I came across this book when I was watching a MOOC video on evolution. The lecturer interviewed Coyne in the course. I read about Coyne and about the book. Then downloaded the book.
I love the theory / logic philosophy of evolution. I do not like the amino acids, genes, chromosome etc part which is more into biology. I can't understand those.
The evolution book seems to me now almost what the doctor ordered.
I have this suspicion that there is something very important I am missing in understanding evolution.
And different people say some things which contradict each other a little. So it's fun.
And I have to verify one thing. That genetic drift or mutation is essential to natural selection And what gets encoded in genes and what doesn't. I want to see how a dinosaur became a bird in say 100,000 years. What happened inside in the gene or DNA. If possible, why.
In a way evolution is like fashion. You never know which will catch on and become a hit and reproduce successfully over generations. If you analyzed the fossil record of fashion in the last 100 years, you may find some were stagnant for a period of time and some changed rapidly in bursts. And someone is always experimenting causing the drift or the mutation. The rest is natural selection.
So much to understand.
Now here are some very interesting quotes from the book. All quotes are indented and without permission.
Now here are some very interesting quotes from the book. All quotes are indented and without permission.
Pg 291
The formation of a new species usually begins when populations are geographically isolated from each other...
Pg 299
This divergence [between species] may have been the result of natural selection acting to reduce competition for food between the two species..
Natural selection acting to? Seems like Parthiban Kanavu...I thought natural selection by itself doesn't cause gene change.
Pg 311
"Further transitional forms don't have to be on a direct line of a descent from an ancestor to a living descendant - they could be evolutionary cousins that went extinct.
My question
How do you know if a species was your direct ancestor (say great great great.... grandfather) or his cousin whose line may or may not have got extinct?
Pg 367
Shows how evolution might have happened and what changes might have occurred at each stage from dinosaur to birds.
Don't know page number
It is vestigial not because it's functionless, but because it no longer performs the function for which it evolved.
Pg 475
How does natural selection eliminate useless features? Unless useless features consume energy and hence cost in terms of survival or reproductive ability
Pg 490
This meant that chickens had all the right genes for making teeth, but were missing a spark that the mouse tissue was able to provide.
Meaning an external attachment added can get an organism to get an organ or behavior which its ancestor only had and which it doesn't normally have.
Meaning during evolution, either genes themselves change or are deleted or they are soft deleted through a flag. Once the flag or external tissue is added or sparked then the old thing reemerges.. so then the question: when does hard delete happen and when only a soft delete?
Pg 495
And once we have the DNA sequence of a given gene, we can usually tell if it's expressed normally- that is if it makes a functional protein [if it's active] - or whether it's silenced and makes nothing [soft deleted].
This is strange.. That a gene itself carries information as to whether active or inactive. So while changing status, the gene itself modifies to include updated status info?
Pg 497
This implies that those [pseudo] genes were also active in a common ancestor and were killed off in some descendants but not in others..out of about 30,000 genes, we humans carry more than 2000 pseudo genes.
Pseudo genes are the soft deleted genes. So if the flag can be activated humans could start doing what our ancestors could..
Pg 512
Sure there is almost no chance of viruses inserting themselves independently at exactly the same spot in two species, this points strongly to common ancestry [and hence to evolution and natural selection]
Pg 518
First an ancestral gene became duplicated a number of times. Such duplication happens from time to time as an accident during cell division. Gradually, the duplicated copies differed from each other, with each binding to a different odor molecule. A different type of cell evolved for each of the thousand OR [Olfactory Receptors] genes. And at the same time the brain became rewired to combine the signals from the various kinds of cells to create the sensations of different odors.
Order of evolution:
Fish amphibian reptiles birds and animals
Pg 548
The really curious thing is that as our [human embryonic] development proceeds, the changes resemble an evolutionary sequence. Our fishlike circulatory system turns into one similar to that of embryonic amphibians. In amphibians, the embryonic vessels turn directly into adult vessels, but ours continue to change - into a circulatory system resembling that of embryonic reptiles. In reptiles, this system then develops directly into the adult one. But ours changes still further, adding a few more twists and turns that turn it into a true mammalian circulatory system complete with carotid, pulmonary and dorsal arteries.
Pg 561
So, far example, a lizard begins development resembling an embryonic fish, then somewhat later am embryonic amphibian, and finally an embryonic reptile.
Pg 565
It is best for things that evolved later to be programmed to develop later in the embryo
Pg 566
As one group evolves from another, it often adds its development program on top of the old one.
Pg 568
Also, the recapitulation is neither strict nor inevitable: not every feature of an ancestor's embryo appears in all its descendants, nor do all stages of development unfold in a strict evolutionary order. Further, some species like plants have dispensed with nearly all traces of their ancestry during development.
Pg 578
Around six months after conception, we become completely covered with a fine, downy coat of hair called lanugo. Lanugo is usually shed about a month before birth, when it's replaced by the more sparsely distributed hair with which we're born. (Premature infants, however, are sometimes born with lanugo, which soon falls off)... Lanugo can only be explained as a remnant of primate ancestry... And, like humans, fetal whales also have lanugo, a remnant of when their ancestors lived on land.
Pg 580
If you have access to an infant, gently stroke the palms of its hands. The baby will show a reflex response by making a fist around your finger. In fact, the grasp is so tight that an infant can, using both hands, hang for several minutes from a broomstick. (Warning: Don't try this experiment at home). The grasping reflex, which disappears several months after birth, may well be an atavistic behavior. Newborn monkeys and apes have the same reflex, but it persists throughout the juvenile stage, allowing the young to hang on to their mother's fur as they are carried about.
Pg 646
Evolutionary theory predicts, and data support, the notion that as species diverge from their common ancestors, their DNA sequences change in roughly a straight-line fashion with time. We can use this "molecular clock" calibrated with fossil ancestors of living species, to estimate the divergence times of species that have poor fossil records. Using the molecular clock, we can match the evolutionary relationships between species with the known movements of the continents, as well as the movements of glaciers and the formation of genuine land bridges such as the Isthmus of Panama. This tells us whether the origins of species are concurrent with the origin of new continents and habitats. These innovations have transformed biogeography into a grand detective story: using a variety of tools and seemingly unconnected facts, biological can deduce why species live where they do.
Pg 666
Convergent evolution - meaning similar condition creates similar characteristics even in disparate locations. If you survive and reproduce better because you burrow underground, natural selection will shrink your eyes and give you large digging claws, be you placental or marsupial.
Pg 672
As for how the marsupials got to Australia, that's part of another evolutionary tale, and one that leads to a testable Prediction. The earliest marsupial fossils, around 80 million years old, are found not in Australia but in North America. As marsupials evolved, they spread southward, reaching what is now the tip of South America about 40 million years ago. Marsupials made it to Australia roughly 10 million years later, where they began diversifying into the 200 odd species that live there today. But how could they Cross the South Atlantic? The answer is that it didn't yet exist. At the time of the marsupial invasion, South America and Australia were joined as part of the southern continent of Gondwana. This landmass had already begun to break apart, unzipping to form the Atlantic ocean, but the tip of South America was still connected to what is now Antarctica, which in turn was connected to what is now Australia. Since marsupials had to go overland from South America to Australia, they must have passed through Antarctica. So we can predict this: there should be fossil marsupials on Antarctica dating somewhere between 30 and 40 million years ago.... And sure enough scientists found them.
Pg 681
If evolution happened, species living in one area should be descendants of earlier species that lived in the same place.
Pg 752
With few exceptions, the animals and plants on oceanic islands are most similar to species found on the nearest mainland. Oceanic islands have birds and insects and flying mammals but no amphibian, reptile and land mammals - because the latter couldn't Cross hundreds of miles of sea.
Pg 768
Very old continental islands which separated from the mainland eons ago, should show evolutionary patterns that fall between those of young continental islands and oceanic islands. Old Continental islands such as Madagascar and New Zealand, cut off from their continents 160 million and 85 million years ago, respectively will have been isolated before many groups like primates and modem plants had evolved.
Pg 825
When biologists say that selection is acting "on" a trait, they're merely using shorthand to say that the trait is undergoing the process. In the same sense, species don't try to adapt to their environment. There is no will involved, no conscious striving. Adaptation to the environment is inevitable if a species has the right kind of a genetic variation.
My question
What does the last line above mean?
The following is beautiful
Pg 826
Three things are involved in creating an adaptation by natural selection. First the starting population has to be variable... Otherwise a trait [color] cannot evolve. Second, some proportion of that variation has to come from changes in the form of genes, that is, the variation has to have some genetic basis (called heritability). Where does this genetic variation come from? Mutations-accidental changes in the sequence of DNA that usually occur as errors when the molecule is copied during cell division. Genetic variation generated by mutation is widespread: mutant forms of genes, for example explain variation in human eye color, blood type and much of our - and other species' - variation in height, weight, biochemistry and innumerable other traits. Scientists have concluded that mutations occur randomly. What this means is that mutations occur regardless of whether they would be useful to the individual. Mutations are simply errors in DNA replication. Most of them are harmful or neutral, but a few can turn out to be useful. The useful ones are the raw material for evolution.
Wowow
My question:
Is there any trait which is not explained by mutation?
Is there any trait which is not explained by mutation?
Pg 839
It is, then, the unique combination of mutation and [natural] selection- chance and lawfulness - that tells us how organisms become adapted.... Richard Dawkins provided the most concise definition of natural selection"it is the non random survival of random variants"
Pg 847
It is telling however that biologists haven't found a single adaptation whose evolution absolutely requires an intermediate step that reduces the fitness of the individual.Here's another requirement. An adaptation must evolve by increasing the reproductive output of its possessor.A gene that knocks you off after reproductive agree incurs no evolutionary disadvantage...It follows that a gene will actually be favored if it helps you reproduce in your youth and kills you in your old age.
One example [of a gene not doing it's job] is one that helps human females survive after menopause.
Pg 851
Nor do we expect to see adaptations in one species that benefit only members of another species.
Pg 855
And adaptations always increase the fitness of the individual, not necessarily of the group or the species.
Example is given of Lions killing unweaned cubs in order to have their own offspring.
Pg 858
As evolution predicts, we never see adaptations that benefits the species at the expense of the individual - something we might have expected if organisms were designed by a beneficent Creator.
This is very important
Pg 859
Most biologists define evolution as a change in the proportion of alleles (different forms of a gene) in a population... Every individual has 2 copies of each gene. The two copies can be identical or different. Every time sexual reproduction occurs, one member of each pair of genes makes it to the offspring, along with one from the other parent. It's a tossup to see which one of the parent's pair makes it to the next generation. The other allele would be lost. The upshot is that, every generation, the genes of parents take part in a lottery whose prize is representation in the next generation. Because the number of offspring is finite, the frequencies of the genes present in the offspring won't be the same as in the parents. If you make only a few tosses of a coin you'll deviate from a 50-50 result of heads and tails.(in 4 tosses for example you have a 12% chance of getting all heads or all tails). And so in small populations, the proportion of different alleles can change over time entirely by chance. And nee mutations may enter the fray and themselves rise or fall in frequency due to this random sampling. Eventually the resulting "random walk" can even cause genes to become fixed in the population (that is rise to 100% frequency) or, alternatively, get completely lost.
Such random change in the frequency of genes over time is called genetic drift. It is a legitimate type of evolution, since it involves change in the frequencies of alleles over time, but it doesn't arise from natural selection....
Genetic drift can change the frequencies of alleles regardless of how useful they are to their carrier. Selection on the other hand always gets rid of harmful alleles and raises the frequencies of beneficial ones.
My question
How can new mutations arise out of genetic drift?
Pg 871
In fact, genetic drift is not only powerless to create adaptations, but can actually overpower natural selection. Especially, in small populations, the sampling effect can be so late that it raises the frequency of harmful genes even though selection is working in the opposite direction. This is almost certainly why we see a high incidence of genetically based diseases in isolated human communities.
Pg 874
Any mutations in pseudogenes have no effect on the organism, and therefore can evolve only by genetic drift.
My question:
Mutations is the only distinct mechanism of changing a gene. Correct?
Genetic drift and natural selection only change the allele frequency.. Neither creates a new gene that didn't exist before. So, how can a mutation in pseudogene be caused by drift.?Only an allele frequency change can happen that way. Not mutation.
My question:
How do we decide that Evolution of a species has happened or a new species created (speciation)?
Pg 920
It is a widespread belief that drug resistance occurs because somehow the patients themselves change in a way that makes the drug less effective. But this is wrong: resistance comes from evolution of the microbe, not habituation of patients to the drugs.
Pg 928
We can then make a reasonable intended: when a population encounters a stress that doesn't come from humans, such as a change in salinity, temperature or rainfall, natural selection will often produce an adaptive response.
My question
Why is there a non human filter above?
Pg 951
Here's another Prediction: under prolonged drought, natural selection will lead to the evolution of plants that flower earlier than their ancestors. This is because during a drought soils dry out quickly after the rains. Of you're a plant that doesn't flower and produce seeds quickly in a drought, you leave no descendants. Understand normal weather conditions, on the other hand, it pays to delay flowering so that you can grow larger and produce even more seeds.
Pg 1049
Many of the birdsongs that delight our ears are actually threats warning other male birds to keep away.
Pg 1059
When a male mates with an already mated female, he uses backward pointing spines on his penis to scoop out the sperm of the earlier mating male. Only after she has been despermed does he transfer his own sperm. In Drosophyla, my own lab found that a male's ejaculate contains substances that inactivate the stored sperm of males who mated previously.
Pg 1120
Sexual selection theory makes testable predictions. If only one sex has bright plumage or antlers, performs vigorous mating displays or builds elaborate structures to lure females, you can bet that it is members of that sex who complete to mate with members of the other. And species showing less sexual dimorphism in behavior or appearance should be more monogamous.
Pg 1171
You could test this theory by producing a truly novel trait in males and seeing if females like it. This was done in two species of Australian grassflinches by Nancy Burley and Richard Symanski at the University of California. They simply glued a single vertically pointing feather to the heads of males forming an artificial crest, and then exposed these crested males, along with uncrested controls to females. Females turned out to show a very strong preference for males sporting white artificial crests over males with either red or green crests or normal uncrested males. We don't understand why females prefer white, but it may be because they line their nests when white feathers to camouflage their eggs from predators.
My question:
If similar animals in similar places in different continents evolve similarly [this has been quoted in the book], then the mutation is not random. Could be Parthiban Kanavu?
Pg 1185
And although there is variation among individuals within a cluster (as all lion researchers know, each lion looks different from every other lion), the clusters nevertheless remain discrete in"organism space". We see clusters in all organisms that reproduce sexually.
These discrete clusters are known as species. And at first sight, their existence looks like a problem for evolutionary theory. Evolution is, after all, a continuous process, so how can it produce groups of animals and plants that are discrete and discontinuous, separate from others by gaps in appearance and behavior? How these groups arise is the problem of speciation - or the origin of species.
Pg 1205
When you ponder cryptic species, and variation within humans, you arrive at the notion that species are different but merely because they look different, but because there are barriers between them that prevent interbreeding.
Groups that are reproductively isolated form a separate species.
Pg 1236
We don't have different species because nature somehow needs them. Far from it. The study of speciation tells us that species are evolutionary accidents. The "clusters" so important for biodiversity don't evolve because they increase that diversity nor do they evolve to provide balanced ecosystems. They are simply the inevitable result of geographic barriers that arise when spatially isolated populations evolve in different directions.
Pg 1226
Suppose for example that an ancestral species of flowering plant was split into two portions by a geographic barrier, like a mountain range. The species may, for example, have been dispersed over the mountains in the stomachs of birds. Now imagine that one population lives in a place having a lot of hummingbirds but only a few bees. In that area flowers will evolve to attract hummingbirds as pollinators; typically the flowers would become red (a color that the birds find attractive), produce copious nectar (which rewards the birds) and have deep tubes (to accommodate hummingbirds' long bills and tongues). The birds on the other side of the mountain may find out pollinator situation reversed: few hummingbirds but many bees. They're the flowers will evolve to attract bees: they may become pink (a color bees favor) and evolve shallow nectar tubes with less nectar (bees have short tongues and don't require a large nectar reward) as well as flatter flowers whose petals form a landing platform (unlike hovering hummingbirds, bees usually land to collect nectar). Eventually the two populations would diverge in the form of their flowers and amount of their nectar and each would be specialized for pollination by only a single type of animal. Now imagine that the geographic barrier disappeared, and the newly diverged populations found themselves back in the same area- an area containing both hummingbirds and bees. They would now be reproductively isolated: each type of flower would be served by a different pollinator, so their genes would not mix by Cross pollination. They would have become 2 different species.
Pg 1244
Steven Pinker describes other striking similarities and differences between the diversification of languages and species in his engrossing book THE LANGUAGE INSTINCT.
Pg 1244
The idea that geographic isolation is the first step in the origin of species is called the theory of geographic speciation... The evolution of genetic isolation between populations requires that they first be geographically isolated.. Splitting a population into two genetically isolated parts is very difficult if they retain the opportunity to interbreed. Without isolation, selection that could drive populations apart has to work against the interbreeding that constantly brings individuals together and mixes up their genes... Speciation is like separating oil and vinegar: though striving to pull apart, they won't do so if they're constantly being mixed.
Pg 1468
Putting this together we see that the genetic divergence between ourselves and chimpanzees comes in several forms- changes not only in the proteins produced by genes, but also in the presence or absence of genes, the number of gene copies and when and where genes are expressed during development.
Pg 1695
Unlike most primates, human females show no visible signs when ovulating. (The genitals of female baboons, for example, swell up and turn red when they are fertile.) There are more than a dozen theories about why human females evolved to conceal their periods of fertility. The most famous is that this is a female strategy to keep their mates around for sustenance and child care. If a man doesn't know when his wife his fertile and wants to father children, he should hand around and copulate with her frequently.
My question:
Are we sure males want to pass their genes ie to father and not just have sex?
Pg 1482
Direct genetic evidence accumulated over the last the decades, shows that only about 10 to 15% of all genetic variation in humans is represented by differences between"races" that are recognized by differences in physical appearance. The reminder of the genetic variation, 85-90% occurs among individuals within races.
Pg 1495
But the cultural change can also produce genetic change. Imagine that a spreading idea or fad involves the preferred appearance of one's mate. An empress in Asia, for example, might have a penchant for men with straight black hair and almond shaped eyes. By creating a fashion her preference spreads culturally to all her female subjects and, lo and behold, over time the curly haired and round eyed individuals will be largely replaced... Moreover sexual selection can often act incredibly fast.
Additional reading:
- http://vbala99.blogspot.com/2018/02/evolution-and-parthiban-kanavu.html
- http://vbala99.blogspot.com/2018/03/high-venus-and-evolution.html
- https://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_39 - explains different types of evolution - migration, drift etc
- http://evolutionfaq.com/faq/category/myths-and-misconceptions
- https://www.wimp.com/david-attenborough-the-evolution-of-the-eye/ - how the eye evolved.
- https://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_18
