The Vital Question

Introduction: Why is Life the way it is?

• Some structures inside complex cells look and behave like bacteria, perhaps they are!

• Lynn Margulis came up with ‘serial endosymbiosis theory’: The idea that complex eukaryotic cells are an ensemble of bacteria.

• But that has far less to support it, there’s nothing in the genes to suggest it.

• Francis Crick, 1958: “Biologists should realise that before long we shall have a subject which might be called ‘portein taxonomy - the study of amino acid sequences of proteins of an organism and the comparison of them between species. It can be argued that these sequences are the most delicate expression possible of the phenotype of an organism and the vast amounts of evolutionary information may be hidden away within them.”

• Indeed, biology is now very much about the info concealed in the sequences of proteins and genes.

• Instead of amino acids, we now compare the sequences of letters in DNA, giving greater sensitivity.

• We know that complex cells arose on just one occasion in 4 billion years of evolution, through a singular endosymbiosis between an archaeon and a bacterium.

• So it seems that there are 3 big unknowns at the very heart of biology today:

  1. why life evolved in the perplexing way it did?
  2. why cells are poweredin such a peculiar fashion?

PART 1: THE PROBLEM

What is Life?

• Your software is built by source code 🖥️. Living organisms are built by genomes 🧬.

• Genomes do not predict the future but recall the past: they reflect the exigencies of history.

• Dialectical materialism: Genes <—> environment, aka nature and nurture. Biology is all about genes, and their behaviour is all about the environment.

• All plants, animals, algae, fungi and protists share a common ancestor - the eukaryotes are monophyletic.

• Almost all the genes inolved (encoding so-called eukaryotic “signature proteins”) are not found in prokaryotes. Conversely, bacteria show practically no tendency to evolve any of these complex eukaryotic traits. There are no known evolutionary intermediates between the morphologically simple state of all prokaryotes and the disturbingly complex ancestor of eukaryotes. All these attributes of complex life arose in a phylogenetic void, a black hole at the heart of biology.

• ‘The Origin of Species’ by Darwin made the point that natural selection actually predicts that intermediate should be lost. In that context, it is not terribly surprising that there are no surviving intermediates between bacteria and eukaryotes.

• Some sort of structural constraint must have acted equally on both of the two great domains of prokaryotes, the bacteria and archaea, forcing both groups to remain simple in their morphology throughout an incomprehensible 4 billion years. Only eukaryotes explored the realm of complexity and they did so via an explosive monophyletic radiation that implies a release from whatever these structural constraints might have been. That appears to have happened just once - all eukaryotes are related.

• The chapter sets up the book’s central argument: that energetic constraints—rather than solely genetic or chemical factors—are pivotal in shaping life’s evolution

What is living?