New science, evolution and human biology

If all thoughts are created and stored and existential reality of our surroundings fed by our senses is processed by the mind/brain then whats the reason behind the origins of gut feeling and being heartfelt? 

In the past 40 years, science has thankfully developed to the extent that it can help us realize what ever our distant ancient forefathers knew to have been existed. Our dismissal of an ancient advanced civilization, based on principles of evolutionary Darwinian theory, however much proven by things we can see, will have to be acknowledged as conceptually limited in scope to the lesser evolved and more primitive beings like plants and animals.

We know for certain that

• in the chain of events - in which superior generations are formed as a result of genetically selected and need based species evolve as a part of natural selection, there is a missing link whereby from chimps to the homo-erectus we have a predictable chain and from then on the neanderthal man simply vanished. Presumed to have become extinct due to non-survivability and arrival of our present dominant species - the homo sapien sapiens, in the same generation! So where the heck did these new guys come from all of a sudden?
• Moreover, in the race to come up with a theory of evolution, which explains and answers the spiritual need for man to know his origins(where do I come from?), we tend to overlook the fact that neither of the animals/plants became dominant in the past purely based on the theory of evolution. Sharks are known to have been in the same state they are in now, because of already having been close to perfection in terms of adapting to their environment since millenia. So why didn't they become better and become the dominant species ruling the earth?
• In the entire history of planet earth, radiometrically dated for age on a material based off of a meteorite, to be ~4.4 Billion years old, the so called evidence of our existence is only about a maximum of 8,000 years(2000 years of AD and the oldest archeological find till now, city of Dwarika, claimed to have been established during the reign of Shri Krishn, 6000 years BC). Evolutionary speaking, this is not even a second. probably a nano second of human time, compared to galactic time counted in light years(dist travelled by light in one year counted at the rate of 300,000 kms per sec!).
• The only species of dominance found in terms of evidence from past are dinosaurs, popularly presumed to have become extinct when a meteorite ~5 miles wide, hit earth, forming the great crater on the south American continent, creating a dust cloud enveloping the entire earth and blocking out all sunlight for ~200 years and rendering the planet uninhabitable.

Based on the aforementioned points, we need to start thinking with a broader set of horizons in order to eventually understand what could have happened and how did we come to be. One would do well to remember that purpose is a very strong motivator which is why even the law needs to know the motive behind a crime in order to punish. Even though we can see the humongous ancient pyramids standing still, and even though if we wanted to build it again today with access to all the technology we have in the present times, we do not go on to build because neither do we feel motivated to do so nor do we have any inclination towards the wasteful exercise which does not promise to answer our deepest questions.

Out of all the uncertainties of the future, why do we some times feel that we already know/knew about an instance which has as yet not taken place or occurred? When we know that our sub-conscious cannot order and can only suggest or tell and our conscious can make decisions by using forces of logic on a primary level, why do we not end up believing in ourselves?

New science is helping us get closer to the truth: (Includes notes from Dr. Deepak Chopra's lecture at the Zeitgeist forum - the Future of well being, neurobiologist/scientist)

1. We now know scientifically, that there is an actual molecular structure to emotions. Emotions ARE things which are influenced by hormones like serotonin(and its reuptake inhibitors), dopamine, melanin, oxytocin etc.,
2. Mind is no more the exclusive owner of our thoughts as previously thought. Gut-feeling and being Heart-felt are real things which have conclusive proofs now. Similar hormones as are produced in the mind are found to be produced/exist in the gut and in the muscular structure of the heart.
3. Body is not a structure, its a process.
4. The mind is a relational and embodied process, that regulates the flow of energy and information. - UCLA psychotherapist.
5. Consciousness creates reality