Writing a book about horizontal gene transfer and non treelike evolution. Bioinformatics, Evolutionary Biology. Pangenomes. Chair in Evolutionary Biology. 🇮🇪 http://github.com/mol-evol/panGPT
James McInerney
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This looks really great. I’ve been following this for a while.
On this last point: the implication is (and I wrote this in the paper) that evolution is not optimising biochemical (or other) activity as a primary focus, but the context-dependent function. And this is liable to change often.
A transformer model trained on raw DNA, with no biological instruction whatsoever, learned to distinguish between genetic codes. Nobody taught it what a codon is. That is just “wow”.
Interesting. www.rte.ie/brainstorm/2...
We have a new Masters programme in Liverpool. Please pass on to anybody you think might be interested: news.liverpool.ac.uk/2026/02/13/n...
those who felt word meanings came from definitions, and those who thought word meaning emerged from context. It just struck a chord & I started from there. I think gene "function" emerges from context (function ≠ biochemical activity, btw) and for the next ten years, I plan on focussing on context.
The entire thing came from watching a youtube video interview with Geoffrey Hinton (en.wikipedia.org/wiki/Geoffre...), who was talking about how the field of language modelling was in two camps 2/3
I'm thankful to MBE for publishing this paper. I wan't sure anybody would. The handling editor (I now know was Jeff Townsend) was great, as were the 2 reviewers. It is not an outcome/product/discovery, it is my way of thinking about HGT & pangenomes 1/3 academic.oup.com/mbe/article/...
