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While inspecting historical temperature graphs, he noticed a strange discontinuity, or "jump" in many locations, all occurring around the time of January, 2000.
These graphs were created by NASA's Reto Ruedy and James Hansen (who shot to fame when he accused the administration of trying to censor his views on climate change). Hansen refused to provide McKintyre with the algorithm used to generate graph data, so McKintyre reverse-engineered it. The result appeared to be a Y2K bug in the handling of the raw data.