In The Origin of Species, Charles Darwin agonized over the gaps in the fossil record. “Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps,” Darwin pined, “is the most obvious and serious objection which can be urged against my theory.”

To address and justify the “serious objection,” Darwin reasoned that “only a small portion of the surface of the Earth has been geologically explored.” However, in the wake of 150 years of unprecedented paleontological research since the publication of The Origin of Species in 1859, the gaps are even more glaring.

As Evan Lerner, the Science News Officer at the University of Pennsylvania explains, the “Cataloging the diversity of life on Earth is challenging enough, but when scientists attempt to draw a phylogeny — the branching family tree of a group of species over their evolutionary history — the challenge goes from merely difficult to potentially impossible.”

The significance of the problem cannot be overlooked since the fossil record is the only direct evidence scientists have about the history of life. In lieu of direct evidence, scientists during the twentieth century increasingly turned to investigating indirect evidence for evolution.

Of the types of indirect evidence, “slight, successive” molecular changes between species emerged as a leading candidate to stand-in for the fossil record gaps. Molecular changes from species to species were expected to parallel evolutionary changes in the fossil record.

This past week, a research team at the University of Pennsylvania announced that their molecular results will be published in the Proceedings of the National Academy of Sciences in the paper entitled “Reconciling Molecular Phylogenies with the Fossil Record.”

“We’ve put contemporary molecular approaches on equal footing with classical paleontological approaches,” says University of Pennsylvania researcher, Joshua B. Plotkin, an associate professor of biology in the School of Arts and Sciences and the Department of Computer and Information Science in the School of Engineering and Applied Science. Plotkin conducted the research along with postdoctoral fellows Helene Morlon and Todd Parsons.

Plotkin and his team developed a new technique for re-tracing the history of species using DNA in cetaceans, a group of species that includes whales, dolphins and porpoises. This DNA reconstructive technique once held prominence in the field of theoretical evolution.

When checked against a group of species that do have a good fossil record, Plotkin’s research team will be reporting that new glaring problems have emerged−DNA evidence cannot account for extinctions. Plotkin explains the problem: “This molecular inference is problematic because it’s known to be false. The fossil record clearly shows extinctions and long periods of diversity loss.”

The disconnection between Darwin’s theory of “slight, successive” evolutionary changes and corresponding genetic changes are now well recognized even within the evolution industry. The once prominent gene-centric theory of evolution, known as the Modern Synthesis theory of evolution rapidly started dissolving earlier in the twenty-first century as a consequence of advances in genomics.

In 2008, evolutionary scientists, Massimo Pigliucci of Stony Brook University and Gerd B Műller of the University of Vienna hosted the convening of the sixteen greatest minds in evolution for the purpose of constructing a non-gene-centric theory for evolution in Altenberg, Austria. The meeting has since been called the Altenberg Summit−the Woodstock of Evolution.

According to Pigliucci, “several of these tenets [Modern Synthesis] are being challenged as either inaccurate or incomplete… “All of these molecular processes clearly demolish the alleged central dogma.”

“The Modern Synthesis was a great intellectual accomplishment in an important era for evolutionary biology. Viewed today it is neither modern nor much of a synthesis,” according to Marc Kirschner of Harvard University and John C Gerhart of the University of California, Berkley.

Evidence from DNA will fail to address the fossil record gaps. Genetics is no longer considered a driving force in evolutionary.

No small wonder why Italian geneticist Giuseppe Sermonti recognizes that “there never really has been a scientific theory of evolution”−a fact re-discovered by Plotkin.