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PostPosted: Thu Jul 22, 2010 6:11 pm 
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Well you certainly were not passing out compliments when you said, "I might have known......"

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PostPosted: Thu Jul 22, 2010 7:07 pm 
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m0002a wrote:
I did not reach my conclusion about folding@home in a vacuum. I was curious about it, so I asked two bio-chemists about it (without giving them any input from me) and they were both skeptical, and didn't know anyone in bio-tech research who used the data that comes from folding@home. These were very well established bio-chemists who work for major bio-tech firms and have fairly impressive CV's.


Show them this page, and see what they say, please?

http://folding.stanford.edu/English/FAQ-Diseases

Quote:
Introduction

The Folding@home project (FAH) is dedicated to understanding protein folding, the diseases that result from protein misfolding and aggregation, and novel computational ways to develop new drugs in general. Here, we briefly describe our goals, what we are doing, and some highlights so far.

We feel strongly that a Distributed Computing project must not just run calculations on millions of PC's, but DC projects must produce results, especially in the form of peer reviewed publications, public lectures, and other ways to disseminate the results from FAH to the greater scientific community. Below, we also detail our progress in these areas as well.

Most updates are announced in the main Folding@home blog, but we will periodically update this page. For the latest news, please see the blog.

What is protein folding and how is it related to disease?

Proteins are necklaces of amino acids, long chain molecules.

Proteins are the basis of how biology gets things done. As enzymes, they are the driving force behind all of the biochemical reactions that make biology work. As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels. As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders. For these reasons, scientists have sequenced the human genome -- the blueprint for all of the proteins in biology -- but how can we understand what these proteins do and how they work?

However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carry out their function (e.g. as enzymes or antibodies), they must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."

What happens if proteins don't fold correctly?

Diseases such as Alzheimer's disease, Huntington's disease, cystic fibrosis, BSE (Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding. When proteins misfold, they can clump together ("aggregate"). These clumps can often gather in the brain, where they are believed to cause the symptoms of Mad Cow or Alzheimer's disease.

Which diseases or biomedical problems are you currently studying?


Alzheimer's Disease (AD)

AD is caused by the aggregation of relatively small (42 amino acid) proteins, called Abeta peptides. These proteins form aggregates which even in small clumps appear to be toxic to neurons and cause neuronal cell death involved in Alzheimer's Disease and the horrible neurodegenerative consequences.

We have many calculations being performed on AD. Our primary goals are the prediction of AD aggregate structure for rational drug design approaches as well as further insight into how AD aggregates form kinetically (hopefully paving the way for a method to stop the AD aggregate formation).

There have been many projects, including 500 series and 700 series. So far, all of them are either Tinker WUs or normal (not bigWU) Gromacs WUs.

2005

* We are currently in the process of submitting our first paper on FAH results.
* FAH researchers Vishal Vaidyanathan and Nick Kelley present the recent FAH results on AD at BCATS 2005. Their work won the best talk award in 2005.
* Prof. Vijay Pande presented recent FAH work on AD at the National Parkinson's Foundation conference (in the session on AD and its connections to PD).

2006

* Our first paper on AD is ready to submit. We hope to start publicly talking about these results very soon.
* We have submitted our first paper for peer review and we're working on the next 2 paper right now. We're very excited about the results!

2007 We have made some significant progress experimentally testing our computational predictions using NMR.

2008 The first of the papers has come out (see paper #58 on our Results page: "Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach").

2009 We have had some exciting results regarding new possible drug leads for Alzheimer's. We hope to be submitting these soon for publication.




Huntington's Disease (HD)

HD is caused by the aggregation of a different type of proteins. Some proteins have a repeat of a single amino acid (glutamine, often abbreviated as "Q"). These poly-Q repeats, if long enough, form aggregates which cause HD. We are studying the structure of poly-Q aggregates as well as predicting the pathway by which they form. Similar to AD, these HD studies, if successful, would be useful for rational drug design approaches as well as further insight into how HD aggregates form kinetically (hopefully paving the way for a method to stop the HD aggregate formation).

2006 We are currently in the process of submitting our first paper on FAH results.

2007 Nick has been working on a new collaboration with Judith Frydman's group to computationally test a new hypothesis for HD aggregation found in the Frydman lab.

2008

* Prof. Pande has presented the results on HD at a variety of Stanford internal conferences and meetings. People have been excited and interested in the results.
* We have also started to apply the drug design methods used in Alzheimer's to HD.

2009 New paper #62: The predicted structure of the headpiece of the Huntingtin protein and its implications for Huntington's Disease. It's still early (since this paper was just accepted), but I wanted to give FAH donors a heads up on our work on Huntington's Disease aggregation, which is just about to come out in the Journal of Molecular Biology.



Cancer and P53

Half of all known cancers involve some mutation in p53, the so-called guardian of the cell. P53 is a tumor suppressor which signals for cell death if their DNA gets damaged. If these cells didn't die, their damaged DNA would lead to the strange and unusual growths found in cancer tumors and this growth would continue unchecked, until death. When p53 breaks down and does not fold correctly (or even perhaps if it doesn't fold quickly enough), then DNA damage goes unchecked and one can get cancer. We have been studying specific domains of p53 in order to predict mutations relevant in cancer and to study known cancer related mutants.

2005

* Our first work on cancer has recently been published.
* We are expanding FAH's p53 work to other related p53 systems
* We are getting some interesting results from recent new FAH p53 projects.
* Two new sets of projects have completed and two new papers are being readied for peer-reviewed publication.

2006 FAH researcher Dr. Lillian Chong presented her work on p53 at a lecture at several US Universities.

2007 Plans have started to take a new approach for using FAH to fight cancer: to develop novel chaperonin inhibitors. FAH researcher Del Lucent is taking the lead.

2008 Del has presented his plans to the NIH Nanomedicine center with a very positive response. Planning for the lab side of this work has begun.

2009 Del has been involved in the development of new software methods (Ocker) for the chaperonin inhibitor project.


Osteogensis imperfecta

In collaboration with other groups at Stanford (especially Dr. Teri Klein's group at Stanford University Medical Center), we are looking at Collagen folding and misfolding. Collagen is the most common protein in the body and mutations in collagen leads to a very nasty disease called Osteogenesis Imperfecta (or OI for short). In many cases, OI is lethal and leads to miscarriage. However, 1 in 10,000 people have some sort of mutational in collagen. For many, where the mutation is not very serious, it lies unknown and misdiagnosed and leads to brittle bones and other more subtle problems. In others, however, mutations lead to more serious morphological disorders (as shown on the right).

We are starting to model collagen folding and misfolding in the 1000 series projects. Follow the link for more information.

2005 FAH's first work on collagen has been accepted for publication

2006 FAH researcher Dr. Sangyhun Park presents his work on collagen at a lecture at Duke University

2007 Our paper on collagen folding has been accepted for publication.

2008 Our paper on collagen folding has come out.

For now, our Osteogensis imperfecta stands still as a pilot project, with the bulk of our efforts going into AD and HD.


Parkinson's Disease (PD)

We have also performed preliminary studies on a key protein implicated in Parkinson's disease. Alpha-synuclein is a natively unfolded protein and its folding/misfolding (see figure on the right for misfolded aggregates) appears to be critically linked to PD. We are evaluating the application of various FAH methods to this problem.

2005

* We have only done a pilot study on PD and are looking for funding to continue our work in this area.
* Prof. Vijay Pande presented recent FAH work on AD at the National Parkinson's Foundation conference (in the session on AD and its connections to PD).

For now, PD stands still as a pilot project, with the bulk of our efforts going into AD and HD.


Antibiotics

The Ribosome is an amazing molecular machine and plays a critical role in biology, as it is the machine that synthesizes proteins. Because of this critical role, and some small but fundamental differences in the ribosomes of mammals and bacteria, the ribosome is the target for about half of all known antibiotics. These antibiotics typically work by preventing bacterial ribosomes from making new proteins, thus killing them. We have several projects on going to study the ribosome. Since the ribosome is so huge, these WUs are big WUs and have required us to push the state of the art of FAH calculations. However, with these new bigWUs, FAH is set up to study more and more complex problems, and if successful, with greater and greater biomedical impact.

2005

* We are working on our first paper resulting from FAH's ribosome simulations.
* Prof. Pande presents ribosome results at a protein folding conference at U Penn.
* Prof. Pande presents ribosome results at a lecture at University of California at San Francisco (UCSF) Medical School.
* Prof. Pande presents ribosome results at a lecture at Rice University.

2006

* Prof. Pande presents ribosome result at the NIH Roadmap center on Nanomedicine.
* We are just about to submit our first paper on the ribosome.
* Our first work units for antibiotic drug design calculations are now running on Folding@home.

2007 We have received a grant from Stanford University to design and study novel antibiotics. This grant is joint with the labs of Chaitan Khosla at Stanford's Chemistry Department (who does small molecule synthesis, design, and some characterization) and Jody Puglisi at the Stanford Medical School (who studies the ribosome and antibiotics experimentally)

2008 Our first ribosome paper has come out in PNAS. See paper #59. Side-chain recognition and gating in the ribosome exit tunnel.

2009 Our second paper on the ribosome has been submitted for publication.

How are these advances possible?

In order to make breakthroughs using distributed computing, new methods are critical. Distributed computing is an unusual way to perform large-scale calculations. While it gives computer resources much greater than a typical supercomputer (e.g. the almost 200,000 actively processing CPUs in FAH vs. 5,000 in a typical supercomputer), these processors are connected by the Internet, not the high speed, low latency interconnects found in supercomputers. Thus, we must develop new methods to use FAH's unusual computational paradigm and capabilities. Moreover, these methods must be tested.

Much of our work in the first years of FAH has been to develop and test these methods on model systems: small proteins that can be easily studied experimentally. With these experimental comparisons, we can test and validate our methods, as well as find out their limitations (which is critical for improving our methods).

To date, FAH has been very successful, with over 40 published works (as of July 2006) directly stemming from FAH calculations. We will continue to work on all fronts: new scientific cores, new server side algorithms, new models for proteins, and new questions related to testing our methods and applications to disease and other biomedical questions.


What about the rest of my post, about saving energy? (BTW, my family are becoming locavores, too.) What are you doing to reduce your carbon output, and start to reduce Global Climate Change?

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PostPosted: Thu Jul 22, 2010 7:17 pm 
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aristide1 wrote:
Well you certainly were not passing out compliments when you said, "I might have known......"

That is not a personal attack, it was just an observation about left wing ideologues who seem to hold logically inconsistent views, IMO.

It does amaze that some people who claim to be rational and open-minded, and who ridicule anyone that thinks there is some reality beyond what science can know, can adopt an almost religious allegiance to something (folding@home), and when someone tries to rationally question their assumptions, they get extremely upset.

This is not really personal. If you don't believe me, find a bio-chemist or someone doing serious medical research in the areas of cancer, Alzheimer's, etc, and ask them what they think about folding@home, or if they have ever thought about using the data captured by that project.


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PostPosted: Thu Jul 22, 2010 7:31 pm 
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NeilBlanchard wrote:
[Show them this page, and see what they say, please?

It is very easy (and common) in the academic world to name-drop diseases such as cancer, Alzheimer's, etc, in order to get grants and research money. The fact is that if you read the 73 articles, there is almost nothing there of any substance (outside the realm of computer science).

I suggest you talk to some bio-chemists doing serious medical research in your area, and then ask them about it. Then you can decide to do whatever you want, or what your conscience dictates.

I already told you my opinion, which is that although you sincerely think you are helping mankind to find a cure to some serious diseases, you are in fact only contributing to global warming and wasting precious energy resources. In the US at least, we have free speech, and that is my opinion. You obviously have the right to disagree.


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PostPosted: Fri Jul 23, 2010 12:18 am 
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m0002a wrote:
Given that Folding is creating untold amounts of green house gases, using up energy supplies that could be put to better uses


I think the biggest problem is that (at least a few years ago when I looked into this) the folding people are not up front about the costs and environmental impact of the project. Estimates of the costs (amount of kw-hours used, greenhouse gasses generated, cost to the contributor) of folding should be prominently posted on the F@H website.

Back in 2007, when I looked into this, they downplayed the costs, and said little or nothing about the environmental impact and inefficiency of the project. They talked about "wasted" cycles, which even then were an anachronism.

(In October 2007 I made a rough estimate:
Quick calculation puts electrical donations to folding on the order of
10,000,000 kilowatt-hours
(worth about $2 million at current prices, and added something like 10,000 metric tons of extra CO2 to the air)

http://www.silentpcreview.com/forums/vi ... sc&start=0

Obviously a lot more since then.

So the big issue is that the costs were [are?] untold (I haven't checked extensively recently - but a quick peek didn't suggest that they are doing any better). The first part of efficiency is knowing what something is costing - then one can have some basis for improving efficiency, or deciding whether it is worth it.

I am inclined to agree that F@H is not an efficient way of contributing to solving those problems. (e.g. if I gave the money directly the government would magnify my contribution by providing a tax write off. Purpose built compute servers could be put closer to energy transformation facilities, or where heating could be used. With the rapid increase in computer speed, waiting to start until machines are faster is often more efficient than trying to run on lots of old, slow processors.)

In the past F@H were not particularly good about weeding out low efficiency processors. Again, bringing the costs more to the fore could help in this regard (especially for neophites).

"This is a sad thread. The High Cost of Folding."
http://www.silentpcreview.com/forums/vi ... highlight=

"What are your points per [day per] watt (PP[DP]W)?"
http://www.silentpcreview.com/forums/vi ... sc&start=0

On the other hand, in the winter using a folding space heater (made from surplus parts - to reduce embodied energy) might well be better than just running the electricity through a resistor. (After one had done sealing, installed insulation, bundled up warm, etc.)

Because there is waste elsewhere is not a reasonable reason to say one shouldn't examine the cost/benefit ratio of this project. The inherent inefficiencies of the folding model and lack of transparency about the costs involved are clearly problems with folding, and reasonable topics for discussion/areas for improvement.


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PostPosted: Fri Jul 23, 2010 9:36 am 
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scdr, thank you for your valuable input. In some places (like Florida, for example) using a computer as a space heater is not a good idea. Because they don't have much need for heaters in FL, almost everyone has electric heating, and when it does get cold (occasionally) they sometimes have electricity blackouts. I was in FL once when the temps got down to 25 F and the electric utility had to cycle the power on and off in 2 hour increments.

The flip side of the efficiency issue is the actual benefit of the data. I had no idea myself, and that is why I asked two different bio-chemists who do cancer and other medical research, and both had no interest in the data and were highly skeptical of the project.

The head of the folding@home project at Stanford has not seemed to have gotten a lot of support from his colleagues in the Chemistry department, as he is still an associate professor (not a full professor). If there was something to this, I would expected that he would have gotten a Nobel Prize by now, but I think most scientists view it as computer science project, rather than a medical research project.


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PostPosted: Fri Jul 23, 2010 3:00 pm 
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Are you folks scientists? Can you specifically critique the scientific output of this project? Do you think that science should only focus on the easy questions, that we would likely find the answers to without much effort?

In what ways are we left-wingers (according to you!) being illogical? Are you our right-winger savior, with all the real answers?

You have conveniently ducked the energy savings I have been doing, to more than offset the electricity that you feel is wasted. What are you doing about Global Climate Change, sir/madam? What kind of science are you participating in, where the trade offs are worthwhile for you?

[moderator's hat]
I strongly suspect that you are taking the intellectually lazy path of sanctimonious criticism of other people's choices, merely to justify your preconceived notions about other people that you think don't agree with you, on some other subjects. If we are wrong about those things, then we are wrong about these things; in your mind? Do you have any positive input, or are you just going to criticize other people?

I took the time to make this thread (after you thoughtfully jammed up another thread), and if you want to "use" it for the purposes of discussing the subject at hand, then please do so! But if you continue to diss other people's choices and actions, and offer nothing in return, then this thread will go away.
[/moderator's hat]

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PostPosted: Fri Jul 23, 2010 3:44 pm 
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m0002a, you keep harping on the associate professor deal, could you offer some more insight into why you think this is such a big thing?

Neil, I think noone should downplay your achievements and efforts in minimizing your enviromental footprint, if everyone did that we'd have a much more comfortable situation when it comes to oil supply, electrical supply (and pricing), etc.
Sadly, joe sixpack tend to look at the buck, and lets it stop there...

My personal opinion on folding@home is that while its nice to help out, I feel they should be working on improving their workloads and clients more, all the points chasing gets tiring, all the hackery you need to do to get the max "points" out of it, etc. Which is why I now run BOINC in the winter instead of F@H.

On the impact F@H and similar projects has on science, I think they dont really have that much of a direct impact, but when that one lucky computer out there in bum***k Indiana finds the "one" protein that cures/prevents alzheimer, its all gonna be worth it in the end.

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PostPosted: Fri Jul 23, 2010 4:51 pm 
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Wibla wrote:
m0002a, you keep harping on the associate professor deal, could you offer some more insight into why you think this is such a big thing?

I wouldn't say it was a huge deal, but he is 40 years old and has had his PhD for 15 years. Given the extravagant claims of folding@home, and that the Pande Lab is named after him, I would have thought he would be a full professor by now. My theory is that, although he seems to be a superstar outside of the scientific community, his colleagues don't think he is doing much chemistry, just mostly computer science or physics instead.

Wibla wrote:
On the impact F@H and similar projects has on science, I think they dont really have that much of a direct impact, but when that one lucky computer out there in bum***k Indiana finds the "one" protein that cures/prevents alzheimer, its all gonna be worth it in the end.

I guess you watched the The Andromeda Strain. Unfortunately that is science fiction. It is interesting how many people are deeply affected by the movies. I think because of the film JFK, many younger people really think the LBJ had something to do with killing Kennedy.

I suppose that folding@home depends on the theory that protein folding is random, and if we just run enough computer simulations that we can figure it out. I don't know the answer to that, but there seems to be very little acceptance of folding@home in the scientific community as a serious player in the fight against the diseases, or understanding how they occur.

Not that everyone has to agree with all theories, but this one is on the fringes of mainstream thinking in the scientific community whose aim is to understand and cure diseases. Of course, Pande is in the chemistry department, and is more interested in bio-physics and computer science than bio-chemistry. He also seems to have a very large ego.


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PostPosted: Fri Jul 23, 2010 11:33 pm 
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Extremely reluctant as I am to actually agree with m0002a on anything, I feel that on this occasion I have to. :cry:

Here's why:

Up until this morning when I happened upon this thread I knew little to nothing about folding@home other than it was some scientific project that caused your computer to run at full bore all the time - using electricity and creating noise, neither of which is good; in my opinion.

I decided to have a look to see what protein folding was all about. First stop, Stanford University folding website. Not a good start - server must have been down or something. /irony/
Next was Wiki where I came upon something known as the Levinthal Paradox, which if I understand it correctly, states that there are 3 to the power of 98 permutations of fold. Given the current 5 petaflops of computation working on folding, I worked out that it would take roughly one thousand million, billion, billion years to go through all the possible permutations. Given that the age of the universe is only of the order of 14 billion years, I feel that an incredible stroke of luck, to say the least, would be required for folding@home to give any kind of meaningful return. Not as bad as an infinite number of monkeys with keyboards coming up with Hamlet but still remote.

Of course I may have completely misunderstood the whole business and/or made an arithmetical mistake on the back of my fag packet but I think I'm in the ballpark at least.


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PostPosted: Fri Jul 23, 2010 11:37 pm 
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NeilBlanchard wrote:
[...] Since each gallon of gasoline (just in the gas itself, not counting all the embedded energy to find, extract,transport, refine, etc.) is worth 33.4kWh of electricity; brings the total savings to the equivalent of 21,042kWh -- that is more electricity than our household uses in about 2.5 years!


Hey Neil, that is a very interesting observation - a gallon (or 3.8 l in my terms :wink:) is equivalent to 33.4kWh of electricity. Is that at power plant efficiency or how do you calculate this? I guess you mean in terms of how much carbon dioxide is released, is this assumption right?

If so, my total electricity consumption last years was equal to 143 l (38 gallons) of gas. That certainly puts things into perspective, considering how I am an eco-hippie who doesn't want to own a car! :lol:

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PostPosted: Fri Jul 23, 2010 11:51 pm 
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judge56988 wrote:
Next was Wiki where I came upon something known as the Levinthal Paradox, which if I understand it correctly, states that there are 3 to the power of 98 permutations of fold. Given the current 5 petaflops of computation working on folding, I worked out that it would take roughly one thousand million, billion, billion years to go through all the possible permutations.


Actually, it's pretty easy to restrict the conformational space by several orders of magnitudes. One approach is to use either the the amino acid sequence or spectroscopic data to take a pretty good guess at the secondary structure (the internal conformations of the protein) and restrict sampling of the the angles of the backbone to the corresponding allowed angles, called a Ramachandran map. Also you don't need to search the entire conformational space, since you're trying to minimize the energy of your sample structures.
Also, the conformational space of a protein it's a continuous space (it's based on bond distances and bond angles, which can take any decimal number), so in principle there is an infinite number of conformations.

The way it works is that you sample a structure (protein conformation) and you calculate the energy of that structure using an energy function. Usually you do a Monte Carlo simulation and try to minimize the energy of the sample structure, and once you're done minimizing the energy, you should have a nicely folded protein, given that your energy function works properly.

EDIT: Also, I did a protein folding myself last month, which took ~400h on 8 cores, using a spectroscopic consistent energy function (but still very cheap) I've been working on for the past six months. So they age of the universe is, in my opinion, not a completely accurate ballpark. But your point remains valid, it's computationally demanding problem, no question. Hence the need for large CPU resources.

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PostPosted: Sat Jul 24, 2010 1:12 am 
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NeilBlanchard wrote:
What kind of science are you participating in, where the trade offs are worthwhile for you?


The following is an example of the sort of investment I think has a pretty decent rate of return.

NeilBlanchard wrote:
We took advantage of a generous rebate from our energy company, to greatly reduce the cost of heating our house by insulating it, and after the $2K rebate, our out-of-pocket expense was just $740. We reduced our natural gas bill (during the winter months) from ~$350 by over $200 per month. So, as far as the costs go, we already more than recouped our costs, and the energy company will recoup theirs in a few short years. That is about a 60% energy savings; thank you very much!


Not only does it provide the direct financial benefits, but reducing the use of unsustainable energy extraction (e.g., burning of fuels, nuclear power) also reduces cancers, etc. (i.e., it helps address some of the same issues that folding trying to address - but with proven benefit.)


Even better rates of return can be had by investing in family planning. In the US, every dollar invested in providing family planning services to those in need of publicly supported services saves more than $4 in short term (<1 year) public medical costs. The savings if you include other costs (education, justice, food, housing, transportation, waste, energy, etc.) or consider longer terms are considerably greater. The savings to the individual of investing in effective contraceptives are also considerably greater.

Another example: Providing modern contraceptives to the 201 million women at risk of unintended pregnancy in developing countries who do not have access to contraception would cost an estimated US$3.9 billion per year. This expenditure would prevent an estimated 52 million unintended pregnancies annually, preventing 1.5 million maternal and child deaths annually, and reduce induced abortions by 64%.
[Source: Susheela Singh, Jacqueline E. Darroch, Michael Vlassoff, Jennifer Nadeau (2003) Adding it Up: The Benefits of Investing In Sexual and Reproductive Health Care. The Alan Guttmacher Institute and UNFPA.]

Because of the multiplicative factor (I=P*A*T, or Impact = Population * Consumption * Technology to extract the goods consumed) and exponential growth, population increase can swamp any gains in efficiency or reductions in consumption. But, by the same token, moving towards a sustainable population is one of the most promising ways out of the current environmental mess.


Those are more applied examples of more worthwhile investments, but getting back to the question posed - there is plenty of science to be done in family planning, population, energy efficiency, etc.


As far as contributing to folding - the most useful thing I see to do is to work to improve the energy efficiency of the system.

As to the energy efficiency of distributed computing systems, this might be of interest.
"In fact, the energy efficiency of computation has doubled about every 1.6 years since 1945"
http://blogs.msdn.com/b/see/archive/200 ... oomey.aspx

Which again lends support to the idea of delayed computation. Rather than starting running an open-ended/seriously long job now. Wait until the computers are faster (and more energy efficient), and do the job then. (In the meantime, you can invest the resources that you would have invested in the computation in something else that gives a high rate of return - for examples, consider above.) Also, improvement in algorithms often nets even better returns than more computing power, so given more time to tune the algorithms, future folding may again be even more efficient than mere machine improvements would predict.


Not meaning to go off topic, but since somebody mentioned the resources used in gaming, thought this article might interest.
http://gear.ign.com/articles/941/941223p1.html


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PostPosted: Sat Jul 24, 2010 1:40 am 
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judge56988 wrote:
Given the current 5 petaflops of computation working on folding, I worked out that it would take roughly one thousand million, billion, billion years to go through all the possible permutations. Given that the age of the universe is only of the order of 14 billion years, I feel that an incredible stroke of luck, to say the least, would be required for folding@home to give any kind of meaningful return.


Good news - it won't take quite so long. You neglected to consider the rate of change of computational power. If compute power doubles every 24 months [Moore's law], then we should wait for a mere 180 years (90 doubling times) before performing the computation. Our computers will then be 1x10^27 times the current speed, and capable of completing the task in a year.


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scdr wrote:
judge56988 wrote:
Given the current 5 petaflops of computation working on folding, I worked out that it would take roughly one thousand million, billion, billion years to go through all the possible permutations. Given that the age of the universe is only of the order of 14 billion years, I feel that an incredible stroke of luck, to say the least, would be required for folding@home to give any kind of meaningful return.


Good news - it won't take quite so long. You neglected to consider the rate of change of computational power. If compute power doubles every 24 months [Moore's law], then we should wait for a mere 180 years (90 doubling times) before performing the computation. Our computers will then be 1x10^27 times the current speed, and capable of completing the task in a year.


Moore's law is by no means a "law" - just an observation based on recent progress; there appears to be a limit as to the rate of increase with current technology however I wouldn't either discount the possibility of a development in processing that could give an orders of magnitude increase in computational power - molecular and quantum computing for instance. Your idea of waiting is a good one, I'm also right with you on a sustainable population being the only long term answer to our other problems but I don't want to stray off topic.

There is also another ethical dilemma that I think needs to be considered: given the finite financial resources available, how much money should be directed at keeping old people alive for greater lengths of time, taking into account not only the cost of expensive treatment but also the ongoing cost of care and pensions? Would that time, money and effort be put to better use in other areas such as better care for younger people or improved education facilities or even research into fusion reactors? The burden of looking after an increasingly aged population will, I think, become too much for Western countries with an ever decreasing number of tax paying younger people. I guess that once the baby boom generation are all dead and gone, the equilibrium will be restored but I wonder what the world will look like then?


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PostPosted: Sat Jul 24, 2010 5:05 am 
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Strid wrote:
Actually, it's pretty easy to restrict the conformational space by several orders of magnitudes. One approach is to use either the the amino acid sequence or spectroscopic data to take a pretty good guess at the secondary structure (the internal conformations of the protein) and restrict sampling of the the angles of the backbone to the corresponding allowed angles, called a Ramachandran map. Also you don't need to search the entire conformational space, since you're trying to minimize the energy of your sample structures.
Also, the conformational space of a protein it's a continuous space (it's based on bond distances and bond angles, which can take any decimal number), so in principle there is an infinite number of conformations.

The way it works is that you sample a structure (protein conformation) and you calculate the energy of that structure using an energy function. Usually you do a Monte Carlo simulation and try to minimize the energy of the sample structure, and once you're done minimizing the energy, you should have a nicely folded protein, given that your energy function works properly.

EDIT: Also, I did a protein folding myself last month, which took ~400h on 8 cores, using a spectroscopic consistent energy function (but still very cheap) I've been working on for the past six months. So they age of the universe is, in my opinion, not a completely accurate ballpark. But your point remains valid, it's computationally demanding problem, no question. Hence the need for large CPU resources.

:shock: :shock: :shock: :shock: :shock: :shock: :shock:
9 am on a saturday morning... WAY too early for this.... back to bed :roll:
Nice to see someone in the field give us feedback.

I don't know how complicated this calculation you did was, but from the time frames you describe, I'm sure a complicated calculation makes sense in the context of the folding@home project !

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frenchie wrote:
I don't know how complicated this calculation you did was, but from the time frames you describe, I'm sure a complicated calculation makes sense in the context of the folding@home project !


Basically the computational expense lies in the speed of generating sample structures and and the speed of evaluating the energy of each sample.

We have a frame work which is very efficient in the first part, and mainly we work with inexpensive energy evaluations. The expensive stuff is when you include stuff such as all atom energies via a force-field. This can easily cost you several days on thousands of cores to minimize even a modest sized protein, which is what for iinstance Rosetta routinely works with. This is not the kind of resources everybody has at their disposal.

If anyone is interested in the motivation of doing protein folding simulations, let me give a few lines. In order to understand the exact function and chemical pathways of how a protein works, one must know the 3D structure, i.e. a set of 3D-coordinates for every atom in the protein.
Usually, the way you get the coordinate sets today is that you hire a master or Ph.D. student to see if it is possible to crystallize the protein. Then IF crystallization is possible (which it is not for ~95% of all proteins) you can use X-ray crystallography to determine the structure, often with very high accuracy. However, since it is extremely difficult to make good protein crystals, this approach does not work for many proteins. Other methods like NMR structure determination is also extremely laborious and does not work for large proteins, and the structures generated are not as high in quality as X-ray structures.
However, if one instead can spend a week or two on a cluster computer and get a usable structure, which it seems like it will be in the future, it's a big thing for bio-technology.

EDIT: For anyone interested, do take a look at what hot-shot David Baker has to say: http://boinc.bakerlab.org/rosetta/rah_welcome.php

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PostPosted: Sat Jul 24, 2010 4:17 pm 
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Strid -- 33.4kWh of electricity has approximately the same BTU content as a typical gallon of gasoline. Source-to-wheels is a whole 'nuther ball 'o wax...

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For someone so concerned about efficient use of energy, he's sure wasting a lot of it in this thread (literally, and figuratively).

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yoitsmeremember wrote:
For someone so concerned about efficient use of energy, he's sure wasting a lot of it in this thread (literally, and figuratively).


Oh, I don't know.
At the moment if you do a google search for environmental impact folding@home, this thread is the top item that shows up.
The impact may be small, or it may not - hard to say where people will go with it, but the energy expenditure of contributing to this thread is tiny compared to the expenditure of even one person running folding.
(As far as the figurative waste - if you look through the archives I believe you will find that some prominent SPCR folks are former folders, partly from similar concerns.)

Never doubt that a small group of thoughtful, committed citizens can change the world; indeed, it's the only thing that ever has.
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PostPosted: Mon Aug 16, 2010 11:59 pm 
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Still, seems like a moot point for several reasons:

1) If you're concerned about the energy cost, simply set something up to offset the cost of your folding--solar panels, wind turbines, whatever is feasible. If nothing physical is, buy green credits from your local power company (as most offer these days).

2) I know those outside the tropics, myself included, may use electric heating during the winter. Why waste the energy and put it directly into heat, when you could do something positive and still get the heat you need?

3) There are much bigger fish to fry. I bet at least some of people who stopped folding drive a car for probably thousands of miles a year. If you want to start somewhere, start there. Don't ride a car? Even things that are ultimately better for the environment--e.g. biking--are still inefficient. The human body is only around 25% efficient at best. The only reason they're better than the car is you're moving less weight. Even then, if you increase your consumption of meat due to your increased energy expenditure, you could probably end up being as bad as if not worse than some cars. Finally, the ultimate irony, is that prolonged sun exposure could cause the very problem folding is trying to solve--cancer. Sure you can wear sunscreen, but who knows if even that's safe.

4) How crazy is it to stop folding completely? People are ultimately the biggest contributors to global warming. Perhaps everyone should just stop having kids. I think it's a modest proposal.

To simply say "everyone should stop folding immediately" is not only narrow and shortsighted, but it can lead to worse efficiency and even worse decisions.

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yoitsmeremember wrote:
There are much bigger fish to fry. I bet at least some of people who stopped folding drive a car for probably thousands of miles a year. If you want to start somewhere, start there.

I think you are missing the point. Very, very few scientists believe that folding@home is worthwhile, regardless of the energy cost. If one drives a car, presumably (hopefully) they do it for some reason, such as to get from one place to another.

There is no rational reason to do folding@home since it is basically just a an erroneous religious belief that it is contributing to curing any diseases. Folding@home may be an interesting computer science project (a hammer looking for nail) rather than a legitimate bio-science project. The Andromeda Strain was science fiction.

The main benefit of folding@home is that it may make you feel better about yourself if you naively believe that you are helping solve the world's problems (even when you are actually doing no such thing, and in fact creating more problems with global warming and/or energy shortages).

One other benefit of folding@home is that gives people an excuse to build a quiet PC, even one that operates at high CPU levels over long periods of time. There is some engineering and entertainment challenge to the hobby of Silent PC's on a folding@home computer, which partly explains why folding@home is (or at least was) so popular on this forum. This is another hammer looking for a nail.


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m0002a wrote:
I think you are missing the point. Very, very few scientists believe that folding@home is worthwhile, regardless of the energy cost.

Do you have any hard evidence supporting this claim? F@H is in the process of getting a paper published that might lead to cures or at least drugs to lesson the effects of Alzheimer's disease. Would this not be beneficial?

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yoitsmeremember wrote:
m0002a wrote:
I think you are missing the point. Very, very few scientists believe that folding@home is worthwhile, regardless of the energy cost.

Do you have any hard evidence supporting this claim? F@H is in the process of getting a paper published that might lead to cures or at least drugs to lesson the effects of Alzheimer's disease. Would this not be beneficial?

Do you have any evidence supporting their claims about folding@home possibly helping cure Alzheimer's?

It is not my responsibility to prove a negative. I did ask two respected bio-chemists involved in finding cures for serious diseases, and neither of them saw benefit in folding@home. That doesn't prove anything, but it makes me very suspicious.

If you look at all of the 73 published papers on the folding@home website, you will find that everyone of them is co-authored by Vijay S. Pande, the person who invented folding@home. There is very little diversity of scientists involved in using the research being gathered, and the vast majority of them are chemists or computer scientists (not bio-chemists) and mostly associated with the Stanford Chemistry department (not may authors from other universities, and none from bio-tech firms that I could find).


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PostPosted: Tue Aug 17, 2010 6:29 pm 
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m0002a wrote:
Do you have any evidence supporting their claims about folding@home possibly helping cure Alzheimer's?

I sure do. Of course, this is all pending peer review.

m0002a wrote:
It is not my responsibility to prove a negative.

If you're going to make the broad claim of "Folding@Home is a completely worthless project", yes, I'd say it is your responsibility. Otherwise, you are likely to be ignored.

m0002a wrote:
I did ask two respected bio-chemists involved in finding cures for serious diseases, and neither of them saw benefit in folding@home. That doesn't prove anything, but it makes me very suspicious.

Who? How can I verify that they are respected without knowing their names? How is their opinion even remotely representative of most scientists, as you so boldly claim in your earlier post?

m0002a wrote:
If you look at all of the 73 published papers on the folding@home website, you will find that everyone of them is co-authored by Vijay S. Pande, the person who invented folding@home.

This is not the least bit surprising.

m0002a wrote:
There is very little diversity of scientists involved in using the research being gathered, and the vast majority of them are chemists or computer scientists (not bio-chemists) and mostly associated with the Stanford Chemistry department (not may authors from other universities, and none from bio-tech firms that I could find).

As far as use of the research, who knows who is actually making use of it? It would not surprise me to discover that pharmaceutical companies have used the research. Clearly, the accuracy of the folding algorithms has been proven experimentally. This alone makes the project worthwhile. The fact that it's published in peer reviewed journals shows that each article is clearly of some value--why else publish it?

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yoitsmeremember wrote:
m0002a wrote:
Do you have any evidence supporting their claims about folding@home possibly helping cure Alzheimer's?

I sure do. Of course, this is all pending peer review.

That does not constitute proof, even in the most remote sense of the word. Even if by some stretch, a drug was actually developed and went into clinical trials, most clinical trials end without FDA approval.

Here is estimate I found on the Internet about Clinical Trials:

What percentage of clinical trials ultimately result in an effective drug?
"About seven to fifteen years. The shortest time I've ever heard of a drug going from lab to actual use was the original HIV protease inhibitor, at the time there was essentially no treatment for HIV/AIDS, and a diagnosis usually meant death in under a year. The FDA basically pulled out all the stops for it.

There's three phases of clinical trials, and precliical before that. The overwhelming majority of drugs die in preclinical trials. About 7-9% of what gets into Phase I trials gets to move forward. It's hard to go with an exact number, because high throughput drug screening - which is where they test a very large number of compounds looking for a specific behavior skews it. Of he compounds that are looked at seriously though, easily under 1% make it to the point where they can be sold."


Regarding the other questions:

It would not do you any good if I told you which bio-chemists I talked to. Find some bio-chemists, and ask them yourself.

Finally, even if there was some value to folding (which has not been proven), there is no evidence that it could not have been done much more efficiently on a central computer, instead of the distributed configuration of folding@home (which is really just a computer science project, masquerading as a bio-chemistry project).

I personally don't care whether you believe what I say since I have no skin in the game. I originally posed the question, and the deeper I got into it, the more questionable it becomes.


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PostPosted: Wed Aug 18, 2010 5:56 am 
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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 ? ;)

m0002a wrote:
If one drives a car, presumably (hopefully) they do it for some reason, such as to get from one place to another.

That's besides the point. What you should have said was : If they really need to drive a car (not to go across the road to the convenience store), they do it for some usefull reason. That's what folding is : You have a computer, it sits there doing nothing (even while browsing this forum) so why not let it do something else in the meantime ?
To get back to the car comparaison, not running folding@home is like buying a car with super xeon lights and dual air conditionning, and running without lights on in the dark and without air conditionning in the heat. After all, the main purpose of a car is to get around, like you said, not to be an airconditionner or a street lighting device, right ?

m0002a wrote:
There is no rational reason to do folding@home since it is basically just a an erroneous religious belief that it is contributing to curing any diseases.

No proof of that, except 2 scientists saying they don't think it's usefull. Do they even work in a field where folding@home could be used ?

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PostPosted: Wed Aug 18, 2010 11:26 am 
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m0002a wrote:
yoitsmeremember wrote:
m0002a wrote:
Do you have any evidence supporting their claims about folding@home possibly helping cure Alzheimer's?

I sure do. Of course, this is all pending peer review.

That does not constitute proof, even in the most remote sense of the word.

I never said it did. You simply asked for evidence supporting my claims, not proof. We'll have to wait and see. Clearly the paper hasn't been rejected yet, and with something that has such a high potential impact, I would not be surprised if it spends more than usual time in peer review. Patience is a virtue.

m0002a wrote:
Even if by some stretch, a drug was actually developed and went into clinical trials, most clinical trials end without FDA approval.

Right, but this is ignoring the fact that several drugs could potentially be developed from the same research. Note that the post says "new possible drugs". Also, how many drugs in the past have been developed from research from a large scale folding project like folding@home? You can't apply the same statistics to different development processes.

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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?

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PostPosted: Wed Aug 18, 2010 6:43 pm 
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yoitsmeremember wrote:
I never said it did. You simply asked for evidence supporting my claims, not proof. We'll have to wait and see. Clearly the paper hasn't been rejected yet, and with something that has such a high potential impact, I would not be surprised if it spends more than usual time in peer review. Patience is a virtue.

Just because the paper is not rejected, does not mean that it will ever lead to any medical remedies.


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