Incoming links: Academic publishing
- experimentalhistory.substack.com/p/the-rise-and-fall-of-peer-review The rise and fall of peer review by Adam Mastroianni (2022)
One of the most beautiful things is how they paywall even public domain works. E.g. here: www.nature.com/articles/119558a0 was published in 1927, and is therefore in the public domain as of 2023. But it is of course just paywalled as usual throughout 2023. There is zero incentive for them to open anything up.
What they don't tell you about academic publishing by Andy Stapleton (2021)
Source. The publishing scandal happening right now by Andy Stapleton (2023)
Source. TOOD get the name of the academic who quit. A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis (1958) Updated 2024-12-15 +Created 1970-01-01
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, very meh, asked rationale on GitHub discussion, and they confirmed as expected that it is to:Oh well.
- to prevent their publication ideas from being stolen. Who would steal publication ideas with public proof in an issue tracker without crediting original authors?
- to prevent noise from non collaborators. They do only get like 2 issues as year though, people forget that it is legal to ignore other people :-)
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.Ciro Santilli once talked to a man who had been working on high-frequency trading for the last six years.
He was quite nice.
Ciro asked him in what way did he feel his job contributed to the benefit of society.
He replied that it didn't contribute at all. It was completely useless. More than that, it so completely useless, that it was even pure. A bit like advanced mathematics, but not even providing beauty for anybody outside of the company, since everything is a closely guarded trade secret, unlike mathematics which is normally published for the vanity recognition.
And so, Ciro was enlightened.
A great mind can work in the most useless branches of finance, without the desire to improve the world, nor make it worse. Not to compete, nor be afraid, nor anxious. A Sand mandala.
Only being. Being, in the exact fraction of a moment where bid meets ask.
From the abstract:
Much money, his student went on to say, is spent by various Governments in attempting to discover those people whose thorough education may be expected to bring in a return of value to the State, and the question how best to discover latent genius is an eminently practical one. After cogitation, Prof. Ostwald came to the conclusion that it is those students who cannot be kept on the rails - that is, who are not contented with methodical teaching - who have within them the seeds of geniusCiro Santilli couldn't agree more... notably students must have a flexible choice of what to learn.
2s/2p energy split in the hydrogen emission spectrum, not predicted by the Dirac equation, but explained by quantum electrodynamics, which is one of the first great triumphs of that theory.
Note that for atoms with multiple electrons, 2s/2p shifts are expected: Why does 2s have less energy than 1s if they have the same principal quantum number?. The surprise was observing that on hydrogen which only has one electron.
Initial experiment: Lamb-Retherford experiment.
On the return from the train from the Shelter Island Conference in New York, Hans Bethe managed to do a non-relativistic calculation of the Lamb shift. He then published as The Electromagnetic Shift of Energy Levels by Hans Bethe (1947) which is still paywalled as of 2021, fuck me: journals.aps.org/pr/abstract/10.1103/PhysRev.72.339 by Physical Review.
The Electromagnetic Shift of Energy Levels Freeman Dyson (1948) published on Physical Review is apparently a relativistic analysis of the same: journals.aps.org/pr/abstract/10.1103/PhysRev.73.617 also paywalled as of 2021.
TODO how do the infinities show up, and how did people solve them?
Lamb shift by Dr. Nissar Ahmad (2020)
Source. Whiteboard Lecture about the phenomena, includes description of the experiment. Seems quite good.www.mdpi.com/2624-8174/2/2/8/pdf History and Some Aspects of the Lamb Shift by G. Jordan Maclay (2019)
Freeman Dyson - The Lamb shift by Web of Stories (1998)
Source. Mentions that he moved to the USA from the United Kingdom specifically because great experiments were being carried at Columbia University, which is where the Lamb-Retherford experiment was done, and that Isidor Isaac Rabi was the head at the time.
He then explains mass renormalization briefly: instead of calculating from scratch, you just compare the raw electron to the bound electron and take the difference. Both of those have infinities in them, but the difference between them cancels out those infinities.
Hans Bethe - The Lamb shift (1996)
Source. Ahh, Hans is so old in that video, it is sad to see. He did live a lot tough. Mentions that the shift is of about 1000 MHz.
The following video: www.youtube.com/watch?v=vZvQg3bkV7s Hans Bethe - Calculating the Lamb shift.
Lamb shift by Vidya-mitra (2018)
Source. Structure of Hen Egg-White Lysozyme: A Three-dimensional Fourier Synthesis at 2 Å Resolution (1965) Updated 2024-12-15 +Created 1970-01-01
www.nature.com/articles/206757a0 on Nature 181, 662-666. Paywalled as of 2022. Has some nice pictures in it.
Structure of Some Crystalline Lysozyme-Inhibitor Complexes Determined by X-Ray Analysis At 6 Å Resolution (1965) Updated 2024-12-15 +Created 1970-01-01
www.nature.com/articles/206761a0 on Nature 206, 761-763. Paywalled as of 2022. Has some nice pictures in it.