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

The thing that drove this home for me were the biovisions animations which got me to go back and basically learn high school biology. Seeing the mechanical nature of gene transciption and chemical signaling blew my mind. ▶ this video link On the other hand, I don't buy his thing about wishing his high school teacher had presented it differently. No on else can make you interested in this stuff. The best they can do is provide resources like the ones above.

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

What a beautiful depiction. Reminds me of high fidelity 3D animation videos I used to watch about DNA replication, cell signalling etc. One of the most fascinating parts to me was DNA transcription. The engineering is quite precise. Found the video I was referring to: ▶ this video

>> I think our brains are machines for predicting what happens next. > Technologist thinks that humans are machines (breaking news) While I also dismiss or at least be careful of the inherent biases of technocratic viewpoints, humans and life in general are very much made of many types of machines. Take a look at these videos: link ▶ this video I.e., life is insane and bewildering.

Reminds me of this pretty common but all the more spectacular: a close-up of super complex production line (gene transcription) driven by DNA strands: ▶ this video / ▶ this video

I like the wehi videos because they take effort to make the molecular motions appear to be random, a result of stuff blundering about: ▶ this video

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.

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

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.

When I watch animations of how the cell works at a molecular level [0], I can't help but wonder how can this level of sheer complexity in dna transcription, protein production, and many other supporting functions in a single cell works in perfect harmony. It's mind boggling. I admit that I'm biased, but I don't think this could have evolved through random processes. I'm a believer in Intelligent Design. link ▶ this video link

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