Ram Neupane, Ph.D.

As someone who did this kind of genome mining work during my PhD, some thoughts on this Anthropic announcement: First, the very simplified version of what they did is that they noticed two genes (one known, one new) sitting next to a weird repeating piece of DNA. More specifically, they described an unusual reverse transcriptase (RT) associated with a repetitive DNA array and an unknown accessory protein. This kind of process was used to understand CRISPR back in 2002 and was key to the gene editing tools we use today. To put this into context, though, people have been finding RTs associated with CRISPR arrays since 2008, and this general kind of genome-neighborhood mining has been used to discover new biological systems for decades. The basic genome-mining strategy is well established, and there are now mature tools and published pipelines for doing much of this. There are papers that discover and experimentally validate dozens of new systems using this approach in a single study. Doing it in bacteriophage genomes is also nothing new (eg CasPhi). Finding a weird cluster of genes and repeats is often the easy part. The hard part, and where the real discoveries come from, is figuring out what the system actually does. Eg for the bridge-RNA discovery in 2024 from @arcinstitute or the discovery of CasPhi in 2020 from @DoudnaJennifer they figured out the pieces of the system and the rules for what makes it work so it can be used. Anthropic does not yet know what this does. They’ve shown that the repeat array produces RNAs, but not what those RNAs do, what the RT does with them, or whether the system has any of the programmable properties that make the CRISPR comparison justified. I’m genuinely rooting for all of the frontier labs to seriously get into biological discovery, and I’m excited about what comes out of it. But announcing these very early, incremental findings with the framing of a major discovery doesn’t help. I’d much rather they set the bar high now, so that when an AI actually discovers a fundamentally new biological mechanism, everyone appreciates how big a deal it is.