There is, of course, a basic contradiction here: the basis of science itself is continuous challenge to scientific ideas. A scientific theory is never considered to be finally confirmed; even the most firmly established ideas are open to challenge; Newton's laws of motion were amended on the large scale by Einstein, and on the small by Bohr, Planck, and, well, Einstein. So, in declaring that the much softer sciences of sociology and economics had reached their final point, Fukuyama was, in effect, embracing the conclusions of the scientific process while rejecting their basis.
Well, the contradiction is out; Fukuyama is now arguing against future development of biotechnology, on grounds that they might justify new forms of social order (a quaint notion that used to be called "progress"). Perhaps he's worried that if things keep changing, he'll have to find a new title for his damn book.