Marketplaces, Banks, and now Stock Exchanges only work their magic on commerce that is directed to your treasury (i.e., not to science or entertainment). If you set science to 100%, banks do nothing for you. Similarly, if science is set to 0%, libraries and universities do nothing (but add culture, that is).
By building marketplaces and banks and keeping your science set at 50%, you do nothing to increase your science beaker accumulation, but should see incresing surpluses going to your treasury (which would, of course, allow you to raise your science slider if you choose to do so).
Catt