Matrix multiplication by Ciro Santilli 40 Updated 2025-07-16
Since a matrix can be seen as a linear map , the product of two matrices can be seen as the composition of two linear maps:
One cool thing about linear functions is that we can easily pre-calculate this product only once to obtain a new matrix, and so we don't have to do both multiplications separately each time.
UniProt for example describes YaaX as "Uncharacterized protein YaaX".
As function is discovered, they then change it to a better name, e.g. to names such as the E. Coli K-12 MG1655 transcription unit thrLABC proteins all of which have a clear name due to threonine.
There are many other y??? as of 2021! Though they do tend to be smaller molecules.
From this we see that there is a convention of naming promoters as protein name + p, e.g. the first gene in E. Coli K-12 MG1655 promoter thrLp encodes protein thrL.
It is also possible to add numbers after the p, e.g. at biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=PM0-45989 we see that the protein zur has two promoters:
  • zurp6
  • zurp7
TODO why 6 and 7? There don't appear to be 1, 2, etc.
That page lists several components of the promoter, which we should try to understand!
After the first gene in the codon, thrL, there is a rho-independent termination. By comparing:we understand that the presence of threonine or isoleucine variants, L-threonyl and L-isoleucyl, makes the rho-independent termination become more efficient, so the control loop is quite direct! Not sure why it cares about isoleucine as well though.
TODO which factor is actually specific to that DNA region?
Mycoplasma genitalium by Ciro Santilli 40 Updated 2025-07-16
Size: 300 x 600 nm
Has one of the smallest genomes known, and JCVI made a minimized strain with 473 genes: JCVI-syn3.0.
The reason why genitalium has such a small genome is that parasites tend to have smaller DNAs. So it must be highlighted that genitalium can only survive in highly enriched environments, it can't even make its own amino acids, which it normally obtains fromthe host cells! And because it cannot do cellular respiration, it very likely replicates slower than say E. Coli. It's easy to be small in such scenarios!
Power, Sex, Suicide by Nick Lane (2006) section "How to lose the cell wall without dying" page 184 has some related mentions puts it well very:
One group, the Mycoplasma, comprises mostly parasites, many of which live inside other cells. Mycoplasma cells are tiny, with very small genomes. M. genitalium, discovered in 1981, has the smallest known genome of any bacterial cell, encoding fewer than  genes. Despite its simplicity, it ranks among the most common of sexually transmitted diseases, producing symptoms similar to Chlamydia infection. It is so small (less than a third of a micron in diameter, or an order of magnitude smaller than most bacteria) that it must normally be viewed under the electron microscope; and difficulties culturing it meant its significance was not appreciated until the important advances in gene sequencing in the early 1990s. Like Rickettsia, Mycoplasma have lost virtually all the genes required for making nucleotides, amino acids, and so forth. Unlike Rickettsia, however, Mycoplasma have also lost all the genes for oxygen respiration, or indeed any other form of membrane respiration: they have no cytochromes, and so must rely on fermentation for energy.
Downsides mentioned at youtu.be/PSDd3oHj548?t=293:
Data:
Lattice Microbes by Ciro Santilli 40 Updated 2025-07-16
GPU accelerated, simulates the Craig's minimized M. genitalium, JCVI-syn3A at a particle basis of some kind.
Lab head is the cutest-looking lady ever: chemistry.illinois.edu/zan, Zaida (Zan) Luthey-Schulten.
Ciro Santilli by Ciro Santilli 40 Updated 2025-07-16
Quick facts:
Other people with the same name are listed at Section "Ciro Santilli's homonyms".
Figure 1.
19th century illustration of the Journey to the West protagonist Sun Wukong
. Source.
Sun Wukong (孙悟空) is a playful and obscenely powerful monkey Journey to the West. He protects Buddhist monk Tang Sanzang, and likes eating fruit, just like Ciro. Oh, and Goku from Dragon Ball is based on him. His japanese name is "Sun Wukong" (same Chinese characters with different Japanese pronunciation) for the love. His given name "Wukong" means literally "the one who mastered the void", which is clearly a Dharma name and fucking awesome in multiple ways. This is another sad instance of a Chinese thing better known in the West as Japanese.
It is worth noting however that although Wukong is extremely charming, Ciro's favorite novel of the Four Great Classic Novels is Water Margin. Journey to the West is just a monster of the week for kids, but Water Margin is a fight for justice saga. Sorry Wukong!
Figure 2.
Ciro Santilli playing with a pipette at the University of Cambridge circa 2017
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The photo was taken in an open event organized by the awesome Cambridge Synthetic Biology outreach group, more or less the same people who organize: www.meetup.com/Cambridge-Synthetic-Biology-Meetup/ and who helped organize Section "How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it".
Taking part in such activities is what Ciro tries to do to overcome his lifelong regret of not having done more experimental stuff at university. Would he have had the patience to handle all the bullshit of the physical word without going back to the informational sciences? Maybe, maybe not. But now he will probably never know?!
Notice the orange high visibility cycling jersey under the lab coat, from someone who had just ridden in from work as fast as possible as part of his "lunch break". It is more fun when it is hard.
Figure 3.
Scribe Jean Miélot, 15th century
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Ciro Santilli fantasizes that he would have make a good scribe in the middle ages, partly due to his self diagnosed graphomania, but also appreciation for foreign languages, and his mild obsession with the natural sciences.
OurBigBook.com is Ciro's view of a modern day scriptorium, except that now the illuminations are YouTube videos.
The job of a Internet-age scribe is basically that of making knowledge more open, legally extracting it from closed copyrighted sources, and explaining your understanding of it to the wider world under Creative Commons licenses on the web. And in the process of greater openness, given a well organized system, we are able combine the knowledge of many different people, and thus make things more understandable than any single/few creator closed source source could ever achieve.
Ciro once saw some cartoon on Wikipedia help pages of a turtle with a book in one hand, and typing into Wikipedia on its computer, TODO find it. That cartoon summarizes well the modern scribe life.
Another analogous version of this fantasy more in touch with Ciro's sinophily is the ideal of the Chinese scholar, notably including their stereotypical attributes such as mastery of the Four arts.
Figure 4.
Ciro Santilli piling boxes as a child
. A natural born engineer.
Figure 5.
Ciro Santilli waving hello in infrared.
More info at: Figure "Ciro Santilli waving hello in infrared".

Pinned article: 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:
  1. 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-calculus
    Articles 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
  2. 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.
    Figure 2.
    You can publish local OurBigBook lightweight markup files to either https://OurBigBook.com or as a static website
    .
    Figure 3.
    Visual Studio Code extension installation
    .
    Figure 4.
    Visual Studio Code extension tree navigation
    .
    Figure 5.
    Web editor
    . 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.
  3. https://raw.githubusercontent.com/ourbigbook/ourbigbook-media/master/feature/x/hilbert-space-arrow.png
  4. Infinitely deep tables of contents:
    Figure 6.
    Dynamic article tree with infinitely deep table of contents
    .
    Descendant 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
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact