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A lot of people think we don't have any idea how life on Earth originated. It seems really likely through experimental evidence that a series of chemical reactions led to formation of life as we know it. Whether this happened on Earth or somewhere in space is still unclear. Even if life did originate somewhere else, it does not mean our alien aunts and uncles are going to show up sometime. They probably wouldn't even recognize us now; we're so grown up.
One misconception about the Miller-Urey experiment is that this experiment showed how all of the necessary compounds for life were formed. Another misconception is that they were wearing pants while doing these experiments. We can neither confirm nor deny this. In actuality, the Miller-Urey experiment did not produce all the essential amino or nucleic acids. Furthermore, several organic molecules not commonly incorporated in biology were also formed. The formation of life on Earth is more complicated than the Miller-Urey experiment would suggest, but it does provide some evidence for a model of the origins.
A lot of old textbooks still cling to the old Linnean taxonomy, where there were only five kingdoms (with prokaryotes listed as the kingdom "monera"). Some old textbooks call for blood-letting… so keep that in mind. There are three domains, and there are heated debates amongst taxonomists over how many kingdoms there are, and what organisms belong in what kingdom. It's like debating which is a better system of copying documents: woodcut or mimeograph. Don't sweat the details, let the lab coats sort it out for themselves.
Many scientists debate what the definition of a multicellular organism is, and life loves to be a pain, so there are many grey areas of multicellular life (such as the previously mentioned multicellular amoebas and volvox). Some biofilms, though not truly multicellular, have aspects of multicellularity. One could argue that if there is a spectrum from unicellular organisms to multicellular organisms, there are quasi-multicellular organisms all along the spectrum at different stages. Moral of the story, don't talk to biologists.
Macroevolution is a commonly misunderstood phenomenon, so there are many common misconceptions (See "Policy"). First, people mistake Lamarckian evolution with Darwinian evolution. The major difference is that Lamarckian evolution predicts that individual experience will affect the ability of offspring to succeed, and Darwinian evolution does not.
Darwinian evolution predicts that minor genetic changes affect fitness, and over the course of many generations, certain traits will be favored in the population. This might be why blondes have the most fun.
Another difference between Lamarckian and Darwinian evolution is the difference between heritable and non-heritable traits. The difference between nature and nurture is blurred with Lamarckian evolution, where non-heritable traits such as ability to cook are passed on to offspring. On the other hand, evolution is purely driven by nature in Darwinian evolution.
Lastly, the difference between saltation, gradualism, phyletic gradualism, and punctuated equilibrium is often times confused, though we can't imagine why, given their simple, easily differentiable, names. Right. Many evolution opponents say saltation is proof that Darwinian evolution is incorrect. They argue that complex evolutionary features have no primitive intermediates (despite evidence contradicting this).
Advances in the fossil record refute the "leaps and bounds" theory associated with saltation. Punctuated equilibrium, on the other hand, states that species do not exhibit much phenotypic change over time, and the only perceptible changes are due to rare speciation events. Punctuated equilibrium is the favored theory of evolutionary biologists, and while evolution is a gradual process, major changes occur faster than you would expect with phyletic gradualism.
Many people like to consider homology as a relative concept; where organisms have DNA or protein sequences that are some percentage "homologous." This is not true. Organisms are either homologous or not. When you're arguing percent similarity in DNA or protein sequence, you would say that two organisms are some percentage "similar."
Reading trees can also be a tricky problem. The important thing to remember is that at any node, the branches can be swapped around. Just because two taxa are next to each other as you read a tree from top to bottom (if it's a horizontal tree) or left to right (if it's a vertical tree), doesn't mean they are the closest relatives. To determine which species are most closely related, you have to add the branch distance from one species to the other and figure out how long that is.
There is strong evidence that most mutations in evolution are not selective, and are in fact "neutral," where there is no change in fitness from a mutation. This is a hot controversy among evolutionary biologists, and it seems like the neutralists have defeated the selectionists. Yay neutralists. When we talk about advantageous or disadvantageous mutations, it is really just a small portion of the total amount of mutations that are mostly neutral.