I think we already do give in to our instincts, by and large.

So one of the things you have to understand about the older parts of the brain is: they work, and they all communicate with each other. Our reptilian brains (the brain stem and cerebellum) are pretty reliable, but rigid. Most people walk essentially the same way. The reptilian brain is what is called into service when we feel jealousy, or when we're fucking.

The "negotiator" of our brain sits in the middle of this: the mid-brain, which is responsible for our two most powerful emotions: love, and fear. There's a tiny area in this called the hypothalamus gland, which serves as a kind of thermostat for various things: it controls the autonomic nervous system, which does a whole host of things: controls breathing, sleep, hunger, maternal bonding. Basically, the ANS does the job of keeping you alive and healthy as best it can, through a pair of competing nerve networks-one speeds you up, one slows you down. At the top of this complex structure (more highly differentiated than our cerebral cortex) are the amygdala, which process our emotions, and create an emotional memory. If you've ever gotten the "creeps" in a strange neighborhood, it's your amygdala talking.

Now, it may sound as if these parts of the brain would make us all brutal and primitive. But this is, in fact, not true, many of the most noble aspects of humanity-a mother's love for her children, an appreciation of beauty, the desire to belong to social groups-these all have their roots in these older parts of the brain. Many aspects of culture derive from this area. An interesting fact about the amygdala is that they are very sensitive to testosterone levels-in other words: men live in more fear than women do. I believe this leads to their more "compartmentalized" thinking-objects of thought which arouse fear are simply avoided. The two main "balancing factors" that allow us to not live a life of terror are the desire for happiness and pleasure, and situations that bring about these are also stored by the amygdala (particularly the one on the left).

We perform a near-constant check on the reactions of those around us: "Am I doing OK, are the others displaying disapproval, or hostility?" Non-verbal cues, such as a nod, or a smile, go a long way towards establishing an emotional equilibrium in which we finally have the chance to do what we call "thinking". The cerebral cortices have the unthankful task of "trying to make sense of all of this". We mostly do this through an internal narrative, which is 90% fabrication. We believe what we think we believe because "it makes sense to us."

In other words, the answers to your questions are:

1. Not particularly relevant, many of the functions of the lower brains are carried out autonomously.
2. Most of it: language, and the science it has yielded are important exceptions.
3. We've confused ourselves, because our inner narratives aren't accurate. Because of their power, we're often afraid of our animal natures-they are not, however, intrinsically malicious.
4. Exactly.

Given this, if you really desire to have your conscious thoughts inform your conscious decisions, you'll have to make those decisions in a peaceful place, where you are free from discomforts. And even then, your feelings will color these thoughts, in ways you cannot control.

It is not so much a question of instincts as of defaults generally, some of which ill serve us in the modern era and a few of which are positively fatal to civil society.

The term "instinct" and "instinctual" tend to carry with them the notion that they are "natural" and therefore inherently beneficial. That association is specious. We are for example heavily prone to confirmation bias and agency inference, which was great when eluding predators on the savanna and really problematic when functioning in a modern, technological, often urban environment. These two mental limitations largely gave us religion, for example, among other things. They are a major impetus to tribalism and toxic discrimination.

So no, we should not give into our "instincts" willy-nilly.

If you're just talking about "gut feelings" then yes and no. Gut feelings still must be constrained by facts and evidence and should be seen as arising out of deep experience and unconscious connections produced by that experience ... not as some kind of mysterious visitation of one's Best Self. Intuitions and hunches are not infallible. They have their place, in the right context, usually in urgent or dangerous situations where you have an opportunity to circle back later when you have more time and/or facts and re-evaluate. You should never "follow your gut" in a vacuum or without question.

When l have ignored my gut feeling, it has most often turned out badly.

Instincts should be reined in when one deems them disadvantageous ideally. I believe we would be better off if we could arrange our lives such that instinct is allowed mostly free reign without judgement yes. But thats very difficult while living in modern society.

Hunter gatherers generally seem much happier, freer, satisfied to be self sufficient. Their hut gets blown down by a storm they laugh and everyone pitches in to build a new one, who cares?

In regard to your last two questions, it's not a binary matter. Both apply. We have restrained our instincts too much and yet we are fooling ourselves into thinking we can escape them. Particularly among puritanical societies, our sexual instincts have been hampered, rerouted and perverted against reality. The resulting societal blueballs seems to drive a lot of militaristic and money/power grubbing dick measuring contests and fuel a lot of our tribalistic animus.

But we're still more driven by instinct than we realize or admit generally. The only people who seem to know this and use it to their advantage are sociologists who informed our advertising and marketing, and the few politicians who are actively playing chess instead of checkers, although its hard to think of a conservative smart enough to give that much credit to for now.

Depends on how you define instinct, but since I am happy to accept genetic determinism, that is what I will call instinct and I will go with my own usage, to say. We are sailing ships. Instinct is the wind, emotion the sail and reason the rudder. Loose any one of the first two and you are a passive lump which goes no where until you starve, loose the last and you are either wrecked, (crime) or lost (religion).

My instincts have served me very well these 79 years and I would never give them up.They have kept me safe ,aided in decision making and in general aided me in a very successful life. Three cheers for instincts.