By just looking at some peaceful verses by directly reading from Koran or cited and shown by proponents of Islamic tolerance to show that no where does Koran commands Muslims to fight or kill non Muslims because they refuse to become Muslims, these non Muslim readers will probably be inclined to apply conservative or accepted methods of logic.
(One can also watch the following video for understanding Rule of Abrogation)
These people are tempted to take presence of these peaceful verses at face value wrongly thinking that just because they are present in Koran their rulings must be applicable and valid today. Much worse is they go on to believe extremists and terrorists are misinterpreting Koran. But the truth is it is these people not terrorists and extremists who are misinterpreting Koran, out of ignorance or lack complete knowledge. Because mere presence of a verse in Koran does not mean that verse or ruling of that verse is applicable or valid. Why? Because of rule of abrogation.
Understanding application of rule of abrogation in holy Koran is central and critical to understanding Islam because Koran is the foundation of Islam. This rule of abrogation is unique to Koran among the existing various religious scriptures. The concept of "abrogation" in the Koran is that Allah chose to reveal a verse that supersedes or erases ruling of earlier verse (or verses) in the same Koran.
When you read Bible or Torah you read it in chronological order and you will also see that context is available for each verse. In Koran it is not like this. It is neither in chronological order nor provides any context for any verse. I already wrote that Suras (Chapters) are not in chronological order, in fact verses in a Sura (Chapter) are also not in chronological order. But as such knowing the chronological order of verses in a Sura is not that important compared to knowing the chronological order of Suras.
Literally abrogation means that, suppose verses ‘a’ and ‘b’ contradict each other or give two different or opposing meanings or rulings then verse among these two which comes later replaces the other one, i.e. suppose verse ‘a’ was reveled in the year 628 AD and verse ‘b’ was reveled in the year 619 AD, then by this rule of abrogation ruling of verse ‘a’ supersedes ruling of verse ‘b’, just by virtue that ‘a’ was reveled later.
That verse ‘b’ will be there in Koran but still it is not applicable, its message or ruling is annulled by message of ‘a’. Here ‘a’ is called abrogator and ‘b’ is called abrogated.
Now let’s dwell more in to this concept of abrogation in the sense that where and how it is mentioned in Koran. The verses mentioning abrogation are 17:86, 13:39, 16:101 and 2:106. And we just look at the verse 2:106 and understand it. Below I pasted this verse from four different translations of Koran.
YUSUFALI: None of Our revelations do we abrogate or cause to be forgotten, but we substitute something better or similar. Knowest thou not that Allah Hath power over all things?
PICKTHAL: Nothing of our revelation (even a single verse) do we abrogate or cause be forgotten, but we bring (in place) one better or the like thereof. Knowest thou not that Allah is Able to do all things?
SHAKIR: Whatever communications we abrogate or cause to be forgotten, we bring one better than it or like it. Do you not know that Allah has power over all things?
Al-Hilali: Whatever a Verse (revelation) do we abrogate or cause to be forgotten, we bring a better one or similar to it. Know you not that Allah is able to do all things?
[Note: All the verses I quote here or any where in this blog from now on will be from translations by Yusuf Ali, Shakir and Pickthall and Al- Hilali. I already gave the links to above translations. Another thing is they were all Muslims.]
If you read carefully two or three times, you will notice the differences between various translations. To understand much better, I suggest you to read the tasfir (exegesis) of Ibn Kathir, a very famous one and respected by all Islamic scholars, regarding this verse 2:106.
Now coming to this verse 2:106, the second part of first statement in all the translations indicates later verses are better. It is only in the first part, translations differ by giving different meanings.
Ali and Pickthall use ‘none of our’ and ‘nothing of our’ while Shakir and Hilali use the word ‘whatever’ as a starting word or a phrase in the verse. But if we observe carefully, Ali and Pickthall contradict them selves because they use the words ‘substitute’ and ‘in place’ in the second part. But logic and convention says that substitution automatically erases or cancels or replaces the original one. This practice of twisting is seen in many verses in translations by Ali and Pickthall.
The verse 2:106 above is clearly making the claim that only when a better verse or similar is available, does Allah change it and cause the older ones to be forgotten. And to drive the point home, the verse continues on that Allah has power over all things. In essence abrogated verse will still be present in Koran but its ruling is invalid.
Now just look at some more verses on this abrogation.
Al-Hilali: Allah blots out what He wills and confirms (what He wills). And with Him is the Mother of the Book (Al-Lauh Al-Mahfûz)
Al-Hilali: And when we change a Verse [of the Qur’an, i.e. cancel (abrogate) its order] in place of another, and Allah knows the best of what He sends down, they (the disbelievers) say: "You (O Muhammad SAW) are but a Muftari (forger, liar)". Nay, but most of them know not.
Yusuf Ali: When we substitute one revelation for another and Allah knows best what He reveals (in stages), they say, "Thou art but a forger": but most of them understand not.
Now it is clear that when the rulings of two verses in Koran contradict each other, concept of abrogation says the later (in the sense of time) ruling is the better one and replaces or cancels the ruling of earlier verse.
What do Muslims say about this concept of abrogation? There are differences among the present day Muslims, for a good reason, but most scholars say abrogation occurs in Koran. More importantly all classical Muslim scholars agree upon abrogation and go on to deride those who read Koran without understanding abrogation. But there are differences among Scholars, both classical and modern, over which are the verses abrogated and which are the abrogators.
I suggest you to read the following article on abrogation.
This is what renowned Islamic scholar Arthur Jeffery wrote on abrogation in his book "Islam: Muhammad and His Religion", page 66, "The Qur’an is unique among sacred scriptures in teaching a doctrine of abrogation according to which later pronouncements of the Prophet abrogate, i.e.: declare null and void, his earlier pronouncements. The importance of knowing which verses abrogate others has given rise to the Qur’anic science known as "Nasikh wa Mansukh", i.e.: "the Abrogators and the Abrogated".
The Encyclopedia of Islam, states on abrogation:
“Rather than attempting to explain away the inconsistencies in passages giving regulations for the Muslim community, Koran scholars and jurists came to acknowledge the differences, while arguing that the latest verse on any subject "abrogated" all earlier verses that contradicted it. A classic example involves the Koranic teaching or regulation on drinking wine, where V, 90, which has a strong statement against the practice, came to be interpreted as a prohibition, abrogating II, 219, and IV, 43, which appear to allow it.”
Sayyid Qutb, Islamic revolutionary, a member of Muslim Brotherhood, Egypt, some commentators call him the father of modern day Jihad, maintains that “partial amendment of rulings in response to changing circumstances during the lifetime of the Prophet Muhammad could only be in the interest of mankind as a whole.” He was the author of the book “milestones”. We see more on abrogation in the second part.