Evolutionary Transitions in Individuality: much more than you wanted to know

I.

For the first half of the 20th century, evolutionary biology was dominated by the Modern Synthesis—the triumphant, mathematically rigorous fusion of Darwinian natural selection with Mendelian genetics. It was a beautiful theory, clean and legible in the exact way that neoclassical economics is clean and legible. Allele frequencies exist in a population; the environment applies a selection pressure; the frequencies update via a localized algorithm.

But the Modern Synthesis treated the actual, physical organism as a black box. A genotype goes into the box, a phenotype comes out, selection acts upon