Ciro Santilli @cirosantilli 37

A really good option to store educational media such as images and video!

Shame that like the rest of Wikimedia, their interface is so clunky and lacking obvious features.

The cool thing about parallel evolution is that it shows how complex phenotype can evolve from very different initial genetic conditions, highlighting the great power of evolution.

We list some cool ones at: polyphyly.

ALSA can be thought as analogous to physical wires linking up machines.

Except that instead of machines, you have separate programs. One such typical link is:

The advantage of this setup is that separate programs can collaborate to make complex sounds.

The disadvantage of this setup is that it makes it very hard to reproduce results, you basically need a Docker image with the exact same version of everything. And some script to launch and connect all programs correctly.

Some composition systems like LMMS reduce that problem by having synthesizers as plugins, so that you don't have to setup any connections yourself.

aconnect vmpk hello world: askubuntu.com/questions/34391/virtual-midi-piano-keyboard-setup/1298026#1298026

This is a good initiative. It doesn't go nearly as deep as it needs to go to fix students must have a flexible choice of what to learn, but it is a start!

Followup to Quantum field theory lecture by Tobias Osborne (2017).

When the word "advanced" precedes QFT, you know that the brainrape is imminent!!!

Big goal: explain the Standard Model.

2022: saddle and seat post stolen near home. Burn in Hell, motherfuckers. Bought a seatpost marked SP342 MICROPOST ALLOY 3 30.4mm. Like this: web.archive.org/web/20220208115055/https://www.ebay.co.uk/itm/Lightweight-Alloy-Micropost-Bike-MTB-Seatpost-25-4mm-Seat-Pin-300m-Long-Silver-/402311713393 but 30.4mm. OK, bought the Park Tool PW-5 15mm pedal wrench tool. Wasn't expensive at all.

TODO understand other markings on receipt: "18 Flourish FS W Sil XS".

The exact specs pages is lost forever. Closest one we've got is the 2020: web.archive.org/web/20200927204537/https://www.liv-cycling.com/gb/flourish-2

Frame: size: XS. Marking near bottom bracket: F/N GY17Z1327 DK: WGI GY17Z1327 F ES:BI-2339.

Seatpost: TODO diameter. Measured in store 30.4mm after original stolen, although 2020 says 30.9. 30.4mm seemed to fit OK, and measuring with ruler gives 30.5/30.6, I don't think a 30.9 can possibly fit.

Saddle: Liv Contact Comfort Plus Saddle, color golden brown. Same as this but blown: www.liv-cycling.com/gb/contact-comfort-plus-saddle-liv Actual color:

Discovered by Marie Curie when she noticed that there was some yet unknown more radioactive element in their raw samples, after uranium and polonium, which she published 6 months prior, had already been separated. Published on December 1989 as: Section "Sur une nouvelle substance fortement radio-active, contenue dans la pechblende".

The uranium 238 decay chain is the main source of naturally occurring radium.

To Ernest Lawrence for the cyclotron.

Variable resistance element.

As of 2020, Ciro Santilli is getting excited about quantum computing, which is a deep tech field.

He's a bit lazy to explain why here, but Googling will be more than enough.

There is a risk it will fizzle and the bubble pop, like any revolution.

But recent developments are making it too exciting to ignore.

2022 page: www.cs.ox.ac.uk/teaching/courses/2022-2023/quantum/ (archive). Assignments are available:

2022 lecturer: Aleks Kissinger

The course would be better named ZX-calculus as it appears to be the only subject covered.

Group of all permutations.

Group of even permutations.

Note that odd permutations don't form a subgroup of the symmetric group like the even permutations do, because the composition of two odd permutations is an even permutation.

UniProt entry: www.uniprot.org/uniprot/P00561.

NCBI entry: www.ncbi.nlm.nih.gov/gene/945803.

The second gene in the E. Coli K-12 MG1655 genome. Part of the E. Coli K-12 MG1655 operon thrLABC.

Part of a reaction that produces threonine.

This protein is an enzyme. The UniProt entry clearly shows the chemical reactions that it catalyses. In this case, there are actually two! It can either transforming the metabolite:Also interestingly, we see that both of those reaction require some extra energy to catalyse, one needing adenosine triphosphate and the other nADP+.

TODO: any mention of how much faster it makes the reaction, numerically?

Since this is an enzyme, it would also be interesting to have a quick search for it in the KEGG entry starting from the organism: www.genome.jp/pathway/eco01100+M00022 We type in the search bar "thrA", it gives a long list, but the last entry is our "thrA". Selecting it highlights two pathways in the large graph, so we understand that it catalyzes two different reactions, as suggested by the protein name itself (fused blah blah). We can now hover over:Note that common cofactor are omitted, since we've learnt from the UniProt entry that this reaction uses ATP.

If we can now click on the L-Homoserine edge, it takes us to: www.genome.jp/entry/eco:b0002+eco:b3940. Under "Pathway" we see an interesting looking pathway "Glycine, serine and threonine metabolism": www.genome.jp/pathway/eco00260+b0002 which contains a small manually selected and extremely clearly named subset of the larger graph!

But looking at the bottom of this subgraph (the UI is not great, can't Ctrl+F and enzyme names not shown, but the selected enzyme is slightly highlighted in red because it is in the URL www.genome.jp/pathway/eco00260+b0002 vs www.genome.jp/pathway/eco00260) we clearly see that thrA, thrB and thrC for a sequence that directly transforms "L-aspartate 4-semialdehyde" into "Homoserine" to "O-Phospho-L-homoserine" and finally tothreonine. This makes it crystal clear that they are not just located adjacently in the genome by chance: they are actually functionally related, and likely controlled by the same transcription factor: when you want one of them, you basically always want the three, because you must be are lacking threonine. TODO find transcription factor!

The UniProt entry also shows an interactive browser of the tertiary structure of the protein. We note that there are currently two sources available: X-ray crystallography and AlphaFold. To be honest, the AlphaFold one looks quite off!!!

By inspecting the FASTA for the entire genome, or by using the NCBI open reading frame tool, we see that this gene lies entirely in its own open reading frame, so it is quite boring

From the FASTA we see that the very first three Codons at position 337 arewhere ATG is the start codon, and CGA GTG should be the first two that actually go into the protein:

ecocyc.org/gene?orgid=ECOLI&id=ASPKINIHOMOSERDEHYDROGI-MONOMER mentions that the enzime is most active as protein complex with four copies of the same protein:TODO image?