Ciro Santilli
OurBigBook.comJust like computers, biological systems can be seen as being composed of several different layers of complexity.
For humans specifically: en.wikipedia.org/wiki/List_of_systems_of_the_human_body
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A cool thought: bacteria like E. Coli replicate every 20 minutes. A human replicates every 15 years. So how can multicellular beings possibly cope with the speed of evolution of parasites?
The answer is that within us, the adaptative immune system is a population of cells that evolves very quickly. So in a sense, within our bodies there is fast cell-level non-inheritable evolution happening daily!
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- journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005268 Could a Neuroscientist Understand a Microprocessor? by Jonas and Kording (2017)
Interview with John White by MRC Laboratory of Molecular Biology (2023)
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Source code: github.com/neuronsimulator/nrn
www.frontiersin.org/articles/10.3389/fninf.2019.00063/fullCoreNEURON: An Optimized Compute Engine for the NEURON Simulator (2019) Merged back into mainstream: github.com/BlueBrain/CoreNeuron
One nerve fiber under a scanning electron microscope: www.quora.com/Is-a-human-head-transplant-possible-in-the-future/answer/Dimitrios-Michmizos
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Studies biology from a more global point of view, if putting all little pieces of an organism make up the final biological function.
Some key activities:
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Very good metabolism database.
Some things that they have of interest which may not be on NCBI:
Hits a free login wall after a few IP hits. And just a very normal casually browsing number of hits. What is this bullshit?
Their YouTube: www.youtube.com/channel/UCR9QDQ_9_N4isZV_YRQg9tA has some good tutorials.
Database of promoter.
E.g. for E. Coli K-12 MG1655: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI For some context see e. Coli K-12 MG1655 gene thrL + e. Coli K-12 MG1655 gene thrA + thrB + thrC all of which are in the same transcription unit.
The bioinformatics database: www.ncbi.nlm.nih.gov/
Here's a good example of what you can get out of it: E. Coli K-12 MG1655
For an example with context, have a look at E. Coli K-12 MG1655 and the second protein of the genome, e. Coli K-12 MG1655 gene thrA.
Each of the omics studies a subset of molecular biology with a data intensive and broad point of view that tries to understand global function or organisms, trying to understand what every biologically relevant molecule does as part of the hole metabolism.
The main omics are:
Omics might be stamp collecting, but maybe it is a bit more like Trading card game/Magic: The Gathering collecting, in which the cards that you are collecting actually have specific uses and interactions, especially considering that most metabolic pathways are analogous across many species.
Integrating multiple omics, comes quite close to whole cell simulation.
- prokaryote models:
- E. Coli: the most well studied
- mycoplasma: a very minimal genus, notable species: Mycoplasma genitalium
- eukaryote
- S. cerevisiae: simplest eukaryote model. Unicellular.
- C. elegans: simplest multicellular organism model
- vertebrate:
- Zebrafish: simplest vertebrate model
- mammal:
- Mus musculus: simplest mammal model
The Evolution of Bacteria on a 'Mega-Plate' Petri dish by Kishony Lab (2016)
Source. They've made a huge Petri dish with bands of different concentrations of antibiotic, and then they visualize Escherichia coli mutations as new strains manage to make their way into the highest antibiotic concentration strip. mind blowing.The exact opposite of argument from poor design!
For specific species:
Allele means "other" in Greek.
For some reason, this is one of the things that makes Ciro Santilli want to puke the most. More than surgery or blood.
- 2024 www.uktech.news/foodtech/alternative-meat-research-centre-20240829A research centre examining the implementation of alternatives to meat, backed by £38m, will be launched by the University of Leeds.The virtual research centre will look into lab-grown meat as well as plant and fungus-based meat alternatives to determine the health, sustainability and feasibility of moving away from traditional meat.
- 2024 techcrunch.com/2024/08/04/even-after-1-6b-in-vc-money-the-lab-grown-meat-industry-is-facing-massive-issues/ "Even after $1.6B in VC money, the lab-grown meat industry is facing 'massive' issues"
- www.reuters.com/markets/commodities/hoxton-farms-raises-22-million-cultivated-animal-fat-2022-10-20/ Hoxton Farms, cultured animal fat
This is something worth investigating!
Bibliography:
- 2023 www.uktech.news/foodtech/investors-lab-grown-meat-startups-regulation-20230216 mentions the company Ivy Farm
- UK
- Higher Steaks then renamed to the boring "Uncommon": uncommonbio.co/
- 2022 vegconomist.com/cultivated-cell-cultured-biotechnology/ivy-farm-europes-biggest-cultivated-meat-facility/ Ivy Farm Unveils Europe’s Biggest Cultivated Meat Pilot Production Facility
- www.crunchbase.com/organization/ivy-farm-technologies
Bibliography:
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One of the biotechnology superstars of the 2000's/2010's.
One of the biotechnology superstars of the 2000's/2010's.
Wikipedia mentions quoting his Nobel Prize biography:
In Monod's studies he discovered that the course work was decades behind the current biological science. He learned from other students a little older than himself, rather than from the faculty.
John Sulston in 2008
. Source. 
Paul's bastardness is more striking than his Nobel Prize and that is awesome.
Family Trees Can Be Dangerous by Paul Nurse
. Source. Fantastic video of Paul describing his bastard story. What a legend. He speaks very well.Sequence alignment is trying to match a DNA or amino acid sequence, even though the sequences might not be exactly the same, otherwise it would be a straight up string-search algorithm.
This is fundamental in bioinformatics for two reasons:
- when you sequence the DNA of a new species, you can guess what each protein does by comparing it with similar proteins in other species that you have already studied
- when doing DNA sequencing, and specially short-read DNA sequencing, you generally need to align the reads to reference genomes to know where you are inside the entire genome, and then be able to spot mutations, notably single-nucleotide polymorphisms
BLAST is a sequence alignment.
The NCBI free-to-use BLAST server: blast.ncbi.nlm.nih.gov/Blast.cgi. Having a centralized query server is fundamental, because the gain of sequence alignment really comes from having one huge database to link information together, which is best centralized.
The bane of multicellularity.
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A cool thought about cancer expressed at Power, Sex, Suicide by Nick Lane (2006) is that cancer it is the direct product of natural selection gone wrong!
Cancer cells are obviously selected against anti-cancer mechanism, which when they manage to evade, they reproduce uncontrollably, gaining more and more momentum.
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Obesity is an extremely serious disease that is very hard to cure, and has deep psychological implications.
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Whatever it is that biology studies.
Some of the software-based artificial life simulators can be used as AI training game.
Ciro Santilli just always feels that what can be classified as "artificial life" simulators have too much focus on beating more continuous population mechanics, and lack the discrete elements which he feels could be important to AGI: Section "The missing link between continuous and discrete AI".
There is great interest in this direction of research however quite clearly.
Unknown real developer name, claims to be from Canada on YouTube channel about: www.youtube.com/@TheBibitesDigitalLife/about, likely because he's a software developer and wants to keep his employer's claws away from his side project.
Appears to be closed source unfortunately, so not suitable for research.
Video 5. "What will happen after 100h of evolution? by The Bibites (2022)" mentions it was started five years ago, so circa 2017.
Appears to be Unity-based, if you download and extract for Linux you get files named
UnityPlayer.so.Author is named Leo Caussan in game credits at startup: www.linkedin.com/in/l%C3%A9o-caussan-560350136/, a Canadian software engineer.
Was not very Linux compatible: www.reddit.com/r/TheBibites/comments/vqk6ac/program_stalls_at_a_blue_screen/ Trying to run 0.5.0 leads to a blank screen after you click "start simulation".
What will happen after 100h of evolution? by The Bibites (2022)
Source. This channel contains several 2D continuous simulations and explains AI techniques used.
The engine appears to be open source: github.com/Primer-Learning/PrimerTools (previously at: github.com/Helpsypoo/primer). Models are closed source however.
They have several interesting multiagent game ideas.
Ciro became mildly jealous of this channel when he found out about it, because at 800k subscribers at the time, the creator is likely able to make a living off of it, something which Ciro thought impossible.
As of 2022 he was at 1.6M followers with only 17 videos! Of course, much of those videos is about the software and they require infinite development hours to video time ratios.
Much of this success hinges a large part on the amazing 3D game presentation.
Well done!
Created by Justin Helps. Awesome name.
To make things better, the generically named channel is also the title of one of the best films of al time: Primer (2004).
Creator of Primer
youtube.fandom.com/wiki/Primer gives real identity:Feels exactly the background you'd expect: disilusioned by the educational system, and working to make education better! Great guy! Reminds Ciro Santilli of himself a bit.
- the name is Justin Helps from Minnesota
- dropped out of his PhD that got boring, and used to work at Khan Academy
- LinkedIn gives PhD subject: www.linkedin.com/in/justin-helps/ as materials science
- twitter.com/helpsypoo personal Twitter account
Face reveal at: www.youtube.com/watch?v=QC91Bf8hQVo
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For the act, see: sex.
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It is not obvious why there have to be two sexes.
Sex itself is obvious: by mixing genes we increase variability.
But having two sexes rather than just being able to reproduce with anyone reduces the possible mating pool by half!
One of the key thesis of Power, Sex, Suicide by Nick Lane (2006).
Also mentioned at:
Analects translation by Robert Eno (2015) 16.7:
He seems highly censored by search engines as of 2024!
Pedobear with the Powerpuff Girls
. Source. A signal that indicates that an animal is ready for mating.
Ciro Santilli is for abortion rights of women, until very late in pregnancy.
But it's not something that he would do himself, unless under extreme cases.
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For Ciro Santilli's unimpressive drug experiences see: Section "Ciro Santilli's drug experiences".
Ciro Santilli supports full legalization of all drugs, because he feels that it would be better overall for the world to have cheaper drugs and more drug addicts, but way, way less organized crime.
These should be extremely controlled of course, with extremely high taxes that puts their price just below the current illegal market, and a complete ban on any positive advertising.
Ciro believes that maybe the government could even go as far as giving free drugs to drug addicts so they don't have to rob to get a fix.
This is notably considering that drug-led organized crime completely dominates and corrupts the politics of many production and trafficking zones, which are already generally poor fucked up places to start with:Ciro's experiences in Brazil such as mentioned at São Remo, the favela next to USP, although much less extreme than the above, also come to mind.
Drug traffic corrupts everything. It prevents development of honest people. It is a cancer, which we have failed time and time a gain to cure. The only cure is to accept the other less insidious of addiction.
Bibliography:
- How to Fix a Drug Scandal (2020) gives a good sense of the relentlessness of the drug war, and how it affects people who are already poor the most
Ancestors
Incoming links
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- 100 Greatest Discoveries by the Discovery Channel (2004-2005)
- The best articles by Ciro Santilli
- Bert Hubert
- Chemistry
- De novo DNA synthesis
- Half-life
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- Natural science
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- How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it
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- Project to explain each Nobel Prize better