The Making of the Fittest
Sean Carroll, W.W. Norton, 2006
Preface: Beyond any Reasonable Doubt
p 14 Story and illustration of use of DNA to free after 16years a man wrongly convicted of assault and murder of his wife and unborn child.
p 15 Discussion of explosively growing database of DNA information
1. Introduction: The Bloodless Fish of Bouvet Island
Very well-written story of the investigation of the fish of this remote island in frigid South Atlantic. The story builds from the discovery of these fish in 1928 to the first detailed examination in 1954.
[Page numbers are from the paperback edition.]
p22 The 1954 examination of the fish revealed the absence of hemoglobin in the blood of the fish. Hemoglobin "had been found in every living vertebrate. Indeed, no other case of bloodless vertebrate has ever been discovered outside of the fifteen or so species of icefish now known."
p23 DNA examined, apparently in the 90s. The findings were "the two genes that normally contain the DNA code for the globin part of the hemoglobin molecule have gone extinct. One gene is a molecular fossil, a mere remnant of a globin gene - it still resides in the DNA of the icefish, but it is utterly useless and eroding away, just as a fossil withers upon exposure to the elements. The second globin gene, which usually lies adjacent to the first in the DNA of red-blooded fish, has eroded away completely. This is absolute proof that the icefish have abandoned, forever, the genes for the making of a molecule that nurtured the lives of their ancestors for over 500 million years."
p23 "What would provoke such a dramatic rejection of a way of life that serves every other vertebrate on the planet? Necessity and opportunity, both of which sprang from dramatic, long-term changes in ocean temperature and currents." This discussion of "chance and necessity" shows that Monod is on his mind.
p23 About 200 species of fish around Antarctica, and all have hemoglobin except the 15 or so species of icefish. Illustrates the time scale projected for these happenings in Fig 1.3, p28
p24 Our blood volume is about 45% red blood cells (hematocrit =45), whereas that of the red-blooded fish of the Antarctic is 15-18%, but is 0% for the icefish. They have only white blood cells in their blood, and only about 1% cells so they "literally have ice water in their veins."
How do they do it?
p24 The myoglobin gene is also mutated and non-functional, so no myoglobin in icefish hearts. He notes that diving mammals like dolphins and whales have an abundance of myoglobin in their heart muscles - binds more tightly to oxygen than does hemoglobin, so can concentrate oxygen in hearts and muscles of these animals to help with long dives. There is some myoglobin in some of the icefish.
p25-26 Discusses the microtubule scaffolding of the cells. This cytoskeleton material is faithfully preserved in all eukaryotes. The tubulin from which it is constructed in most cells is unstable below 50 F, so there has to be a change in the microtubules - a genetic change.
p25-26 Discusses the "invention" of antifreeze in the plasma. The antifreeze molecules are 4 to 55 repeats of 3 amino acids. Cheng, et al studied this and concluded that the gene for this was a piece broken off the gene for a digestive enzyme - a 9-letter code makes the antifreeze.
p26 "As a resident of a cold climate, I have to admire the icefishes' grit and ingenuity. We take various measures to keep our cars running on subzero Wisonsin days, but the icefish has managed to change its whole engine while the car was running. It invented a new antifreeze, changed its oil (blood) to a new grade with a remarkably low viscosity, enlarged its fuel pump (heart), and threw out a few parts along the way - parts that had been used in every model of fish for the past 500 million years."
p26 Uses this as an example of the "making of the fittest": "Icefish evolved from warm-water, red-blooded ancestors ill suited to life in the cold. Their adaptation to the changing environment of the Southern Ocean was not a matter of instant design, nor just a one-way "progressive" process. It was an improvised series of many steps, including the invention of some new code, the destruction of some very old code, and the modification of much more."
Time scale of the development of the icefish.
 | This is Carroll's projected timeline for the events surrounding the icefish. Adapted from Fig 1.3, p28. |
p27 All the Antarctic notothenioid fish have the antifreeze gene, and he projects these fish to about 25 million years ago. The icefish are projected to 8 million, and the mixed picture on the myoglobin gene suggests that the loss of myoglobin was more recent and perhaps still ongoing.
p27 The story of the icefish is extremely well done. It makes clear the fact that evolution has taken place that made a major change in species - from a red-blooded fish to one without hemoglobin, so that would have to be considered to be macroevolution.
p27-31 In his "Darwin Redux" section he outlines Darwin's main points with quotes and briefly tells the story behind "Origin ..".
p31 "The esteem we biologists have for Darwin is manifold. Sure, 'On the Origin of Species' is the most important single work in biology." That esteem we know about from biologists. Esteem, yes, but for those of us in other science disciplines, it is held a lot more tentatively and nervously, and there are reasons for that reserve.
p32 "The eminent biologist and writer Richard Dawkins .. 'It is almost as if the human brain were specifically designed to misunderstand Darwinism, and to find it hard to believe.' " Yeah .. I can identify with that.
2. The Everyday Math of Evolution: Chance, Selection and Time
p45 Cites Thomas Huxley as "Darwin's greatest ally", but Huxley favored "saltations" as the explanation for change. Both went to their graves without knowing of Mendel's development of genetics from the pea plant experiments of the 1850's and 1860's. The world took note of Mendel about 1900.
p46 Bateson also opposed Darwin's small changes, favoring saltation. Thomas Huxley quote "science warns me to be careful how I adopt a view which jumps with my preconceptions, and to require stronger evidence for such beliefs than for one to which I was previously hostile."
p46 Another name is William Castle of Harvard who m over toward the small variation line of Darwin because of hooded rat experiments around 1914.
p48. With R C Punnett and the help of mathematician H T J Norton, a kind of compound interest model of the effects of mutations was developed, with "selection coefficient" taking the place of interest rate.
p50. Brings J B S Haldane into the story with R A Fisher and Sewall Wright.
p51 Table of margin of error, but doesn't say what kind of distribution.
p52 Peppered moth melanism. Haldane involved in the study. Graph of p53.
p53 Seven year study of falcon predation on feral pigeons. Davis, CA. 5235 pigeons banded, 1485 falcon attacks logged. White-rumped pigeons had advantage in early studies. Actually swapped the white patches to those which had not to control for the white patch and reversed the survival statistics.
p56 Story of the stickleback fish that adapted from ocean water to fresh water lake and reduced their number of spines in a matter of decades.
p57 Pinning down the basics. "The source of all variety is mutation." "The mutation process is blind, natural selection is not."
p58. Discusses types of mutations in DNA. 175 new mutations in each person out of 7 billion DNA letters.
p60-64 Melanism in mice. Expect 1 mutation in specific gene in 500,000 individuals. Black mice in lava areas, light mice in sandy areas. Mutation in MC1R gene 1 in 25 million.
3.Immortal Genes: Running in Place for Eons
p69 Discussion of the discovery of thermophylic organisms around the hot springs of Yellowstone, some of which could live even in boiling water! This was the discovery of the Archaea, a third domain or division of life to add to prokaryotes and eukaryotes.
p70 "A heat-stable enzyme that could copy DNA at high temperatures was isolated from Thermus aquatics. This enzyme led to the invention of a new, efficient, and very fast technique for the study of genes in any species." Story of the impact of this discovery.
p71 "Still preserved in the DNA of these primitive organisms are many pieces of DNA code that also exist in humans and all other eukaryotes."
p71-72 "The fact that such ancient text has endured over eons of time, against the steady bombardment of mutations that could have erased it many times over, is itself remarkable. But these "immortal" genes are also powerful evidence of two key elements of the evolutionary process - the power of natural selection to preserve the DNA record and the descent of life from common ancestors."
The ideas in this chapter are things I hadn't thought about. I had the picture of an advantageous mutation being preserved by natural selection, and a harmful one being removed by natural selection, but had not thought about the role of natural selection in preserving a well-functioning gene over vast lengths of time, warding off any changes that would damage it. Carroll calls this process "running in place".
p73 General review of proteins, bases, amino acids, genetic code, transcription, translation
p74-75 Non-coding DNA, junk DNA.
p75 Discusses "the immortal core" Table of number of genes on p77.
p79 "when we compare the genomes of Archaea, bacteria, fungi, plants and animals, we find about 500 genes that exist in all domains of life." Because of the short generation time of bacteria and the "bombardment" of mutations, we would expect all similarities to have been long since erased, so this points to the preservative power of natural selection according to Carroll.
p79 Compares genome of poisonous puffer fish to human, characterized as "the gourmand stupid enough to eat this deadly creature (human)" and notes 7350 genes shared between them even though they separated about 450 million years ago. His point is that mutations are not simply allowed to accumulate over time.
p79 "Immortal genes have survived not because they avoid mutation- they are as vulnerable to mutation as all other genes." Goes on to talk about the role of redundancy in the genetic code.
p80 In analysis of mutations, some mutations change the bases, but code for the same amino acid and are called synonymous mutations. But non-synonymous mutations are favored by probability by 441 to 135 of the 576 possibilities, or almost 3:1 in favor of the nonsynonymous. But when actual genes are examined, it is found that the ratio is just the reverse, with 1:3 in favor of the synonymous mutations! In response to "why?" he responds "Natural selection. There is no other explanation. This skew in ration is very clear evidence of a type of selection, called purifying selection, that maintains the 'purity' of the amino acid sequences of proteins by ridding them of changes that would compromise their function."
p81 Table of sequence of protein "elongation factor 1-alpha" for which he shows amino acids that have not changed in 3 billion years. In comparing a tomato to a human on p82 he notes that the bases of the DNA sequence are identical in 65 of 78 positions (83%) but because of redundancy in the genetic code, the amino acids coded for are identical in 25 of 26 positions (96%). So the redundancy of the genetic code protects the integrity of the proteins.
p81 "many of the proteins involved in the making of key pieces of machinery for decoding mRNA are shared among all species."
p84 "The new wealth of data from genomes offers unique insights into the deep past that could not be deciphered from any other source."
p84 Embarks on the proposal that present eukaryotes were derived from a combination of archaea and bacteria. Sketches on p87 and 89 outline the proposal.
p88 Lynn Margulis' proposal that mitochondria and chloroplasts, the energy-producing organelles, arose from bacteria living within eukaryotes. "This view is now widely accepted."
4. Making the New from the Old
p90 Story of the Colobus monkey, which has full color vision to help it select the young red leaves to ruminate in its large multi-chambered stomach. He chooses this animal as an example of "the invention and fine-tuning of species capabilities." Embarks on a discussion of the development of color vision.
p93 "the ultraviolet .. birds, insects, and many other animals use to find food, mates, and each other."
p93 "the genes underlying color vision and its evolution have been studied perhaps more intensely than those affecting any other trait."
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5. Fossil Genes: Broken Pieces of Yesterday's Life
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6. Deja Vu: How and Why Evolution Repeats Itself
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7. Our Flesh and Blood: Arms Races, The Human Race, and Natural Selection
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8. The Making and Evolution of Complexity
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9. Seeing and Believing
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10. The Palm Trees of Wyoming
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