Scientists Search Deep Sea Reefs for Wonder Drugs

ScienceDaily is reporting that a team of scientists will be venturing some 2000-3000 feet below the ocean surface in order to explore deep-sea reefs discovered last December. From the article: "A primary goal of the upcoming expedition, which is funded largely by the State of Florida's 'Florida Oceans Initiative,' will be to search for marine organisms that produce chemical compounds with the potential to treat human diseases such as cancer and Alzheimer's."

Comments

Curse of the Blue Gold

[eldavojohn]

First off, this isn't really 'news' as it is an alarm. When a new coral reef is discovered, we aren't sending people to look for new species or attempting to preserve it ... instead we're sending people to take samples to see if we can benefit medically from the reef.

Modern man has an impeccable record for destroying the natural environment that produces his fruits & resources. Then we sit and bitch about how it went away. Reefs are probably going to be no different. They're harder to get at, but if the run-off doesn't destroy them, I'm sure our medical companies will.

There's a report written by the UN University that details the problems being raised by this treasure of "blue gold."

Significantly, the ratio of potentially useful natural compounds to compounds screened is higher in marinesourced materials than with terrestrial organisms. There is, therefore, a higher probability of commercial success. Potential applications for marine organisms include: pharmaceuticals; enzymes; cryoprotectants; cosmaceuticals; agrichemicals; bioremediators; nutraceuticals; and fine chemicals. All the major pharmaceutical firms, including Merck, Lilly, Pfizer, Hoffman-Laroche and Bristol-Myers Squibb, have marine biology departments. Estimates put worldwide sales of marine biotechnology-related products at US$ 100 billion for the year 2000. Profits from a compound derived from a sea sponge to treat herpes were estimated to be worth US$ 50 million to US$ 100 million annually, and estimates of the value of anti-cancer agents from marine organisms are up to US$ 1 billion a year.

One of the interesting sources it cites is Blue Genes: Sharing and Conserving the World's Aquatic Biodiversity (another interesting document on the global problem of sharing the world's oceans).

Hypothetical scenario time! So, Pfizer's scientists find that a fairly common sponge produces a natural chemical that slows the growth of cancer. Unfortunately, each sponge only produces an ounce of this chemical when refined and there is no way to naturally synthesize it on a mass scale. Pfizer tries to buy the rights to harvest the sponge at a restricted rate in Florida. But they have to get permits from the local, state & federal governments and it costs them a lot of money because they send people down to the reef to hand pick the sponges. Instead, they find a supplier in a third world country (possibly around Indonesia) that promises them mass quantities of the sponge at a reduced rate. Now, the government there forbids it too but an official receives a large sum from this company and suddenly Pfizer has got incoming shipments of the sponge. The problem is that the company working for Pfizer is doing so with total blatant disregard for the ecosystem & probably its workers.

A farfetched scenario? Or something that's happened so often in the past, we'd be naïve to imagine it to stop here?

Re:Curse of the Blue Gold

[TheMeuge]

Any chemical that can be synthesized biologically should be perfectly capable of being synthesized in-vitro. Any protein can be cloned and synthesized en masse. This scenario isn't very realistic, and smacks of ultra-enviromentalist garbage... like anti-GM-crop people.

Re:Curse of the Blue Gold

[fain0v]

Even if you could sythesize anything that nature can make, there isnt enough matter in the universe to make every small molecule that might be of interest to medicinal chemists. So how do you screen out the useless molecules and find ones that might have an effect on a druggable target? You use millions of years of evolution to your advantage and isolate compounds made by organisms. These "natural products" can be used to do high-throughput screening on your drug target.

Here is a lab that does this.
http://www.umich.edu/~lsi/institute/labs/sherman/s ponge.html

Re:Curse of the Blue Gold

[archeopterix]

Any chemical that can be synthesized biologically should be perfectly capable of being synthesized in-vitro.

Synthesized in-vitro? Perhaps.

Synthesized in-vitro on a commercial scale? Look at Taxol. It took over 20 years to design a commercially viable synthesis method.

Galanthamine? To my knowledge, no commercially viable method exists.

Re:Curse of the Blue Gold

[Red Flayer]

"Any chemical that can be synthesized biologically should be perfectly capable of being synthesized in-vitro."

Should be != is. Particularly since development of the process for complex compunds can be extrmely expensive.

"Any protein can be cloned and synthesized en masse."

Protein folding is still a tricky business for a lot of proteins, and not necessarily reproducible in a lab. Plus, you've got to isolate the gene(s) responsible for the protein production, successfully insert them into bacteria or yeast to produce a viable colony, and then ferment them. By no means automatic. It's not a simple matter of 'cloning' a protein.

Cost is also a huge issue. As the GP alludes to, the availability of a cheap supply will often preclude synthetic production -- regardless of whether that supply is truly cheap in the long run (i.e., in his example, the public value of the reefs/natural sponges in the environment is not included in the cost equation for the drug company).

Sure, as the natural supply becomes more limited, it gets more expensive, and synthesis of the compound becomes an economically viable alternative for the company. But in the meanwhile, overharvesting of a natural resource can have pretty dire consequences.

Re:Curse of the Blue Gold

[jocknerd]

The CEO of Shell Oil was on the Today Show this morning, and he even admits that global warming is real and its here. Frankly, I was a bit surprised. I figured that he would have the same opinion as President Bush which is more studies need to be done. He said the discussion should be over. Scientific evidence is overwhelming. And we need to do something about it.

Re:Curse of the Blue Gold

[onepoint]

>>The CEO of Shell Oil was on the Today Show this morning, and he even admits that global warming is real and its here

this should be referenced to a web site where others can find it.

I am very glad to here that an oil company exec. is willing to commit to the thinking that the global warming issue is real. if anything, this might guild funds to better long term resource usages.

Onepoint

Re:Curse of the Blue Gold

[darkmeridian]

Any chemical that can be synthesized biologically should be perfectly capable of being synthesized in-vitro. Any protein can be cloned and synthesized en masse. This scenario isn't very realistic, and smacks of ultra-enviromentalist garbage... like anti-GM-crop people.

This statement is categorically untrue. Tamiflu is made from an element of Chinese star anise. Are you surprised by the fact that 90% of the Chinese star anise in the world is used to make Tamiflu? Imagine if Chinese star anise is rarer than it is.

Re:Curse of the Blue Gold

[Johnny5000]

The problem is that the company working for Pfizer is doing so with total blatant disregard for the ecosystem & probably its workers.

I'm the last person to make apologies for some company, but I'd like to think they're probably smart enough to not kill the golden goose. If they're making billions of dollars from reef extracts, it wouldn't do them any good to destroy the reef and lose that potential source of profits.

Of course, I could be wrong.. they could decide that they'll destroy the reef at a rate that will take 100 years (or 50, or 10) and decide that's a good window of time to make a huge profit, and by the time the reef is destroyed, they will have perfected an in-vitro method of production or been able to move onto the next wonder drug, or whatever.

Re:Curse of the Blue Gold

[Dr. GeneMachine]

And what exactly is your agenda, spamming this completely off-topic drivel here?

Re:Curse of the Blue Gold

[LunaticTippy]

I'd say that the reef would be destroyed at a rate calculated to coincide with patent expiration.

Re:Curse of the Blue Gold

[AndersOSU]

If you're going to rip-off an article the least you can do is provide a link to it.
http://magic-city-news.com/article_5888.shtml

All this in light of yesterdays article about plagerism .

Re:Curse of the Blue Gold

[Oligonicella]

Your entire fifth paragraph falls apart logically. Use the northwestern yew as an example. Extremely rare species which supplies a useful anticancer compound. Were they harvested to extinction? No. Were they replaced by other yews from around the world? No. Why? It is that species which has the compound. Your paragraph falls apart historically. Which, ironically, is the very rational you use to promote it. Odd, that.

Re:Curse of the Blue Gold

[John Newman]

You've got to isolate the gene(s) responsible for the protein production, successfully insert them into bacteria or yeast to produce a viable colony, and then ferment them. By no means automatic. It's not a simple matter of 'cloning' a protein.

You just described the simple matter of "cloning", as it's used in the laboratory sense. It is, in fact, quite simple.

- A friendly neighborhood molecular biologist

Re:Curse of the Blue Gold

[lubricated]

Actually usually the people going are going because they want to explore the stuff and usually are most interested in it's biology and how to preserve it. The whole medicine thing is how you get funding.

Re:Curse of the Blue Gold

[John Newman]

This statement is categorically untrue. Tamiflu is made from an element of Chinese star anise. Are you surprised by the fact that 90% of the Chinese star anise in the world is used to make Tamiflu? Imagine if Chinese star anise is rarer than it is.

The same Wikipedia article says that a complete synthesis protocol was developed this year. Like for Taxol, it took a while but proved possible. And happened much faster than Taxol, probably showing the effect of improving organic chemistry science and tools.

I find it surprising, though, that both syntheses came out of academic labs - not from the pharmaceutical companies that sell the drugs. You'd think they'd have enormous incentive, and more than enough resources, to do such work themselves. If they aren't interested in actually making drugs, what exactly is it that they do?

Re:Curse of the Blue Gold

[Red Flayer]

Simple in theory, not always so in practice -- cloning of peptide sequences starts getting rough at around 30 peptides, IIRC -- though likely most drug products would be small. Also, we're looking at a commercial scale here. Plus the fact that proteins are a poor structure for most drugs, due to the delivery mechanism (IV or IM injection only, with rare exceptions), storage requirements, lability, etc.

So really, the bigger concern should be how to produce non-peptide drugs, which are not always so easy to synthesize.

Re:Curse of the Blue Gold

[hackstraw]

Scientific evidence is overwhelming. And we need to do something about it.

Eat more chicken!

Re:Curse of the Blue Gold

[EatHam]

I would personally kill every animal on the planet if it would prevent me from catching a cold.

Re:Curse of the Blue Gold

[hexi]

http://www.guardian.co.uk/climatechange/story/0,12 374,912530,00.html

This google thing actually seems to work... :)

Re:Curse of the Blue Gold

[Anonymous Coward]

While some of your comments are rational, some of them don't apply to these particular reefs.

They are 2-3km deep -- coastal runoff is largely irrelevant, and they aren't going to be hand-collected by divers.

On the more negative side, the life at these locations probably grows very, very, very slowly (low temperature, low nutrient supply), and would be easy to damage or destroy. However, ordinary fishing operations in the vicinity of these deep sea reefs already do *immense* damage in some parts of the world. Compared to that, harvesting anything for medical purposes would be a minor effect. If it is worth protecting these deep-sea reefs (and I think it is), then it is more important to protect them from the harvesting and damage that is already occurring than it is to worry about any additional effect from potentially new applications such as medicine. If anything, a medical use for some of the biota there might provide the incentive for fishing operations to cease or adopt a less damaging approach than dragging gear across the bottom (which tears down the corals and other biota as destructively as if you were clear-cutting trees).

I guess the bottom line, from my perspective, is that these deep sea reefs are relatively poorly understood, and yet they are being severely impacted in some regions by fishing, so it makes sense to try to understand them via studies like this. Opposing the studies only because of the *chance* it could make the situation worse is silly. We need more information about them *in*order* to try to protect them. While scientific studies can pave the way for irresponsible exploitation, they can also be the means for preservation. Either way, you aren't going to have an effective management of anything if you don't know anything about what you are trying to manage.

Re:Curse of the Blue Gold

[cashman73]

Now that we're beginning to understand genomics, it's becoming a lot easier to synthesize complex biomolecules. If we can identify the genes that are involved in making the proteins that go into how certain organisms produce a particular compound, we can modify those genes, put them in a particular order, then place those same genes into a bacterium and let nature do our dirty work for us! ;-)

Re:Curse of the Blue Gold

[Ryan Amos]

If they aren't interested in actually making drugs, what exactly is it that they do?

Pharmaceutical companies are not interested in drugs that cure diseases, nor have they been for quite some time.

They are more interested in "maintenance drugs," which do nothing to cure the ailment, but merely treat the symptoms. This way you have to keep taking the drug (and paying for it) for the duration of the ailment (which could be the rest of your life.) It's generally left up to academia to find the cure.

Re:Curse of the Blue Gold

[Ponga]

I think you ment to say this:
I'd say that the reef would be destroyed at a rate calculated to coincide with patient expiration

Re:Curse of the Blue Gold

[Mutatis Mutandis]

Relatively far-fetched, I would say. Look at the fluorescent proteins that probably make up most of that cited $100 billion per year (in 2000) for marine-biotechnology derived products. Very few people would use "wild type" fluorescent proteins for research, as these are not very efficient for our purposes. Instead researchers have developed the original jellyfish or coral proteins in entire families of mutated proteins with desirable fluorescent and other properties -- similar in structure, but a small change can turn a blue-fluorescent protein in a red-fluorescent protein.

The same is true for drugs. Pharmaceutical companies are looking for novel chemical structures and proteins in marine organisms to feed their chemistry libraries, but they are unlikely to be able to use these as drugs in their original form. Something an invertebrate uses as a toxin for self-defence may be a potential anti-cancer drug, but is likely to be too dangerous for use in humans. Instead chemists will study the structure-activity relationship for a family of related compounds in the hope of deriving a compound that is more active and safer. But that means that the end product will probably have to be synthesized.

Besides, it is an expensive chore to extract and purify a product that a primitive animal might be making minute quantities. It makes much more economic sense to go for expression in genetically modified cells.

Re:Curse of the Blue Gold

[darkmeridian]

The wiki article says no such thing. From the article:

"Although it is produced in most autotrophic organisms, star anise is the industrial source of shikimic acid, a primary ingredient used to create the anti-flu drug Tamiflu. Tamiflu is regarded as the most promising drug to mitigate the severity of bird flu (H5N1); however, reports indicate that some forms of the virus have already adapted to Tamiflu.

A shortage of star anise is one of the key reasons why there is a worldwide shortage of Tamiflu (as of 2005). Star anise is grown in four provinces in China and harvested between March and May. The shikimic acid is extracted from the seeds in a ten-stage manufacturing process which takes a year. Reports say 90% of the harvest is already used by the Swiss pharmaceutical manufacturer Roche in making Tamiflu, but other reports say there is an abundance of the spice in the main regions - Fujian, Guangdong, Guangxi and Yunnan."

A more efficient method of doing another portion of the synthesis was recently discovered, but shikimic acid still comes from Chinese star anise.

Re:Curse of the Blue Gold

[Grab]

Ever heard of factory ships like the Atlantic Harvester? They're busy doing to the West African coast what the Canadians did to the Grand Banks. But they're handing out money to the relevant African countries, and the leaders of those countries don't care that a few fishermen are going to lose their livelihoods, never mind caring about the environment and what's down there.

In my own back yard, we've got another classic. For the last 10-15 years, scientists have been telling the EU that cod stocks in the North Sea are going the same way as the Grand Banks. Is anything happening? Is it fuck. There's some rules about maximum catches, but those maximum catches have always been orders of magnitude more than what the scientists say is the most optimistic replacement level, bcos the fishermen's lobby puts money the right way. And even then, the fishing bastards complain like they've got a right to strip-mine the place.

Grab.

Re:Curse of the Blue Gold

[Frozen Void]

First kill the animal above.

Re:Curse of the Blue Gold

[Kent Recal]

Of course, I could be wrong.. they could decide that they'll destroy the reef at a rate that will take 100 years (or 50, or 10) and decide that's a good window of time to make a huge profit...

I think you're dead-on. Having worked with large-company execs (and wannabe-execs) I can tell that
the amount of greed and sheer ignorance that it apparently takes to get into such a position and the resulting ruthlessness should not be underestimated.

The droids that I was unfortunate to deal with were kind of mindlocked on terms like
quarterly-revenue, ROI, dividends etc.

*If* destruction of some reef promises a positive, worthwhile bottom line
I doubt that many of the type would spare a second thought. Who needs reefs anyway...

Re:Curse of the Blue Gold

[Mahou]

wow looks like someone was waiting to get mod points and then mod my posts down. what a pathetic little shit

Cancer

[PrivateDonut]

Sorry, but cancer isn't a disease... its a mutation. You can't cure mutations, only give your body the ability to remove the mutated cells.

Re:Cancer

[Whiney Mac Fanboy]

but cancer isn't a disease... its a mutation.

Are you sure? Disease:

1. A pathological condition of a part, organ, or system of an organism resulting from various causes, such as infection, genetic defect, or environmental stress, and characterized by an identifiable group of signs or symptoms.

2. A condition or tendency, as of society, regarded as abnormal and harmful.

Re:Cancer

[GundamFan]

WMF,

Take it down a notch man... He (or she) was likely just joking...

And yeah us daily posters are sick in the head... did that come as a shock to you?

Hopefully, it won't be like...

[magores]

Hopefully, it won't be like...

The rainforest(s).

Lots of potential, but wasted.

This is pretty common, actually

[Dr.Enormous]

If you read biology journals, you'll see that just about every third or fourth paper consists of "we pureed some sea sponge in a blender and extracted this compound. And look, it kills cancer cells (*cough* and non-cancerous cells too *cough*)!" The only thing different here is a somewhat deeper venue for collection. (this isn't to say that it's not important scientific work, just that it's rather commonplace and rarely leads to much of anything)

Re:This is pretty common, actually

[955301]

It certainly reeks of someone's pet project. I cannot imagine that everything between our current elevation and the spot they chose has been thoroughly investigated and that this is our last bastion of naturally occurring medicines.

If someone were to do a cost analysis on this, I'm betting they could fund several, if not tens of similar projects on dry land. Having said that, it's not likely you will get shot or kidnapped while searching in the depths of the ocean as oppose to wandering about in the jungles or forests of a hostile land (*cough* mississippi *cough*).

Re:This is pretty common, actually

[Frumious Wombat]

Coming from the deliberately-synthesized school of chemistry, I was surprised when I sat on a PhD committee recently, and asked the student what the sponge did with the chemical she was discussing. I got a blank stare from the student, and one of the committee members told me that nobody knows, and the natural-product researchers just pick an organism, puree it (or some part of it), make separations, then try them on anything they'd like to cure/killl, and see what works.

As much as I applaud my colleagues for getting the state to fund their diving expedition, it would be nice if some of that money went to trying to understand what role the compounds have in the original organism, then working outward from there to design new pharmaceuticals. It might give us to the tools to stop prospecting, and instead rationally design our molecular targets to fit the application.

Of course, if you read this week's New Yorker, you can see how much effort has gone into rationally designing a replacement for sugar in food, versus how much success on the other end.

Re:This is pretty common, actually

[brianerst]

On top of that, there is the annoying habit of the mass media's description of any type of medical research as having the potential to treat "cancer or Alzheimer's" (or AIDS or Parkinson's).

These types of bioassays are the ultimate in crap shoots - there is no specific reason to suspect that brain coral just happens to secrete a substance that treats brain cancer. We're just looking for all sorts of oddly shaped proteins and hoping that one of them fits a receptor somewhere. It's just as likely that we'd find a substance that reduces flatulence, but we'd probably miss that one because no one is looking for it.

If I read one more article claiming that stem cells will cure everything from cancer to acne, I think I'm gonna scream...

Re:This is pretty common, actually

[John Newman]

If you read biology journals, you'll see that just about every third or fourth paper consists of "we pureed some sea sponge in a blender and extracted this compound. And look, it kills cancer cells (*cough* and non-cancerous cells too *cough*)!"

Once in a blue moon, it does work. Search PubMed for "ecteinascidin" or "Et-743". The compound was isolated from pureed Caribbean sea squirt, and is showing great promise for hard-to-treat sarcomas.

On the other hand, that's the only example that comes easily to mind.

Re:This is pretty common, actually

[cashman73]

Coming from the deliberately-synthesized school of chemistry, I was surprised when I sat on a PhD committee recently, and asked the student what the sponge did with the chemical she was discussing. I got a blank stare from the student, and one of the committee members told me that nobody knows, and the natural-product researchers just pick an organism, puree it (or some part of it), make separations, then try them on anything they'd like to cure/killl, and see what works.

This is not even half of the whole drug design process! It is, however, a great way that we get a good lead compound for further studies. To really analyze the effectiveness of a compound as a drug, you'd have to add a bit more than this oversimplified approach ... molecular modeling studies and QSAR would be important, a database and literature search in the process as well (find out if anyone's come across anything remotely similar and what difficulties they've encountered), and we haven't even gotten to the Phase I, II, and III Clinical Trials, yet!

All in all, the whole process of going from finding a compound in pureed sea squirt to being stocked in your local pharmacy shelf is going to take about 15 years and something on the order of $1 billion, if you're lucky. And people wonder why drugs cost so much?

But articles such as this serve a purpose. For one, they stress the need for additional spending on pharmaceutical research, because generally, curing cancer and alzheimer's makes people feel good. And for another, the article points out the need to take care of our environment, not necessarily in the sense of complete, left-wing, liberal, untouched save-the-world kind of attitudes. But more in the sense of, "we don't want to kill off anything that could be potentially economically useful and/or save lives," kind of sense.

Sea Exploration

[gmiley]

We really need to get back on this train. Oceanography wasn't really even around until relatively recent times. Even once it started catching on, it quickly died off. To date, one of our biggest contributions to oceanography and marine biology has been the H.M.S. Challenger in the 1870's, it's three year mission to explore strange... well, nevermind you get the picture. Sure we have made some large steps since then, but nothing that comes close.

Re:Sea Exploration

[icebrain]

Sounds eerily familiar, like the space program... we get one (or a couple) good efforts going, finally start learning stuff... and then people drop it with the mentality of "all right, that's good enough." I'm sure there's a good supply of young people who would be very willing to do out on new oceanographic research trips... but I'm betting they're either lured away by bigger research grants in other areas, or no one wants to fund them for the above-mentioned reason. And I think the public perception of the field is either of Mr. Cousteau ("a dead guy who lived on a boat") or Robert Ballard ("oh, the guy that found the Titanic"). And everyone thinks oceanography is finding old shipwrecks, and they quickly turn to thoughts of salvaging an old wreck or finding some hidden conspiracy... (or maybe that's just my lack of coffee speaking). The above probably holds true for most areas of science... people want lots of amazing new scientific discoveries fast, thrilling, and cheap. They don't understand how science works, and write it off as boring and useless... then move on to "American Idol."

Re:Sea Exploration

[gmiley]

You are correct, you do see this in many fields of scientific research. An idea catches on, and just as quickly it fades away. In the 1930's two men invented what is called the "bathysphere", it was eventually made by GE (General Electric), the home appliance company. The two men were Barton and Beebe, they got to a depth of around 1,400 feet.

After that, in 1953, a Swiss explorer, Auguste Piccard, made a record shattering dive to almost 7 miles. This vessel, the Trieste, was sponsored by the U.S. Navy. After that they funding stopped citing it as a waste of money. Man has not since been back to that depth (AFAIK), making it strikingly similar to the space program and the Lunar projects. =/

Re:Sea Exploration

[DerekLyons]

We really need to get back on this train. Oceanography wasn't really even around until relatively recent times. Even once it started catching on, it quickly died off. To date, one of our biggest contributions to oceanography and marine biology has been the H.M.S. Challenger in the 1870's, it's three year mission to explore strange... well, nevermind you get the picture. Sure we have made some large steps since then, but nothing that comes close.

How did this nonsense get modded insightful? Even a minute of googling on 'oceanography' and 'marine biology' shows them to be extremely active fields.

HMS Challenger's mission was a three year one - because it took that long to get from the UK to anywhere interesting in the Pacific, and back. Today, rather than sending a handful of scientists on a three year mission - thousands are flying or sailing across the globe on a daily basis.

Re:Sea Exploration

[DerekLyons]

Sounds eerily familiar, like the space program...

Sound eerily like you not only don't have a clue, but lack the wit to use Google as well.

we get one (or a couple) good efforts going, finally start learning stuff... and then people drop it with the mentality of "all right, that's good enough."

Hasn't happened with with oceanography - or space. What has happened is that both have become common enough that it's no longer 'sexy'.

I'm sure there's a good supply of young people who would be very willing to do out on new oceanographic research trips...

Indeed there is - and there are new research trips made each and every year.

Re:Sea Exploration

[DerekLyons]

You are correct, you do see this in many fields of scientific research. An idea catches on, and just as quickly it fades away. In the 1930's two men invented what is called the "bathysphere", it was eventually made by GE (General Electric), the home appliance company. The two men were Barton and Beebe, they got to a depth of around 1,400 feet.

After that, in 1953, a Swiss explorer, Auguste Piccard, made a record shattering dive to almost 7 miles. This vessel, the Trieste, was sponsored by the U.S. Navy. After that they funding stopped citing it as a waste of money. Man has not since been back to that depth (AFAIK), making it strikingly similar to the space program and the Lunar projects. =/

I'm always astonished when people write arrant nonsense, close it with an 'AFAIK' - and then treat it as if it was fact. Does no one ask questions any more? Do they lack the curiosity and wit to even try and educate themselves?

At any rate, the answer to you unasked question is, No, they have not stopped funding deep ocean research.

Re:Sea Exploration

[zippthorne]

Ahh but therein lies the "problem" that's not really a problem per se, but still an interesting challenge:

Deep ocean research, like the space program, is tremendously expensive. (and like the space program, robots have made it significantly cheaper/safer.) And both programs have the problem that the average joe can't really participate beyond monetary support: It takes a very lot of money to support even a few scientists.

Astronomy on the other hand has the benefit of an army of amateur astronomers with varying degrees of professionalism making literaly millions of independant observations, many of which are actually scientifically usefull. On an enthusists budget, telescopes can be purchased/built that exceed the specifications of a few "professional" telescopes, and have been.

Ocean research however has only recreational scuba-diving as its amateur community. Physical limits of the human body prevent amateurs from going very deep, which also limits the area observable to near coasts of some kind. The next step up from scuba is incredibly expensive, and so is restricted to the domain of professional researchers.

The challenge has therefore been laid: bring down the cost of manned submersibles capapable of reaching mid-ocean depths to the point that a particularly dedicated hobbyist could afford to purchase/build one.

It is a difficult challenge. If you could build a submersible out of scrap as easily a shown in "Surface" people'd have been doing it for years now.

Odd. . .

[Limburgher]

Now I have "Octopus's Garden" running through my head. How strange.

Re:Odd. . .

[neoform]

I dunno about you, but when i saw that headline i was thinking "Man, where can i score some of these wonder drugs and where's the nearest rave?!"

Reef Etiquette

[schweinhund]

For those who are not familiar with coral reefs and may go for a casual snorkel or swim sometime, please do not physically touch the coral itself as this kills it. Because of this, federal law requires swimmers to wear flotation jackets when nearby to avoid contact.

It takes 30,000 years to grow 1 cubic inch of coral, and the mistreatment of the reefs around Florida (1960s dynamite fishing, jewelry harvesting, etc.) has made it so that the reef off of the Florida Keys is the last living coral reef in the region.

Re:Reef Etiquette

[Anonymous Coward]

For those who are not familiar with coral reefs and may go for a casual snorkel or swim sometime, please do not physically touch the coral itself as this kills it. Because of this, federal law requires swimmers to wear flotation jackets when nearby to avoid contact.

As an ex-marine aquarist (I stopped when I found out that 99% of the animals are from the wild! Don't let some pet-store schmuck tell you otherwise), I've placed a few corals in my tank. The ones that are sold in stores are hardy enough to have survived the transportation from some place around the globe that's still exploiting their reefs for this trade. Most corals are very delicate and they feel like slimy rocks (the hard corals) and like stiff snot (the soft corals). So, if you want to know what a coral or reef feels like, pick your nose when you have allergies or a cold and then pick up a rock.

Re:Reef Etiquette

[Whiney Mac Fanboy]

It takes 30,000 years to grow 1 cubic inch of coral,

Source?

I thought it was more like 1/2 inch per year

Re:Reef Etiquette

[Bromskloss]

It takes 30,000 years to grow 1 cubic inch of coral

That doesn't make much sense. What happens if you have two reefs growing simultaneously? Do they grow at half speed as to stay within this speed limit? Or, for that matter, what happens if you have two spots on the same reef, growing simultaneously (which they of course do)?

Re:Reef Etiquette

[Whiney Mac Fanboy]

I thought it was more like 1/2 inch per year

Ahem, sorry, (I'm not used to working in British imperial units, they're so old fashioned!)

I should have said 1/20th inch per year

(around 13mm, I lost a zero converting)

Re:Reef Etiquette

[Whiney Mac Fanboy]

Source? :P

Fair enough :-)

Some species of coral grow only a millimeter per year, and even quick sprouters add less than an inch.

From my memory it was 13 millimeters. But I was wrong (that was one species only)

Re:Reef Etiquette

[Wooster_UK]

Eh? 13mm *is* half an inch.

Re:Reef Etiquette

[Whiney Mac Fanboy]

Eh? 13mm *is* half an inch.

*snort* you're right *sighs* Where the hell did I leave my brain this afternoon.

Just goes to show, we should get rid of those units & get everyone on to metric asap!

Re:Reef Etiquette

[gmiley]

Just a quick google search found:

Ariel Roth of the Geoscience Research Institute has commented on the fact that estimates of net reef growth rates vary from 0.8 millimetres per year to 80 millimetres per year, whereas actual measurements based on soundings at depth are many times these estimates.3 Roth suggests a number of reasons for this difference.

source And from Wikipedia:

Formation of the calciferous exoskeleton involves deposition of calcium carbonate by the polyps from calcium ions isolated from seawater. The rate of deposition, while varying greatly between species and environmental conditions, can be as much as 10 g / m2 of polyp / day (0.3 ounce / sq yd / day). This is however hugely dependent on light, with production reduced by 90% at night compared to the middle of the day[6].

source

Re:Reef Etiquette

[Whiney Mac Fanboy]

It sounds to me as if you were trying to be alarmist

Incorrect. Reread the thread.

The gp thought he'd overestimated the growth rates, not underestimated.

Re:Reef Etiquette

[Council]

It takes 30,000 years to grow 1 cubic inch of coral

. . . that's a confusing statistic for something that is inherently parallel in nature. It could take 30,000 years to grow 1 cubic inch of coral, and next to it another cubic inch of coral, and then you could say it takes 30,000 years to grow 2 cubic inches of coral. I mean, more than 1 cubic inch of coral grows every 30k years. Is that 1 cubic inch built up per square inch of area? Then it should be phrased differently, probably as 1 inch of thickness added.

Re:Reef Etiquette

[pembo13]

Tell that to the coral reefs in the Cariibean where I come from.

Re:Disease

[icebrain]

Apparently, a lot of people tend to associate "disease" purely with illnesses directly caused by bacteria, virus, or protozoan...

Humans are not that unique in the world

[BinaryOne]

The fact is, most of the health problems (or most of the problems, period) we face as humans, ie: cellular degeneration, bacterial infections, etc. have some analog in other forms of nature.

The production of antibiotics by fungi and other bacteria to reduce the population of competing organisms has been honed by centuries of evolution. If preserved, supported and studied the processes, and the compounds are there to be used.

The science is slow and tedious, but many of the cultures that live in these rich habitats are well versed in the properties of the flora they have around them.

Cancer and Alzheimer's... or..

[layer3switch]

V1@Gr4 ... time for me to update spamassassin filter to include "deep sea reef"

Reefs

[Sqreater]

How can we be expected to destroy them if we don't know where they are? Let's put more money into hunting down these "reef" things so we can pit-mine them for a solution to athlete's foot.

Or, maybe we can just leave them the hell alone. How about it scientists? Just a thought.

Re:Reefs

[Frumious Wombat]

If people with scientific and engineering mindsets just "left things alone", you'd be sitting in a cave wondering why rocks weren't edible.

Most likely, as the natural product needs to be modified before being an effective pharmaceutical, the compounds of interest will be identified. Then either the necessary gene sequence will be cloned into a workhorse organism, such as yeast or E. coli, or retrosynthetic techniques will be used to make the compound and derivatives thereof under abiotic conditions.

Translation: no company expecting to sell billions of dollars worth of product would rely on such a low-yield source such as mining coral reefs for drugs. Even Taxol( (R) Bristols-Meyer-Squibb) http://www.bris.ac.uk/Depts/Chemistry/MOTM/taxol/t axol.htm/, which could be grown on vast yew ranches, is preferrentially synthesized via standard organic chemistry techniques. Our methods of finding new molecules may be from the Dark Ages, but our methods of synthesizing them are not.

Re:Reefs

[gmby]

"for a solution to athlete's foot."
Try vinegar 1 cup per gallon water. Soak feet for a good while. Spray a little in the shoe if you can't wash the shoes. If you can wash the shoes then use bleach and a little vinegar in the wash.
Oh... and always buy shoes that are on the top shelf and have not been tried on by an "athlete!"

PS. If you have a problem with "athletes foot" then please "GO TO THE SHOE STORE WITHOUT YOUR SHOES ON!" BUY CLEAN SOCKS BEFORE TRYING ON NEW SHOES! Use the above remedy to help with your fungi problem!

Remember; to kill a plant just change the PH!

Re:Reefs

[Sqreater]

The main piece said they were doing it to find drugs, not preserve the reefs. Also, once they find new deep-sea reefs, the information will probably be public and it will serve to target those previously-unknown deep-sea reefs for commercial fisheries.

If cancer isn't a disease, then the reason is...

[jack_call]

In most cases of cancer(as I recall it it's about 70%), it is found that the protein p53 is in someway defect. p53 is the protein responsible for during a "checksum" of the DNA string, and is damaged instruct the cell to repair its DNA or undergo apoptosis.
The damage to the p53 can, amongst other things, be caused by disease.

Depths can't be right.

[Anonymous Coward]

This doesn't really make sense to me. I had been taught that coral reefs required the photosynthesis of the Zooanthelae algae which therefore, restricted such reefs to shallow waters where sunlight could penetrate. This article is talking about coral reefs 2,000 to 3,000 feet deep! That makes no sense.

For those that don't know, sunlight doesn't penetrate into the depths. It is noticeably dimmer at 120 feet (an approximate limit for sport SCUBA divers.) and it is quite dark at 300 feet. No light whatsoever reaches 2,000 feet or deeper.

Further investigation shows that the originally discovery was coral reefs 200-300 feet down which, while quite deep for coral, is far above the darkness of 2,000 feet.

Re:Depths can't be right.

[cutedinochick]

Nope, only some corals utilize zooxanthellate algae. It's estimated that over 2/3 of all coral species do not use algae, do not need sunlight, and live in the deep sea. Huge coral reefs, some of the largest (a huge on off the coast of Norway) live along the continental shelf, which is very deep, past the photic zone.

Not the First Time

[giafly]

FTA "the Miami researchers believe this is the first time an AUV has been used to map deepwater coral reefs". Seems they never use Google.

"New Underwater Imaging Vehicle Maps ... deepwater coral reefs" - Jul 29, 2003

Scientists Search Deep Sea Reefs for Wonder Drugs

[slushbat]

Of all the stupid places to drop your stash of wonder drugs over the side of the boat.

With rainforests gone, we'll NEED to look harder

[malsdavis]

It makes sense really. Since we've cutting all the rainforests down to grow soya, we can no longer draw upon the most widely used source of drug inventions. Over 25% of modern drugs contain chemicals originally discovered in rainforest plants & animals. These discoveries then normally allow synthetic mass-production.

Once the rainforests are gone, discovering these chemicals and constituants will get much tougher and many drugs simply wont be invented. Reefs may help produce some drugs, but the article ignores the fact that the diminishing rainforests and other similar natural sources provide far better places to look for potential drug ingredients!

This is always a needle in haystack deal....

[King_TJ]

A friend of mine with a biology background took a job involving searching for new plants and herbs with potential scientific/medical uses. He was sent on expensive trips to remote parts of Africa and other locations to examine the plants and flowers - and after years of it, found absolutely nothing useful. Did this mean he was a "failure" or lost his job over it? Heck no... That was pretty much what they *expected* would happen. It's just that there's so much money involved if someone DOES hit upon a useful one, they'll throw wads of money at the problem.

This strikes me as the same thing, only in the ocean rather than on land. Exploring is all well and good, but if there's sufficient risk of doing major damage to the landscape - it seems like the negatives outweigh the lottery-winning like chances of finding a benefit from it.

Sealab 2021

[Jamesjoh1337]

Stimutax anyone?

Human Papilloma Virus

[TerranFury]

Actually, you'd be surprised. Nothing gets into your cells and screws up your DNA like a virus.

Have you heard of HPV (Human Papilloma Virus)? It's a very-common (family) of sexually-transmitted viruses. We've known for a long time that certain types of HPV are the cause of cervical and ovarian cancer in women and testicular cancer in men (e.g.: these cancers are STDs), and more recent research has shown that HPV is also linked to certain forms of skin cancer.

In other words: Yes, cancer can be and often is caused by infectious diseases!

Re:Human Papilloma Virus

[ShakaUVM]

Uh, no. HPV is a major cause of cervical cancer. So much so that a HPV vaccine is being hailed as a cure for cervical cancer.

You can read more about HPV and cancer here:
http://www.cancer.gov/cancertopics/factsheet/Risk/ HPV

State of Fear?

[CrazedWalrus]

I read State of Fear (Michael Crighton) a while ago. Good book. I don't remember it word for word, obviously, but it seems like it fits.

Agree with Crighton or not, he cites his sources in the book, which is more than I can say for most of the GW scaremongering I've ever seen. Usually it's just "[experts|scientists] [say|warn]", which bothers the shit out of me.

Notice to all sea sponges: Don't panic

[paiute]

Although it may seem that if a promising drug is found in a deep sea organism, the rapacious drug companies will get all Constant Gardener on them and start the dredging, that is not how it goes. If a compound is isolated from a sponge that had some desirable bioactivity in humans, that compound is isolated and its stucture is determined. Now the reason this compound has some activity in humans - a species the sponge has had no evolutionary contact with - is most usually due to the way some corner of the chemical sticks into a receptor or enzyme in the mammalian cell. This corner, by no means the whole thing, is called a pharmaphore - the actual working part of the molecule. The rest of the compound is unnecessary. The drug company doesn't need to waste money making that part, or squeezing out gallons of sponge juice. They set their hundreds of medicinal chemists to work preparing a simpler, easier to manufacure, compound that contains the necessary pharmaphore.

DiscoveryHD program on the reef

[dmt99]

The DiscoveryHD channel has a program, "Predators of the Great Barrier Reef" which shows a natural enemy to the worlds reef population, the Crown Of Thorns Starfish. These starfish are demolishing the reefs at a very fast rate. During the show, they discuss the fact that certain sea animals (fish, eels, sea-snakes) have venom which can help with pain management and possibly cure some illnesses. http://dhd.discovery.com/tvlistings/episode.jsp?ep isode=0&cpi=110507&gid=0&channel=DHD

Inside joke alert!

[tgv]

Isn't this known as a "fishing expedition"?

Why?

[Frankie70]

Why are they searching for meds there?
Why not search the Sahara desert or the
moon or the African jungle or something?

Why the deep sea reef?

Re:Why?

[Locus Mote]

Why are they searching for meds there? Why not search the Sahara desert or the moon or the African jungle or something? Why the deep sea reef?

It is most likely that there are other groups studying the life of the Sahara desert and African jungles, however, it is most unlikely that studying biodiversity on the moon will turn up much that is useful. (As far as we know, there is no life there!) More fruitful for the moon would be a search for life at all. Once we find it, then we can study it.

When searching for novel organic compounds scientists will often examine places with high-biodiversity or intense living pressures, like near-surface coral reefs or rainforests. The more ecological niches there are in a locale, the more intense the evolutionary pressure to adapt. When species adapt to these circumstances, they often produce organic chemical compounds which are highly complex and completely unique. Scientists prize these compounds for their ability to perform various funcitons in the human body.

Why deep sea vents and reefs? They are not easy places to live and therefore are likely locations for intense adaptation among resident species.

If Mother Nature Keeps Fucking Us...

[enjahova]

We better fuck her back!

"Oceans lash our coasts. Deserts Burn. The sky provides no shelter. Turmoil of Biblical proportions threatens not just our weather but life itself."

Don't those sound like great reasons to fight back? :)

In all seriousness I feel totally out of the loop on global warming, but Al Gore's scaremongering movie makes me think the current attitude is exaggerated. I believe that there is truth to global warming, but I am starting to disbelieve anything that threatens impending doom (this includes terrorism).

Every generation thinks theirs is the last, why should ours be any different?

Re:If Mother Nature Keeps Fucking Us...

[Johnny5000]

"Oceans lash our coasts. Deserts Burn. The sky provides no shelter. Turmoil of Biblical proportions threatens not just our weather but life itself."

"Oh, so mother nature needs a favor? Well, maybe she should have thought of that when she was besetting us with droughts and floods and poison monkeys." -Monty Burns

Seriously, you missed a perfectly good Simpsons quote?
What kind of Slashdotter are you?

Okay so what about this...

[Maxo-Texas]

I read speculation that fungus develops anti-microbial toxins because it competes with bacteria for living space.

Soooo... in addition to searching deep sea reefs, how about putting various kinds of cancer cells into competition with fungi and bacteria until some develop randomly that kill the cancer. Then see what they did to achieve that.

It might be cheaper.

Re: Scientists Search Deep Sea Reefs for Wonder Dr

[nihaopaul]

reminds me of a night dive on scubacat i was leading in thailand at the similan islands, i had a group of 5 with me, i found 1 tea spoon, some rubbish and 1 bottle of jhonny walker blacklabel 12yr in box which couldn't have been more than 2 hours old underwater, of course i was really removing rubbish!

OrgWHAT?

[Aeonite]

For a moment, I thought that said "A primary goal of the upcoming expedition... will be to search for marine orgasms..."

I was much more interested in the article until I re-read that sentence.

Are you on the endangered ideologies' list? : )

[Scrameustache]

honed by centuries of evolution.

Wow! A young-earth evolutionist! :-P

OH!

[spankey51]

" Scientists Search Deep Sea Reefs for Wonder Drugs"

So THATS where the term "reefer" comes from!

Re:OH!

[Joebert]

Can't wait to see the headlines after the trade devolops "reefers" as a slang name for the scientists.

"Reefer cures cancer !"

Odder Yet...

[Red Flayer]

FTFS: "I'd like to be under the sea
In an octopus' garden in the shade
He'd let us in, knows where we've been
In his octopus' garden in the shade " (emphasis mine)

Funny, it's the YRO articles about the NSA that make me think of Octopus' Garden.

Re:Yadda yadda...

[cutedinochick]

The scientists probably just want to study it just for the sake of studying it (we know very little about the deep seas, and discover on average 2 new species with EVERY dive), but no one gives you money to do that. Having a better "purpose" (i.e. economically viable) may be the only way to get funding.

Curse of the Depleted Environment

[reporter]

eldavojohn (898314) surmises, "Modern man has an impeccable record for destroying the natural environment that produces his fruits & resources."

What is amazing is that even as modern man harvests his latest wonder drugs from the environment, he simultaneously wrecks it by (1) dumping chemicals into the seas, (2) burning the rain forests, etc.

One of the key forces spurring the destruction of the environment is population growth. Expanding populations need living space: in a battle between human population and mother nature, the human population always wins. Indeed, Consider the recent attempt to add immigration-control to the platform of the Sierra Club: immigration-control would curb the population growth of the United States. The attempt completely failed because no one cares about the environmental destruction that population growth facilitates.

To quote a cliched phrase, "the earth does not belong to man; man belongs to the earth." Wrecking the earth is equivalent to long-term suicide.

Re:With rainforests gone, we'll NEED to look harde

[slughead]

Once the rainforests are gone, discovering these chemicals and constituants will get much tougher and many drugs simply wont be invented. Reefs may help produce some drugs, but the article ignores the fact that the diminishing rainforests and other similar natural sources provide far better places to look for potential drug ingredients!

In other news, cleaning my counter with bleach could kill microbes which produce the cure for obsessive compulsive disorder.

There are unumerable (well, we'll call it 10^30 or something) chemicals being produced by organisms in the world. It hardly matters if the cure for cancer is hiding in a slime mold under a rock, because it's more likely a synthetic cure would be invented before we find cures in the wilderness.

Re:With rainforests gone, we'll NEED to look harde

[fain0v]

If you want to find a treatment for obsessive compulsive disorder, you need to find what causes it. An enzyme for example. You would then need to find a small molecule that interacts with that molecule. You create an assay where you can detect changes in the enzyme, and then you add small drug-like molecules to the assay. This will help you determine what interacts and what could become a drug.

You could theoretically make every single small molecule that is drug sized and use it for the assay. The problem is that you would need more matter than is contained in the universe to create just one of every molecule. You need a starting point. Nature is the starting point. Organisms create molecules to defend themselves, interact with the environment, etc. Billions of years of evolution has allowed for optimization of these interactions.

Medicinal chemists need something to start with and nature often provides the answer.

Re:LOL

[Gulthek]

How about Texas A&M?

NOAA?

Re:LOL

[BitterAndDrunk]

I completely approve of those! :)

A week's not complete without at least one downmod on slashdot.

Re:With rainforests gone, we'll NEED to look harde

[malsdavis]

Synthetic drugs don't just get made. 95% of the time they are modelled on naturally produced sources, they can then get made artifically once the source process has been well researched.

Your kitchen surface is not likely to produce chemicals useful for drugs either mainly because their not surviving in a niche enviroment. Rainforests for example contain lots of good candidate chemicals because trillions of different types of organisms live in often carefully etched out niche's where funky chemical processes allow them to survive predators. These funky processes are the ones BY FAR most likely to produce "wonder-drugs" if they can be made to do funky stuff in humans aswell. ...with rainforests gone, wonder-drug's will be A LOT harder to discover. That is my point!

Taxol, BMS, and NCI

[falconwolf]

I noticed the wiki article on Taxol doesn't mention that Bristol-Myers Squibb paid the NCI, National Institute of Cancer, less than the NCI spent developing Taxol. Having paid little for the rights to exclusive use of the Taxol data, MBS has made billions of dollars off of Taxol.

Falcon

pharmaceutical research

[falconwolf]

I find it surprising, though, that both syntheses came out of academic labs - not from the pharmaceutical companies that sell the drugs. You'd think they'd have enormous incentive, and more than enough resources, to do such work themselves. If they aren't interested in actually making drugs, what exactly is it that they do?

It's cheaper for the pharmaceutical companies to let government and univserities to do the research then to come in and buy the drug. Taxol, a cancer drug previously mentioned, is a good example. Bristel-Meyer Squibb, who has exclusive rights to the data gathered by the National cancer Institute (NCI), paid the NCI less than half the cost NCI paid to develop Taxol from the Pacific Yew tree. The additional money BMS has spent on it has been in reducing their own costs of producing Taxol. The cost for one cancer treatment with Taxol cost several thousand dollars yet BMS's cost is less than $100. And Taxol has made $billions for BMS.

Falcon

Pacific Yew tree

[falconwolf]

Your entire fifth paragraph falls apart logically. Use the northwestern yew as an example. Extremely rare species which supplies a useful anticancer compound. Were they harvested to extinction? No. Were they replaced by other yews from around the world? No. Why? It is that species which has the compound. Your paragraph falls apart historically. Which, ironically, is the very rational you use to promote it. Odd, that.

Actually a species of the yew tree has been found to at least augment if not replace the Pacific Yew tree as a source for Taxol. Researchers at FSU found a Yew tree native to the area that can be used to manufacture Taxol.

Falcon

Sierra Club and immigration

[falconwolf]

One of the key forces spurring the destruction of the environment is population growth. Expanding populations need living space: in a battle between human population and mother nature, the human population always wins. Indeed, Consider the recent attempt [usatoday.com] to add immigration-control to the platform of the Sierra Club: immigration-control would curb the population growth of the United States. The attempt completely failed because no one cares about the environmental destruction that population growth facilitates.

The Sierra Club did the right thing in opposing immmigration control. For anyone who's against immigration I have one question and depending on what the answer to it is then maybe a second. First, what Native Amwerican Indian Tribe are they from? If they aren't NDN then what tribe signed their or their ancestors who immigrated to America documents? White Northern Europeans invaded and colonized the Americas and now the descendents of those who came to the USA want to prevent anyone else from immigrating here as well.

Falcon

Florida Keys

[falconwolf]

It takes 30,000 years to grow 1 cubic inch of coral, and the mistreatment of the reefs around Florida (1960s dynamite fishing, jewelry harvesting, etc.) has made it so that the reef off of the Florida Keys is the last living coral reef in the region.

Ah, Key Largo's an excellent place for scuba diving. While it's not done in the Keys now, dynamite fishing is done frequently in the Indian Ocean. That and the use of cyanide. Shark finning is also popular, especially for shark fin soup.

Falcon