DNA animation (2002-2014) by Drew Berry and Etsuko Uno wehi.tv #ScienceArt

It takes downloading one of these files, gunzipping them, extracting the tar and opening up a JSON file at random to really understand just how distant the title of the project is from its contents. I fully realize this is about natural language processing, but... this is beyond reach. You'd have to teach a computer to become a doctor first. Feels like where AI (and computing in general) should go in case of Covid-19 and other illnesses is analyzing and simulating how the heck we work to begin with. Take a few minutes to watch these videos of supercomputer simulations that show -- fragments -- of the fundamentals of how we exist. Multi Scale Modeling of Chromatin and Nucleosomes - [link] DNA animation showing realtime DNA replication - [this video] Somewhere in these mind-boggling processes is where the disruption called Covid-19 puts a stick in our wheels. Compared to the complexity of the simulations, abstract ideas contained in these files are so macroscopic by comparison. It's both humbling and awe-inspiring.

Some other good ones: [this video] [link] The GP is right in that our intuitions aren't cutting it down at the bottom. All these animations tend to edit out the water molecules so that the audience can understand better. The proteins aren't colored blobs at all. At these scales you'd clearly see individual atoms instead of blobs. But watching a bunch of really detailed atomic ball-stick models would be confusing. And not only are the H2Os battering everything like TIE fighters in the Hoth asteroid field [0], there are ions in there too (Na, K, Cl, etc) that really effect the cell. The membranes are also edited, as many cells are porcupined with receptors like an over crowded wave pool [1]. In addition to the water/saline being edited out, most of the other proteins, vesicles, and interior membranes are also gone for the sake of clarity. There is nearly no free 'space' in the cell, think of a really crammed subway car [2], with the air being like the water/saline. But only much much tighter. The cell is more like a frantically efficient liquidy crystaly thingy than a wonky wobbly blobby poofed-up juice box. And each one is utterly deeply profoundly fascinating. [0] [link] [1] [link] [2] [link]

ATP synthase is amazing. It uses the driving force from the potential gradient (aka voltage) built by the proton pump in the first video to spin at ~21,000 rpm and crank out ATP. I read that your body creates (and then consumes) about its own weight in ATP every day. This channel has a ton of great videos: [link] Here's one on kinetichore and mitosis (which also shows kinesin and dynein which are comically odd) - [link] There's a collection of their DNA ones here: [this video] Here's another view of the ATP synthesis process that shows the chaos a bit more: [link] When I think of these systematically I just wonder what the intermediate steps were. The proton pump uses energy to create the potential gradient that ATP synthase runs on. You can't have a proton gradient without the proton pump, and without the proton gradient you don't have ATP. So these two exquisitely complex machines depend on each other and had to evolve together. It boggles my mind. Edit: Ah! Was looking for this one, sodium potassium pump - [link] This is how our neurons propagate signals. They are driven by ATP.

I'm working on a project in malaria genetics this summer, and I was shocked to find out that the entire analysis toolkit is entirely based on math and statistics (and some non-trivial stuff too, e.g. hidden Markov models to predict CNV). Genotype likelihoods throw an extra wrench into the process, since even basic stuff like predicting allele frequencies requires a maximum likelihood estimator instead of simple counting. This whole area was quite eye-opening, and I'm still amazed that reading billions of base-pairs in DNA sequencing reliably works. Also gotta shout out to these incredible molecular animations by WEHI: [this video]

Even if that narration is something easily relatable by software developers, the simplification is too big to allow the reasonable comprehension of the subject. So I still suggest anybody interested to really try to learn more about the actual science topics, instead of comforting themselves falsely believing they "understood" anything. For the start, I would suggest the nicely produced courses: [link] [link] Just to illustrate how non-intuitive our "common sense" is, the current estimate of the number of human cells in human body is 30,000,000,000,000 (30e12). The current estimate of the number of bacteria in human body (in the mouth and guts) is 3 times more. The size of human genome (present in each human cell) is around 3 billion (3e9) base pairs (encoding information units of DNA [link] ). But not all the information is in the DNA alone. The biochemical reactions happen in parallel even when a single cell is observed. The reconstruction of gene transcription, also played in the speed it actually happens: [this video]