Student or Learner
Descartes declared that the whole of nature was a machine, and that phenomena which seemed to be “alive” were really just automata with no soul or mind. Later Newton showed that the “machine” of the universe operates according to a number of rigid laws, and that all things (including living beings) are just arrangements of inert elementary particles.
--- Does it mean "that all things are made up of inert elementary particles"?
Yes, made of them put together (arranged) in a certain way.
It's a rather bleak view of humanity, isn't it?
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.