A discovery is about something that is found out that was already there, but one did not know. This can be determining the existence of a substance in nature. This is not patentable.

An invention is something new; in the practice it requires human intervention of a technical nature. This is patentable, if it fulfuls the other patentability requirements. In other words, if a substance is freely occuring in nature, there is a distinction between whether it is just a discovery or whether it is subsequently isolated and then used for a techncal purpose. The latter is an invention.

For example, identifying a gene sequence occuring in nature is a discovery and not an invention. Isolating a gene or a piece of DNA, and determining its utility, is an invention and can be patented.

In the guidelines of the European Patent Office it is described as follows:

To find a substance freely occuring in nature is also mere discovery and therefore unpatentable. However, if a substance found in nature has first to be isolated from its surroundings and a process for obtaining it is developed, that process is patentable.

Moreover, if that substance can be properly characterised either by its structure, by the process by which it is obtained or by other parameters and it is "new" in the absolute sense of having no previously recognised existence, then the substance per se may be patentable.

An example of such a case is that of a new substance which is discovered as being produced by a micro-organism.
(Artical 52(3) EPC-Discoveries. EPO guidelines for examination (Part C, Ch. IV,2).