Nick Lane

biochemist at University College, London

Oxygen, The Molecule that made the World Oxford, 2002

• p215: James Lovelock estimates respired oxygen damage equivalent to whole body dose of 1 Sv (100 rem) per year.
  • Fukushima was about 300 Sv to workers and population. At 1 cancer / 1000 Sv, that's about 0.3 cancers. The cancers caused by the coal plants Fukishima replaced are in the thousands.

Life Ascending - The 10 Great Inventions of Evolution 2009

The overall message: Life is an optimized version of the easiest steps.

• 008 The Origin of Life Undersea alkaline vents produce small-celled nickle-iron compartments, and energetic chemical reactions that are much like living organisms use today. This is the best part of the book, because it provides a plausible high-probability organic chemistry path from primordial conditions to the first living cells. This is a complementary description to Linton and Watsons Revolutions that Made The Earth, which focuses on life's slow chemical restructuring of that environment.

• 034 DNA - RNA may have begun as a template molecule for guiding the formation of biomolecules. But RNA is fragile and structurally limited, so it expanded its repertoir with the aid of other molecules (leading to ribosomes), while DNA evolved to accurately duplicate RNA. The precursors of RNA codons are found in those alkaline vents.

• 060 Photosynthesis is the combination of two Photosystem 2 and Photosystem 1, evolving in separate prokaryotes and combining in eukaryotes. Once. This generated oxygen, slowly, until the world was transformed.

• 088 The Complex Cell Mitochondria. Another prokaryote fusion. This separates mutation-generating combustion from most of the cell's genetic material, including most of the genetic material of modern mitochondria. Some remains, for regulation.

• 118 Sex evolved to allow varied immunity to pathogens. Clones have identical immune systems, and rapidly-evolving pathogens can duplicate and exploit that. Dandelions are clones (p121) - which over time ought to make them vulnerable to epidemics. However, the real advantage of sex and variation is that it allows rapid exploitation of changing environments.

• 144 Movement Myosins, actins, kinesins, dyneins, and motor proteins powered by ATP.

• 172 Sight Lensed eyes are more accurate, but lensless eyes are more sensitive.

• 205 Hot Blood - high CO₂ levels produce low nitrogen, low protein, high carb plants. In high CO₂ eras, sufficient protein required eating lots of plants, and burning off the excess carbs.

• 232 Consciousness up to 10,000 synapses per neuron, 240 trillion synapses in the cerebral cortex. Phased locked oscillations, neural handshaking. Magic quantum effects are BS, and can't possibly operate at macroscale in a turbulent chemical environment.

• 260 Death ... happens after we no longer contribute to offspring. Natural selection cannot improve what it is blind to - old age.

The Vital Question

Energy, Evolution, and the Origins of Complex Life

• In essence, proton flow drives all lifeforms. Power flows permit eukaryotes and multicellular organisms.

• This is a densely detailed book, too much to summarize in a few pages.
• The merger of bacteria inside an archaeon to make eukaryotes a one-time event, took billions of years to happen.
• Mitochondria use proton flow through outer membrane to power ATPase
• Carbs to energy, protons flow from carbohydrates to oxygen down a very carefully tuned tunnelling cascade.
  • Small changes in molecules can change spacing by angstroms and tunnelling rates by orders of magnitude
• p21 "My argument in this book is that there are in fact strong constraints on evolution - energetic constraints - which do make it possible to predict some of the most fundamental traits of life from first principles."

• p24 ancient zircons (submillimeter zirconium silicate crystals) suggest liquid water > 4GYA

• p33 If ambient oxygen was key, polyphyletic radiation, multiple phyla adapt and diverge

• p35 but all eukaryote are made the same way
• likes Margulis original endocytosis, but serial endocytosis was nonsense
• Archezoa are a sidebranch of eukaryote tree, not the root (which has no living examples, no surviving intermediates )
  • all eukaryotes have radiated from LECA, Last Eukaryotic Common Ancestor, probably one single individual cell
  • Metazoa (like humans) branched from 3489 genes shared with LECA, plants from 3204 genes, 4133 LECA genes in all supergroups
• p83 life is all about proton gradients, the other machinery in bacterla and archaea are very different
• p124 Fig 15 Carl Woese phylogenetic tree for small subunit ribosomal DNA shows clearly branching tree from LUCA, however other bacterial genes each have different trees. Because bacteria laterally exchange so many genes so often, they have a merged history and LUCA cannot be determined easily.

• p125 As much as 30% of the genome can vary in different strains of E. coli

• p127 Bill Martin's disappearing tree, 48 genes conserved across all life, all produce a different "tree" 1 GYa, making LUCA impossible to pin down
• p130 LUCA was chemiosmotic with ATP synthase and DNA, but did not have a modern membrane or respiratory proton pumps or modern DNA replication (archaea and bacteria differ!). This does not make sense in open ocean, but does in alkaline hydrothermal vents.
• p131 acetyl CoA pathway

• p146 SPAP Sodium proton anti-porter enabled survival on smaller H⁺ gradients. Archaea and Bacteria evolved different proton pumps. That permitted the evolution of modern membranes and free living in open oceans.

• p178 Eukaryote metabolic rate per gene 30K to 300K higher than bacteria.
• p241 10x respiration rate changes per angstrom of respiratory chain spacing
  • since most mitochondrial genes come from central nucleus, and a few genes are in the mitochondria, they must carefully coevolve
  • Mitochondrial genes (exclusively from mother) evolve 10-50 times faster than nuclear genes
• mitochondrial membrane voltage potential 150 to 200 mV, 30 MV per meter field
• p273 Antioxidants - free radical leaks power respiration, antioxidants can disrupt this
• rest and inactivity can be bad because low ATP consumption raises membrane potential, respiratory complexes fill with electrons, and leak more free radicals.

• Barry Halliwell and John Gutteridge, Free Radicals in Biology and Medicine: "By the 1990s it was clear that antioxidants are not a panacea for ageing and disease, and only fringe medicine still peddles this notion"

• PSU RB170 .H35 1999 OHSU 3rd Ed Closed Stacks, Addall, cheap in UK but about $20 with shipping
• Amazon 4th edition 978-0198568698 2007 704p $20.64+3.99 acceptable, 5th edition 2015 896p 978-0198717485 $78.29+3.99 new