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Life Inside a Cell 79

Posted by ScuttleMonkey
from the 30-percent-perhaps-a-bit-ambitious dept.
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."

Life Inside a Cell

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  • AAARRRG! (Score:2, Insightful)

    by jstomel (985001)
    Why won't they they release fucking Flash 9 for Linux? Grrrrrr
    • Re: (Score:3, Interesting)

      by Bromskloss (750445)
      Why won't they they release fucking Flash 9 for Linux? Grrrrrr
      It would be no problem if people could just stop using flash things on their web pages. An Ogg Theora would be perfectly fine with me.
      • Flash can be useful. YouTube and Google Videos is a good starting point. Newgrounds for small, simple and amusing games and movies. (Albeit a lot are poor.) But as design for a full website - navigation and the like - it's just poor practice.
        Install AdBlock/Flashblock, and actually get the benefit of Flash without the downsides. It's only as harmful as JavaScript, and that's easy to work around with Firefox or any decent browser.
      • by ATMD (986401)
        wine + firefox.exe + flashplayer.xpt

        Works like a charm. But I know what you mean.
      • What the world needs instead of Flash is "Animated SVG".

        (Now go create it :) )

    • Re: (Score:3, Informative)

      They're working on it. http://blogs.adobe.com/penguin.swf/ [adobe.com]
    • 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...
  • by Anonymous Coward
    What constitutes 30% improvement when you're already giving out 90% "A"s?
    • by Veetox (931340)
      Well, I'm sure that there are some Harvard students that get worse grades than others [at Harvard]. However, I am a little surprised that there are enough students in an Ivy League school having a problem understanding undergraduate biology principles to constitute making a video for them.
      • Re: (Score:2, Funny)

        There are always enough business majors that could not get into History of Music that have to take Biology as an elective instead. They would probably do 50% better with a power point on the subject.....
      • Re: (Score:3, Interesting)

        by Two99Point80 (542678)

        This would be very useful for those of us whose learning mode is primarily visual. It is possible to read a description of something and recognize it as parseable without really "getting" it, then see the same information in visual form and have the "AHA!" of grasping the concept.

        Keep in mind that advances such as the double

  • by creimer (824291) on Saturday September 02, 2006 @12:32PM (#16030091) Homepage
    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.
  • by Pfhor (40220) on Saturday September 02, 2006 @12:33PM (#16030092) Homepage
    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/ [proscopehr.com]) the other day, I was able to actually see the capillary action in my own finger.
  • Anywhere?
  • Cache (Score:1, Informative)

    by LeDopore (898286)
    here [nyud.net]
  • by Animats (122034) on Saturday September 02, 2006 @12:45PM (#16030133) Homepage

    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 [studiodaily.com].

    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.

    • Re: (Score:2, Insightful)

      by MustardMan (52102)
      You know, with the number of us who post on every single fucking roland spam article bitching, you'd think the slashdot editors would give us a way to filter them. Then again, taking the time to read the thread and bitch about roland means slashdot is getting more advertising dollars from us.
      • Re: (Score:2, Insightful)

        by LiquidCoooled (634315)
        Actually, I would imagine the problems with inserting a whole layer of filtering to the section article selection would be problematic.
        I am also sure that if you wanted to have a try yourself at implimenting the code within slash they would gladly accept and consider any carefully thought out patches you would like to submit.

        I don't care where the articles come from and tbh I don't care if slash pays him all I know if Roland is some kind of 24/7 internet roving geek who just has a REALLY good knack at diggi
        • Re: (Score:1, Offtopic)

          by FLAGGR (800770)
          Here's some C++ pseudocode:

          if (story->author == "Roland Piquepaille" || search(story->links, "http://www.primidi.com/")) {
          delete story;
          blocksubmissionsfrom (story->author.ip);
          return 0;

          I kid, I kid.
    • by nucal (561664)
      I assume (hope) that this was actually a trailer and there are more in depth animations either available or in the works.

      Another gripe, they were inconsistent with how they altered the time scale. For instance, kinesin dragging around a vesicle was slowed down, while the cell migration through the blood vessels was speeded up.

      Still, it's nice to see animations based on real molecular structures ... finding a way to incorporate real principles of signal transduction and intermolecular interactions wou
    • Re: (Score:1, Offtopic)

      by houghi (78078)
      We can vote on posters. It would be nice to vote on both publishers and editors and filter out that way. The same reasons and rules can be used that already exist. That is unless they think that this whole voting system won't work.
  • Animations? (Score:3, Funny)

    by bigdavex (155746) on Saturday September 02, 2006 @12:55PM (#16030174)


    Right, because dead students don't perform well. Sounds like a kick-ass research program, by the way.

    • by jd (1658)
      Yeah, but which scores better in tests - zombies, ghouls, ghasts or skeletons? Personally, I'd have thought do better by performing a spirit transfer - minor demons would likely do well in a student body. It would fit the image better, too.
  • 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.
  • Youtube Link (Score:4, Informative)

    by blackbearnh (637683) on Saturday September 02, 2006 @01:10PM (#16030202)
  • 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.

      I've had engineering classes where the average on a test was 40% (transport sucked).
      "Furthermore, 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

  • by Anonymous Coward
    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.
  • Dude...
  • What's going on (Score:5, Informative)

    by SiliconEntity (448450) on Saturday September 02, 2006 @07:02PM (#16031157)
    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.
    • Re:What's going on (Score:5, Informative)

      by jrau (880696) on Saturday September 02, 2006 @09:15PM (#16031461)
      Well, I am a bit of a biologist (I'm a med student with a masters in physiology), so I'll see if I can't provide a bit more detail...

      The initial shot of a blood vessel is way bigger than a capillary (more like an arteriole), but those are certainly WBCs crawling along the inside. Those aren't cilia, but rather a variety of different cell adhesion molecules (CAMs), and cell recognition proteins.

      The "platforms" floating around on the exterior surface of the cells are likely lipid rafts (which are quite fascinating, actually - a select, extremely hydrophobic lipid type accumulates around some proteins, and in some cases seems to dictate how and where they move around the exterior of the cell. In fact, they seem to be connected to the cytoskeleton on the inside of the cell - really cool stuff).

      Most of what we see from here on out is not specific to WBCs, but rather processes that all cells go through. Those are actin microfilaments which form a mesh for structural support on the outer edge of the cell (near the membrane). Throughout the cell there are microfilaments, intermediate filaments, and microtubules, which give the cell structure, and more importantly, a framework for the movement of various organelles and vesicles around the inside of the cell (as we see in a little bit).

      These are actin filaments being assemble initially (and then cleaved, and disassembled), and then after that microtubules are formed. They actually form in a very ordered linear manner like this. MT's form in long sheets that then fold over and seal to form a tube, then upon disassembly chip off, almost like shards of glass. MT's frequently fracture/shatter, while actin just breaks.

      The part with the vesicle being towed along the MT is very cool - the parent post is quite right about the unrealistic steadiness of this molecule, but of course this is really the case for all the molecules. That tow molecule is probably either a kinesin or a dynein - these molecules are kind of like myosin (myosin and actin are what allow your muscles to contract), and one moves in one direction down a MT and the other moves in the opposite direction. We also see a distance shot of some centrioles (which are also composed of microtubules). Centrioles serve to anchor the microtubules that connect to the chromosomes and pull them apart during cell division. There are MT strands shooting out in all directions from the centrioles. One side anchors them to the cellular membrane and the other connects to centromere of the chromosomes.

      Yep, those are definitely mRNA's shooting out of the nuclear pores. They form a ring as the two ends form a complex that initiates translation of the mRNA into protein. The ribosomes then latch on and start cranking out protein. As the protein emerges from the ribosome we can see it start it folding process. Protein folding is a very complicated and intricate process. If a protein is misfolded it may simply not work, or it may cause a disease state. Creutzfeldt-Jakob disease (caused by mad cow disease in some instances) is caused by misfolded proteins that then cause other proteins to misfold (it's a prion encephalopathy).

      We then see some sort of protein-protein interaction occurring randomly out in the cytosol of the cell. This could be any number of things, but looks to me like a signaling protein interaction. That newly formed protein dimer could then float off and effect some other cellular process (presumably something those two proteins couldn't do by themselves). Also, that big gray thing in the background that they float by - if I had to wager a guess, I'd say that was a mitochondria.

      We then see a protein fold through a membrane in the rough ER.

      We then see what looks like vesicles budding off of the ER and floating off, presumably to the Golgi apparatus, which is what we see next, right after more of the vesicle being towed again. The Golgi preps things for extracellular and intracellular transport. The golgi often sends the proteins it modifies
      • Re: (Score:3, Informative)

        by SiliconEntity (448450)
        One thing the movie is not completely consistent about is speed. This is a slowed-down view of life within the cell, but the slow-down factors are not always the same.

        The "keep on truckin'" kinesis molecule towing the blobby vessicle along the microtubule will take in real life about 100 steps per second. We see it taking about 1 step per second so this is a slowdown by a factor of 100.

        The translation of mRNA to protein by a ribosome occurs at a rate of about 60 steps per second, each step adding a single a
  • by neurocutie (677249) on Saturday September 02, 2006 @10:11PM (#16031569)
    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.
  • by ModernGeek (601932) on Saturday September 02, 2006 @11:15PM (#16031670) Homepage
    I like the music, what kind is it? Anyone know what genre it would be classified as or what the specific author/title is?
  • by Bertie (87778) on Sunday September 03, 2006 @06:28AM (#16032164)
    Imagine my disappointment on seeing "Roland Piquepaille" and "Life inside a cell", and getting this instead of the prison diaries I so hoped for...
  • 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:

    http://www.scripps.edu/mb/goodsell/illustration/ce ll/ [scripps.edu]

    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 bact
  • 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
  • I have to say it was pretty impressive as an advertisement. Graphics on par with hollywood cartoons, music well selected.

    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.

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