Many people come to look at the brain from some variation on a particular set of preconceived attitudes.

1. Most and all important thinking happens in the neo-cortex.
2. There are two independent thinking systems: unconscious and conscious.
3. There is a big divide between how humans think and how animals think.
4. Introspection is a trustworthy means to understand ‘conscious thought’.
5. Without human language it is not possible to have concepts.
6. It is impossible to have morality and responsibility without free will and impossible to have free will without a ‘conscious mind’.

All of these notions are probably false. They may not be but they certainly can be mistaken. The important thing is to keep an open mind when interpreting research results. It hampers us to carry Freud, Descartes, Chomsky and others like millstones around our necks.

The more reasonable way to look at things can be laid out.

1. The whole of the forebrain and parts of the midbrain are important in normal thinking. In particular the cortex does not work without the thalamus and vice versa. The more ancient parts of the cortex, such as the hippocampus, are extremely important to thought and memory, not just the neo-cortex.
2. Being conscious of thoughts should not be confused with the actual thinking any more than being conscious of a tree should be confused with the actual tree. It may be that there is one undivided thinking process and that we are aware of some of the process but not all of it (or even most of it).
3. In evolutionary history, we have only recently, diverged from our sister species. There is no reason our brains differ in kind, rather than degree, from other animals.
4. Introspection may be largely an exercise in spin or self deception. We would not know if it was from within introspection.
5. There is non-verbal thinking even though some people resist and downplay the idea. You can think something and not be able to find words to express the idea.  
6. We make decisions and that should be sufficient for owning our actions and accepting responsibility for them. What that means morally and legally needs to be decided as it has been in the past. Conscious free will is a red herring.