Humans are controlled by their brains, and by their endocrine systems.
Brains are autonomous massively parallel processors. They control themselves - and it can be easily demonstrated that external influences on the brain are limited to easily detected sensory inputs; there cannot be any unknown external influence, as there is no force that could propagate such an influence without destroying the brain.
Souls are not possible, other than as a metaphorical description of self-reference and feedback within the brain.
The 'brain' is made of molecules just like the rock.
Yet the brain can freely 'decide' to pick up the rock, lifting it in the opposite direction of gravity.
When was the last time gravity 'decided' to move a rock?
Your error here is to assume that if two things are both made of molecules, that must imply that they share other characteristics. However that assumption is very obviously false.
Table Sugar and Potassium Cyanide are both made of molecules. But you would not be wise to put the latter into your coffee.
Atoms and molecules interact in accordance with the principles discovered by Chemistry; and these principles can be shown to derive from the Physical law described by Quantum Electrodynamics; specifically, all chemistry derives from electron/photon interactions at the periphery of atoms, as atoms cannot approach each other arbitrarily closely, due to the inability of electrons to occupy the same space.
Most chemical reactions have a significant energy balance - when you combine hydrogen and oxygen to make water, a lot of excess energy is released, and to split water back into hydrogen and oxygen therefore requires a lot of energy - so it rarely happens spontaneously.
A few reactions have much closer starting and finishing energies, and these tend to settle into equilibrium states with the proportions of the various molecules determined by the energy available. However this can be a very slow process, because there is still an 'activation energy' required to get things started - which is why hydrogen and oxygen can be mixed together without reacting, until a spark provides the initial 'push'.
The activation energies of many reactions can be significantly reduced by the presence of catalysts - molecules whose shape encourages other molecules to react.
As it turns out, because the properties of carbon allow it to link with up to four other carbon atoms, that element can form structures of a huge variety of shapes and sizes, and can act as a framework on which other structures and groups of atoms can be supported. This allows cyclic chemical reactions to take place, that can move energy from one area to another, and can store energy in chemical bonds. A system that is able to perform such cyclic energy transfers, and which by so doing is able to build more copies of itself, is quite possible; however such systems are able to generate increasing complexity, through the simple survival of those structures that are most effective at using the ambient energy and available chemicals. We call these highly complex systems of interacting chemicals 'life'.
The idea that a complex system of interacting dynamic equilibria between trillions of large and complex self-catalysing carbon-based molecules, and a simple lump of slightly impure silicate, should be similar in their behaviour because they are both 'just molecules' reveals, once again, a mind-boggling level of ignorance on your part.
You are not only unqualified to engage in debate on this topic; you are unqualified to determine your level of qualifications in this field of knowledge.
You need to stop talking, and start learning. Come back and talk when you know enough not to make a complete clown of yourself. This stuff isn't that hard to learn; but you can't just assume that you can understand it without learning it, anymore than you can just pick up a violin for the first time, and play like a maestro.
Learn some physics, and some chemistry first - then you can talk about molecules without coming across as a complete mong.