For those of us who are non-believers, the concept of free will poses a special challenge. 
We think of the universe, and the citizens living in it, following laws of science and not spirituality. These laws can already explain a lot of what we see and experience, and, we believe that what cannot be yet explained will be in the future. 
In this picture, there is no place for the concept of soul as a separate entity from the body. Soul is not molecules and atoms, and the laws of physics do not dictate what it does. According to the non-believers, soul cannot exist. However, if soul does not exist, how does one explain that I have the freedom to identify choices and make decision on which one to select? What law of science explains that fuzzy, non-deterministic aspect of our experience? 
A recent book by Sam Harris provides one theory of how to reconcile this quandary. http://www.samharris.org/free-will 
He, of course, is a very vocal non-believer and I like his rational thinking, so I am inclined to believe in what he says.
Basically, his explanation is based on two points:
- Our brain is under the illusion that it is      freely identifying options and making choices, when it is not. One needs      to dig deeper to find out what is going on. For example, you cannot decide      what you will decide to do. Nor      can you choose to choose what to choose. In other words, it is your      physical being that decides what you will decide to do or choose what you      will choose to choose. Sam cites scientific studies in which the body had      made a decision before the      person thought he made the decision based on free will. 
- To make the matter more      complicated, as yet we do not know what this human “system” exactly is or      how it will behave given a certain input. It is as yet an unexplained      black box. However, it is a system formed through nature and nurture      guided by laws of science. Genetics, environmental factors, neuron      connections formed through experience---all are involved in making the      system what it is.
Now this my sound like a play on words surrounded by uncertainties. However, it does provide a framework to explain free will without resorting to the concept of soul. 
Just as science has cracked (or making good progress in cracking) tough nuts like creation of universe, evolution of life, or prediction of weather, it will make in roads in explaining the very essence of our existence like free will. 
I feel confident.
 

Non-believers can certainly take a breather, because nobody has ever said that a "soul" is required to exercise free will (believers will certainly argue this point). However, what is forgotten in the reasoning mentioned here is the fact that the body also has a "mind". It is this Mind (nothing to do with soul) that exercises free will. There is a famous scientist named Albert Einstein, who should be expelled from the scientific community for saying thus: "The intuitive mind is a sacred gift and the rational mind is a faithful servant. We have created a society that honors the servant and has forgotten the gift."
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