Monday, November 9, 2015

In the right order and right place

I finished reading the book Why Evolution is True by Jerry Coyne. The book lays out the overall reasons why evolution, not Creationism or Intelligent Design, is the way of the world. It is good to see it all in one place. I found the book readable – written for the general public, not the scientist – and quite fascinating.

The big reason for the book is that the general public will take what a scientist says in stride – except when the subject is evolution. That is particularly true in America. The opposition is, of course, driven by the Fundies, but there is still high skepticism in the general public not associated with the Fundie churches. Coyne devotes a whole chapter to that.

We start with six basic concepts. Evolution means that a species undergoes genetic change over time. Over time a species may become quite different because of changes in the DNA. These changes originate as mutations.

Evolution operates through gradualism. It takes many generations, sometimes hundreds of thousands to millions of years. When an environment is stressed, a change may occur quickly, but in an environment for which the species is well suited evolution slows down.

There is speciation. Environmental isolation usually causes two groups in a species to evolve in different directions, eventually becoming two species.

The flip side of that is common ancestor. Pick any two species and there is a species somewhere in the past that is a common ancestor species to both. This lineage can be traced through DNA sequencing or the fossil record. When we say that humans and chimpanzees are closely related it does not mean humans evolved from chimps. It does mean there is a species of primate from which both humans and chimps evolved. That ancestor species may have characteristics that are identifiably human and others identifiably chimp.

In 1735 botanist Carl Linnaeus began classifying animals into groups. Evolution eventually confirmed those classifications – each group was shown to have common ancestors. That means a natural classification system is proof of evolution.

Evolution works through natural selection. A gene mutation may make an organism better able to reproduce, may make no difference in reproduction, or may make an organism less able to reproduce. If the first one, the gene soon spreads through the descendants and the species has changed. For example, consider mice who live in an area that has dark dirt near pale sand. Hawks are better able to pick off dark mice on the sand and light mice on the dirt. Soon there are two groups of mice, light colored on the sand and dark colored on the dirt.

An example of a mutation that doesn't (or didn't) make a difference is the gene that manufactures vitamin C. In humans this gene doesn't work. That mutation also occurs in several other primates and can be traced back to an ancestor that first carried the mutant form of this gene. That mutation didn't matter because there was enough vitamin C in the diet. But now that humans have spread away from the tropical climate vitamin C isn't as readily available in our diet.

The last concept is processes other than natural selection can cause evolutionary change. An example of this is genetic drift.

Evolution is a science. It is testable and can make verifiable predictions. It can be shown to fit the facts better than alternative theories. Creationism and Intelligent Design cannot be tested and are not science.

Coyne spends much of the rest of the book discussing the predictions made by evolution and showing how they were verified.

Making fossils is hard. An organism must die in calm waters and be quickly covered over by sediment so it doesn't decay or get eaten. That doesn't happen too often. So fossils are relatively rare. There are lots of species in our evolutionary history that did not leave a fossil record. Yet, there are enough to show evolution.

Fossils are encased in rock. In 1945 geologists showed it was possible to determine the age of rocks and thus the age of the fossils in them. They also showed that sedimentary rocks are in layers with younger rocks over older ones.

The fossils we have clearly show species change over time and there are "missing link" fossils that show transitional forms between water and land animals, between reptiles and dinosaurs, and between dinosaurs and birds. Coyne explores several evolutionary paths.

The fossil record is clear. It shows gradual changes within lineages, splitting of lineages, and transitional forms. It also shows these changes are in the right order and the right place. Early bird fossils appear after dinosaur fossils and before modern bird fossils. The steps from land mammal to a whale in the sea can be traced and those steps appear in the fossil record in order. Fossils for early Australian marsupials are in Australia, not Europe. Fossils for early man are in Africa as are the fossils for other early primates. There have never been fossils out of order or in the wrong place.

Because evolution works from small mutations features of an ancestral species are remodeled into new features of the descendant species. The stout limbs of fish become legs of land animals. The middle ear bones of mammals are remodeled from the jawbones of reptiles. Bird wings are remodeled from forelegs of dinosaurs.

We can see some of that refashioning as we watch embryos develop. Very young human embryos look a lot like fish embryos (which is not the same as looking like fish). In many species various features begin to develop, then are reversed, such as hind legs in a dolphin embryo. Coyne traces the gill arches of a fish into the middle ear bones, thyroid bone and larynx, carotid artery, and neck muscles of a human.

If there was an intelligent designer why are there vestiges? A kiwi bird can't fly, so why would a designer bother giving it nubby, yet useless, wings? Why do whales have hip bones that aren't connected to any other bones? Many cave dwelling animals can't see – no need in the perpetual darkness – so why were they created with eyes that don't work?

If there was an intelligent designer why are there bad designs? In a human why does the nerve that connects the brain to the larynx travel down into the chest and loop around an aorta just off the heart? Why is a flatfish born with eyes on both sides of its head then one eye migrates over the skull until both eyes are side-by-side?

A reason why evolution leads to what we see as bad designs is that in natural selection each mutation must be an improvement (or make no difference) to what is already in the organism. A mutation cannot undo or be a redesign. The mutation cannot be a step back so that a better version can emerge later. This mutation must move the species forward. A mutation cannot be a benefit for another species. It must benefit the species which contains the mutation. Scientists haven't studied all situations in which one species apparently does something for the sole benefit of another species.

Evolution explains biogeography. Certain species occur in some places and not in others, even if the habitat is the same. Plants and animals in the desert of Arizona are different from those in the Sahara and both are different from the Australian Outback. That's because they evolved separately. Many fossils and species are similar in South America and in Africa because in (evolutionarily) recent times the two were part of one continent.

Islands that used to be parts of continents – Britain and Madagascar – have a broad range of species that are similar to the continents from which they separated. But oceanic islands – Hawaii and the Galapagos – do not have the full range of native species. These islands have the native plants, birds, and insects, all of which could travel over oceans (plant seeds usually traveling in bird guts). But oceanic islands do not have native land mammals, reptiles, amphibians, or freshwater fish. These could not cross the ocean. In addition, oceanic islands frequently have a wide variety of a small number of kinds of birds. The Galapagos are famous for their wide variety of finches, which Charles Darwin studied in his travels.

Coyne discusses natural selection as the engine of evolution. But that takes time, usually in time scales longer than a human life. But there are modern and fast examples. Natural selection takes too long? Let's look at artificial selection, otherwise known as animal and plant breeding. A big and well known examples of artificial selection is dog breeding. All 150 breeds – Chihuahua, Saint Bernard, greyhound, dachshund, retriever, and Pomeranian – as well as all the mutts descend from one ancestral species, likely some sort of wolf. All this variety happened in less than ten thousand years. Think of the diversity that could happen in millions of years.

Evolution has played a role in modern medicine. Antibiotics, introduced in the 1940s, were seen as the solution to infectious diseases. But an antibiotic usually doesn't kill off all of an infecting bacteria. The ones that survive are the ones a bit more resistant to the drug. When that happens enough times we end up with superbugs – diseases that can no longer be treated with known antibiotics. This is a major medical concern these days.

Coyne also includes a discussion of sex. Why does a peacock have such a showy tail and the peahen doesn't? The male invests little in bearing offspring, so spreads his genes best by having lots of mates. The female invests a great deal in bearing offspring, so spreads her genes best by being choosy in mates. She usually chooses the mate with the showiest tail (which can also be an indication of the health of the male). But there are limits. If the tail is too big it becomes a hindrance to living (too difficult to escape predators) and the male doesn't live long enough to reproduce.

Coyne discusses what is a species and how do we get new ones? A species is a group of organisms that can interbreed. Almost always a new species will develop when two groups of a species become geographically isolated (such as another island of the chain) and their genetics evolve in separate directions. Coyne cites a species of shrimp in the Pacific Ocean near Panama. It's closest genetic relative is a species of shrimp in the Atlantic Ocean. Before Panama rose out of the ocean there had been only one species.

The changes between species might only be in mating habits. Two organisms from either side of a divide might still produce fertile offspring. But they don't breed because they no longer see each other as potential mates and are thus separate species.

Many people say, well, evolution may be true for animals, but humans are different. Humans were created. So Coyne spends a chapter discussing the evolution of humans from primates. He documents some of the species of hominins (a more accurate term than hominid) that appeared in the last seven million years. Creationists will look at these fossils and draw a line, saying those are primate, these are human. That usually allows that there has been more than one species of human. But there is one problem – different creationist leaders draw that line in different places.

Coyne is well aware that most of the time when scientist discuss race it is usually to justify racism. Coyne notes there is much more variation within races than between races. Yes, there are visible differences between a Finn, a Japanese, a Masai, and a Navajo. These differences can be attributed to adaptation to different environments and to sexual selection and cultural preferences. He speculates that in evolutionary time races are way "too young to have evolved important differences in intellect and behavior."

Now back to the reason why Coyne wrote the book. Why are humans so resistant to believing that evolution is true? He can lay out all the evidence there is and some people still won't believe. Behind the shouting that evolution denies God there are two complaints, evolution denies purpose and it denies morals.

If belief in God supplies purpose and morals (and many believe that morals can only be supplied through belief in God), then denying God also negates the purpose and morals defined by God. But the scientific method isn't set up to define morals.

Don't our behaviors evolve along with our genetics? There is a field of evolutionary psychology and it does explain some features of human behavior. But a great deal of the field is unprovable speculation that is only a parlor game.

Genes are not behavioral destiny. Some of our behaviors likely did evolve with our genetics. But we are not "marionettes dancing to the strings of evolution." The world is full of immorality and injustice. It is also full of kindness and altruism. All these acts are a choice, not of genes.

Evolution may operate without a purpose. But that doesn't mean our lives are without purpose. We supply our own purpose, meaning, and morality.

Is evolution just a theory? Perhaps. But all of a great deal of evidence found so far supports it. And there hasn't been any evidence to refute it.

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