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Does anyone know of resources or groups with a focus on educationally conveying a feel for foundational biochemistry mechanics: extreme violence; random; crowde

Does anyone know of resources or groups with a focus on educationally conveying a feel for foundational biochemistry mechanics: extreme violence; random; crowded; with locality and concentration enhancement? For instance, there's a video of simulated viral icosahedral capsid assembly, where the panels are tethered together to maintain proximity, so you get to see realistic assembly and disassembly and reassembly, temporary misfits and irreversible fails, and just a whole lot of flailing and slamming around until something clicks. It's ok for showing 10 nm scale object violence, but I've never seen anything good for 1 nm or 100 nm scale violence. And for concentration enhancement, I've only ever seen nice slides in research talks. Given how pervasive related misconceptions are, it'd be interesting to have a page to point to where the best available misconception antigens are slowly accumulated.

jfarlow 6y ago
One issue is that the scales don't well-match. And there are actually many time-scales beneath us, not just a few (and that biology/life is working at them all - including those on the order of millions of years. An event like a "protein folding" can take milliseconds, in a tube [1]. While atomic/biophysical/biochemical simulations have time-steps of femto-seconds. [1] https://www.youtube.com/watch?v=gFcp2Xpd29I https://www.youtube.com/watch?v=gFcp2Xpd29I From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890418/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890418/ "Traditional MD [Molecular Dynamics (protein folding)] simulations are limited in length by timestep limits. Studies by our group and others have shown that traditional MD is limited to timesteps of about 2 fs due to high-frequency resonance frequencies.1–3 Many biologically relevant motions occur on the microsecond to millisecond range, which is 9 to 12 orders of magnitude greater than the timesteps possible with traditional MD. Further, each step requires a costly force calculation (O(N) to O(N2)). As such, simulating medium-size proteins often requires months of computer time on a large distributed cluster such as Folding@home4,5 to simulate milliseconds of dynamics, while simulating a large protein (e.g. the β-2 Adrenergic Receptor) on biologically-relevant time scales (milliseconds through hours) using a standard desktop computer would take years. Thus, it is not feasible to simulate timescales of biological interest without substantial advances in MD methods." 12 orders of magnitude of difference in time is akin to the difference between causal events happening once per millisecond and those happening once per century. How do you show a movie capturing the nuance of someone's blink reflex, along with their birth life and death... https://www.youtube.com/watch?v=uHeTQLNFTgU https://www.youtube.com/watch?v=uHeTQLNFTgU https://www.youtube.com/watch?v=VdmbpAo9JR4 https://www.youtube.com/watch?v=VdmbpAo9JR4
- mncharity 6y ago
  > One issue is that the scales don't well-match. [...] many time-scales Indeed, teaching of scale pervasively fails. Physical, temporal, and other. But it's also taught very very badly. Thus it seems an open question how well it might be taught, and to whom. Might we teach it better? This[1] (mine) illustrates one speculative approach to teaching size down to atoms, for a young and outreach audience. And here's[2] an old attempt at helping develop a feel for torque, down to picoNewton-nanometers. Many years back I started on a temporal zoomer - don't know if it would have worked, but I've not seen anything similar since. I recall some work on teaching deep time in intro geology as being rather nice. Interactives with physically realistic molecular motion are vanishingly rare, and I've never seen a one with temporal zoom. So I suggest we're not even trying yet to explore whether we can teach this well. Those last two "Inner Life ..." videos are regrettably even more misleading than the original. Motion in the original was aphysical, but at least it was simple. Those two retain that aphysicality, and add aphysical jiggle, further obscuring how badly you're being misled. Creating educational content to support an excellent understanding of science is ghastly hard. So much so, that I suggest we're not even really trying yet. Which would mean how hard it will be to teach, once such content exists, is necessarily an open question. I wish I knew of folks exploring it. [1] first section of http://www.clarifyscience.info/part/Atoms http://www.clarifyscience.info/part/Atoms (page loads slowly - was meeting prep, not intended to be public) [2] http://www.clarifyscience.info/part/ZoomB?v=A&p=CK6Ji&m=torque http://www.clarifyscience.info/part/ZoomB?v=A&p=CK6Ji&m=torq...
  - jfarlow 6y ago
    Very cool! I've actually built similar models for myself to build that intuition. They're so helpful and generally hard to find. I agree that scale is generally poorly taught. I personally think having even a modest intuition for how to map physical knowledge to its appropriate 'scale' (time/space, from plank to universe) is one of the most straightforward ways to be "smart". And a great way to get to know the limits of our knowledge. I still haven't seen a video that matches my intuition. Which is unfortunate. I want to build a version of your scaler there, but for VR that you can slide up and down along at least time/scale axes - and maybe additional ones too.

jfarlow 6y ago

One issue is that the scales don't well-match. And there are actually many time-scales beneath us, not just a few (and that biology/life is working at them all - including those on the order of millions of years. An event like a "protein folding" can take milliseconds, in a tube [1]. While atomic/biophysical/biochemical simulations have time-steps of femto-seconds. [1] https://www.youtube.com/watch?v=gFcp2Xpd29I https://www.youtube.com/watch?v=gFcp2Xpd29I From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890418/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890418/ "Traditional MD [Molecular Dynamics (protein folding)] simulations are limited in length by timestep limits. Studies by our group and others have shown that traditional MD is limited to timesteps of about 2 fs due to high-frequency resonance frequencies.1–3 Many biologically relevant motions occur on the microsecond to millisecond range, which is 9 to 12 orders of magnitude greater than the timesteps possible with traditional MD. Further, each step requires a costly force calculation (O(N) to O(N2)). As such, simulating medium-size proteins often requires months of computer time on a large distributed cluster such as Folding@home4,5 to simulate milliseconds of dynamics, while simulating a large protein (e.g. the β-2 Adrenergic Receptor) on biologically-relevant time scales (milliseconds through hours) using a standard desktop computer would take years. Thus, it is not feasible to simulate timescales of biological interest without substantial advances in MD methods." 12 orders of magnitude of difference in time is akin to the difference between causal events happening once per millisecond and those happening once per century. How do you show a movie capturing the nuance of someone's blink reflex, along with their birth life and death... https://www.youtube.com/watch?v=uHeTQLNFTgU https://www.youtube.com/watch?v=uHeTQLNFTgU https://www.youtube.com/watch?v=VdmbpAo9JR4 https://www.youtube.com/watch?v=VdmbpAo9JR4

mncharity 6y ago
> One issue is that the scales don't well-match. [...] many time-scales Indeed, teaching of scale pervasively fails. Physical, temporal, and other. But it's also taught very very badly. Thus it seems an open question how well it might be taught, and to whom. Might we teach it better? This[1] (mine) illustrates one speculative approach to teaching size down to atoms, for a young and outreach audience. And here's[2] an old attempt at helping develop a feel for torque, down to picoNewton-nanometers. Many years back I started on a temporal zoomer - don't know if it would have worked, but I've not seen anything similar since. I recall some work on teaching deep time in intro geology as being rather nice. Interactives with physically realistic molecular motion are vanishingly rare, and I've never seen a one with temporal zoom. So I suggest we're not even trying yet to explore whether we can teach this well. Those last two "Inner Life ..." videos are regrettably even more misleading than the original. Motion in the original was aphysical, but at least it was simple. Those two retain that aphysicality, and add aphysical jiggle, further obscuring how badly you're being misled. Creating educational content to support an excellent understanding of science is ghastly hard. So much so, that I suggest we're not even really trying yet. Which would mean how hard it will be to teach, once such content exists, is necessarily an open question. I wish I knew of folks exploring it. [1] first section of http://www.clarifyscience.info/part/Atoms http://www.clarifyscience.info/part/Atoms (page loads slowly - was meeting prep, not intended to be public) [2] http://www.clarifyscience.info/part/ZoomB?v=A&p=CK6Ji&m=torque http://www.clarifyscience.info/part/ZoomB?v=A&p=CK6Ji&m=torq...
- jfarlow 6y ago
  Very cool! I've actually built similar models for myself to build that intuition. They're so helpful and generally hard to find. I agree that scale is generally poorly taught. I personally think having even a modest intuition for how to map physical knowledge to its appropriate 'scale' (time/space, from plank to universe) is one of the most straightforward ways to be "smart". And a great way to get to know the limits of our knowledge. I still haven't seen a video that matches my intuition. Which is unfortunate. I want to build a version of your scaler there, but for VR that you can slide up and down along at least time/scale axes - and maybe additional ones too.