Folding Forum

many advanced methods projects are not mentioned on the main page. check psummary.

To me, it's just another indicator of the lack of transparency here, usually couched in the "lack of resources" defense. How many years has bigadv and influenza research been done? And nobody could bother to update the main page?

Yes the sarcasm was intended to show the absurdness of your focus.

The objective is to investigate folding as it relates to disease . full stop.

Because some diseases are listed as examples, does nothing to exclude other possible examples or areas of exploration.

Your question, and attitude is the antithesis of research. The objective is to expand, not contract the dissemination of knowledge.

I'm sorry the introduction does not contain enough boilerplate,( possible inclusions in addition to the items listed) to meet your definition of full disclosure.

I have always been an advocate of transparency, (hence my signature) but you are making a conspiracy where none exists.

No one can predict where knowledge will lead inquisitive minds. That is the exciting thing about research.

I don't think anyone, here or anywhere else, will apologize for this.

I do understand where the OP is coming from. I've wondered about this myself. I don't mind that a lot of effort is put into the flu, but make a mention of it on the diseases page and what progress you guys have.

We apologize for the omission on the diseases studied page and have amended it to add information on influenza. There is also now a link to my group's web page with some of the papers on our influenza work. Finally, as influenza-related papers have been published from our FAH work, we have posted in the forum and updated the Papers page on folding.stanford.edu. A look through the forum archives should yield some of these.

Thanks for folding!

kasson wrote:We apologize for the omission on the diseases studied page and have amended it to add information on influenza. There is also now a link to my group's web page with some of the papers on our influenza work. Finally, as influenza-related papers have been published from our FAH work, we have posted in the forum and updated the Papers page on folding.stanford.edu. A look through the forum archives should yield some of these.

Thanks for folding!

Thank you very much Dr. Kasson! Perhaps I'm missing something obvious here, but unfortunately I don't see any new papers on the Results page (http://folding.stanford.edu/English/Papers) and it says that bottom that the page was last modified on October 21. Is this not the page you were talking about? Sorry I didn't see your forum post either, since I thought it would pop up in the New Posts category. Thanks though for responding and changing the Diseases Studied page, I for one very much appreciate that.

Hi Jesse_V

The link at the end of Viral Disease description will get you there. http://www.stanford.edu/~kasson/Research_Interests.html click on the research headers at the top of the page. http://www.stanford.edu/~kasson/Publications.html

Grandpa_01 wrote:Hi Jesse_V

The link at the end of Viral Disease description will get you there. http://www.stanford.edu/~kasson/Research_Interests.html click on the research headers at the top of the page. http://www.stanford.edu/~kasson/Publications.html

Thank you very much. I'll take a look.

Jesse V.

Dr. Kasson, thank you for updating the pages to include a description of viral diseases including influenza. I think greater ease of access to information about where donor's resources go will help them make decisions about where to donate those resources.

One question remains, though - does your area of influenza research use protein folding in the investigation of the infection process, or is this a different type of simulation?

I don't like how Punchy is "attacked" here for his questions. I think we donors have the right to know what is going on in this "f@h project" and where the focus is.
So many people think they are fighting cancer or Alzheimer's (look at the many team forums), they would be disappointed with this influenza focus, wouldn't they ? PG (and not their devoted followers) should explain more to us scientific laymen - in layman's terms.
I'm thinking about changing my rigs to WCG crunchers and cancer projects because of all this.

Punchy, it's a little of each.

We're doing some work on protein folding in the membrane: when the viral protein is inserted into the host cell, how does it fold and what does it do.
But to understand what it does, we also want to simulate the viral entry reaction (membrane fusion) that the protein folding controls. So we've spent a fair amount of effort doing that too. The key question is why we should care about the protein conformation: if the protein mutates a little bit in the wrong way, it no longer works, and we don't understand why. So we're trying to figure this out by studying both the protein in isolation, the underlying reaction, and the two together.
We've also done some work on protein refolding or conformational change: when the protein has one shape and then something makes it refold into another shape. This kind of conformational change is though important to a lot of biological signaling. (One debate in the field right now is how much proteins have one stable fold and move to another stable fold versus how much they exist in or move through a partially disordered state along the way. We're not directly examining this at the moment in the viral work, but it's important to think about.)
So it's all related to protein folding, but some is protein folding by a strict definition and some is a set of related simulations to allow us to understand the disease context better.

In general, work in my lab tends to be disease-focused. We do a lot of basic research, and we do some methods development, but we're always asking the question of what will best allow us to chase the disease questions we're interested in. We've chosen a set of disease problems that are both medically important and general (i.e. we think that progress here will help us for a broad range of biomedical problems).

Once again, thank you very much Dr. Kasson. That is quite interesting, and thank you for explaining. I wish some of the Project Descriptions were more informative in explaining all that, and you seem to imply that influenza research extends beyond just influenza. There are a large variety of viruses after all.

While it's a good idea to have all that information on the main folding.stanford.edu page, if people would like more information on what F@h studies and what it has accomplished, please see its article on Wikipedia. http://en.wikipedia.org/wiki/F@H I have put a lot of time into making that page as informative as reasonably possible, especially in the Biomedical Significance section.

Magic Michael wrote:I don't like how Punchy is "attacked" here for his questions. I think we donors have the right to know what is going on in this "f@h project" and where the focus is.
So many people think they are fighting cancer or Alzheimer's (look at the many team forums), they would be disappointed with this influenza focus, wouldn't they ? PG (and not their devoted followers) should explain more to us scientific laymen - in layman's terms.
I'm thinking about changing my rigs to WCG crunchers and cancer projects because of all this.

Agreed. And I also think quite some SMP users will be schocked to find out they've been only flu WU's. But then again, all this information was available if they simply looked which projects they were folding for. F@H is doing protein folding research, not cancer or alzheimer's research. I personally would welcome more diseases being researched.

Besides, Alzheimer's is probably still the biggest focus of PG with all the unicore and GPU WU's out there (don't forget that GPU's are still much faster than bigadv). I do agree that not enough attention is going to cancer, though. By far most people fold to fight cancer, and some are leaving to Help Conquer Cancer.

Here's more info about viral diseases research and Folding@Home:

http://folding.typepad.com/news/2007/09 ... eam-1.html

Interesting note: Peter Kasson helped develop SMP & BigAdv cores/clients, it's obvious that he's using those for his research.

Well I'm willing to apologize for being overly sarcastic.

However, it was not really an attack on anyone.

Just trying to point out that everything is inter-connected....that ideas are applied in different directions...that the synergy of research and application should be applauded as one of the greatest goods...

If you are really keen to be assured that the research you are funding only will go to cancer research that is great. However, you need to understand there are as many "causes" of cancer as their are tools to treat it. Virus, genetics, environmental exposures, over-use, etc. etc. etc.

So, can understanding the proteins (folding abnormality or not) have applications in CANCER, VIRUS, GENETIC DISEASE, DRUG DESIGN, STEM CELL RESEARCH, and BIO-ENGINEERING to name just a few?

Yes.

Can you have the expectation that the research is directed to the primary goals listed? Sure.
Can you have the expectation that the research will never be applied to other areas? I don't think so.

My initial response was to the accusatory tone of the inquiry. I didn't see any attempt to deceive donors into donating time for "folding diseases" when the application of understanding the folding process has so many other applications. (viruses and Flu for example as discussed)

In my mind, it is like accusing a math research project of helping the energy industry.

Yes, complex equations will be used in the oil, natural gas, and even the nuclear industry.
However, they will also be used in the solar, and wind, battery design, and Cellulosic Ethanol applications.

Advanced math is a tool, just like understanding protein folding is a tool.

Trying to dictate prior restraint on where that tool will be used just seems futile and counter-productive.

I don't disagree with any of the above,
but from previous donor comments some were not aware that Bigadv was mainly researching influenza,
so take another analogy,
Someone attracted to donating straight $$ to feed starving children by graphic images in the charities advertizing would expect their $$ to go to food and food only ?
but food alone would be useless without clean drinking water, so the charity would rightly support wells, filtration etc to provide that, and state that's part of their work
somewhere in their literature,
So is not having anything about clean water on the front page of some brochure somehow deceiving ?
With Folding you can just "sign up" and run standard clients, Gpu clients if you choose, or smp and Bigadv if you want high performance (and high ppd), or carefully look through the project descriptions and choose the client that runs the project you wish to support,
I do feel though that considering the hardware needed for Bigadv projects there should've been more information about what it was working towards at the time of it's release.