You're confusing sophistry with science.
Spontaneous generation comes to us by way of Aristotle. It was finally challenged by the emerging field of science.
Lamarckian inheritance was not borne out by empirical evidence, so was effectively discounted. Modern understanding of genetics does recognize some mechanisms that resemble Lamarckian inheritance.
Miasma is an ancient greek magical revenge curse. Emperical scientists like Ignaz Semmelweiss worked away from that idea. For his trouble, he ended up dismissed from his position and replaced by Carl Braun, who stopped the handwashing program Semmelweiss had started and introduced a ventilation system to extract miasmas. The death rate went back up by an order of magnitude from when Semmelweiss was in charge.
Bloodletting goes back to belief in the four humours, which comes down from Hippocrates. Science is what has partially dispelled these ideas in modern times.
Aether is the fifth of the traditional Greek four elements. Once again, the idea comes down from fairly non-scientific thought. The name has cropped up to describe a number of different concepts in science, generally to describe something that may fill the universe in spaces in between regular matter. Science has mostly ruled out most of those theories. The general idea still lives on a bit in concepts such as the quantum foam.
Java Man... You've really got us there. A scientist dug up fossils of ancient hominids and... um... what's the smoking gun supposed to be there?