All IP ranges have some holes in them for which we don't have a domain name.

It is because there was nothing there, or just because we don't have a good enough reverse IP database?

It is possible that DomainTools could help with a more complete database, but its access is extremely expensive and out of reach at the moment.

Censys is another option that would be good to try.

Putting 140 USD into WhoisXMLAPI to get all whois histories of interest for possible reverse searches would also be of interest.

Materials paywalled e.g. www.cs.ox.ac.uk/teaching/courses/2022-2023/modelsofcomputation/

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

This section is about the version of the course offered on Hilary term 2023 (January).

It can't be HTML crawl because presumably there wouldn't have been links to those websites? Presumably this is why Common Crawl doesn't seem to have any hits.

So they must have had some kind of DNS A record database?

Or would IPv4 sweep have worked, without the Host header with the CIA's setup?

The same question also applies to the 2013 DNS Census. It has less hits, but still has many.

Whatever they did, we are so so glad that they did!

.com and .net are very dominant. Here we list other choices made:

I wonder where the spray painted sign went: twitter.com/profgalloway/status/1229952158667288576/photo/1. As mentioned at officechai.com/startups/amazon-first-office/ and elsewhere, Jeff did all he could to save money, e.g. he made the desks himself from pieces of wood. Mentioned e.g. at youtu.be/J2xGBlT0cqY?t=345 from Video 4. "Jeff Bezos presentation at MIT (2002)".

Bibliography:

Previously it was unclear if there were any .org hits, until we found the first one with clear comms: web.archive.org/web/20110624203548/http://awfaoi.org/hand.jar

Later on, two more clear ones were found with expired domain trackers:further settling their existence. Later on newimages.org also came to light.

Others that had been previously found in IP ranges but without clear comms:

.org is very rare, and has been excluded from some of our search heuristics. That was a shame, but likely not much was missed.

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.

This is a dark art, and many of the sources are shady as fuck! We often have no idea of their methodology. Also no source is fully complete. We just piece up as best we can.

In order to explore IPs in known IP ranges, what we need are good DNS databases.

This is our primary data source, the first article that pointed out a few specific CIA websites which then served as the basis for all of our research.

We take the truth of this article as an axiom. And then all we claim is that all other websites found were made by the same people due to strong shared design principles of the such websites.

2022 page: www.cs.ox.ac.uk/teaching/courses/qsoft/ Half of the problems are Jupyter Notebooks, not bad.

Like Quantum Processes and Computation course of the University of Oxford, also ZX-calculus-heavy.

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?