Missing Verses (Part 1): What "Divine Wisdom" Justified Removing the Stoning Verse from the Quran?

Allah does not appear before us in person. His angels do not show up either. No miracle is shown to us today. Yet we are expected to recognize Allah by observing His commandments.

But when we actually look at those commandments, instead of any "divine wisdom," what starts becoming visible is a distinctly "human fingerprint."

Let us examine the verse of stoning (rajm) from this angle.

What is the Core Problem with the Stoning Verse?

• According to Muslim scholars, a verse prescribing the punishment of stoning (rajm) for married adulterers was revealed in the Quran.
• But that verse does not exist in the Quran today. Critics therefore present this as evidence of the "corruption of the Quran" (tahrif).
• Muslim apologists respond to this by claiming: "It is part of Allah's system that He may preserve the ruling of a verse while abolishing its recitation from the Quran."
• Non-Muslim critics counter that this principle — that a ruling can remain in force while the actual verse is removed — is not stated anywhere in the Quran or hadith. They argue it is a later excuse invented by Muslim generations to shield the Quran from accusations of corruption.

When Muslim scholars are asked what "divine wisdom" could possibly justify keeping a ruling in force while removing its verse from the Quran, no convincing divine wisdom is ever offered.

Instead, the discussion is typically ended with a new deflection:

"You atheists are incapable of understanding divine wisdom with your limited human minds, which is why Allah did not explain to you the wisdom behind keeping the ruling of the stoning verse while removing the verse itself from the Quran."

This argument carries no weight that would justify continuing the debate with them.

So let us leave the scholars to themselves and move forward to examine the "human fingerprint" visible in this case.

Table of Contents

Islamic Law of Fornication: Divine Perfection or Human "Trial and Error"?

For a being that is "All-Knowing and All-Aware," whose knowledge encompasses every corner of the past, present and future, it would not even be a minor challenge to reveal a law or command that is complete, clear and permanent from the very first attempt.

An ordinary human, by contrast, simply does not have the capacity to craft a perfectly complete law on the first try. Because of limited intellect, changing circumstances and short-sighted foresight, a human being always travels an evolutionary path. Along this journey he stumbles, experiments and gradually tries to fix the flaws in things by learning from his mistakes over time.

When we take a historical look at the Islamic law of fornication, it does not appear at all like a perfect divine law delivered in one complete package. Instead it visibly passes through a long journey of evolutionary stages, amendments and abrogations — a journey that is purely a reflection of human behavior.

This entire structure provides evidence that no all-knowing God sitting in the heavens was revealing these commands. Rather, the Prophet Muhammad was himself arranging these laws in response to the shifting political, social and domestic circumstances of Medina. And since he was only a human being with the limited reach and understanding of a human being, he was working under the natural law of "Trial and Error." He would first make a law, and then when its flaws emerged in real life, he would revoke the previous command and patch the deficiencies in his human rulings with a new one.

Let us examine the first stage of this evolutionary journey from the pages of history — a stage that fully exposes the "human hand" hidden behind this so-called "divine law."

Stage One: A Vague and Unclear Command of Lifelong Imprisonment and Physical Punishment

The evolutionary journey of the law of fornication begins with this initial and temporary command found in Surah An-Nisa (verses 15-16):

Verse 15: "Those of your women who commit indecency... confine them to their homes until death takes them or until Allah opens a way for them (in the future)."
Verse 16: "And those two among you who commit it, punish them both..."

If we accept for a moment the Muslim belief that Allah is "All-Knowing of the Unseen" and that He knew from day one that He would eventually establish laws such as "a hundred lashes" or "stoning" (rajm) as the final punishment for fornication, then why was there any need to say something as intensely vague and uncertain as "or until Allah opens another way for them" in that very first stage? Was the All-Wise, All-Powerful God of the universe so helpless that He could not establish a clear and final law from the very beginning?

This initial divine confusion plainly reveals that the lawmaker (meaning the Prophet Muhammad) did not himself know at that point what permanent solution to establish for this crime in the future. He was, like an ordinary human being, "searching for a path" as time went by and deciding on a course of action by observing unfolding circumstances. This is not a specimen of divine foresight, but it was the initial attempt of an ordinary human lawmaker who was looking for temporary solutions before arriving at a final decision.

Stage Two: A General Command of a Hundred Lashes and Persistent Ambiguity

As time passed and it became apparent that the temporary method of confinement and physical punishment was not effective, the first command was abrogated and a new law took its place in Surah An-Nur (verse 2):

Verse 2: "The fornicatress and the fornicator, flog each of them with a hundred lashes..."

According to this Quranic verse, this law applies to every type of fornicator without distinction, whether married or unmarried.

The question is, if Allah's ultimate destination was the law of "stoning" (rajm) for married adulterers, why was He unable to state this distinction clearly in this very clear and explicit verse?

If the author of divine scripture had wanted Muslims to stone the married offender and flog the unmarried one, why could He not simply write in clear and plain language in this very verse of Surah An-Nur: "Stone the married adulterer and give a hundred lashes to the unmarried one"? Was writing one sentence really that difficult for the Creator of the universe? Was there some "heavenly obstacle" preventing God from writing this truth in His own book?

In a matter involving the ending of a human life, a law being this vague, incomplete and generic cannot reflect any divine wisdom or heavenly insight. It plainly mirrors a temporary human decision made under the pressure of the moment, a decision that later had to be completely revised to handle the contradictions and new ground realities that emerged.

Stage Three: The Command to Stone Married Persons (The "Revelation" of the Stoning Verse)

This evolutionary journey does not stop here. After establishing the general Quranic law of a hundred lashes, the lawmaker (Muhammad) apparently felt that this punishment was insufficient for married persons. So a new decision was made, and now a command for stoning (rajm) married adulterers was introduced in the form of a separate Quranic verse:

Sunan Ibn Majah, 2553 and Sahih Bukhari, Hadith 6830:

`Umar bin Khattab said: “I fear that after a long time has passed, some will say: 'I do not find (the sentence of) stoning in the Book of Allah (ﷺ),' and they will go astray by abandoning one of the obligations enjoined by Allah (SWT). Rather stoning is a must if a man is married (or previously married) and proof is established, or if pregnancy results or if he admits it. I have read it (in the Quran). “And if an old man and an old woman commit adultery, stone them both.” The Messenger of Allah (ﷺ) stoned (adulterers) and we stoned (them) after him.' ”  
Grade: Sahih

The Jewish Background of Stoning: Heavenly Revelation or Imitation of the Law of Moses?

We now move to the most important part of this article, one that usually remains completely hidden from the human eye in traditional debates. Yet reflecting on these possible historical and earthly factors can provide us the most important help in understanding this entire puzzle.

At this stage, one question has remained unanswered, i.e. what was the urgent "reason" that compelled the Prophet Muhammad to set aside the two previous Quranic commands (lifelong imprisonment and the general hundred lashes) and then introduce a completely new command of "stoning" through a third verse?

The answer to this question does not lie in any transcendent "divine wisdom." The answer is hidden in the earthly circumstances, political pressures and human factors that Muhammad was facing in the state of Medina.

When Muhammad migrated from Mecca to Medina, Jews were already living there who practiced the Law of Moses (Torah).

And in the Torah, the commandments regarding the punishment for adultery had been completely clear, unambiguous and fully definitive from the very first day. For example:

Leviticus 20:10: "If a man commits adultery with another man's wife... both the adulterer and the adulteress are to be put to death."
Deuteronomy 22:22: "If a man is found sleeping with another man's wife, both the man who slept with her and the woman must die."

The Prophet Muhammad was not literate and was also unaware of the commandments of the Torah. This is why he had first established the "human law" of imprisonment and then a hundred lashes in the Quran.

But then later an incident occurred that brought the Torah's hidden command to light before Muhammad:

Sahih Bukhari, Hadith 6841:

The jews came to Allah's Messenger (ﷺ) and mentioned to him that a man and a lady among them had committed illegal sexual intercourse. Allah's Messenger (ﷺ) said to them, "What do you find in the Torah regarding the Rajam?" They replied, "We only disgrace and flog them with stripes." `Abdullah bin Salam said to them, 'You have told a lie the penalty of Rajam is in the Torah.' They brought the Torah and opened it. One of them put his hand over the verse of the Rajam and read what was before and after it. `Abdullah bin Salam said to him, "Lift up your hand." Where he lifted it there appeared the verse of the Rajam. So they said, "O Muhammad! He has said the truth, the verse of the Rajam is in it (Torah)." Then Allah's Messenger (ﷺ) ordered that the two persons (guilty of illegal sexual intercourse) be stoned to death

On the surface this appeared to be an intellectual victory for Muslims over the Jews, but this incident created a very large intellectual and political contradiction for Muhammad's own claim and raised the question:

"If the God of Muslims and the God of the Jews (Yahweh) are the same being, and Muhammad claims to be a continuation of the same Abrahamic chain, then why has the law of death (stoning) for married adulterers been crystal clear in the Law of Moses from day one, while Muhammad's law is still tangled in the incomplete commands of flogging? Has God forgotten His own laws over time?"

This was the point at which Muhammad had no choice left but to claim the revelation of a "third verse" (the verse of rajm) in order to prove the Abrahamic continuity of his prophethood and to show his law as aligned with and equivalent to the Mosaic law.

Therefore, this sudden and contradictory decision regarding stoning was not any divine or heavenly necessity. It was a purely human, political and religious effort to restore confidence in his own law against the backdrop of the Law of Moses in the environment of Medina and to resolve that contradiction.

Stage Four: The Verse Removed from the Quran (Abrogation of Recitation While the Ruling Remains)

But the story does not end here. The problem is that this verse commanding stoning does not exist in the Quran today.

What a surprise.

Muslim scholars answer this problem by saying that this verse was removed from the Quran (naskh al-tilawa), but its ruling (stoning) was kept in force.

Upon hearing this answer from Muslim scholars, your human reason will immediately and involuntarily cry out that this statement goes against logic.

This fourth stage brings forward the most dangerous question of all, one that demolishes the very idea of any "wise God."

Observe the cruel irony of "divine wisdom": Allah kept in the Quran forever the verse that was not to be acted upon (the hundred lashes verse), yet Allah removed from the Quran the very verse that was supposed to be acted upon until the Day of Judgment (the verse about married adulterers).

Is this "divine wisdom" or "divine hide-and-seek"?

Stage Five: Even the Stoning Ruling Changed and a New "Compound Punishment" Emerges

This spectacle of legal evolution does not stop even upon reaching stoning. The story moves one step further. In this fifth stage, Muhammad changes even the standalone command of stoning present in that verse and introduces a new procedure. According to this new procedure, a married adulterer is not only to be stoned but must first be flogged as well:

Sahih Muslim, Hadith 1690a:

(The Messenger of Allah said): "And if a married man commits adultery with a married woman, their punishment is a hundred lashes and then stoning (rajm)."

This compound punishment is also confirmed by the conduct of the fourth Caliph Ali ibn Abi Talib:

Musnad Ahmad ibn Hanbal, 716:

When Ali (may Allah be pleased with him) stoned a woman of Kufa, he flogged her on Thursday and stoned her on Friday, and said: "I flogged her according to the Book of Allah (the Quran) and stoned her according to the Sunnah of Allah's Prophet ﷺ."
Ruling: Authentic (link)

Here a question mark is raised once again over "divine wisdom." If the "All-Knowing and All-Aware" God of the universe had already settled in the third stage that the final punishment is stoning, why did He not reveal the complete law (100 lashes plus stoning) all at once at that very moment? What was the need to pass through the maze of a fourth and fifth stage?

Religious apologists at this point offer the usual excuse: "Allah did so according to the principle of gradualism and so as not to burden human beings, because having both punishments revealed at once would have been mentally too harsh for the companions."

But this excuse proves completely hollow on the scales of logic, because:

• When the command had already been given to stone a person to death by pelting them with rocks (rajm), which is in itself the most terrifying and exemplary death in the world, then adding 100 lashes before this horrific death was not such a great shock that it would have been impossible for the companions to bear.

• When the fate of the criminal was "death" in both scenarios anyway, what significance would the punishment of lashes hold in the face of that inevitable death? Can any sane mind accept that the companions who immediately agreed to stone one of their own to death with rocks would rebel against Allah over the command to merely administer 100 lashes before the stoning?

Presenting any excuse of "gradualism" or "consideration for human psychology" here is tantamount to burying reason itself. The reality is simply this that it was not heavenly planning. It was a flawed and inconsistent human approach where the lawmaker was repeatedly getting entangled in his own decisions and patching the flaws and contradictions of previous decisions with new commands.

The Possible "Human Factors" Behind the Change in the Stoning Penalty in Stage Five, in the Light of History

Looking at history, it appears that on one hand Muhammad wanted to align Islamic law with the Law of Moses, but on the other hand, out of hostility toward Jews, he also wanted to "oppose" them.

This pattern of opposition appears in multiple places, for example:

1. The Fast of the Tenth of Muharram (Ashura):
After arriving in Medina, Muhammad first gave the command to fast on the tenth of Muharram in order to align with the Law of Moses (Sahih Bukhari, Hadith 2004). But then later in 9 AH (one year before his death), while commanding opposition to Jews out of enmity, he said: "Observe the fast of Ashura and oppose the Jews in it by fasting either one day before it or one day after it too." (Sahih Muslim, 1134 and Musnad Ahmad, 1/241)

2. Trimming the Moustache:
Muhammad commanded: "Oppose the polytheists by letting beards grow and trim the moustaches." (Sahih Bukhari, Hadith 5892)

3. Dyeing the Hair:
Jews and Christians did not like dyeing their white hair (or did not dye it for religious reasons). In Sahih Bukhari (5899) it is narrated that the Prophet ﷺ said: "Jews and Christians do not dye their hair so you should do the opposite of what they do." The purpose of opposition here was clearly to create a difference in outward appearance.

4. Praying with Shoes On:
Jews would remove their shoes before entering their places of worship (just as Moses was commanded in the sacred valley). In Sunan Abi Dawud (652) it is narrated: "The Messenger of Allah (ﷺ) said: Act differently from the Jews, for they do not pray in their sandals or their shoes." (Meaning that praying with shoes on, as long as they are clean, was designated as a way of opposing the Jews.)

In the case of stoning, the same pattern is visible. First, to align with the Law of Moses, Muhammad claims the revelation of the stoning verse. But later, when opposing the Jews comes to mind, he removes the stoning verse from the Quran and issues a new command, i.e., flog a hundred times first and then stone.

But this approach is not the reflection of any perfect divine procedure, one that should have included the hundred lashes penalty from the very first stage (or at minimum alongside the stoning command in the third stage). Rather it is a "non-perfect" human approach where commands are flawed in the first stage and deficiencies are corrected step by step.

PS (Postscript):

The incident of the fast of the tenth of Muharram is an excellent example for understanding this "human behaviour." From the first year AH right through to 9 AH after arriving in Medina, for eight or nine continuous years, Muhammad observed only the fast of the tenth of Muharram, and throughout this long period the principle of opposing the Jews never occurred to him at all (even though he had already used the principle of opposing Jews in several other matters on multiple occasions before this).

But then after nine years, when the contradiction of this fast matching Jewish practice was suddenly raised by people around him, Muhammad hastily changed the command in the very last year of his life (9 AH) and issued an order to fast two days instead of one. This nine-year delay, and then the reaction upon realizing the mistake, is a reflection of purely human behaviour.

If the maker of the law had truly been an all-knowing God of the universe, He would not have needed to wait until 9 AH to turn His attention to this issue. At the very time He gave the general principle of opposing Jews, He would have changed the law about the tenth of Muharram fast from day one as well.

This incident is a clear proof that all of this was a human process of "trial and error", and not any "divine wisdom."

What "Divine Wisdom" Is It to Create Confusion in the Community by Revealing Legal Commands in Such a Flawed Manner?

Hudud cases hold the status of the most serious punishments in Islam. Yet even in the punishment for fornication, one of the most important of these punishments, the community is gripped by confusion, and this confusion has been going on for the past fourteen centuries:

• Hanafis and Malikis say: the punishment for a married adulterer is stoning alone.

• Shafi'is and Hanbalis say: the punishment for a married adulterer is first a hundred lashes and then stoning afterward.

• And then there are the Quranists today who say: the punishment for a married adulterer according to the Quran is only a hundred lashes.

What "divine wisdom" is there in creating this confusion in the community on such an important matter?

And when Muslim scholars have no satisfying answer to this, the excuse of the "divine wisdom" that created all this confusion is offered: اختلاف الأمة رحمة i.e., "Disagreement within the community is a mercy."

In fact, because of this "divine wisdom," this disagreement was not only among Muslim sects later on, but it existed right from the beginning among the companions themselves.

For example, there was disagreement between Umar ibn al-Khattab and Ali ibn Abi Talib on the punishment for a married adulterer, and this disagreement was on two points.

The first disagreement was that Umar ibn al-Khattab's entire emphasis was on stoning being part of the "Book of Allah" (even if its recitation was later abrogated). His actions and his sermons show that he believed the punishment for married persons was stoning alone. In the stoning cases that took place during his era (such as the case of Ma'iz al-Aslami), there is no mention of any flogging before stoning.

Ali ibn Abi Talib, by contrast, believed in the compound punishment of first a hundred lashes and then stoning afterward.

The second disagreement between them was that Umar ibn al-Khattab accepted the punishment of stoning because of a Quranic verse, one that was subsequently removed from the Quran while its ruling of stoning was kept in force.

Ali, unlike Umar, did not consider stoning a Quranic verse at all. He regarded it solely as "the Prophet's Sunnah." Look again closely at the narration regarding Ali:

Musnad Ahmad ibn Hanbal, 716:

When Ali (may Allah be pleased with him) stoned a woman of Kufa, he flogged her on Thursday and stoned her on Friday, and said: "I flogged her according to the Book of Allah (the Quran) and stoned her according to the Sunnah of Allah's Prophet ﷺ."
Ruling: Authentic (link)

This means Ali did not consider the hundred-lashes verse (24:2) revealed in the second stage to be abrogated, whereas Umar ibn al-Khattab considered it abrogated.

And according to Ali, no verse of stoning was ever revealed, but the Prophet established stoning through his Sunnah alone. Umar ibn al-Khattab, on the other hand, believed in the revelation of the stoning verse.

In all this confusion, what glimpse of any "divine wisdom" can be seen?

"Abrogation Upon Abrogation Upon Abrogation Upon Abrogation" (Four Abrogations): "Divine Wisdom" or Simply Pointless Logic?

Reflect calmly on this entire chain. In the single matter of stoning, we find not just one, but four instances of "abrogation."

A command came, then it was changed, then it was changed again, then it was changed one more time.

1. First abrogation: The command of imprisonment (4:15) was abrogated and replaced with 100 lashes (24:2).

2. Second abrogation: The 100 lashes (for married persons) were abrogated and replaced with "stoning."

3. Third abrogation: The "recitation" of the stoning verse was abrogated (removed from the Quran), but its ruling was kept in force.

4. Fourth abrogation: Then even the ruling of that standalone stoning verse was abrogated, and a new command, "first 100 lashes and then stoning", was put in its place.

When a human being makes a law, he engages in trial and error. He first makes a weak law and then improves it. This is a sign of human limitation.

A divine God, however, possesses absolute knowledge. He knows everything, past, present and future. So if Allah has absolute knowledge, why did He need to engage in this "trial and error"? Could He not have revealed the "final" and "perfect" law from the very start? This is not the work of an "All-Knowing of the Unseen." This is the work of a lawmaker who himself does not know what is going to happen next and is gradually removing deficiencies from his commands in accordance with time and circumstances.

Has the Purpose of Our Lives Been Reduced to Getting Stuck in These Pointless Debates?

The entire community, from the companions up to today, has been embroiled in these debates about abrogation and counter-abrogation. And all probability points to this chain continuing in the same way going forward till Qiyammah.

Think about it: Has the purpose of our lives been reduced to merely wasting centuries going round and round these pointless and contradictory debates? Should the purpose of humanity have been the pursuit of knowledge and art, the conquest of the universe and the welfare of one another, or is it to dust off these decaying pages whose hidden contradictions are themselves crying out as testimony to their "human" origin?

Think about it: If even the guidance of a perfect God leaves human beings confused for 1400 years, then in what sense is that guidance perfect?

Think about it: Is this the "heavenly guidance" that came to unite us, or is this the "human fingerprint" that has divided the community into sects, factions and endless quarrels?

Think about it: When God Himself keeps changing His own commands, by what right do those who question the mistakes of human beings pick up stones?

Please also read part 2 of this series:

• Missing Verses (Part 2): What "Divine Wisdom" Justified Removing the Five Breastfeedings Verse from the Quran?