Science Literature

The assumptions underlying molecular clocks are all dependent on the "Darwinian model of continual and gradual change". What happens if these assumptions are probed, tested and subjected to critical scrutiny? This is the exercise undertaken by Schwartz and Maresca.
The first part of the paper addresses historical aspects of "molecular systematics" to better understand the "theoretical and methodological underpinnings." The authors are concerned to find out "how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central, especially to paleoanthropology." This they do with an incisiveness rarely appearing on the printed page of refereed journals. The MA (molecular assumption) is acknowledged to be dominant but to rest on theoretical rather than empirical foundations. "No doubt because it was completely Darwinian, the MA continued to dominate the increasingly influential field of what was now often called molecular systematics."
The authors go on to look at the topic of DNA hybridization, showing that the data may be telling us something about "primitive retention" rather than "closeness of relatedness". They show that although the authors of MA studies use the language of cladism, they are mistaken: "In light of this procedure of hypothesis testing, it is obvious that any molecular analysis based on the MA is not cladistic."
They show that comparisons based on structural genes can be interpreted in ways that are quite different from the MA advocates. "Phylogenetic relationships among metazoans might, therefore, be better revealed through comparing developmentally regulated genes, because changes in their expression can alter phenotypes."
It has been a major problem for Darwinism that its foundations are regarded as inviolable and a 'given'. "Our review [...] reveals that, no matter how sophisticated their mathematical models, molecular systematists have not questioned the basic assumptions upon which they are based. Thus, while refining computer programs to analyze molecular data phylogenetically continues apace [...] with statements of certitude about results following suit, no algorithm is more viable than the assumptions that inform it." The authors offer the hope that their critical review will open the way for a more integrated approach to systematics.
This is a paper that will disturb the Darwinists, but it will offer encouragement to all who want to see less ideology in evolutionary thinking and who want to follow the evidence wherever it leads.

Do Molecular Clocks Run at All? A Critique of Molecular Systematics
Jeffrey H. Schwartz and Bruno Maresca
Biological Theory, Fall, 2006, Vol. 1, No. 4, Pages 357-371 | doi:10.1162/biot.2006.1.4.357 (Open Access)

Abstract: Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the "molecular assumption."

See also:

Prof Questions Darwinian Dogma, Scienceagogo, 12 February 2007