Quantinuum H1 by Ciro Santilli 35 Updated +Created
History of polarization by Ciro Santilli 35 Updated +Created
Particularly cool is to see how Fresnel fully understood that light is somehow polarized, even though he did not know that it was made out of electromagnetism, clear indication of which only came with the Faraday effect in 1845.
spie.org/publications/fg05_p03_maluss_law:
At the beginning of the nineteenth century the only known way to generate polarized light was with a calcite crystal. In 1808, using a calcite crystal, Malus discovered that natural incident light became polarized when it was reflected by a glass surface, and that the light reflected close to an angle of incidence of 57° could be extinguished when viewed through the crystal. He then proposed that natural light consisted of the s- and p-polarizations, which were perpendicular to each other.
Sample collection by Ciro Santilli 35 Updated +Created
As you would expect, not much secret here, we just dumped a 1 liter glass bottle with a rope attached around the neck in a few different locations of the river, and pulled it out with the rope.
And, in the name of science, we even wore gloves to not contaminate the samples!
Figure 1.
Swans swimming in the river when during sample collection
. Source. Swam poo bacteria?
Figure 2.
Tying rope to bootle for river water sample collection
. Source.
Figure 3.
Dumping the bottle into the river to collect the water sample
. Source.
Figure 4.
Measuring the river water sample temperature with a mercury thermometer
. Source.
Figure 5.
Measuring the river water sample pH with a pH strip
. Source. The strip is compared with the color of a mobile app that gives the pH for a given strip color.
Figure 6.
Noting sample collection location on the water bottle
. Source.
Video 1.
Dumping the bottle into the river to collect the water sample
. Source. That was fun.
Conclusions by Ciro Santilli 35 Updated +Created
  • against all odds, the experiment worked and we got DNA out of the water, despite a bunch of non-bio newbs actively messing with random parts of the experiment
  • PuntSeq and Biomakespace people, and all those tho do scientific outreach, are awesome!
  • biology is hard
  • creating insanely media rich articles like this is also hard, but the following helped enormously:
    • Wikimedia Commons to store large media files out of Git
    • Asciidoctor extensions to easily include those media files. The lessons learnt in this article were then an important motivation for Ciro's OurBigBook Markup, to which this article was later migrated.
    • Nomacs to give Google Photos photos meaningful names and to edit people's faces out of pictures ;-)
  • some scientific Wikipedia pages may or may not have been edited with better pictures during the course of writing this article
better-sqlite3 Node.js package by Ciro Santilli 35 Updated +Created
As claimed on their README, their operation truly appears to be 10x faster than the node-sqlite package!! It is insane!! How can that other package still exist at all?
The only big problem was the lack of ORM, but people are looking into that by adding it to Sequelize:
Isomer by Ciro Santilli 35 Updated +Created
Isomers were quite confusing for early chemists, before atomic theory was widely accepted, and people where thinking mostly in terms of proportions of equations, related: Section "Isomers suggest that atoms exist".
Mars sample-return mission by Ciro Santilli 35 Updated +Created
Not done yet as of 2020! Will be done one day for sure.
Fabry-Pérot interferometer by Ciro Santilli 35 Updated +Created
Video 1.
Fabry Perot Interferometer by JFC UCL (2016)
Source. Description only, reasonable animations. Considers the case of two nearby beam splitters.
Video 2.
Fabry-Perot Introduction by Williams College Physics (2020)
Source.
Shows a working device. Confocal optical cavity, one of the mirrors scans back and forward moved by a piezoelectric motor, this is called a "scanning Fabry-Perot interferometer".
Does not produce an interference pattern, only an on/off blob, which is then fed into an oscilloscope for analysis. The oscilloscope shows both the mirror displacement (which is given by a voltage) and the light detector output.
Video 3.
Aligning a Scanning Fabry-Perot Interferometer by University of South Florida (2016)
Source. Very detailed, and shows of some nice equipment and techniques.
feathersjs/feathers-chat by Ciro Santilli 35 Updated +Created
The main FeathersJS hello world demo. Notable missing things...
E. Coli K-12 MG1655 gene thrA by Ciro Santilli 35 Updated +Created
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:
  • "L-homoserine" into "L-aspartate 4-semialdehyde"
  • "L-aspartate" into "4-phospho-L-aspartate"
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:
  • the edge: it shows all the enzymes that catalyze the given reaction. Both edges actually have multiple enzymes, e.g. the L-Homoserine path is also catalyzed by another enzyme called metL.
  • the node: they are the metabolites, e.g. one of the paths contains "L-homoserine" on one node and "L-aspartate 4-semialdehyde"
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 are
ATG CGA GTG
where 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:
Aspartate kinase I / homoserine dehydrogenase I comprises a dimer of ThrA dimers. Although the dimeric form is catalytically active, the binding equilibrium dramatically favors the tetrameric form. The aspartate kinase and homoserine dehydrogenase activities of each ThrA monomer are catalyzed by independent domains connected by a linker region.
TODO image?
Arago spot by Ciro Santilli 35 Updated +Created
Continental drift by Ciro Santilli 35 Updated +Created
Ubuntu 21.10 by Ciro Santilli 35 Updated +Created
GDM crashes sometimes when switching windows right after opening a new window: bugs.launchpad.net/ubuntu/+source/gdm/+bug/1956299
Node.js SQLite bindings by Ciro Santilli 35 Updated +Created
SQL isolation level example by Ciro Santilli 35 Updated +Created

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