Transformer: The Deep Chemistry of Life and Death, Nick Lane, 2022, 390 pages, Dewey 572, ISBN 9780393651485
The book is largely about the Krebs cycle,Transformer: The Deep Chemistry of Life and Death, Nick Lane, 2022, 390 pages, Dewey 572, ISBN 9780393651485
The book is largely about the Krebs cycle, which provides energy and organic molecules inside cells. He gives us not just what's known, but also a sense of how amazing it is that anything /can/ be known of details of chemical reactions deep within cells. None of it is visible. Experimenters had to be very clever. Science is not a collection of dusty facts but a way of exploring the unknown. p. 273. We learn how some of the findings were made; he touches on the origins of life, and on metabolic causes of cancer. A page-turner despite the biochemical details.
Cells rarely live alone, but collaborate in the most intimate ways to optimize the driving forces of each other's metabolism. p. 171.
GEOCHEMISTRY BIRTHS BIOCHEMISTRY
Life could begin only in an oxygen-poor environment: hydrogen must react with carbon dioxide to form organic molecules. But hydrogen reacts instead with oxygen where available. p. 157.
At hydrothermal vents on the floors of alkaline seas, hydrogen and carbon dioxide flowed through porous metallic rock, which catalyzed organic-compound formation. Fatty acids spontaneously form enclosed membranes. At pH eleven, 70ºC, and ocean salinity, protocells self-assemble. Acetyl phosphate forms adenosine triphosphate, ATP, the energy supply of mitochondria. Ferric iron (Fe3+) catalyzes its formation. pp. 132-154.
Life began 4 billion years ago. Photosynthesis (in cyanobacteria from at least 2.3 billion years ago p. 176, which evolved into chloroplasts p. 221), produced O2 as waste. When O2 levels were high enough, animals developed that could reverse the Krebs cycle—burning organic compounds in oxygen, rather than assembling them from carbon dioxide. This enabled the Cambrian explosion of animal species, 640 million years ago. p. 158.
When people say that life on earth is "carbon-based," carboxylic acids are your basic hand of cards. p. 41. Five occur in all life: acetate (C2), pyruvate (C3), oxaloacetate (C4), succinate (C4) and alpha-ketoglutarate (C5). p. 123.
CANCER AND AGEING
When succinate accumulates in a cell, as it would if disease reduced oxygen delivery, genes switch on to promote inflammation and cell growth—as might be required in the event of illness or injury. If these genes stay switched on too long, cancer can result. pp. 209-213.
"Ageing reminds me of that absurd scene in Monty Python's /The Life of Brian/, where Brian admonishes the crowd that they don't need to follow anyone—they're all individuals. The crowd chants back, 'Yes, we're all individuals!' apart from one lone, doleful voice who says, 'I'm not.' " p. 263.
All your cells have the same genes. Epigenetics—which genes are switched on or off—make the difference between, say, kidney cells and nerve cells. Epigenetic changes cause us to age. The state of a cell results from one billion to 30 billion metabolic reactions per second. You comprise at least 30 trillion cells: in the last second you were sustained by 10^23 reactions. "In my mid-fifties, my wrinkles and aches and pains are the product of about 10^32 reactions, roughly 10^9 times the number of stars in the known universe. How many didn't work properly? It's astonishing I'm alive at all." p. 269.
CONSCIOUSNESS
Almost the only thing we know about consciousness is that it is, so to speak, soluble in ether, chloroform and a variety of other solvents. While it is not known to what extent fruit flies are conscious, they are most definitely unconscious when exposed to chloroform or ether. —Luca Turin. p. 276.
Every dogma has its day. p. 77. What if they were barking up the wrong tree? p. 83. Problems dogged them from the beginning. p. 84.
And yet—the finding that citrate synthase can run backward, threw the cat among the pigeons. p. 111.
Animals hasten the heat death of the universe, by turning free energy into heat energy. p. 32. (Don't worry. On the timescale of its heat death, the current age of the universe is minuscule.)
"Probably only a tenth of the material I wanted to write about actually made it into the book." p. 228.
Some of the "books that have most influenced me:"
Erwin Schrödinger, /What Is Life?/. Wrong on plenty of details, but an unparalleled example of how far vision and clear thinking can take you in science. p. 306.
Philip Ball, /Molecules: A Very Short Introduction/, 2003. Briefly covers the Krebs cycle and some basic metabolic biochemistry as part of a wider canvas. p. 309.
Eric Smith and Harold J. Morowitz, /The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere/, 2016. Clearly presents new ideas. Balanced. Exhaustive. pp. 330-331.
Nick Lane, /Life Ascending: The Ten Great Inventions of Evolution/, 2009. p. 340.
Tim Lenton and Andrew Watson, /Revolutions that Made the Earth/, 2013. p. 340.
Ron Milo and Rob Phillips, /Cell Biology by the Numbers/, 2016. p. 363.
Be told that in the nothing-ever-happens interpretation of quantum mechanics, every event spawns a universe where it doesn't happen. No matter what, there's always some universe where you never die. You're immortal.
In the real world, act on that belief. Go on. Could an interpretation of quantum mechanics be wrong?
Read instead a novel of (view spoiler)[the futility of life (hide spoiler)] in French from mid-20th Century, in German from early 20th Century, or in Russian from any time.
A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution, Jennifer A. Doudna, Samuel H. Sternberg, 2017, 281pp. (246pp. text +A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution, Jennifer A. Doudna, Samuel H. Sternberg, 2017, 281pp. (246pp. text + endmatter), ISBN 9780544716940, Dewey 576.5072, Library-of-Congress QH440
The authors are biochemists.
Viruses can splice new genetic information into the DNA of host cells. p. 16. Eight percent of the human genome is viral. p. 19.
Streptococcus thermophilus makes milk into yogurt or cheese. Streptococcus pyogenes causes .5 million human deaths annually. It causes strep throat, scarlet fever, toxic shock syndrome, and necrotizing fasciitis (flesh-eating bacteria). The two species of bacteria contain "all the same genes." pp. 72-73.
Bacteriophages--bacteria-destroying viruses--are the most prevalent life forms on Earth. They outnumber bacteria 10-to-1. Every day, 40% of all ocean bacteria are destroyed by phages. p. 48.
Bacterial DNA contains "Clustered Regularly Interspaced Short Palindromic Repeats" (CRISPR): between the repeated palindromes are snippets of DNA the bacteria have absorbed from viruses. The bacteria use these to match with and recognize attacking viral DNA; then to cut and destroy the attacking viral DNA. CRISPR is part of the bacterium's immune system. pp. 43-59. The bacteria's DNA is a template to make 2 kinds of RNA, and to make various enzymes. The RNA identifies and cuts the attacking viral DNA; the enzymes complete the destruction. pp. 62-81.
By modifying the swatch of DNA it matches, the CRISPR RNA, with its "tracrRNA," can be used to snip out /any/ bit of DNA. Not just viral DNA. The technique can work for human DNA too. pp. 81ff.
The author and her colleagues submitted their paper suggesting this to /Science/, June 8, 2012. It was published 20 days later and changed the field. p. 85.
"But should we?" pp. 113-246.
The author is oddly worrisome about the prospect that parents may interfere with nature to the extent of preventing their unborn child from being born with a congenital defect. Yet she's oddly OK with the idea of using the techniques to edit genes to cause the extinction of mosquitoes (and all the life forms that depend on them). She feels that /she/ should have a say in how people are permitted to use these techniques.
In any case, Pandora's box is open. Crops, domestic animals, wild animals, and humans are being modified using the techniques.
The author's description of the pace of advance makes this, her 2017 book, seem already dated in 2019....more
Thomas Ray
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