Molecular clocks take another hit

Here's an interesting article in Revista di Biologia / Biology Forum. I have always had doubts about the molecular clock hypothesis, which is the idea that we can estimate divergence rates between organisms based on rates of change in their DNA. Admittedly, some the DNA and protein sequences Huang uses in his paper are hotly debated as to their validity, but the paper is intriguing nonetheless.

Huang, S. “Ancient Fossil Specimens of Extinct Species Are Genetically More Distant to an Outgroup than Extant Sister Species Are.” Biology Forum / Rivista di Biologia, v. 101, 2008, p. 93-108.

Abstract. There exists a remarkable correlation between genetic distance as
measured by protein or DNA dissimilarity and time of species divergence as
inferred from fossil records. This observation has provoked the molecular
clock hypothesis. However, data inconsistent with the hypothesis have steadily
accumulated in recent years from studies of extant organisms. Here the published
DNA and protein sequences from ancient fossil specimens were examined
to see if they would support the molecular clock hypothesis. The hypothesis
predicts that ancient specimens cannot be genetically more distant to an
outgroup than extant sister species are. Also, two distinct ancient specimens
cannot be genetically more distant than their extant sister species are. The
findings here do not conform to these predictions. Neanderthals are more
distant to chimpanzees and gorillas than modern humans are. Dinosaurs are
more distant to frogs than extant birds are. Mastodons are more distant to
opossums than other placental mammals are. The genetic distance between
dinosaurs and mastodons is greater than that between extant birds and
mammals. Therefore, while the molecular clock hypothesis is consistent with
some data from extant organisms, it has yet to find support from ancient
fossils. Far more damaging to the hypothesis than data from extant organisms,
which merely question the constancy of mutation rate, the study of
ancient fossil organisms here challenges for the first time the fundamental
premise of modern evolution theory that genetic distances had always increased
with time in the past history of life on Earth.