If you need any reminders that the middle east is not the USA, remember the hikers that are still hanging out in Iranian prison for being spies with no proof or evidence.
Uh, I'm no fan of the Iranian rulers, and I can think of many other reasons why the American system of government is vastly better to Iran's, but we've held a lot more foreign nationals indefinitely without evidence in the last decade. And although lots of Iranians have died under "questioning" in their prisons, so far there's no indication that any of the hikers have been tortured, let alone killed - and our record there isn't too great either. I hope the remaining two get out soon, and I hope our government presses for their release, but this is one case where we have no basis for a smug feeling of moral superiority.
Nor can I use my newspaper or TV company to stump for them, any more than a newspaper could give free classifieds for a year to the local fire marshal in exchange for, or hopes of, "forgetting" the fire inspection. That's not free speech. It's bribery.
Bullshit. "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances." It doesn't get any clearer than this. You can say nearly anything you want in this country, short of directly inciting violence. If you're unhappy with this, move to Saudi Arabia or Iran or China, and enjoy the enlightened political environment that comes with a properly regulated media.
Concerning the distinction between corporations and people, it's irrelevant in this case. If I write a blog about politics, and I think that putting hypothetical Candidate X in the White House would directly lead to the destruction of Western Civilization, should this be allowed? What if I'm the publisher of a major newspaper, shouldn't I be allowed to say the same thing on my paper's editorial page? If the shareholders of the newspaper collectively decide this, why should they be prohibited from saying so? At what point does a group of citizens become large enough (or rich enough) that they collectively lose their 1st Amendment rights?
If there is an actual quid-pro-quo involved, then certainly, send the fuckers to jail. But this is almost never the case, even for news organizations that are blatantly biased towards a particular candidate. Proving it, anyway, is nearly impossible. Where do you draw the line between self-interest (which is entirely legitimate - if often unpleasant - in a pluralistic, democratic society) and acting in the public good? Would newspapers that loudly supported abolitionist candidates in the 1850s be muzzled by your hypothetical "anti-bribery" laws? Do you really think that federal regulators should waste time trying to parse out the personal motivations of everyone involved?
There's no technical reason not to launch all the equipment the settlers would need to be self sufficient in those areas all at once in a Project Orion [wikipedia.org] vehicle.
No, but there are dozens of practical obstacles, such as convincing the US taxpayers to spend hundreds of billions of dollars on a massive spaceship that will spew radioactive waste into our atmosphere and violate the nuclear test ban treaty. Or, if you're only going to use nuclear pulse propulsion starting from orbit, you substitute the technical obstacle of getting all that mass into orbit in the first place.
I work for the DOE (at a different lab), and from what I've seen, patented technology is almost always licensed to American companies. If it wasn't, a major argument for the existence of the national labs goes out the window, and Congress would probably throw a fit. I don't know if patent licenses come with strings attached (like "thou shalt not offshore manufacturing"), but my guess is that any company wanting to profit from publicly-funded basic research has to tread carefully.
(Obvious disclaimer: I speak for no one except myself - I'm just a lowly programmer anyway.)
To be honest, it's not clear to me why they aren't imaging individual protein molecules directly. It can't be that hard to make a small hard X-Ray synchrotron and appropriate imaging hardware.
You wouldn't use a synchrotron for this; you need something called a "free electron laser". This science is in its infancy, and single-molecule imaging with FELs is still only theoretically possible. And it still isn't clear whether the resolution limit will be as good as we can get with crystallography. It's a very promising avenue of research, but it will probably take another decade for it to become truly practical, and decades longer (if ever) for it to supplant crystallography. (And FELs are neither small nor cheap - not that a state-of-the-art synchrotron is either, for that matter.)
It really is the perfect example, as you only need to grow one crystal of every protein, then you can take it down to earth and do X-ray crystallography.
Well, there are at least two problems with this:
1. Protein crystals are sensitive to vibration (and many other external factors); some don't age well either. 2. We usually freeze protein crystals in liquid nitrogen to protect against radiation damage. Unfortunately, this also tends to decrease crystal quality a great deal, which we accept because we can get away with blasting them with synchrotron X-rays.
It also turns out that many of the advantages of microgravity can often be simulated in other ways to obtain equally good crystals. I'm fuzzy on the details, but I think using an agarose matrix to slow diffusion is one method. And there are many, many other tricks to improve crystallization that are vastly less expensive or troublesome than shipping the protein into space. In fact, because the resources up there are so limited, you need to have already identified a set of conditions that you know will get at least marginal crystals, before doing the microgravity experiment.
Will the contributions the space station makes to Science and society at large be sufficient to provide a $4 billion/year real rate of return in perpetuity, give or take? Does it even come close?
No, and I totally agree with the premise that the ISS is a waste of money. That said, I'm hesitant to endorse a system that only judges basic research expenditures based on the eventual return. Hubble is a terrific example of a project that cost a fair amount of money and probably won't pay back very much of it, but it did some spectacular science for many years. I do think there is some intrinsic value in the acquisition of new knowledge, and it's also very difficult to quantify payoffs for basic research that doesn't lead directly to a tangible product. The problem with the ISS is that the so-called science it supported wasn't even very interesting. (I'm familiar with the microgravity protein crystallization research, and it has done very little for the field. The underlying idea is sound, but the cost and practical obstacles are a deal-breaker.)
It's a complicated problem, and I'm honestly not sure what the best course is, but I think that in our current economic and political system, our basic research expenditures and the resulting economic gain are about as optimal as can be hoped for. (Semi-obvious disclaimer: yes, I'm a government scientist, so hardly disinterested. I won't be voting tomorrow, however.) I'd be much happier if the entire scientific enterprise - and space exploration too, for that matter - were completely in private, non-profit hands instead of having to rely on either the government or corporations to fund it. On the other hand, when we're spending more on two unwinnable wars each year than the ISS has cost in its entire lifetime, I'm not going to get my panties in a knot over the relatively small portion of my tax dollars going to NASA. Based on past experience, I suspect the poster to whom I was replying is very selective in his outrage.
There is nothing about research that makes me pay for a non-existent product.
Most basic research takes decades to turn into a marketable product. To take my favorite example, X-ray crystallography, it took 25 years from the first experiments with protein crystals to actually determine a structure, then another 25 years for the method to mature enough for pharmaceutical companies to use it. Simultaneously, it also took 25 years for a particular type of particle accelerator to be recognized as useful for crystallography. There is simply no profit to be had in a reasonable amount of time from this kind of fundamental groundwork. The particle accelerators in particular cost hundreds of millions of dollars to build. Only a handful of companies in the world have enough money to spend on blind research like this. Even some of those would probably be at risk of shareholder lawsuits if they were devoting hundreds of millions on research of questionable use.
I won't get into the issue of morality, because it's simply impossible to argue with someone who claims that "taxation is theft." Strictly from a free market standpoint, there is no financial incentive to invest in basic research without any hint of a future product. I personally think that the ISS has been a waste of time and money that has detracted from more promising space exploration projects, but none of this would happen if left to companies like, say, GE. (Private charities? I wish - only a handful of those can afford mega-projects, and they risk alienating major donors if something turns out to be a blind alley.)
This was not an ab initio, calculation. It's all atom MD, which itself is an approximation
Sorry, I meant "ab initio MD", although I realize that to a chemist or physicist this is a total oxymoron. (My background is molecular biology and bioinformatics, where we try not to think about quantum chemistry.) I should have written "physically-based", if you prefer, as opposed to the knowledge-based approaches that have been most successful for de novo structure prediction. (I think most MD "force fields" are ultimately based on genuinely ab initio QM calculations.)
That's a little unfair to Folding@Home. Shaw has a lot of resources to pour into this project - he's lured faculty members away from universities to work for him instead and has the equivalent of several large labs worth of advanced researchers. He also has an immensely larger budget than most non-profit labs, and he's self-employed so he doesn't have to answer to granting agencies or tenure committees. I think what he's doing is great but he's really one of the only people who could have pulled this off. It's difficult to know what approach will work best in advance, and both Shaw and Vijay Pande have been very innovative in approaching the problem from completely different angles.
By the way, this approach has been tried before with less stellar results - I'm thinking of the MD-GRAPE project in Japan. You're also assuming that every problem is equally well suited towards custom ASICs, but actually, molecular dynamics is far easier to do this with than many other methods. For instance, Rosetta (Rosetta@Home and Fold.It) is doing structure prediction, not folding, using a mostly statistics-based energy function and Monte Carlo sampling, and this isn't something you can trivially offload to a specialized chip. In that case, distributed computing is by far the most efficient solution.
The actual research articles are hard science - this was just a news story for a general audience. The official publication of the results in Science magazine appears to be a pretty serious piece of work, and it's significant enough that the editors allowed them to make it reasonably long instead of a (severely compressed) three- or four-page summary article like most of what they publish. There are lots of valid criticisms of those two journals, starting with their length requirements, but they're not Scientific American, and publishing in one of these is practically a prerequisite for getting a faculty position in biosciences at a major research university.
The best way is to just compare them to the actual structure which is known from x-ray crystallography and NMR studies.
And so far, this is the only way that most researchers are willing to trust. There is a very good reason why these folding studies tend to focus on a small group of well-defined model systems, because the folded native structure is already very well understood, and it provides an essential constraint on the interpretation of results. Using ab initio physics calculations like this for truly blind structure prediction would be a complete waste of time, and the entire field figured this out decades ago.
The only problem is getting out of our gravity well.
Not only are you forgetting about cosmic radiation, which is a severe hindrance, you're vastly oversimplifying the problem of the gravity well, since sustaining a human presence on an asteroid would require regular shipments of supplies at exorbitant cost. I'm also curious how you expect the raw materials to make it back down to Earth. Actually refining many of these metals in space would also be a pain in the ass, but landing asteroids wouldn't be very easy either.
Which elements are actually that rare, anyway? For instance, Wikipedia claims that "The main mining areas [for gadolinium] are China, USA, Brazil, Sri Lanka, India and Australia with reserves expected to exceed one million tonnes. World production of pure gadolinium is about 400 tonnes per year." That's a lot to ship back from the asteroids, and I'm not sure I see any financial benefit.
Which is worse, saying we should believe everything scientists say, or being anti-scientist?
Both are a bad idea, and as a scientist myself, I've learned to keep my BS detector set to "11". But when faced with a choice between believing actual scientists versus the propagandists at the Discovery Institute, I'll side with the scientists every time.
It is interesting (and very bigoted of you) to assume anyone who is a AGW skptic is anti-science and pro-intelligent design.
I realize that this isn't universally true, but I've noticed a large overlap - specifically, the vast majority of creationists appear to be "AGW skeptics", and they are certainly anti-science, and very militant about it. When I see the cretins from the Discovery Institute reading from the same script as the anti-AGW crowd, I'm naturally suspicious of the latter. This may seem unfair to you, but it's no more unfair than accusing climate scientists of wanting to force society back to a pre-industrial state.
Which brings up a more accurate point: while the "skeptics" may not all be anti-science, they definitely come across as anti-scientist.
While this technique avoids the inherent difficulties of producing crystals (a process that can take decades for some samples), until very recently it has been difficult to achieve high resolution structures using this method. The cryo-EM adenovirus structure is one of only a handful of atomic resolution cryo-EM structures that have been solved to date.
A large part of the reason why this is possible is the high internal symmetry of viral particles; I think all of the atomic-resolution cryo-EM structures so far have also been of highly symmetric structures like bacterial chaperonins, or other viruses. (The same symmetry also makes crystallography easier, for different reasons.) The only other EM structure that I'm aware of at better than 4 Angstrom resolution is also of a virus, published a few months ago by the same group at UCLA. For highly asymmetric structures such as ribosomes, crystallography is still far ahead of EM as far as resolution is concerned - although the bottleneck of crystallization remains a major problem.
it is interesting that the Medical Daily focuses only on the x-ray crystallography study from Scripps. . . Perhaps Medical Daily needs to do a better job of doing their homework.
If you scroll to the end of the story, you'll see "Provided by Scripps Research Institute" in tiny gray letters. It's just a press release from Scripps, in other words - standard operating procedure for research institutions when someone scores a high-profile article.
The article is horribly misleading - it suggests that the FoldIt users came up with better structures completely on their own. What they were actually doing was improving the automatic structure predictions. If you actually read the Nature article, it shows comparisons of the initial model, final model, and experimental structures. The initial model has the overall fold correct, but with some gross errors which the FoldIt players corrected, leading to an even better model. This is still an impressive result, but it simply doesn't mean what Ars Technica says it means. The author sort of admits that Rosetta helped at the end, but it sounds completely ignorant of how difficult it is to even guess the overall fold correctly. I'm wondering if the writer even bothered to read the original article or just read the PR material.
what makes the real proteins not get "stuck" in the local energy minimums that the program keeps getting stuck in?
Several good answers below, but there isn't really a single simple one. This is called Levinthal's paradox, and it's one reason why ab initio molecular dynamics simulation turned out to be a terrible way to predict 3D structure. It turns out that Folding@Home (not FoldIt) requires petaflops of computing power because of the same problem: it runs ab initio simulations, and most of them get stuck, but spread out over that many CPUs, they can extract enough data to get a trajectory to the final folded state (which they already know).
forget about Foldit! Just download Folding@Home and let your CPU/GPU do it for you!
FoldIt and Folding@Home are doing completely different things. FoldIt (or more specifically, the Rosetta software underneath it) is attempting to guess the final structure of novel protein sequences, using a variety of clever tricks such as mining the database of known structures for peptide motifs. It contains energy functions to evaluate candidate structures, but it is not simulating physical processes, and it tells you nothing about how the linear chain of amino acids forms the 3D structure. Folding@Home is used to study the process of protein folding, where the end result is already known; it isn't useful as a structure prediction tool. Both programs require a massive amount of computing power, but for very different reasons. Both are very useful, but there is almost no overlap in their practical applications. (And it should go without saying that while they can both be an excellent complement to experimental studies, neither can replace them.)
How about the fact that hundreds of NASA employees will not be thrown out of work? How about the fact that hundreds if not thousands of current commercial suppliers to NASA will not be thrown out of work? How about the fact that there will still be jobs created because there will still be development outsourced from NASA?
So basically, you're saying that NASA should be used as a welfare program for existing dependent companies and key congressional districts, regardless of whether the projects it works on actually advance science and technology?
How about the fact that these people are basically complaining because they won't get any corporate welfare?
Certainly, but the Senate bill is basically written to address the concerns of the existing recipients of corporate welfare. Since it comes down to a fight between private interests, I'll still side with the plan that I think spends our tax dollars most effectively towards what I believe NASA's goals should be. None of those goals involve locking ourselves in to spending billions of dollars on solid rocket boosters built by ATK.
Okay then, what facts did the article leave out? So far all you've contributed to the discussion is bashing everyone who opposes the goals of the bill.
"I won't be able to exploit the government and workers so this bill sucks."
Your sarcasm would be more convincing if this weren't the same complaint that we've been reading about Obama's proposals for NASA.
Every single one of the named sources is attached to and gets money from commercial space interests in some way.
So what? The facts about the Senate bill are a matter of public record and not in dispute. Any plan NASA comes up with is guaranteed to be kicked around like a football by all of the commercial space interests and Congresspeople that stand to gain or lose from it; this is unavoidable. The article was in a North Florida paper and was largely discussing the potential effect on the North Florida economy, but those of us who've been paying attention to this silly controversy are aware that it's much more complicated. People can make up their own minds what they think of the bill; I suspect most Slashdot readers who oppose it don't care about North Florida or the poor, unloved commercial space interests. Personally, I think it's appalling, and I don't work for NASA or any aerospace contractor, and won't gain or lose either way.
That would be perfect because everything produced by the govornment is in the public domain.
Not even close. The AC who replied covered some of the major points, but it's pretty complex. Basically, the Bayh-Dole act (passed in 1982, I think) allows a great degree of latitude in commercialization of research done with government funding - the idea being to encourage economic development AND turn raw technologies into useful consumer products ("consumer" used in the broadest possible sense, since these technologies could become anything from specialty laboratory instruments costing $500,000 to OTC medications). How this is actually interpreted varies in practice, but the general consensus (as far as I can tell) is that it's an imperfect system but no one can think of a better alternative.
I actually work for the DOE writing software, and none of what I do is "public domain". Some of it is Free Software (BSD-ish license), the rest is free-as-in-beer for academics, and companies have to pay (they get the code too, but can't redistribute it). This is a pretty typical arrangement (in our case, the rules are dictated more by the funding source, which is the NIH). A large part of the reason for this is that the licensing revenues help pay for the research - I'm sure as f*** not getting rich off this. I'd be happier if it was all Free Software, but mostly because I think it would make my job easier and get more people to use our software. Compared to many of the other licensing arrangements that scientists invent for government-funded research, ours is pretty reasonable. The NIH is starting to get stricter about what they allow - some funding specifically requires that the source code be made available, and programs need to be free for academics. But public domain (or Free Software, which I think you're confusing it with) has never been a requirement.
And we all know that a career bureaucrat would never, ever lie to the media. Can you show me any evidence that NASA has actually acted (or wasted money on) this supposed "priority"?
You're so quick to believe this because it confirms your biases, but every time Obama or one of his political appointees tries to pander to the free-market crowd by talking about privatizing launch vehicles, every right winger screams "bullshit!" (And for all I know you're correct; it seems just as probable to me that he's trying to fuck over the politically connected contractors who've grown fat off NASA contracts.) Meanwhile, he's ordering drones into Pakistan to kill Taliban, along with more than a few civilians, and the pseudo-conservatives accuse him of caring too much about Muslim public opinion because he gave a speech in Cairo.
Slashdot Mirror
If you need any reminders that the middle east is not the USA, remember the hikers that are still hanging out in Iranian prison for being spies with no proof or evidence.
Uh, I'm no fan of the Iranian rulers, and I can think of many other reasons why the American system of government is vastly better to Iran's, but we've held a lot more foreign nationals indefinitely without evidence in the last decade. And although lots of Iranians have died under "questioning" in their prisons, so far there's no indication that any of the hikers have been tortured, let alone killed - and our record there isn't too great either. I hope the remaining two get out soon, and I hope our government presses for their release, but this is one case where we have no basis for a smug feeling of moral superiority.
Nor can I use my newspaper or TV company to stump for them, any more than a newspaper could give free classifieds for a year to the local fire marshal in exchange for, or hopes of, "forgetting" the fire inspection. That's not free speech. It's bribery.
Bullshit. "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances." It doesn't get any clearer than this. You can say nearly anything you want in this country, short of directly inciting violence. If you're unhappy with this, move to Saudi Arabia or Iran or China, and enjoy the enlightened political environment that comes with a properly regulated media.
Concerning the distinction between corporations and people, it's irrelevant in this case. If I write a blog about politics, and I think that putting hypothetical Candidate X in the White House would directly lead to the destruction of Western Civilization, should this be allowed? What if I'm the publisher of a major newspaper, shouldn't I be allowed to say the same thing on my paper's editorial page? If the shareholders of the newspaper collectively decide this, why should they be prohibited from saying so? At what point does a group of citizens become large enough (or rich enough) that they collectively lose their 1st Amendment rights?
If there is an actual quid-pro-quo involved, then certainly, send the fuckers to jail. But this is almost never the case, even for news organizations that are blatantly biased towards a particular candidate. Proving it, anyway, is nearly impossible. Where do you draw the line between self-interest (which is entirely legitimate - if often unpleasant - in a pluralistic, democratic society) and acting in the public good? Would newspapers that loudly supported abolitionist candidates in the 1850s be muzzled by your hypothetical "anti-bribery" laws? Do you really think that federal regulators should waste time trying to parse out the personal motivations of everyone involved?
There's no technical reason not to launch all the equipment the settlers would need to be self sufficient in those areas all at once in a Project Orion [wikipedia.org] vehicle.
No, but there are dozens of practical obstacles, such as convincing the US taxpayers to spend hundreds of billions of dollars on a massive spaceship that will spew radioactive waste into our atmosphere and violate the nuclear test ban treaty. Or, if you're only going to use nuclear pulse propulsion starting from orbit, you substitute the technical obstacle of getting all that mass into orbit in the first place.
I work for the DOE (at a different lab), and from what I've seen, patented technology is almost always licensed to American companies. If it wasn't, a major argument for the existence of the national labs goes out the window, and Congress would probably throw a fit. I don't know if patent licenses come with strings attached (like "thou shalt not offshore manufacturing"), but my guess is that any company wanting to profit from publicly-funded basic research has to tread carefully.
(Obvious disclaimer: I speak for no one except myself - I'm just a lowly programmer anyway.)
To be honest, it's not clear to me why they aren't imaging individual protein molecules directly. It can't be that hard to make a small hard X-Ray synchrotron and appropriate imaging hardware.
You wouldn't use a synchrotron for this; you need something called a "free electron laser". This science is in its infancy, and single-molecule imaging with FELs is still only theoretically possible. And it still isn't clear whether the resolution limit will be as good as we can get with crystallography. It's a very promising avenue of research, but it will probably take another decade for it to become truly practical, and decades longer (if ever) for it to supplant crystallography. (And FELs are neither small nor cheap - not that a state-of-the-art synchrotron is either, for that matter.)
It really is the perfect example, as you only need to grow one crystal of every protein, then you can take it down to earth and do X-ray crystallography.
Well, there are at least two problems with this:
1. Protein crystals are sensitive to vibration (and many other external factors); some don't age well either.
2. We usually freeze protein crystals in liquid nitrogen to protect against radiation damage. Unfortunately, this also tends to decrease crystal quality a great deal, which we accept because we can get away with blasting them with synchrotron X-rays.
It also turns out that many of the advantages of microgravity can often be simulated in other ways to obtain equally good crystals. I'm fuzzy on the details, but I think using an agarose matrix to slow diffusion is one method. And there are many, many other tricks to improve crystallization that are vastly less expensive or troublesome than shipping the protein into space. In fact, because the resources up there are so limited, you need to have already identified a set of conditions that you know will get at least marginal crystals, before doing the microgravity experiment.
Will the contributions the space station makes to Science and society at large be sufficient to provide a $4 billion/year real rate of return in perpetuity, give or take? Does it even come close?
No, and I totally agree with the premise that the ISS is a waste of money. That said, I'm hesitant to endorse a system that only judges basic research expenditures based on the eventual return. Hubble is a terrific example of a project that cost a fair amount of money and probably won't pay back very much of it, but it did some spectacular science for many years. I do think there is some intrinsic value in the acquisition of new knowledge, and it's also very difficult to quantify payoffs for basic research that doesn't lead directly to a tangible product. The problem with the ISS is that the so-called science it supported wasn't even very interesting. (I'm familiar with the microgravity protein crystallization research, and it has done very little for the field. The underlying idea is sound, but the cost and practical obstacles are a deal-breaker.)
It's a complicated problem, and I'm honestly not sure what the best course is, but I think that in our current economic and political system, our basic research expenditures and the resulting economic gain are about as optimal as can be hoped for. (Semi-obvious disclaimer: yes, I'm a government scientist, so hardly disinterested. I won't be voting tomorrow, however.) I'd be much happier if the entire scientific enterprise - and space exploration too, for that matter - were completely in private, non-profit hands instead of having to rely on either the government or corporations to fund it. On the other hand, when we're spending more on two unwinnable wars each year than the ISS has cost in its entire lifetime, I'm not going to get my panties in a knot over the relatively small portion of my tax dollars going to NASA. Based on past experience, I suspect the poster to whom I was replying is very selective in his outrage.
There is nothing about research that makes me pay for a non-existent product.
Most basic research takes decades to turn into a marketable product. To take my favorite example, X-ray crystallography, it took 25 years from the first experiments with protein crystals to actually determine a structure, then another 25 years for the method to mature enough for pharmaceutical companies to use it. Simultaneously, it also took 25 years for a particular type of particle accelerator to be recognized as useful for crystallography. There is simply no profit to be had in a reasonable amount of time from this kind of fundamental groundwork. The particle accelerators in particular cost hundreds of millions of dollars to build. Only a handful of companies in the world have enough money to spend on blind research like this. Even some of those would probably be at risk of shareholder lawsuits if they were devoting hundreds of millions on research of questionable use.
I won't get into the issue of morality, because it's simply impossible to argue with someone who claims that "taxation is theft." Strictly from a free market standpoint, there is no financial incentive to invest in basic research without any hint of a future product. I personally think that the ISS has been a waste of time and money that has detracted from more promising space exploration projects, but none of this would happen if left to companies like, say, GE. (Private charities? I wish - only a handful of those can afford mega-projects, and they risk alienating major donors if something turns out to be a blind alley.)
This was not an ab initio, calculation. It's all atom MD, which itself is an approximation
Sorry, I meant "ab initio MD", although I realize that to a chemist or physicist this is a total oxymoron. (My background is molecular biology and bioinformatics, where we try not to think about quantum chemistry.) I should have written "physically-based", if you prefer, as opposed to the knowledge-based approaches that have been most successful for de novo structure prediction. (I think most MD "force fields" are ultimately based on genuinely ab initio QM calculations.)
That's a little unfair to Folding@Home. Shaw has a lot of resources to pour into this project - he's lured faculty members away from universities to work for him instead and has the equivalent of several large labs worth of advanced researchers. He also has an immensely larger budget than most non-profit labs, and he's self-employed so he doesn't have to answer to granting agencies or tenure committees. I think what he's doing is great but he's really one of the only people who could have pulled this off. It's difficult to know what approach will work best in advance, and both Shaw and Vijay Pande have been very innovative in approaching the problem from completely different angles.
By the way, this approach has been tried before with less stellar results - I'm thinking of the MD-GRAPE project in Japan. You're also assuming that every problem is equally well suited towards custom ASICs, but actually, molecular dynamics is far easier to do this with than many other methods. For instance, Rosetta (Rosetta@Home and Fold.It) is doing structure prediction, not folding, using a mostly statistics-based energy function and Monte Carlo sampling, and this isn't something you can trivially offload to a specialized chip. In that case, distributed computing is by far the most efficient solution.
Nature and Science are not for hard science.
The actual research articles are hard science - this was just a news story for a general audience. The official publication of the results in Science magazine appears to be a pretty serious piece of work, and it's significant enough that the editors allowed them to make it reasonably long instead of a (severely compressed) three- or four-page summary article like most of what they publish. There are lots of valid criticisms of those two journals, starting with their length requirements, but they're not Scientific American, and publishing in one of these is practically a prerequisite for getting a faculty position in biosciences at a major research university.
The best way is to just compare them to the actual structure which is known from x-ray crystallography and NMR studies.
And so far, this is the only way that most researchers are willing to trust. There is a very good reason why these folding studies tend to focus on a small group of well-defined model systems, because the folded native structure is already very well understood, and it provides an essential constraint on the interpretation of results. Using ab initio physics calculations like this for truly blind structure prediction would be a complete waste of time, and the entire field figured this out decades ago.
The only problem is getting out of our gravity well.
Not only are you forgetting about cosmic radiation, which is a severe hindrance, you're vastly oversimplifying the problem of the gravity well, since sustaining a human presence on an asteroid would require regular shipments of supplies at exorbitant cost. I'm also curious how you expect the raw materials to make it back down to Earth. Actually refining many of these metals in space would also be a pain in the ass, but landing asteroids wouldn't be very easy either.
Which elements are actually that rare, anyway? For instance, Wikipedia claims that "The main mining areas [for gadolinium] are China, USA, Brazil, Sri Lanka, India and Australia with reserves expected to exceed one million tonnes. World production of pure gadolinium is about 400 tonnes per year." That's a lot to ship back from the asteroids, and I'm not sure I see any financial benefit.
Which is worse, saying we should believe everything scientists say, or being anti-scientist?
Both are a bad idea, and as a scientist myself, I've learned to keep my BS detector set to "11". But when faced with a choice between believing actual scientists versus the propagandists at the Discovery Institute, I'll side with the scientists every time.
It is interesting (and very bigoted of you) to assume anyone who is a AGW skptic is anti-science and pro-intelligent design.
I realize that this isn't universally true, but I've noticed a large overlap - specifically, the vast majority of creationists appear to be "AGW skeptics", and they are certainly anti-science, and very militant about it. When I see the cretins from the Discovery Institute reading from the same script as the anti-AGW crowd, I'm naturally suspicious of the latter. This may seem unfair to you, but it's no more unfair than accusing climate scientists of wanting to force society back to a pre-industrial state.
Which brings up a more accurate point: while the "skeptics" may not all be anti-science, they definitely come across as anti-scientist.
While this technique avoids the inherent difficulties of producing crystals (a process that can take decades for some samples), until very recently it has been difficult to achieve high resolution structures using this method. The cryo-EM adenovirus structure is one of only a handful of atomic resolution cryo-EM structures that have been solved to date.
A large part of the reason why this is possible is the high internal symmetry of viral particles; I think all of the atomic-resolution cryo-EM structures so far have also been of highly symmetric structures like bacterial chaperonins, or other viruses. (The same symmetry also makes crystallography easier, for different reasons.) The only other EM structure that I'm aware of at better than 4 Angstrom resolution is also of a virus, published a few months ago by the same group at UCLA. For highly asymmetric structures such as ribosomes, crystallography is still far ahead of EM as far as resolution is concerned - although the bottleneck of crystallization remains a major problem.
it is interesting that the Medical Daily focuses only on the x-ray crystallography study from Scripps. . . Perhaps Medical Daily needs to do a better job of doing their homework.
If you scroll to the end of the story, you'll see "Provided by Scripps Research Institute" in tiny gray letters. It's just a press release from Scripps, in other words - standard operating procedure for research institutions when someone scores a high-profile article.
The article is horribly misleading - it suggests that the FoldIt users came up with better structures completely on their own. What they were actually doing was improving the automatic structure predictions. If you actually read the Nature article, it shows comparisons of the initial model, final model, and experimental structures. The initial model has the overall fold correct, but with some gross errors which the FoldIt players corrected, leading to an even better model. This is still an impressive result, but it simply doesn't mean what Ars Technica says it means. The author sort of admits that Rosetta helped at the end, but it sounds completely ignorant of how difficult it is to even guess the overall fold correctly. I'm wondering if the writer even bothered to read the original article or just read the PR material.
what makes the real proteins not get "stuck" in the local energy minimums that the program keeps getting stuck in?
Several good answers below, but there isn't really a single simple one. This is called Levinthal's paradox, and it's one reason why ab initio molecular dynamics simulation turned out to be a terrible way to predict 3D structure. It turns out that Folding@Home (not FoldIt) requires petaflops of computing power because of the same problem: it runs ab initio simulations, and most of them get stuck, but spread out over that many CPUs, they can extract enough data to get a trajectory to the final folded state (which they already know).
forget about Foldit! Just download Folding@Home and let your CPU/GPU do it for you!
FoldIt and Folding@Home are doing completely different things. FoldIt (or more specifically, the Rosetta software underneath it) is attempting to guess the final structure of novel protein sequences, using a variety of clever tricks such as mining the database of known structures for peptide motifs. It contains energy functions to evaluate candidate structures, but it is not simulating physical processes, and it tells you nothing about how the linear chain of amino acids forms the 3D structure. Folding@Home is used to study the process of protein folding, where the end result is already known; it isn't useful as a structure prediction tool. Both programs require a massive amount of computing power, but for very different reasons. Both are very useful, but there is almost no overlap in their practical applications. (And it should go without saying that while they can both be an excellent complement to experimental studies, neither can replace them.)
They should just mandate that NASA builds a space elevator by 2020 and be done with it...
Are you being sarcastic, or just delusional?
How about the fact that hundreds of NASA employees will not be thrown out of work?
How about the fact that hundreds if not thousands of current commercial suppliers to NASA will not be thrown out of work?
How about the fact that there will still be jobs created because there will still be development outsourced from NASA?
So basically, you're saying that NASA should be used as a welfare program for existing dependent companies and key congressional districts, regardless of whether the projects it works on actually advance science and technology?
How about the fact that these people are basically complaining because they won't get any corporate welfare?
Certainly, but the Senate bill is basically written to address the concerns of the existing recipients of corporate welfare. Since it comes down to a fight between private interests, I'll still side with the plan that I think spends our tax dollars most effectively towards what I believe NASA's goals should be. None of those goals involve locking ourselves in to spending billions of dollars on solid rocket boosters built by ATK.
Okay then, what facts did the article leave out? So far all you've contributed to the discussion is bashing everyone who opposes the goals of the bill.
"I won't be able to exploit the government and workers so this bill sucks."
Your sarcasm would be more convincing if this weren't the same complaint that we've been reading about Obama's proposals for NASA.
Every single one of the named sources is attached to and gets money from commercial space interests in some way.
So what? The facts about the Senate bill are a matter of public record and not in dispute. Any plan NASA comes up with is guaranteed to be kicked around like a football by all of the commercial space interests and Congresspeople that stand to gain or lose from it; this is unavoidable. The article was in a North Florida paper and was largely discussing the potential effect on the North Florida economy, but those of us who've been paying attention to this silly controversy are aware that it's much more complicated. People can make up their own minds what they think of the bill; I suspect most Slashdot readers who oppose it don't care about North Florida or the poor, unloved commercial space interests. Personally, I think it's appalling, and I don't work for NASA or any aerospace contractor, and won't gain or lose either way.
That would be perfect because everything produced by the govornment is in the public domain.
Not even close. The AC who replied covered some of the major points, but it's pretty complex. Basically, the Bayh-Dole act (passed in 1982, I think) allows a great degree of latitude in commercialization of research done with government funding - the idea being to encourage economic development AND turn raw technologies into useful consumer products ("consumer" used in the broadest possible sense, since these technologies could become anything from specialty laboratory instruments costing $500,000 to OTC medications). How this is actually interpreted varies in practice, but the general consensus (as far as I can tell) is that it's an imperfect system but no one can think of a better alternative.
I actually work for the DOE writing software, and none of what I do is "public domain". Some of it is Free Software (BSD-ish license), the rest is free-as-in-beer for academics, and companies have to pay (they get the code too, but can't redistribute it). This is a pretty typical arrangement (in our case, the rules are dictated more by the funding source, which is the NIH). A large part of the reason for this is that the licensing revenues help pay for the research - I'm sure as f*** not getting rich off this. I'd be happier if it was all Free Software, but mostly because I think it would make my job easier and get more people to use our software. Compared to many of the other licensing arrangements that scientists invent for government-funded research, ours is pretty reasonable. The NIH is starting to get stricter about what they allow - some funding specifically requires that the source code be made available, and programs need to be free for academics. But public domain (or Free Software, which I think you're confusing it with) has never been a requirement.
The director seems quite sincere
And we all know that a career bureaucrat would never, ever lie to the media. Can you show me any evidence that NASA has actually acted (or wasted money on) this supposed "priority"?
You're so quick to believe this because it confirms your biases, but every time Obama or one of his political appointees tries to pander to the free-market crowd by talking about privatizing launch vehicles, every right winger screams "bullshit!" (And for all I know you're correct; it seems just as probable to me that he's trying to fuck over the politically connected contractors who've grown fat off NASA contracts.) Meanwhile, he's ordering drones into Pakistan to kill Taliban, along with more than a few civilians, and the pseudo-conservatives accuse him of caring too much about Muslim public opinion because he gave a speech in Cairo.