Cell and Molecular Biology Animated Textbooks • Hacker News Board

Re: Cell and Molecular Biology Animated Textbooks

#31

Post by mncharity » Wed, Oct 30, 2019, 8:24 PM UTC

droithomme wrote: post #27

mncharity wrote: post #18

Earlier quoted context omitted.

> 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 bein…

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,…

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.

Re: Cell and Molecular Biology Animated Textbooks

#32

Post by mncharity » Wed, Oct 30, 2019, 9:12 PM UTC

1auralynn wrote: post #26

mncharity wrote: post #17

Earlier quoted context omitted.

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 realist…

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…

> 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.

Re: Cell and Molecular Biology Animated Textbooks

#33

Post by tasty_freeze » Wed, Oct 30, 2019, 9:15 PM UTC

droithomme wrote: post #27

mncharity wrote: post #18

Earlier quoted context omitted.

> 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 bein…

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,…

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.

Re: Cell and Molecular Biology Animated Textbooks

#34

Post by 1auralynn » Wed, Oct 30, 2019, 9:28 PM UTC

mncharity wrote: post #32

1auralynn wrote: post #26

Earlier quoted context omitted.

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…

> 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 pul…

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 ;)

Re: Cell and Molecular Biology Animated Textbooks

#35

Post by 1auralynn » Wed, Oct 30, 2019, 9:38 PM UTC

mncharity wrote: post #29

1auralynn wrote: post #26

Earlier quoted context omitted.

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…

> 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…

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.