Evolution (useful notes)

One general law, leading to the advancement of all organic beings, namely, multiply, vary, let the strongest live and the weakest die.
—Charles Darwin, Origin of Species

The word "evolution" in its most basic terms simply means "change over time". In biological terms, it is the inheritance of genetic traits within populations of organisms through successive generations. Evolution is one of the strongest-supported scientific theories, and is in fact the cornerstone of modern biology.

Evolution has two main components. The first is descent with modification. An offspring is like its parent(s) but not exactly like its parent(s). The reason for this is the random changes that occur in the propagation of genes between generations. Parent DNA is copied faithfully, but not exactly to the child. Sometimes part of the code gets pasted in backward, sometimes a chunk moves from page 1003 to page 1209, sometimes a bit is left out or another bit tacked on. There are a number of ways for information to be added, subtracted, or simply changed in a gene sequence.

Whereas an error in a computer program will cause it to crash and stop running, organisms can be more flexible. Sometimes a mutation can be crippling or fatal, other times it is a superficial change, and on some occasions the change is beneficial. The vast majority are completely neutral, either occurring in non-coding DNA or not changing the performance of the gene in which it occurs. You yourself are the heritor of some 120 (average number for humans) changes and aren't particularly crippled or enhanced by them. A specific mutation will typically only occur once and then spread through the population. Some mutations spread by virtue of being beneficial while others spread completely by chance in a process known as genetic drift. It is through genetic drift and mathematical models that scientists can trace evolutionary paths and genetic mutations back through history, in a process similar to the study of how language mutates over time.

The second component of evolution is a selection process--stated succinctly, that which survives to reproduce becomes more widespread. This is often referred to as natural selection, but in principle, we see selection processes every day. Whether you use Firefox or Chrome or Internet Explorer is a complex process of artificial selection, for example, and there are many reasons why different browsers control their respective market shares. Like organisms, companies, charities, even whole political systems spawn, grow, and die. What makes the evolution of organisms "natural" is that it has to do with conditions of adaptability, fertility, and more--what determines an organism's ability to propagate itself are factors derived from nature. And in the most trivial case, an organism that can't reproduce in some way (whether it's true sexual or asexual reproduction or simply the mechanism of a virus forcing a host cell to make copies) dies off and, well, vanishes.

Major factors that drive speciation through selection are geographical or climatological in nature: when populations get separated by mountains or rivers, the split-off groups can diverge; when the local weather patterns turn more rainy or warmer, creatures built for cold, dry weather die off. Additionally, a creature may have a competitive advantage for limited resources. Plants that grow higher than others get a clear, unobstructed path to sunlight. Animals that are faster, bigger, or tougher can more easily kill their prey, or those that are fast and quick can outrun predators that might hunt them, or those that are smaller and weaker require less food and so do not starve. Organisms that are more attractive to the opposite sex can have more offspring. There are too many factors to list, of course; this is just a sample of what all affects an organism's ability to reproduce, to survive selection and the passage of time. In the end, no matter the cause, that which survives to reproduce becomes more prevalent, whatever that may be. It's a misconception to think only the "fittest" survive; this is not true. There's an element of chance (anyone can get hit by a falling rock). Plus, a great number of organisms survive to have children; it's whether they have more surviving children and grandchildren that determines the course of change.

Some dates to keep in mind regarding the history of life on Earth, according to evolutionary biology:

The Earth itself is ~4.5 billion years old
The first simple life (that is, prokaryotic and single cellular) appeared around 3.5 billion years ago. Multicellular life did not appear until around 1 billion years ago.
Animals (everything from jellyfish to scorpions to elephants) have only been around for 550 million years or so (probably).
Our genus, Homo, is only about 2.5 million years old. That includes our earlier bipedal ancestors. "Modern" humans only really popped up around 200,000 years ago, and Cro-Magnons (the first homo sapiens) 50,000 years ago.
While photosynthesis is absolutely ancient, flowering plants didn't appear til around 130 million years ago.

Notably, a number of conservative Christians have had issues reconciling evolutionary biology with The Bible's creation account in Genesis. Some have decided to take Genesis as metaphorical and/or believe that God drove the evolutionary process. Others say that the two views are irreconcilable and side with the Biblical account (while they don't deny the selection process or genetic drift on a small scale, they believe it only goes as far as forming different breeds within a species, not entirely different species). Be careful when broaching the subject, though, as both sides tend to consider their views Serious Business.

A note, while all serious biologists agree that evolution is a real process, like any scientific field of study, there is still some quibbling over certain details, such as the speed at which it occurs (phyletic gradualism, or a slow accumulation of changes over time, vs. punctuated equilibrium, or periods of little or no noticeable change interrupted by periods of great change in a short amount of time, like what might be caused by mass extinction events or population bottlenecks). There also is some debate between the Darwinist school of thought which holds random mutations as the primary source of evolutionary innovation, and a relatively newer theory of Symbiogenesis which instead emphasizes associations with other organisms that provide novel traits as a result of symbiotic relationships during times of environmental stress.

This is compounded by the fact that evolution is a bit trickier to follow in bacteria since they have the ability to pass their genes to other bacteria they encounter through a process called "horizontal gene transfer", and so bacterial populations have the ability to gain new traits from processes other than random mutation. The most famous example of this is probably the acquisition of antibiotic resistance genes across bacterial strains. Because of this ability, some scientists goes as far as to argue that you can't even classify bacteria strictly into separate species since the classical biological definition of a "species" can't be applied to them!

Because of this wackiness with single-celled prokaryotes, most of the larger misconceptions that are addressed on this page have to do with animals and plants, as they are the organisms that most people are more familiar with and understand the best.

Also, keep in mind, despite these certain differences and disagreements, it all still assumes the fundamental tenets of evolution, that all populations of organisms have variations in their genetic information (no matter whether they come from mutations or were picked up from other organisms), and that not all of them will be able to produce offspring to carry on that information in the population.

King Phillip Came Over For Good Soup. Motherfucker loved soup.

Linnaean taxonomy classifies organisms based on their morphological characteristics into a hierarchical system. For example, humans are in Kingdom Animalia, Phylum Chordata, Class Mammalia, Order Primates, Family Hominidae, Genus Homo, Species Sapiens. Unfortunately, not everything fits into this neat arrangement, especially once common descent is taken into account.

The Linnaean Taxonomy has precedents stretching back to antiquity, organizing life by kind and in a kind of ladder. God above man above animals above plants. However the hierarchy breaks down in the face of history, as single-celled organisms are more numerous and diverse than multi-cellular organisms. They had three billion years plus to evolve, so this makes sense, but it flies in the face of the anthropocentric world-view that holds life in a hierarchy with ourselves at the top. Further, the divisions between groups break down when you consider, for example, the monotremes and marsupials, animals with characteristics common to reptiles and mammals, or when you learn that the birds are closely related to and recently descended from reptiles, making them closer cousins to crocodiles than crocodiles are to turtles, even though both of the latter are clearly reptiles!

The solution is a difficult one, particularly as Phillip and his Soup are so pleasing to the memory and to the aesthetic sensibilities of schoolchildren, but biology is switching over to cladistics. A clade is any group of organisms descended from a species. So in plants you could have the clade that includes mosses, ferns, conifers, and flowering plants. Or you could move up, pick a different ancestor species, and define a subclade that excludes mosses (who split earlier from the other plants), but which includes ferns, conifers, and flowers.

In the same fashion, you have the clade of all dinosauria, which includes birds and non-avian dinosaurs. Go back to an earlier ancestor and you have the archosauria, which clade includes the birds, non-avian dinosaurs, and crocodylomorphs (crocodiles). Go back further and your clade includes both archosauria and squamata, the lizards and snakes. Further still, and your clade includes the testudines, the turtles. At that point your clade includes all living reptiles and, under the Linnaean system, would have been considered Kingdom Animalia, Phylum Cordata, Class Reptilia. However, your clade also includes the birds, which under Linnaeus were sorted into the separate Class of Aves.

Cladistics means that our understanding of life is less tidy and hierarchical, but considerably more organic. The tree of life now has three main branches of Archaea, Bacteria, and Eukaryota. Eukaryota has a sub-clade of multi-cellular organisms, some of which developed the protein collagen, which includes a sub-clade of bilateral animals (which excludes the octopus and starfish, but includes insects), with a sub-clade of vertebrates (which includes all the fish), with a sub-clade of tetrapods (we're up to land animals, now), some of which developed amnions to help birth along, some of which developed hair and mammary glands, some of which developed an upright, bipedal posture and started smoking cigarettes because smoking is cool.

The Linnaean system has been retrofitted and adapted to help continue to organize life, but the tree of life is many-branched, as can be seen in this chart of the human taxonomy, which lists fifty-six clades, beginning with biota (all life) and ending with our subspecies, sapiens sapiens. Cladistics allows us to clearly sort ourselves and our ancestors, some of whom were mammals, some of whom were not, and some of whom had many characteristics common to mammals and absent in non-mammals but which clearly were not mammals. Rather than invent subphyla and superphyla and legions and metalegions, it makes more sense to consider this a historical science rather than a categorical science, and do our best to understand what happened when.

Myths

Some myths have become attached to evolution and natural selection over the years:

Myth: Evolution picks winners.

It's actually the other way around: Evolution picks losers. Organisms which are ill-suited to their environments, and the genes that make them ill-suited, are selected against. In a sense, "winning" evolution would be having children who have children who have children ad infinitum. There are no winners, just organisms that haven't lost yet.
Particularly tragic is the myth of Superior Species, particularly in the form of Social Darwinism. No creature is inherently "better" than another. A cheetah is particularly well adapted to running down fast prey, but it will never outfight a bear, which will never be as deft with its paws as a raccoon, who can't swim with the fishes, who don't know how to do math. We are each of us what we are, with nearly the same 3.5 billion years of evolutionary history behind us. And a tree won't have nukes, anger and lower back problems.

Myth: Evolution is leading somewhere, or knows where it's going, and that place is human intelligence.

Evolution is simply a combination of random change and environmental pressure. What happens is that poorly adapted individuals die or reproduce less, not that something will magically appear that is perfectly suited to the environment. Happening as it does over hundreds of generations, modification and selection only guarantees you the minimum necessary to survive to this moment, not the best of all possible worlds. So, while you might be best-adapted today, that doesn't mean you will be tomorrow when something new evolves--or shows up by some other method. Take for example extremely isolated islands; in the absence of small mammals, birds adapted to fit the various niches that rodents would have occupied, but were then lethally out-competed when rodents showed up on European ships.
And no, humans are not specifically the target of evolution. Were you to rewind history a few million years and play it forward again, there is no guarantee that a species would emerge that was a) bipedal, b) as intelligent as we are today and/or c) derived from apes, all of which are significant components of Homo sapiens. Were humanity to disappear today, it's questionable as to whether another species would achieve high intelligence, much less the other two.
- There are two schools of in the field of biology. The first, represented by Richard Dawkins is that if you were to rewind history prior to the emergence of our hominid ancestors, you would see the rise of bipedal, intelligent apes. They wouldn't be precisely human; the details would be different, but the overall organism would be very similar. The other, represented by Stephen J Gould, is that evolution is essentially stochastic (non-deterministic) and our hominid ancestors could easily go in another direction and intelligence might never appear.
- Research has actually been done on this point, and it turns out that both schools make valid points. The research was to follow populations of E. Coli for tens or hundreds of thousands of generations under varying conditions (which, given their life cycles, only takes a few weeks/months) and observe the result. Under tightly controlled conditions, the first school of thought holds; the result is the same overall, with varying details. Where conditions are more variable, the results are more variable and the second school of thought holds. Thus the argument has morphed to "Is the environment on Earth such that intelligence is an inevitable result or is intelligence a product of random exploration of the landscape of possible forms?" Until and unless we get the opportunity to observe alien biological histories, or the independent rise of intelligence multiple times on Earth, we may never know.

Myth: Evolution is nothing but chance.

One of the arguments thrown at evolution is that "none of this could have just happened by chance" (see above re: religion). No evolutionary biologist argues that this is the case. Chance is flipping a million coins and having them all land on heads. Evolution by descent with modification and natural selection is flipping a million coins, keeping the heads, flipping the rest, keeping the heads, flipping the rest... If you think about it, the whole point of evolution is to accumulate "luck" in this way.

Myth: Evolution churns out perfection.

Evolution gives us organisms that are able to survive in their environments not organisms that are the best at surviving in their environments. Remember what was stated above, evolution doesn't pick winners, it selects against "losers", or those that aren't able to produce offspring. As long as you're able to pass on your genetic information, whatever traits and adaptations you have will be kept in the gene pool, even if they aren't the most ideal traits for organisms to have. Some organisms may have certain traits not because they give any sort of appreciable benefit at all, but just because that's the trait that happened to be dominant through genetic drift or other random occurrences.
- Remember, evolution is not guided with any sort of specific end or goal in mind, and it is only focused on the ability of the organism to produce offspring. So negative traits that only show up AFTER the individual has reproduced are not selected against. This is why some degenerative conditions like Huntington's disease are still present in human populations, whereas other genetic disorders are selected against because they eliminate individuals before they reach reproductive maturity.

Myth: Evolution is about the origin of life

Evolution tells us how life changes once it's already here, not how it formed in the first place. The latter is known as abiogenesis and is the realm of biochemists and organic chemists. Not evolutionary biologists.
And not having the answer to this question doesn't invalidate natural selection or common descent anymore than gravity and thermodynamics are invalidated by physics not having the answer to how matter and energy came into existence(also known as the first cause argument and/or complexity of the universe argument). To put it another way, not knowing who your father is doesn't mean you didn't have one.

Myth: If people evolved from monkeys, why are there still monkeys?

There are two incorrect assumptions present in this (naggingly persistent) question. The first incorrect assumption is simple to correct, but the second is more pernicious.

The first incorrect assumption is that modern humans evolved from modern monkeys, or at least from ancestors that would be fully classed as monkeys. This is false. Modern monkeys and modern humans do share a common ancestor, but the most recent common ancestor was far enough in the past that monkeys had not yet emerged. It would be more correct to ask "If people evolved from apes ...".
The second incorrect assumption is that evolution is a ladder of progress, and that an entire species must evolve into a different species leaving no members of the original species behind. Evolution, in fact, is not a ladder so much as a branching tree of contingency. Speciation usually occurs when a small group from a much larger population is reproductively isolated from the rest of that population, most often through geographic isolation. This smaller population continues to breed amongst themselves, and will generally be operating under different selection pressures than the population they came from. Eventually, so many genetic differences will accrue that the members of this new population can no longer interbreed with the other population, and it's at this point that we say a new species has arisen. We started with one species, and ended up with two species.
- This same mechanism happened with our ancient ancestors: We started with one large population pool in Africa that was pretty much chimp-like, then about 4-6 million years ago some of those chimp-like ancestors got separated from the rest of them and began exploiting a slightly different biological niche in a different part of Africa, until they'd diverged far enough from their ancestors that they could no longer interbreed with the rest of the chimp-like creatures. Meanwhile, because those original chimp-like creatures were now isolated from us, they went on to become modern chimps.
- Thus, the question being asked is: "If you're descended from your grandparents, why are they still alive?" And it would be better put, "If you're descended from your grandparents, why do you still have cousins?"

Myth: The theory of natural selection is a tautology.

This is usually phrased thusly: natural selection is all about survival of the fittest, but fitness is determined by what survives, and 'round we go. Thus it has no real informational content; it doesn't describe the world any more than the statement that all chairs are chairs.

In fact, fitness is defined as the average contribution by a particular organism/genotype/phenotype to the gene pool of the succeeding generation. This isn't the nebulous "survival" (recall that no one survives in the long run), but is in fact a mathematical definition that allows the comparison of genes, gene-plexes, organisms, populations, etc.
Further, evolution doesn't occur in a vacuum; we observe it within a functional ecology and can make predictions about which genes will survive and propagate. The classic example would be the moths of England. In the absence of soot-producing coal fires, black moths were selected against as being highly visible against tree bark; once England industrialized and the background was darkened with soot, the rate of success changed. Presented with the two kinds of moths and the information that soot is darkening the countryside, a prediction about the relative fitness is easy and inevitable.
Finally, in studying fitness, we have to recognize that two genotypes may have absolutely no competitive edge over one another. Neither is more fit, and how each fares will be the result of genetic drift, or allelic drift, in which the survival of each will be the result of random chance rather than natural selection. One might disappear, or both might continue. In the absence of an actual definition of fitness (as proposed by the myth), genetic drift and an absence of fitness would be incoherent concepts, which they are not.

Myth: Evolution predicts chimeras.

Behold, the mighty Crocoduck! This myth states that the transitional forms of species are the melding of two existing species. That is to say, something that is half cat, half dog. A mermaid, a hippogriff, a chimera. In fact, a transitional form is a form intermediate between a currently living form and its ancestor. For example, Darwin himself reasoned that birds are descended from a family of ancient reptilians, and predicted that there should therefore be a transitional form sharing characteristics common to both birds and reptiles. Just two years after the publication of Origins, Archaeopteryx was discovered with a snout containing teeth, feathers on half-formed wings, wingbones not fully fused, and other qualities placing it intermediate between the two forms. This remarkable predictive power is why evolution is today the fundamental theory of biology.
A related misconception is about common ancestry. Bears, dogs, and cats (all members of the order carnivora) are related, and bears and dogs are more closely related to each other than either is to cats (bears and dogs are both members of the suborder caniformia, while cats are members of feliformia). Thus you go back a certain amount of time and you find the common ancestor to both the bear and the dog. It is not a beardog. Rather, it shares characteristics common to both (hair, carnivorous diet), some that are unique to either (the ancestor was walked on its toes like dogs [digigrade] whereas the bear family walks flat on its feet [plantigrade, like us]), and some that are found in neither. The ancestor looked more like a badger (it wasn't one) than like either bears or dogs, but had a wider, more bearlike head; a snout longer than a bear's and shorter than a dog's; and it was about the size of a raccoon. You would have to go back even further to find the common ancestor of dogs, cats, and bears, and you'll find that it's not a fusion of the three modern forms. Instead it is a less well-defined, creature, with broader characteristics and without the specific adaptations any of them have today. What it did have was traits suited to its time and place that had the potential to turn into what those creatures became.
The closest living relatives of the bears today are the pinnipeds; the seals, walruses, and sea lions. The hyena isn't a caniform at all! They're descended from a civet-like creature, making them feliforms more closely related to the mongoose! This is an example of convergent evolution and explains why biology is such a difficult and complex science; also, why you shouldn't judge a book by its cover and the power of genetic studies.