1 reply [Last post]
Joined: 08/24/2010

From it's inception foldit has accomplished many things. A fellow player wanted to know what these advancements were. Here is that conversation, at a glance:



Real Science or just another Video Game ?

Case number: 699969-989556
Topic: General
Opened by: itskimo
Status: Resolved
Assigned: zoran
Priority: 1-High
Type: Question
Opened on: Friday, April 15, 2011 - 11:38
Last modified: Monday, April 18, 2011 - 19:33

somehow when i started Foldit i thought it had something to do with solving science problums. I was wrong. Guide puzzles are not science, they already have the guide. de novo puzzles are not science, spegetti solutions have no value to science. interface puzzles are usualy just frustrating, so where is the science?

If all these puzzles are suppose to teach us how to fold why are there no advanced tutorials?

If this is realy for Science, what and where is the feedback on what we have done to advance the science of Foldit? what original solution in the past 6 months has made a contrabution to science. I for one would like to know what it was and where is it?

(Fri, 04/15/2011 - 11:38  |  5 comments)




Joined: 08/24/2010
Send private message

whoa kimo kimo calm down :)

1. Advanced tutorials will eventually be developed for the wikis

2. they think chaperones may use a "fusing" technology in combination with friction (heat) to aid protein folding

3. molecular weight is vital in structure prediction

..the breakthroughs are coming :)

B_2's picture
User offline. Last seen 26 min 38 sec ago.
Offline
Joined: 11/29/2008
Groups: Go Science
Send private message
Add buddy

None of which seems to answer the OP's question.

1. Wikis are useless - people won't read wikis, the tutorials need to be hands on, interactive, with very detailed and non-biologist-understandable explanations of exactly WHY we should be doing what is being demonstrated. The current alignment and exploration tutorials are good examples of useless tutorials, since they do not explain nearly enough in plain language what we're supposed to do and WHY. They may explain the mechanics of using the tool, but that's it.

2. What's a "chaperone" in this context?

3. Huh? Molecular weight? Never heard that term associated with foldit so far.

Kimo is correct - without proper context and feedback, what we are doing is simply a video game for the highest scores, regardless of whether what we're producing makes sense.

vixynn's picture
User offline. Last seen 1 hour 4 min ago.
Offline
Joined: 03/26/2011
Groups: None
Send private message
Add buddy

I wasnt aware that ALL the puzzles were to teach us how to fold.

My understanding was that it was up to us to find ways of doing things and achieving outcomes that may..or may not.. benefit some part of the scientific community with respect to how proteins can be manipulated etc

Unless you are a highly qualified scientist, then you cannot state whether the de novo puzzles or spaghetti structures have any intrinsic value or not.

As for being frustrating, it isnt meant to be easy.

Why does there need to be advanced tutorials?..who is going to do them?. What are these advanced tutorials for?

What kind of science are you wanting?

Yes, more feedback on a more regular basis would be helpful, on that I agree.

@Brick, the wiki is there, if people are too lazy to read it , that is their issue, noone elses.

You can lead a horse to water...you cannot make it drink.

If you guys are so dissatisfied, there is always... Farmville

Pletsch's picture
User offline. Last seen 3 hours 55 sec ago.
Offline
Joined: 04/21/2010
Send private message
Add buddy

I think maybe there is more expectation here than should be, I don't see our role to be that of amateur scientists hell bent on finding a big solution to some mysterious problem. We are more like parts in the process trying to help out to furnish large amounts of results in order to assist the research of a "real" scientist. The "work" we do here is not the role of scientific research, it's more akin to the role of scientific equipment. Because the equipment is not sophisticated enough to complete tasks quickly and return amazing results there is an opportunity for us to contribute meaningful results in a way which may help to create better machines at some point. What we are doing is essentially providing data that can be analyzed so that better computing programs can be devised to replace us at some point. I don't see this as a bad thing, only a fun source of recreation that may aid in creating useful tools someday. The chance of finding a real solution, or getting lucky and making a breakthrough are enticing, and attractive to many, but ultimately I do think it's more about the game, contributing, and seeing how people stack up vs. machines, and to allow those programming the machines to perhaps learn something about what people do differently than existing programs which may help to replace us someday. Of course the opportunity to discover something really huge is there, though I think it's an extremely slim chance, and the expectation of valid real world results is a bit out of line with the tasks which this program tackles. I may be wrong, but that's just my two cents.

The game does accomplish real science, just not in the way many people like to think imho.


zoran's picture
User offline. Last seen 30 min 27 sec ago.
Offline
Joined: 11/10/2007
Groups: Window Group
Send private message
Add buddy
Status: Open » Resolved
Assigned: Anonymous » zoran

Actually, in fact we currently have 3 papers in submission, and a number more pending. here's the summary:

1. a protein that has not been solved for 15 years has recently been resolved by foldit players and confirmed by x-ray crystalography. the paper is currently submitted to science. The group that produced the solution is on the author list.

2. analysis of macros used by fodlit players lead to a comparison of those macros against the state of the art algorithms. we found that some of the frequently used macros outperform standard proteomics algorithms, and are actually a variant of fast relax protocol that is currently not published but is known to outperform other methods. the paper is in preparation to be sent to PNAS.

3. a new enzyme has been developed AND confirmed in the lab that has improved over other known enzymes focusing on Diels-Alder reactions. In this case the scientists used the novel backbone configuration from the foldit players, and redesigned the sidechains. the paper is in preparation.

So in summary, over the 2 years of foldit life, we have both shown that foldit players can outperform known computatonal methods, discovered the structure of an unsolved protein, discovered novel automated methods for protein relaxation, and designed new proteins that are confirmed in the laboratory. I don't think any individual lab in the world could boast with these kinds of outcomes in just 2 years. Of course, i only expect us to do even greater things in the future.

So no need to lower the expectation. Foldit player should be proud of what they have accomplished. In my view, the most important outcome of this game is that we may have tripled of quadrupled the numer of world experts in protein science in two years.

Joined: 06/17/2010
Blog post about all that:
Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons