Cell and Molecular Biology Animated Textbooks • Hacker News Board

Re: Cell and Molecular Biology Animated Textbooks

#11

Post by 1auralynn » Wed, Oct 30, 2019, 3:22 AM UTC

tasty_freeze wrote: post #9

The illustrations and videos are good at conveying the relative scale of things. But one mistake they make is common to just about every cartoon depiction I've seen: the molecules seem to have intent. they fly into the scene and an atom is exchanged with the binding site, then then remainder flys away again. the stochastic nature everything is completely missing.

I've made a fair amount of these kinds of animations in the past, and it's much harder than it would seem to portray the random nature of interactions. Another common criticism is that a lot of these visualizations don't show how completely packed full of molecules/cells each of these environments are.

You're tasked with the almost-impossible goal of clearly conveying accurate information, visually, in realms where a) though there are a lot of structural data, the visual relationship of things gets VERY complex, b) not everything is actually known, and c) the time and visual scales aren't naturally perceptible to humans.

It's definitely not impossible (see Drew Barry's work, and from the glimpses of this project I've seen it looks pretty great actually), just difficult, and there's not a huge amount of money in it unless you want to work for pharma. Personally, I've been moving more towards 3D interactive content vs. linear videos because you can show a lot more layers, and having users drive what they're focusing in on can be a lot more powerful than trying to design one animation for every learning style.

Re: Cell and Molecular Biology Animated Textbooks

#12

Post by throwaway_n » Wed, Oct 30, 2019, 3:33 AM UTC

If you want something more accessible, I highly recommend the BBC documentary "The Hidden Life of the Cell": https://www.dailymotion.com/video/x6agslv

If this course is at the same level of production values, I would buy it just for entertainment purposes. It beats watching CGI explosions from movies! It looks like it's just $65 dollars for independent students. The samples look decent: https://www.smart-biology.com/life-unit-1-from-atoms-to-cell...

Re: Cell and Molecular Biology Animated Textbooks

#13

Post by TeMPOraL » Wed, Oct 30, 2019, 4:57 AM UTC

1auralynn wrote: post #11

tasty_freeze wrote: post #9

The illustrations and videos are good at conveying the relative scale of things. But one mistake they make is common to just about every cartoon depiction I've seen: the molecules seem to have intent. they fly into the scene and an atom is exchanged with the binding site, then then remainder flys away again. the stochastic nature everything is completely missing.

I've made a fair amount of these kinds of animations in the past, and it's much harder than it would seem to portray the random nature of interactions. Another common criticism is that a lot of these visualizations don't show how completely packed full of molecules/cells each of these environments are. You're tasked with the almost-impossible goal of clearly conveying accurate information, visually, in realms where a…

RE random and packed, the first video on the page (about bacterial flagella) manages to pull out both by exploiting the time domain. First, it shows the usual but misleading view focused on the flagellum, but near the end, it fills in all the other missing activity in the displayed cutout - giving a sense of how it fits into the whole.

Re: Cell and Molecular Biology Animated Textbooks

#14

Post by TeMPOraL » Wed, Oct 30, 2019, 5:00 AM UTC

Koshkin wrote: post #3

A picture is worth a thousand words; a video is worth, well, 24 pictures per second... (Times two, if it’s 3D.)

It's not, really. Someone needs to make a more accurate version of this saying that's rooted in information theory, to show that video isn't worth 24picturelength in seconds, but picture + whatever is communicated in how it changes over time (which is much, much less than a picture's worth).

Re: Cell and Molecular Biology Animated Textbooks

#15

Post by 1auralynn » Wed, Oct 30, 2019, 5:00 AM UTC

TeMPOraL wrote: post #13

1auralynn wrote: post #11

Earlier quoted context omitted.

I've made a fair amount of these kinds of animations in the past, and it's much harder than it would seem to portray the random nature of interactions. Another common criticism is that a lot of these visualizations don't show how completely packed full of molecules/cells each of these environments are. You're tasked with the almost-impossible goal of clearly conveying accurate information, visually, in realms where a…

RE random and packed, the first video on the page (about bacterial flagella) manages to pull out both by exploiting the time domain. First, it shows the usual but misleading view focused on the flagellum, but near the end, it fills in all the other missing activity in the displayed cutout - giving a sense of how it fits into the whole.

Yeah! I've been seeing bits and pieces of this project over the last few weeks, and it really does look great.

Re: Cell and Molecular Biology Animated Textbooks

#16

Post by OldGuyInTheClub » Wed, Oct 30, 2019, 5:17 AM UTC

Armando Hasudungan's hand illustrated biology and medicine videos are also excellent. https://www.youtube.com/user/armandohasudungan/videos

Re: Cell and Molecular Biology Animated Textbooks

#17

Post by mncharity » Wed, Oct 30, 2019, 5:33 AM UTC

1auralynn wrote: post #11

tasty_freeze wrote: post #9

The illustrations and videos are good at conveying the relative scale of things. But one mistake they make is common to just about every cartoon depiction I've seen: the molecules seem to have intent. they fly into the scene and an atom is exchanged with the binding site, then then remainder flys away again. the stochastic nature everything is completely missing.

I've made a fair amount of these kinds of animations in the past, and it's much harder than it would seem to portray the random nature of interactions. Another common criticism is that a lot of these visualizations don't show how completely packed full of molecules/cells each of these environments are. You're tasked with the almost-impossible goal of clearly conveying accurate information, visually, in realms where a…

An educational graphic where some aspects are carefully accurate, and others utterly bogus, used by students unable to tell which are which, is going to prolifically foster misconceptions... when used in isolation. So, why do that?

Software limitations, or visualization clarity, or pedagogical focus, or budget, may require a misleadingly empty cell. But why then use it in isolation?

Why not start by showing a realistically crowded and packed representation? Briefly, like 2 seconds. Static. Drawn with crayons. By a 5 year old. Sorry, it's a pet peeve of mine. A problem with these recurring... I'll call them "excuses", is that they depend on a silent addendum. That something has been prioritized over reducing misconceptions, over slapping on secondary misconception-antidote representations. Sometimes it's "that wouldn't be pretty" (almost a quote), or sometimes it's couldn't be bothered, or just don't care. Sigh.

For conveying the random violence of nanoscale, I like simulation of virus icosahedral capsid assembly. The panels are tethered together, so they can't wander off. They just keep variously smashing into each other. Disassembling, misassembling, and finally, sometimes, succeeding. The panel size/speed, and collision and attachment rates, make realism watchable. Maybe with some skipping ahead.

Apropos 'not naturally perceptible' scale... I've a hobby project around teaching scale down to atoms for early primary. It's funny or sad or something, that it's not that hard to give at least some children, a firmer grasp of the size of cells, than that of at least some first-tier medical-school graduate students. It's a very low bar.

There's a lot of "We tried teaching really really badly, and wow, surprisingly, that didn't work out. So we drew the obvious conclusion: students aren't developmentally ready to understand so complex thing".

But as you say, XR is a source of hope. And personalized instruction. And when MIT did a VR cell biology app, pulling in and interviewing researchers for domain knowledge, they reported a reoccurring challenge was... getting the enthusiastic researchers to leave and end the interviews. So there's seems hope for gathering the needed expertise as well.

Re: Cell and Molecular Biology Animated Textbooks

#18

Post by mncharity » Wed, Oct 30, 2019, 6:03 AM UTC

droithomme wrote: post #10

tasty_freeze wrote: post #9

The illustrations and videos are good at conveying the relative scale of things. But one mistake they make is common to just about every cartoon depiction I've seen: the molecules seem to have intent. they fly into the scene and an atom is exchanged with the binding site, then then remainder flys away again. the stochastic nature everything is completely missing.

> the molecules seem to have intent Take a look at dynein and kinesin walking along microtubules while dragging along their cargo. It's pretty neat. Unknown is how the really simple microtubules get to their destination while building themselves just ahead of the walkers or how the walkers know which turns to take. https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=gbycQf1TbM0 https://www.you…

> It's pretty neat

And very very misleading. Those video frames are strobe-like snapshots, very carefully cherrypicked and arranged to spin a very bogus tale.

Those smoothly and carefully walking legs? They're really a cross between Monty Python and Cirque du Soleil, insanely flailing all around. Including backwards. The not-quite-random walking only makes net progress.

And those stately-moving barge-like things being towed as if by a donkey? Picture instead a helium balloon, held by its string. By a crazed drunk mouse clinging to rope. In a cat 5 hurricane. And that's still not flailing violently enough. Between one step and the next, that "stately barge" explores the entire parameter space it can reach given its tether. Even in politics, we'd not call that spin, but more of a bald- and boldface lie. But "pretty".

Re: Cell and Molecular Biology Animated Textbooks

#19

Post by mncharity » Wed, Oct 30, 2019, 6:42 AM UTC

Myrmornis wrote: post #4

mncharity wrote: post #2

Computer graphics and XR are part of an opportunity to transformatively improve science education content, pre-K to graduate. And we're going to spend years aggressively declining the opportunity. As with that "Unit 1" video at the top of the page... by analogy, " We will get to know the animal kingdom, starting with these airliner-sized mice wearing pink tutus and playing poker. Look at how beautifully rendered they…

Could you clarify what you're saying? I thought the free sample video looked pretty promising. Did you?

The "Unit 1" video presents atoms using aphysical cartoons misrepresenting size, behavior, structure, and properties. Nuclei size by more than 3 orders of magnitude.

One might argue that it's so obviously physically unrealistic and representational, that it's "clearly" iconic. Except that it could easily be made more clearly iconic, but wasn't. And arguments of the form "that's so clearly unrealistic, it won't cause misconceptions" are... just not what happens.

Then there are all the usual problems with computer graphical representations of chemistry, biochem, cell and tissue biology. Where "pretty"-but-misleading is prioritized over the messy multiple representations needed to avoid nurturing a rich ecology of misconceptions.

> thought [...it] looked pretty promising. Did you?

Better than many paper textbooks, yes. Doing the things we know are needed to produce good student outcomes... there's a ways to go. Promising? 3D graphics in general, oh very yes. But this project in particular, I've no idea. The incentives around education content are very dysfunctional. So actually providing deep transferable understanding... is usually not the metric of interest.

Re: Cell and Molecular Biology Animated Textbooks

#20

Post by mncharity » Wed, Oct 30, 2019, 7:23 AM UTC

tasty_freeze wrote: post #9

The illustrations and videos are good at conveying the relative scale of things. But one mistake they make is common to just about every cartoon depiction I've seen: the molecules seem to have intent. they fly into the scene and an atom is exchanged with the binding site, then then remainder flys away again. the stochastic nature everything is completely missing.

> are good at conveying the relative scale of things

The atom-sized atomic nuclei in that first video are a mere... 3 orders of magnitude oversized?

> molecules seem to have intent. they fly into the scene

Like little spaceships, doing rendezvous and docking. When watching CG chemistry videos, I sometimes hear the Blue Danube waltz from "2001". Hmm, if that's an infectious meme... sorry?

> the stochastic nature everything is completely missing

The nanoscale mosh pit from hell, and biological binding energies hovering just above thermal dissolution, high enough for satisficing stability, but low enough for cheap dis/assembly, are critical core concepts for understanding biology. So of course they're almost never taught.