The Cambrian Explosion, in which multitudes of new species began to appear in the fossil record is considered to have happened so amazingly fast (only a few million years) that many consider it a refutation of evolution all it’s own. Meanwhile, the fact that we haven’t directly observed a single speciation event* in the 150 years since Darwin is also refutation of evolution. In other words a few million years isn’t enough time for evolution to work, but 150 years is so much time that if evolution worked we’d have seen it directly by now.

* I’m going to steal another guys references here. Over at Corny’s blog (a favorite of mine…he’s hilarious) someone posted a bunch of references to directly observed speciation events. Please note that, being the lazy bastard that I am I didn’t actually go to verify any of these, so feel free to mock me mercilessly for being an evolutionist tool if these turn out to be bogus.

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella.
BMC Genomics. 2009 Dec 27;10:633.

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes.
http://www.ncbi.nlm.nih.gov/pubmed/20331780
Mol Ecol. 2010 Mar;19 Suppl 1:197-211.

Adaptive radiations: from field to genomic studies.
http://www.ncbi.nlm.nih.gov/pubmed/19528644
Proc Natl Acad Sci U S A. 2009 Jun 16;106 Suppl 1:9947-54. Epub 2009

Evolution in the Drosophila ananassae species subgroup.
http://www.ncbi.nlm.nih.gov/pubmed/19377294
Fly (Austin). 2009 Apr-Jun;3(2):157-69. Epub 2009 Apr 12.

Ahearn, J. N. 1980. Evolution of behavioral reproductive isolation in a laboratory stock of Drosophila silvestris. Experientia. 36:63-64.

Boraas, M. E. 1983. Predator induced evolution in chemostat culture. EOS. Transactions of the American Geophysical Union. 64:1102.

Crossley, S. A. 1974. Changes in mating behavior produced by selection for ethological isolation between ebony and vestigial mutants of Drosophilia melanogaster. Evolution. 28:631-647.

Dobzhansky, T. and O. Pavlovsky. 1971. Experimentally created incipient species of Drosophila. Nature. 230:289-292.