Cell and Molecular Biology Animated Textbooks
smart-biology.com
smart-biology.com
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.
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 <some topic> 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.
Totally agree on XR and scientists - biologists LOVE visualization, particularly XR. That's definitely not the problem. In fact, one of the things I've been trying to do is to make XR tools for scientists to make their own visualizations using their datasets (http://10k.systems). There just aren't enough headsets yet, but it's possible Quest will change this.
Have you any thoughts on helping them with that process?
For instance, educational graphics for atomic nuclei, and electron density, are very stereotyped and unrealistic. Some good data exists for both, but it's in these tiny communities. Education content creators have little interest or incentive to pull, and the researchers have no incentive to push, with non-trivial effort, something for which there's no interest.
So I've been wondering, might one facilitate the process? To speed progress. Perhaps say create a free Unity asset, with a set of more realistic atomic nuclei graphics. So the next time an XR content creator is reaching for a graphic, at least there's an easily accessible one that isn't the usual ball of colored marbles.
So yeah, there are lots of people working on little bits, all over the place, duplicating efforts again and again. In my opinion, what is needed is real funding and a coordinated effort to establish open source tooling, or at least some kind of platform that brings everyone together. And then more money on top of that ;)
I agree with the challenge, but suggest parts of the compromise are not being squarely faced.
Have you seen a Jackie Chan action film, where mixed into the ending credits, is a blooper reel of stunt fails and injuries? It serves to correct the reality distortion of the film itself, to reduce viewer injuries from emulation misjudgement. If Hollywood held itself to a similar standard, there would be less paralysis from "we had to move them, before the car exploded", and less drowning with "but... it was so quiet".
A microbiologist writing a young children's picture book, included an errata page. Describing the liberties taken, and at least some of the errors made. And if just maybe, one might uncharitably suggest that maybe it was motivated a bit more by concern for being seen by ones colleges as having made an mistake, and perhaps a bit less for the conceptual integrity of readers, still it served to remind of the latter, and perhaps helped.
Yes, resources are always limited, and engineering and content creation are fundamentally about tradeoffs.
But you know how expense escalates, as one moves from thought to sketch to storyboard to crufty draft to professionally polished prettiness? That means one can always afford to add something crufty, if motivated to do so.
I'd have no problem if people said, "yeah, we could have reduced that misconception, but given our resource limitations, it would have been an unprofessionally hackish job mixed into our otherwise nice work, and we prioritized polish over the misconceptions, which maybe sucks, but it has to be viable as a product".
But I've never heard that. I've never heard "we prioritized polish over student outcomes". But I have heard lots of comments about software limitations, and pedagogical constraints, and so on. But the implicit constraining context, that "pretty" is prioritized as more important than "works", that's usually not looked at straight on.
And sure, part of that is the dysfunctional way that content is created, which in turn results from the way it's funded. I talked with a PBS science creator, who commented, sure, we'd love to try iterative creation and testing, rather than creating a thing, tossing it over the wall into the world, and never being sure how all our efforts and tradeoffs actually worked out... and just as soon as we find someone willing to fund that, we'll try it.
So my suggestion is that if we were more heads up about our choices, and their costs, we might be making different and better choices.
> headsets
I'm looking forward to the 1080p Nreal Light AR glasses early next year. I've found resolution limitations more of a bottleneck than market, but then for me it's merely a hobby for now. Thanks for the 10k link.
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
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".
http://biovisions.mcb.harvard.edu/
It was produced with the oversight of cellular biologists and lead by Dr. Robert A. Lue. (https://www.mcb.harvard.edu/directory/robert-lue/) Yet you say it is a fantasy, misleading, and cherry picked.
Since you consider Harvard University's cellular biologists incompetent and misleading, could you direct us to some accurate videos and name some more competent universities that are not backwater Monty Python loony bins like you consider Harvard? Also would be great if you could provide a critique of all the deficiencies in Dr. Lue's training and background that provided the substrate of total incompetence and ignorance you have discovered in his animations that you assess as "bold and bald faced lies". Thank you!
Also if you have a chance, what sort of egregious errors led to Harvard being ranked the #1 University in the world for Molecular Biology and the only one with a subject ranking of 100?
https://www.usnews.com/education/best-global-universities/mo...
The problem isn't that the authors think proteins are actually bright cartoonish colors. Nor that such colorization isn't pedagogically useful. The problem is that many students, unsure which aspects of what they are seeing are real, and which are artistic license, are known to get it wrong. Are known to end up believing that bodies and cells are big empty-ish spaces, and that molecular motion isn't extremely violent.
As here. That stately motion, is artistic license, not reality.
The critique of the authors, is that they are failing to do some things which would reduce the creation and reinforcement of these student misconceptions. They could have for instance, retained the stately motion for its pedagogic value, but added a brief clip of more realistic motion, to inoculate against the misconception. But they failed to do that.
Hmm, as for the cartoon colors, I don't actually know if some students end up believing they are real. I'd expect so. I do know many students believe blood changes from red to blue, based on the colors in a common circulatory system diagram, reinforced by vein color observed through skin.
I've a paper around here, somewhere, on kinesin towing physical dynamics, if that's something you'd care about.
Form reading "The Machinery of Life" by David Goodsell I also got the same impression as the person you are responding to. The brownian motion at the molecular scale is more akin to being in a hurricane than the stately walking this animation shows. It progresses in a herky jerky N steps forward M steps back where N > M manner.
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.
As with that "Unit 1" video at the top of the page... by analogy, "<Attenborough voice> 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 are! You can just feel the feathers on their flippers. You're students will find that highly engaging." Ah well, MVP mumble mumble.
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.
If someone progresses to the point where these misconceptions really become an issue I think they would be corrected organically.
Or alternately, perhaps it's like students struggling with high-school stoichiometry, with atom conservation, because they've managed to remain unclear on the simple core concept that atoms are real objects, are real, physical, little balls.
> think they would be corrected organically
Yeah, that's a widespread impression. That say high-school misconceptions will disappear as students become undergraduate majors, and then graduate students. It's not been well studied, at least the last time I checked. But at a minimum, there are notable exceptions. If your 5-year old wants to know which finger-paint color to use for the Sun, asking a first-tier astronomy graduate student is likely to get them the wrong answer. Misconceptions turn out to be highly resilient. Which is why creating and reinforcing them is not something to do lightly.
I'm planning to spend some time learning three.js in the coming months, but does anyone else have advice for getting into this kind of work? Should I go deep into linear algebra and the math behind the graphics? Or just keep things simple and focus on the actual creative / artistic representation of scientific ideas? (The latter certainly seems like the harder part).
Also curious where one could find paid work doing these kinds of things.
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...