Theoretical Biology Reading Group

Check out Koonin’s book (www.google.com/books/editio...) and the paper his discussion of introns is based on (www.nature.com/articles/nat...). At our next session, we’ll be discussing
@birchlse.bsky.social’s The Philosophy of Social Evolution. More details coming soon.

Finally, this story suggests an intermediate position in the "junk DNA" debate. While most of the eukaryotic genome is junk, it is structured junk; this structured junk is a massive pool of variation that evolution has tinkered around with to build many of our lineage's most essential innovations.

Increases in evolutionary complexity, then, are often associated with population bottlenecks because bottlenecks relax the pressure of purifying selection, allowing populations to explore areas of the fitness landscape further from their local peak.

Overall, the prevailing evolutionary trend is likely toward genomic streamlining--in fact, that is precisely what happened in many unicellular eukaryotes, whose large population sizes have allowed them to evolve genomes which are nearly intron-free.

Koonin argues (after Mike Lynch) that the null hypothesis for the evolution of genomic complexity should be that it is neutral--genes duplicate, parts of one or the other break, and now two genes are needed where only one was before.

What does this story tell us about evolution? First, the evolution of complexity is not by any means necessarily adaptive. Though the intron-exon structure of eukaryotic genes today allows for combinatorial gene expression, its origin in an invasion of genetic parasites was massively maladaptive.

Model of the structure of the human spliceosome, from Zhang et al. 2017 - An Atomic Structure of the Human Spliceosome

The spliceosome, the RNA-protein complex which in all eukaryotes removes introns from mRNA, is composed of snRNAs derived from bacterial Group II intron genes and proteins, such as Sm, of archaeal origin.

How did eukaryotes deal with this problem? They evolved a nucleus, which separated transcription from translation, allowing for sequestration of aberrant transcripts. But more surprisingly, they evolved tools to inhibit the translation of introns using genes derived from the introns themselves.

This massive stress likely contributed to a reduced population size among these proto-eukaryotes. This population bottleneck only exacerbated the problem, as the lower the population size, the less effective is purifying selection to rid the population of introns.

Perhaps the worst part of this genetic barrage was the introns, mobile elements which can actively catalyze their own excision and insertion into DNA, and thus proliferate rapidly throughout a genome.

When these bacteria broke open, they spilled their genes into the cytoplasm; over generations, these genes recombined into random sites in the archaeal genome, breaking functional elements left and right.

When the alpha-proteobacterium which was to become the mitochondria took up life inside its archaeal host, the archaeal genome faced an unprecedented challenge.

The cover of Eugene Koonin's The Logic of Chance: The Nature and Origin of Biological Evolution. The title and author's name are written in a serif font over a photograph of a bare birch tree and twigs.

Last Thursday, we discussed Eugene Koonin's The Logic of Chance. Koonin tells the story of how genomics, particularly bacterial and viral genomics, has changed our understanding of how evolution works. One episode in this story is the evolution of eukaryotic introns and the spliceosome.

Poster with low-contrast black-and-white background image, a scanning electron micrograph of the archaeon Candidatus Prometheoarchaeum syntrophicum, strain MK-D1 (image from Imachi et al. 2020 - Isolation of an archaeon at the prokaryote-eukaryote interface). The poster text reads "the Theoretical Biology Reading Group will be discussing Eugene Koonin's The Logic of Chance. 5pm, 2/26, Daley Library Rm 4-191". In the bottom right corner is a QR code and a link to theoreticalbiology.github.io and an email address, theoreticalbiology@proton.me.

On February 26th, we'll be discussing Eugene Koonin's The Logic of Chance. The meeting will take place at 5pm at the Daley Library at UIC, Room 4-191. Please RSVP at theoreticalbiology.github.io.