This image: https://davidskernick.com/midwest-gal... makes it look like, "That place is amazing! Worth a trip!" But if you look at an ordinary picture of it, https://hangarkafe.com/ , you see that being there would not be as amazing as the photo makes it look. (For one thing, it's taken with a fisheye lens, which makes it look much larger than it is. And the lighting and camera angle are perfect.)
The photos are exceptional; the subject matter is worthy. I wouldn't want to own a copy, though.
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.
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
The Serengeti Rules, Sean B. Carroll, 2016, 213 pp. ISBN 9780691167428
Carroll tells us about how researchers find out how living systems (ecologies orThe Serengeti Rules, Sean B. Carroll, 2016, 213 pp. ISBN 9780691167428
Carroll tells us about how researchers find out how living systems (ecologies or individuals) work—usually by noticing the effects of a change. Change can have unlooked-for effects. We need to know the consequences of changes—and mitigate them.
Introduction:
In 1804, world human population reached 1 billion [up from perhaps 5,000–15,000 after the Tova eruption in Indonesia, 72,000 BCE—but Carroll doesn’t mention it]. Now, we’re adding a billion every 12 years. (p. 5) Ecologists estimate that Earth can sustainably regenerate enough plants and animals to support 4 billion humans. That line was crossed in 1980. The 2016 7-billion-human economy is using up Earth’s resources at about seven-fourths of the rate at which Earth can replenish them. (pp. 8–10) [This gives mass extinctions, mass destruction of unique habitats, catastrophic climate change. But Carroll doesn’t hit that note too hard in this book.]
In 1966, world lion population was 450,000. In 2016, it was 30,000: 40% in Tanzania. Zero in 26 African countries of its 1966 range. Ocean shark populations have fallen 90–99% in these 50 years. (p. 8) In 2016, there were 31 black rhinos in the Serengeti: once over 1000 there.
Chapter 1: effect of emotion on digestion.
Chapter 2: food chains.
Chapter 3: induction of enzyme production within cells.
17,500 feet elevation is the world’s highest permanent human population, on Mount Aucanquilcha, Chile. (p. 73)
Men with cholesterol over 260 mg/dl have 5 times the heart attack risk of men with cholesterol below 200 mg/dl. (p. 76)
Chapter 5. genetic causes of cancers.
Chapter 6: keystone species, without which biodiversity plummets.
A predator may be a keystone species: by preventing one prey species from exploding in population, the predator makes room for many other species. Examples:
Starfish in a tide pool keep mussel populations in check; many other species share the pool. Starfishless pools explode with mussels, excluding everything else.
Bass keep minnows in check, letting plants grow.
Sea otters keep anemones in check, letting kelp forest grow, which harbors a profusion of life. Seals and sea lions provide orcas something to eat besides sea otters, letting sea otters survive. Orcas extirpate sea otters where there are no seals, dooming the kelp forest.
Or, grazers can be a keystone: grazers eat the grass, so there’s less fuel in the dry season, so fewer fires, so trees can grow, so more species can exist that use trees. Dry areas of East Africa with too few grazers have many fires, few trees, few giraffes, few tree-using birds and other animals.
Chapter 7: In the Serengeti (among lions and hyenas), herbivores smaller than 300 kilograms usually die from predation; herbivores larger than 300 kilograms rarely die from predation.
[Hey! /We/ are smaller than 300 kg!! We’re gonna need some fire, sharp sticks, projectile weapons—whatever it takes!!!]
Chapter 8: human food requires keystone species too!
Shark overfishing off the Eastern United States allowed cownose ray populations to explode—which then extirpated the scallops that had been a millions-of-pounds-per-year human food source—down to zero.
Insecticide use killed the spiders that kept the insects from eating all the rice—causing Indonesia to become the world’s largest importer of rice. The insects gained immunity to the pesticides, and increased their egg-laying by a factor of 2.5 in the presence of pesticide. All leading to an 800-fold increase in rice-eating-insect density, without the spiders.
Fewer lions in Africa allowed baboons to explode in population, preying on human crops.
Chapter 9: Reintroducing keystone species.
Lake Mendota in Madison WI: without many bass and pike, small fish proliferated, zooplankton plummeted, and algae proliferated. Reintroduction of large fish (with fishing limits!) kept the small fish in check, allowed the zooplankton to increase, which ate the algae and made the water clearer. Just the reintroduction of big fish wouldn’t’ve done so much, but there was a massive dieoff of small cisco fish in a very hot summer. [Lake Mendota had clear water in the early 1960s, before Cherokee Marsh Subdivision was built—but Carroll doesn’t tell us that. He may not know. Carroll first saw Lake Mendota in 1987; he was at the University of Wisconsin–Madison 1987–2018. He’s now at Maryland. http://biology.umd.edu/sean-carroll.html also http://seanbcarroll.com/about/]
Yellowstone wolves were extirpated in 1926. Seventy years later, 95% of the aspen trees were over 75 years old. Without the wolves, elk proliferated, browsing almost all new trees down to the ground. Wolves were reintroduced in 1995. Ten years after releasing 31 wolves, there were 301. Winter elk population dropped from 17,000 to 8,000 by 2004. Trees are coming back. Beaver rebounded from 1 colony to 12 colonies in Lamar valley by 2009. But beaver have not returned to the streams most heavily eroded during the 70 overbrowsed years. Also, coyotes are down, so small pronghorn antelope are up. Ranchers lose 1% of sheep, 0.01% of cattle to wolves yearly. (pp. 179–180. Update: nps.gov/yell/learn/nature/wolves.htm)
Chapter 10: restoring Gorongosa National Park in Mozambique.
Gorgongosa is so lush it can support some 8,000 kg of animals per square kilometer. (p. 200)
A violent faction in Mozambique expelled the Portuguese in 1975, becoming a violent government. Civil war destroyed the park: animals were slaughtered for meat; forests were cut for fuel.
Restoration was a combination of bringing back extirpated species, anti-poaching and anti-lumbering enforcement, and creating value for local people in preserving the park rather than continuing to despoil it. Locals were hired as law-enforcement rangers; shade-grown coffee was introduced, to earn locals more than they could by deforesting to grow maize; tourism was redeveloped, to give locals employment; hospitals and schools were started. Much of this was funded by a U.S. telecom billionaire [as a tax-free way to remake the world in his image, out of the /interest/ on his wealth. Applause for what he accomplished. Thumbs down on monopoly profit and tax-avoidance.]
Afterword
Smallpox was eradicated in 15 years, from 1965—10 million cases, 2 million deaths, in 59 countries containing 1.1 billion people—to 1980—zero cases. [The virus exists now only in biological-weapons labs in the United States and Russia. What could go wrong?] Smallpox was eradicated by an army of dedicated, imaginative health workers who did not know that experts said it was impossible. See the book, House on Fire, by Bill Forge, for the full story of how it was done. Forge lists 18 lessons from the effort, of which a few:
Global efforts are possible.
We don’t have to live in a world of plagues, disastrous governments, conflict, uncontrolled health risks, pollution, mass extinction, erosion, climate catastrophe. By good management and teamwork, we can bring about a better future.
Coalitions are powerful.
The objective may be global; implementation is always local. Local cultures and needs determine which tactics are successful. The global effort will be the sum of countless local initiatives.
Optimism can be a self-fulfilling prophesy. There’s a place for pessimism, but not on the payroll!
The measure of civilization is how people treat one another.
Sean Carroll adds these:
Nothing gets conquered everywhere at once. Progress is important wherever it can be made.
Don’t wait until everyone gets on board. The experts thought smallpox-eradication wasn’t worth trying. Get started.
Individuals’ choices matter.
So—the book was mostly about ecology; some about physiology and medicine. Carroll’s book titles, and chapter titles, give little clue to what it’s about. It ends well, with the positive message, get together, do what you can.
397 pages, each with a National Geographic photo both pretty and rare. 11.5" x 9.5" x 1.5". 4.5 lb.397 pages, each with a National Geographic photo both pretty and rare. 11.5" x 9.5" x 1.5". 4.5 lb....more
Nick Lane, The Vital Question: Energy, Evolution, and the Origins of Complex Life, 2015, 360pp. ISBN 9780393088816
Bleeding-edge science for the generaNick Lane, The Vital Question: Energy, Evolution, and the Origins of Complex Life, 2015, 360pp. ISBN 9780393088816
Bleeding-edge science for the general reader. Lane has plausible, partly detailed explanations for how life may have arisen from natural geochemical processes—and how complex life may have arisen from bacteria and archaea.
He has new ideas—including testable hypotheses, and is testing some of them.
The atmosphere 4.4–4 billion years ago was mainly carbon dioxide, water vapor, nitrogen, sulfur dioxide—oxidized volcanic gases.
Conditions for new life:
Alkaline hydrothermal vents in mildly acidic, metal-rich sea: thermal currents of carbon- and energy-rich fluids through microporous semiconducting iron-sulfur catalytic rock, proton gradients form across thin walls. Proton gradient drives formation of methyl thioacetate and acetyl phosphate; carbon and energy metabolism; ‘dehydrate’ to form polymers including nucleic acids and proteins. (pp. 135, 148) Organics accumulate. Vents persist at least 100,000 years, 10^17 microseconds (pp. 110–120). Organics interact; fatty acids precipitate into vesicles; amino acids and nucleotides could polymerize into proteins and RNA.
Lane and his team have built a reactor to mimic these conditions, and are testing their ideas. “We’ve produced ribose and deoxyribose, acetyl phosphate, and other organics” (p. 119, 134).
Geochemistry gives rise seamlessly to biochemistry. (p. 27)
Cells form:
Lipid bilayers form spontaneously from fatty acids. (p. 135)
Genetic code forms; heredity; self-replication. (p. 135–136) Catalytic dinucleotides could generate amino acids from simpler percursors.
Today’s oceans are no longer conducive to starting new life in that way: there’s too much oxygen and too little carbon dioxide now. (p. 112)
Life arose on Earth perhaps 4 billion years ago—half a billion years after Earth was formed—including archaea and bacteria, which had Earth to themselves for 2 billion years. Eukaryotes arose maybe 1.7 billion years ago—cells with a membrane-bound nucleus, mitochondria, straight chromosomes, dynamic cytoskeleton, and other complex structures, and sexual reproduction: plants, animals, algae, fungi, protists. (pp. 26, 160)
Complex life (eukaryotes) likely started from a bacterium entering an archaeal cell as an endosymbiont. The endosymbionts became mitochondria, losing all but 13 of their protein-coding genes to the host cell’s nucleus, and specializing in energy production.
Nick Lane is a good writer and a voracious reader, collaborator, researcher and author in his field.
Whereas a university student can spend a scholastic career learning only orthodox dogma, what was learned in bygone generations—in this book Lane introduces us to big questions to which the answers aren’t known. But the answers to some of them might be knowable. He lets us in on how he and his colleagues are trying to find out. Well done.
Thomas Ray
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