Learning (And Harvesting) from Extremophiles 192
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."
Oh. (Score:5, Funny)
Re:Oh. (Score:1)
Re:Oh. (Score:2)
easy, put the two in a room together, generate heat energy from friction
Re:Oh. (Score:1)
Re:Oh. (Score:2, Offtopic)
Re:obligatory: You read the article?!?! (Score:2)
Re:obligatory: You read the article?!?! (Score:2)
Simple minds are easily amused...
It's not like its strip mining (Score:5, Insightful)
Re:It's not like its strip mining (Score:5, Funny)
Man, them cotton swabs is deadly weapons, I'm tellin' ya.
KFG
Re:It's not like its strip mining (Score:4, Funny)
Read the Article: more patents than ecosystems. (Score:2, Informative)
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 informat
That class... (Score:2)
My paper's [mtu.edu] there too
In my view, probably one of the best classes I took while I was there..
Extremophiles (Score:5, Funny)
Brilliant. (Score:5, Insightful)
Re:Brilliant. (Score:5, Funny)
Well, at least the cavemen in the parallel universe finally accepted fire...
Re:Brilliant. (Score:2)
Re:Brilliant. (Score:3, Insightful)
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)
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)
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)
- 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.
Re:Brilliant. (Score:2)
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)
Re:Brilliant. (Score:2)
Re:Brilliant. (Score:4, Funny)
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)
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.
Re:Brilliant. (Score:2)
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
Re:Brilliant. (Score:2)
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
Re:Brilliant. (Score:2)
-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?
Re:Brilliant. ; (Score:2)
There is a bad joke here someplace... (Score:5, Funny)
...and tend to congregate at Slashdot...
Sorry, had to be said...
Re:There is a bad joke here someplace... (Score:5, Funny)
Stupid git.
KFG
Re:There is a bad joke here someplace... (Score:3, Funny)
Re:There is a bad joke here someplace... (Score:3, Funny)
KFG
Re:There is a bad joke here someplace... (Score:2)
No, pedophiles are people with foot fetishes.
Re:There is a bad joke here someplace... (Score:2)
Re:There is a bad joke here someplace... (Score:2)
People for the Eating of Tasty Animals. Who knew?
Clueless hack (Score:2)
Invitrogen (Score:5, Insightful)
Re:Invitrogen (Score:1)
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:1, Funny)
Maybe you went to a school that wasn't allowed to teach science. That's ok, the rapture will come soon enough. Right?
Re:Invitrogen (Score:3, Insightful)
Re:Invitrogen (Score:5, Insightful)
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)
Re:Invitrogen (Score:2)
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)
not invitrogen, not the harvesting (Score:5, Informative)
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.
Re:Invitrogen (Score:1)
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)
extremophiles?! (Score:2, Insightful)
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)...
Re:extremophiles?! (Score:1)
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.
Re:extremophiles?! (Score:2)
-2C is damn extreme? (Score:2)
Re:extremophiles?! (Score:2)
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.
Re:extremophiles?! (Score:2)
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)
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)
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).
Re:You can't have it both ways.... (Score:2)
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
Re:You can't have it both ways.... (Score:2)
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
Re:You can't have it both ways.... (Score:2)
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
Re:You can't have it both ways.... (Score:2)
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.
Re:You can't have it both ways.... (Score:3, Informative)
Re:You can't have it both ways.... (Score:2)
>example).
But thneeds are what everyone, everyone, EVERYONE needs.
-l
(unless)
why not open source science? (Score:5, Interesting)
Because science is expensive (Score:2, Insightful)
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)
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.
Re:Not much bias there, eh? (Score:2)
hyperstable macromolecules (Score:3, Funny)
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)
I've changed my mind.
For those who have no idea whats this about. (Score:5, Informative)
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)
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
Re:"literal gold mine" (Score:2)
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
Antartic (Score:2)
On the horizon... (Score:5, Funny)
Alternatives to Exploiting Evolution's Accidents (Score:5, Interesting)
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)
Re:Alternatives to Exploiting Evolution's Accident (Score:2, Informative)
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)
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)
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.
Re:Alternatives to Exploiting Evolution's Accident (Score:2)
Those are designer drugs, not designed drugs (Score:2)
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,
Re:Alternatives to Exploiting Evolution's Accident (Score:2, Insightful)
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)
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)
Can I call my browsing of the stranger Y! Member Profiles scientific research now?
re potential discoveries (Score:2, Insightful)
Glycoprotien is more than one. (Score:5, Informative)
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)
Re:You have got to be kidding me! (Score:2)
Re:You have got to be kidding me! (Score:2)
Hmm (Score:3, Informative)
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)
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)
Cool (Score:5, Interesting)
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)
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,
Crock is a bit of an exaggeration. (Score:3, Informative)
They've been getting really good at this, modern methods improving the amount that can be flash-frozen
Re:Crock is a bit of an exaggeration. (Score:2, Interesting)
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.
A cat in the box ? (Possibly OT) (Score:2)
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)
So can we indiscriminantly drop that on Mars? (Score:2)
Antarctica patent code AQ (Score:2)
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.
Re:The human race is doomed (Score:4, Insightful)
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