be, check out this and this

  30. Re:Alternatives to Exploiting Evolution's Accident by Anonymous Coward · · Score: 3, Interesting

    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 millenia?

    Soon we might design drugs, rather than find drugs, but not yet. Not yet. I personally believe it won't happen in my lifetime, and this is based on the belief that we won't have AI in my lifetime either.

    Beware. Someone might be watching.

  31. Re:Alternatives to Exploiting Evolution's Accident by Anonymous Coward · · Score: 2, Informative

    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. While we could do this for abundant proteins without these enzymes, we can't do it for low abundance proteins, because they require an engineered bacterium to produce them in large enough quantities for structure determination. To do that, you need to know the DNA sequence, so you need to have sequenced the gene in question. To sequence it, you need to isolate enough of it to sequence. PCR is the method for doing that.

    And besides, people have been trying purely in silico drug design for years now. I'm not aware of there being more than half a dozen or so pharmaceuticals in production that were discovered that way.

  32. Hmm by Perianwyr+Stormcrow · · Score: 2, Informative

    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.

    --

    What we call folk wisdom is often no more than a kind of expedient stupidity.-Edward Abbey

  33. Re:Alternatives to Exploiting Evolution's Accident by Anonymous Coward · · Score: 4, Interesting
    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 a pretty readable article that explains more.

  34. what about the extremophiles? by Anonymous Coward · · Score: 0

    (Wont somebody please think of the extremophiles?)

    1. Re:what about the extremophiles? by Anonymous Coward · · Score: 0

      hey stop doing that!!

  35. Extremophile? by phrostie · · Score: 0, Redundant

    isn't that like an adrinaline freak?

  36. Re:Alternatives to Exploiting Evolution's Accident by Apogee · · Score: 4, Informative

    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).

    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.

  37. obligatory: You read the article?!?! by funkyjunkman · · Score: 1

    New here to slashdot, eh?

    1. Re:obligatory: You read the article?!?! by proj_2501 · · Score: 1

      the factor of 10 between my userid and yours doesn't clue you into anything? at all?

    2. Re:obligatory: You read the article?!?! by funkyjunkman · · Score: 1

      Yep. Clued me to one thing. I may have a newer userid, but I can roll out the most cliched joke on slashdot with the best of 'em.
      I chuckled anyway.

    3. Re:obligatory: You read the article?!?! by proj_2501 · · Score: 1

      "I chuckled anyway."

      Simple minds are easily amused... :)

  38. Clueless hack by rs79 · · Score: 1

    Posers read and post. Real extremophiles create alt groups.

    --
    Need Mercedes parts ?
  39. Food chain? by SimianOverlord · · Score: 1, Informative


    Interesting article, but why write "let me remind you of something called the food chain?"
    The article describes a risk from the industry that grows up around the extremophiles, with exploitation of a natural resource that should be available to all. The submitter seems to confuse this with a risk to the organisms themselves.

    I'm not arguing that harming the extremophiles wouldn't have knock on effects eventually for humans, but in terms of the article, it is beside the point. Reading some of the posts above seems to show people have confused this, or haven't actually bothered to read the article.

    --
    Meine Schwester ist sehr, sehr reizvoll - Nietzsche
  40. The solution is obvious by rs79 · · Score: 0, Offtopic

    Get SCO to patent Antactica.

    --
    Need Mercedes parts ?
  41. I've been eating... by Anonymous Coward · · Score: 0

    Blue-Green Algae and Spirulina for years...this is news. The stuff grows like mad...it's ALGAE!

    1. Re:I've been eating... by Harmotech · · Score: 1

      Sorry, blue-green algae is not really an algae: it's a class of photosynthetic bacteria called cyanobateria.

  42. No Doubt by Anonymous Coward · · Score: 0

    I've been eating blue-green algae for years.

  43. -2C is damn extreme? by WebCowboy · · Score: 1

    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...

    1. Re:-2C is damn extreme? by Anonymous Coward · · Score: 0

      Bit chilly, eh?

  44. Computer Modeling and Synthetics by Seanasy · · Score: 3, Interesting

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

    .
  45. 21st Century Hacking is Taking Off by smchris · · Score: 1

    glycoprotein, which prevents Antarctic fish from freezing

    Cool. We won't need aquarium heaters.

    Will they still glow in the dark?

  46. this is not like clearcutting rainforests. by caino · · Score: 4, Insightful

    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.

  47. Read the Article: more patents than ecosystems. by 2marcus · · Score: 2, Informative

    If you read the BBC article, rather than the Hemos summary, you get a very different feeling for what the "threat" is. The BBC article mostly concentrates on the problems of intellectual property and patenting that may stifle scientific research...

    Economists recognize that patents are a double edged sword. Without patents, there is no incentive for companies to invest in basic research that can then be duplicated by freeriders. With patents, you slow down further scientific advances because the information isn't freely accessible.

    This is where universities can (potentially) help - there is a parallel incentive system of "grants" and "ego feeding through publications and awards" that give professors the incentive to do basic research that becomes instantly publically available.

    -Marcus

  48. Because science is expensive by Anonymous Coward · · Score: 2, Insightful
    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 testing process. Each failure is an expensive failure, so you need some way to recover the costs of taking these risks. The only way we know of is to give the agency making the discovery (or more specifically the agency that manages to make something that is actually useful from this original discovery) some porprietary protection so that they can recover enough profit to justify all of the failures.


    It is these proprietary interests that allow you to even use a computer, so maybe you should cut them some slack and genuflect in the direction of the USPTO every time you boot your computer. It is not benevolent sharing of knowledge that drove the CPU, disk drive, and RAM manufacturers to invest in the processes and technology that enabled them to produce these products so cheaply.


    Greed is good. It provided the comfortable world you enjoy today and continues to provide the environment that makes open source software possible in the first place. The truth can be a bitter pill to swallow, but get over it. The tools and techniques that enable you to prosper are the direct result of proprietary and secret knowledge that recovered its investment and then became open knowledge.

  49. Cool by Pedrito · · Score: 4, Interesting

    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.

    1. Re:Cool by pclminion · · Score: 2, Informative
      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, these ice crystals don't have a chance to form and the water instead gels into a more amorphous structure where ice crystals are small, or perhaps not even present.

      That being said, I don't think I would want my body frozen while there's still a chance of getting it fixed in this century :-) It's the kind of thing I might consider if I knew that I would certainly die soon anyway.

  50. Kary Mullis, PCR, patenting, and BRCA1 by 2marcus · · Score: 1

    I actually think that the patenting of the Taq enzyme for use in PCR is actually a great example of both the wonders and pitfalls of patenting. Before Kary Mullis, copying DNA was a pain. So, with the incentive of getting a worthwhile patent, Cetus funded Mullis' research to develop PCR. And the invention of PCR revolutionized biology.

    The questions this raises: would PCR have been invented without patents? How much did Cetus' (and then Roche's) patent slow down the use of PCR by others (given how widespread it is, in this case I'd have to say not much)? If what we care about is improving the welfare of the world, does this mean that in this case, patenting was a good thing? I would say probably yes.

    In a slightly different case, Myriad Genetics tried to patent a breast cancer gene, BRCA1. Here, they were patenting a gene, not a process. Their incentive to discover that the gene was linked to breast cancer was the possibility of a patent. However, having shown that BRCA1 is the key gene, it is impossible to patent every way of detecting BRCA1, so they tried to patent the gene itself. Ethically dodgy? Possibly. But if they had thought that there was no chance of making a profit, they might never have done the research to discover the gene, and then one of the most valuable breast cancer susceptibility tests would not exist. Again, if we care about society's welfare, is allowing this type of patent good? Possibly.

    The final question becomes, is there an alternative? There needs to be some reward system in place to provide incentives. Perhaps a government funded system to give money to companies that make good discoveries if those discoveries are made public domain? And now we have the university research system... But that system isn't perfect either, and there will always be a tension between university research and privately funded research, and that is what we are going to see in Antarctica as the patenting goldrush begins...

    -Marcus

    http://www.myhealthspan.com/mullis.shtm
    http:// www.ssgm.ch/sections/News/brca1testing.htm

  51. That class... by abhisarda · · Score: 1

    a little OT but in spring,01 I took that class.
    My paper's there too :)
    In my view, probably one of the best classes I took while I was there..

  52. Re:Lack of draft animals by Anonymous Coward · · Score: 0
    The research I've read says they probably never made the leap to the wheel because of their lack of draft animals.

    What they only had animals in cans and bottles? Probably couldn't sell them on Sunday either.

  53. Re:The human race is doomed by Anonymous Coward · · Score: 0

    Uh, in the 60s everything was already transistorized and/or in IC form. Hell, they even had GUIs with mice and some guy even got a woman to wear a transducer suit and animate a character on a tv screen. In 1968.
    Oh, and they had oscilloscopes with analog bandwidths in the 4GHz region.

  54. Re:The human race is doomed by Anonymous Coward · · Score: 0

    what the fuck does this have to do with anything...

  55. Re:Alternatives to Exploiting Evolution's Accident by Idarubicin · · Score: 1
    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).

    Quite. What the present system of drug discovery aims to do is find compounds that have a biological effect--any biological effect--and then try to figure out how they work. They use the natural compounds as a starting point for future development. Such a trick usually shrinks dramatically the space you have to search to find useful drugs.

    If you started out with completely random compounds, you'd be reinventing a lot of wheels. Nature already has developed compounds that do almost anything we would want a particular drug to accomplish.

    --
    ~Idarubicin
  56. So what about collecting pregnant-horse urine? by TheTranceFan · · Score: 1
    I see your point. But...

    Premarin, a drug used in estrogen replacement therapy, is produced by collecting and processing the urine of pregnant horses. The mares in question are kept constantly pregnant (and one would guess well-hydrated).

    How does this practice fit into the hierarchy of exploitation? (Not judging - just wondering.)

    1. Re:So what about collecting pregnant-horse urine? by Anonymous Coward · · Score: 0

      Oh, probably no worse than the Dairy industry.

      Compare it to early methods of getting taxol. Pacific Yew trees were considered by the logging industry to be a junk species. Not much concern was given to logging them down, but no one sought them out, either. Now taxol comes out, and the initial source was from them. Now everyone is going through their woods (Natl Forest) stripping bark off of Pac Yew trees, and concerns about all the trees being killed start becoming apparant.

      Now taxol is industrially synthesized, and the Pacific Yew was "saved".

      I think a more obvious problem is harvesting of animals for their body parts: bear bladders, shark fins, rhino horns, elephant tusks, etc. (alligators are farmed in Florida for use by the leather industry), whether it be for real or imagined medical effect, epicurean delight, or whatever, or not figuring out how to replicate environments for "super algae", extremophiles, etc, instead focusing on mining (mining = taking w/o replenishment) them from their natural environment.

      Patent law also comes into play...

  57. I have cancer, but... by rbanzai · · Score: 1

    ...I'm not willing to destroy the environment for a cure. If people (and corporations) showed any kind of restraint or sense of proportion in the way they made use of what the world has to offer we wouldn't have to discuss this kind of thing.

    1. Re:I have cancer, but... by Anonymous Coward · · Score: 0

      Is the use and destruction of other life forms acceptable?

      What's the difference?

  58. A cat in the box ? (Possibly OT) by fygment · · Score: 1

    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.

    --
    "Consensus" in science is _always_ a political construct.
  59. Crock is a bit of an exaggeration. by Derek+Pomery · · Score: 2, Informative

    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 at once by freezing inside and outside of your basic frozen head simultaneously.

    I'm not pinning my personal hopes on cryonics, but good to know it is getting better.

    --
    -- perl -e'print pack"H*","6e656d6f406d38792e6f7267"' /. ate my old sig. Bastards.
    1. Re:Crock is a bit of an exaggeration. by Anonymous Coward · · Score: 0

      But isn't the whole cryonics thing putting the horse in front of the cart, in a manner of speaking?

      We have not figured out how to reenergize an electrochemically body yet, and somehow I do not think that Mr. Ashcroft would look too keenly on an operation that was freezing live people.

      Oh, I see...it's based on "hope". Well...I can't wait to get a new Ted Williams autograph in 50 years.

    2. Re:Crock is a bit of an exaggeration. by Derek+Pomery · · Score: 2, Interesting

      erm... "reenergize" ?
      Is this based upon that magic belief some people have that there is a vital force without which there is no life?

      Freezing and unfreezing embryos is routine. Cells can be frozen and their chemistry just start up again.
      More complex things need to be warmed evenly, and other complications, but it isn't as insurmountable as your average vitalist would think.

      --
      -- perl -e'print pack"H*","6e656d6f406d38792e6f7267"' /. ate my old sig. Bastards.
  60. Renumeration by canineK9 · · Score: 2, Insightful

    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?

  61. -1: Retarded by Anonymous Coward · · Score: 0

    Ice cubes are not alive. It was not a typo.

    1. Re:-1: Retarded by PitaBred · · Score: 1

      Ice cubes are not alive. It was not a typo.

      Or you might be the retard. Remember that little bit about the "natural antifreeze"? Yeah. That would keep something, say, not an ice cube? Hrm. Funny how that works. And FYI, seawater can get much colder than fresh water before it freezes.
    2. Re:-1: Retarded by Anonymous Coward · · Score: 0

      Name one microorganism that reproduces at -15 C. You are retarded as well.

    3. Re:-1: Retarded by Anonymous Coward · · Score: 0

      Cryotendolithotrophs

    4. Re:-1: Retarded by Anonymous Coward · · Score: 0
      Cryotendolithotrophs

      Does everything you know come from trivia questions?

      Point 2: "Cryotendolithotrophs" is found only once by your beloved google search, and not at all in the scientific literature.

      Point B: "Cryotendolithotrophs" would not be the name of an organism, even if they exist.

      Point 11: You are retarded.

      Point 4: Surviving and reproducing are separate issues. Lots of morcoorganisms can survive at temperatures much lower than -15 C, but only reproduce when thawed.

      Point e^pi: You fail it.

      I mock your value system. You also appear foolish in the eyes of others.

  62. It's All About the Money by ml10422 · · Score: 1

    Sounds like the prospectors are mostly a threat to the "real" scientists' grant money.

  63. Re:Alternatives to Exploiting Evolution's Accident by khallow · · Score: 2, Insightful
    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?

  64. You know what's not funny? by phossie · · Score: 1

    Organic regs don't say a whole lot about pesticide use, just that those pesticides must be organic and legal. "Organic," at any specificity of definition, says nothing about toxicity. It's sad that people don't realize that.

    I'm all for organic food, but I prefer mine without lots of neurotoxin. And that means that I need to know my providers personally, and trust them, or I need to grow my own.

    In particular, I almost prefer chemfarmed apples - organic apples need to be sprayed an average of about twice a week. Commercial apple strains tend to be pretty weak... which means that I don't eat many apples. :(

    --

    [|]
  65. are you nuts? by Anonymous Coward · · Score: 0

    "Although we may have much to learn from nature, we approach the day when no longer need this haphazard ancient dataset."

    The day we no longer need the haphazard ancient dataset *which includes us*, then we will have figured out life, the universe, and everything. And that's not going to happen anytime soon, if ever.

  66. Re:The human race is doomed by Anonymous Coward · · Score: 0

    obviosuly we are doomed.

    the universe wouldnt have it any other way

  67. More technology? by FlyingOrca · · Score: 2, Insightful

    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.

    --
    Corruptissima re publica plurimae leges.
  68. Re:Brilliant. ; by DonGar · · Score: 1

    How do you know they weren't?

    --
    plus-good, double-plus-good
  69. Re:Alternatives to Exploiting Evolution's Accident by Mal-2 · · Score: 1

    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.

    Designed drugs have already happened. They just happened in areas you probably aren't studying -- namely, the pharmacology of psychedelia.

    Phenethylamines I have Known and Loved, by Alexander and Ann Shulgin.

    MDMA came from efforts such as this, and would have been discovered by the above effort even if it hadn't yet been studied (and widely used).

    Mal-2

    --
    How is the Riemann zeta function like Trump rallies? Both have an endless number of trivial zeros.
  70. So can we indiscriminantly drop that on Mars? by tjstork · · Score: 1

    We ought to be able to genetically engineer stuff that can being terraforming Mars. Full speed ahead!

    --
    This is my sig.
  71. Antartic by BiggerIsBetter · · Score: 1

    Why the Antartic? Has everything in the Artic been killed off already?

    --
    Forget thrust, drag, lift and weight. Airplanes fly because of money.
  72. Those are designer drugs, not designed drugs by Apogee · · Score: 1

    What you're describing is not de novo drug design, but rather tinkering, which indeed happens regularly in the drug development process.

    The whole zoo of phenethylamine derivates comes from a process of optimization. That part of "drug design" is in fact very common in drug development (not only in psychoactive drugs, but drugs in the common sense of therapeutic substance).

    The initial, biologically active, substance usually has some beneficial properties (i.e. it is active), but some undesired properties, such as causing side effects (not specific enough), or having low activity (low bioavailability [basically, it isn't taken up well in the blood stream, or isn't taken up properly by the target organ]). In these cases, medical chemists start playing around with side-groups of the molecule, trying to enhance the desired pharmacological, pharmacokinetic and pharmacodynamic properties. The way I understand it, this process is half science, half art.

    What I was referring to when I talked about rationally designed drugs is more than just tinkering. It's saying "We have this disease that's caused by an overactivity of protein XYZ. Let's have a look at protein XYZ and design a completely new compound that will bind to it and dampen that activity", for instance. This is what maybe one day will be possible, but not yet.

    To come back to your example, as far as I know, there's no way even within the phenethylamines to look at the structure of two members of this class, and just by looking at the structure predicting what exact effects each of them will have. It's more a kind of trial-and-error process, hardly rational drug design.

  73. Antarctica patent code AQ by Richard+Kirk · · Score: 1
    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.

  74. Bioengineered crops for the third world ? by RedLaggedTeut · · Score: 1
    Genetically engineered corn will not do anything good to the third world for several reasons:
    • the first reason is that GEC is not free. It needs to be paid for by a high annual fee. Sometimes special herbicides are part of the package.
    • next the company selling the corn forbids the farmers to keep part of their harvest for seeds as is customary. Where the company cannot control that these restrictions are followed it will use political pressure to destroy any of their crops found and will not offer their corn. Companies like this distribution model because their profits are protected by patents.
    • the GECs genes can cross over to other corn and seeds owned by farmers. Farmers will get sued, disowned and be forbidden to use their seeds.

    Of course this means that GECs will make us in the developed countries own the third world, so hell, lets do it.

    --
    I'm still trying to figure out what people mean by 'social skills' here.
  75. All I want to know is by Anonymous Coward · · Score: 0

    why hasn't someone spliced the 'glow in the dark' gene from fish and fire flys into the mosquito?