There are a number of ways of knowing involved in a person's sense of moral duty, that is, his sense of the natural law. Involved are intuition, connatural knowledge, self-knowledge, and reasoning. And a large portion of that knowledge, in most people at least, is not explicit and conscious, but remains implicit and pre-conscious, albeit very real.
Aquinas argued that every human being, whether he realizes it or not, possesses a natural knowledge of God; it is a confused and general knowledge - this is true even for the "atheist". It is this knowledge that is the source of the moral sense, a natural awareness of a moral order that includes a host of duties. This moral sense can be dulled or enhanced, depending upon how we choose to respond to its command in the deepest recesses of our conscience, that is, whether we choose to obey it out of reverence for a good we know is larger than ourselves because it embraces everyone, or whether we choose to disregard it for the sake of the delectable. The evidence for this natural knowledge is in man's behavior, in his search for 1) the sufficient reason that explains the existence of things, and 2) in his desire for happiness.. Allow me to explain what this means.
I would like to begin with the principle of sufficient reason, which runs thus: "Everything which is, to the extent to which it is, possesses a sufficient reason for its being so that it is capable of explaining itself to the intellect. In other words, whatever is, has that whereby it is."
Consider the example of a broken window. You come home one evening and find that your living room window has been smashed. You immediately wonder how that happened. In other words, you seem to know that there is a sufficient reason for this window being broken. Now, "whatever is, has that whereby it is"; and so this broken window has that whereby it is broken (i.e., the reason), either in itself or in another. If it has "that whereby it is" in itself, then it contains within itself, within the very notion of "broken window", the reason for its being broken. If that were the case, then just knowing that this window is broken is enough to know the sufficient reason for its being so, and thus you would not ask the question: "Why is this window broken?" The reason would be contained in itself, and so it would explain itself. But that is clearly not the case, which is why you wonder how the window got broken.
Notice, however, that you do not wonder how you are able to carry on an intelligent conversation with a friend; there is nothing about that which you find puzzling. The reason is that the "sufficient reason" for the conversation is contained within your friend's very nature, for he or she is a human person, that is, a rational animal. An individual with a rational nature is capable of communicating concepts through language - that's what it means to be rational. But a flower is not capable of such communication, and so if a flower were to pose a question to us, we'd be wonder struck.
If that which is has that whereby it is through another, then it depends upon that 'other'. Thus the broken window has its sufficient reason in something outside of it.
Now when we see something existing, or an inanimate thing moving, we naturally inquire of the reason until we possess the sufficient reason, at which point we are sufficiently satisfied. The reason for the moving ball is the pitcher's act of throwing (the efficient cause). Knowing the efficient cause, however, is not always sufficient. If a neighbor tells us that the boy down the street threw the ball through the window, we continue to search for the reason until we find the sufficient reason - a "throwing arm" is insufficient. It is not enough that his arm was moving and caused the ball to move through the air, thus breaking the window. We know that arms don't throw things; it is the agent as a whole that throws things, and so we naturally want to know "why" he threw the ball in the first place. In other words, we're looking for the final cause of the action (the end, or purpose). If it is determined that he threw the ball to his friend during play and the pitch was wild and thus he accidentally broke the window, we now possess the sufficient reason. But if that is not the case, we continue to search for the reason. If we learn that he threw the ball at the window because he was angry with you and wanted revenge for an injustice he believes you committed, then we are coming closer to the sufficient reason that explains the broken window.
Now, consider the principle of identity: each being is what it is (a carrot is a carrot, an oxygen atom is an oxygen atom, etc). There is quite a bit packed into that first self-evident principle. In knowing anything at all, I know first and foremost that it is (it exists). Being is first in my knowledge of anything. I may not understand who or what is approaching, but I know generally and confusedly that something is approaching. After a while, I come to realize that it is an animal. After a bit more time, I realize that it is something possessing a canine nature. Finally, I realize it is my pet dog that was lost. That realization is accompanied by a sense of relief.
In this apprehension of my approaching dog, I know "what" it is (a canine creature), and I know "that it is" (my dog has existence). The formulation of the principle of identity - "each being is what it is" - contains two apprehensions: the simple apprehension of a being's nature or essence (what it is) and the judgment of its existence (that it is). But my dog's existence is not contained in her nature (canine) - otherwise I would not have been worried that she might have been killed; for whatever belongs to a thing's nature belongs to it necessarily. Thus, the ability to think belongs necessarily to a rational nature, "3 sides" belongs necessarily to a triangle, etc, and so if behind this door there is a human being, it is necessarily the case that he or she has a rational nature and thus cannot not be rational, and if there is a triangle behind this wall, it may not be made of wood and painted yellow, but it necessarily has 3 sides (it cannot not have 3 sides).
Existence, however, does not belong necessarily to my pet dog's nature; otherwise my dog would necessarily exist, and could not not exist (just as a triangle cannot not have 3 sides, etc). In other words, the sufficient reason for my dog's existence is not contained in its nature, but is outside of it. More to the point, the existence of anything that I apprehend, whether it is a human, a cat, a plant, or a mineral of some kind, etc, is not contained in the nature that I grasp through simple apprehension. I apprehend existence through a distinct act of the intellect, namely existential judgment.
And that is precisely why we wonder why there is anything rather than nothing at all. We want to know the ultimate meaning of things, the purpose of life, the origin of existence, etc. We do so because the sufficient reason for the existence of things is outside the things themselves that we know, and so we are constantly seeking to discover the causes of things. Sure, we now know why your eyes are blue, and why your cells multiply, and why you should moderate sodium in your diet, etc, but we continue to seek for more answers to our questions, for we want to know why you and everything else exists in the first place. We have a desire to know the ultimate causes of things, the first causes, and being (existence) is absolutely first. To know the cause of the origin of the whole is to understand the whole.
Of course, most people do not have all this worked out in explicitly formulated concepts and first self-evident principles, but they do, nevertheless, have a knowledge of the "insufficiency of being", even if it is only a preconscious one. But there is more to this. If I possess - even confusedly and pre-consciously - a knowledge of the insufficiency of things to explain their very existence, then I know that things depend on something outside of them in order to exist (to be and continue to be). In other words, if the sufficient reason for their being is not within them, it is outside of them, in another. And since the most obvious agents of a living thing's generation are its parents who are themselves beings whose sufficient reason for being is outside of them, whose parents in turn are beings whose sufficient reason for being is outside of them, and so on, etc, I am aware (even confusedly and perhaps pre-consciously) that all things depend for their existence on a being who contains within himself the sufficient reason for his own existence, that is, a being whose existence and essence are one and the same, and who is thus independent.
If I were to provide an analogy, think of a beautiful chandelier hanging above your head in a ballroom, but you are positioned in the room such that you cannot see the ceiling, only the chandelier and the links of the chain by which it is suspended. Now in your mind, it matters not how many links in the chain there are; the ceiling could be so high as to require hundreds, even thousands of links. Nevertheless, each link is dependent upon another (i.e., the one is holding up the link below it because it is being held up by the one above it, which in turn is being held up by the one above it, etc.). The very fact that there are hundreds of dependent links makes no difference to your knowledge of the insufficiency of the links as an explanation for the chandelier being suspended above. Multiplying them into the millions, even trillions, does not in the long run satisfy you by offering you the sufficient reason for its suspension. You know that there must be a ceiling from which the links are attached - millions of dependents do not amount to an independent.
And so, one does not even need to see the ceiling, but one knows nonetheless that there is a sufficient reason for the chandelier being continually suspended above our heads, which is why if we want an explanation for its suspension, we look to see the ceiling, or whatever it is that is radically different from the dependent links in between. Whatever it is, we know it is a stable origin that enjoys an independence not belonging to the links.
Now, it is not necessary to think of this in terms of a long series of causes stretching back into the past; that would be to misunderstand the point being made. If the sufficient reason for a thing's very act of existence is not contained within it, then there is no need to search for it in another being in the same predicament (i.e., a parent). Every being in such a predicament is immediately dependent upon this efficient cause who is the sufficient reason for the existence of all things.
Human beings have a more or less confused knowledge of this, and they've always had this knowledge. This is what most people have always referred to as God. But those who refuse to do so, i.e., atheists, are nonetheless still in search for "the origin" that they expect will explain and thus provide the sufficient reason for the very existence of the universe. In other words, their search for this sufficient reason shows that they understand, even if only pre-consciously, that there really exists a sufficient reason, otherwise there would be no "reason" to search.
There is also another angle from which we can look at all this. You and I are moved to act, to pursue, to search, to work, to accomplish, etc. Whatever we choose to do, we do so for the sake of an end (final cause).
Consider any activity whatsoever - your neighbor fixing his car, for example. Why is he doing that? He's acting for an end, namely, that the car will continue to function. And why would he want the car to function? So that he can get from one place to another. And why would he want to drive from his home to, let's say, his workplace? Well, he wants to work. Why does he choose to work? In order to support himself, etc.
As we can see, it is the end that gives meaning (direction) to one's activity, and it is an end that is the reason (the cause) for the previous movements or actions. The end is the final cause, or that for the sake of which there is activity. The final cause (end) is the mover that moves the agent to action. The ultimate end is the ultimate reason, that is, the ultimate mover of one's actions.
So let us ask the question: "What is the ultimate reason why we do anything at all"? The answer is happiness. We seek happiness, and the happiness we seek has certain characteristics. We seek a happiness that is enduring and unqualified; for example, were we to achieve that happiness, we would not say to ourselves: "I want this to come to an end". We want a happiness that is endures. We want a happiness that does not depend upon contingent factors like the weather. We seek a happiness that is complete, that is desired entirely for its own sake and not for the sake of something else, and one that is sufficient unto itself, not one good among others, but a final good that transcends all others. That's why we continue to seek, regardless of how much we already possess, for our current state of happiness is always qualified, incomplete, and not entirely self-sufficient.
The human heart (will) is restless. It is always searching for more, no matter how much it already possesses. Now if we seek this unqualified good (end), it must mean that we know it in some way; for we do not desire what we do not know - the will can only tend towards what the intellect presents to it. So what is it that we know, which is behind the will's tendency to it? We know there is a universal good, an unqualified good, otherwise we would not desire it. We may not know clearly and explicitly what that is, but we know it confusedly and generally at least, which is why we continually tend to it.
This is the good that we love before and above all things, and this ultimate end is the reason why we recognize the goodness in all other human goods in our life, i.e., our friendships, our work, our leisure, our insights, etc, just as our neighbor sees all those things that contribute to his achieving his end, which is the functioning of his car, as good; for example, he sees his tools as good, his garage as good, his tires as good, oil as good, etc. They are all good in view of the good of a functioning automobile, but a functioning automobile is good in view of his work, which is good in view of his very life that his work helps to sustain.
My life and all other human goods are good because they are related to the ultimate end, which I naturally love more than I love myself - for I am not the bonum universale, for if I were, I would no longer seek anything outside myself. Indeed, my life is good for its own sake, but it is also relatively good, that is, in relation to higher goods that are specific to my nature. For example, it is good to be alive, and so I know that food and shelter are good for the sake of that life. But I seek more than just living. Indeed, it is good to be alive for its own sake, but I also want to live in order to continue to possess truth, to love, to raise my children, pursue justice, etc. I pursue a life rich in human goods, but behind all this is a pursuit of something supremely good, a self-sufficient happiness that I do not find within myself or as yet in the world. I certainly desire my own perfection, my own fullness of being, but that desire is for something other than me. In possessing it, I seem to be aware that I will possess perfection and thus happiness - otherwise I would not pursue it. I desire a universal good, an unqualified good that will bring me an unqualified happiness.
This self-sufficient happiness, which is the ultimate end of everything I do, coincides with the sufficient reason for the being of all beings. My search for the sufficient reason for being and my search for happiness converge towards the same point. Being Itself (that being whose nature is to be) and the universal good (the possession of which constitutes my perfect happiness) are one and the same.
This one end is God, whether we are explicitly aware of it or not. In fact, Aquinas' demonstrations of God's existence are simply ways of showing that what we already know confusedly and generally is in fact what we mean by God. To repeat, although an atheist rejects the idea of God's existence, he pursues nonetheless the origin that he expects will explain and provide the sufficient reason for existence. Perhaps he thinks that sufficient reason is going to be located in a particle, or in an equation for a theory of everything, etc, but it is the difficult work of philosophy that involves attempting to determine whether these or other such things constitute the sufficient reason for the existence of things. Similarly, a person might believe that his greatest happiness, the ultimate end, is the possession of power or unlimited wealth or fame, etc. So too, it belongs to philosophy to test that supposition through reasoning. Regardless of this, what is clear is that these people, and everyone else, are aware of a sufficient reason for being and a bonum universale (universal good), for their actions reveal such an awareness.
There is much more to this pre-conscious and confused knowledge of the universal good than what we've unpacked up to this point. We experience reality as intelligible, good, and beautiful, even though its goodness, intelligibility and beauty are limited. Now, all these properties (intelligibility, goodness, and beauty) have to do with order. This is especially obvious in the case of beauty; a beautiful symphony is ordered, harmonious, and radiant with meaning. We speak of beautiful days, beautiful sunsets, beautiful skies, etc. If there is beauty to reality, there is an order to reality.
That is why we have a sense that the origin, the sufficient reason for existence, is intelligent, good and beautiful; for we all know intuitively the principle of causality, that for every effect, there is a cause, and the effect cannot possess what the cause is lacking, for that would suggest that something comes from nothing (or that nothing and something are identical, which is absurd). And that is why human beings, from as far back as we know, have an awareness of a God (or gods) that is in some sense personal (intelligent and volitional) and who is deserving of acts of gratitude and thanksgiving. He is the origin of the order found in things, considered in themselves and taken as a whole.
Now the world we live in is characterized by movement. Things are in motion; there is change in the universe, and every agent moves for the sake of an end, a final cause. A thing's final cause tells us the good of the thing, that is, it tells us what completes it. A plant moves, but its motion is towards its own completion, i.e., a rose develops in order to be a rose most fully and completely. That is why we understand what constitutes a good and healthy rose, a good and healthy dog, etc. Without that knowledge, we couldn't treat diseases in plants and animals, for we can only know a pathology in light of the good of the thing.
Now I know from within that I am inclined to an ultimate end, namely happiness. I also know from within that I am inclined towards a number of ends (human goods, such as life, the possession of truth, the knowledge and appreciation of what is beautiful, personal friendships, marriage and family, a just social order, etc). I also know that this and that person over there are of the same nature as myself (human), and I know through observing their behavior that they too are inclined to these goods, and ultimately to the universal good, because everything they do is also for the sake of happiness. We all experience our own lives and the lives of one another as fundamentally good.
And so I know that the good is much more than my own private good; I know that it is much more than your private good. I know, therefore, that there is a common good that is larger than my own private good, just as each player on a soccer team is aware of a common good, which is the team's victory. Each player will share in the victory and will be glorified by it. This common good, however, is larger than the individual player's private good, for example, the player's individual scoring record. Note that the team's strategy is ordered for the sake of victory (the common good). Every action on the part of the individual players is ordered towards the common good, and a player's acts are judged to be good to the degree that they are ordered to the common good, which is victory. To score is good because it contributes to the end to which all their actions aim, but if a player were to get carried away and begin performing dazzling tricks with the soccer ball, which then leads to the other team scoring a goal, his actions would be judged by his teammates as bad - albeit skilled. Were he to continue in that vein, he would eventually be benched, because his behavior is harmful to the team (and thus every player on the team, including himself). His actions lack order towards the good of the whole, perhaps as a result of having an inflated ego, a passion for praise, etc. He has the potential to be a great player, but does not achieve excellence because his actions on the field lack due order towards the good of the whole, that is, the common good.
Each one of us has a sense of a moral order which includes us (our own good), but which is also larger than us considered individually (it embraces the good of everyone). I know from within that I am a moral agent, and that I have a natural inclination towards the universal good that I can't do anything about (I necessarily will my own happiness), but I am aware that I have the freedom to make choices that establish me in a certain relationship with my ultimate end, this personal God, who is the origin of the order of creation. If I sense that He is personal, even confusedly and pre-consciously, then I sense He has a will and that the order of creation manifests His will, just as the order I behold in a work of art is an expression of the will of the artist.
Plants and animals are not moral agents. The movement of a plant is such that as long as it is watered and planted in the proper environment, it will mature and become what it is inclined to become by nature. So too is this the case with brute animals. Both plants and animals achieve their own good naturally. But human beings, on the other hand, have the ability to freely determine themselves towards their own fullness of being or in a way that arrests that maturation. A moral agent can choose to fulfill his nature or destroy it.
As a moral agent, I have the ability to think and make free choices, thus determining myself to be a certain kind of person, that is, shaping a moral identity for myself. This is what we mean by moral character. By my free choices, I determine myself to be a person of good character, or a person of deficient (evil) character. I am either the kind of person who freely chooses to love the moral good before the delectable good - which involves freely choosing to love your good and everyone else's (the common good), thus God's goodness expressed in the order of creation - , or I am the kind of person that loves my own private pleasure (the delectable good) over the moral good.
The human person detects within himself a law, a command or rational dictate, to which he feels called to obey, and it is a command to respect the order of creation in all things, in himself and in the social order. He knows from within that he respects that moral order by freely choosing to do what he understands to be good as such, as opposed to what is simply pleasurable for him.
For example, I know that you are of the same nature as myself (through simple apprehension), and I know from within that it is good for me to be alive (I desire to live). Now I desire to possess certain property for the sake of preserving my life, for example, I own a pair of shoes, a jacket, my own lunch box, etc. I know that you too possess property for the same reason, and that it is good for you to do so - in other words, it is "right" (Latin: jus) and ordered for you to do so, not disordered - property is ordered towards the preservation of life, which in turn is ordered towards knowledge, personal relationships, and other human goods, and finally the ultimate end (the bonum universale). The social order, which includes the economy and the order of justice, exists for our shared good (common good), and I know that I would not want you to take my shoes and lunch box just because you happen to like them (I need them), and so I know from within that I ought not to take yours (because I know that you are of the same nature as myself), even though possessing them would bring me some kind of emotional satisfaction.
If it is right and ordered for you to own them, it is wrong and disordered for me to take them simply because I like them. If my emotions are moving me to take your property when you are not looking, simply because I desire them, I now have a choice before me: to resist that temptation for the sake of an order larger than me, or give into it, thus choosing my own emotional satisfaction (pleasure) over the order of justice. In choosing the latter, I am choosing to treat myself preferentially. Although I know you to be equal in dignity to me, I am treating you in a way that fails to respect that equality, and thus that order. I am twisting that order, elevating my desire for emotional complacency above your right to own and share in the good. I am aware that I am violating a natural law, that is, a natural command or dictate of reason to respect an order that is larger than me.
Think of how a crook behaves when he is caught and confronted - he often reacts with violent indignation. And how does a criminal behave when he discovers he's the victim of a theft? Also with violent indignation; thus he is aware that theft is a violation of a right, but he is indifferent to the rights of others and incensed when confronted with the truth of his disordered character.
Just as a bad but skilled soccer player behaves without order towards the good of the whole, so too a morally bad person chooses without due regard for the good of the whole, that is, the entire moral order. In doing so, he goes against his deepest awareness of that order, that is, he violates his conscience. He is disordered within himself, for his emotions are not disposed to submit to the demands of reason, thus he is intemperate, and he lacks the fortitude to sacrifice his own love of the delectable good for the sake of the good of the whole. Moreover, he is an unjust person, for by his own will he is a disordered part of the social whole.
Now the human person naturally loves God more than he loves himself. I know, for example, that I am not the "universal good". I also naturally love the good of the whole more than the good of the part. For example, if someone comes towards me swinging a baseball bat, I naturally raise my arms to defend myself. I am placing a part of myself in harm's way in order to protect the whole, thus I naturally love the whole more than the part, for the whole is a greater good than the part, which is good on account of the whole. Similarly, I see that I am part of a larger social whole (not a mere part, to be sure), and I naturally love the social whole more than myself. All this is natural and inevitable; there is no moral nobility in this. But as a moral agent, I must now freely choose in accordance with that natural inclination. For me to choose my own private satisfaction over the good of the social whole (which reflects back on me for my well-being, as a team's victory is also the good of the individual player), that is, for me to choose to disobey my knowledge of the natural law, my awareness of the command to revere that order of creation, is for me to choose in a way that is contrary to my own natural inclination (my own good). In other words, immoral choices put me on a path to self-destruction. Furthermore, I never do experience the "pleasurable good" that I choose above the moral good, at least not in any lasting and significant way, because the delectable good and the moral good are not necessarily opposed; rather, the former (bonum delectabile) is the fruit of the latter (bonum honestum). Immoral choices only succeed in bringing fragments of the delectable good, temporary pieces that lack breadth and depth, which is why immoral choices lead to greater restlessness, not greater peace. An immoral person is his own worst enemy, not to mention an enemy of the civil community as a whole.
Consider that by virtue of the close relationship between the moral sense and the sense of God's existence, it is no coincidence that moral reasons are and have always been at the root of atheism. To violate that moral order of which my conscience makes me aware is to dampen that voice, to suppress that sense of a natural and personal command or dictate (natural law). To eradicate that sense completely is, I suspect, difficult to do, and even more difficult to dampen that sense consistently, which is why those of depraved character will expend a tremendous amount of energy trying to show that God does not exist and that to believe so is delusional and infantile. It is also no coincidence that atheists and agnostics who choose to obey the directives of that moral sense as it is made known to them in the deepest recesses of their conscience, very often come to a more explicit awareness of God's existence and become great converts.
All that we've unpacked and made explicit up to this point is known, more or less confusedly, vaguely, and pre-consciously, by every human person who has reached a certain level of reason. What is particularly disturbing, however, is the increasing number of people who choose every day to place their own pleasure (bonum delectabile) above the moral good (bonum honestum), in little acts of theft, lying, deception, cutting corners, insurance fraud, etc. In doing so, they not only place themselves on a path of self-destruction (personal dis-integration or dis-integrity), they also create disorder in the world, for their disordered actions have wide and costly social repercussions to which they are frankly indifferent. But they know this fundamental conflict within themselves, they are aware of it and are ashamed of it, they don't love it, which is why they spend a great deal of energy trying to hide it, for they know that others, persons of virtue in particular, would find them unsightly, as they find themselves unsightly.