Do Molecular Clocks Run at All? A Critique of Molecular Systematics

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."

Genetic recombination as DNA repair

“…We predicted the clock rate dependence on generation time (there are empirical observations of this dependence (Avise et al 1992)) and explained how weakly and strongly conserved genes can have constant but different clock paces. Both of these phenomena can not be (as easily) explained by conventional theories (Schwartz and Maresca 2006). We showed that population size has no influence on GI storage in equilibrium conditions.…”

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

“…Concerning molecular systematics, critical attention has been paid recently to the problems of inferring evolutionary distances from patterns of similarity between sequences (Schwartz and Maresca, 2006). According to the basic, and generally accepted assumption by Zuckerkandl and Pauling (1962), the degree of molecular similarity reflects the degree of relatedness.…”

Reply to “Humans as second orangutans: sense or nonsense?”

“…Thus, while Zuckerkandl and Pauling (3) demonstrated decreasing similarity in hemoglobin between human, gorilla, horse, chicken, and fish, they acknowledged inference of phylogenetic propinquity upon assuming that if lineages continually change, more recently divergent taxa should be more similar molecularly than distantly divergent taxa as a function of the amount of change accumulated since time of divergence. They then sought corroboration of their ''molecular assumption'' (MA) (4) from the accepted, morphologically based theory of decreasing relatedness among these taxa. Thereafter, the MA (also (5) ) morphed into fact.…”

“…This is not hypothesis testing. Not widely appreciated is the confinement of DNA sequence analyses primarily to the region coding for metabolically active proteins, enzymes, etc (reflecting adaptation, not organismal change), (4) which constitutes only c. 2-3% of the metazoan genome; (21) since mtDNA is metabolically functional it can be treated similarly. (4) Thus, while assertions such as demonstrating c. 99% similarity between humans and chimpanzees in a 90 kb stretch of coding DNA (22) are generalized to ''humans and chimpanzees are c. 99% similar in their DNA'', (22) this extrapolation derives from a minimal fraction of the genome.…”

“…If molecular change was real and random, it should mostly impact the vast non-coding region, causing failure of developmental processes, organismal death, and/or wanton emergence of novel features. (4) Yet,…”