How does your soul fit into your brain?

Many people also believe that the soul is the "real you" - your Id in a perfect world. This line of thinking leads people to believe that, for example, when a baby dies it's "real" self will live on, not as a baby but as an adult mind. This makes sense, otherwise all babies that die and go to heaven would still be babies there, which wouldn't be much use, really - knowing practically nothing and not being able to communicate or interact with other souls except by screaming and crying. It seems that no matter what state of development you were in at the moment of death, be it a helpless infant, a severely mentally handicapped person, or an eighty-year old with advanced Alzheimer's Disease, up in heaven you magically acquire all the mental faculties and knowledge you would have had as person in the prime of mental health.

The soul, apparently, must be somehow separate from the brain.

There are a number of gaping flaws in this idea (as is often the case with religious pseudo-science). The most obvious one is this:

If a person has a major physical change to their brain (due to injury, surgery, disease or oxygen starvation), it will often bring about a major change to their personality. Many people who suffer accidents that cause brain injury also undergo a personality change. It used to be common practice to lobotomise (surgically remove the frontal lobes of the brain) dangerously violent people as this brought about a dramatic change in their personality - they became much more subdued and docile.

There have been several cases where a person went into hospital for an operation, something went tragically wrong, perhaps with the anaesthetic, and the person suffered massive brain-damage as a result. Healthy, thinking, reasoning person before the operation, and a vegetable afterwards. What happened to the soul? Did the material drugs damage the immaterial soul?

Sometimes a baby is starved of oxygen during birth, and suffers irreparable brain-damage because of this. Is this evidence that God, for some reason, installs a "damaged" soul into the baby, coincidentally at the same time that the baby's brain is being starved, or is it evidence that your mental state is inextricably related to the physical state of your brain?

This begs the question: how can a change to a person's physical being have such a large effect on that person's non-physical being - their soul / personality?

Maybe the brain is just the soul's connection to the physical world? That is, the soul floats along inside our heads and use the brain the drive all the various muscles etc. that express the soul's desires and feelings. In that case, why do we have such a large brain? Mice and other small mammals get along quite well with a brain the size of a pea, so why can't humans? A mouse has a similar set of bodily organs and muscles to a human. Many dinosaurs had large bodies and tiny brains, so a big brain is not required to move big muscles. Why do we, with our average-sized body, have such a disproportionately large brain? Does a complex soul require a large brain to connect it to the physical world, or is our intelligence due to the hundreds of trillions of neural connections inside our heads?

Are memories stored in the brain or the soul? Some people partially lose their memory when their brain is injured. This implies that the brain stores memories, in which case how does your soul remember anything after brain-death? Does it take a copy of your memories and store them somewhere? If so, why can't it do this before death, giving us all perfect memories throughout our lives? What happens to those memories that are forgotten or lost? Does the soul somehow retrieve them so that you have a complete memory of every single second of your life, or does it only get those things that your conscious mind can normally remember?

If the brain is the soul's connector, why do other animals have brains at all? Do they have small, simple souls? Many religions teach that only humans have souls, and yet many animals are able to express their desires and feelings quite adequately (ask any cat-owner at feeding time). If a soulless animal can obviously express happiness or fear, is this caused purely by its brain or by some sort of mini-soul acting via the brain? If animals have some sort of soul, do they go to Heaven when they die, or is their existence simply extinguished (just as if their personality was indeed caused by the brain)?

If the brain is simply a link-point for the soul, then how can drugs affect the state of the soul? If you take some mind-altering drugs, the chemical balance in your brain will be altered, but how can chemicals have any effect on the immaterial soul floating along with the brain? How do antidepressant drugs stop a nonphysical soul from feeling depressed? Why do souls need sleep? Why does your soul cease to be aware while your brain slumbers?

The answer is quite simple, and not to the liking of theists. Your personality is a direct product of that physical organ in your head, your brain. If your brain is altered, your personality (your "soul") is altered. When your brain dies, your soul dies with it.

Nothing else makes sense and, as usual, the theistic explanations only raise more problems than they solve.