Is this true? Answer from Stanford if poss!!

[lennytiger]

Originally Posted by Ol'man:

I quit folding for now cause the way they made it sound at Stanford was that they wanted to learn how to simply make totally new polymeric prion proteins which to me is not finding a cure for alzheimers. I compare it too creating new viruses that cause cancer. And if you think viruses don't cause cancer think again. Instead of making new polymeric prions they should be concentrating on the 3 or 4 prions that cause alzheimers, mad cows disease and KURU. They have even found radical prions in the deer and elk around where I live. That is some scary shi#. Nope these folk want to figure out how to make totally new prions. Buncha BS if you ask me. Until someone shows me that they are simply trying to find a cure then I may fold again but I am not going to help create new and possibly more deadly prions.

What about that? Any Ideas?
Vijay??

*This is not a flame to anyone*
Just sounds very true, they just use our cpu power for whatever they want?!!

[flounder43]

I don't think that they are going to be actually creating these prions and setting them loose...

They are doing fundamental research on an area about which little is known. They are building a solid knowledge base upon which to expand. I do believe it is useful research.

BTW, a friend of mine's father actually died of CJD, which is often referred to as the human equivalent of Mad Cow. It is unknown where he got it. One theory was that he had hunted and eaten deer, elk, and other game animals in the Western U.S.

This is a very mysterious area, and I fully support Stanford's research.

[Kendan]

I believe the next set of proteins that we are going to be working on directly relate to alzheimers.

[Ploaf]

I believe that they are complimentary and the end result will be working toward a cure. Has anyone asked for a response on this on the Folding 2 message board?

[lennytiger]

Not yet whats the url I may do that...

[Kendan]

Originally posted by lennytiger
Not yet whats the url I may do that...


http://groups.yahoo.com/group/folding2

there you go. Folding, Folding, Folding, Folding, Folding,

[Ploaf]

<Doh> beat me to it :D

[Ploaf]

Just something I was thinking about. Most of our problems such as alzheimers, CJD, etc. are caused by a LACK of understanding. We know that something happens and we know that certain things are directly related to the disease but we often do not know how they relate to each other besides the fact that they are related.
Accidents in the lab generally come from Not knowing. Not knowing what happened. Not knowing how it happened. Not knowing why it happened. We are working on finding out what, how, why this happens at the lowest possible levels. Does that mean replicating it in a lab in real life? Yes. It could also mean that to reduce or eliminate the effect of the prions that new proteins may be necessary to combat the problem. I don't know. Are there dangers involved in this type of discovery? There is no doubt in my mind that dangers do exist.

Here's what I do know. We are not the only ones working on this. There are companies right now that are working on this. What's the difference? Well, for one, I am not being paid to find a result. For another, all of the results from this project will be freely published on the internet available to anyone who wants to see them. Will the companies do the same? Who knows what they will do with what they find? If mistakes are made in a lab because of what we find the base information will be available to the anyone capable of looking for a solution. If there are mistakes made in a lab with information based on results that are locked in a safe then the resources available to find a solution will be severely limited. I'd rather that this information remain available to the public rather than having it locked away somehwere away from prying eyes.

[ol' man]

Here is a quote from a recent thread I started.

http://forums.overclockers.ws/vb/showthread.php?s=&threadid=46477

One of our project goals is to simulate protein folding in order to understand how proteins fold so quickly and reliably, and to learn how to make synthetic polymers with these properties.

Right there they are saying they want to form polymers with these properties. So are we working on finding a cure for Alzheimers or doing work on finding a way to make protein polymers as the above quote suggests? Sure it is one of the most common ways to find cures by making a mistake in the lab. I have made plenty myself.

For instance I found that in a aqueos/organic phase seperation the immersion of the sep funnel into a sonicator decreased the time it took for the seperation of the phases to complete. Definatly not what I was planning on doing but never the less a good find for a lab rat.

I am not sure what kind of mistakes these people hope to make but I think trying to make prion polymers is not the way to go about it. That sounds too "mad scientist" for me. I want them to find a cure for this.

The problem with the radical prions is that they form beta bonds instead of alpha bonds. If you know anything about sugar and protein you will know that beta bonds or beta pleated sheet proteins are the proteins in your muscles and and are what give them strength. Also a common beta bonded sugar we all know is cellulose which is what gives paper its strength as also wood. Alpha bonded sugar would be sucrose which is broken easily.

Back to proteins...

What happens in the brain, is that these radical proteins are forming essentially muscle like fiber in the brain. Which when get large enough form cavities in which I think the amygdoloid plaques grow. In the end I think it is a good place for mold and fungus replication. I have seen pictures of people with huge spots of fungus growth in the brain where the growth was the size of a marble. ICK to say the least. I have come to find that there are fungal infections in the intestines that cause whole proteins or large sections anyway to enter own blood stream and this is a problem. Proteins are not supposed to enter our blood stream as a whole but be comletely broken down into the essential amino acids. You see the fungus opens up its own channels in the intestines directly into the blood stream through which larger proteins enter. Maybe that could be some of the casue right there. It is known that first one must injest this radical prion to get it started. But once there it can take other non radical prions which are natural in our bodies of course and form the radical ones from them. Not sure how but it happens.

I don't do any folding or seti type of distibuted computing for anyone and would really like to know what in tarnation they are doing. You can suger coat anything enough to make it sound good but take a few licks and it could be bitter as vinegar. If in fact there main end goal is to find a cure for prion related diseases then it is fine but otherwise once again I am not going to take part in anything that is just someone throughing a bunch of crap together to see what they can make.

I have though about emailing Stanford my self but maybe someone else would like to make the effort. Iam too busy;)

[Ploaf]

Ol' man

What you may want to do is ask in the Yahoo Folding2 group. Vijay loves these kind of questions since it's his field of expertise, and you may get the answer you are looking for. It seems to me that you are the most qualified to ask this question of them. If you don't want to join the group or ask them then I, or somebody else here, could post your question, either one, in the group and see what they say.

[ol' man]

Forgot to add that my professor compared these proteins in the brain to the protein silk which as you know comes from the silk worm. I guess they have close to the same structure. His definition was that they are proteins in a spiral helix with methyl groups pointing out which account for it lipophilicity.

[Ebola]

Originally posted by kendan
I believe the next set of proteins that we are going to be working on directly relate to alzheimers.

I've been folding for about 8 months now and I have folded several alzheimers (or however you spell it) proteins.

[ol' man]

Originally posted by Ebola


I've been folding for about 8 months now and I have folded several alzheimers (or however you spell it) proteins.

How do you know it was a alzheimers related protein. All I see is that on the side it says either villin or native villin and at the top it says "Stanford Alzheimers and Amydloidogenic Disease Research Program." Where do you find out what exactely this protein is.

[Ploaf]

A lot of the information is duplicated between the old and the new F@H sites, but there seems to be more in the old site. There are 2 Yahoo groups. The Yahoo group for Folding1 seems to contain more of the type of information that you are looking for.
Here are some links.
There are some articles they are doing here -
http://www.stanford.edu/group/pandegroup/papers.html

http://folding.stanford.edu/papers.html

http://www.stanford.edu/group/pandegroup/Cosm/ - This link is for the old page. If you scroll down you'll see some published results, although most of it was a test of the scientific method.

I don't remember folding the Alzheimer protein but haven't been doing it quite as long. Vijay posted a message in the Yahoo 2 group stating that the next protein is directly related to Alzheimers.

[Ebola]

Originally posted by ol' man


How do you know it was a alzheimers related protein. All I see is that on the side it says either villin or native villin and at the top it says "Stanford Alzheimers and Amydloidogenic Disease Research Program." Where do you find out what exactely this protein is.

You know how the current proteins are called villins. well these were called Alzheimers.

villin
l
l
l
l
V

[lennytiger]

I got one called AlzheimerB42xx something like that, thats the only thing it ells you what i would like to see is more information on each protein in the f@h program.

[ol' man]

Originally posted by lennytiger
I got one called AlzheimerB42xx something like that, thats the only thing it ells you what i would like to see is more information on each protein in the f@h program.

Yeah I would too. I got 3 wu's under my belt and a 4th one half ways done. I can do one every 9 hours. How is this on average? Faster or slower?

[Ploaf]

It depends on the speed of your processor. I'm at 1.4 (amd) and did 55/100 frames villin in 4:20 so far.

[lennytiger]

My 1.2 does about 100Frames of vilin 22:50secs, thats when I'm doing something on the comp tho...

[Ploaf]

I've been having problems on and off the last few days with things locking up, etc. Thought it was something I had installed. Anyway. I noticed last night that it was getting really hot sitting at my desk. The hot air from the furnace was blowing all the way across the room right at this PC. Checked the temps and was hitting 53C ..argh. Closed the register until a solution can be found, but I think it was affecting my times and causing the client to slow down. :( Lapping the heatsink had helped some, but the furnace ran more last night than it had previously because it was much colder.

[lennytiger]

I just got my desktop back from the ship, (I moved to south africa recently) and found that with the delta the whole machine vibrates the shippers must have knocked it or something and its disslodged the fan... the temps aren't affected tho

[Ploaf]

Originally posted by lennytiger
I just got my desktop back from the ship, (I moved to south africa recently) and found that with the delta the whole machine vibrates the shippers must have knocked it or something and its disslodged the fan... the temps aren't affected tho

Big Ouch. Glad it's still working.

[lennytiger]

well now the temp is 52C Full load they must have dislodged the hsf or something!! DAMN!!

[ThePunkGeek]

Originally posted by Ploaf
It depends on the speed of your processor. I'm at 1.4 (amd) and did 55/100 frames villin in 4:20 so far.

is that 22 min or hours?

[Ploaf]

Originally posted by ThePunkGeek


is that 22 min or hours?

I had to think for a minute :) It was 4 hours 20 minutes.