You're being purposely reductive in describing the brain - the most complex object in the known universe - and its processes as "only a set of chemical reactions." But yes. All thought, argument, emotion, sense of being, etc are bound within the brain and the body and the physical universe and its laws. It's all physical. There is no "soul" or any other paranormal aspect to any of it.

So the squashing of a tomato or a human or a civilization -- they're just different rearrangements of matter and energy. Our feelings about each are also just chemical reactions. Any feeling or argument to the contrary has nothing to stand on. There's no such real thing as better or worse ultimately -- only better or worse within a context but not ultimately.

If you're on a hike and you see blueprints for a working automobile, you don't assume it assembled itself by mere chance. There's a language of a working design and you assume some minds created it.

But at the same time you interact with humans who have a working blueprint expressed in a 4-letter language and suddenly deny there is any mind behind any design?

Values are real, the same way real numbers are real