Pharyngula

Molecular machines!

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If you’ve ever wondered what the heck Behe was smoking when he claims there are literal trucks trundling about on literal highways with literal traffic signals inside of cells, well, I don’t have an answer for you…but there is a wonderful Flash movie that will show you the Inner Life of a Cell so you can see what “molecular machines” look like, more or less. It’s a spectacular show. What you’ll see is the series of events that transpire when a lymphocyte encounters a cell surface signal that triggers emigration out of a capillary and into other tissues; it zooms rather abruptly from a cellular view to the molecules on the surface interacting with one another, then into the interior of the cell to see the response. All kinds of cool stuff fly by: actin and microtubule assembly and disassembly, kinesin-mediated vesicle transport, protein synthesis on ribosomes, ER processing, vesicle fusion, etc.

I do have a couple of gripes, though. One is an understandable shortcut: the cell is far too uncluttered, and events proceed in too directed a manner—there ought to be much more stochastic noise at the molecular level. We’re seeing chemistry in action, after all. Another is that there is no explanation at all for anything we’re seeing, it’s simply a weird and trippy voyage into a subcellular world. This clip was created under the auspices of Harvard scientists, so I hope there is a viewing guide somewhere, otherwise it’s only going to be appreciated by people who have already read Molecular Biology of the Cell(amzn/b&n/abe/pwll). I think it also needed a disclaimer somewhere that this video too is a visual metaphor for cellular activity.

But I’m being picky. Otherwise, it’s an excellent introduction to the profound weirdness of the processes going on inside a cell.

Comments

  1. #1 Blake Stacey
    September 3, 2006

    PZ wrote:

    If you’ve ever wondered what the heck Behe was smoking when he claims there are literal trucks trundling about on literal highways with literal traffic signals inside of cells, well, I don’t have an answer for you…

    The cell isn’t a truck. It’s a series of tubes!

  2. #2 craig
    September 3, 2006
  3. #3 John Evens
    September 3, 2006

    Well, I liked it, but then I’ve read MBOTC! I agree with you about the ‘directed-ness’ of it! I wonder what it would look like if you included every molecule – would we be able to see any order in it at all? Since the solvent plays a big role in all the processes, it’s a shame that it’s just shown as a void.

    However, from the point of veiw of showing *what* molecular interaction go on in a cell, it’s very good, even if the *how* is not perfect.

    Do you think we’ll ever be able to film that kinda stuff for real?

  4. #4 Rosie Redfied
    September 3, 2006

    This appears to be the 3-minute demo version; I think Harvard has a full-length (10-minute) version.

    Maybe the reason there’s no narration is so the students can be asked to do the intellectual work of connecting what they’re seeing to what they’ve read about in their textbook or heard in lectures. I hope so – if the instructor provides the explanation it will just be a flashier classroom video. The detailed graphics won’t change the fundamental problem that students never really learn much by sitting and watching.

  5. #5 Theron
    September 3, 2006

    Cool – but yeah, I didn’t know what most of that was. The “inference by design” folks will insist, upon seeing this, that it could “never happen by accident.”

  6. #6 jbark
    September 3, 2006

    Very cool, but yeah, I didn’t have the foggiest idea what was going on.

  7. #7 Neoteny
    September 3, 2006

    As a bio undergrad, I got most of it. Quite amazing in my opinion. The microtubule assembly and the kinesin motors were particularly cool. If there’s a 10 minute video, I definitely want to see it.

  8. #8 Jeff Knapp
    September 3, 2006

    Very cool animation, very nicely done – from an animation perspective. The shading and texturing, lighting, motion, camera work were all nicely done.

    As an animator, I understand completely the need to simplify and and make it less “cluttered” for the purposes of illustrating a process. I am assuming the purpose is educational and illustrative (while using fairly realistic imagery) rather than a literal recreation of what one would see if one were to put a nano-camera inside a real cell to film these processes. My only criticism is the editing – too many cuts and dissolves poorly timed to the rhythm of the motion in the animations. It did have the feel of an animation demo reel.

    (For once I get to comment on something I am actually qualified to comment on in these blogs. I am a 3D animator and visual effects artist by profession.)

  9. #9 arensb
    September 3, 2006

    Okay, ‘fess up: who else was reminded of the opening credit sequence in Fight Club (the pull-out from the “fear center of the brain”, through a pore, and onto Tyler’s gun)?

    the cell is far too uncluttered

    Yeah, that’s what I was thinking, too: shouldn’t all this be happening in a soup of water and ten thousand other chemicals? And in the bits where the microtubules assemble themselves, I assume there are other molecules catching the components out of the soup and bringing them into position. But obviously including those parts would’ve made the animation hopelessly dense, and obscured those parts they wanted to show.

  10. #10 Caledonian
    September 3, 2006

    You *couldn’t* put a nanocamera into a cell and see much of anything. The wavelength of light determines how small an object can be and still be clearly seen in that light — objects that are roughly as large as the wavelength scatter the light around themselves and smaller objects can’t be distinguished at all. That’s why electron microscopes are necessary to get clear images of very small things. Visible-light images of things as small as cytoskeletons and microfilaments would be a blank blur.

    There seems to have been a new technique developed, called Stimulated Emission Depletion microscopy, that can actually resolve things on the 50~70 nm scale… but the images it produces aren’t anything like what we see with our eyes.

  11. #11 Julia
    September 3, 2006

    Fascinating! It ought to have some success as an educational tool. It certainly made me want to learn more.

  12. #12 Martin C
    September 3, 2006

    The video was amazing to me, I had no idea those kinds of things were happening in us!

    I had a lot of difficulty with the switches in scale in the video, I’ve watched it 3 times now and I think I’m starting to get what is the same between scales. For me it certainly would have helped if there were some clues as to the scale so if for example they’d just zoomed in 10x I could look for things that would be 10x bigger compared to the previous sequence.

    I’m a software engineer as well, so I had no clue what each thing was, I had to get my pathologist girlfriend who happened to be here to explain it all to me. Fascinating stuff!

  13. #13 Steve
    September 3, 2006

    Fantastic! I remember thinking as a high school and college student how much easier many scientific concepts would be to understand if they could be shown visually — and now here’s a movie that does just that.

    Here’s a question: What’s the thing that looks like a walking twig carrying a giant water balloon on a rope?

  14. #14 PZ Myers
    September 3, 2006

    That’s kinesin. It’s actually fudging a bit — there’s some argument now about exactly how it moves, and the animation is of the “hand over hand” model, while some think it’s more of an “inchworm” movement.

  15. #15 miko
    September 3, 2006

    add to the the disclaimers and caveats that everything is happening several orders of magnitude slower than in a cell.

    i hope in whatever form this is published it makes clear that it is a symbolic cartoon model that does not physically resemble things in cells. i mean, it should be a dense, quivering mass of molecules packed tight together, even in slow motion it wouldn’t make any sense.

    the lipid raft is hilarious. i suppose if undergrad bio majors like watching it after bong hits, it’s worth it.

  16. #16 j
    September 3, 2006

    That was really, really awesome.

  17. #17 KevinC
    September 4, 2006

    It was a real neat video, skipping the real soup is ok for lower level biology, but by college one should know it is not that simple. Plus, biological actions do not react in beat to the background music.

  18. #18 lo
    September 5, 2006

    thx for the link.
    Other than that it already says it is a render. It`s a great simplification for students and educators alike.
    There are quantum dynamically modelled versions of the mere ribosome and polymerase out there of course all of this itself is incredibly simplified. Just imagine that the ribosome is at times interacting with all sorts of other enzymes in an unfavorable way coming even to a halt perhaps and perhaps there are other yet undiscovered chemicals that entangle those two.

    However those new syncrotron and femtosecond lasers projects are making headway to shed light on even very fast molecular kinetics.

    In the end one of my concerns is that the students of biology a.s.o. should actually understand that the underlying effects are of quantum mechanical nature. And afaik they at least are tought some understanding of that in the 21st century curriculum. What remains the biggest mystery to me however is how a BIOCHEMIST like BEHE has such a great educational lack.

  19. #19 Don Culberson
    September 5, 2006

    As predicted, the ID hacks are gleefully pointing fingers and exclaiming, “See we were right all along!!! Take that, nasty natural selectionists…” and so forth, for instance:

    http://www.uncommondescent.com/index.php/archives/1554

    I rather enjoyed the video, showed it to my BIO101 class this morning, with the caveat that depth and complexity were assuredly sacrificed for clarity and watchability. And I kinda like the music, but thats just me.

    What mystifies me is how IDers can view a video animation and think it is proof of intelligent design, as per this quote from the first comment on Uncommon Descent, “Animations like these should make students think about whether ID is as silly as the science powermen tell them.” Huh?
    Uncle Don

  20. #20 Steven Sullivan
    September 5, 2006

    The ribosome pooping out a protein into the endoplasmic reticulum was very cool, as was the kinesin ‘walker’.

    Where can I/we see the full 8 min version?

  21. #21 Martin C
    September 6, 2006

    I’ve been emailing with the Production Coordinator at XVIVO and she has told me that Harvard owns the full video but are considering making it publicly available later this year. Anyone have contacts at Harvard?

  22. #22 @rno klein
    September 19, 2006

    tremendous visualization!
    it would be fun to have an epilogue animation taking into account the aforementioned points (accuracy in temporal and spatial scales, overwhelming kinetic crowdedness of a chemical soup, alternative models for kinesin, etc.). thank you!

  23. #23 judith h
    September 30, 2006

    Anybody know the composer and title of the music and if it was written especially for this film.

  24. #24 Douglas Steele
    October 14, 2006

    From another blog.

    Thanks! The music was composed, performed and recorded by Matt Berky. His company is called Massive Productions. Check him out at:

    http://www.massiveproductions.com/

    He does most of the sound work for XVIVO. He always does an amazing job!

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