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PostPosted: Wed Aug 18, 2010 6:50 pm 
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Strid wrote:
I'm not sure you guys are aware of how much protein structure determination is a bottle neck in modern bio-chemistry.

Ask anyone within the field if they'd like to be able to have a computer predict the protein structure, rather than having a Ph.D. student employed for three years, trying to figure out how this one protein crystallizes so they can get an X-ray structure.

This is just one of the major benefits, if/when in silico protein structure determination becomes a reality (other than as proof of concept).

If you're making the statement that research in protein folding is useless... then LOL. If you're making the statement that specifically the folding@home project serves no purpose, then okay... ..but I strongly disagree.

Surely, you think that Rosetta@home is useful, right?

The bio-chemists I talked to said that they can get whatever computer time they need, if they need it. Given that some of this is in "proof-of-concept" phase, and the energy requirements/inefficiencies involved, it seems more than a little dubious to me.

The lack of acceptance by the general scientific community for folding@home is rather obvious IMO. But if any of you want to continue, go ahead. I am tired of hearing all of this unsubstantiated propaganda that is nothing more than an excuse to get research grants and build academic empires.


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PostPosted: Wed Aug 18, 2010 6:56 pm 
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frenchie wrote:
m0002a wrote:
Very, very few scientists believe that folding@home is worthwhile, regardless of the energy cost.

All those scientists... you mean those 2 (two) you talked to ? ;)

I read the abstracts of all 73 papers on the subject that have been "published" on the Folding@home website. There is striking lack of diversity of scientists who authored the papers (if you know anything about the scientific community). No bio-chemists, no one from a bio-tech company (who are the ones who create drugs), almost everyone connected to Standford, and every single one of the articles is co-authored by Panda (the founder of folding@home). Many of the articles are written by computer scientists, which is why I previously said that folding@home is an interesting computer science project, but not all that useful in the real world of bio-technology.


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PostPosted: Wed Aug 18, 2010 8:27 pm 
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Well, it looks like you've done a good job convincing yourself that you are the white knight. However, you've made the same tired arguments with no solid evidence to support it, and I will no longer argue with you, as it is about as fruitful as yelling at a brick wall. Enjoy your global warming.

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PostPosted: Thu Aug 19, 2010 3:59 am 
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Yes sir/madam m0002a,

What else are you doing to stop your contributions to Global Climate Change? I'm sure that you are aware that all the computers and the entire Internet use about 1% of the electricity. Air conditioning and industrial users are a huge majority consumers. Lighting is something 15%.

And transportation and heating and industrial and agriculture are the enormous users of oil and gas. So, electricity used to run Folding@Home is a drop, nay -- a molecule in the ocean...

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PostPosted: Thu Aug 19, 2010 5:46 pm 
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NeilBlanchard wrote:
Yes sir/madam m0002a,

What else are you doing to stop your contributions to Global Climate Change? I'm sure that you are aware that all the computers and the entire Internet use about 1% of the electricity. Air conditioning and industrial users are a huge majority consumers. Lighting is something 15%.

And transportation and heating and industrial and agriculture are the enormous users of oil and gas. So, electricity used to run Folding@Home is a drop, nay -- a molecule in the ocean...

I "could" explain what else I am doing (I have actually done so in other posts) but that is irrelevant as to whether folding@home is worthwhile given the energy required to do it (do it at all, or do it more efficiently at a central computer at aresearch facility).

It is a logical fallacy to associate folding@home with any other energy use, since each should stand on its own merits vs costs, which is why it is becoming clear to me that folding@home is a religious cult rather than a real scientific endeavor. The defenses of folding@home are mostly irrational, and the whole project is based on faith and hope, rather than rational logic and proof. After spending a lot of time looking at the folding@home website, the claims made by them are ridiculous, and I believe that the founder and director of folding@home (Vijay Pande) is cult leader and megalomaniac (and just a academic who wants more research grants). The rhetoric of the cult followers who defend folding@home is no different from what one find regarding any other religious cult.

Regarding air conditioning, more of it is required when you run a computer (since computers heat up living spaces), especially at the kinds of CPU loads that folding@home puts on a system. Even it is only done in winter, electrical heating is very inefficient. So your calculations may be off.


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PostPosted: Thu Aug 19, 2010 9:32 pm 
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NeilBlanchard wrote:
I'm sure that you are aware that all the computers and the entire Internet use about 1% of the electricity.


What is your source on this? Estimates I have seen put it rather higher.
(e.g. about 3% of US electricity use almost a decade ago).

http://enduse.lbl.gov/projects/InfoTech.html
http://www.cosn.org/Initiatives/GreenComputing/InterestingFacts/tabid/4639/Default.aspx
http://uclue.com/index.php?xq=724

How is it changing? Even if it is 1% - if increasing rapidly would still be much more of a concern than if stable or declining. Computer and network use seems to still be increasing (more devices, more users, more uses, etc.) This may be countered to some extent by some increase in efficiency.

NeilBlanchard wrote:
So, electricity used to run Folding@Home is a drop, nay -- a molecule in the ocean...


If a project that consumes something like a billion watt-hours a year is small potatos, what do you consider a worthwhile savings? Seems unlikely that m0002a (or any of us in our individual efforts) would have saved anything comparable.

(From another thread [green computing - Environmental impact of Kill-A-Watt purchase?]).
NeilBlanchard wrote:
We gotta' start saving a lot of energy, and we have to start somewhere. If we talk ourselves out of trying to solve problems before we even start, then we are guaranteed to fail.


I agree that it makes sense to measure and look critically at costs and benefits of energy used. Not just on an individual basis, but even more so for larger things (like folding).

[Edited to fix typo in number of watt-hours, watt hours based on my 2007 estimate, see previous post in this thread.]


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PostPosted: Fri Aug 20, 2010 5:53 am 
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m0002a wrote:
The defenses of folding@home are mostly irrational, and the whole project is based on faith and hope, rather than rational logic and proof. [...] The rhetoric of the cult followers who defend folding@home is no different from what one find regarding any other religious cult.

Like capitalism, right ? You'll get more (money, intelligence, women)/(folding points) if you (buy)/(upgrade your computer) more.
Sure, why not. Just don't forget that folding still does something that can be seen, contrary to any religious cult.
And maybe it IS a computer science project... So what ? It's just a proof that a computer science project can be usefull to other people than the no-life-geek-sitting-behind-his-computer. Read (again) what Strid said in his posts, it is very interesting (thanks to him for spending time explaining things).

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PostPosted: Fri Aug 20, 2010 7:34 am 
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frenchie wrote:
And maybe it IS a computer science project... So what ?

Because it is burning up the planet and creating energy shortages which cause collateral geo-political problems. Maybe if we generated 80% of our electricity from nuclear like France, it would not be a problem, but that is not the case in the USA.

The only usefulness of folding@home is to generate grant money to prove that it can be done. This is what we call "hammer looking for a nail." Someone (or something) is going to be hurt when the hammer starts swinging for no good reason other than to prove that the hammer works.


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PostPosted: Fri Aug 20, 2010 1:07 pm 
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Hard to say if m0002a is right or wrong, so lets keep a cool head about it. Regarding m0002a's belittling someone for being an associate professor at Stanford, it can take quite a lot of time to become a full professor. Plenty of very smart people where I work take quite a while to get full professorship. Even though I'm just staff, I work at one of the handful of institutions that would be considered better than Stanford.

As an aside I don't run folding@home for the same reason as m0002a. I don't claim to know that I am right in doing what I do however.

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PostPosted: Fri Aug 20, 2010 1:34 pm 
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tay wrote:
Hard to say if m0002a is right or wrong, so lets keep a cool head about it. Regarding m0002a's belittling someone for being an associate professor at Stanford, it can take quite a lot of time to become a full professor. Plenty of very smart people where I work take quite a while to get full professorship. Even though I'm just staff, I work at one of the handful of institutions that would be considered better than Stanford.

As an aside I don't run folding@home for the same reason as m0002a. I don't claim to know that I am right in doing what I do however.

I wouldn't say I belittled Pande for "only" being an associate professor, but based on the claims of folding@home (which Pande founded is the director of the Pande Lab that runs it) and the fact that he co-authored all 73 papers on the subject, one would have thought he would be awarded a Nobel Prize by now. When I investigated folding@home (to decide whether to do it) I was trying to determine what Pande's peers thought of him. I did speculate that perhaps his peers in the Chemistry department are not amused, and don't consider his project to be anything more than a community computer science project as opposed to chemistry or bio-chemistry. Other universities could offer him a full professorship if they wanted to (universities do recruiting just like anyone other organization). That doesn't mean that protein folding is useless, but whether it is really being advanced by folding@home is another matter.

If anyone is interested in finding out if folding@home is worthwhile given the cost (energy use), then I would advise that them to find some bio-chemists who are involved in medical drug research and ask their opinion. That's what I did. I don't expect anyone to change their minds just because of what I post, but I also would advise others to not take the claims of folding@home at face value without some other opinions.

Actually I think Pande should be awarded a full professorship in the computer science department.


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PostPosted: Sat Aug 21, 2010 11:43 am 
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m0002a wrote:
Maybe if we generated 80% of our electricity from nuclear like France, it would not be a problem, but that is not the case in the USA.


That would be nicely ironic - massively increasing people's exposure to ionizing radiation in order to study cancer. Well, it would result in a lot more cancer cases to study. :roll:


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PostPosted: Sat Aug 21, 2010 12:41 pm 
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Three percent for all computers everywhere is a bit too high -- industrial electrical use is huge, especially for things like aluminum smelting. Air condition is a massive portion of our electricity use, and lighting is a significant use -- like 10%? Appliances like refrigerators use a significant amount of power; and hot water heaters too.

And certainly, Folding@Home (and SETI@Home and any of the other distributed computing projects) only use a small fraction of the the power used in all computers, and they only add some use to an already running computer.

Driving gas guzzling cars absolutely swamps the power used by computers -- like 1,000X times more energy is wasted driving an extra 1-2 tons of overweight cars around. As I mentioned earlier, by ecodriving, I have averaged ~45+ MPG instead of the 30MPG that the EPA rates my car -- and that saved gasoline was equivalent to ALL the electricity our household of four people used in the same 2 1/2 years. So, for people who get 10-15MPG now, that is by far a more important way to conserve than to get all worked up about running Folding@Home!

And you know what? Folding@Home is a LOT better than simply wasting the energy -- it is making significant headway in the science of proteins. They would not be going through all the work to get it set up and maintain it if it wasn't. Or, they would buy a supercomputer or rent time on one -- but they didn't. They are using the CPU time on people who volunteer the use of their computers.

It's your choice to do F@H or not. I choose to, and I have more than compensated for the energy it uses. My iMac uses just 116 watts on full load, so it isn't very much power, anyway.

Oh, and yes it would be wonderful to switch over to renewable energy for all our power -- then we would stop our carbon footprint, and if we felt like "wasting" power, there would be no guilt.

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PostPosted: Sat Aug 21, 2010 12:57 pm 
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NeilBlanchard wrote:
And you know what? Folding@Home is a LOT better than simply wasting the energy -- it is making significant headway in the science of proteins. They would not be going through all the work to get it set up and maintain it if it wasn't. Or, they would buy a supercomputer or rent time on one -- but they didn't. They are using the CPU time on people who volunteer the use of their computers.

There is no proof whatsoever to the claim that folding@home is "making significant headway in the science of proteins." The only people who claim that are those that are involved in the project, and who have financial connections relating to research grants, etc. These kind of statements are nothing more than faith-based statements that is reminiscent of a cult (hmm, Mac is another cult, so I see a trend here).

If there was any chance that protein folding studies would lead to a drug that was even partially effective for Alzheimer's or cancer, then bio-tech companies would (or maybe already have) put their own massive computers to the task, since the payoff would be in the tens of billions of dollars per year for such a drug.


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PostPosted: Sat Aug 21, 2010 7:02 pm 
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Bio tech companies have no interest whatsoever in doing fundamental science themselves. The ones telling you that are liars. Too expensive and no idea when - or even if - the return of investment will happen. However, they will use the results of that science if somehow they feel they can use it.

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PostPosted: Sat Aug 21, 2010 7:42 pm 
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frenchie wrote:
Bio tech companies have no interest whatsoever in doing fundamental science themselves. The ones telling you that are liars. Too expensive and no idea when - or even if - the return of investment will happen. However, they will use the results of that science if somehow they feel they can use it.

There is not a single bio-chemist who has co-authored any of the 73 articles on folding@home. Not in academia, not working for the government, not working for a bio-tech company.


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PostPosted: Sat Aug 21, 2010 10:43 pm 
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NeilBlanchard wrote:
Three percent for all computers everywhere is a bit too high -- industrial electrical use is huge, especially for things like aluminum smelting.


Do you have a source for that? The Lawrence Berkeley Lab has been a reasonably reputable source on matters of energy. Consider that 3% includes the manufacture and decomissioning/recycling of the computer equipment, and, if memory serves, the climate control to support the computers as well. It includes commercial and industrial computer use, not just domestic. Many things have less than obvious computers (embedded systems, control systems, communications, etc.)

Certainly the LBL estimate is for the United States, but the US uses a huge portion of the world's energy (it was about 1/4, if memory serves). So US proportions have an even larger on world energy use than the population proportion would suggest. In addition, computers are heavily used worldwide, and use has grown.

Certainly industrial use is huge, but there are billions of people chatting on (and throwing out) cellular phones, huge data centers for everything from google to facebook, millions of smart meters, computers monitoring and controlling everything from cars to aluminum smelters, etc. I wouldn't be too quick to discount the total.

NeilBlanchard wrote:
Oh, and yes it would be wonderful to switch over to renewable energy for all our power -- then we would stop our carbon footprint, and if we felt like "wasting" power, there would be no guilt.


Just being renewable doesn't mean no carbon footprint, non polluting and no-impact energy. (Wood and biofuels can be renewable, but burning them still causes pollution. Hydropower is to some extent renewable, but still silts up streams.)


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PostPosted: Thu Sep 16, 2010 3:44 pm 
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Folding proteins is now a computer game:

http://www.npr.org/templates/story/story.php?storyId=129914162

Quote:
In a new game called Foldit, players move computerized versions of proteins to give researchers new combinations to try as they seek to cure diseases like Alzheimer's and Parkinson's. David Greene talks to one of the creators of the game, Zoran Popovic, a professor at the University of Washington.

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 Post subject: Re: Is Running Folding@Home Worthwhile?
PostPosted: Tue May 24, 2011 6:40 pm 
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I would like to address of few of the concerns posted by m0002a.

In m00002a's first post, there was an unsupported exaggeration. m00002a claimed "significant harm to the environment" and yet m00002a knows nothing about the persons that posted nor how they fold, or even in what country they folded. As m00002a said, if they happened to be in France, not that much damage. Or if they owned solar panels. Or if they offset their FAH power usage by upgrading regular light bulbs to CFLs. Or as others in this thread mentioned, they used alternate forms of transportation, and had reduced their red meat consumption, etc. They could actually be helping the environment much more than the average person, and still be running FAH. m00002a simply has no basis to make this outlandish claim.

Next, asking 2 Bio-whatevers about FAH means very little when considering the large numbers of Bio-whatevers in the world. FAH doesn't have to be "world famous" to make positive contributions to science. 2 random guys you asked mean nothing to us, especially when you won't disclose those 2 Bio-WEs credentials. They could be Larry and Moe from the Bio-Institute of Stooges for all we know. You'll need to step up on that one or withdraw that claim. For example, my brother has a BS in EE, MS in CE, and PHD in Genetics. He is an associate professor at the University of Iowa, working in the Center for Bioinformatics and Computational Genomics lab. And my brother did not come to the same conclusion as m0002a's unmentioned Bio-dudes. He was impressed by the scale of the project, and that FAH had placed very well in several contests that predicted protein shapes using FAH software as compared to actual known shapes. He also expressed some concerns, but overall he liked the idea of the project. And he withheld any further conclusions without having done more research in to the project. An educated person does not just off-handedly shoot down a project without knowing more about it like m00002a's examples did.

Okay, next let's talk about Published papers.

1. Published papers are a measuring stick of scientific production as conducted by a research project. The papers are all "Peer Reviewed" before they are allowed to be published. That means other "Bio-whatevers" in the same scientific fields review the research, and have approved each paper as being valid. So at least 73 other Bio-whatevers disagree with m00002a's bio-dudes. And usually the peer review is a committee, so it's more like 2 or 3 times that 73 value. And as a measuring stick, Folding@home has published more research paper than any other @home distributed computing project, and FAH is by no means the oldest project.

Most professors spend their entire research careers as an "associate professor." At a prestigious school like Stanford, only a small number of top professors ever become full professors. There are also a limited number of "department heads" to get that title. I also suggest you read a bit more about what an associate professor is before you lambast them. Associate Professors are tenured positions. And how many people do you know that has a PHD from MIT? How many DC projects hold a world record for being the most powerful? 1! Folding@home. :roll:

You should also read more about how papers are published. Co-authorship is common. Grad students do not typically publish papers as a soloist. ;)

2. One thing m00002a got right is that most of the published papers are about the science of simulating how proteins fold, not about folding actual proteins (although actual proteins has picked up as of late). This also demonstrates how little m00002a knows about the project. Folding@home is not Rosetta@home. Folding's first goal, as defined on their project web site, is to understand how proteins fold, and misfold. FAH studies the process of how proteins get from A to Z, and how they break at G or R and cause Alzheimers or Cancer. Rosetta only tries to go from some point C to some other predicted point L, and doesn't care about anything else as long as they get to L. FAH has to learn to walk before they could run. FAH is now running.

3. The vast majority of the authors are from Stanford, because that is where the vast majority of the research is being done. This claim by m00002a also show's a short-sightedness in how research at the University level is conducted. But the research has grown from Stanford, to Notre Dame, Virginia, Hong Kong, and Sweden. FAH has project servers all over the world. And if you look at the project home page, FAH has top tier corporate supporters. Google, Intel, Apple, AMD, NVIDIA, Dell, etc. The corporation doesn't have to be on the research paper for it to be a good paper. Again, read WIKI on how papers are published.

4. I don't know what your hang-up on bio-chemists and bio-chemistry is, but you should seek professional help for that. ;) Okay, that's a cheap shot. Sorry. When FAH uses computer programming and physics algorithms to simulate a biological process, they tend to need more computer programmers and physics majors than bio-chemists. And FAH has all 3, so the composition of their research team does not concern me. Pande Group has associate appointments across multiple disciplines at Stanford. They can tap any kind of expertise they need at any time.


m00002a, in another post, claims to know what most bio-chemists think about simulating protein folding. One, I doubt m00002a is a mind reader, and two, does note have the resources to poll that many people. And again, shows a lack of knowledge about protein folding. Many proteins are so small, and fold so quickly in real life, that they cannot be studied in a test tube by a bio-chemist. Nor can a bio-chemist stick a microscope in to a human brain to watch proteins mis-fold and cause Alzheimers. Ask your bio-chemist friends... where, when, and on whom is the majority of Alzheimers research done! Where, in the morgue, after death, on dead people. That's where. Not a great place to watch live proteins do their thing.

m00002a, in several more posts, lists "suspicions" and "personal conclusions" all of which are unsupported. Folding@home is a mix of computer science and bio-science. That does not preclude the project from doing good works on the Bio side of the equation. For example, my brother supervises research in human genomics. But the majority of the work is done on and by a computer. The genome sequencers are all computerized. The results are all computerized in to a huge relational database of thousands of volunteers, and they do data mining on the strings of proteins looking for genetic markers, or combinations of markers that potentially cause specific diseases. It's the bigger hammer approach, but they can only study a handful of genes at any one time, otherwise the database gets too large to produce meaningful data.

Anyway, m00002a makes interesting assumptions, and claims to have correct conclusions, but again, almost none of it is supported or backed up with actual data in any way. And when one of m00002a's claims is refuted with actual data, m00002a falls back to one of the other unsupported yet unrefuted claims. Repeating the same personal conclusions over and over does not make them any truer.

I got a big laugh where m00002a mentions "left wing ideologues" and "religious allegiance" in the same post. It's rather ironic. :) I also find it humorous the whole second page of this thread is m00002a repeating the same things over and over. Associate professor this, and only computer science that, and ask a fellow bio-whatever. False arguments repeated again and again. m00002a, PLEASE read through that WIKI material I linked. Dr. Pande got his PHD 15 years ago, yes. But you try to make it sound like all 15 years has been at Stanford, and that someone should have been a full professor in all that time. And that's not true. Dr. Pande did post-doctoral work at MIT through 1999. Then at UC Berkeley for a few years, and on and on. Dr. Pande has worked on multiple projects in the last 15 years. Only 10 at Stanford.

Another unsupported claim was that Dr. Pande wasn't like well by peers because he was still an associate professor. Okay, here is the real proof that he is well liked. Dr. Pande was an assistant professor for 5 years at Stanford. And then was PROMOTED to associate professor of Chemistry. And in the last 5 years, has been given 3 more Assistant Professor titles, and 2 more Associate Professorships, in Structural Biology and Computer Science. One does not advance at a Uni like Stanford unless you are doing well. Again, read a little Wikipedia...

And again, the all bio-chemists claim that FAH is BS has grown to "all scientists" in a later post. Wow. That's serious BS. Again, this was unsupported drivel.

And the one time m00002a actually posted real information (about clinical trials) it had absolutely nothing to do with FAH. Folding doesn't produce drugs. Folding doesn't do clinical trials. And any information produced by Folding would be shared openly, for the drug companies to do with as they please. That's why all these claims about a lack of a big pharma presence on the FAH team is such BS. Folding isn't about drug research. Folding is about figuring out how diseases work on the most fundamental biological scale. And once that is figured out, Pharma can swoop in and start building a drug to fit the data.

m00002a wrote:
Because it is burning up the planet and creating energy shortages which cause collateral geo-political problems. Maybe if we generated 80% of our electricity from nuclear like France, it would not be a problem, but that is not the case in the USA.

The only usefulness of folding@home is to generate grant money to prove that it can be done. This is what we call "hammer looking for a nail." Someone (or something) is going to be hurt when the hammer starts swinging for no good reason other than to prove that the hammer works.


Such outlandish unsupported claims. One might think that m00002a was an anti-cultist. FAH is a drop in the ocean compared to all energy usage. FAH is NOT burning up the planet. And FAH is a world wide project. One of the top 10 teams is from France, so at least in part, they are using a lot of nuclear energy.

And the hammer looking for a nail is a funny analogy. It might have applied if the project were only a year or two old. Or was 5 years old, but grants and participation were decreasing. But after 10 years, with grants increasing, and participation increasing, the hammer has clearly found the nail, nailed it squarely on the head, and driven it home.

Finally, I could not have summarized this better than NeilBlanchard ...

NeilBlanchard wrote:
I strongly suspect that [m00002a] is taking the intellectually lazy path of sanctimonious criticism of other people's choices, merely to justify [] preconceived notions


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