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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."
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.
Is some great white hunter scientist with a cotton swab and a sequencer really going to be a threat to Antarctica?
Is that one of those Audiophiles that buys all the best equipment and scoffs at CD audio in favor of DVD audio?
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.
...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
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!
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)...
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.
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
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.
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.
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. --
I've changed my mind.
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.
I was going to put a sig here, but I had already submitted the message.
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.
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.
Can I call my browsing of the stranger Y! Member Profiles scientific research now?
Hopefully I didn't put any [] around my words.
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
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?
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.
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.
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"
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.
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.
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
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.
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.
You don't harvest extremophiles for these substances. You model the substance and find a synthetic analog
.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.
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
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.
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.
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"'
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?
Nature has been creating new drugs for hundreds of millions of years. Why shouldn't we use this valuable resource?
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.