[tasty_freeze]

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.

[1auralynn]

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.

[hagy]

For those curious, here are some animations by Drew Berry, https://www.wehi.edu.au/wehi-tv. They're visually stunning, accurate, and highly informative.

[TeMPOraL]

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.

[1auralynn]

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

[busyant]

Just a small correction for anyone looking for this person via Google: it's Drew Berry https://en.wikipedia.org/wiki/Drew_Berry

[mncharity]

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 <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.

[1auralynn]

I mean, why try to do anything? There are tons of science educators working on low-tech tools like you describe, with success. My point is, we can all be armchair critics, but from my experience when you actually try to make one of these visualizations "right", you run into a never-ending torrent of complex decisions that need to be made, both on the scientific end of things and pedagogical, most of which end in some kind of compromise that others can pick apart. There's also a severe lack of funding to support this kind of work.

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.

[mncharity]

> I've been trying to do is to make XR tools for scientists to make their own visualizations using their datasets

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.

[1auralynn]

I have lots of thoughts - I made a platform for them and am partnering with various collaborators to see how they want to use it. Right now, you can import and visualize any PDB file, among other formats. There is also an open source plugin called UnityMol that has more standard molecular visualization features. My interests have always tended towards visualizing larger amounts of proteins together, so I'm not using it in my platform.

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 ;)

[mncharity]

> I mean, why try to do anything? [...] compromise [...] severe lack of funding

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.

[1auralynn]

You're welcome! I guess what I'd say is, you are more than welcome to join the effort to create this kind of content on shoestring budgets. Then in 5 years we can have a conversation about tradeoffs, etc.

[droithomme]

> 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.youtube.com/watch?v=y-uuk4Pr2i8

[mncharity]

> 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".

[droithomme]

That first one was commissioned by Harvard University's BioVisions project and is directed at Cellular Biology students, utilizing in Harvard's words "rigorous scientific models of how biological processes occur".

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...

[mncharity]

Are proteins bright cartoonish colors, or sort of clear? Are cells empty spaces with some few things in them, or packed almost solid? Are molecules moving along trajectories with intent, or slamming about with shocking violence and randomness?

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.

[tasty_freeze]

Harvard very well may be the top university for this particular discipline but that doesn't mean that every statement by every person there is gospel.

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.

[mncharity]

> 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.