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Biologists define evolution as a change in the gene pool of a population over time. One example is insects developing a resistance to pesticides over the period of a few years. Even most Creationists recognize that evolution at this level is a fact. What they don't appreciate is that this rate of evolution is all that is required to produce the diversity of all living things from a common ancestor.
The origin of new species by evolution has also been observed, both in the laboratory and in the wild. See, for example, (Weinberg, J.R., V.R. Starczak, and D. Jorg, 1992, "Evidence for rapid speciation following a founder event in the laboratory." Evolution 46: 1214-1220). The "Observed Instances of Speciation" FAQ in the talk.origins archives gives several additional examples.
Even without these direct observations, it would be wrong to say that evolution hasn't been observed. Evidence isn't limited to seeing something happen before your eyes. Evolution makes predictions about what we would expect to see in the fossil record, comparative anatomy, genetic sequences, geographical distribution of species, etc., and these predictions have been verified many times over. The number of observations supporting evolution is overwhelming.
What hasn't been observed is one animal abruptly changing into a radically different one, such as a frog changing into a cow. This is not a problem for evolution because evolution doesn't propose occurrences even remotely like that. In fact, if we ever observed a frog turn into a cow, it would be very strong evidence against evolution.
"Evolution violates the 2nd law of thermodynamics."
This shows more a misconception about thermodynamics than about evolution. The second law of thermodynamics says, "No process is possible in which the sole result is the transfer of energy from a cooler to a hotter body." [Atkins, 1984, The Second Law, pg. 25] Now you may be scratching your head wondering what this has to do with evolution. The confusion arises when the 2nd law is phrased in another equivalent way, "The entropy of a closed system cannot decrease." Entropy is an indication of unusable energy and often (but not always!) corresponds to intuitive notions of disorder or randomness. Creationists thus misinterpret the 2nd law to say that things invariably progress from order to disorder.
However, they neglect the fact that life is not a closed system. The sun provides more than enough energy to drive things. If a mature tomato plant can have more usable energy than the seed it grew from, why should anyone expect that the next generation of tomatoes can't have more usable energy still? Creationists sometimes try to get around this by claiming that the information carried by living things lets them create order. However, not only is life irrelevant to the 2nd law, but order from disorder is common in nonliving systems, too. Snowflakes, sand dunes, tornadoes, stalactites, graded river beds, and lightning are just a few examples of order coming from disorder in nature; none require an intelligent program to achieve that order. In any nontrivial system with lots of energy flowing through it, you are almost certain to find order arising somewhere in the system. If order from disorder is supposed to violate the 2nd law of thermodynamics, why is it ubiquitous in nature?
The thermodynamics argument against evolution displays a misconception about evolution as well as about thermodynamics, since a clear understanding of how evolution works should reveal major flaws in the argument. Evolution says that organisms reproduce with only small changes between generations (after their own kind, so to speak). For example, animals might have appendages which are longer or shorter, thicker or flatter, lighter or darker than their parents. Occasionally, a change might be on the order of having four or six fingers instead of five. Once the differences appear, the theory of evolution calls for differential reproductive success. For example, maybe the animals with longer appendages survive to have more offspring than short-appendaged ones. All of these processes can be observed today. They obviously don't violate any physical laws.
"There are no transitional fossils."
A transitional fossil is one that looks like it's from an organism intermediate between two lineages, meaning it has some characteristics of lineage A, some characteristics of lineage B, and probably some characteristics part way between the two. Transitional fossils can occur between groups of any taxonomic level, such as between species, between orders, etc. Ideally, the transitional fossil should be found stratigraphically between the first occurrence of the ancestral lineage and the first occurrence of the descendent lineage, but evolution also predicts the occurrence of some fossils with transitional morphology that occur after both lineages. There's nothing in the theory of evolution which says an intermediate form (or any organism, for that matter) can have only one line of descendents, or that the intermediate form itself has to go extinct when a line of descendents evolves.
To say there are no transitional fossils is simply false. Paleontology has progressed a bit since Origin of Species was published, uncovering thousands of transitional fossils, by both the temporally restrictive and the less restrictive definitions. The fossil record is still spotty and always will be; erosion and the rarity of conditions favorable to fossilization make that inevitable. Also, transitions may occur in a small population, in a small area, and/or in a relatively short amount of time; when any of these conditions hold, the chances of finding the transitional fossils goes down. Still, there are still many instances where excellent sequences of transitional fossils exist. Some notable examples are the transitions from reptile to mammal, from land animal to early whale, and from early ape to human. For many more examples, see the transitional fossils FAQ in the talk.origins archive, and see http://www.geo.ucalgary.ca/~macrae/talk_origins.html for sample images for some invertebrate groups.
The misconception about the lack of transitional fossils is perpetuated in part by a common way of thinking about categories. When people think about a category like "dog" or "ant," they often subconsciously believe that there is a well-defined boundary around the category, or that there is some eternal ideal form (for philosophers, the Platonic idea) which defines the category. This kind of thinking leads people to declare that Archaeopteryx is "100% bird," when it is clearly a mix of bird and reptile features (with more reptile than bird features, in fact). In truth, categories are man-made and artificial. Nature is not constrained to follow them, and it doesn't.
Some Creationists claim that the hypothesis of punctuated equilibrium was proposed (by Eldredge and Gould) to explain gaps in the fossil record. If you read all this, well you'll find you must be extremely bored, and I have just copied/pasted and randomly highlighted crap. I just wanted to join in with the long posts that no one reads. Actually, it was proposed to explain the relative rarity of transitional forms, not their total absence, and to explain why speciation appears to happen relatively quickly in some cases, gradually in others, and not at all during some periods for some species. In no way does it deny that transitional sequences exist. In fact, both Gould and Eldredge are outspoken opponents of Creationism.
"But paleontologists have discovered several superb examples of intermediary forms and sequences, more than enough to convince any fair-minded skeptic about the reality of life's physical genealogy." - Stephen Jay Gould, Natural History, May 1994
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