I understand there is debate and angst regarding this subject, so I will not comment, but simply place this lengthy quote on evolutionary biology and a second insertion (abstract) that claims a new theory that diminishes the importance of natural selection. I also would encourage those interested to obtain some articles in which biologists are debating the very notion of species within the context of neo-Darwinian theory.
"In making this claim, Muller and Newman are careful to affirm that evolutionary biology has succeeded in explaining how preexisting forms diversify under the twin influences of natural selection and variation of genetic traits. Sophisticated mathematically-based models of population genetics have proven adequate for mapping and understanding quantitative variability and populational changes in organisms. Yet Muller and Newman insist that population genetics, and thus evolutionary biology, has not identified a specifically causal explanation for the origin of true morphological novelty during the history of life. Central to their concern is what they see as the inadequacy of the variation of genetic traits as a source of new form and structure. They note, following Darwin himself, that the sources of new form and structure must precede the action of natural selection (2003:3)–that selection must act on what already exists. Yet, in their view, the genocentricity and incrementalism of the neo-Darwinian mechanism has meant that an adequate source of new form and structure has yet to be identified by theoretical biologists. Instead, Muller and Newman see the need to identify epigenetic sources of morphological innovation during the evolution of life. In the meantime, however, they insist neo-Darwinism lacks any theory of the generative."PROCEEDINGS OF THE BIOLOGICAL SOCIETY OF WASHINGTON 117(2):213-239. 2004 The origin of biological information and the higher taxonomic categories Stephen C. Meyer.
I add an abstract of a paper that does not directly deal with identifying species (transitional or otherwise) but challenges the primacy of natural selection, to illustrate the topic is not as cut and dried as some comments seem to indicate.
"The new mutation theory of phenotypic evolution Masatoshi Nei*
Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802
Edited by Daniel L. Hartl, Harvard University, Cambridge, MA, and approved June 13, 2007 (received for review April 16, 2007)
Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance."