7 ms·

The issue with these animations is that they're getting rid of all the thermal noise. In reality, single proteins are flying around the whole length of the cell

by knzhou 6y ago

The issue with these animations is that they're getting rid of all the thermal noise. In reality, single proteins are flying around the whole length of the cell many times a second, just from their thermal motion. And when processes like DNA transcription happen, they're not like a regular conveyor belt -- a fraction of the time the machine will even accidentally run steps in reverse! However, if any of this were shown, the animations would become impossible to understand.

changoplatanero 6y ago
just once i would like to see the realistic animation though even if it's impossible to understand
- InDemoVeritas 6y ago
  It would be pretty boring, proteins bouncing around randomly and occasionally honking up, substrates flying around like rifle bullets sometimes hitting the target, and everything smooshing around in random directions. If you’ve seen Brownian motion, you’ve seen what is happening to all the molecules but at 1/100 the length scale. Nothing stays put. Everything is moving fast and far on the scale of proteins and small molecules.
  - wrycoder 6y ago
    Fast, yes. Far, well, the mean free path in a cell is very short.
- satori99 6y ago
  https://www.youtube.com/watch?time_continue=42&v=uHeTQLNFTgU https://www.youtube.com/watch?time_continue=42&v=uHeTQLNFTgU This comes close -- It shows the jittery thermal motion of this tiny machinery, instead of nice smooth glides.
  - mncharity 6y ago
    Oh my that facepalm dreadful. Thank you! That gives me a new high-water mark for misleading biomolecular visualization computer graphics content. Snagged a copy. When most everything is unmoving, it's "obvious"... well no, not to students, but... there's no pretense of doing anything other than stitching together an extremely selective set of "snapshots", to tell a completely bogus narrative of smooth motion. Here it seems something like a Maya "jiggle all the things" option has been turned on. Making it sort of kind of look like you're being shown more realistic motion. But you're so not. It's the same bogus smooth narrative, now with a bit of utterly bogus jiggle. Those kinesin legs still aren't flailing around randomly. Nor only probabilistically making forward progress. And the thing it's towing still isn't randomly exploring the entire bloody space it can reach given the tether, between each and every "step". It still looks like a donkey towing a barge, rather than frog clinging to rope holding a balloon in a hurricane. And given that the big vacuole or whatever should be flailing at the timescale defined by the kinesin feet, consider all those many much smaller proteins scattered about, just hanging out, in place, with a tiny bit of jiggle. Wow - you can't even rationalize that as being selective in "snapshots" - those proteins should just be blurs and gone. And that's just the bogosity of motions, there's also... Oh well. So compared with older renders, these new jiggles made it even harder to recognize that all the motion shown is bogus. And not satisfied with the old bogus motion, we've added even more. Which I suggest is dreadful from the standpoint of creating and reinforcing widespread student misconceptions. Sigh.
    - satori99 6y ago
      Well, OP did say "even if it's impossible to understand" so if it is in fact in any way misleading, then my lawyers assure me that I may claim the full privileges of a contextual get-out-of-jail-free card for linking to it, and am hereby fully absolved of any intellectual harm caused to any and all individuals who may have viewed it.
      - mncharity 6y ago
        Ha. I've wondered if increasing embarrassment might reduce long-term stable misconceptions in education content. Like astronomy texts getting the color of the Sun wrong. Or wing lift discussed elsewhere. But making textbooks liable for intellectual harm... wow. What might the internet, media, politics, thought and conversation look like, if we were all liable for negligent intellectual harm?
- JabavuAdams 6y ago
  https://youtu.be/5JcFgj2gHx8 https://youtu.be/5JcFgj2gHx8 EDIT> Also: https://www.youtube.com/watch?v=4Z4KwuUfh0A https://www.youtube.com/watch?v=4Z4KwuUfh0A
JabavuAdams 6y ago
Yes to getting rid of thermal noise. No ish? to single proteins flying around the cell that fast. The cytosol is incredibly jam-packed and things are getting hung up on other things so we'd expect the mean free path to actually be quite small for the larger biomolecules.

by knzhou 6y ago

changoplatanero 6y ago

just once i would like to see the realistic animation though even if it's impossible to understand

InDemoVeritas 6y ago
It would be pretty boring, proteins bouncing around randomly and occasionally honking up, substrates flying around like rifle bullets sometimes hitting the target, and everything smooshing around in random directions. If you’ve seen Brownian motion, you’ve seen what is happening to all the molecules but at 1/100 the length scale. Nothing stays put. Everything is moving fast and far on the scale of proteins and small molecules.
- wrycoder 6y ago
  Fast, yes. Far, well, the mean free path in a cell is very short.
satori99 6y ago
https://www.youtube.com/watch?time_continue=42&v=uHeTQLNFTgU https://www.youtube.com/watch?time_continue=42&v=uHeTQLNFTgU This comes close -- It shows the jittery thermal motion of this tiny machinery, instead of nice smooth glides.
- mncharity 6y ago
  Oh my that facepalm dreadful. Thank you! That gives me a new high-water mark for misleading biomolecular visualization computer graphics content. Snagged a copy. When most everything is unmoving, it's "obvious"... well no, not to students, but... there's no pretense of doing anything other than stitching together an extremely selective set of "snapshots", to tell a completely bogus narrative of smooth motion. Here it seems something like a Maya "jiggle all the things" option has been turned on. Making it sort of kind of look like you're being shown more realistic motion. But you're so not. It's the same bogus smooth narrative, now with a bit of utterly bogus jiggle. Those kinesin legs still aren't flailing around randomly. Nor only probabilistically making forward progress. And the thing it's towing still isn't randomly exploring the entire bloody space it can reach given the tether, between each and every "step". It still looks like a donkey towing a barge, rather than frog clinging to rope holding a balloon in a hurricane. And given that the big vacuole or whatever should be flailing at the timescale defined by the kinesin feet, consider all those many much smaller proteins scattered about, just hanging out, in place, with a tiny bit of jiggle. Wow - you can't even rationalize that as being selective in "snapshots" - those proteins should just be blurs and gone. And that's just the bogosity of motions, there's also... Oh well. So compared with older renders, these new jiggles made it even harder to recognize that all the motion shown is bogus. And not satisfied with the old bogus motion, we've added even more. Which I suggest is dreadful from the standpoint of creating and reinforcing widespread student misconceptions. Sigh.
  - satori99 6y ago
    Well, OP did say "even if it's impossible to understand" so if it is in fact in any way misleading, then my lawyers assure me that I may claim the full privileges of a contextual get-out-of-jail-free card for linking to it, and am hereby fully absolved of any intellectual harm caused to any and all individuals who may have viewed it.
    - mncharity 6y ago
      Ha. I've wondered if increasing embarrassment might reduce long-term stable misconceptions in education content. Like astronomy texts getting the color of the Sun wrong. Or wing lift discussed elsewhere. But making textbooks liable for intellectual harm... wow. What might the internet, media, politics, thought and conversation look like, if we were all liable for negligent intellectual harm?
JabavuAdams 6y ago
https://youtu.be/5JcFgj2gHx8 https://youtu.be/5JcFgj2gHx8 EDIT> Also: https://www.youtube.com/watch?v=4Z4KwuUfh0A https://www.youtube.com/watch?v=4Z4KwuUfh0A

JabavuAdams 6y ago

Yes to getting rid of thermal noise. No ish? to single proteins flying around the cell that fast. The cytosol is incredibly jam-packed and things are getting hung up on other things so we'd expect the mean free path to actually be quite small for the larger biomolecules.