At the first time when few colleagues of Darwin urge him to publish his findings on the possibility of evolution, the fear in the face of actor Paul Bettany, was perhaps very close to that of any person who is faced with the challenge of may be contradicting the long-prevalent thought on the "belief-based" philosophy. As the protagonist says, we live in a society and it is bound together by the belief system that while might be improbable, but certainly floats and manages to keep the fabric of society together. It is very difficult to build plank by plank the very vessel in which the entire society sails. I image such are the thoughts of many world-changing ideas. It does take some mettle to stand for such thoughts.
All of nature is a battle field, survival of the fittest is a thought that is new to the world. "What are you so scared of?, asks Annie to Darwin. Only brutal survival was only a theory. The imagery of Darwin's daughter was perhaps his own contradiction in mind trying to give him the courage to speak his thoughts to the world.
As a scientist, Darwin's character mentions that he has been holding back his thoughts and has been living in a limbo. What if the then persistent ( and still persistent) faith belief creator existed and what if he faces the consequences of not believing in it. Perhaps he didn't want to take a chance of being away from his family (in heaven).
At one point in his life, Darwin gets strong of opinion that he will tell the world about his thoughts on evolution when one of the faith-based teacher punishes his daughter Annie when she expresses her father's findings of dinosaurs (based on theory of evolution). There happens a silent struggle within Darwin about accepting the validity of his theory of evolution.
In the movie, there is a scene where the fox hunts the rabbit. Darwin's daughter Annie explains her thoughts that the hunt has to happen for the survival of the fox and its babies. In nature, things might seem unfair, but they have to happen to keep the balance and equilibrium. Various thoughts of Darwin's recollection of his daughter Annie give him courage to take the responsibility to publish his evolution based findings, for the sake of his children. "On the origin of Species" is the chosen title of Darwin's book. It is mentioned in the movie, Darwin takes personal attention to keep the creator out of his book.
"Logic isn't everything" was the statement that the protagonist mentions in the movie. I am personally confused at this statement of the character of Darwin. Himself being a scientist, why does he say so? perhaps the reality that his daughter Annie was diagnosed with some unknown ailment (that takes her life eventually) makes him think that logic isn't everything? The reality of being human cannot be neglected ever. After all we are humans.
Wallace, another scientist from another country (not UK) publishes a 20 paged paper about his independent findings on evolution theory. Darwin sees that paper and feels a little dejected as his 250 paged book is not complete and because of his procrastination in publishing his findings. Darwin's procrastination in publishing his book is perceived as a failure by him. He almost gives up the hope of writing, but Darwin's friend visits him and encourages him to complete his book. This scene of the movie highlights the human limitations of the mind, sometimes feeling elated at new scientific findings and sometimes being worried of social relations/consequences.
As portrayed in the movie, after the death of his daughter Annie, Darwin seems to have lost belief on faith-based thoughts. Perhaps this event gives him the impetus to finish his book.
"Taking comfort from faith-based thoughts", is it necessary to live in the world peacefully-in-mind? The dreadful alternation of hope and no-hope sickens the soul.