Molecular biology feels like systems programming by 
Ciro Santilli 35 Updated 2025-01-29 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-01-29 +Created 1970-01-01Whenever 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:
Now that we've done one section manually, let's graduate and use the
readelf -S of the other sections: [Nr] Name Type Address Offset
Size EntSize Flags Link Info Align
[ 2] .text PROGBITS 0000000000000000 00000210
0000000000000027 0000000000000000 AX 0 0 16.text is executable but not writable: if we try to write to it Linux segfaults. Let's see if we really have some code there:objdump -d hello_world.ohello_world.o: file format elf64-x86-64
Disassembly of section .text:
0000000000000000 <_start>:
0: b8 01 00 00 00 mov $0x1,%eax
5: bf 01 00 00 00 mov $0x1,%edi
a: 48 be 00 00 00 00 00 movabs $0x0,%rsi
11: 00 00 00
14: ba 0d 00 00 00 mov $0xd,%edx
19: 0f 05 syscall
1b: b8 3c 00 00 00 mov $0x3c,%eax
20: bf 00 00 00 00 mov $0x0,%edi
25: 0f 05 syscallIf we grep
b8 01 00 00 on the hd, we see that this only occurs at 00000210, which is what the section says. And the Size is 27, which matches as well. So we must be talking about the right section.This looks like the right code: a
write followed by an exit.The most interesting part is line to pass the address of the string to the system call. Currently, the This modification is possible because of the data of the
a which does:movabs $0x0,%rsi0x0 is just a placeholder. After linking happens, it will be modified to contain:4000ba: 48 be d8 00 60 00 00 movabs $0x6000d8,%rsi.rela.text section. University of Oxford spinout company by Ciro Santilli 35 Updated 2025-01-29 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-01-29 +Created 1970-01-01
Pinned article: ourbigbook/introduction-to-the-ourbigbook-project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivative - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.
Figure 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. . You can also edit articles on the Web editor without installing anything locally. Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. - Internal cross file references done right:
- Infinitely deep tables of contents:
Figure 6. Dynamic article tree with infinitely deep table of contents.Live URL: ourbigbook.com/cirosantilli/chordateDescendant pages can also show up as toplevel e.g.: ourbigbook.com/cirosantilli/chordate-subclade
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
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