Incoming links: Ciro Santilli
Ciro Santilli believes that molecular biology technologies will be a large part of the next big things as shown at: Section "Molecular biology technologies".
Bibliography:
- www.youtube.com/watch?v=mS563_Teges&list=PLQbPquAyEw4dQ3zOLrdS1eF_KJJbUUyBx Biophysical Techniques Course 2022 by the MRC Laboratory of Molecular Biology. Holy crap that playlist is a tour de force of molecular biology techniques in 2022!
Whenever 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:
As of 2019, the silicon industry is ending, and molecular biology technology is one of the most promising and growing field of engineering.
Ciro Santilli is especially excited about DNA-related technologies, because DNA is the centerpiece of biology, and it is programmable.
First, during the 2000's, the cost of DNA sequencing fell to about 1000 USD per genome in the end of the 2010's: Figure 2. "Cost per genome vs Moore's law from 2000 to 2019", largely due to "Illumina's" technology.
The medical consequences of this revolution are still trickling down towards medical applications of 2019, inevitably, but somewhat slowly due to tight privacy control of medical records.
Ciro Santilli predicts that when the 100 dollar mark is reached, every person of the First world will have their genome sequenced, and then medical applications will be closer at hand than ever.
But even 100 dollars is not enough. Sequencing power is like computing power: humankind can never have enough. Sequencing is not a one per person thing. For example, as of 2019 tumors are already being sequenced to help understand and treat them, and scientists/doctors will sequence as many tumor cells as budget allows.
Then, in the 2010's, CRISPR/Cas9 gene editing started opening up the way to actually modifying the genome that we could now see through sequencing.
What's next?
Ciro believes that the next step in the revolution could be could be: de novo DNA synthesis.
This technology could be the key to the one of the ultimate dream of biologists: cheap programmable biology with push-button organism bootstrap!
Just imagine this: at the comfort of your own garage, you take some model organism of interest, maybe start humble with Escherichia coli. Then you modify its DNA to your liking, and upload it to a 3D printer sized machine on your workbench, which automatically synthesizes the DNA, and injects into a bootstrapped cell.
You then make experiments to check if the modified cell achieves your desired new properties, e.g. production of some protein, and if not reiterate, just like a software engineer.
Of course, even if we were able to do the bootstrap, the debugging process then becomes key, as visibility is the key limitation of biology, maybe we need other cheap technologies to come in at that point.
This a place point we see the beauty of evolution the brightest: evolution does not require observability. But it also implies that if your changes to the organism make it less fit, then your mutation will also likely be lost. This has to be one of the considerations done when designing your organism.
Other cool topic include:
- computational biology: simulations of cell metabolism, protein and small molecule, including computational protein folding and chemical reactions. This is basically the simulation part of omics.If we could only simulate those, we would basically "solve molecular biology". Just imagine, instead of experimenting for a hole year, the 2021 Nobel Prize in Physiology and Medicine could have been won from a few hours on a supercomputer to determine which protein had the desired properties, using just DNA sequencing as a starting point!
- microscopy: crystallography, cryoEM
- analytical chemistry: mass spectroscopy, single cell analysis (Single-cell RNA sequencing)
Ciro is sad that by the time he dies, humanity won't have understood the human brain, maybe not even a measly Escherichia coli... Heck, even key molecular biology events are not yet fully understood, see e.g. transcription regulation.
One of the most exciting aspects of molecular biology technologies is their relatively low entry cost, compared for example to other areas such as fusion energy and quantum computing.
Molecular Sciences Course of the University of São Paulo Updated 2025-06-02 +Created 1970-01-01
Good Portuguese overview: www.scielo.br/scielo.php?script=sci_arttext&pid=S1806-11172017000300301&lng=pt&tlng=pt
A fantastic sounding full time 4-year course that any student could transfer to called that teaches various natural science topics, notably mathematics, physics, chemistry and molecular biology.
Many past students Ciro talked to however share a common frustration with the course: in the first 2 years at least, the "basic cycle", you have infinitely many courses, and no time to study, and no choice of what to study, it is only in the latter 2 years (the advanced cycle) that you get the choices.
Also, if you get low grades in a single subject, your out. And exams are useless of course.
Here's a Quora question in Portuguese about the course: pt.quora.com/Como-funciona-o-tal-do-curso-secreto-da-USP, the only decent answer so far being: pt.quora.com/Como-funciona-o-tal-do-curso-secreto-da-USP/answer/Victor-Soares-31. Very disappointing to hear.
On the advanced cycle, you have a lot of academic freedom. You are basically supposed to pick a research project with an advisor and go for it, with a small amount of mandatory course hours. Ciro was told in 2022 that you can even have advisors from other universities or industry, and that it is perfectly feasible to take courses in another university and validate the course hours later on. Fantastic!!!
Students from the entire University of São Paulo can apply to transfer to it only after joining the university, with the guarantee that they can go back to their original courses if they don't adapt to the new course, which is great!
Around 2007, they were in a really shady building of the University, but when Ciro checked in 2021, they had apparently moved to a shiny new entrepreneurship-focused building. Fantastic news!!!
One of the Brazilians who came to École Polytechnique together with Ciro was from this course. The fact that he is one of the most intelligent people Ciro knows gave further credit to that course in his eyes.
Cryptocurrency with focus on anonymity. Was almost certainly the leading privacy coin since its inception until as of writing in the 2020s.
Ciro Santilli has received and held considerable quantities of Monero, notably 1000 Monero donation. so bias alert.
As mentioned at Section "Are cryptocurrencies useful?", Ciro Santilli believes that anonymity is the most valuable feature that really matters on crypto coins, and therefore if he were to invest in crypto, he would invest in Monero or some other privacy coin.
localmonero.co/knowledge/monero-stealth-addresses?language=en gives an overview of the privacy mechanisms:
- ring signatures, which hide the true output (sender)localmonero.co/knowledge/ring-signatures Gives an overview. Mentions that it is prone to heuristic attacks.Uses a system of decoys, that adds 10 fake possible previous outputs as inputs, in addition to the actual input.So the network only knows/verifies that one of those 11 previous outputs was used, but it does not know which one.TODO so how do you know which previous outputs were spent or not?
- RingCT which hides the amounts.
- stealth addresses, which hides who you send toThis forces receivers to scan try and unlock every single transaction in the chain to see if it is theirs or not.The sender therefore can know when the money is spent, but once again, not to whom it is being sent.
Based on en.wikipedia.org/wiki/CryptoNote and like Satoshi Nakamoto created by under the pseudonym "Nicolas van Saberhagen" www.reddit.com/r/Monero/comments/7v2obe/offering_a_bounty_for_a_video_of_the_speech_by/
Coinbase has actually stayed away from trading it even as of 2019 when Monero was the third largest market capitalization crypto because of fear of regulatory slashback: decrypt.co/36731/heres-why-coinbase-still-hasnt-listed-monero. Although it must be said, the value of privacy crypto is greatly reduced when everyone is trading it on exchanges, which require a passport upload to work.
To Ciro Santilli, a key observation is:Clearly the rich will be much, much more shielded by keeping large parts of their wealth in shares... from this point of view, it is insane to print money!!! Tax the rich instead...
The rich are more easily able to avoid the harm than poor and middle-class people [...] they are more likely to have large amounts of non-cash assets to shield themselves from inflation.
The Holy Hand Grenade of Antioch scene from Monty Python and the Holy Grail
. Source. When a young Ciro Santilli played Worms Armageddon, he almost shat himself of laughter when he first threw a Holy Grenade. Little did he know it was actually a Monty Python reference.By Esther Wojcicki, Sergey Brin's ex-mother-in-law:So basically strong focus on self-directed learning.
A moonshot classroom is a fundamental shift to give students more autonomy and agency in the classroom and entrusts them with greater ownership of their learning outcomes.
Also:so along the lines of project-based learning. Ciro Santilli specifically likes the "authentic audience" part, related: Section "Projects must aim for novelty"
Real World Work. Students must produce learning projects with real world applications and an authentic audience.
No, they are basically not-for-profits, or more precisely in british legal terms, "charities". By taking government funding (directly or indirectly through subsiding enrolment fees?), they have to follow some government rules, and all major ones do it seems: academia.stackexchange.com/questions/49187/in-what-sense-are-uk-universities-public/49188
In the University of Cambridge for example, all MA degree holders or higher appear to have some voting power: www.cam.ac.uk/about-the-university/how-the-university-and-colleges-work/governance (archive)
This adds an extra layer of difficulty for the average taxpayer to make changes to university policy, e.g. making universities publish all material with Creative Commons licenses. At most, voters could require this indirectly through the government funding requisites. It is a mess.
Not even the Open University seems to be very open!
Ciro Santilli once attended a round table in the early 2020s where a University of Oxford official from the IP licensing department. The University of Oxford took a 20% equity on spin-off companies, not an uncommon University IP ownership policy at the time. At one point, the officer clearly justified this along the following very official sounding lines (paraphrased):While noble sounding, this immediately reminded Ciro of instrumental convergence, in the field of AGI philosophy. Or in other words, of course the best approach to maximize education and research outcomes of society is to first take over the world, and then implement those goals from there! See also Why Not Just: Think of AGI Like a Corporation? by Robert Miles (2018)
The university is a charity with the goal of promoting education and research. All money obtained is reinvested in furthering education and research.
Notably, the University of Oxford was extremely protective of its learning material at that time, which was highly paywalled behind university logins, presumably with the rationale of having unique learning materials to enroll more paying undergrads. How can giving out free information to all not be the optimal way to "promoting education and research" is very hard to envision.
Bibliography:
- www.hepi.ac.uk/2023/06/07/most-universities-are-charities-so-what/ Most universities are charities: so what? by Mary Synge (2023) on the
After learning this term, Ciro Santilli finally understood that his actual major was MR, and not bullshit like applied mathematics or control theory.
Ciro Santilli's jaw dropped when he learned about this concept. A Small Talent for War, are you sure?
Ciro Santilli took courses once upon a time, maybe that has influenced his passion? Ciro Santilli's musical education.
Ciro Santilli often wonders to himself, how much of the natural sciences can one learn in a lifetime? Certainly, a very strong basis, with concrete experimental and physics, chemistry and biology should be attainable to all? How much Ciro manages to learning and teach in those areas is a kind of success metric of Ciro's life.
Article likely written by him: www.theguardian.com/commentisfree/2010/feb/22/home-schooling-register-families
“Especially my father. He was doing most of it and he is a savoury, strong character. He has strong beliefs about the world and in himself, and he was helping me a lot, even when I was at university as an undergraduate.”An only child, Arran was born in 1995 in Glasgow, where his parents were studying at the time. His father has Spanish lineage, having a great grandfather who was a sailor who moved from Spain to St Vincent in the Carribean. A son later left the islands for the UK where he married an English woman. Arran’s mother is Norwegian.
One of the articles says his father has a PhD. TODO where did he work? What's his PhD on? Photo: www.topfoto.co.uk/asset/1357880/
www.thetimes.co.uk/article/the-everyday-genius-pxsq5c50kt9:
Very very good. Those nice pre-Dot-com bubble vibes.
Might be freely watchable? Wikipedia links to:
But they do start with an FBI warning about copyright. So... erm.
Part 1 - Networking The Nerds talks about the TCP/IP and early machines implementing it:
- 21:00: shows inside The Pentagon. The way the dude who works there opens a his locked office door with an electric switch is just amazing. Cringely also mentions that there's an actual official speed limit in the corridors as he rides a carrier bike slowly through them.
- 21:45: the universities weren't enthusiastic, because people from other locations would be able to use your precious computer time. But finally ARPA forced the universities' hands, and they joined.
- 24:24 mentions that some of the guys who created ARPANET were actually previously counting cards at Casinos in Las Vegas, just like in the 21 (2008) film
- one of the centerpieces of development was at UCLA. The other was the BBN company. 33:55 shows the first router, then called them Interface Message Processor
- the first message was from UCLA to Stanford University. He was trying to write "Login", and it crashed at the 'g'. Epic. They later debugged it.
- towards the end talks about ALOHAnet, the first wireless computer communication done
Part 2 - Serving the Suits
- Robert Metcalfe. He's nice. Xerox PARC. Ethernet.
- Explains what is a "Workstation", notably showing one by Sun Microsystems. This is now an obscure "passé" thing in 2020 that young people like Ciro Santilli have only heard of in legend (or in outdated university computer labs!). Funny to think that so many people have had this idea before, including e.g. the Chromebook
- 10:46 mentions that all of Cisco, Silicon Graphics and Sun Microsystems and where founded at Margaret Jacks Hall, Building 460, at Stanford University.
- he then talks a lot about Sun. Sun became dominant in Wall Street.
- 19:05: Novell, from Utah. How they almost went bust, but were saved at the last moment by Ray Noorda, who refocused them to their NetWare product which was under recent development. It allowed file and printer sharing in IBM PCs. 22:55 shows how they had a live radio host for people waiting on customer support calls!
- 33:56 mentions how The Grateful Dead had in impact on the Internet, as people wanted computers to be able to access The WELL online forum. They still own the domain as of 2022: www.well.com/. It is interesting how Larry Page also liked The Grateful Dead as mentioned at The Google Story, his dad would take him to shows. Larry is a bit younger of course than the people in this documentary.
- 37 show McAfee
- 43:56: fantastic portrait of Cisco
Part 3 - Wiring the World:
- Berners-Lee at CERN and the invention of the URL.
- 1992: US Government allow commerce on the Internet
- Web browser history, Mosaic and Marc Andresseeen.
- 20:45: America Online
- 23:29: search engines and Excite. Google was a bit too small to be on his radar!
- 25:50: porn
- 27: The Motley Fool and advertising
- 30: Planet U grocery shopping
- 31:50: Amazon
- 33:00: immigrant workers, Indians playing cricket, outsourcing, Wipro Systems
- 41:25: Java
- 46:30: Microsoft joins the Internet. The Internet Tidal Wave Internet memo. Pearl Harbour day talk.
- 56:40: Excite Tour. If they had survived, they would have been Google with their quirky offices.
An IBM made/pushed term, but that matches Ciro Santilli's general view of how we should move forward AGI.
Framework built on top of React.
gothinkster/realworld blog example by Ciro Santilli: node Express Sequelize Next.js realworld example app.
Basically what this does is to get server-side rendering just working by React, including hydration, which is a good thing.
Next.js sends the first pre-rendered HTML page along with the JavaScript code. Then, JavaScript page switches just load the API data.
Next.js does this nicely by forcing you to provide page data in a serialized JSON format, even when rendering server-side (e.g. the return value of
getServerSideProps). This way, it is also able to provide either the full HTML, or just the JSON.Some general downsides:
- it does feel like they don't document deployment very well however, especially non-Vercel options, which is the company behind Next.js. I'm unable to find how to use a non Vercel CDN with ISR supposing that is possible.
- Next.js is very opinionated, and like any opinionated library it is sometimes hard to know why something is/isn't happening, and sometimes it is hard/impossible to do what you want with it unless they add support. They have done good progress, but even as of 2022, some aspects just feel so immature, some major-looking use cases are not very well done.
In theory, Next.js could be the "ultimate frontend framework". It does have a lot of development difficulties that need to be ironed out, but the general concepts, and things it tries to integrate, including e.g. webpack, TypeScript, etc. are good. Maybe the question is when will someone put it together with an amazing backend library and dominate and finally put an end to the infinite number of Js Frameworks!
In-tree examples at: github.com/vercel/next.js/tree/canary/examples
In order to offer its amazing features, Next.js is also extremely opinionated, which means that if something wasn't designed to be possible, it basically isn't.
No prerender with custom server? It forces you to write your API with next as well? Or does it mean something else?
TODO can it statically generate pages that are created at runtime? E.g. if I create a new blog post, will it automatically upload a static page? It seems that yes, and that this is exactly what Incremental Static Regeneration means:However, Ciro can't find any mention of how to specify where the pages are uploaded to... this is pat of the non-Vercel deployment problem.
- github.com/vercel/next.js/discussions/25410
- vercel.com/docs/next.js/incremental-static-regeneration
- github.com/vercel/next.js/discussions/17711
- www.reddit.com/r/nextjs/comments/mvvhym/a_complete_guide_to_incremental_static/
- github.com/vercel/next.js/discussions/11552#discussioncomment-115595
- stackoverflow.com/questions/62105756/how-to-use-aws-with-next-js
- github.com/vercel/next.js/discussions/17080
- github.com/vercel/next.js/discussions/16852
Can't ISR prerenter by URL query parameters:
That plus the requirement to have one page per file under
pages/ leads to a lot of useless duplication, because then you are forced to place the URL parameters on the pathnames."Module not found: Can't resolve 'fs'" Hell. The main reason this happens seems to be the that in a higher order component, webpack can't determine if callbacks use the require or not to remove it from frontend code. Fully investigated and solved at:
Overviews:
- www.reddit.com/r/reactjs/comments/8evy5d/what_are_the_downsides_to_nextjs/ 2017 What are the downsides to Next.js?