Social science is that branch of intellectual enquiry (which seeks to study humans and their endeavors in the same reasoned, orderly, systematic, and dispassioned manner that natural scientists use for the study of natural phenomena.)

但正常来说，从句应该是in the same manner that natural scientists did(in the same manner整体做从句谓语方式状语)

而这句话that 指代manner，manner还可以做从句动词use的宾语吗？

句子没有错因为我看到了:Mutant proteins were prepared by PCR as previously described and purified in the same manner that was used for the wild-type enzyme.这个句子，同样的用法。从句改写成：the manner was used (for the wild-type enzyme)