Complex sentence: In the case of the panda's thumb, the argument isn't that it works, the argument is that the "design" is poor--as a real digit would be functionally more effective than modified wrist bones.
Split into simpler sentences: In the case of the panda's thumb, the argument is not that it works. The argument is that the "design" is poor, as a real digit would be functionally more effective than modified wrist bones.