Ciro Santilli
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Whenever Ciro Santilli learns about molecular biology, he can't help but to feel that it feels like programming, and notably systems programming and computer hardware design.
In some sense, the comparison is obvious: DNA is clearly a programmable medium like any assembly language, but still, systems programming did give Ciro some further feelings.
- The most important analogy perhaps is observability, or more precisely the lack of it. For the computer, this is described at: The lower level you go into a computer, the harder it is to observe things.And then, when Ciro started learning a bit about biology techniques, he started to feel the exact same thing.For example when he played with E. Coli Whole Cell Model by Covert Lab, the main thing Ciro felt was: it is going to be hard to verify any of this data, because it is hard/impossible to know the concentration of each element in a cell as a function of time.More generally of course, this is exactly why making any biology discovery is so hard: we can't easily see what's going on inside the cell, and have to resort to indirect ways of doing so..This exact idea was highlighted by I should have loved biology by James Somers:
For a computer scientist, a biologist's methods can seem insane; the trouble comes from the fact that cells are too small, too numerous, too complex to analyze the way a programmer would, say in a step-by-step debugger.
And then just like in software, some of the methods biologists use to overcome the lack of visibility have direct software analogues:- add instrumentation to cells, e.g. GFP tagging comes to mind
- emulation, e.g. E. Coli Whole Cell Model by Covert Lab
- The boot process is another one. E.g. in x86 the way that you start in 16-bit mode, largely compatible into the 70's, then move to 32-bit and finally 64, does feel a lot the way a earlier stages of embryo development looks more and more like more ancient animals.
Ciro likes to think that maybe that is why a hardcore systems programmer like Bert Hubert got into molecular biology.
Some other people who mention similar things:
- I should have loved biology by James Somers highlights the computer abstraction layer analogy between the two:
Everywhere you look - the compiler, the shell, the CPU, the DOM - is an abstraction hiding lifetimes of work.