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Discussion (30 Comments)Read Original on HackerNews
“The Machinery of Life” by David Goodsell is full of illustrations like the ones show in the article and really gave me a sense of what k might imagine when reading about the cell.
“Cell Biology by the Numbers” by Ron Milo and Rob Philips is full of order of magnitude calculations of about the processes of the cell. How fast are they, over what distance, how much, etc.
Every part of this passage is a shockingly accurate description of myself. I felt that I was bad at math and did a biochem degree because it meant I could skip Cal III. Now, I'm a computational biologist and I've mostly made up with math.
One of the most fascinating parts to me was DNA transcription. The engineering is quite precise.
Found the video I was referring to: https://www.youtube.com/watch?v=7Hk9jct2ozY
For illustration, consider the classic animation of a walking kinesin towing a vesicle. One could jiggle-ify it. But that won't convey that during every step, the vesicle has done a "balloon in a hurricane" exploration of every possible position it can reach while remaining tethered. Won't clarify that the very very misleading "I'm just a peaceful barge" vibe is entirely animation fantasy. Secondary content could have been added to defuse this negative educational impact, but the choice was made to optimize for, and I'm quoting, "pretty".
Jiggle-ification takes perhaps the biggest educational downside of these animations, and makes it even more misleading.
One thing that these animations always remind me of is that speeds at that level are tied to size. We're use to a world where birds and cars are faster than pollen and insects (mostly), but the fidgety twerking of all those big proteins is due to collisions with higher-velocity, invisibly small molecules like water (Brownian motion). When was the last time a pollen grain made you flinch? Everything is kinetic/EM energy exchange; everything is in the gray area between Newtonian and quantum physics. (Shout out to Einstein, but also Boltzmann through Dirac.)
I didn't get the "miles of DNA" reference. A single strand of DNA is approx 3 meter in length when uncoiled. Now I'm thinking how many strands may be replicated at a time.
The painting is wonderful. Yes, it's a snapshot in time of a dynamic state. All paintings are!
The first few Units cover all the basics: chemistry of life and energy, molecular biology, cell biology, and genetics. From there you can branch out into anything.
Maybe an educational text for the laymen has summarised this recently but I'm not aware of one. Most Biology from your school days have been rewritten.
I will have to re-read Molecular Biology of the Cell, 7th Edition, 2022. I read the 3th edition and it has changed dramatically since.
You can download it on Anna's Archive or order it at the usual suspects https://www.amazon.com/s?k=Molecular+Biology+of+the+Cell%2C+...
> The first time I did these calculations, I felt an intense appreciation for biology. And now, I want everyone else to feel the same. We ought to teach students of biology to think as mathematicians: to carefully quantify biology, to think in absolute units, and to develop a feeling for the organism.
It was interesting to read this article, but I think I would’ve understood a lot more if this entire piece had been (or were) an animated video that described it. Text and a few animations don’t do enough justice for the passion, knowledge and detail that’s in this article, IMO.
Hold up, My own inexpert "numerical intuition" is having problems here.
If polymerase converts 40 bases/sec, and travels ~20m /sec, how on earth is one base pair 2 meters long?
I assume what the author means is that the average conversion work done by each protein is 40 base pairs per second, however it spends most the time "seeking" rather than "converting"?
Bit nitpicky here but ... he wrote a typical E. coli cell.
Naturally bacteria have different size ranges, depending on many factors - nutrients, temperature, genome and so forth; e. g. look at how huge Thiomargarita namibiensis is.
But the 1 µm as average here given for E. coli, is not correct:
https://bionumbers.hms.harvard.edu/bionumber.aspx?id=117344&...
Length 1.78±0.54 μm
So while +/- at the lower end may be 1.24 µm, the max range here would be 2.42 µm, which is what I had more in mind (e. g. roughly about 2µm). I don't have all of the data to be able to say which is the exact value, but I think the website at bionumbers.hms.harvard.ed is more realistic, so I would say that E. coli's best average is more at 2µm than 1µm.