Homunculus is one of those great words to have in your back pocket. You never know when it might come in handy, and it is a fun word to say. Traditionally, the homunculus was a small physical representation of a human used in the practice of alchemy during the 16th century to symbolize their attempts to re-create human life by artificial means.
Psychologically, the idea of the homunculus is the inescapable feeling that there is a “little person” inside my head, something like a crane operator, looking out through my eyes, listening through my ears, and manipulating my appendages in order to act on my human volition. Most human religions have even given the homunculus the supernatural power to live indefinitely beyond (or even before) the lifespan of its host body. This is, in “God language,” my soul.
The problem is that the harder you look inside the brain to find your homunculus, that “little person” controlling you, the faster it disappears into the mass of individual brain cells which have only very limited and specialized individual abilities.
Take this sense of “seeing through your eyes.” For starters, images of the outside world are inverted by the lenses in our eyes, and are projected upside down on the backs of our retinas. So our brain is first doing an internal reversion of the image, a neat trick in itself. In addition, our eyes are constantly blinking and shifting their point of focus slightly (called “saccades”), yet we “see” in nice clear, stabilized motion. Human peripheral vision does not see in color, and we have two big blind spots on our retinas, yet I will swear that I see an uninterrupted sweep of full-color landscape in front of me. My brain is constantly filling in the missing details from my (often faulty) memory. 
Our sensory intelligence is distributed throughout our brain, and even likely distributed throughout our entire bodies. The idea of distributed intelligence is something we already know, but we are reluctant to apply this knowledge to our own sense of consciousness and intelligence. Swarms of ants, bees and termites demonstrate an impressive “collective intelligence” that emerges from very limited individual “parts,” each with very limited decision-making power. But surely, this “intelligence” is vastly different from my human intelligence, right?
This is not to say that we don’t have a “soul,” which is more a “faith statement” than a scientific one.  But just as we learned that heaven is not just above the clouds, we are finding that this homunculus is not a “thing,” rather it is the “collective me,” distributed throughout my brain, and even the rest of my body. If I have a stroke in, or an injury to, a small portion of my brain, a part of “me” can disappear, perhaps never to reappear.
And part of this “collective me” is a “centering function” that creates my homunculus perception of being in the “middle of things.” It is a fragile function. “Virtual reality” games are very effective at altering this brain function, and “out of body” experiences sometimes associated with “near-death experiences” have been replicated in a variety of neuroscience experiments.
Our human “intelligence parts” even appear to include the functions of the microbial “biome” living inside our intestinal tract, which appears to impact our brain function and emotions.  And without this rich and individualized mix of gut bacteria and other creepy-crawlies living in symbiosis with us, we would literally die. The classic scenario in H.G. Wells’ War of the Worlds, where the invading aliens die because of foreign microbes, may not be that far off for the human species itself.
The “good microbes” keep us alive, and the “alien” ones can kills us. My gut biome is a critical part of me.  There is even an interesting perspective that human beings are the “domesticated animals” of our gut biome organisms. They often decide what foods they will point us toward eating, as we “graze” at their command, and tell have their unique ways of telling us which foods to avoid. They shape our daily routines, and they wreak their revenge if we disobey them. And they will outlive us when we die, perhaps even moving on into another living body.
Needless to say, the disappearing homunculus can present some theological challenges. This is called the mind-body problem. Is our “mind” a function of our physical brain or is it something separate? In my view, the mind-body problem presents more theological challenges to traditional religion than does the reality of Darwinian evolution.  And yet few believers even seem to know that the problem exists.
So, even though I know that my homunculus is not really “there” in the sense that I normally perceive it, I still go through life mostly pretending it is there anyway. And likely so do you.
- Stafford, Tom. Mind Hacks: Tips & Tools for Using Your Brain. O’Reilly Media, 2010. This is a book of fascinating experiments you can try on yourself to demonstrate how your “sense of senses” is largely created on the fly.
- See my post on paleontologist’s Stephen Jay Gould’s attempt to bridge this divide here.
- Stein, Rob. “Gut Bacteria Might Guide The Workings Of Our Minds.” NPR, 18 Nov. 2013.
- I have once had an illness where the treatment made many of the “good biome” organisms inside my gut die. Trust me, you don’t want that to happen.
- See my discussion on evolution here.