Hi Everyone

My background is in biology and 3D animation/art, and my work generally combines the two-- mostly I have worked on biology educational outreach projects.

I have been communicating with David Baker over the last couple of weeks about the possibility of producing a series of animations and video footage that would bring more users to the project as well as explain the science behind Rosetta to new users. These videos would be on the website and could also be used for general publicity such as news spots, promo dvds, educational resource for schools, etc.

We would like to flesh out our concepts for this project with help from the users on this board.

Basically we were thinking of four major animations or videos

1. The biology of protein folding and the protein folding problem, with narration.

2. Footage of the Rosetta Team explaining the science behind Rosetta

3. An animated diagram of the boinc screensaver graphics explaining all of the different aspects

4. An explanatory video on how to actually install Rosetta

I have been working on an animation that is a contextual intro to the biology behind the project-- basically, the central dogma of biology. I'll probably use it in some form in the first animation; the science of protein folding. There are 4 parts to it, the last two of which are extremely rough. The final animation I am envisioning will be much more streamlined and directed (probably less emphasis on transcription/translation and definitely more in depth on protein folding- the actual protein folding section is just a placeholder). The animation details DNA->RNA (transcription) RNA-->protein (translation) and then the protein folding placeholder + experimental rosetta animation.

Intro to Folding Animation

I think that generally it would be useful to hear what you all think the major topics are that should be addressed in the Baker Lab video footage. Basically, help us come up with a set of interview questions and general concepts that would be useful to new users and other laypersons. Also, we could use some help with developing simple installation instructions that could possibly be turned into a video. I know that there are other threads similar to this one, but I'd like to kind of refocus the conversation to this one option for expanding usership.

Any input would be appreciated!

I'll expand upon this thread as well as my ideas progress. Let me know if you want clarification on anything.

Thanks
-Laura Gonzalez

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nice, really nice

Great! Sounds like you've got JUST the skills that will be needed for some of the major promotional ideas that have been bouncing around. Good to have you on the task!

I too have been working on the question of how to express something so abstract as atomic level folding. When reading the thread that started by Dr. Baker on the specific diseases they are studying and how they are hoping to cure them, it morphed into a discussion of how HIV works, and why it is an especially difficult target.

I feel that an animation that's less scientific, and more, almost, cartoonish might have some merit (in addition to those you are describing). Perhaps as an intro. to the science stuff. I picture this rough "script"...

{setting... battlefield, virus vs. immune system}

{immune scout:} "HQ, we've got an invasion force here."

{scene: field, line of viruses holding shields}

{HQ:} "What do ya need down there to handle it?"

{scout zooms in too much into one virus shield and sees a narrow verticle hole}

{scout:} "Send in the sharpshooters. The enemy has narrow verticle holes that we can penetrate."

{scene: large numbers of specialized immune cells arrive on the front line the following day, they take aim and look through there scopes}

{Specialized immune cell:} "I thought they said these things had narrow verticle holes"

{scene: back to virus forces, 1% of them still have narrow verticle holes in their shields and fall dead on the battlefield. The virus march continues.}

{HQ:} "What's goin' on down there? What's the hold up?"

{scout:} "The enemy has illuded us Sir." (he again zooms in to one virus shield) "Send in the sharpshooters. The enemy has holes in their shields shaped like triangles."
...new specialized troops arrive (different color), again 1% success rate, show the shields morphing to change shape of holes and patch them up.

{narrator:} "Without some NEW approach, the body continues to send sharpshooters and cannot win the battle against HIV. The vaccine we are working on will allow that scout to call in the trip line troops. Hit HIV in the feet, it's true weakness. This will wipe out 99% of them rather than 1%. Those that remain have no feet, and cannot continue the advance. The enemy is defeated. ...let's take a look at how a virus works, and see how they can be defeated..."

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Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

A post on the WCG points out:

I have had more success on recruiting by explaining to people the LIFE they SAVE might be their OWN or someone they LOVE or care about. I tell them this program attacks HIV...that it is like finding a key to a lock...a weakness...seems most people tend to need to be shown the light and realize they have a personal stake or interest in it as we are SELFISH driven creatures mostly.

I wanted to post that here in hopes that you can incorporate that "make it personal" idea in to the work you produce.

I think the timeline is important to. That we're probably going to have this work done in time for my own retirement years, and MAY have a cure for cancer before my father knows he needs one.

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Hello All,

One thing that has tripped me up many times in my recruitment efforts is the use of jargon. Amazingly enough, people want things explained to them on what amounts to a 9th grade level. The use of anything more technical is a real turn-off.

So there lies another challenge. To translate what is going on here to very simple plain english. The analogy of the explorers jumping out of airplanes looking for the dead sea. That was used a while back was excellent.

I used this device many times in my own efforts to explain things with much success.


Ciao all.......

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Oh WOW! You've really come a long way over what was originally posted there. Others, please take a second look and offer comments.

I just looked at it again. Takes FOREVER to download (warning to other reviewers, not criticism as download won't be the most common way this message gets delivered I don't think).

I like the way you show the natural processes, and then relate Rosetta back to that natural process. Do you have a draft of a narration for it?

For video #4, installing Rosetta, might I suggest the footage be of a 10-12 year old... conveys that it's not hard. And perhaps would be related to by the teens we've been talking about targetting to help crunch Rosetta.

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Hi, thanks!

I really like the idea of using a 10-12 yr old for the installation tutorial, we'll see if that is possible.

Did you mean that the video takes forever to download? It should be streaming and start playing pretty much immediately. I can make a smaller version and put up a link so you can right click and download that way if people want.

I'm trying to put together a draft narration as well as what topics should be covered in the interviews with the Rosetta team. I should have something to show in a day or two.

Yeah, so, basically that is the idea behind the animations, to give people a sense of the biological context of the project. My philosophy is, seeing is understanding. This takes care of the problem of jargon-laden explanations. The final animation will probably have some simple text labels (like DNA will be labeled and the ribosome will be labeled) and then a simple guiding narration. Then, in the interview section, we can have some of the standard analogies that explain Rosetta and possibly more in depth scientific explanation of the project.

I'll update soon.

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Perhaps you can work some stills from this animation into the interviews. I mean as the interview answers lead to references you've made in this first video, you could bring up a still of that "concept" during their answer. This would further help correlate terms and concepts.

I for one would LOVE to see an animation that goes down to the atomic level, where these degrees of freedom are driving us nuts. I want to see why it can take so many shapes.

I realize noone's really offered up any interview questions, so let me take a stab... I know some of the answers, but feel they should be included in your video explaination. So, please, no comments here with answers. She asked for suggestions for interview questions.

1) Everyone KNOWS that "protein gets OUT protein", and can destroy a virus... so what makes your project new and scientifically significant?

2) Why does it take SO MUCH computing time to solve the problem?

3) Do you think Rosetta will really be used to devise treatments for disease in our lifetimes?

4) Who owns the computer models you are developing?

5) Why do other scientists feel that other approaches to devising treatments will work? Are you both right somehow?

6) If you can use X-ray crystilography to determine the ACTUAL structure of the proteins, then why don't you just do that?

7) If the sequence of amino acids is known, why is it so hard to determine shape?

8) What if your technology falls in to the "wrong hands"? Could this same technology be used to devise viruses?

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Larelin,

It was beautiful... better than some of the animations I've seen elsewhere online. One thing I noticed, though was that during the translation sequence, you can't see the amino acids being added very well. I knew what to expect and had trouble finding them right away. Maybe if the camera angle was on the other side of the ribosome, so you could more clearly see the aa chain growing, it would be a little more understandable??

Of course, this comes from someone whose stick people are barely recognisable...

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Take a look inside my brain

I was going to do a kind of segue animation between translation and the protein folding section that gave a quick overview of amino acids, their properties, and peptide bond formation... basically I would zoom into the ribosome (or have a box highlighting that site on the ribosome and then fade the ribosome out to show the amino acids and tRNAs more) to see this happening up close. I was planning on the protein folding segment having more to do with the interactions on the atomic level, degrees of freedom and bond rotation etc. What is there now is a placeholder.

As far as splicing stills into the footage of the Rosetta team, good idea... I was thinking of having several different video formats available-- like, you could view the 4 seperate items on the website but also there will be a kind of documentary-style overview of the project that will have the first 3 items edited together- for general publicity, a trailer of sorts.

Anyway, feet1st- thank you for the interview questions, they are great! I'll compile a list of them as well as an outline of what will be included in the narration. I want to make a simple narration that will augment the 1st animation but I also want to make it so that the animation can be viewed and understood without sound. Still workin on that...

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Another interview topic for you. I was discussing the subject with a friend at lunch today, and explained how once we understand how the protein folds, then "game over", we can create another protein that fits in all the right places and knock it out... ok it's not quite that simple, and ya still have ta figure out how to produce and deliver that protein, but his response was "so 'they' claim". So this leads me to the question:

9) Once the computer model accurately finds the native state of the protein, how do you know you'll be able to make a vaccine for bird flu? Or SARS? Or anthrax or whatever the malidy that requires a treatment?

I think the answer is something to the effect of "this is what medical science has been doing for centuries, they just found treatments via other, more difficult and error prone means". But perhaps some "proof" of what "they claim" could be delivered in the response.

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I think it is best explained by telling these people that this is the basic way that we can understand these diseases. These are the fundamental structures that we must understand in order to eventually conquest them. Other than than that I am not sure what your concern is..

(I'm quite happy you have made good headway with my 'tell a friend' idea)

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Founder of BOINC GROUP - Objectivists - Philosophically minded rational data crunchers.

These are the fundamental structures that we must understand in order to eventually conquest them.

I'm hoping for a definitive statement about how the treatments work against disease. Something I could bring back to my friend as incontestable evidence that once this (the disease's protein native state) is known, then that (a cure) can be done. His "that's what 'they' say" retort makes me feel he believes that statement about as much as he trusts his government to represent his best interests. So, if it is possible to relate the process back to how the small pox vaccine works, or how penicyline (sp?) works or something that's well known and understood by people, that would be helpful. Then you could just say "ya, it's the same way that's been working for 150 years".

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I totally agree, feet1st.

We need an easy to understand example of the benefits, just as a marketing tool.
Can any of you guys come up with something my mum could understand (she's not a biologist, nor a computer scientist, and she's turning 70 :o) ) ?

Vulgarizing the work done could really help our cause by smashing the first doubts and reticences.

Or maybe one of us is a marketing or PR expert? :)

- Trib'

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The explanation that was written about at other places is that normal searches for cures go along the lines of noticing that people that eat lots of garlic are less prone to catching a particular ailment. The claim is tested. Then they examine garlic and try to find just the one compound in garlic that keeps people from catching the ailment.

A.
They test each of the compounds against the ailment; and if they're lucky, they find the magic compound. (And it didn't turn out that the reason they didn't catch the ailment was that they reeked so bad, the infected people stayed away from them.. )

If they didn't know of something like garlic that had been linked to not catching the ailment.. then they have millions of compounds to test against, and they may somehow run through enough tests to randomly find a compound or two that show promise against the ailment in question. Testing time for this stage is measured in years.. to never if the research is too expensive.

B.
Once you have a collection of compounds that show promise with anti-ailment properties, they move on to studies for effectiveness, and then to animal based testing, and then to human studies (which take years.)

What we're doing is helping develope a better way to eliminate most of Step A. The Rosetta client will be able to be used by DC projects targetting specific ailments (Cancer, HIV, Aids (if HIV ends up being a symptom, not the cause of Aids), Malaria, your favorite genetic disease, or the latest forms of bird flu, etc.) Once enough information is known about how a particular ailment spreads, is caught, or damages its human host, then a DC project can spring up to use the Rosetta client to find compounds that will block the way it spreads, protect against it being caught, or keep it from causing damage to the human host. It chops years off of step A.. or makes getting through step A even possible.

Unfortunately, we then go back to Step B.. and have to wait through the various stages of trials before it's pronounced safe for human use. (And hopefully, it's actually been proven safe.. as a number of USDA approved drugs weren't safe.)

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All you need is good salesmanship....it's frustrating..

If I make a bit of time I'll see what I can do. No promises.

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Founder of BOINC GROUP - Objectivists - Philosophically minded rational data crunchers.

I totally agree, feet1st.

We need an easy to understand example of the benefits, just as a marketing tool.
Can any of you guys come up with something my mum could understand (she's not a biologist, nor a computer scientist, and she's turning 70 :o) ) ?

Vulgarizing the work done could really help our cause by smashing the first doubts and reticences.

Or maybe one of us is a marketing or PR expert? :)

- Trib'

Let's try this one....and it's simplistic but that is what you are asking for. I can provide a couple of others using different metaphors later if needed. Please don't flame me too much...but criticism is ALWAYS welcome. Remember, this is SUPPOSED to be simplified.

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"People's bodies are made up of cells. These cells are comprised of proteins and amino acids which make up proteins. Without these proteins our cells would not be alive and therefore we would not be able to live! Neither would fish, frogs, alligators, or even dinosaurs!

All of these proteins fit together to make a 'jigsaw puzzle' in living things....like you!

If we can figure out how they fit together properly and in the right way we can help stop diseases that affect us. The problem is there are just too many jigsaw pieces out there! Soooo...

Rosetta tries to solve this by looking at many of these proteins with computers! Rosetta tries to solve the big jigsaw puzzle. The Rosetta project tries to put alot of these puzzle pieces together to make the 'big picture'...

It is just one big jigsaw puzzle! And your computer helps!

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Founder of BOINC GROUP - Objectivists - Philosophically minded rational data crunchers.

I totally agree, feet1st.

We need an easy to understand example of the benefits, just as a marketing tool.
Can any of you guys come up with something my mum could understand (she's not a biologist, nor a computer scientist, and she's turning 70 :o) ) ?

Vulgarizing the work done could really help our cause by smashing the first doubts and reticences.

Or maybe one of us is a marketing or PR expert? :)

- Trib'

Tribaal? As an unscientific experiment would you let your mum read what I posted above and see if that makes sense to her? Input most welcome after, please....
[edit---scientists/developers/ if my simplification is too off base then tell me. No offense taken.]

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Founder of BOINC GROUP - Objectivists - Philosophically minded rational data crunchers.

People's bodies are made up of cells. These cells are comprised of proteins and amino acids which make up proteins.

...I'm afraid you lost many people right there. I don't think it passes the "mum" test.

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Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
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Uh oh....I'll redo it and fix it...thanks.

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Founder of BOINC GROUP - Objectivists - Philosophically minded rational data crunchers.