Incoming links: Bert Hubert
Co-founder of PowerDNS, an open source dNS implementation.
Homepage: berthub.eu/ says:.
All stuff Ciro cares about too! Cool dude! In particular Ciro loved his quote of I should have loved biology.
All stuff Ciro cares about too! Cool dude! In particular Ciro loved his quote of I should have loved biology.
He's writing a fun-sounding book about molecular biology as of 2022: berthub.eu/dna-book. Appears to be closed source though. Ciro wonders if he really needs to sell the book for money after all those years though, rather than just publishing it online for free.
Looking at Bert just brings the Dutch Golden Age, and more in particular Antonie van Leeuwenhoek to mind. Epic.
How life is Digital by Bert Hubert (2021)
Source. Just a "boring" overview of the central dogma of molecular biology ;-)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:
The natural sciences are not just a tool to predict the future.
They are a reminder that the lives that we live daily are mere illusions, religious concepts such as Maya and Samsara come to mind.
We as individuals perceive nothing about the materials that we touch every day really work, nor more importantly how our brain and cell work.
Everything is magic out of our control.
The natural sciences allow us peek, with huge concentrated effort, into tiny little bits a little of those unknowns, and blow our minds as we notice that we don't know anything.
For all practical purposes in life, there is a huge macro micro gap. We are only able to directly perceive and influence the macro events. And through those we try to affect micro events. Because for good or bad, micro events reflect in the macro world.
It is as if we live in a different plane of existence above molecules, and below galaxies. The hierarchy of Figure "xkcd 435: Fields arranged by purity" puts that nicely into perspective, shame it only starts at the economical level, not going up to astronomy.
The great beauty of science is that it allows us to puncture through some of the layers of reality, either up or down, away from our daily experience.
And the great beauty of artificial intelligence research is that it allows to peer deeper into exactly our layer of existence.
Every one or two weeks Ciro Santilli remembers that he and everything he touches are just a bunch of atoms, and that is an amazing feeling. This is Ciro's preferred source of Great doubt. Another concept that comes to mind is when you see it, you'll shit bricks.
Perhaps, the feeling of physics and the illusion of life reaches its peak in molecular biology.
Just look at your fucking hand right now.
Do you have any idea of each of the cells in it work? Isn't is at least 100 times more complex than the materials of the table you hand is currently resting on?
This is the non-science fiction version of the lotus-Eater Machine.
Alan Watts's "Philosopher" talk mentions related ideas:
The origin of a person who is defined as a philosopher, is one who finds that existence itself is exceedingly odd.
The toddler of a friend of Ciro Santilli's wife asked her mum:Our perception of the macroscopic world is so magic that children have to learn the difference between living and non-living things.
Why doesn't my tiger doll close its eyes when we sleep?
James Somers put it very well as well in his article I should have loved biology by James Somers, this quote was brought to Ciro's attention by Bert Hubert's website[ref].The same applies to other natural sciences.
I should have loved biology but I found it to be a lifeless recitation of names: the Golgi apparatus and the Krebs cycle; mitosis, meiosis; DNA, RNA, mRNA, tRNA.In the textbooks, astonishing facts were presented without astonishment. Someone probably told me that every cell in my body has the same DNA. But no one shook me by the shoulders, saying how crazy that was. I needed Lewis Thomas, who wrote in The Medusa and the Snail:For the real amazement, if you wish to be amazed, is this process. You start out as a single cell derived from the coupling of a sperm and an egg; this divides in two, then four, then eight, and so on, and at a certain stage there emerges a single cell which has as all its progeny the human brain. The mere existence of such a cell should be one of the great astonishments of the earth. People ought to be walking around all day, all through their waking hours calling to each other in endless wonderment, talking of nothing except that cell.
Alan Watts' "Philosopher" talk (1973)
Source. Lecture given at UCLA on 1973-02-21. Some key quotes from the talk:The origin of a person who is defined as a philosopher, is one who finds that existence itself is exceedingly odd.