excerpt from Matt Ridley in the Wall Street Journal 4/16/11:
Even climate science has encountered cause-effect confusion. When in 1999 Antarctic ice cores revealed carbon-dioxide concentrations and temperature marching in lockstep over 400,000 years, many—including me— found this a convincing argument for attributing past climate change to carbon dioxide. (About 95% of carbon dioxide in the atmosphere is natural, coming from the exhalations of living things. In the past, carbon-dioxide levels rose as the earth warmed at the end of ice ages and fell as it cooled at the end of interglacial periods.)
Then four years later came clear evidence from finer-grained analysis of ice cores that temperature changes preceded carbon-dioxide changes by at least 800 years. Effects cannot precede their causes by eight centuries, so temperatures must drive carbon dioxide, chiefly by warming the sea and causing carbon dioxide dissolved in water to "out-gas" into the air.
Climate scientists fell back on a "feedback" hypothesis, arguing that an initial change, probably caused by variations in the earth's orbit that affect the warmth of the sun, was then amplified by changes in carbon-dioxide levels. But this made the attribution argument circular and left the reversal of the trend after a period of warming (when amplification should be at its strongest) still harder to explain. If carbon dioxide is still driving the temperature upward but it falls instead, then other factors must be stronger than expected.
Some climate scientists see cause-effect confusion at the heart of climate modeling. Roy Spencer of the National Aeronautics and Space Administration argues from satellite data that the conventional view has one thing backward. Changes in cloud cover are often seen as consequences of changes in temperature. But what if the amount of cloud cover changes spontaneously, for reasons still unclear, and then alters the temperature of the world by reflecting or absorbing sunlight? That is to say, the clouds would be more cause than consequence. Not many agree with Mr. Spencer, but it is an intriguing idea.