Added
ourbigbook --format-source automatic code formatting. I implemented it for the following reasons:- I want to do certain automatic modifications to source code on web, e.g.:
- later on, much later, this will allow WYSIWYG export to plaintext
This also ended up having one unexpected benefit: whenever a new feature is added that deprecates an old feature, by converting the large corpus from github.com/cirosantilli/cirosantilli.github.io to the new feature I can test the new preferred feature very well.
For example, converting
\x[blue cat] en masse to the new insane syntax <blue cat> found several bugs with the new insane syntax.This seemed somewhat easy at first, so I started it as a way of procrastinating more urgent Web features (web scares me, you know), but it ended being insanely hard to implement, because there are many edge cases. Also, most bugs are not acceptable, as they would corrupt your precious source code and potentially output.
But well, it is done!
Notably, it does not undergo crossover.
All pages below are from the second edition from 2018. It seems that there weren't any changes in the text, the updated preface mentions
As it happens, nearly 15 years have passed since the 1st edition of Power, Sex, Suicide was published, and I am resisting the temptation to make any lame revisions. Some say that even Darwin lessened the power of his arguments in the Origin of Species through his multiple revisions, in which he dealt with criticisms and sometimes shifted his views in the wrong direction. I prefer my original to speak for itself, even if it turns out to be wrong.
This is partly addressed in the preface of the second edition from 2018.
Central thesis:
- there are two sexes because of mitochondria
- the acquisition of mitochondria was one of the most important steps in the evolution of eukaryotes.There are no known eukaryotes which never had mitochondria. Having mitochondria appears to be a requisite for being an eukaryote.Contrast this for example with multicellularity, which is highly polyphyletic.
- Apoptosis is largely regulated by mitochondria
- there are two main theories for how the mitochondria endosymbiosis started:
- parsitic hypothesis of mitochondrial endosymbiosis: a parasitic option rather than cooperative
- hydrogen hypothesis: a cooperative option rather than parasitic
Smaller points:
- 10% of our body weight (dry presumably?) is mitochondria. Also quoted at: www.nature.com/scitable/blog/student-voices/mighty_mitochondria. TODO confirm.
- eukaryotes can do phatocytosis due to their cytoskeleton
- paints a colorful picture of Peter Mitchell. Some Wikipedia edits are warranted!
- it is hard for complex organisms to evolve because longer DNA means longer replication time
- cancer is natural selection gone wrong
- multicellular organisms are not utopias where every cell lives happily. Rather, they are dictatorships, where any dissident is forced to commit seppuku. Lu Xun's petition quote comes to mind.
Nitpicks:
- the book calls ATP synthase "ATPase" in several points, which is confusing because -ase means "something that breaks", and in 2020 parlance, there are ATPases which actually break ATP: en.wikipedia.org/wiki/ATPase. The book itself acknowledges that on page 135:
The ATPase is freely reversible. Under some circumstances it can go into reverse, whereupon it splits ATP, and uses the energy released to pump protons up the drive shaft, back across the membrane against the pressure of the reservoir. In fact the very name ATPase (rather than ATP synthase) signifies this action, which was discovered first. This bizarre trait hides a deep secret of life, and we’ll return to it in a moment.
Some criticisms:
- some of the later chapters are a bit more boring, like the stuff about warm-blooded animals. Perhaps is it that Ciro Santilli is more interested in the molecular aspects than macro
- the author talks about some very recent research at the time. While this does highlight his expertise, some of the points mentioned might still be in a state of flow. This is acknowledged by the author himself on the 2018 updated preface however.
Same motivation as Galilean invariance, but relativistic version of that: we want the laws of physics to have the same form on all inertial frames, so we really want to write them in a way that is Lorentz covariant.
This is just the relativistic version of that which takes the Lorentz transformation into account instead of just the old Galilean transformation.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Sequencing by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16With X-ray crystallography by David Chilton Phillips. The second protein to be resolved fter after myoglobin, and the first enzyme.
Published at: Structure of Hen Egg-White Lysozyme: A Three-dimensional Fourier Synthesis at 2 Å Resolution (1965). The work was done while at the Davy Faraday Research Laboratory of the Royal Institution.
Phillips also published a lower resolution (6angstrom) of the enzyme-inhibitor complexes at about the same time: Structure of Some Crystalline Lysozyme-Inhibitor Complexes Determined by X-Ray Analysis At 6 Å Resolution (1965). The point of doing this is that it points out the active site of the enzyme.
This is basically what became the dominant formulation as of 2020 (and much earlier), and so we just call it the "mathematical formulation of quantum mechanics".
- 1982 www.pnas.org/doi/pdf/10.1073/pnas.80.6.1579 DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels by Fischer and Lerman (1982). It is possible then.
- www.nature.com/articles/d41586-019-02209-z The four biggest challenges in brain simulation (2019)
Sponsored by National Academy of Sciences, located in Long Island.
Some photos at: www.nasonline.org/about-nas/history/archives/milestones-in-NAS-history/shelter-island-conference-photos.html on the website of National Academy of Sciences, therefore canon.
This is where Isidor Rabi exposed experiments carried out on the anomalous magnetic dipole moment and Willis Lamb presented his work on the Lamb shift.
It was a very private and intimate conference, that gathered the best physicists of the area, one is reminded of the style of the Solvay Conference.
QED and the men who made it: Dyson, Feynman, Schwinger, and Tomonaga by Silvan Schweber (1994) chapter 4.1 this conference was soon compared to the First Solvay Conference (1911), which set in motion the development of non-relativistic quantum mechanics.
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!
Intro to OurBigBook
. Source. 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/derivativeVideo 2. OurBigBook Web topics demo. Source. - 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 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. 
- Infinitely deep tables of contents:
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