"The assumption is that [penguins] evolved from an auk-like ancestor," Speakman continued. "This would involve a progressive reduction in wing size, which makes diving more efficient and flying less so. read more
Birds evolved from flighless dinosaurs with fossils( in fact birds themselves are actually considered dinosaurs). These evolved flight and then penguins and other birds lost it again. So you go from flightless to flying to flightless again. read more
Postscript (5/26/14): Another study, published this month in Science, compared ancient DNA from elephant birds to DNA from modern ratites and came to the same conclusion: flightless ratites evolved several times, independently, from a flying ancestor. read more