One promising way to find more of those would be with IP searches, since it was stated in the Reuters article that the CIA made the terrible mistake of using several contiguous IP blocks for those website. What a phenomenal OPSEC failure!!!

The easiest way would be if Wayback Machine itself had an IP search function, but we couldn't find one: Search Wayback Machine by IP.

viewdns.info was the first easily accessible website that Ciro Santilli could find that contained such information.

Our current results indicate that the typical IP range is about 30 IPs wide.

E.g. searching: viewdns.info/iphistory and considering only hits from 2011 or earlier we obtain:

Neither of these seem to be in the same ranges, the only common nearby hit amongst these ranges is the exact 68.178.232.100, and doing reverse IP search at viewdns.info/reverseip/?host=68.178.232.100&t=1 states that it has 2.5 million hostnames associated to it, so it must be some kind of Shared web hosting service, see also: superuser.com/questions/577070/is-it-possible-for-many-domain-names-to-share-one-ip-address, which makes search hard.

Ciro then tried some of the other IPs, and soon hit gold.

Initially, Ciro started by doing manual queries to viewdns.info/reversip until his IP was blocked. Then he created an account and used his 250 free queries with the following helper script: ../cia-2010-covert-communication-websites/viewdns-info.sh. The output of that script can be seen at: github.com/cirosantilli/media/blob/master/cia-2010-covert-communication-websites/viewdns-info.sh.

Ciro then found 2013 DNS Census which contained data highly disjoint form the viewdns-info one!

Summaries of the IP range exploration done so far follows, combined data from all databases above.

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

A memorable quote from Tinker Tailor Soldier Spy:

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.

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?