This is an interesting point, and this very background may have found its way into the ruling. Specifically, that the judge has a background in chemistry and directly speaks to the difference in perspective between biologists and chemists :

"We recognize that biologists may think of molecules in terms of their uses, but genes are in fact materials having a chemical nature and, as such, are best described in patents by their structures rather than by their functions" [1]

The blogger goes on to state in more plain terms :

"In other words, this ruling affirms that molecular biology is, in fact, chemistry, if you want to look at it that way."

[1]http://pipeline.corante.com/archives/2012/08/17/the_myriad_g...

This makes perfect sense... I could easily see how a chemist could come to one conclusion, whereas a biologist would come to a completely different conclusion. In this case, I think the judge's chemistry training actually worked against him.