RICHARD DAWKINS - NOTES FROM "THE ANCESTOR'S TALE"

•  Evolutionists can be said to "triangulate" an ancestor by comparing two (or more) of its surviving descendants.

• Agriculture also arose, probably independently in China and along the banks of Nile, and completely independently in the new world.
• Archaelogy suggests that something very special began to happen to our species around 40000 years ago.
• Earlier than the Great Leap Forward, man-made artefacts had hardly changed for a million years. Some think that it coincided with the origin of language.
• About 80 percent of individuals in any generation will in theory be ancestors of everybody alive in the distant future.
• Our AB0 polymorphism is present in chimpanzees.
• Neanderthal mitochondria are quite distinct from those of all surviving humans, suggesting that Neanderthals are no closer to Europeans than to any other modern people.
• Deliberately built camp fires magnetise the soil in a way that distinguishes them from bushfires and from burnt-out stree stumps.
• Some say the speech areas of the brain were already enlarged before 2 million years ago. Others concluded that even Neanderthals as recently as 60000 years ago were speechless.
• For many palaeontologists, the large brain is the distinguishing feature of our genus.
• The modern human brain is about six times as big as it should be, for a mammal of equivalent size.
• Louis Pasteur: Fortune favours the prepared mind.
• The evolution of bipedalism to free the hands for carrying.
• The chimpanzee resolves sexual issues with power; the bonobo resolves power issues with sex.
• About half of human DNAconsists of multiple copies of meaningless sequences.
• The G-C pairing is chemically stronger than the A-T one.

• Neighbour-joining is quick to calculate, but do not incorporate the logic of the evolutionary process. They are purely measures of similarity. Parsimony means economy of explanation. The most parsimonius explanation is the one that postulates the least quantity of evolutionary change. Differences that are unique to a single species of animal, are uninformative. The neighbour-joining method uses them, but the method of parsimony ignores them completely. Parsimony relies upon informative changes; ones that are shared by more than one species.
• Bayesian phylogenetics is an alternative approach to maximum likelihood. Instead of believing in the single most likely tree, we should look at all possible trees, but give proportionally more credence to the more likely one. Probabilities are automatically calculated when using the Bayesian method.
• Bootstrap method resamples different parts of the data repeatedly to see how much difference it makes to the final tree.
• Similar methods are "jackknife" and the "decay index". All are measures of how much we should believe each branch point on the tree.
• Different parts of DNA can have different trees.
• Mammals in general probably have the poorest colour vision among vertebrates.
• The genes that make our green and red opsins are very similar to each other, and they are on the X chromosome.
• Polymorphism is the simultaneous existence, in a population, of two or more alternative versions of a gene. For a stable polymorphism in a population there area two main suggestions:

1- Frequency-dependent selection (green monkeys-green fruit / red monkeys-red fruit)

2- Heterozygous advantage (sickle-cell anemia; heterozygote individuals are protected against malaria. Cystic fibrosis whose gene, in the heterozygous condition, seems to confer protection against cholera.

• Men suffer more frequently from red-green colourblindness than women.
• Various studies have found that a typical human gene has an average probability of duplication of about 0,1 to 1 percent per million years.
• The living primates can be divided into the lemurs and their kin, and the rest.
• Gondwana houses about 5% of all the plant and animal land species, more than 80% of them being found nowhere else.
• Recent molecular evidence shows that a couple of species on the African mainland are more closely related to some Madagascan rodents than some Madagascan rodents are to each other. This might seem to indicate multiple immigration from Africa. But the single founder is from India. The ancestors of the African species came from India via Madagascar.
• If you wiped out Madagascar, you would destroy only about a thousandth of the world's total land area, but fully 4% of all species of animals and plants.
• Captive beavers imprisoned in a bare, unfurnished cage, with no water and no wood, seem to be placing virtual wood into a virtual dam wall, pathetically trying to build a ghost wall with ghost sticks, all on the hard, dry, flat floor of their prison.
• Not all Carnivora are carnivores (Panda).
• Hippos are closer cousins to whales than hippos are to anything else including other even-toed ungulates such as pigs.

• God was having a bad day when he created the platypus. Finding some spare parts left over on the workshop floor, he decided  to unite rather than waste them.
• Extinction is the eventual fate of nearly all species. Perhaps 99% of all species that have ever existed have gone extinct. Nevertheless, the rate of extinctions per million years is not fixed and only occasionally rises above 75%, the threshold arbitrarily recognised for a mass extinction.
• Trout are closer cousins to humans than they are to sharks.
• Mammal-like reptiles flourished before the rise of the dinosaurs.
• In 1896 the Ilinois State Agricultural Lab. started breeding for oil content in maize seeds.
• Geoffrey Miller argues that up to 50% of human genes express themselves in the brain.
• Evolution is now universally accepted as a fact by thinking people.
• Some biologists regard a human as a juvenile ape.
• Mudskippers can jump more than half a metre; climbing fish can climb mangrove trees looking for prey.
• Almost all animal embryos go through gastrulation stage, which presumably means it is a very ancient feature indeed. During gastrulation the ball indents to form a cup with two layers.
• Protostome means "mouth first", deuterostome means "mouth second". Protostomes have a much greater number of animal phylia.
• It has been estimated that "the eye" has evolved independently more than 40 times in various parts of the animal kingdom.
• If all humans were wiped out except for one local race, the great majority of the genetic variation in the human species would be preserved.
• If you take blood and compare protein molecules, or if you sequence genes themselves, you will find that there is less difference beween any two humans living anywhere in the world that there is between two African chimpanzees.
• Chimpanzees did not pass through a genetic bottle neck very long ago.

• Sympatric speciation is commoner among insects than "true" geographical speciation. It could even be that most speciation events -for insects- are sympatric.
• Some early fossil insects had three pairs of wings.
• Hox genes have been found in almost every animal; but not found in plants, nor in fungi, nor in the single celled organisms. Plants and fungi have homeobox genes but not Hox genes.
• A Hox gene is a gene whose mission in life is to know whereabouts in the body it is, and so inform other genes in the same cell.
• The homeobox itself is this diagnostic sequence of 180 code letters, and a "homeobox gene" is a gene that contains the homeobox sequence somewhere in its length. The name Hox is used not for all homeobox genes but only for the linear arrays of genes that determine position along the length of an animal's body and which have turned out to be homologous in nearly all animals.
• Pax 6 is responsible for telling cells to make eyes. The same gene makes eyes in animals as different as Drosophilla and mouse, even though the eyes produced are radically different in the two animals. In a similar way to Hox genes, Pax 6 doesn't tell cells how to make an eye. It only tells them that here is the place to make an eye.
• Tinman genes are responsible for telling cells to make a heart.
• The bdelloids are highly successful group of animals; not a single male has ever been found. An entire asexual class, now numbering 360 species.
• There are hints of older animal diversity. Twenty million years before the start of the Cambrian, in the Ediacaran Period of the late Precambrian, there was a worldwide flourishing of a mysterious group of animals called the Ediacaran fauna named after the Ediacara Hills in South Australia.
• J.B.S. Haldane proposed a unit of evolutionary rate, the darwin, which is based upon proportional change per generation.
• Molecular clocks ultimately depend on calibration by fossils.
• Trichoplax has the smallest genome and the simplest bodily organisation of any multicellular animal. It has only four cell types in its body, compared to more than 200 in us. And it appears to have a single Hox gene. Trichoplax is our most distant cousin among the true animals.
• Impressive feat of simbiotic co-operation, basidiomycetes and -independently evolved again- ascomycetes form associations with algae or cyanobacteria to create lichens.
• The largest single living organism Sequoiadendron giganteum is over 30 metres in circumference and over 80 metres tall, with an estimated weight of 1260 tonnes. More than 3000 years old and the bark alone is about a metre thick.

• What had been magnetic north suddenly becomes magnetic south for some thousands of years, then flips again. this has happened 282 times during the last 10 million years. The magnetic north pole in any case seldom coincides exactly with the true, geographic North Pole. During the "flip" there is an interregnum of magnetic confusion, with large and complicated variations in field strength and direction, sometimes involving the temporary appearance of more than one magnetic north and more than one magnetic south.
• Paleomagnetism can be observed in sedimentary rock.
• Nuclear transformation has an occasional tendency to change at an unpredictable instant, though with predictable probability.
• In alpha decay, nucleus loses an alpha particle (2 protons and 2 neutrons stuck together). Mass number therefore drops by four units. U 238 ✒ Thorium 234
• In beta decay, one neutron turns into a proton. So the mass number remains the same.
• When neutron-proton replacement happens, neutron knocks one proton out; so the mass number stays the same. K 40 ✒ Ar 40
• C 14 decays to N 14 with a half-life of 5730 years.
• A few atoms of N 14, the most abundant gas in the atmosphere, are continually being transformed, by bombardment of cosmic rays, into C 14. The rate of creation of C 14 is approximately constant.

• Chloroplasts are distant descendants of once free-living green bacteria.
• Some chloroplasts show evidence of having entered plant cells indirectly; the evidence is that some chloroplast have a double membrane. Presumably the inner one is the wall of the original bacterium, the outer one is the wall of the alga.
• Yet our own cells, unaidedi wouldn't know what to do with oxygen. It is only mitochondria, and their bacterial cousins, that do.
• Mitochondria themselves have lost much of their original genome.
• Both chloroplasts and mitochondria have their affinities with the eubacteria, not the other prokaryotic group, the Archaea. But our nuclear genes are slightly closer to Archaea.
• Chemically, we are more similar to some bacteria than some bacteria are to other bacteria.
• An Amoeba is scarcely distinguishable from a human when viewed through the "eyes" of bacteria.
• Animals, plants and fungi constitute just three small branches of the tree of life.
• A chain letter needs a good supply of idiots, with evolved brains educated at least enough to read.
• The first replicator worked de novo, ab inito, without precedent, and without help other than from the ordinary laws of chemistry.
• Life couldn't originate on any planet with free oxygen in its atmosphere. 
• Whatever its ultimate merits as the original replicator, RNA is certainly a better candidate than DNA.
• There is a set of small transfer RNAs (tRNA), each about 70 building blocks long. Each of the tRNAs attaches itself selectively to one, and only one, of the twenty kinds of natural amino acids. 
• Hypercycle is a dependency like, fish numbers depend on the population of Daphnia (water fleas) on which they feed. In turn, fish numbers affect the population of fish-eating birds. The birds provide guano, which assists blooms of algae on which the Daphnia flourish. 
• Double helix system lends itself to proof-correction. Proofreading based on this principle reuces mutation rates to the order of one in a billion, which is what makes large genomes like ours possible.
• The wild RNA (QB) after 74 generations (of test tubes) has evolved from 3600 beads long to a mere 550.
• The alleged distinction between  macroevolution and microevolution: macroevolution (evolution on the grand scale of millions of years) is simply what you get when microevolution (evolution on the scale of individual lifetimes) is allowed to go on for millions of years.

JAMES C. DAVIS - Notes from "The Human Story"