an accidental click -- what the Vleeptron CPU does when it has nothing better to do

Clicking -- probably a good idea.

This is a model of the Folding@Home update window
which just appeared on my screen. The F@H project
recognizes my PC as belonging to Elmer Elevator, of the
Yankee Magnetic Software team. The window shows
the molecule my PC is computing.

The top diagram, from F@H, illustrates the process of protein folding and protein synthesis.

I just clicked on something accidentally and Lo! up popped a very elaborate What's Happenin window all about the Folding@Home distributed computing thingie I shoved into the bowels of my PC maybe 3 years ago, and haven't had to think about since.

For all I know, that software could have been running a high-stakes strip-poker game in my CPU for three years.

But this fancy-schmantzy window claims that the Folding@Home software I've been hosting is steaming ahead, using my CPU, to solve the fundamental mystery of Protein p2095.

It's fairly easy these days (dictionary definition 12g. of "easy") to know the precise nucleotide sequence of this protein's precursor strand of RNA. It might, for example, look much like this:

CUUAGACCCCAGUCAGUUA

but probably a lot longer, maybe 400 or maybe 4000 letters. I'm not a professional Protein RNA Biochemical Analyst. It's just a hobby with me.

(Amy could help me out a lot here if she were Kind.)

Our full and precise knowledge of the RNA sequence is, sadly, pretty useless for understanding what Protein p2095 does inside a living thing (maybe a living human thing, maybe an asparagus). RNA and its precursor, DNA, are marvels of functional, simple, straightforward, compact, nearly errorless information storage and copying. RNA is a long 1-dimensional string containing only four possible beads, or nucleotides: Cytosine, Guanine, Adenine and Uracil. (In DNA, it's Thymine rather than Uracil.)

Don't get bored yet, don't turn that dial.

My computer has apparently not been playing strip poker or surfing for molecule porn, but has spent the last three years computing the biochemical intimacies of:

Alzheimer's Disease
Cancer
Huntington's Disease
Osteogenesis Imperfecta
Parkinson's Disease
Ribosome & antibiotics

(The action of almost all antibiotics is to slow protein production in the Ribosome.)

In a recent post, I mentioned Woltman's Inequality:

5000 PCs > 1 Supercomputer

and that's what's going on here. My PC is linked via the Internet to about 200,000 other PCs all over the fucking planet, all of whose owners have likewise agreed to let the Folding@Home software use their PC's Spare Thinking Time (that's most of the time most PCs are powered up).

Most of the time your PC is doing essentially Nothing, waiting for its Owner to make some trivial computational demand, which it executes, and 0.0031 seconds later your PC goes back to Doing Nothing again.

George Woltman was the first to figure out how to harness the Doing Nothing Time of thousands of computers simultaneously, to solve Very Difficult Computational Problems. This is Distributed Computing. It rawks.

As Distributed Computing's first challenge, Woltman chose what was commonly reckoned as about the most stubborn, intractable, difficult problem in all mathematics: How to determine if some huge Integer is or isn't a Prime Number.

The tools are perfectly known and most are very simple, and can verify that 56565656565661 is Prime and 56565656565663 is Not Prime in fairly short order on an ordinary computer.

Short order stretches to hours, days, months, years -- on the world's most powerful computers -- as the Integer grows far larger. Mathematically, a few Wonderful Shortcuts have been discovered during the last 150 years. The Wonderful Shortcuts have shrunk the year of computing to 11 months, ten years to a mere nine years. This is a violently intractable and frustrating problem.

Woltman's G.I.M.P.S. -- the Great Internet Mersenne Prime Search -- has now barfed out perhaps a dozen ever larger Largest Prime Numbers Ever Discovered [most recently (2^30,402,457) - 1 on 15 December 2005] using thousands of ordinary PCs from all over the world interconnected via the Internet and working on these problems simultaneously, in coordinated harmony. Each Big Problem is carved into a gazillion Small Problems, and as soon as my PC finished computing one Small Problem, G.I.M.P.S. sent it another.

Seti@Home sends snatches of Radio Stuff From Deep Space to thousands of PCs, where the parasite software analyses the Stuff to find a Message From An Extraterrestrial Sentient Entity. Something or Someone Smart Out There sending messages to our part of the Melkweg.

When the first Sentient Message is finally discovered -- we may have a hard time understanding it, but it will reek of Order and Non-Randomness and a Logical Structure, it will reek of being Tremendously Un-natural -- the actual Physical Locus of Discovery will be inside some ordinary grrrl's or ordinary dude's ordinary PC, because two or three years ago the PC owner downloaded Seti@Home.

I used to run G.I.M.P.S. But now my work with vast Primes is done.

I have moved on to solving the Mystery of Protein Folding.

When it's time to manufacture a Protein, the RNA sequence acts as an Information Template, and in less than a minute assembles a precise complement chain of Amino Acids (any of a possible 20), and this chain suddenly springs into a 3-Dimensional macromolecule with a fantastically complex and irregular shape called a Protein. (Like the illustration at the top.)

The Protein's irregular shape is the Business End of Life. Other biomolecules float around and bump up against the Protein, and when a highly specific Key surface floats into contact with its complement Lock surface, catalysis happens, and that sucker starts chemically pumping out another important biochemical. Other uses for a protein's specific 3D shape include the protein's function as a transport for other molecules to various locations around a living organism (e.g., hæmoglobin, which carries oxygen to all the tissues of all red-blooded animals).

How does the long and structurally trivial 1-Dimensional string of beads become a fantastically irregularly-shaped 3-Dimensional Protein? How does the folding take place? By what Laws?

More inspirationally: Given a particular RNA sequence, can we precisely Predict the final (Tertiary) shape of its Product Protein? (When we can, this should in theory allow us to design pretty much any useful biochemical we want.)

We know all the Laws. They're the simple electrochemical bonds we had to pass a test on in high school or college Chemistry. And one or two others you don't learn until 201 or 301, like the Van der Waals bond. But the handful of reasonably simple Laws have been perfectly understood for a half-century or more.

But (like the Prime Factoring Problem) when the RNA sequence becomes long, and the product protein is consequently very large (this is measured in Daltons or kiloDaltons -- a Dalton is the equivalent mass of one hydrogen atom), computing the simultaneous mutual effects of the handful of Laws on hundreds of atoms becomes a monster of computation. The problem has traditionally been viewed as insoluble, not because things are unknown, but because there are gazillions of Small Known Things all influencing all the other Small Known Things.

In planetary astronomy, using Newton's classical laws of gravitational attraction, the n-Body Problem is comparable -- understood, but beyond human or machine power to compute. The mutual motions of two or three massive bodies are computable, but as the number of planets and moons in the mutual system increases -- our Solar System has one Sun, nine (uhhh, maybe ten) planets and dozens of moons, all influencing each other -- the computations required become vast and unwieldy.

~ ~ ~

Enough for now, I'm a bit exhausted. Are you interested in this? There's more. F@H has apparently already made many significant discoveries in molecular biology, one of them involving HIV Integrase -- the molecular mechanism by which the virus HIV, a primitive protein creature, inserts itself into the genetic machinery of human beings. Leave A Comment.

At the Folding@Home website is a world map which has colored dots which represent the approximately 200,000 CPUs around the world devoted to Folding@Home. Some big dots, typically in cities in North America, Europe and East Asia, represent clusters of hundreds or thousands of devoted PCs.

There are two dots in Iran. The dot in Tehran represents a single PC, the other, apparently in Mashhad, where the big university is, represents from 2 to 5 PCs working on F@H. So at this moment there are as many as six Iranians whose PCs are working on F@H. For a few people on Earth, finding the answer to this fundamental Mystery of Life at the biochemical level transcends political, religious, cultural and ideological differences. Our computers have serious work to do when we're not using them to buy and sell tchatchke on e-Bay.

Here is the Folding@Home introductory page in Farsi. It will be a Computer Miracle if it displays on Vleeptron.

~ ~ ~

پروتئین ها و بیماریهای ناشی از آن

پروتئین چیست و دلیل تاخوردگی آن چیست؟ پروتئین ها کارگران زیستی هستند — یا به عبارتی "ماشینهای ریز". قبل از اینکه پروتئین ها اعمال بیوشیمیایی خود را انجام دهند، باید خود را سرهم نموده و یا دچار "تاخوردگی" شوند. با وجود نقش اصلی و اساسی در زیست شناسی، روند تاخوردگی پروتئین ها به صورت یک راز باقی مانده است. بنابراین جای تعجب نیست زمانیکه پروتئین ها به طور صحیح تا نمی خورند (بدتاخوردن)، سبب ایجاد اثرات جدی شامل بسیاری از بیماری های آشنا مثل آلزایمر، جنون گاوی، CJD، ALS و پارکینسون می گردند.

Folding@Home چه کاری انجام می دهد؟ Folding@Home یک طرح محاسبه توزیعی (Distributed Computing) می باشد که تاخوردگی پروتئین، بدتاخوردن، تهاجم و بیماریهای ناشی از آن را مورد مطالعه قرار میدهد. ما از روشهای محاسباتی جدید و محاسبه توزیعی بسیار گسترده استفاده می کنیم تا مقیاس زمانی معادل هزاران تا میلیونها برابر طولانی تر از آنچه در گذشته قابل دستیابی بود را شبیه سازی نماییم. این به ما اجازه داد تا برای اولین بار تاخوردگی پروتئین را شبیه سازی کنیم و هم اکنون روش خود را برای بررسی بیماریهای ناشی از تاخوردگی به کار گیریم.

نتایج حاصل از شیبه سازی ویلین با استفاده از Folding@Home

چگونه می توانید کمک کنید؟ شما می توانید به طرح ما از طریق دانلود و اجرای نرم افزار ما کمک کنید. الگوریتمهای ما طوری طراحی شده اند که با اضافه شدن هر کامپیوتر به طرح، افزایش سرعت شبیه سازی متناسب را بدست خواهیم آورد.

همچنین می توانید با اهدا وجه از طریق دانشگاه استنفورد به این طرح کمک کنید.

تابحال چقدر پیش رفته ایم؟ ما موفقیت های بسیاری داشته ایم که شما می توانید در مورد آنها در صفحه علمی، بخش نتایج بخوانید و یا مستقیم به صفحات انتشارات و مقالات بروید.


از 1 اکتبر 2000، بیش از 500.000 CPU در سراسر جهان در Folding@Home شرکت کرده اند. هر CPU اضافی توان ما را در اجرا افزایش می دهد که به ما امکان می دهد از عهده مشکلات سخت تر بر آمده و یا این تحقیق را سریعتر و دقیق تر به انجام برسانیم.

می خواهید که بیشتر بدانید؟ جهت دانلود یا اطلاعات بیشتر برروی لینک های طرف چپ کلیک کنید. همچنین شما می توانید خلاصه ای از جانب ما را دانلود کنید که به صورت PDF بوده و برای توزیع مناسب است.