Every aspect of life is a biochemical phenomena - even solving differential equations boils down to biochemistry in brain. I thnik that's not what you wanted to state
There is the Gestalt viewpoint, that we are more than the sum of our parts.
No contradiction here. "Parts" are biochemistry, "more" can be classified as emergent properties. Ting is, this new quality is often treated as something that can't be explained by interactions of the parts - which is obviosuly not true, as there are no other parts and no other interactions. Complexity of the explanation may be well beyond our understanding or beyond processing power of our computers, but it doesn't mean there is no explanation.
Diffusion is a good example. Diffusion is a macroscopical scale process, described by Fick's laws that doesn't tell a thing about single particles movements, as if the diffusion was something completely new and different, independent of the particles interactions. Yet if you know how, Fick's laws can be derived from random particles movements/bouncing.
Can a thinking person force a different arrangment of chemicals in the brain? Is thinking enough to cause an increase or decrease of neurotransmitters?
Yes - when you think there are measurable chemical changes in the brain. That's how large part of neuropsychological research is done these days.