Rosetta video/outreach project

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Profile Dimitris Hatzopoulos

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Message 16114 - Posted: 12 May 2006, 23:20:13 UTC
Last modified: 12 May 2006, 23:54:44 UTC

I watched it a couple of times and here is some feedback:

1/ You should explain project significance and medical relevance ( E.g. "-David Baker- mutations in proteins cause disease") in layman's terms early in the video. Perhaps mention that proteome is the natural next step after decoding the Human Genome. Also mention some diseases worked on by name cancer, AIDS, malaria (with Bill's piece elaborating on HIV)

2/ Give some idea of the technology / computational aspect, BOINC, the server(s), the 500-node Linux cluster etc and how work in R@H flows. This is where most volunteers get "involved" personally.

3/ People should try to talk slower, in particular if one has a little accent (i.e. English isn't their native language) and look a bit into the camera once in a while :-)

4/ Certainly a pic of the whole team in the end
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Message 16136 - Posted: 13 May 2006, 4:15:39 UTC - in response to Message 16085.  

-David Baker- elevation analogy

I like the elevation analogy a lot - however, minor correction, Jupiter is a socalled "gas giant", and a such does not have a surface one can parachute down to. ;-) See here.
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Message 16143 - Posted: 13 May 2006, 6:10:55 UTC

Well, It is hard to offer critical commentary with some tact but I will try. I shoot and edit a lot of video myself, so rather than focus on the content let me discuss the video itself.

While I like the backdrop you selected and the informality of the speakers, you need to have some front lighting with that much backlight.

The audio suffers from echo in the room, but you can take some of that out in post, enough to be acceptable. this would not be as big an issue if the speech was slower, but you are almost better off not trying to direct inexperienced talent too much.

While I prefer the wide screen format you have selected, having the subject off center may be an issue for multi-purposing the final video. This will not be a big problem so long as it is kept in a web or computer based medium, but you are really close to the safe action limits on some shots. While I did not check the Safe title for your titles some of them may be a problem on an NTSC monitor.

Video quality looks good, and you mpg looks good as well. I assume you are shooting in DVcam, or DVCPRo and running direct digital to the edit suite which would account for the quality. Your mpg codex works well too.

Just out of curiosity what edit platform are you using (AVID, Final Cut, Premier, other)? Do you plan on putting this out on a DVD as well?

Regards
Phil

PS - Jupiter really is a gas giant. People trying to land there will all meet near the middle as a crushed pool of proteins, amino acids and DNA.

We Must look for intelligent life on other planets as,
it is becoming increasingly apparent we will not find any on our own.
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Message 16148 - Posted: 13 May 2006, 9:15:45 UTC - in response to Message 16143.  
Last modified: 13 May 2006, 9:53:06 UTC

Yeah, this is a very rough edit, as I mentioned :) I am mostly looking for a critique of the content/order. The sound has not been edited at all. The segments suffering from excessive backlighting will be fixed. I use Vegas Video, my editing program of choice for the last 3-4 yrs. Everything is within the safe action/safe title area (actually playing around with cropping with this edit so all of the footage is actually well within safe action) and the final output will be of professional quality. We are planning on making a promo DVD, along with streaming mpeg and perhaps a mov as well on the rosetta@home website.

p.s Yes, Jupiter is a gas giant, we have been planning on re-shooting David's analogy to say "a planet the size of jupiter" or "a large planet." Sorry, should have clarified that in the original post. Any suggestions on shorthand for "a large planet" that brings to mind an immediate mental picture besides "jupiter"?







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Message 16161 - Posted: 13 May 2006, 14:32:06 UTC

I tried to watch the graphic. I took forever to download, and when I played it, there was no sound, looked nice though. I suspect this is an issue with IE7 which has more bugs then a biology lab.
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Message 16162 - Posted: 13 May 2006, 14:35:21 UTC - in response to Message 16148.  

p.s Yes, Jupiter is a gas giant, we have been planning on re-shooting David's analogy to say "a planet the size of jupiter" or "a large planet." Sorry, should have clarified that in the original post. Any suggestions on shorthand for "a large planet" that brings to mind an immediate mental picture besides "jupiter"?


Why not just use good old Earth as an example in the planet analogy?

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Message 16165 - Posted: 13 May 2006, 15:16:33 UTC - in response to Message 16162.  

p.s Yes, Jupiter is a gas giant, we have been planning on re-shooting David's analogy to say "a planet the size of jupiter" or "a large planet." Sorry, should have clarified that in the original post. Any suggestions on shorthand for "a large planet" that brings to mind an immediate mental picture besides "jupiter"?


Why not just use good old Earth as an example in the planet analogy?

Everest, Dead Sea. see Extremes on Earth

The moon, while not large, is something most people can relate to, and getting there is a big part of the problem in taking measurements, just like with a protein. The getting there part is analogous to finding the computing resources to do the search in the first place.

It is remote and untouchable, but still a big part of everyones life like a protein. Moreover all the information on topology is from remote sensing just like with proteins.

So what you get is - like the moon proteins have an effect in the lives of everyone (tides, night-light whatever), and finding the resources and applying them to search for protein structures is difficult and expensive but now we have BOINC. The search is done by use of remote sensing (our computers, electron microscopy), and the more computers we have ....

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Message 16166 - Posted: 13 May 2006, 15:17:13 UTC - in response to Message 16162.  
Last modified: 13 May 2006, 15:26:49 UTC

p.s Yes, Jupiter is a gas giant, we have been planning on re-shooting David's analogy to say "a planet the size of jupiter" or "a large planet." Sorry, should have clarified that in the original post. Any suggestions on shorthand for "a large planet" that brings to mind an immediate mental picture besides "jupiter"?


Why not just use good old Earth as an example in the planet analogy?

Everest, Dead Sea. see Extremes on Earth

Yes, why not use the example from the "lecture" (death valley vs. dead sea). Rocky planets (the ones with a surface one can stand on) larger than Earth nowadays are called super-Earths, though I think it is not clear whether super-Earths the size of Jupiter are even possible. Due to the large gravity the height of mountains would at any rate be much smaller than on Earth.
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Message 16207 - Posted: 14 May 2006, 4:11:29 UTC
Last modified: 14 May 2006, 4:20:49 UTC

So lemme get this straight... I drop a rope into a gravityless box and it falls in different ways?

I agree about the rapid speech. Anytime a new speaker is brought in to the picture, it takes you a little bit to get a feel for how they speak, what they sound like. And if they're starting right out with words you may have never heard before it makes it difficult to feel you're really getting it. So, two ways around it, and perhaps both would be best solution. Introduce the terms before the speaker uses them. And have the speaker speak with a consistent pace and not rush through "Amino acid sequence" or any of the 3 or more sylable words used to describe the science. Keep in mind MANY of the viewers will not have English as their primary language, and almost none will have heard of these scientific concepts and terms before.

I really like the point about the child that's going to come along and beat you at your own game, because they grew up and essentially absorbed and devised a way of thinking about the problem that's new and different.

I think Dr. Baker's explorers analogy might be more meaningful if he could relate it somehow back to the Rosetta calculations of low energy. I mean the analogy actually means more to HIM than to the listener. Because HE knows that when mathematically "exploring" a protein, he finds cases where things seem to be going "up hill" an then suddenly finds a huge drop that you wouldn't have expected to see. Dr. Baker sees it from ground level, like the explorer... but when we hear the analogy, we see it from the level of the airplane or spaceship that's dropping the explorers... so it doesn't convey all that's intended.

If you could leave the plane out of it, and just play through the role as a single explorer, with limited time, and you're getting discouraged with your findings, and then you make the long arduous climb to the highest peak to look around for the lowest valleys and suddenly realize there are dozens of others on peaks nearby doing the same thing. When you contact them, they tell you there are a million of us dropped on the planet. ...now things seem more hopeful! More possible/achievable!

Perhaps you can reinforce the analogy during the explaination of the graphics?
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Message 16227 - Posted: 14 May 2006, 5:45:42 UTC - in response to Message 16207.  
Last modified: 14 May 2006, 5:51:51 UTC

...I agree about the rapid speech. Anytime a new speaker is brought in to the picture, it takes you a little bit to get a feel for how they speak, what they sound like. And if they're starting right out with words you may have never heard before it makes it difficult to feel you're really getting it. ...

One way around this would be to actually introduce each speaker, and have them say a few words about themselves, where they come from, how they got into this, and where they think they may be heading in their careers. That allows the listener to tune their ear to each new presenter.

I think Dr. Baker's explorers analogy might be more meaningful if he could relate it somehow back to the Rosetta calculations of low energy. I mean the analogy actually means more to HIM than to the listener. ...

This needs to be in terms that people are familiar with. Things they have seen in their own lives. Who has not played with a pair of magnets and wondered at how they attract one way and repel the other? How many people have not seen velcro by now? How about this-

Look at this along the lines of a tinker toy or erector set, (or for the younger among you, legos).

You have a pile of 22 parts (amino acids) in a variety of unique rounded shapes that can fit together in a number of ways. These parts have velcro on them in places and inside each part are a number of magnets arranged in different ways. From these parts you can build an amazing variety of objects (proteins), creating different shapes. But there are limits. Some of the velcro areas can stick together, but in some cases the magnets inside repel the parts with so much force that they will not stay together the way you would like.

The magnets are exerting forces that push and pull the parts in different ways and put tension on the finished object (Energy). In some cases the objects you build will not stay in a shape you select because the magnets do not line up properly and are stronger than the velcro. In some cases when they are close to each other they snap together in way you do not want, and prevent the use of other parts in proper order. Sometimes the object holds its shape, but because of the forces exerted by the magnets everything is under a great deal of stress and tension (high RMSD). In other cases the object is very stable, and the tension between the parts is very low (Low RMSD).

Rosetta knows the type, order and number of the parts in an object, but not the final shape of the object. They do know that the most likely stable shape will not be under a lot of tension (low RMSD). But, it is possible that there can be more than one shape for the object that has a low energy.

So Rosetta is looking for a stable shape made from a certain number of these 22 parts, in a certain sequence, that is under the lowest possible level of stress. To do that they have to try every possible shape for the combination of parts they are looking at and measure the energy of each. They eliminate the unstable ones, the high stress ones, and pick the best possibility from what is left.

While this specific example might not work for the video, it might help someone come up with something that will.



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Message 16311 - Posted: 15 May 2006, 14:56:40 UTC

I've said once before somewhere that there is a danger in taking the explorer analogue too seriously. On Earth, and terrestrial type planets, it is unlikely that the lowest point of the planet would be in the middle of a high lying area.

This is because the forces that shape the surface of such planets are not the same as those that create the energy landscape of a protein. A protein may well have it's lowest energy point surrounded by relatively high energy configurations.

If you must use it, why not use the planet Zig, a large rocky planet orbiting Beta Pictoris or some other equally imaginary place? There is not really a suitable planet in our solar system, they are either too small, too well known, or of inappropriate type.

Nobody can claim to have prior knowledge of Zig's appearance.
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Message 16314 - Posted: 15 May 2006, 15:29:42 UTC

Thank you all for the helpful criticism. Divya and I will have to reshoot with more accurate analogies...
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Message 16335 - Posted: 15 May 2006, 19:38:22 UTC - in response to Message 16227.  
Last modified: 15 May 2006, 19:39:24 UTC

I think Dr. Baker's explorers analogy might be more meaningful if he could relate it somehow back to the Rosetta calculations of low energy. I mean the analogy actually means more to HIM than to the listener. ...

This needs to be in terms that people are familiar with. Things they have seen in their own lives.


I think the analogy will be fine in the context of the biological animations and other explanatory graphics (once it is re-filmed). Like I said, only at most 1/2 of the info that will be in the final video is actually in the interview portion. The animations will explain all about amino acids, why proteins' actual shapes are the ones that have the lowest energies, etc, etc. Plus the analogy will segue into a depiction and explanation of the screen saver.

Perhaps some of the ideas for extended scenes where the Rosetta team members tell all about themselves and give long detailed analogies can be added later as supplemental material on the website-- the video is already going to be ~8 min long when I wanted it to originally be under 5 min.
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Message 16338 - Posted: 15 May 2006, 19:54:10 UTC

I had no idea what they looked like until this video. I was picturing Dr's and Scientists as some middle aged, slightly balding, grey haired people, wearing labcoats. Out of my own selfish thoughts (something I try to work on), my first thought while watching was "I've got underwear older than these people".

LOL
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Message 16342 - Posted: 15 May 2006, 22:19:36 UTC

In defense of the paratroopers - while drifting down, they'd have a view of everywhere they could travel before their air system gave out while floating through the atmosphere. On the Earth, many/most of them would have drowned when landing in really large bodies of water that they can't swim out of in time.

It just brings to mind a quote from Bones.. "Damnit Jim.. I'm a doctor not an Astrophysicist" (Or Astrogeologist..)

While watching this video, I noticed a lot of jargon that I'm now familiar with, but many others would have problems with. How about recommending it be watched through once.. link to a dictionary of the science related terms used in the video, and have them watch the video again.

(Reading the dictionary first.. or viewing the dictionary after pausing the video and looking up the unknown phrase would be options, as well.)




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Message 16346 - Posted: 15 May 2006, 23:31:36 UTC - in response to Message 16342.  
Last modified: 16 May 2006, 4:55:27 UTC

...On the Earth, many/most of them would have drowned when landing in really large bodies of water that they can't swim out of in time.
...

At rosetta those kinds of events are "bad workunits". The ones that land in volcanos and forest fires are "bugs". But occasionally the volcanos have the lowest RMSD at the bottom.
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Message 16371 - Posted: 16 May 2006, 8:01:22 UTC

Divya and I will have to reshoot with more accurate analogies...


As an analogy, to protein newbies, it works reasonably well.

The reason I made the point I did was that people seemed to be getting hung up on the details of the analogy, and losing sight of the fact that it is just an analogy and should not be taken literally.

If you wanted to find the lowest point on a rocky world, you'd use an orbiting high resolution radar altimeter, and get the job done right in a fraction of the time.

Your homolog approach is king of like using a very low resolution radar altimeter to identify areas which may be promising to send explorers.

Hell, I'm getting hung up in the anlogy now, I'll shut up!


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Message 28558 - Posted: 26 Sep 2006, 22:38:41 UTC

OK everyone, it's been a long time coming but I have the edit done. Still working on sound-- going to re-record the voiceover, tone down background noise, and add a bit of music.

http://www.lauralynngonzalez.com/things/rosettateam/bakerSmall.mpg

Comments are welcome, things I specifically want input on are:

1. Does the script work?
2. Does my voice work for the voiceover? I'm going to re-record as I said, and it shoudl turn out a little clearer/cleaner. I may get this australian guy to do it, but I thought that having a female voice is better.
3. Do you think that the screensaver explanation should be seperate from the film?

Voiceover script:

NARRATOR

The sequence of amino acids that makes up proteins is directly determined from the genetic code, otherwise known as the sequence of molecules in DNA.

DNA, like proteins, is also made of molecular subunits with specific properties. Within the nucleus, a kind of imprint of DNA is transcribed into a similar molecule called RNA.

Carrier molecules transport amino acids to an enormous structure called a ribosome. The ribosome translates the information in RNA into a chain of amino acids.

NARRATOR

A strand of amino acids, the order of which has been determined by the genetic code, can indeed be thought of as rope- or chain-like. However, the properties of the links, in this case, amino acids, cause portions of the chain to be attracted to or repelled from one another, as well as elements in the cellular environment.

What the Rosetta program does, is calculate the likelihood of these interactions between segments of the chain based upon favorable energy levels. The most likely 3D structure of the chain will take the least amount of free energy to fold.

NARRATOR

Each work unit that your computer processes through Rosetta@home consists of what are called trajectories. The end product of each trajectory is a predicted structure for a protein.

When Rosetta is ‘searching,’ it is trying out different moves on the protein chain. It then calculates the energy and ‘accepts’ a particular move. The ‘low energy’ box keeps track of the lowest energy shapes seen so far in the trajectory. If it is know, the experimentally determined true shape of the protein is shown in the ‘native’ box. Rosetta also produces a graph which plots how close the currently accepted structure is to the native state versus the energy of each accepted move in the trajectory. All of the low energy calculations from these trajectories, calculated by your computers, are used to find the very lowest energy structure for a protein


THANKS!

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Message 28563 - Posted: 27 Sep 2006, 3:24:36 UTC
Last modified: 27 Sep 2006, 3:29:01 UTC

HURRAY!!! It's here! Can you tell us how many megabytes the movie is currently? Wondering if it will fit on the CDs that Ethan has made.

Oh, and your voice is just fine. Sounds like maybe stay a bit further from the mic when you rerecord, but I agree with all the other male voices, it is a nice contrast.
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Message 28564 - Posted: 27 Sep 2006, 3:30:16 UTC - in response to Message 28563.  

its ~60 mb right now

I'm planning on making available a high quality version. Also maybe a divx compression. Also, YouTube.
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