Feet1st, mentioning oil, you've struck a nerve.

I'll never understand people, why they don't REVOLT against this kind of abuse. After bleeding financially for years and years. How can they possibly believe people who are lying to them in the most blatant and obvious way?

You're expectng logical behaviour there. Which is NOT going to happen in a society that is told by adverisers that the cool vehicle they have to own burns about 80% of a pint of gas each mile it goes.

Hummer Fuel Stats

Look at the 2004 H2 SUV and weep.

Also, (to quote John Lennon) "You say you want a revolution ..." How exactly are we supposed to revolt?

Naimi said Saudi Arabia had always worked on market stability "in the interest of consumer countries, producer states and in the interest of the world economy in general".

"There is no doubt that the initiatives taken by my country and by other oil producers, within or without OPEC, will sooner or later return stability to the market," Naimi said.

Naimi said since the beginning of his career in the oil sector, he had never seen as many disagreements and agitation, noting this could partially be explained by a short-term rise in oil prices and "rumours about an assumed exhaustion, limits in excess production capacities and effects on the environment".

"It is preferable to us, government officials, business men and intellectuals, to be realistic, to avoid resorting to intimidation or exaggeration despite what this might accomplish in terms of attention and short-term political advantages."

BTW: Was that "Internal benchmark" compared with a credited
benchmark program ?
eg: Sisoft Sandra
http://downloads.guru3d.com/download.php?det=177

SiSoft Sandra's integer and floating point benchmarks are optimized to produce the higest possible results. That's all well and good, but it's not REALLY important exactly what numbers Boinc comes up with in it's results, as long as it's reasonably good at linearly giving a score that matches the speed of the machine. If you take the time to optimize the benchmark so that it gives a better score, would it actually give a fairer result? Probably not...

4 years ago, I was told that an RMSD of 4 angstroms was the point where predictions started being useful. Has the point of being useful suddenly dropped to an even smaller RMSD?

"I'm a guy who was once associated with one of labs/projects mentioned above. I was working on the problem for years, and have a great deal of expertise in the area. I can also tell you that the project is complete and utter crap, from a scientific perspective. The PI routinely misrepresents the project goals, claiming "possible" results that could never, ever come from the type of research performed. In general, the "science" is poorly-conceived and improperly controlled, and most of the "experiments" are methodologically flawed. I can't post my name here...it would be career suicide. As one of the authorities to whom you seem so desperate to appeal, let me assure you: if you are devoting your resources to this project, the world would be a better place if you simply turned your computer off."
Making the assumption (yes, it is a big assumption) that he is right, now I wonder which one he was talking about... I'm lousy at detective work

"A similar approach, Rosetta@Home, led by the most respected protein folding group in the world, The David Baker Lab, uses an algorithm with is much more likely to yield useable results. Last year they used distributed computing to vastly outperform every other protein folding lab in the world."

In terms of scientific contribution, neither of these projects is really worth a great deal. They're both quite speculative, with long-range benefits, if any.

Still, if you have to give one project the benefit of the doubt, it's Folding@Home. Rosetta may "work" better than other ab initio methods, but that isn't saying a whole lot. Ab initio protein structure prediction is just one step above useless, scientifically. A nice game, good for PR and flashy pictures, but the results are usually dismal.

That said, you can still find value in the methods, but only if they give us some scientific insight as to the process of protein folding. The thing is, Rosetta doesn't do that. It can't. It's a heuristic algorithm, and the best you can possibly ever do with it, is say that you're confident to some probability that a particular prediction may be "correct" (in case you're wondering, this probability is usually quite low).

In contrast, Folding@Home is based on a physical model of the world. It may not work very well at structure "prediction," but it's a much better algorithm for other, more realistically-attainable problems (like small-molecule binding). It's also based on actual physical models, and so there is a chance that it can contribute to our understanding of the basic physics of protein folding.

In short: if you truly want scientific relevance, devote your time to other projects. If you insist on helping this field, however, use Folding@home.

(incidentally: I am a computational biologist who has a PhD in the field.)

writing that after two years in computational chemistry for what is now GlaxoSmithKline, "I became strongly convinced that computers do not find cures for diseases - or even give you much understanding of illnesses. Molecular modeling is so far from being able to model in vivo molecules that it's practically worthless. ... [W]e already know that trials at this stage are poorly correlated with actual drug usefulness, simulations are just as much a waste of resources as SETI. ... It seems to me that molecular modeling is actually one of those hard 'macho' (but ultimately pointless) projects that gets funding because to criticize it makes you seem anti-drug, anti-therapy and anti-human-progress. (I'm not saying people shouldn't try to model molecules. This is a great blue-sky goal. But people who are trying to find drugs or therapies shouldn't be wasting their time with such techniques.)"

The screensaver project has produced a large number of 'hits'; molecules predicted to be potential inhibitors of proteins and possible leads for drug discovery. The bottle neck to exploitation of these predictions is the potentially costly synthesis of the compounds and their biological testing.
For two of the series we have passed that stage and the results are very encouraging.
One of the more interesting and challenging targets is the phosphatase.
Much of biology is a balance between phosphatases and kinases. The latter have been important commercial targets for anti-cancer drugs for many years, but the phosphatases have proved more difficult as for one thing the biding site into which the drug must bind is rather ill-defined. The project produced some 128,000 hits for this target. We analysed the results and produced a list of 400 good hits of differing chemical types. These were synthesized and tested. Over 40 [~10%] proved to be genuine inhibitors which is very good by industry standards and what is more they are uncharged molecules which are very different from known inhibitors. We are trying to find pharmaceutical companies to take this further.
For a second series where the target is urokinase plasminogen activator [implicated in prostate cancer] we have again had hits synthesized and tested, this time by collaborators at the Arizona Cancer Center. This too has produced encouraging novel active compounds . These results were presented at the American Association for Cancer Research and a poster giving details is being put on the Oxford Chemistry web site

Um, I don't understand what you mean by the people should "revolt". Do you mean demonstrations at the refineries? Protests in the streets?

I'm not talking about refineries or BigOil. Ofcourse they're profiteering off a broken pricing mechanism and pretend all is well and are shedding crocodile tears about how sorry they are.

I mean to change the BROKEN mechanism used to set the price of oil, off the price of derivatives whereas there is no real link between derivatives and physical. Isn't it obvious?

When you have even the #1 exporter of oil in the world tell you BLUNTLY that oil should be selling for no more than $50 (see yesterday's Reuters story) and now it's 50% higher, just what more do people need?

If we were talking about the market for apples instead of oil barrels, and you saw the price go up and up and at the same time the producers tell you can't sell their apples, wouldn't you think the market is "broken"? Why don't people do the same for oil?

Apparently people have the misconception that international "open markets" set the price for oil, but due to technical aspects -explained earlier- the oil derivatives markets are neither free nor fair. They're cornered, but unlike a similar situation that might happen in a piece of paper i.e. stock, oil is a basic commodity which everyone HAS to buy and it's getting awfully expensive!

Um, I'm not disagreeing with you at all, Dmitri. <kindly said>

I'm just asking about the "How" of it all. What would you like people do to get this changed?

Best regards.


Edit: P.S. I'm seeing the price disconnect at the supermarket every day, on apples and other products. There's a complete disconnect there too. Prices are based solely on demand monitored in real time by the retailers' computers. Only a drop in demand succeeds in lowering prices. These new price disconnects we're seeing are a feature of new computer-enabled business savvy in many fields, I think.

Of course as anonymous can't tell who wrote what, so perhaps this other comment is from the same person, or maybe not... (in response to the question Is "Human Proteome Folding" the same as Folding@Home, the one run by Stanford?)
"They are competitors. Or rather... "Human Proteome Folding" would like to compete, but haven't been able to. Just look at the amount of _hard_ results coming out of Folding@Home in the form of scientific papers and your choice is easy. The "Human Proteome Folding" project claims they are heading into "phase2", yet haven't published any real results public journals.
Yes, I'm in the field, but no, I'm not related to the Pande group, but I find their recent work _very_ impressive scientifically."

Feet1st, mentioning oil, you've struck a nerve.

Dimitris, I hope you didn't take my carberator reference personally. I didn't intend for it to be a reference to your thread in the cafe. Your analysis goes beyond the guy asserting that such a carberator exists and is being suppressed. I didn't mean to go off-topic. I think we should leave the oil discussion to the cafe.

One of the problems with using something like a GA in Rosetta@Home is communication. While it's plausible to have each computing node with an independently evolving population of structures, that process is limited by the number of structures that can be constructed on that single node in a reasonable amount of time. The most straightforward approach to adding this information would be prohibitively expensive in terms of communication, especially when we consider the number of users that we have on intermittently active or slow connections.

...yet they seem MORE then willing to ask everyone to band together and NOT buy gasoline on ONE day next week... and they think this will lower the gas prices. Meanwhile they floor the accelerator when the light turns green and get it up over the speed limit in a block so they can slam on their brakes for the next red light which was clearly visible from the first. And they complain about the corporate conspiracy to NOT make cars that get better mileage. And how the oil companies have the auto companies on their payroll. Hey look, if there really IS a carborator out there that makes a car get 100MPG... and you know about it... then SELL IT! Don't keep it to yourself! ...and if you really don't have any first-hand knowledge of such... then shut up.
[dismount soapbox]

What can be done?

There's tons of explanations of why the price is so high and won't come down. Listening to the radio, or reading the paper, I gather that the 'glut' of storage oil on the market has now affected OPEC so badly that they're storing oil in old tankers (and running out of them!). They're looking (begging) for people on the open (spot) market to buy oil.

Inflation, inflation everywhere!

Pretty soon, the producers are going to have to start ramping back, correct? And when that happens, the price IS gonna be pretty much set in stone, correct?

Most of the charts and articles you've referenced here reflect the month of April, and they mostly talk about the Western world (specifically the US). What's going on in China? And to a lesser extent, India? Things haven't changed much in three months. It's such a fast changing world, too.

I'm not an economist, but I would say those "orange" people have something to do with whats going on, too! Maybe these 'speculators' ain't so happy that the world is going flat without them?

Another interesting thing is that the European price for fuel has always been a lot higher than the US. I remember paying something like 4.50 a liter in Italy 10 years ago. Is that right?

So, my question is what mechanism could you use to artificially inflate the price of light sweet crude and sustain it, in order to develop new technology that will in the end, defeat it? And to further aggravate the question, who would be developing the new technology? Hate to be an outsider holding on to a bunch of light sweet crude when that happens, but either way, someone is always living behind a dumpster at a 7-Eleven.

Crude oil closed above $70 a barrel for the first time, highlighting a phenomenon reshaping the petroleum world: investment flows into oil futures are supplanting nitty-gritty supply-and-demand data as prime drivers of prices

In contrast to past bull markets in crude, this year's run-up has occurred even though oil inventories in the U.S., the world's largest market, have swelled to their highest levels in nearly eight years....

The answer to the puzzle posed by rising prices and inventories, industry analysts say, lies not only in supply constraints such as the war in Iraq and civil unrest in Nigeria and the broad upswing in demand caused by the industrialization of China and India. Increasingly, they say, prices also are being guided by a continuing rush of investor funds into oil markets. Institutional money managers are holding between $100 billion and $120 billion in commodities investments, at least double the amount three years ago and up from $6 billion in 1999, says Barclays Capital, the securities unit of Barclays PLC....

Since early 2005, the crude-oil market is in what traders call contango, meaning futures contracts for a given product are priced higher than that same good for near-term delivery. The price of oil to be delivered four months from now is about $3 more than oil to be delivered next month.
Flooded oil storage near Port Arthur, Texas
oil_storage2.jpg

In short, it pays for refiners and other oil-market players to buy and hold oil now to sell it down the road. Making that trading opportunity possible, says Colorado-based oil analyst Philip K. Verleger, is the huge volume of new buyers on the other side: investors who he estimates have put more than $60 billion into U.S. crude-oil futures since 2004.

Indeed, San Antonio-based Valero has been operating with its crude tanks full since the start of the year. When the market is in contango, "you tend to operate at the top of your tanks," says Bob Beadle, Valero's senior vice president in charge of crude oil, supply and trading. Mr. Beadle estimates that in the U.S., the difference between the industry operating at full tanks and at minimum operating levels amounts to as much as 75 million barrels of oil, or about three days of supply.