Polyhedron Updated 2025-07-16
Ernest Hemingway Updated 2025-07-16
List of compilers Updated 2025-07-16
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Overview of the experiment Updated 2025-07-16
For those that know biology and just want to do the thing, see: Section "Protocols used".
The PuntSeq team uses an Oxford Nanopore MinION DNA sequencer made by Oxford Nanopore Technologies to sequence the 16S region of bacterial DNA, which is about 1500 nucleotides long.
This kind of "decode everything from the sample to see what species are present approach" is called "metagenomics".
This is how the MinION looks like: Figure 1. "Oxford Nanopore MinION top".
Oxford Nanopore MinION top open
. Source. 
Before sequencing the DNA, we will do a PCR with primers that fit just before and just after the 16S DNA, in well conserved regions expected to be present in all bacteria.
The PCR replicates only the DNA region between our two selected primers a gazillion times so that only those regions will actually get picked up by the sequencing step in practice.
Eukaryotes also have an analogous ribosome part, the 18S region, but the PCR primers are selected for targets around the 16S region which are only present in prokaryotes.
This way, we amplify only the 16S region of bacteria, excluding other parts of bacterial genome, and excluding eukaryotes entirely.
Despite coding such a fundamental piece of RNA, there is still surprisingly variability in the 16S region across different bacteria, and it is those differences will allow us to identify which bacteria are present in the river.
The variability exists because certain base pairs are not fundamental for the function of the 16S region. This variability happens mostly on RNA loops as opposed to stems, i.e. parts of the RNA that don't base pair with other RNA in the RNA secondary structure as shown at: Code 1. "RNA stem-loop structure".
This is how the 16S RNA secondary structure looks like in its full glory: Figure 5. "16S RNA secondary structure".
Since loops don't base pair, they are less crucial in the determination of the secondary structure of the RNA.
The variability is such that it is possible to identify individual species apart if full sequences are known with certainty.
With the experimental limitations of experiment however, we would only be able to obtain family or genus level breakdowns.
Sandy Maguire Updated 2025-07-16
Lots of similar ideologies to Ciro Santilli, love it:
- sandymaguire.me/blog/reaching-climbing/: don't be a pussyOne is also reminded of Gwern Branwen. Sandy is also into self-improvement stuff, so even more like Gwern. This is a point Ciro diverges on. Ciro works actively on self-worsening.
Last Friday was my final day at work. According to my facebook profile, I am now "happily retired." As of today, I don't plan to do another day of "traditional work" in my life. That's not to say that I'll be sitting idle playing tiddly winks. I want to build things, to dedicate my life to independent study, and to get really, really good with building communities. I don't have time for any of this "work" stuff that somehow pervades our entire culture, choking our inspiration and sapping our energy away from the things we'd rather be doing.
- he thinks university is useless:
- sandymaguire.me/blog/where-uni-fails/ Where University Fails (2018), mostly talking about backward design
- sandymaguire.me/blog/gatekept/ rejected from Imperial College PhD program due to grade being slightly too low for their stupid requirements, even though he had a referral already, and an amazing CV
- he likes jazz: sandymaguire.me/blog/too-smart/
Other interesting points:
- sandymaguire.me/blog/sandy-runback/ he changed his own name to Sandy because he didn't like it, he was born Alexander
- algebradriven.design/ closed source books though, ouch. At least they seem to have been made with leanpub though, could be worse.
Scientific Autobiography by Max Planck translated by Frank Gaynor (1949) Updated 2025-07-16
Published as Scientific Autobiography and Other Papers by Max Planck translated by Frank Gaynor (1949) which also contained other papers.
This section refers just to the translation of Scientific autobiography by Max Planck (1948).
Fall term Updated 2025-07-16
Procedural generation Updated 2025-07-16
Self-driving car company Updated 2025-07-16
Summer term Updated 2025-07-16
This actually happens in spring. But because they are so euphemistic winter had to be removed from the calendar, it gets shifted a left.
Forward secrecy Updated 2025-07-16
Four Gentlemen Updated 2025-07-16
Plum, orchid, bamboo, chrysanthemum Chinese painting by Zheng Xie
. Source. This is an example of bird-and-flower painting, of which the Four Gentlemen are a common theme. TODO date. Fourier basis is complete for Updated 2025-07-16
Riesz-Fischer theorem is a norm version of it, and Carleson's theorem is stronger pointwise almost everywhere version.
Note that the Riesz-Fischer theorem is weaker because the pointwise limit could not exist just according to it: norm sequence convergence does not imply pointwise convergence.
Freely licensed Bibles Updated 2025-07-16
How can you make a translation of the Bible and not put it in the public domain???? You tell me, you tell me.
With Falun Gong it's even more fun: the words of God Himself are will be copyrighted for a while after Li Hongzhi dies!!!
How can I be as great by Justine Musk Updated 2025-07-16
www.quora.com/How-can-I-be-as-great-as-Bill-Gates-Steve-Jobs-Elon-Musk-or-Sir-Richard-Branson/answer/Justine-Musk is a fantastic ansewr by Justine Musk, Elon Musk's ex-fife, to the question:One of her key thesis is Many successful people are neurodiverse:
How can I be as great as Bill Gates, Steve Jobs, Elon Musk or Sir Richard Branson?
These people tend to be freaks and misfits who were forced to experience the world in an unusually challenging way. They developed strategies to survive, and as they grow older they find ways to apply these strategies to other things, and create for themselves a distinct and powerful advantage. They don't think the way other people think. They see things from angles that unlock new ideas and insights. Other people consider them to be somewhat insane.
Freeman Dyson Updated 2025-09-09
Ciro Santilli's admiration for Dyson goes beyond his "unify all the things approach", which Ciro loves, but also extends to the way he talks and the things he says. Dyson is one of Ciro's favorite physicist.
Besides this, he was also very idealistic compassionate, and supported a peaceful resolution until World War II with United Kingdom was basically inevitable. Note that this was a strategic mistake.
Dyson is "hawk nosed" as mentioned in Genius: Richard Feynman and Modern Physics by James Gleick (1994) chapter "Dyson". But he wasn't when he was young, see e.g. i2.wp.com/www.brainpickings.org/wp-content/uploads/2016/03/freemandyson_child-1.jpg?resize=768%2C1064&ssl=1 It seems that his nose just never stopped growing after puberty.
He also has some fun stories, like him practicing night climbing while at Cambridge University, and having walked from Cambridge to London (~86km!) in a day with his wheelchair bound friend.
Ciro Santilli feels that the label child prodigy applies even more so to him than to Feynman and Julian Schwinger.
Bibliography:
- QED and the men who made it: Dyson, Feynman, Schwinger, and Tomonaga by Silvan Schweber (1994) chapter 9 Freeman Dyson and the Structure of Quantum Field Theory
Frequency modulation Updated 2025-07-16
Front-end web framework Updated 2025-07-16
You need those because it is hard to do the following:
- client JavaScript sends a request to server
- server sends back data
- client updates what the user sees
This is hard to do notably because when the update happens, several things might need to change on the webpage at the same time.
Notably, new elements might need to be added to the webpage, which in turn means that new bindings such as button clicks have to be added to those, in a way that keeps the page working.
The only way to do this basically is to have a functional dependency graph that keeps everything in the page in working state as updates come.
OurBigBook.com Action plan Updated 2025-07-16
The steps are sorted in roughly chronological order. The project might fail at any point, and some steps may be carried in parallel:
- create a basic implementation of the website, without advanced features like PageRank sorting and WYSIWYG. This is not much more than a blog with some extra metadata, so it is definitely achievable with constrained resources.
- Ciro would like to volunteer to work for free for this teacher and students to help the students learn.Ciro would start by mapping the headers of the lecture notes onto the website, and then slowly adding content as he feels the need to improve certain explanations.Finding teachers willing to allow this will be a major roadblock: how to convince teachers to use CC BY-SA.
- once some level of validation as been done, Ciro will start looking for charitable charitable grant opportunities more aggressively
- if things seem to be working, start adding more advance features: PageRank-like ranking sorting and WYSIWYG editingThe recommendation algorithms notably is left for a second stage because it needs real world data to be tested. And at the beginning, before Eternal September kicks in, there would be few posts written by well educated university students, so a simple sort by upvote would likely be good enough.
Ciro decided to start with a decent markup language with a decent implementation: OurBigBook Markup. Once that gets reasonable, he will move on to another attempt at the website itself.
The project description was originally at: github.com/cirosantilli/write-free-science-books-to-get-famous-website but being migrated here. The original working project name was "Write free books to get famous website", until Ciro decided to settle for
OurBigBook.com and fixed the domain name. There are unlisted articles, also show them or only show them.