Live data from Hacker News

Cell and Molecular Biology Animated Textbooks

smart-biology.com

21–30 of 35 posts

Re: Cell and Molecular Biology Animated Textbooks

#21

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…

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

Re: Cell and Molecular Biology Animated Textbooks

#22

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…

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.

Re: Cell and Molecular Biology Animated Textbooks

#23

Earlier quoted context omitted.

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…

This seems to me like someone criticizing introductory physics courses because they're not taking into account air friction and all the other minutiae from the very beginning.

If someone progresses to the point where these misconceptions really become an issue I think they would be corrected organically.

Re: Cell and Molecular Biology Animated Textbooks

#26

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…

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 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.

Re: Cell and Molecular Biology Animated Textbooks

#27

Earlier quoted context omitted.

> 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 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, 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...

Re: Cell and Molecular Biology Animated Textbooks

#28
This is pretty awesome to see. I have longed dreamed of doing this kind of work, building interactive tools for teaching science (whether in an academic setting or in science news media).

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.

Re: Cell and Molecular Biology Animated Textbooks

#29

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 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.

Re: Cell and Molecular Biology Animated Textbooks

#30

Earlier quoted context omitted.

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…

This seems to me like someone criticizing introductory physics courses because they're not taking into account air friction and all the other minutiae from the very beginning. If someone progresses to the point where these misconceptions really become an issue I think they would be corrected organically.

> seems to me like [...] minutiae

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.

Post reply on HN