His first claim is demonstrably false. If you look at historical, statistical evidence you can rapidly demolish his position. Start with Stephen Pinker's Ted talk: http://www.ted.com/talks/steven_pinker_on_the_myth_of_violen...
His second claim is probably true, but irrelevant. Humans do seem to naturally love hierarchies. And in the grand sweep of time and place, freedom is still a tiny blip.
But So. Fucking. What. Humans are naturally inclines to die of infectious diseases, too.
The author admits that science does progress. And more importantly, the capital structure of society progresses along with it, symbiotically. That puts the lie to the rest of his argument, because ideas from science have demonstrably altered human behavior, and science is already on the cusp of altering human nature directly at the molecular level.