He beats the The European Union is a failure drum pretty well.
- www.youtube.com/watch?v=iVxaTC7Qp44 The Global Minotaur: The Crash of 2008 and the Euro-Zone Crisis in Historical Perspective (2011)
- youtu.be/vNhkYXhYSSs?t=368 proposes that there is something missing from utility maximization, citing a lotus-Eater Machine idea
github.com/CovertLab/WholeCellEcoliRelease is a whole cell simulation model created by Covert Lab and other collaborators.
The project is written in Python, hurray!
But according to te README, it seems to be the use a code drop model with on-request access to master. Ciro Santilli asked at rationale on GitHub discussion, and they confirmed as expected that it is to:
- to prevent their publication ideas from being stolen. Who would steal publication ideas with public proof in an issue tracker without crediting original authors? Academia is broken. Academia should be the most open form of knowledge sharing. But instead we get this silly competition for publication points.
- to prevent noise from non-collaborators. But they only get like 2 issues as year on such a meganiche subject... Did you know that you can ignore people, and even block them if they are particularly annoying? Much more likely is that no one will every hear about your project and that it will die with its last graduate student slave.
The project is a followup to the earlier M. genitalium whole cell model by Covert lab which modelled Mycoplasma genitalium. E. Coli has 8x more genes (500 vs 4k), but it the undisputed bacterial model organism and as such has been studied much more thoroughly. It also reproduces faster than Mycoplasma (20 minutes vs a few hours), which is a huge advantages for validation/exploratory experiments.
The project has a partial dependency on the proprietary optimization software CPLEX which is freeware, for students, not sure what it is used for exactly, from the comment in the
requirements.txt the dependency is only partial.This project makes Ciro Santilli think of the E. Coli as an optimization problem. Given such external nutrient/temperature condition, which DNA sequence makes the cell grow the fastest? Balancing metabolites feels like designing a Factorio speedrun.
There is one major thing missing thing in the current model: promoters/transcription factor interactions are not modelled due to lack/low quality of experimental data: github.com/CovertLab/WholeCellEcoliRelease/issues/21. They just have a magic direct "transcription factor to gene" relationship, encoded at reconstruction/ecoli/flat/foldChanges.tsv in terms of type "if this is present, such protein is expressed 10x more". Transcription units are not implemented at all it appears.
Everything in this section refers to version 7e4cc9e57de76752df0f4e32eca95fb653ea64e4, the code drop from November 2020, and was tested on Ubuntu 21.04 with a docker install of
docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full with image id 502c3e604265, unless otherwise noted.By Tagkopoulos lab at University of California, Davies.
- www.nature.com/articles/ncomms13090 Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli (2016)
- www.sciencedaily.com/releases/2016/10/161027173552.htm
The conventional starting point is not at the E. Coli K-12 MG1655 origin of replication.
biocyc.org/ECOLI/NEW-IMAGE?type=EXTRAGENIC-SITE&object=G0-10506 explains:If it is a bit hard to understand what they mean by "origin of transfer" though, as that term is usually associated with the origin of transfer of bacterial conjugation.
This site is the origin of replication of the E. coli chromosome. It contains the binding sites for DnaA, which is critical for initiation of replication. Replication proceeds bidirectionally. For historical reasons, the numbering of E. coli's circular chromosome does not start at the origin of replication, but at the origin of transfer during conjugation.
The mandatory xkcd: xkcd 927: Standards.
It is hard for complex organisms to evolve because longer DNA means longer replication time by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16Because DNA replication is a key limiting factor of bacterial replication time, such organisms are therefore strongly incentivized to have very minimal DNAs.
Power, Sex, Suicide by Nick Lane (2006) 7 "Why bacteria are simple" page 169 puts this nicely:
Bacteria replicate at colossal speed. [...] In two days, the mass of exponentially doubling E. coli would be 2664 times larger than the mass of the Earth.Luckily this does not happen, and the reason is that bacteria are normally half starved. They swiftly consume all available food, whereupon their growth is limited once again by the lack of nutrients. Most bacteria spend most of their lives in stasis, waiting for a meal. Nonetheless, the speed at which bacteria do mobilize themselves to replicate upon feeding illustrates the overwhelming strength of the selection pressures at work.
All indefinite orthogonal groups of matrices of equal metric signature are isomorphic by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16Following the definition of the indefinite orthogonal group, we want to show that only the metric signature matters.
First we can observe that the exact matrices are different. For example, taking the standard matrix of :and:both have the same metric signature. However, we notice that a rotation of 90 degrees, which preserves the first form, does not preserve the second one! E.g. consider the vector , then . But after a rotation of 90 degrees, it becomes , and now ! Therefore, we have to search for an isomorphism between the two sets of matrices.
For example, consider the orthogonal group, which can be defined as shown at the orthogonal group is the group of all matrices that preserve the dot product can be defined as:
The Horrible Horrendous Terrible Tremendous Mining Pool inscribed a few cute Coinbase messages during their operation in 2012-2013.
Many of their messages also mention
SockThing, which was part of their mining infrastructure:Starting from their very first ASCII transaction on block 197602 (2012-09-07), there is what seems to be a poem spread across several transactions. Some of the lines are repeated, presumably because they didn't update the current line to a new line and so mined the same thing multiple times:The sentences are not very coherent together, perhaps this is because lines were chosen by different miners one at a time.
I am a pretty princess
covered in mud and blood
water with stuff in it
like everything else that wiggles or jiggles
screaming might not be your waY
see no reason to operate otherwise since
came into the world naked, wet and screaming
but silence will never be mine
until I am dead
but the smell will also give that away
gather all my things
load them in a big boat
airlift that to Kansas
and light it on fire
drop it from 7,000 feet
then railgun my corpse straight down
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