ryan

wtf now my agents found the first bacteria to use new stop codons!! After this TAG result, a chat w/ friend inspired the question: do any bacteria use other stop codons? Overnight, my guys found myxobacteria that stop at TTA, normally read as an amino acid. Evidence: 1) These bacteria lost the tRNA that normally reads TTA as leucine. 2) Their RF2, the protein that recognizes stop codons, has two changes: one in its codon-reading tip (SPF → SPY) and one nearby (L → F). No other species in GTDB has both. 3) We compared the same genes in these bacteria and their closest relatives. Where a relative's gene ends at a normal stop but the gene here keeps going, the very next codon is TTA 11% of the time (252 of 2,339 genes). In the relatives, it's 0.05% (1 of 2,025). 4) TTA swaps with the normal stop codons. Where one of these genomes ends a gene at TTA, another genome from the same group ends that gene at a normal stop 78% of the time. Method: Claude agents on my Mac mini scanned all 199,923 bacterial and archaeal genomes in GTDB for amino-acid codons unusually common near the ends of genes, where a hidden stop would sit. In 4,599 genomes, they then matched each gene to corresponding proteins and checked which codon sits exactly where the known protein ends. Closest prior work: TTA works as a stop in some mitochondria and plastids (Barcytė et al. 2025), and CGA was proposed as a stop in Asgard archaea (Melnykov 2026, PNAS), but none in bacteria until now. One of these bacteria, 1-FT3.2, is kept alive in Finland (Demina et al. 2025). Possibly its proteins can be measured to confirm this.

Data and code: github.com/ry-xu/genome-rese… I think at this point, getting this in front of people in the field is the most important next step. To validate results, discuss followups, and hopefully collaborate. Please reach out if you find this interesting or if you know someone who would. @phylogenomics @jcamthrash @OmicsOmicsBlog

While this is fresh... my AI agents recently ALSO found possibly unmapped sites in Mexico. Not Maya though, these are in the Huasteca. Dozens of raised earth platforms in a cow pasture. Could also be modern earthworks - unverified and reported to INAH.

Training on self outputs degrades model performance

visualizing raw data in ways before unseen pt 3: seismometers are able to pick up human activity!! American is silent on Christmas

visualizing raw data in ways before unseen pt 2: 73 magnetic observatory compass readings during the May 2024 solar storm

visualizing raw data in ways before unseen pt 1: 153 seismometer readings following Tōhoku M9.1 earthquake

aliens could land tmr and it would be the 4th most surprising thing that's happened recently

They thought he was speaking gibberish but he was just Hungarian 😭

Looking at the reasoning trace, astra identified the games by: 1) which of the 10x10 grid cells had strong weights 2) which actions had large biases E.g. - Pong: only up and down actions have strong biases - Breakout: bottom row for paddle, bricks at top - Freeway: strong bias towards moving upwards - Pac-Man: maze is visible from grid input weights Still cool, but probably a game enthusiast would have figured it out in a few minutes in a similar way.