Your friend has a very limited understanding of physics. Quantum mechanics and field theory, which are the most precise scientific theories known, are clearly NOT deterministic. Knowing everything about atoms will not tell you what will happen. For starters, it has been shown over and over that there is a limit on what we can know about particles (see Heisenberg's Uncertainty principle). What we can know is a cloud of probabilities (see Schrodinger's Wave equation), but not which one will come to pass. Lastly, there is the case of emergence. When there are many, many members of a system doing their own things locally new behaviors emerge that cannot be traced to the original members of the group (e.g. atoms). None of this is speculative. It is the basis for modern life: computers, cell phones, GPS, you name it. Things like dark matter only make things less deterministic.