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Life Inside a Cell
Roland Piquepaille writes "Harvard University has decided to use animations as a tool to enhance the performance of its students in biology. And it selected XVIVO's animation studio to take Harvard University students on a 3D journey. Among other realizations, the company delivered an eight minute animation titled 'The Inner Life of the Cell,' which was presented at Siggraph 2006 in a condensed form. This extraordinary animation explores 'the mechanisms that allow a white blood cell to sense its surroundings and respond to an external stimulus.' Harvard University expects a performance improvement of its biology students of almost 30% by using such visualization tools."
Why won't they they release fucking Flash 9 for Linux? Grrrrrr
What constitutes 30% improvement when you're already giving out 90% "A"s?
A down-on-his-luck American guy having a deep philosophical discussion with two Mexican cockroaches in a jail cell south of the border. If I'm not mistaken, I think Hemingway wrote that.
I just hope they do something to make it free for school and educational use, I know a lot of science teachers who would love to integrate this into their curriculums.
*shameless plug*
The scary thing is, after playing with a proscope (http://www.proscopehr.com/) the other day, I was able to actually see the capillary action in my own finger.
Anywhere?
HAD
here
Expected time to finish is 1 hour and 60 minutes.
No, he doesn't. He just "digs stuff up" by rehashing other people's material. If he wanted to contribute to Slashdot, he could link the originals just like the rest of us do, instead of plugging his goddamn blog.
The man is your typical blogwhore, more interested in page views than anything else. And he's a plagerist. Don't try to elevate him above that.
This is just a press release. How did this get in? Oh, right.
As usual, Roland the Plogger posts the link he's paid to post. Here's a better story about the animation.
The animation itself is nice (and you can see it from the link above), but it has that MTV/Discovery Channel style of too many short segments. There's a musical background, but no explaination of what you're looking at.
It also gives the incorrect impression that some of the self-assembly processes shown are much more organized than they really are. Watching those tubes self-assemble makes it look as if all the molecules have active guidance and propulsion. In reality, self-assembly just means that when the right molecules in the right orientation happen to bump, they stick.
...just tell the students that "cells got boobies!"
afraid filthy viruseseses will melt and eat your porn?
FTA: "Preliminary evaluation shows that using animations as a part of their study resource enhances performance on questions requiring data interpretation followed by hypothesis building in the cellular context by almost 30%," says Dr. Lue.
Meaning that it is only expected to improve perfomace on some specific questions in a specific field. Way to extrapolate, Roland.
Man is a slave because freedom is difficult, whereas slavery is easy.
Right, because dead students don't perform well. Sounds like a kick-ass research program, by the way.
-Dave
Guantanamo Bay, Abu Ghraib, umm, Prison Break.
Yap we've seen lots of pictures already.
This is my sig. There are thousands more, but this one is mine.
i spent the last year working in one of the biocomputational labs as a system admin, and this isn't exactly news. before i even arived, we already had this great setup of dual, polarized projections, displaying on a legit silver screen, powered by python, that allowed student and professors to toss on somespecial glasses and see cells, dna, and all sorts of other componds in very crisp and realistic 3d.
mat
http://www.youtube.com/watch?v=5NDI0lojaeI
30% improvement!?
Assuming they mean 30% better than they currently are, that the average student is making at best 77/100 on their grades. (And if that were the case, they expect 100/100 as the new average. So it's got to be much lower than that.)
If they meant straight grades, that means 70/100 was the average, at best.
What does this say about the ability of their teachers? Nothing, that's what... because that 30% number is complete and total bullshit.
"If you make people think they're thinking, they'll love you; But if you really make them think, they'll hate you." - DM
Those microscopes do sound pretty cool. How did you get your hands on one (assuming you're not just astroturfing for the company)?
I am teaching at a larger university in Cambridge as well as at local highschools once in a while. Over time is has turned out that the most powerful tool for teaching geography is Google Earth and some my collegues who are teaching history are saying that their best tool has proven the History Channel, not books.
30% better at what? Navigation through a virtual cell with a computer?
I just got 30% better at posting articles. Thanks slashdot.
It occurs to me this probably got more money thrown at it than the actual animation department at Harvard...(of which I am a student)
You can order them from the site he linked to.
Stupidity is like nuclear power, it can be used for good or evil. And you don't want to get any on you.
curricula
occultae nullus est respectus musicae - originally a Greek proverb
Fuck totally off, you cockeared midget.
I first read that as "playing with a proctoscope"...
If you look at the linked article, it directs to the XVIVO site, not his blog. In the past he often linked to his blog which linked to the article, but lately his ways seem to have changed. Clicking his name will still take you to his blog, but I don't see anything wrong with that.
Help I'm a rock.
My uncle lives in a cell. It's ten foot by twelve and he has to read the same boring, old magazine everyday.
ROTFLMAO, I thought I was the only one :)
Dude...
I can tell you a little bit about what's going on here. I should warn you, I'm not a biologist, just a fan.
We start off of course seeing white blood cells moving through a capillary blood vessel. Then a close up showing cilia from the white blood cell interacting with the cells lining the capillary wall.
We then cut to a confusing looking picture of a "platform" with some large molecules floating on a fluctuating surface. The surface is the cell membrane of the WBC, I'm not sure if this is the inside or the outside. Probably the inside. The molecules moving together are what they all a macro-molecular complex.
We then pull back and see a meshwork or net-looking arrangement. This is a structure just inside the WBC wall. These protein fibers give the WBC its semi-rigid shape, and by tugging on them it is able to change its shape and move around. Much of the interior of a cell is criss-crossed by these fibers, of various sizes. By building and disassembling them, the cell is able to control its shape.
We see some shots of these fibers and larger micro-tubules self-assembling. As noted above this is a little too "choreographed" and it is a more random process. We then see one being cleaved and beginning to disassemble, and some more disassembly.
One of the more striking sequences seems to show a big blob being towed along by a sort of foot that walks along. This is a vessicle being transported along a microtubule. It is destined to merge with the cell wall and dump its contents outside the cell. We don't see the fusion process, but near the end we see the completion of this, as a deep well in the membrane surface flattens out, and its contents are dispersed into the intracellular medium.
The "walking" process is again a little too regular. It is thought to be much floppier than this. The front end of the "foot" flops around until it hits the right spot, where it sticks. At that point an ATP molecule must bind (this is not shown) which drives the rear foot free of the tubule. It will then flop around itself until it sticks up front. This is a "brownian motor (or ratchet)" which is used in many places in cells.
We see a bunch of squiggly things shooting out of holes in some surface. I believe these are messenger RNA molecules coming out of the nucleus. The nucleus creates these molecules based on the genes which are inside the nucleus, and they go out into the cells where they serve as a guide to construct proteins.
That's what we see next, a greenish blob, the ribosome, slides along the mRNA and out the side of it comes a squiggly, new protein. What is not shown here is that there are millions of interactions with amino acids that are used to build the protein.
Many ribosomes are free floating as shown here but many are also attached to what is called the endoplasmic reticulum, a membrane within the cell that has a complicated shape. That's what we see next, a ribosome going down and attaching to the ER where it continues to work, producing a protein, then it detaches and separates into its two constituent pieces.
Next we see our friend the vessicle being towed along, and then a blobby, somewhat cylindrical object comes into view. Look close and you will see free-floating blobs moving through it. This big thing is a Golgi body, and its purpose is to prepare protein products for excretion from the cell. The vessicles move through it and some kind of last minute chemical processing is done (this is not shown, I'm not sure it is understood very well what happens there).
Back to a brief shot of the towed vessicle and then suddenly we see the end of its merging process, the volcanic upwelling as the vessicle completes its attachment to the cell membrane and finishes disgorging its contents.
Presumably this is some kind of signal the WBC is sending to neighboring cells, perhaps to prepare them for its entry.
We are back on the surface now, and see some molecules on the WBC link up to molecules on the adjacent cells. This is meant to represent the first steps by which the WBC "grabs hold" and is able to pull itself into the gap between the cells. That's how the movie ends, with the WBC disappearing into the body.
What the world needs instead of Flash is "Animated SVG".
(Now go create it :) )
-- Sig down
If what you're "aarrrg"ing about is the video not being playable under Linux... the file is downloadable and its a FLV file, playable using VLC (http://www.videolan.org/vlc) among others...
Look, people don't really mind blogspam, so even if the link went to his page it wouldn't cause that big of a deal on its own. What people hate about Roland was the rampant plagiarism he did in the past. I don't blame them, what he used to do was incredibly lame.
--
WHO ATE MY BREAKFAST PANTS?
This one has a 100x magnification for $10c tId=2103694&cp=&origkw=microscope&kw=microscope&pa rentPage=search
http://www.radioshack.com/product/index.jsp?produ
Very pretty, and I suppose it might help you remember certain interactions and players, but it comes from the Fantasic Voyage school of portraying medical biology. Remember when the requisite hottie of the movie, Rachel Welch bumps into some tissue, injurying it ... and these antibodies come streaming along and target her precisely ? For the most part, molecules and proteins such as shown in this animation do not move so purposefully, flying through the void in perfect formation, bumping into precise what they are intended to interact with, amidst the largely empty void (void of what?!? there is plasma/saline everywhere filled with molecules not that much smaller than some of these proteins and polypeptides). Interactions occur mostly by mass-action, PASSIVE diffusion and RANDOM encounters, which then *might* use specific affinities to start specific interactions.
So contrary to the very purposeful, specific and sparse view of interactions portrayed, the first and most predominant level of molecular "interaction" (bumping into each other) is random, driven by passive processes and mass action (many, many more molecules of all types around). Specificity only can kick in after chance encounters permit the right pairing.
You can animate an SVG image by manipulating the SVG's DOM with script.
I like the music, what kind is it? Anyone know what genre it would be classified as or what the specific author/title is?
Sig: I stole this sig.
it's not the future of George W. Bush, Dick Cheney, etc.
Dog is my co-pilot.
Imagine my disappointment on seeing "Roland Piquepaille" and "Life inside a cell", and getting this instead of the prison diaries I so hoped for...
I'm surprised educational videos are not used more often. especially in difficult subjects like physics and maths.
Harvard University has decided to use animations as a tool to enhance the performance of its students in biology.
Viagra for 19 year old college students?
They are pictures and not movies, and kind of 2 1/2 dimensional, but I really like the artwork of Scripps Institute professor David Goodsell. See some examples of the interiors of cells here:
e ll/
http://www.scripps.edu/mb/goodsell/illustration/c
These give a much better idea of how crowded it is inside cells. Even though Goodsell only shows the macromolecules and leaves out the water and ions, everything is just packed together.
For example, the picture on that page shows a bit of the cell membrane of a bacterium. A flagellum is curving away - the bacterium spins this for propulsion. The external surface is coated with sugar-protein molecules to make it slimy. Just inside is a meshwork of protein filaments (shown just as a green line of molecules here). Inside the body of the bacterium are lots of ribosomes, shown in purple, emitting whitish squiggles of newly synthesized proteins. And just inside that, taking up much of the body, is the bacterium's DNA, wrapped around its spools to keep it neat, shown in yellow. A bacterium doesn't have a nucleus so the DNA is right out there with everything else. And they're really small so much of the cell is taken up with DNA.
This kind of picture gives a more accurate impression of what it is really like inside cells, but it would not lend itself to 3D visualization because you wouldn't be able to see far enough through the cell. It's just too crowded.
I love it, but in many ways it perpetuates a misleading notion of the way the nanoscale machinery of a cell behaves. For example, it looks as if the growing microtubule is actually attracting tubulin monomers, when the reality is that they are bouncing around randomly until they happen to encounter the growing end of the microtubule. I can certainly understand why they've chosen to do this; if they were to display tubulin molecules at a realistic concentration and moving at a realistic speed relative to the rate of growth of the microfilament, it would probably look like you were in the middle of a swarm of angry bees, and you wouldn't be able to see what was going on. Still, it would be nice to see an occasional tubulin monomer bind and then dissociate, for example. And of course, all of the protein molecules look too rigid. If you've ever seen a molecular dynamics simulation of a protein, you know that they should be wiggling like they're made of jello. The robotic-looking movement of the kinesin molecule, resembling one of the animated brooms from Fantasia, is particularly misleading. It's unfortunate to see the the two-steps-forward-one-step-back Brownian nature of molecular interactions sacrificed, because one of the most remarkable things about biochemistry is the yin-yang way that apparently purposive behavior emerges out of randomness, two things that many people mistakenly imagine to be in opposition.
I wish i was paid for it. My company does sell it (or a division of it does, I work in another part) but I was helping them do some beta testing on friday, it is really cool to see the sweat come out of your pores on your finger tip. I honestly do like the project and get excited about materials to help teach science.
i can safely say that was the coolest, most moving 3d animation i have ever viewed baked
If they included captions, explaining what they were portraying, I would pay $10 to see the full length version. I would prefer captions to a voice over, as it would be less intrusive, allow the music to capture my artistic side, and would probably result in shorter descriptions.
excitingthingstodo.blogspot.com