Metaethics and AtheismOne of the most often heard critique of atheism is that any system of morality that is premised on it is necessarily arbitrary - which means that morality becomes a matter of personal preferences - leading to moral relativism. The point then is that Hitler can legitimately say he personally thinks it is okay to kill six million Jews and that would be the end of the matter. Furthermore, the question is normally asked: since the atheist says there is no God, why should one be moral? We will look at these two issues here.
Does this mean that morality and ethics are subjective and not objective? There are atheist philosophers who take positions on one or the other side of the subjective/objective divide. Michael Martin has written a book, Atheism, Morality and Meaning (2002), arguing the case for an objective morality without God, while J.L. Mackie argued for subjective morality (or "moral skepticism") in his book Ethics: Inventing Right and Wrong (1977). However I think that the disagreement between these two are purely semantics. [a]
It is first important to understand the meaning of the terms objective and subjective and how they are being used here.
The adjective objective is normally used in one of the two senses below: [b]
As an example we can find things which are "subjective" in the sense of having no ontological existence, yet is "objective" in the sense of being verifiable by others. Take any field of mathematics - say calculus. The concepts of calculus have no real existence outside of the logical system developed by humans. However calculus is objective in the sense that calculations performed can be checked and verified by others as either being "correct" or "wrong". Thus calculus is subjective in the sense of "S1" and objective in the sense of "O2".
Let me bring in another example which is a little closer to what we want to discuss; since it will involve an epigenetic rule: color perception. We have already discussed color perception in some detail elsewhere, but here we will use it again as an example.
When we look at a daisy, we perceive the color of its petals as "yellow". This perception is the result of the interaction of electromagnetic waves of a certain wavelength reflected from the surface of the petals with the cones cells in the retina of our eyes and its representation in our brain. Now color perception is objective in the "O2" sense that any other human being who does not have color impaired vision will be able to verify that the color is yellow. [c]
Yet we know that this color perception is subjective in the "S1" sense. Entomologists have long discovered that flowers, such as daisies have evolved petal pigmentation which leads insects towards their nectar - at the center of the flower. Thus a petal that would look like it has a single uniform color yellow to us actually has an inner portion that absorbs ultraviolet light. When photographed with an ultraviolet sensitive film, it can be seen that the inner portion of the flower petals are "dark", compared to the "light" outer side. We know that insects are able to perceive these color differences (which we cannot) because in experiments where the petals where reversed by scientists, the bee pollinator move towards the outside of the flower rather than towards the center where the nectar are. This shows that the bees are able to perceive differences in the colors of the petals that we could not. Thus when the same insect look at the same "yellow" daisy as we do, it will see the petals not as consisting of a single color, yellow, but as distinct two-color toned petals [with an inner portion which absorbs ultraviolet light and an outer portion that does not]. Thus the insect will "see" two different colors on the flowers when we only see one. 
Thus the color yellow has no objective existence ("O2") outside the interaction of reflecting surfaces, electromagnetic waves and percepting neurological systems.
Since we have shown elsewhere that our moral senses are based on epigenetic rules, the color perception is more than an unrelated analogy; it shows the biological implications very clearly.
That "yellow" has no ontological existence does not make it impossible for human beings to agree with each other what things have this color. Similarly, although our sense of morality does not transcend the human species it does transcend individual humans. Thus morality is objective in the sense that different human beings from different cultures, given all the facts and free from all dogmatic bias can normally come to an agreement as to what is "right" and what is "wrong". The fact that there are moral universals that extends through all human cultures is proof of the objective ("O2") nature of morality.
Of course no one is denying that there are some differences between various cultures as to what is moral and what is not. The strong Muslim revulsion for pork and the devout Hindu avoidance of beef showing some relative differences between cultures. And certainly moral values change over time within the same culture. However this does not lead us to "moral relativism" - the ideas that all moral values - across different cultures and across different times - are merely personal preferences with which no outsider has a right to criticize. As Michael Ruse noted, these differences are "secondary modified consequences of a shared primary moral imperative." In other words the specific conditions of the external and internal environment requires such a modification to the moral system. I quote an example from Ruse:
Thus when it comes to basic ethical principles - loving your family, not cheating on friends, not causing unhappiness unnecessarily etc - humans have a shared moral sense. We have this shared moral sense because we share the same (more or less) genes and the same evolutionary history. In what culture do we find it acceptable to neglect a friend for no reason? In what society do we find gratuitous torture of children as a moral norm? In what stage of our history do we find lying and cheating being the over-riding call to virtue? In which normal human being do we not find guilt or shame as the accompanying emotion for having done a wrong? Do we know of any non mentally disturbed people who do not feel a sense of pride or righteousness in doing what is right? 
Thus the charge that an ethical system that is not objective (in the "O1" sense) leads to moral relativism is pure nonsense.
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 As Micheal Ruse noted:
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