The long-awaited Oxide and Friends bookclub! Bryan and Adam were joined by special guest--and real life biologist--Greg Cost to discuss Philip Ball's terrific book, How Life Works: A User’s Guide to the New Biology. Spoiler: Alan Turing makes a very expected appearance!In addition to Bryan Cantrill and Adam Leventhal, we were joined by special guest Greg Cost.Some of the topics we hit on, in the order that we hit them:The Turing patternRNA as a precursor to DNAXenopus frogXenobotsAnton computerBryan's reading notesCentral themesPower and limitations of metaphor – especially mechanical onesThe fundamental, diametrical opposition between life and machines. (Nature does not use simulations!)Rejecting the neo-Darwinian paradigmPassages of note:p. 91: “of the common SNPs seen in human populations, fully 62 percent are associated with height” … “the most common genomic associations for complex traits like this are in the noncoding regions” What is cognition? p. 137: “Life is, as biologist Michael Levin Jeremy Gunawardenaand philosopher Daniel Dennet have argued, ‘cognition all the way down’” AlphaFold2 p. 148 “AlphaFold does not so much solve the infamously difficult protein-folding problem as sidestep it. The algorithm makes no predictions about how a polypeptide chain folds, but simply predicts the end result based on the sequence.”p. 156: allostery refers to how a? p. 160: “The popular view that science is the process of studying what the world is like needs to be given an important qualification: science tends to be the study of what we can study.”p. 166: “The misfolding pathology of PrPs (prion proteins) is the price paid for the benefits of disorder. … Disordered proteins can increase the complexity and versatility of our regulatory networks, but at the cost of increased risk of toxic aggregates formed from misfolded proteins.”p. 181: “The [training] analogy is far from perfect, not least because proteins don’t need to be ‘trained’ to acquire their roles.” Ball himself loves to use computing a metaphor, even when it is inapt or imperfect!p. 189: “What you’re really looking at here is a diagram not of a molecular event but of a failed paradigm.”p. 201: Clifford Brangwynne: “Many of the textbooks and even our language conveys this kind of factory-floor image of what goes on inside the cell. But the reality is that the computational logic underlying life is much more soft, wet and stochastic than anyone appreciates.” To which I would add: the information machine is MUCH more deterministic than anyone appreciates!p. 205: “Because the binding of BMPs to BMP receptors can be altered by other molecules, the BMP pathway can interact with other pathways to create crosstalk between cells during development.” Mike Olson’s observation of everything working through side-effect. ? p. 212: “It seems likely that metazoans have evolved this evolvability. One of the odd features of transcription factors that bind to DNA is that, in eukaryotes, the base sequences that they recognize are often surprisingly short – perhaps six or so base pairs long. … But there’s no reason the selectivity has to be this approximate; in prokaryotes the binding sites are longer and therefore more specific. It seems that eukaryotes have, so to speak, chosen this sloppiness – probably because it allows new regulatory pathways to develop.”p 217: “While causal emergence seems to be a general design principle for life, it is rarely evident in our own technologies.” Disagree with: “...maybe the better computers of the future will be more causally emergent.” We can’t even get asynchronous systems working!? p. 222: “Is there, after all, really such an obvious advantage to being multicellular? If so, we don’t know what it is.” … “If [evolutionary biologist Michael] Lynch is right, the implication is humbling: we are here not because the multicellular lifestyle of metazoans like us is superior or even advantageous, but because chance mutations created possibilities for new re