This is a list presenting points of disagreement between the authors of the books on my booklist for the upcoming honors course Wonderful Life. This list is certainly not an exhaustive one. F. Deis

1. Hot, Cold, Surface, Deep? Darwin imagined a "warm little pond" as the place for prebiotic soup. Stanley Miller surrounded a similar pond with a reducing atmosphere and lightning striking and came up with a variety of spontaneously formed amino acids. There are people who imagine the earliest cells as psychrophiles (cold lovers) but most people these days think of them as thermophiles instead. And the "deep" environment, near volcanic vents at the ocean floor or even underground, has a rich chemistry and good conditions for concentrating the molecules of life into a prebiotic "stew." This is important now that scientists have concluded that there probably was not a strongly reducing atmosphere at the time life started.

2. RNA World or Protein first? The problem here is that what we see looking back from modern Biochemistry doesn't match what we can easily imagine about the earliest life forms. Today, all protein is built by ribosomes made of RNA. Many fundamental processes are conducted by Ribozymes, and cofactors tend to have attached RNA nucleotides. This implies that RNA had a more important role in earlier cells. But "prebiotic soup" experiments have never produced nucleotides, the building block of RNA. So some people see the RNA world as a midway point between modern life and something earlier, perhaps a thioester-driven early protein world.

3. Introns Early or Introns Late? Proponents of the RNA World like the "Introns Early" hypothesis, because it would help to explain how RNA genes could keep from getting involved as ribozymes in the cell. Intentional interruptions make a lot of sense, and when the "gene product" is also RNA, it can become activated by intron removal. This corresponds well to what is observed in modern eucaryotes, except that the genes are of course DNA. Walter Gilbert is a major exponent of "Introns Early." The problem is that there appears to be reasonably good evidence for "Introns Late" in which most or all introns came from "jumping genes" or transposons.

4. Contingency. Stephen Jay Gould suggests that if you "reran the tape" of the evolution of life on Earth, you would get a completely unrecognizable assortment of creatures, different phyla etc. He also thinks that it's highly unlikely that the planet would develop intelligent life. Many other authors, notably Christian deDuve, say things like "No two streams follow exactly the same course down a mountain, but all may end up in the same valley." This faction argues that the development of intelligence was foreshadowed by the first neuron, and that while the details of evolution might have differed, the products of evolution would be recognizable.

5. Fast Oxygen, slow Oxygen. We know that roughly 2 billion years ago, oxygen entered the Earth's atmosphere. And we also know that most modern phyla do not appear in the fossil record until the Cambrian, starting about 550 million years ago. A possible explanation would be a slow increase in atmospheric oxygen which would only gradually allow vigorously moving animals to develop. The evidence for oxygen levels is hard to read, and comes in the form of paleoweathering, isotopic abundance, etc. Lynn Margulis maintains that the oxygen levels quickly came up to roughly modern levels 2 billion years ago, and stayed there. Others, including Andrew H. Knoll postulate that the oxygen came up slowly and didn't reach modern levels until the Cambrian or later.

6. Gradualism vs. Punctuated Equilibrium. Stephen Jay Gould has been one of the main exponents of punctuated equilibrium. In fact the fossil record appears to more or less stabilize for millions of years, and then abruptly shift. The naming of geologic eras is based on this. Darwin described a very slow process, a gradual process of evolution. It troubled him that fossils did not seem to support the idea. In more recent years it seems that nearly every geologic era ended with some sort of catastrophe, a meteor, great volcanic activity, or a huge ice age. These catastrophes support the idea of punctuated equilibrium.

7. Unit of Selection. Darwin portrayed the individual as the unit of evolutionary selection. More recent thinkers have been creative in attempting to extend this idea. Richard Dawkins has argued that the gene itself is selected for or against. Gould has suggested that groups could be "units" within natural selection.

8. What are Archaea? This hardly seems to be controversial by now, but one of the principal exponents of her own version of taxonomy, Lynn Margulis, considers Archaea as "just another procaryote" and sprinkles them through the first kingdom as equals of the Eubacteria. This overlooks enormous differences between Archaea and Bacteria. Archaea use terpenes in their cell membranes, have ribosomal RNA sequences that resemble eucaryotes more than "true" procaryotes, live in the most extreme environments, and generally have no cell walls. They have multiple chromosomes like eucaryotes, they splice out introns like eucaryotes. Methanogens have biochemical pathways unlike any true procaryote, with special cofactors (Coenzyme M) etc. Carl Woese pointed out that they are different enough to have their own "Kingdom" and only a handful of recalcitrant old schoolers resist this idea, including Margulis. This appears to be due to a wish that all microbes should be classified through a light microscope. Things are not that simple.

9. What are Nanobacteria? This is extremely controversial, and at the moment only a small handful of scientists defend the concept that there might be such a thing as nanobacteria. These have received attention since it was claimed that "nanofossils" were found in a Martian meteorite. The proponents of nanobacteria say that they are quite easy to find, but that microbiologists tend to find only what they are looking for. Nanobacteria are roughly 200 nm in diameter (some known microbes such as Mycoplasma are known to be that small). This issue is far from being resolved, with most scientists claiming that the tiny "bugs" are merely artifacts of some sort. It may be significant though that objects of that size are just less than the resolving power of a light microscope. Recently claims have been made that shell-forming nanobacteria are responsible for the formation of kidney stones in humans.

10. The Gaia Hypothesis. James Lovelock spent years studying the chemistry of the Earth's atmosphere. He decided that the non-equilibrium composition of the gases is maintained by the blanket of life on the Earth, and that the Earth and its life make up a self- maintaining system. Lynn Margulis likes the idea of the Earth as an organism, with the various species as contributing symbiotes. Both of the proponents make some good points, but other scientists generally dismiss the claim that the Earth is an organism, with comments such as "Planets don't have kids" so evolution is impossible.

11. Creationism. When it comes to the origin of life, science and religion form non- overlapping domains. There are many religious scientists who view the Bible or other sacred texts as a poetic view of the real events from the perspective of pre-scientific mankind. But arguments that deny evolution and seek to replace it with one religious perspective or another (remember that there are other religions besides the Judeo-Christian tradition. Hindus like the idea of life on Mars, whereas Christians can find life elsewhere problematical) are generally specious and hardly worth addressing. One of the better books on the subject, "Why People Believe Weird Things" by Michael Shermer compares the debating style of prominent "Creationists" to that of people who deny the Holocaust.

Controversies - Evolution and Origin of Life F. Deis