Considering that the universe is 13.7 billion years old, consciousness and intelligence are relatively new phenomena in the universe. The seeds of these phenomena were planted when life first arose, some 3.7 billion years ago. Life introduced animate beings into a universe that had previously had only inanimate objects.
Life also introduced motility to the universe. Motility is the ability to move in a self-directed way. Motility is probably the root cause of consciousness because without motility there would be no impetus to think. The reason is that motility enabled early lifeforms to move away from danger: the impetus was to survive – to avoid being eaten. In return, many predatory organisms were forced to pursue their meals or go hungry. This led to evolutionary refinements of sense organs and nervous systems to detect predators or prey and escape or pursue them. These rudimentary nervous systems eventually evolved into brains that could execute or anticipate evasive strategies.
There is little doubt that consciousness is shared by many animals. However, self-consciousness and intelligence is a different matter. There's evidence that some apes and other mammals have a primitive form of intelligence but none of them come close to the mental abilities of humans.
If there is a God, then the single greatest endowment he gave to us is our intelligence. Science is the pinnacle of human intelligence and makes the greatest, most disciplined, use of our special endowment. If there is a God, surely he would be pleased at our achievements (if not concerned about our direction).
Science is not a replacement for religion. It does not claim to have the truth or all the answers. It demands skepticism -- NOT faith. The history of science is a history of paradigm shifts: Euclidean, Newtonian, Darwinian, relativity, quantum mechanics, string theory, multiverses, etc. Our quest for understanding seems to step up from one plateau to the next. And when our understanding takes these steps, those who professed certainty (i.e. faith) in the prior paradigm find themselves extremely embarrassed.
Today, there are materialists who believe everything can be explained by their smallest components. Many of these physical reductionists are so focused on the minutiae, that the big picture escapes them. The fact is; not everything can be explained by their most basic components. Many times, the whole is more than the sum of its parts. That's the nature of "emergent properties" found in "complex systems". Consciousness and intelligence are emergent properties of life that defy physical reductionists. I believe it is emergent properties of complex systems that foreshadow the next paradigm shift.
I hope we will (perhaps soon) have an explanation for life, consciousness, intelligence and free will. I suspect that there's much more to the universe than is currently realized or conjectured by our science.
This short essay is a synopsis: not a treatise. It is intentionally simplified and brief. My intention is to flesh out more details as your responses warrant (or not).