Living cells are very fast and crowded places (2012)

In my experience, K-12 and 4-year college were all about "useful abstractions and assumptions" to help people understand concepts, and grad material was about slowly peeling away those assumptions and abstractions that made it convenient to learn and teach but were never really there (at least not guaranteed to be there).

One of the best teachers I had forced us to write or assumptions down every time for every problem on the test. If you didn't write any, you got zero credit. "What's the point in learning equations if you don't know when they stop applying?" You also got _negative_ credit if you applied the wrong assumptions because you were just guessing or going on habit.

Luckily, someone did an experiment similar to this one. They wrote the genome (and ONLY the genome) of a unicellular organism synthetically. Then they've removed the genome of an existing cell of a different species. The've then inserted the genome they created from scratch. The genome worked and produced versions of everything it needed, and cell division happened etc. Everything was produced & worked.

So - they bootstrapped that genome using machinery of the empty cell w/o the genome, but from that point on, the new genome produced everything needed for many other cells & itself. (Venter's papers creating synthetic life)

In fact, following that, the same team refactor that genome to create a minimum viable genome, the MVP of genomes if you will, just to see how few genes you can get away with!

Here's an article: http://www.nature.com/news/minimal-cell-raises-stakes-in-rac...

> cells are extremely crowded and busy places

Cells are extremely crowded and busy... and random and violent places.

Molecular biology dances in a nano moshpit from hell.

The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of Goodsell's crowded proteins, fading to sparseness, could have reduced its reinforcement of the "big empty cell" misconception.

And it doesn't just hide almost everything (crowded), or slow everything way down (busy), or show completely aphysical rendezvous and docking (random), but it also strings together carefully selected snapshots to tell a misleadingly peaceful narrative (violent).

That kinesin walking along, towing a vesicle? Its "feet" are actually madly flapping around. It is randomly "stepping" back and forth - only its net motion is biased. And between one net step and the next, that big vesicle has been slammed around to every position within reach of that tether. It's a random walk on a leash. Reality isn't a donkey quietly towing a slowly-moving barge. It's a balloon flapping madly in a hurricane, tethered to an intoxicated panicked mouse clinging to a rope.

Biology rides a ragged energetic edge, between things being too strong, too expensive to dis/assemble, and being smashed to pieces too quickly.

More generally, the video illustrates a pervasive problem with science education media. Even when done "well", some aspects are done with great skill and care, while other aspects are silently left utterly bogus. Pity the students, who lack the knowledge to sort out which is which. So rich ecologies of misconceptions are established. And are intractably expensive to displace. It's so easy to create content that leaves students worse off than if they had seen nothing at all. So that's, in general, what we create.

The violence of nanoscale is a critical, defining characteristic. That so many biology undergrads are unclear on it, let alone high-school and primary students, shows just how very far we have to go before teaching deep understanding, transferable knowledge, and cross-cutting principles, finally becomes a reality. Or more upbeat, how breathtakingly awesome science education might eventually become.

(FWIW, the top section of my very crufty http://www.clarifyscience.info/part/Atoms might help some with getting a handle on at least the size aspect of small things.)

> It's a balloon flapping madly in a hurricane, tethered to an intoxicated panicked mouse clinging to a rope

Welp, my desk is now covered in coffee. Thanks for that one, I'll be stealing it ;)

It may be better to think of a cell as more of a liquid crystal than anything else, considering the densities. The synapse of neurons is incredibly dense with structures and scaffolding proteins. Even most grad students still think that the ER is a soma kinda thingy, but it goes all the way up the dendrite to just kiss the synaptic buton. The ER is really more of a cell inside a cell, or rather the cell membrane is just a latex bodysuit for the ER.

It's always amazing to me when I heard guys like Elon and Kurzweil talking about MMIs and how you are never gonna actually die, you'll just upload your brain, somehow. Like, they really have no idea how clueless we are in biology. Eric Schmidt goes to parties in West LA about living forever. It's crazy. We are decades away from even a cursory understanding of 1 cubic mm of brain tissue, with all the neurons, astrocytes, glia, mesenchymal cells, etc. Like, we just found out that the immune system is in your brain too, like 3 years ago. I actually think Elon has better odds of putting 0.6 of a Saturn V on Mars and not having it explode before we have a MMI.