2006 and 2007 have been years in which a number of key science papers addressed things we know - that ain't so. For example, there have been serious challenges to the long contested "molecular clock" theory. The theory - which has been around since the 1960s - is that molecular data based on assumed rates of Darwinian evolution can be used to reconstruct evolutionary relationships. As an article on the University of Maryland Department of Geology site puts it,

A molecular clock is a gene or protein common in the cells of all living things, from bacteria to plants to animals. According to some researchers, these molecules change, or mutate with clock-like regularity. Over geological time mutations begin to build up within the molecular clocks of different animal groups, or phyla, once they split off from a common ancestor. Scientists calibrate the speed of these genetic clocks by counting up the number of mutations that have accumulated over a known interval of time, in specific groups of modern fish; skeletons of the earliest fish are well preserved in rocks that have already been dated using geological clocks. Thus by knowing the speed of the molecular clock, researchers need only count up the number of genetic mutations in a wide range of animal groups to project back to the time, before there were fossils, when each phyla evolved.

In other words, we could run the clock backward and find out what happened in the history of life. In that case, we should expect to find that the fossil record and the molecular data match. The problem is that they often don't match. In one example,

Foote's team chose to analyse placental mammals (the group of mammals that produce live young nurtured through a placenta in the mothers womb - including humans, bats, whales, elephants and mice). Fossil evidence suggests placental mammals first appeared on Earth some 65 million years ago while the biochemical data suggests a date of 130 million years. The team asked the question: "Is the fossil record so poor that the group could have been undetected for 65 million years?" - "Fossils cast doubt on molecular clock" News in Science (February 26, 1999)

They don't think so. They argue, based on evidence, that the fossil record is fine and the clock is not. In the science literature, many adjustments are offered to make the fossil record and molecular data match. Of course, some adjustment is certainly inevitable, but after a while a question arises. One can live with a clock that is routinely ten minutes slow. But if it is variably slow, slower at some times than others, there may come a point when one asks, why consult a clock anyway? Or, more to the point, should this device properly be called a clock? The clock may not have run at all, according to a 2006 paper by Jeffrey H. Schwartz and Bruno Maresca, "Do Molecular Clocks Run at All? A Critique of Molecular Systematics," in the journal Biological Theory.

The abstract of the Schwartz and Maresca paper reads:

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.”

Addressing the fallout, British physicist David Tyler commented earlier this year,

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." [ ... ] 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.

There's also this December 2006 paper, "Dates from the molecular clock: how wrong can we be?" by Mário J F Pulquério and Richard A Nichols in Trends in Ecology and Evolution, which makes a similar point,

Large discrepancies have been found in dates of evolutionary events obtained using the molecular clock. Twofold differences have been reported between the dates estimated from molecular data and those from the fossil record; furthermore, different molecular methods can give dates that differ 20-fold. New software attempts to incorporate appropriate allowances for this uncertainty into the calculation of the accuracy of date estimates. Here, we propose that these innovations represent welcome progress towards obtaining reliable dates from the molecular clock, but warn that they are currently unproven, given that the causes and pattern of the discrepancies are the subject of ongoing research. This research implies that many previous studies, even some of those using recently developed methods, might have placed too much confidence in their date estimates, and their conclusions might need to be revised.

Actually, challenges to the molecular clock are not new. In 1990, Michael Behe published a paper in Trends in Biochemical Science, "Histone deletion mutants challenge the molecular clock hypothesis"(15: 374-376) on the subject, and uncertainty and adjustments are regularly acknowledged in professional sources.

But information in the school system may portray much more certainty than the science literature allows. For example, here's information on the molecular clock destined for the school system (notice the advertisement for lesson plans). Also, notice how much more certain Berkeley's Evolution 101 sounds than the scientists do.