Custers & Aarts have a paper in the July 2 Science called "The Unconscious Will: How the pursuit of goals operates outside of conscious awareness". It reviews work indicating that people's brains make decisions and set goals without the brains' "owners" ever being consciously aware of them.
A famous early study is Libet et al. 1983, which claimed to find signals being sent to the fingers before people were aware of deciding to move them. This is a dubious study; it assumes that our perception of time is accurate, whereas in fact our brains shuffle our percept timeline around in our heads before presenting it to us, in order to provide us with a sequence of events that is useful to us (see Dennett's Consciousness Explained). Also, Trevina & Miller repeated the test, and also looked at cases where people did not move their fingers; and found that the signal measured by Libet et al. could not predict whether the fingers would move.
Fortunately, the flaws of Libet et al. were not discovered before it spawned many studies showing that unconscious priming of concepts related to goals causes people to spend more effort pursuing those goals; and those are what Custers & Aarts review. In brief: If you expose someone, even using subliminal messages, to pictures, words, etc., closely-connected to some goals and not to others, people will work harder towards those goals without being aware of it.
This was no surprise to me. I spent the middle part of the 1990s designing and implementing a control structure for an artificial intelligence (influenced by Anderson's ACT* architecture), and it closely resembled the design that Custers & Aarts propose to explain goal priming. I had an agent with a semantic network representing all its knowledge, goals, plans, and perceptions. Whenever it perceived a change in the environment, the node representing that change got a jolt of activation, which spread to the connected concepts. Whenever it perceived an internal need (hunger, boredom), the node representing that need got a jolt of activation. Whenever it decided to pursue a subgoal, the node representing the desired goal got a jolt of activation. And when this flowing activation passed through a node representing an action that was possible at the moment, it carried out that action, modulo some magic to prevent the agent from becoming an unfocused, spastic madman. (The magic was the tricky part.) Goal-setting often happened as the result of an inference, but not always. Actions usually occurred in pursuit of a chosen goal; but not always. Merely seeing a simulated candy bar in a simulated vending machine could cause a different food-related action to fire, without any inference. I did not need to implement consciousness at all.
When I say "I", I mean the conscious part of this thing called Phil. And when I say "I", I like to think that I'm talking about the guy in charge, the thinker-and-doer. Goal priming suggests that I'm not. Choosing goals, planning, and acting are things that your brain does with or without you. So if you don't always understand why "you" do what you do, and it seems like you're not wholly in control, it's because you're not. That's not your job. Wonder why you want coffee so much, when you don't like the taste? Why you keep falling for guys who disrespect you? Sorry, that's on a need-to-know basis. You aren't the leader and decider. Your brain is. It's not part of you. You're part of it.
You only use 10% of your brain. Something else is using the other 90%.
So if making decisions isn't what we do, what do we do? What are we for?
My theory is that we're the "special teams" guy. We're punters, not quarterbacks.
Think of those movies where a group of quirky but talented people team up to steal a diamond from a bank, or information from a computer. There's always a charismatic leader who keeps everybody on task and working together, and some technical guys who work out the tricky details of the leader's plan. In Sneakers, Robert Redford is the leader. David Strathairn is the technical guy. In Ocean's Eleven, George Clooney is the leader. Some guy whose name even the internet doesn't know is the technical guy.
We all want to be the leader. We think we'd make a good leader; but when we try, we screw up. We think that we, the rational part, can do a better job of managing our team. But a lot of cases where "we" benefit from rationality, like wearing a condom or planning for retirement, are where our goals are different from the team's - not where we're better leaders. It doesn't come naturally to us; it's not what we were meant for.
(Someday, AIs may be sufficiently rational that the technical guy part can run the show. Then again, our brains work the way they do because it works; the AI may likewise assign their technical guys a subsidiary role. Maybe consciousness is a bad quality for a leader, that impedes swift decision. Insert political comedy here.)
So, when we're trying to be rational, conquer our instincts and biases, what are we doing? Well, remember all those episodes of Star Trek where an alien parasite takes over someone's brain and makes them do things that they don't want to? That's you. Unless you're content with being technical support guy.
Am I saying we're the bad guy? That we should know our place, and obey our inner leader? Hell no. Screw George Clooney. I hate all those smug leading-man bastards.
I'm saying, when you struggle to stay in control, when you find "yourself" acting irrationally again and again, don't beat yourself up for being a poor manager. You're not the manager. You're the subversive parasite executing a hostile takeover. Don't blame yourself. Blame George. Lick your wounds, figure out what went wrong, and plan how you're going to wipe that smile off his face next time.
Ruud Custers and Henk Aarts (2010). . Science 2 July: 47-5.
Benjamin Libet, Curtis Gleason, Elwood Wright, Dennis Pearl (1983). Time of conscious intention to act in relation to onset of cerebral activity (readiness-potential). Brain 106:623.
You can find more papers on free will and consciousness thanks to David Chalmers.