The Computer Conservation Society (CCS) is an organization aimed at preserving and promoting the history of computing. Founded in the United Kingdom in 1989, the society focuses on the conservation of historic computers and the documentation of their development, as well as promoting awareness and understanding of the impact of computing technology on society. The CCS often collaborates with museums, educational institutions, and other organizations to restore historic computing equipment and to create exhibitions that showcase the evolution of computing technology.

As of 2025, you can check if someone with a given name was at polytechnique and at which year at: programmes.polytechnique.edu/en/about/ecole-polytechnique/list-of-graduates

Public facing GitLab instance: gitlab.binets.fr/, e.g. a repo in Ciro's account: gitlab.binets.fr/ciro.duran-santilli/china-dictatorship

The Cranfield experiments refer to a series of information retrieval experiments conducted at Cranfield University in the United Kingdom during the 1960s. These experiments were foundational in the development of modern information retrieval systems and methodologies used to evaluate the effectiveness of information retrieval processes. The key aspects of the Cranfield experiments include: 1. **Evaluation of Retrieval Systems**: The experiments were designed to assess various information retrieval techniques and systems by using a structured methodology.

NCBI taxonomy entry: www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145 This links to:

KEGG entry: www.genome.jp/pathway/eco01100+M00022

BioCyc promoter database query URL: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI

The Generalized Distributive Law is a mathematical concept that extends the classical distributive law of multiplication over addition in algebra.

Transcription factor for E. Coli K-12 MG1655 operon thrLABC as shown at biocyc.org/ECOLI/NEW-IMAGE?object=TU0-42486.

Note that this is very close to the "end" of the genome.

NCBI: www.ncbi.nlm.nih.gov/gene/948874

UniProt: www.uniprot.org/uniprot/P0A9Q1

TODO DNA assembly structure.

David Caminer is a noted figure in the field of computing and is best recognized for his contributions to the development of early computer systems and software. He played a significant role in the evolution of data processing and has been associated with various projects related to the application of computing in business and scientific domains.

In the 19th century, India saw various developments in the field of physics, though the recognition of Indian physicists as formal scientists, particularly in the modern sense, evolved later. Some notable figures and contributions from the period include: 1. **Jagadish Chandra Bose (1858-1937)**: Although he worked primarily in the late 19th and early 20th centuries, Bose made significant contributions to the study of radio waves, plant physiology, and experimental science.

The **Annual Review of Astronomy and Astrophysics** is a scholarly journal that publishes comprehensive review articles on significant developments and current topics in the fields of astronomy and astrophysics. The journal aims to summarize and synthesize the latest findings, theories, and research in various subfields within these disciplines, making them accessible to researchers, educators, and students. Each volume of the Annual Review typically includes several articles written by experts, focusing on recent advancements, emerging trends, and key questions in the field.

The 19th century was a significant period for physics in Italy, with several notable physicists making important contributions to various fields. Here are a few key figures: 1. **Alessandro Volta (1745-1827)**: Although his most influential work was done in the late 18th century, Volta's impact extended into the 19th century.

David May is a British computer scientist known for his contributions to computer architecture, programming languages, and software engineering. He has worked on various aspects of computer systems, including hardware design and the development of languages that enable more efficient programming and system interaction. One of his notable contributions is in the area of concurrent programming, particularly with the development of the Occam programming language, which was designed for programming the Transputer, a pioneering piece of hardware in parallel computing.

All gene names that start with an Y such as:appear to be proteins of unknown function.

UniProt for example describes YaaX as "Uncharacterized protein YaaX".

As function is discovered, they then change it to a better name, e.g. to names such as the E. Coli K-12 MG1655 transcription unit thrLABC proteins all of which have a clear name due to threonine.

There are many other y??? as of 2021! Though they do tend to be smaller molecules.

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?

UniProt entry: www.uniprot.org/uniprot/P0AD86.

NCBI gene entry: www.ncbi.nlm.nih.gov/gene/944742.

The first gene in the E. Coli K-12 MG1655 genome. Remember however that bacterial chromosome is circular, so being the first doesn't mean much, how the choice was made: Section "E. Coli genome starting point".

Part of E. Coli K-12 MG1655 operon thrLABC.

At only 65 bp, this gene is quite small and boring. For a more interesting gene, have a look at the next gene, e. Coli K-12 MG1655 gene thrA.

Does something to do with threonine.

This is the first in the sequence thrL, thrA, thrB, thrC. This type of naming convention is quite common on related adjacent proteins, all of which must be getting transcribed into a single RNA by the same promoter. As mentioned in the analysis of the KEGG entry for e. Coli K-12 MG1655 gene thrA, those A, B and C are actually directly functionally linked in a direct metabolic pathway.

We can see that thrL, A, B, and C are in the same transcription unit by browsing the list of promoter at: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI. By finding the first one by position we reach; biocyc.org/ECOLI/NEW-IMAGE?object=TU0-42486.