There are few more famous phrases in American history than the Declaration of Independence’s affirmation of life, liberty, and the pursuit of happiness as inalienable, God-given rights. These rights, especially liberty, have come to be pillars of American culture. But the increasing emphasis on the radical autonomy of each human being has led in our time to a divorce between freedom and any notion of an objective order of truth. This is especially evident in various ethical theories that identify man’s dignity merely with the act of choice.
It is true that freedom is a distinguishing human characteristic, but such freedom is grounded in an objective order of value; in fact, without such a grounding, without an essential ordering to what is true, freedom becomes a caricature of its real meaning. In our culture, it seems easy to forget, as President Obama has several times recently, that, in the original context, liberty and our inalienable rights have their source in the Creator.
One manifestation of this modern tendency to separate freedom from truth can be found in arguments about the primacy of conscience. Often appeals to this principle are at the core of justifications for dissent from the Church’s teachings on a wide range of moral questions. Such arguments have been particularly attractive to many Americans, accustomed as they are to look at themselves and their society in terms of individual freedom and autonomy. The primacy of conscience, thus, seems to express a moral imperative.
As with human freedom, the role of conscience in moral decisions is a central tenet of Christian belief. But conscience and its primacy need to be understood correctly. In both popular culture and in the more sophisticated writings of some moral theologians, conscience has changed into something quite different from its traditional sense.
Conscience is the act or condition of knowing the appropriate course to follow in a given situation. From the Latin cum scientia (conscientia), which means “with knowledge,” conscience is a habit or disposition of the intellect concerning specific human behavior. It is a judgment of practical reason rather than of speculative reason; that is, it is a judgment about praxis, about a course of action to be taken or an evaluation of action already performed. The obligation to follow one’s conscience flows from what conscience is. The summons of conscience to do what is good in particular concrete circumstances demands obedience only because it is the application of the objective and universal moral good.
The error into which many fall is to think that to judge an action to be good makes it good. But the judgment conscience makes is not infallible; one’s conscience could be poorly formed or one could act in ignorance, not knowing that a particular act is evil. Those who think that moral maturity, and hence moral well being, are only constituted by the autonomous decision of one’s conscience, misunderstand the role of conscience.
John Paul II: In conscience “the link between freedom and truth is made manifest.”
Conscience is not some independent capacity to decide what is good and evil. Conscience functions within the moral order; it does not constitute that order. The moral imperative to follow one’s conscience is an obligation in the practical order not the speculative order: conscience commands behavior, it does not determine truth. Pope John Paul II made this point with great clarity in his encyclical, Veritatis Splendor:
In the practical judgment of conscience, which imposes on the person the obligation to perform a given act, the link between freedom and truth is made manifest. Precisely for this reason conscience expresses itself in acts of judgment which reflect the truth about the good, and not in arbitrary decisions. The maturity and responsibility of these judgments – and, when all is said and done, of the individual who is their subject – are not measured by the liberation of the conscience from objective truth, in favor of an alleged autonomy in personal decisions, but, on the contrary, by an insistent search for truth and by allowing oneself to be guided by that truth in one’s actions. 
Both conscience and freedom are ultimately unintelligible apart from an order of truth and goodness. The first principle of practical judgment, that is, of human action, is to do good and avoid evil. Practical judgment presupposes an understanding of good and evil by which it then measures the rightness or wrongness of particular actions. Both reason and faith allow man to discover that primordial insight about good and evil.
The recognition that some acts are inherently immoral regardless of the intention of the agent (e.g., abortion) is either a conclusion of speculative reason or a matter of revelation and is not called into question, much less invalidated, by the fact that a particular individual’s conscience might lead him to behave as though these acts are good.
No matter how much one intends to do good, inherently wrong acts remain evil and thus are detrimental to the well-being of the agent, even if the agent is ignorant of that evil. I might drink a glass of sulfuric acid, intending to satisfy my thirst, unaware of what the glass contains. Nevertheless, the effect of such action is physical illness. So too with evil acts, which necessarily result in moral illness, regardless of whether one judges them to be good.
American individualism is particularly susceptible to the error of making human subjectivity, expressed in the distorted notion of the primacy of conscience, the criterion of human dignity. Such a view involves the denial of true freedom and dignity; it leads to a society in which human choice serves as its own justification. What is right becomes nothing more than what is chosen.