Incoming links: Ciro Santilli
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Updated 2025-07-16
This article gives an idea of how this kind of biological experiment feels like to a software engineer who has never done any biology like Ciro Santilli.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it External links to this page Updated 2025-07-16
- 2021-03-25: Oxford Nanopore Technologies retweeted this article, that's awesome!
- 2021: hackaday.com/author/wd5gnr1/ "SEQUENCING DNA FOR METAGENOMICS" by Al Williams (2021). This came after Ciro Santilli self promoted at: stackoverflow.blog/2021/02/03/sequencing-your-dna-with-a-usb-dongle-and-open-source-code/#comment-1411921
Paco de Lucía Updated 2025-07-16
Watching www.youtube.com/watch?v=-SbZZPX-y9g in 2022, who was one of his inspirations, made Ciro miss his guitar so much... one day, maybe, one day.
Parenteral nutrition Updated 2025-07-16
For some reason, this is one of the things that makes Ciro Santilli want to puke the most. More than surgery or blood.
Paris Updated 2025-07-16
Ciro Santilli lived in Paris for a few years between 2013 and 2016, and he can confirm the uncontroversial fact that "Paris is Magic".
Not just one type of magic though. Every quarter in Paris has its own unique personality that sets it apart and gives it a different mood.
Ciro knows Paris not from its historical facts, but from the raw feeling of endless walks through its streets in different times of the year. Ciro is a walker.
Maybe one day Ciro will expand this section to try and convey into words his feelings of love for the city, but maybe the effort would be pointless. Maybe such feelings can only be felt by other free-roaming walker souls living in the city, and that is both beautiful and a shame.
Ciro had written the following in the past before he lived in smaller cities, started cycling and joined the Street reclamation movement he thought:Perhaps compared to São Paulo City, which is what he knew before that was true. But no, his standards have improved since. Paris has way too many cars. The noise of internal combustion engine vehicles is extremely annoying. And because there are too many personal vehicles, cars have to horn a lot to fight for space. Fuck cars. Paris has been making a big cycling push in the early 2020's, and that is great. But it is still far, far from good.
Paris is a friendly city to walkers, as it is not too large, and does not have too many extremely busy roads, you can basically cross all of it on foot.
PATH environment variable Created 2024-12-13 Updated 2025-07-16 Path to AGI Updated 2025-07-16
There are two main ways to try and reach AGI:Which one of them to take is of of the most important technological questions of humanity according to Ciro Santilli
- AI training robot: expensive, slow, but realistic world
- AI training game: faster, less expensive, but possibly non-realistic-enough realistic
There is also an intermediate area of research/engineering where people try to first simulate the robot and its world realistically, use the simulation for training, and then transfer the simulated training to real robots, see e.g.: realistic robotics simulation.
Paul Dirac Updated 2025-07-16
Eccentric nerdy slow speaking physicist mostly based in University of Cambridge.
Created the Dirac equation, what else do you need to know?!
QED and the men who made it: Dyson, Feynman, Schwinger, and Tomonaga by Silvan Schweber (1994) chapter 1.3 "P.A.M. Dirac and the Birth of Quantum Electrodynamics" quotes Dirac saying how being at high school during World War I was an advantage, since all slightly older boys were being sent to war, and so the younger kids were made advance as fast as they could through subjects. Exactly the type of thing Ciro Santilli wants to achieve with OurBigBook.com, but without the need for a world war hopefully.
Dirac was a staunch atheist having said during the Fifth Solvay Conference (1927)[ref]:
If we are honest - and scientists have to be - we must admit that religion is a jumble of false assertions, with no basis in reality. The very idea of God is a product of the human imagination. It is quite understandable why primitive people, who were so much more exposed to the overpowering forces of nature than we are today, should have personified these forces in fear and trembling. But nowadays, when we understand so many natural processes, we have no need for such solutions. I can't for the life of me see how the postulate of an Almighty God helps us in any way. What I do see is that this assumption leads to such unproductive questions as why God allows so much misery and injustice, the exploitation of the poor by the rich and all the other horrors He might have prevented. If religion is still being taught, it is by no means because its ideas still convince us, but simply because some of us want to keep the lower classes quiet. Quiet people are much easier to govern than clamorous and dissatisfied ones. They are also much easier to exploit. Religion is a kind of opium that allows a nation to lull itself into wishful dreams and so forget the injustices that are being perpetrated against the people. Hence the close alliance between those two great political forces, the State and the Church. Both need the illusion that a kindly God rewards - in heaven if not on earth - all those who have not risen up against injustice, who have done their duty quietly and uncomplainingly. That is precisely why the honest assertion that God is a mere product of the human imagination is branded as the worst of all mortal sins.
Paul Dirac and the religion of mathematical beauty by Royal Society (2013)
Source. Personal Genome Project Updated 2025-07-16
Philip Seymour Hoffman Created 2024-09-03 Updated 2025-07-16
This guy just shows up in so many films Ciro Santilli loves. Little by little Ciro started to realize that he is amazing!
Physics Updated 2025-07-16
Physics (like all well done science) is the art of predicting the future by modelling the world with mathematics.
Ciro Santilli doesn't know physics. He writes about it partly to start playing with some scientific content for: OurBigBook.com, partly because this stuff is just amazingly beautiful.
Ciro's main intellectual physics fetishes are to learn quantum electrodynamics (understanding the point of Lie groups being a subpart of that) and condensed matter physics.
Every science is Physics in disguise, but the number of objects in the real world is so large that we can't solve the real equations in practice.
Luckily, due to emergence, we can use uglier higher level approximations of the world to solve many problems, with the complex limits of applicability of those approximations.
Therefore, such higher level approximations are highly specialized, and given different names such as:
Unifying those two into the theory of everything one of the major goals of modern physics.
xkcd 435: Fields arranged by purity
. Source. Reductionism comes to mind.
Physically accurate genie by Psychomic
. Source. This sane square composition from: www.reddit.com/r/funny/comments/u08dw3/nice_guy_genie/. Physics and the illusion of life Updated 2025-07-16
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.
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.
Place de la République Updated 2025-07-16
Planned obsolescence Updated 2025-07-16
2019 cell phones are glued together with adhesive, which makes them impossible to repair them unless you have a heat gun, spend hours and hours learning and planning, and accept the risk of breaking the screen
Repairability scores: www.ifixit.com/smartphone-repairability
If you take a phone less than 300 dollars to a repair shop in the first world, they will say: I've never repaired this crap, and likely for the price of the repair you should just buy a new one, and so to the trash goes the old one, polluting the planet, and in comes a new one, enriching the manufacturer further.
Oh, there is some 2017 EU action actually: (archive) www.europarl.europa.eu/news/en/press-room/20170629IPR78633/making-consumer-products-more-durable-and-easier-to-repair
plasticboy/vim-markdown Updated 2025-07-16
Ciro Santilli contributed a bit to this, and was even given push rights, see also: see also: Ciro Santilli's minor projects.
Pokemon Mania Updated 2025-07-16
Pokemania Comes to America by ABC News (1999)
Source. Ciro Santilli was a part of it! Especially during Ciro Santilli's 10 month stay in Coventry, United Kingdom, in the year 2000! Polish a turd Updated 2025-07-16
Ciro Santilli learned this expression from Angry Video Game Nerd.
Political correctness Updated 2025-07-16
Ciro Santilli believes it generally hurts more than it helps.
Especially when you can't even mention censored things to criticize them. You have to pretend they never existed. So people will forget about them, and do them again in the future.
Polymerase chain reaction Updated 2025-07-16
This is an extremely widely used technique as of 2020 and much earlier.
If allows you to amplify "any" sequence of choice (TODO length limitations) between a start and end sequences of interest which you synthesize.
If the sequence of interest is present, it gets amplified exponentially, and you end up with a bunch of DNA at the end.
You can then measure the DNA concentration based on simple light refraction methods to see if there is a lot of DNA or not in the post-processed sample.
Even Ciro Santilli had some contact with it at: Section "How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it", see: PCR!
One common problem that happens with PCR if you don't design your primers right is: en.wikipedia.org/wiki/Primer_dimer
Sometime it fails: www.reddit.com/r/molecularbiology/comments/1kouomw/when_your_pcr_fails_again_and_you_start/and a comment:
Nothing humbles you faster than a bandless gel. One minute you’re a scientist, the next you’re just a pipette-wielding wizard casting spells that don’t work. Meanwhile, physicists are out there acting like gravity always behaves. Smash that upvote if your reagents have ever gaslit you.
PCR = Pray, Cry, Repeat
Popular science Updated 2025-07-16
On one hand, yes, we need knowledge at all levels, and it is fine to start top-to-bottom with an overview.
The problem is, however, that there is a huge knowledge gap between the one liner "this is the truth" and the much more important "this is how we know it, these are the experiments" as mentioned at how to teach and learn physics.
Therefore, if you have that extremely rare knowledge, you should be writing that in addition to the dumbed down version with an open knowledge license. It takes time, but that's what really changes the world.
Ciro Santilli has always felt that there is a huge gap between "the very basic" and "the very advanced", as mentioned at: Section "The missing link between basic and advanced", which existing scientific vulgarization is not doing enough to address. In a sense, filling out this "middle path" is the main goal of OurBigBook.com.
Ciro really enjoyed the description of the "Arindam Kumar Chatterjee" YouTube channel:
Theoretical/mathematical physics at the graduate level and above. This is NOT a popular science channel. Here you find real theoretical physicists doing real theoretical physics. We think it is important for people to get a taste of the real deal, and for aspiring theoretical physicists to see what they are working towards, i.e., to provide the public with something beyond the ubiquitous Michio Kaku and Brian Cox.
One thing must be said however: there seems to be an actual bias against researchers tho try to create vulgarization material: How To Get Tenure at a Major Research University by Sean Carroll (2011), and that is terrible.
There is often more value in a tutorial by a beginner who is trying to fully learn and explain a subject, than by an expert who is trying to "dumb it down" too much.