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Just like computers, biological systems can be seen as being composed of several different layers of complexity.
Figure 1. Cell type tree of blood cells. Source. Fantastic diagram!
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!
Video 1. Interview with John White by MRC Laboratory of Molecular Biology (2023) Source.
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
Studies biology from a more global point of view, if putting all little pieces of an organism make up the final biological function.
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?
Database of promoter.
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.
Figure 2. Hierarchical diagram of the major omics.
Integrating multiple omics, comes quite close to whole cell simulation.
Video 2. 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.
This is something worth investigating!
Video 3. Inside the Quest to Make Lab Grown Meat by WIRED (2018) Source.
Interviews with a few startups in the area, most of the time with Eat Just.
youtu.be/QO9SS1NS6MM?t=217 taught Ciro Santilli something he really appreciated: uncanny valley.
Bibliography:
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.
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:
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.
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.
Obesity is an extremely serious disease that is very hard to cure, and has deep psychological implications.
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 4. "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".
Video 4. 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.
Claims Unity-based, so has the downside of relying on a non-FOSS engine.
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).
Video 5. Simulating Foraging Decisions by Primer (2020) Source.
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.
This section is about the male/female trait.
For the act, see: sex.
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).
Analects translation by Robert Eno (2015) 16.7:
The junzi has three cautions.
When he is young and his blood and energy are not yet settled, he is cautious about sex.
When he is in his prime and his blood and energy have newly achieved strength, he is cautious about combativeness.
When he is old and his blood and energy are declining, he is cautious about acquisitiveness.
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.
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:

Ancestors

  1. Natural science
  2. Science
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