A prion is a protein that, when misfolded, can [i]induce[/i] the misfolding of another protein of the same sequence. Once one prion protein becomes misfolded (the scientists here use urea and vinegar to denature the protein) then it can effectively _produce_ more prions. What you get is a positive-feedback loop where more misfolded proteins induce the misfolding of even more misfolded proteins and so forth. The misfolded proteins can't be properly degraded by cells and so the proteins start to clump together into fibers which then cause damage.
The experiment they performed was to artificially create a prion protein, inject it into mice, and watch whether the mice became sick.
One other possibility is...
-- The protein they injected is actually a regulatory protein for gene expression. The activation or repression of specific genes then causes the disease. This same regulatory protein are also expressed by these genes and so the disease may be transmitted by the transferral of these regulatory proteins. Note that gene expression is still the cause of the sickness, but the regulatory proteins cause the genes to turn on/off.
So the evidence is interesting because their hypothesis is not disproved. But I still think they need to eliminate the other possibility.
The math behind Einstein's relativity is closely related to the work of Maxwell, Gibbs, and Dirac (among others). What do you think Eistein read while he was working in the Swiss patent office? Papers on what he was interested in!
Most people think Einstein pulled the idea out of the air, but that's only because most people do not understand relativity or the math behind it. I don't want to sound inconsiderate towards Einstein, because his theory was a major paradigm shift in physics. I just wanted to remind you that science almost never materializes out of thin air and, even for the most 'unique' theories, it always originates from previous work of some type.
The catalyst: The techies in the computer lab in my school put it on the desktop for all to use.
When I immediately converted: When the NYtimes.com's popup was instantly blocked. Coool. I knew Firefox could do this, but seeing is believing, I guess.
So how exactly does Dtrace benefit application optimization? I code simulation programs to model physical systems. The applications can be CPU or I/O intensive and I'd like to know if Dtrace will help me optimize my code more than it already is.
Can it suggest areas of vectorization, loop unrolling, parallelization, etc?
Does it primarily give you stats on usage of functions, disk I/O, etc?
The numerical methods I use are probabilistic, making them very hard to debug sometimes. (Imagine a bug occurring only 1e-4% of the time, although it will always occur before you get the answer you want.;)
There's a guy at Stanford who was able to correctly fold a small protein (80 AAs) by performing _numerous_ MD simulations for small times. There is a small, but non-zero probability of the protein folding within a small time (if the folding process is first order). The guy organized a massive distributed computing project to perform like 100,000 MD simulations of 1 nanosecond or so, along with some intelligent (re)sampling of initial conditions.
Btw, if you're interested in MD simulations of protein-lipid interactions, please check out Himanshu Khandelia/Yiannis Kaznessis of the University of Minnesota (one of my group members). He does MD sims of antimicrobial peptides and their effect on bacterial lipid bilayers.
Does the U.S govt have a team of 100,000 agents spoofing your packets to see if you're talking about the government? Probably not, considering that U.S citizens are allowed to criticize their government any time, any place. Not just on the Internet.
Or, if you disagree, how did Farenheit 9/11 ever make it to the theaters?
There's a big difference between civil liberties in the U.S and China. If you can't tell the difference, then you're either ungrateful or ignorant.
Because IPv4 sucks for surveillanc and censorship
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China Deploys IPv9 Network
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· Score: 1, Interesting
The Chinese government is notorious for watching its 'citizens' and what they're doing on the Internet. I don't know if IPv9 is real or not, but if it is it's only purpose is to invade privacy and catch 'dissidents'.
If I had the time or the patience, I could surely put together a better argument than this.
But since I have real work to do, I'll only say this:
For a 'historian', you use phrases like "straw man argument" and "Bizarro Moore from a parallel dimension" much too much for my tastes. It's like you're trying to say something..but not doing it very well.
Anyways...I don't care to argue with you. It's like...we're in parallel dimensions and someone is hitting me with a straw argument. Doesn't that sound stupid? How do you sound?
Moore didn't hold his point of view (and that's all it really is..), so why should I? And have you forgotten my freedom to speech? Moore is free to write his 'documentary', but I'm equally free to trash it.:)
Remember, though, that Moore is not a politician. Neither is Rush Limbaugh, Ann Coulter, Bill O'Reilly, etc etc. They are entertainment, at best.
Actually, that should have been "Like the 50% of Americans who disagree with Moore are complete morons."
I have known many people, some of them friends, who assert that, because people disagree with them, that they must be idiots.
That type of attitude has spawned the highly polarized opinions we see today and the lack of critical judgement. If you can't change your mind based on new information, why the hell do you bother to make up your mind in the first place?
I disagree..it's not that good of a rebuttal (authored by jefgodesky). Let me quote a few lines to demonstrate this.
First off, Hitchen's main point is that Moore wants to have his cake and eat it too. Ie., he wants to complain that Bush did and that's bad, but also say that Bush did not do and that's also bad!
Hitchen's rebuttal then gives a few examples of his point from Moore's movie.
As for this rebuttal of the rebuttal, here are some choice lines and I'll let you decide how good it is:
"FDR's pre-knowledge of Pearl Harbor is, at this point, not only a valid historical theory, it's almost accepted as a historical fact. Will we, in retrospect, see Bush's actions on 9/11 in a similar light?" -- accepted? By nutjobs, sure.
"Hitchens then moves to arguing against Moore's treatment of pre-war Iraq. His lack of any mention of Saddam's cruelty is somewhat suspect, I agree; on the other hand, it was refreshing to see a different view of pre-war Iraq. In every country on earth, most people are just trying to get by." -- Except for the occasional secret police visit...no problems! Saddam was a just misunderstood good guy, right....right?!
"Hitchens describes Moore's treamtent by saying, "In fact, I don't think Al Jazeera would, on a bad day, have transmitted anything so utterly propagandistic." This ignores the fact that, while it is seen as an anti-American organization in the West, it is more often called a mouthpiece of American imperialism in the Arab world. In fact, Al Jazeera's coverage has sparked riots in some cities -- because it was so pro-American!" -- In what Universe is Al-Jazeera a mouthpiece for American Imperialism?
"In actuality, Moore's words were very carefully weighed; he said that Iraq had never attacked America, never threatened to attack America, and had never murdered an American." -- Iraq regularly attempted to shoot down Americans patrolling the UN-sanctioned NO-fly zone over Kurdish Iraq. I'd consider that an attack.
"And though Iraq did fire on planes enforcing the no-fly zones for the better part of the 1990s, whether this constituted an "attack on America" or continuing conflict from Iraq's attack on Kuwait is a matter of debate. " -- Although this guy doesn't seem to agree with me.
"That Saddam wanted to get WMD's from North Korea only buttresses the fact that he didn't yet have them; and even having them does not constitute a threat to attack the United States, anymore than Pakistan and India's recent acquisition of such weapons constitutes a threat to attack the United States." -- Sure, let's WAIT until he has them and then ask politely for him to get rid of them. That worked with the bio/chemical weapons, right. Right..?! And Saddam would _never_ extort the U.S by threatening to attack Israel in exchange for $$ or lifting sanctions. Saddam is really just a nice guy...misunderstood, of course!
Besides the above quotes, this author likes to insult Hitchens after every paragraph. That's just annoying.
You mean Moore's side and Moore making fun of the other side?
Moore does not even mention 'the other side'. He ignores it. Like the 50% of Americans are complete morons. (Which is actually what he says to foreigners when he gives interviews.)
To Moore, if you don't agree with him, you're stupid. To Moore, if a fact does not support his viewpoint, he ignores it. Yes, a fine, fine journalist....
There's quite a few species of bacteria that like to uptake metals and oxidize them for energy. In addition to copper, one major application is the absorption of heavy metals, such as uranium/etc, from the soil by bacteria. The bacteria are then much easier to remove from the soil than the heavy metals they absorbed.
Salis
Re:Good point -- the very weak dollar doesn't help
on
Out of Gas
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· Score: 1
hard currencies like platinum show a clearer picture.
For a second, I thought you meant EverQuest platinum. With all of the (latest) analysis of EQ's GDP, it seemed all too possible!
Re:Could You Choose Beta Release Medicine?
on
Cure for Cancer?
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· Score: 1
Well, I don't know where it's been published (or even if it's true), but I do know that the Weissman Institute is working on 'DNA computers' (ie. computation via hybridization of DNA strands and excising using restriction endonucleases). It's just one more step to using the same principles to 'detect' and treat cancer.
I think it's more hype than reality, though.
Re:Could You Choose Beta Release Medicine?
on
Cure for Cancer?
·
· Score: 2, Interesting
Otter,
I bet it's using anti-sense mRNA to interfere with protein production of some protein that contributes to the continuation of cancer. So not really a drug..more like RNA interference. The article doesn't mention names (??), but I wouldn't be surprised if it came out of the Alon group.
I don't like it when the media portrays DNA hybridization as 'computation'. It's really a giant misnomer.
The idea is to create a retrovirus which will replicate in your cells wildly, creating numerous regulatory sites for HIV proteins that ultimately 'suck up' or titrate the HIV proteins out of solution. (This is from memory however, but I believe this is the only mechanism proposed.)
By lowering the number of HIV proteins in solution, you make it more difficult for the HIV to replicate itself wildly and turn into AIDS. The term is 'lowering the setpoint' of HIV becoming AIDS. HIV is still there. It can still turn into AIDS. But the chances of it doing so are less likely, BUT NOT IMPOSSIBLE.
In fact, the most interesting part of the paper (to me), was that if the retrovirus vector is too efficient in killing HIV then the therapeutic vector loses its own mechanism of infection (ie. the HIV capsin proteins) because these capsin proteins are no longer being produced.
It's a fantastic idea, but it's not a viable therapy. Yet. Using the same principles, it'll be possible to more directly kill HIV (in the future).
The energy required to make the Hafnium emit those X-rays might very well be GREATER THAN the energy released from the Hafnium.
Why? Most of the X-rays fired at the Hafnium might just pass through with no interaction.
And how exactly do you intend to get the Hafnium to emit those X-rays in the battlefield? Strap an X-ray machine next to the Hafnium "golf ball" and throw it towards the enemy? Wouldn't the combined X-ray machine + Hafnium 'ball' be larger than traditional chemical explosives?
IF *I STRESS IF* the Hafnium phenomenom is real (it still has not been experimentally proven) then its uses are still limited.
And before you judge other people's intelligence, I suggest measuring your own.
Similar to the 'liquid body armor' reported on Slashdot a while back, cornstarch + water is a "sheer-thickening" fluid, or a fluid that increases its viscosity when it experiences sheer (or tangential force).
Perhaps the interaction between the cornstarch/water and the vibrations cause the cornstarch/water to increase its viscosity and "hold" up the walls of the hole.
The Airforce was looking at Hafnium for that purpose: Let Hafnium power the battery that makes your UAV fly..for a long, long time.
But, the problem with that is that you need the X-ray machine to make the Hafnium emit X-rays. If your efficiency isn't really, really high, you can easily expend more energy (in making the Hafnium emit X-rays) than you get back from the Hafnium.
Not all of the dental X-rays are able to make Hafnium emit more X-rays. There's a loss of energy there. And not all of the energy from the Hafnium X-rays would be converted to work. There's another loss of energy there. At that point, it turns into an engineering problem..to make it both technologically and economically possible. But, in the mean time, it probably isn't even technologically feasible..it just plain doesn't work at all.
Like the end of the report (linked in the slashdot article) mentions, even if Hafnium does indeed emit 2.5MeV X-rays when hit by a 20 keV X-ray then it still could not be used to make a bomb.
A bomb requires that a chain reaction occur so that the energy released from the initial X-ray emission propogates and hits other Hafnium atoms, making them emit more X-rays. There are two reasons why the bomb will never 'explode':
1) The possibily bogus research report stated that only a 20 KeV (or a 10 KeV, whatever) would trigger Hafnium emissions. So there would be no propogation from one Hafnium emission to the next.
2) The 2.5 MeV photons would interact with other particles (electrons, itself, etc) and sap away that energy before it came into contact with another Hafnium atom.
Slashdot Mirror
Now where is that edit button? Right, there is none.
+HTML tags
-are / +is, yay grammar
Here is the hypothesis of prion-induced disease:
A prion is a protein that, when misfolded, can [i]induce[/i] the misfolding of another protein of the same sequence. Once one prion protein becomes misfolded (the scientists here use urea and vinegar to denature the protein) then it can effectively _produce_ more prions. What you get is a positive-feedback loop where more misfolded proteins induce the misfolding of even more misfolded proteins and so forth. The misfolded proteins can't be properly degraded by cells and so the proteins start to clump together into fibers which then cause damage.
The experiment they performed was to artificially create a prion protein, inject it into mice, and watch whether the mice became sick.
One other possibility is...
-- The protein they injected is actually a regulatory protein for gene expression. The activation or repression of specific genes then causes the disease. This same regulatory protein are also expressed by these genes and so the disease may be transmitted by the transferral of these regulatory proteins. Note that gene expression is still the cause of the sickness, but the regulatory proteins cause the genes to turn on/off.
So the evidence is interesting because their hypothesis is not disproved. But I still think they need to eliminate the other possibility.
Even Einstein did not operate in a vaccuum.
The math behind Einstein's relativity is closely related to the work of Maxwell, Gibbs, and Dirac (among others).
What do you think Eistein read while he was working in the Swiss patent office? Papers on what he was interested in!
Most people think Einstein pulled the idea out of the air, but that's only because most people do not understand relativity or the math behind it.
I don't want to sound inconsiderate towards Einstein, because his theory was a major paradigm shift in physics. I just wanted to remind you that science almost never materializes out of thin air and, even for the most 'unique' theories, it always originates from previous work of some type.
By your logic, I'm famous.
But I'm not, so your logic is wrong.
I use supercomputers all the time.
And it's greeeeeat.
The catalyst:
The techies in the computer lab in my school put it on the desktop for all to use.
When I immediately converted:
When the NYtimes.com's popup was instantly blocked. Coool. I knew Firefox could do this, but seeing is believing, I guess.
So how exactly does Dtrace benefit application optimization? I code simulation programs to model physical systems. The applications can be CPU or I/O intensive and I'd like to know if Dtrace will help me optimize my code more than it already is.
;)
Can it suggest areas of vectorization, loop unrolling, parallelization, etc?
Does it primarily give you stats on usage of functions, disk I/O, etc?
The numerical methods I use are probabilistic, making them very hard to debug sometimes.
(Imagine a bug occurring only 1e-4% of the time, although it will always occur before you get the answer you want.
Thanks for any info!
I'll shuffle into the conversation... :)
There's a guy at Stanford who was able to correctly fold a small protein (80 AAs) by performing _numerous_ MD simulations for small times. There is a small, but non-zero probability of the protein folding within a small time (if the folding process is first order). The guy organized a massive distributed computing project to perform like 100,000 MD simulations of 1 nanosecond or so, along with some intelligent (re)sampling of initial conditions.
Btw, if you're interested in MD simulations of protein-lipid interactions, please check out Himanshu Khandelia/Yiannis Kaznessis of the University of Minnesota (one of my group members). He does MD sims of antimicrobial peptides and their effect on bacterial lipid bilayers.
Does the U.S govt have a team of 100,000 agents spoofing your packets to see if you're talking about the government? Probably not, considering that U.S citizens are allowed to criticize their government any time, any place. Not just on the Internet.
Or, if you disagree, how did Farenheit 9/11 ever make it to the theaters?
There's a big difference between civil liberties in the U.S and China. If you can't tell the difference, then you're either ungrateful or ignorant.
The Chinese government is notorious for watching its 'citizens' and what they're doing on the Internet. I don't know if IPv9 is real or not, but if it is it's only purpose is to invade privacy and catch 'dissidents'.
Technology doesn't have to be empowering.
If I had the time or the patience, I could surely put together a better argument than this.
But since I have real work to do, I'll only say this:
For a 'historian', you use phrases like "straw man argument" and "Bizarro Moore from a parallel dimension" much too much for my tastes. It's like you're trying to say something..but not doing it very well.
Anyways...I don't care to argue with you. It's like...we're in parallel dimensions and someone is hitting me with a straw argument. Doesn't that sound stupid? How do you sound?
Moore didn't hold his point of view (and that's all it really is..), so why should I? And have you forgotten my freedom to speech? Moore is free to write his 'documentary', but I'm equally free to trash it. :)
Remember, though, that Moore is not a politician. Neither is Rush Limbaugh, Ann Coulter, Bill O'Reilly, etc etc. They are entertainment, at best.
Actually, that should have been
"Like the 50% of Americans who disagree with Moore are complete morons."
I have known many people, some of them friends, who assert that, because people disagree with them, that they must be idiots.
That type of attitude has spawned the highly polarized opinions we see today and the lack of critical judgement. If you can't change your mind based on new information, why the hell do you bother to make up your mind in the first place?
I disagree..it's not that good of a rebuttal (authored by jefgodesky). Let me quote a few lines to demonstrate this.
First off, Hitchen's main point is that Moore wants to have his cake and eat it too. Ie., he wants to complain that Bush did and that's bad, but also say that Bush did not do and that's also bad!
Hitchen's rebuttal then gives a few examples of his point from Moore's movie.
As for this rebuttal of the rebuttal, here are some choice lines and I'll let you decide how good it is:
"FDR's pre-knowledge of Pearl Harbor is, at this point, not only a valid historical theory, it's almost accepted as a historical fact. Will we, in retrospect, see Bush's actions on 9/11 in a similar light?" -- accepted? By nutjobs, sure.
"Hitchens then moves to arguing against Moore's treatment of pre-war Iraq. His lack of any mention of Saddam's cruelty is somewhat suspect, I agree; on the other hand, it was refreshing to see a different view of pre-war Iraq. In every country on earth, most people are just trying to get by." -- Except for the occasional secret police visit...no problems! Saddam was a just misunderstood good guy, right....right?!
"Hitchens describes Moore's treamtent by saying, "In fact, I don't think Al Jazeera would, on a bad day, have transmitted anything so utterly propagandistic." This ignores the fact that, while it is seen as an anti-American organization in the West, it is more often called a mouthpiece of American imperialism in the Arab world. In fact, Al Jazeera's coverage has sparked riots in some cities -- because it was so pro-American!" -- In what Universe is Al-Jazeera a mouthpiece for American Imperialism?
"In actuality, Moore's words were very carefully weighed; he said that Iraq had never attacked America, never threatened to attack America, and had never murdered an American." -- Iraq regularly attempted to shoot down Americans patrolling the UN-sanctioned NO-fly zone over Kurdish Iraq. I'd consider that an attack.
"And though Iraq did fire on planes enforcing the no-fly zones for the better part of the 1990s, whether this constituted an "attack on America" or continuing conflict from Iraq's attack on Kuwait is a matter of debate. " -- Although this guy doesn't seem to agree with me.
"That Saddam wanted to get WMD's from North Korea only buttresses the fact that he didn't yet have them; and even having them does not constitute a threat to attack the United States, anymore than Pakistan and India's recent acquisition of such weapons constitutes a threat to attack the United States." -- Sure, let's WAIT until he has them and then ask politely for him to get rid of them. That worked with the bio/chemical weapons, right. Right..?! And Saddam would _never_ extort the U.S by threatening to attack Israel in exchange for $$ or lifting sanctions. Saddam is really just a nice guy...misunderstood, of course!
Besides the above quotes, this author likes to insult Hitchens after every paragraph. That's just annoying.
Both sides?
You mean Moore's side and Moore making fun of the other side?
Moore does not even mention 'the other side'. He ignores it. Like the 50% of Americans are complete morons. (Which is actually what he says to foreigners when he gives interviews.)
To Moore, if you don't agree with him, you're stupid. To Moore, if a fact does not support his viewpoint, he ignores it. Yes, a fine, fine journalist....
There's quite a few species of bacteria that like to uptake metals and oxidize them for energy. In addition to copper, one major application is the absorption of heavy metals, such as uranium/etc, from the soil by bacteria. The bacteria are then much easier to remove from the soil than the heavy metals they absorbed.
Salis
hard currencies like platinum show a clearer picture.
For a second, I thought you meant EverQuest platinum. With all of the (latest) analysis of EQ's GDP, it seemed all too possible!
Well, I don't know where it's been published (or even if it's true), but I do know that the Weissman Institute is working on 'DNA computers' (ie. computation via hybridization of DNA strands and excising using restriction endonucleases). It's just one more step to using the same principles to 'detect' and treat cancer.
I think it's more hype than reality, though.
Otter,
I bet it's using anti-sense mRNA to interfere with protein production of some protein that contributes to the continuation of cancer. So not really a drug..more like RNA interference.
The article doesn't mention names (??), but I wouldn't be surprised if it came out of the Alon group.
I don't like it when the media portrays DNA hybridization as 'computation'. It's really a giant misnomer.
Are you going to the Synthetic Bio conference at MIT later this June?
Should be fun!
The idea is to create a retrovirus which will replicate in your cells wildly, creating numerous regulatory sites for HIV proteins that ultimately 'suck up' or titrate the HIV proteins out of solution. (This is from memory however, but I believe this is the only mechanism proposed.)
By lowering the number of HIV proteins in solution, you make it more difficult for the HIV to replicate itself wildly and turn into AIDS. The term is 'lowering the setpoint' of HIV becoming AIDS. HIV is still there. It can still turn into AIDS. But the chances of it doing so are less likely, BUT NOT IMPOSSIBLE.
In fact, the most interesting part of the paper (to me), was that if the retrovirus vector is too efficient in killing HIV then the therapeutic vector loses its own mechanism of infection (ie. the HIV capsin proteins) because these capsin proteins are no longer being produced.
It's a fantastic idea, but it's not a viable therapy. Yet. Using the same principles, it'll be possible to more directly kill HIV (in the future).
The energy required to make the Hafnium emit those X-rays might very well be GREATER THAN the energy released from the Hafnium.
Why? Most of the X-rays fired at the Hafnium might just pass through with no interaction.
And how exactly do you intend to get the Hafnium to emit those X-rays in the battlefield? Strap an X-ray machine next to the Hafnium "golf ball" and throw it towards the enemy? Wouldn't the combined X-ray machine + Hafnium 'ball' be larger than traditional chemical explosives?
IF *I STRESS IF* the Hafnium phenomenom is real (it still has not been experimentally proven) then its uses are still limited.
And before you judge other people's intelligence, I suggest measuring your own.
Similar to the 'liquid body armor' reported on Slashdot a while back, cornstarch + water is a "sheer-thickening" fluid, or a fluid that increases its viscosity when it experiences sheer (or tangential force).
Perhaps the interaction between the cornstarch/water and the vibrations cause the cornstarch/water to increase its viscosity and "hold" up the walls of the hole.
Those 20 keV photons would collide with electrons and undergo photovoltaic effects, making them propogate poorly as well.
To compare, atomic bombs use neutrons for the propogation of the chain reaction.
The Airforce was looking at Hafnium for that purpose: Let Hafnium power the battery that makes your UAV fly..for a long, long time.
But, the problem with that is that you need the X-ray machine to make the Hafnium emit X-rays. If your efficiency isn't really, really high, you can easily expend more energy (in making the Hafnium emit X-rays) than you get back from the Hafnium.
Not all of the dental X-rays are able to make Hafnium emit more X-rays. There's a loss of energy there. And not all of the energy from the Hafnium X-rays would be converted to work. There's another loss of energy there. At that point, it turns into an engineering problem..to make it both technologically and economically possible. But, in the mean time, it probably isn't even technologically feasible..it just plain doesn't work at all.
Like the end of the report (linked in the slashdot article) mentions, even if Hafnium does indeed emit 2.5MeV X-rays when hit by a 20 keV X-ray then it still could not be used to make a bomb.
A bomb requires that a chain reaction occur so that the energy released from the initial X-ray emission propogates and hits other Hafnium atoms, making them emit more X-rays. There are two reasons why the bomb will never 'explode':
1) The possibily bogus research report stated that only a 20 KeV (or a 10 KeV, whatever) would trigger Hafnium emissions. So there would be no propogation from one Hafnium emission to the next.
2) The 2.5 MeV photons would interact with other particles (electrons, itself, etc) and sap away that energy before it came into contact with another Hafnium atom.
So, don't worry about a bomb, it's all vaporware.