One of the most salient passages in the Quran is 2:106, which shows us the basis for the doctrine of abrogation: "We do not abrogate a verse or cause it to be forgotten except when we bring forth one better than earlier verse or similar to it.  Do you not know that Allah is over all things competent?"

Abrogation has an impact on the arguments about the true nature of Islam.  At endless interfaith dialogues, the early tolerant verses are quoted to show the nature of Islam as peaceful.  When both verses are quoted and then abrogation is applied, we see that the later verse trumps the earlier tolerant one.  Jihad abrogates tolerance.  In general, the Medina Quran abrogates the Meccan Quran.  There are several verses of tolerance that are abrogated by jihad against Christians.

But the earlier verse is still acceptable and in use.  Abrogation does not negate the early verse.  Indeed, the earlier "peaceful" verse that is abrogated is the one most apt to be used in public discourse.

This creates a logical problem, since if two things contradict each other, at least one of them must be false.  This is a fundamental element of Western unitary logic.  In Quranic logic, two statements can contradict each other, and both are true.  This is dualistic logic.

To put it simply, Allah changes revelations as he pleases, and the latter revelations supersede the earlier ones.  There are deviations among Muslim theologians as to which verses have been abrogated and replaced, but the overall idea has been clear.  When Muslims are weak and in a minority position, they should behave peacefully according to the Meccan passages (which reflect the early time, when Muhammad was vulnerable and building his power base), and when strong, they are obligated to wage war according to the later Medina passages.

An alternative explanation is that the early verses are the first stage in a process, like a seed, and the later verses are a second stage, like a plant.

There is truth to this, but the process model does not take into account the fact that both truths are available at the same time.  To go back to the analogy, you don't have the seed and the plant at the same time.  The verses contradict each other.  This is dualistic logic.  The contradictions are usually explained by abrogation, the classical doctrine, but the principle of abrogation is limited to the Quran.  Duality includes the special case of abrogation and it explains how the entire doctrine of the Quran and Sunna work.

Another dualistic aspect of Islam is its ethics.  One of the chief features of Islam is the doctrine of the kefir.  It treats kefirs dreadfully.  No one would ever want to be treated as a kefir is treated in the Trilogy.  This leads us to the Golden Rule.  There is no Golden Rule in Islam because of the division of humanity into believer and kefir.  The Golden Rule is to treat all people as you would be treated.  Since no one wants be treated like a kefir, and the kefir is so central to Islamic doctrine, it proves that Islam has no Golden Rule.  Islam has one set of rules for Muslims and another set of rules for kefirs. This is dualistic ethics.

Practicing Tolerance

We are told it is only civil to respect or at least tolerate other peoples' beliefs, even if you do not agree with them – a sort of "live and let live" attitude.  As a general principle, this position is admirable.  Yet there are exceptions.  A case in point is when people say, "Let Muslims believe what they want."  I strongly disagree with letting Muslims believe what they want to believe when they hold that I, as a non-Muslim, have no right to live.  Or if I am to live, I must live a subservient life to that of Muslims.  Wherever they are in power in the world, Muslims do everything they can to make non-believers' lives dreadful and deadly.

I don't tolerate the belief and practices of Islam, in the same vein as I reject fascism and all other exclusionary oppressive systems of belief.

As they say, tolerating evil is not tolerance.  It is a crime.