Comments on: I have to tell you, none of us were high for this

I have to tell you, none of us were high for this

nickmark — Wed, 17 Sep 2025 12:19:04 -0800

This is not a post about the 1971 film Protein Synthesis: An Epic on the Cellular Level, produced on the campus of Stanford University. That's available on YouTube and through the UCSD library, and we've already had two posts about it specifically, plus it was included in a 2010 MegaPost on bioanimation and other science education tools. No, this post is instead about the making of the 1971 film Protein Synthesis: An Epic on the Cellular Level, produced on the campus of Stanford University.

By: darkstar

darkstar — Wed, 17 Sep 2025 12:36:44 -0800

Oh my. I hadn't seen this video before. It's glorious.

By: BobTheScientist

BobTheScientist — Wed, 17 Sep 2025 13:32:30 -0800

Jane Gitschier, the "making of" author, is ~~fakkin' A~~ kind of amazing. For 10 years between 2005 and 2015 she interviewed N=45 'famous scientists' in a regular PLOS Genetics column. Archived here. Her leads and questions yield a great insight into the process of science and creativity. Should be a book. Heck, Gitschier doesn't even have a page on Wikipedia.

By: mpark

mpark — Wed, 17 Sep 2025 14:10:27 -0800

Great read; thanks, nickmark! Very amused by this bit

"I have to tell you, none of us were high for this," said Redding.

and the author's response

Thank you for clarifying.

By: darkstar

darkstar — Wed, 17 Sep 2025 14:13:50 -0800

Thank you for this post, nickmark -- it is highly relevant to my interests, and I'm shocked that I've not seen it before. I teach university Chemistry (General and Organic). In my General Chemistry lab, when I'm teaching kinetics (second semester college chemistry), we use a common experiment called the "Iodine Clock Reaction". It uses a color change in an iodine-containing solution to determine the rate of reaction, which can be modulated based on the temperature at which the students run the reaction. They are able to determine the rate constant, rate law, etc. -- it's a really useful experiment for probing these basic kinetics concepts. The experiment involves a number of interconnected chemical reactions, however, so students aren't able to easily grasp exactly what's going on in solution, why we add thiosulfate, etc. To facilitate the learning, I developed a short "play" that the class performs. We have students portray iodine molecules, thiosulfate ions, peroxide ions, starch molecule, etc. I have them move around the room and engage with each other as I narrate what is happening. When an un-reduced iodide ion finally makes it past all of the exhausted thiosulfates, and finally encounters a starch molecule to "turn blue", students have enacted the whole process. I have run pre- and post-quizzes to assess student understanding of the chemical processes in this experiment, and the "play" has a dramatic (heh) effect in helping students understand what is going on throughout this experiment. I've heard anecdotally from many students that they really appreciated being able to visualize these reactions in this way. As I'm looking at the 1971 video, I'm struck how it brings poetry, music, and dance to bear on visualizing what is otherwise a very complex series of biochemical reactions. It is furthermore striking that this piece of performance art also leverages the end result of centuries of scientific inquiry to elaborate an understanding a key cellular process of biochemical life. This marriage of teaching a fundamental, existential set of biochemical processes with the expressivity and passion of the performing arts is absolutely inspiring, and I will be honest that I teared up while watching the video. Thank you again for posting this treasure.

By: darkstar

darkstar — Wed, 17 Sep 2025 14:43:41 -0800

Argh: "When un-reduced iodine finally makes it past all of the exhausted thiosulfates..." which permits it to form the tri-iodide ion, and then forms the iodine-starch complex that has the distinctive blue color.

By: nickmark

nickmark — Wed, 17 Sep 2025 14:59:50 -0800

I can't take much credit; my (not-on-MeFi) wife sent me both the article and the YouTube video. I've been familiar with the film since college; one of the biology professors made it a standard part of the curriculum and despite never taking any bio I somehow got exposed to it in those days. But my wife actually understands the stuff going on and gets very excited about it. It was a topic of conversation last night when one of our teens was helping the other with high school biology homework; you can't really mention protein synthesis around my wife without her making you watch the film. (The aforementioned biology professor was one of her favorite profs in college.) Personally, as a non-scientist, I actually think there are some limitations to this approach: a lot of the language we use to describe biochemistry (and evolution and genetics) tends to imply a degree of intentionality in the reactions (this compound "wants" to bond with this other, the DNA carries "instructions"). This approach, to me, leans into some of that and emphasizes it. For me, that was always kind of confusing; I never really understood the idea that a molecule could "deliver instructions." What it's really doing, of course, is kicking off a new set of reactions, which will kick off more, etc. To me, using intentional (or maybe "anthropomorphizing" is what I really mean) language kind of obscures the amazingness of the fact that those tiny, totally involuntary interactions are what life is really made of. But it's also true that my high school science education was... less than ideal, even when I was paying attention, so maybe I was always going to be prone to confusion.

By: darkstar

darkstar — Wed, 17 Sep 2025 15:21:04 -0800

Yes, this is a challenge we constantly have to be on guard for and speak about intentionally in class. "When we say that these particles "want" to do such and such, we must remember that there is no intent...just energy minima, thermodynamics, kinetics, steric hindrance, solvent effects, orbital overlap, etc." A classic example is the fantastic video developed for Harvard, "The Inner Life of the Cell." This superb educational video actually makes many artistic decisions in order to streamline and declutter what would otherwise be a huge muddled mess of interacting particles, so you can see what is going on in the process. The most well-known segment begins at 1:17 in the video, when a kinesin is shown proceeding in what appears to be a very intentional, "step-by-step" walking motion along microtubules, using ATP as its energy source. Each step, around 8 nanometers, is taken by one of its two "feet" (motor domains), coordinated by conformational changes that occur when ATP binds and is hydrolyzed. This process allows kinesin to efficiently transport cellular cargo from the cell's center to its periphery. However, in reality, this is greatly oversimplified in its depiction. In fact, there is both forward and backward motion at each step in the process, but it just happens that there is an energy minimum in the forward direction, so that when the forward step is made, it is energetically preferred. So the kinesin is juddering all about, and when it locks in to the forward step, it advances that step, and then is in position for another dance forward and backward until the next forward step locks in. There is no "intentionality" to this process at all. It's the equivalent of a chemical "ratchet" which energetically favors movement in one direction along the microtubule. That did not stop some Intelligent Design advocates from pointing to this video, and specifically to this segment, to show how "obvious" it is that there is intelligent design to this process, since the kinesin is moving with such evident purpose. If I recall correctly, they started playing this video in their presentations, making these unscientific claims, which led to -- I believe -- a copyright infringement claim, to stop them from doing so. After which, the ID folks then re-created their own video so they could use it, but in doing so, they made what were clearly derivative artistic decisions that were also infringing. (The cellular processes really are much more muddled, compacted, and confounded than the video depicts.) But I still sometimes find myself self-correcing when I use anthropomorphizing language when talking about biochemical phenomena. (The nucleophile is not "looking for" a center of electron deficiency, etc.)

By: darkstar

darkstar — Wed, 17 Sep 2025 16:04:24 -0800

Heh, and it just occurs to me: even the term we use for "nucleophile" has an implicit anthropomorphizing etymology ("nucleus-loving")!

By: chromecow

chromecow — Wed, 17 Sep 2025 16:08:11 -0800

This may be the best science film I have ever seen.

By: BobTheScientist

BobTheScientist — Thu, 18 Sep 2025 04:10:27 -0800

darkstar: The most well-known segment begins at 1:17 in the video, when a kinesin is shown proceeding in what appears to be a very intentional, "step-by-step" walking motion along microtubules, using ATP as its energy source. HoHo. In ~2015, that kinesin clip was out-taked and tagged as "What you see is a myosin protein dragging an endorphin along a filament to the inner part of the brain's parietal cortex which creates happiness. Happiness. You're looking at happiness.". I blogged a rebuttal that hinged on relative sizes of the supposed players "It's a cartoon! And whatever is going on, the caption doesn't match the scaling. Myosin is a long string of a protein about 2000 AA / 160nm long. Endorphins OTOH are chunky but much smaller molecules about 30 AA long. The huge green thang in the gif could be a cell - 10,000nm in diameter - but it looks too small to be 100x wider than the myosin is long. So I'm at a loss but my skeptic hat is throbbing . . . Silly me. If it's too big to be a macromolecule and too small to be a cell it must be a sub-cellular organelle". Google shoved my explanation up its algorithm, so that post was famous for 15 minutes and remains my most pageviewed contribution to the collective.

By: fantabulous timewaster

fantabulous timewaster — Thu, 18 Sep 2025 13:47:16 -0800

I have been seeing that kinesin clip out of context for ages, and I'm glad to finally know where it came from. Folks who like this genre might also enjoy Clockwork, a YouTube channel which produces biochemistry animations. Clockwork's animations have a bit of a herky-jerky feel to them, which is totally appropriate for a physical situation where you are going to have contributions from Brownian motion and other stochasticity.

By: indianbadger1

indianbadger1 — Thu, 18 Sep 2025 14:38:20 -0800

Speaking on protein synthesis at the cellular level, this image of what a cell looks like when you have all the stuff in one place always fascinates me. There's a lot of stuff crammed into a tiny space!

By: BobTheScientist

BobTheScientist — Wed, 24 Sep 2025 23:26:35 -0800

Nikon Small World in Motion Comp 2025 features a baby echinoderm dragging itself forward one tube-foot at a time [YT 30sec] just like that kinesin molecule but 10,000x bigger. Nature? So fractal