Noah's Ark- is the Qur'an more believable than the Bible?

Many Muslims, including such dubious luminaries as Maurice Bucaille and Zakir Naik, claim that the story of Noah and the Flood as related in the Qur'an does not contradict common sense or archaeological evidence as does the Flood story in the Bible. The main reason for this it seems is that the Flood as described in the Qur'an was not the global catastrophe that all Christians have been brought up to believe, but a much more credible LOCAL affair. They thus dismiss the Biblical flood narrative as childishly naive, scoffing (see later for more on "scoffing") at the idea of Noah having to load his Ark with every animal and of a world-wide inundation.

Here is an excerpt from Zakir Naik's book on the subject:

The Biblical description of the flood in Genesis chapter 6, 7 and 8 indicates that the deluge was universal and it destroyed every living thing on earth, except those present with Noah (pbuh) in the ark. The description suggests that the event took place 1656 years after the creation of Adam (pbuh) or 292 years before the birth of Abraham, at a time when Noah (pbuh) was 600 years old. Thus the flood may have occurred in the 21st or 22nd Century B.C.This story of the flood, as given in the Bible, contradicts scientific evidence from archaelogical sources which indicate that the eleventh dynasty in Egypt and the third dynasty in Babylonia were in existence without any break in civilisation and in a manner totally unaffected by any major calamity which may have occurred in the 21st century B.C. This contradicts the Biblical story that the whole world had been immersed in the flood water. In contrast to this, the Qur’anic presentation of the story of Noah and the flood does not conflict with scientific evidence or archaeological data; firstly, the Qur’an does not indicate any specific date or year of the occurance of that event, and secondly, according to the Qur’an the flood was not a universal phenomenon which destroyed complete life on earth. In fact the Qur’an specifically mentions that the flood was a localised event only involving the people of Noah.It is illogical to assume that Prophet Muhummad (pbuh) had borrowed the story of the flood from the Bible and corrected the mistakes before mentioning it in the Qur’an. 

This all seems very credible until we read the Qur'anic version more closely. For if experience has taught us anything, it's to take with a giant ladle of salt anything Muslim miracle seekers tell us.

So what about 71:26-27 which plainly states that NO-ONE, NOT A SINGLE PERSON will be left alive on Earth?
71:26 And Noah, said: "O my Lord! Leave not of the Unbelievers, a single one on earth!
71:27 "For, if Thou dost leave (any of) them, they will but mislead Thy devotees, and they will breed none but wicked ungrateful ones.
That doesn't sound like a LOCAL flood to me.

Or how about 11:40-42 which says that the waters gushed over the face of the Earth and talks of the waves being the size of mountains and requires Noah's Ark to act as a depository for breeding pairs of EACH animal? LOCAL flood? Hmm...
11:40  [And so it went on] till, when Our judgment came to pass, and waters gushed forth in torrents over the face of the earth, We said [unto noah]: "Place on board of this [ark] one pair of each [kind of animal] of either sex,  as well as thy family -except those on whom [Our] sentence has already been passed  -and all [others] who have attained to faith!"-for, only a few [of noah's people] shared his faith.
11:42  And it moved on with them into waves that were like mountains. At that [moment] noah cried out to a son of his, who had kept himself aloof [from the others]: "O my dear son!  Embark with us, and remain not with those who deny the truth!" 

So, just to re-cap: we have
1. Noah asking God to drown ALL the non-believers so that NOT A SINGLE ONE is left on Earth so they can't breed again (a pretty big ask for a LOCAL flood!).
2. We also see Noah being told (just like in the Bible) to load breeding pairs of ALL animals onto the ark (to what purpose if this is a local flood? Wouldn't it be easier simply to restock from an area unaffected by the LOCAL flood? You'd also avoid the inherent risk of having future animal stock forever cursed with genetic problems from the inbreeding necessarily required when you restock from just one breeding pair.)
3. And we have waves the SIZE OF MOUNTAINS.
4. And we have the waters covering the FACE OF THE EARTH.

And we're asked to believe that this story is MORE believable than the errant nonsense in the Bible?

Come on Muslims! Challenge the patronising jerks who feed you this nonsense! Ask your immams to explain.

And if they can't, then ask yourself why. Why might a supposed holy book contain a story so full of holes an intelligent six year-old can see the logical flaws- "Er, Daddy - how big did you say the ark was? And Noah had ALL the animals in his boat....? For HOW long...?"

I'm not for one moment suggesting that a disastrous flood (or two) didn't happen at some stage in our pre-history. Why should there otherwise be so many FLOOD MYTHS. Look at the Gilgamesh flood story, for example. In fact it might be enlightening for any reader who believes the story of Noah to be original and hence divine to google it right now. Go on - I dare you! You'll find disturbing echos of the Biblical/Qur'anic story right down to birds being sent out to test if the waters had receded.

Note: i. Since the Flood and the building of the Ark, we are apparently supposed to regard all ships and boats as signs from God. Did you know that?
54:15  And, indeed, We have caused such [floating vessels] to remain forever a sign [of Our grace unto man]:  who, then, is willing to take it to heart? 
         ii. It's interesting to see how much "scoffing" went on at the time. Look at this, for example:
11:38 And  set himself to building the ark; and every time the great ones of his people passed by him, they scoffed at him. He said: "If you are scoffing at us-behold, we are scoffing at you , just as you are scoffing at us. 
and then remember how the style of the Qur'an is supposed to be utterly inimitable and perfect. So perfect and inimitable, in fact, that no-one can write a verse like it. Hmm.... (Sorry - doing a bit of scoffing here myself, I've just realised.)

Muslims, you are allowed to drink!

Keen students of the Qur'an will know of the theory of abrogation - when Allah sends down a verse which seemingly contradicts a previous one Muslims must follow the doctrine that the latter verse supersedes the older verse. This docrine is explained in the Qur'an itself:
"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?" 16:101
Abrogation is important when one is trying to understand the reasons behind the strict Islamic ruling which states that Muslims are not allowed to drink. For it seems that the Qur'an is not as clear on this matter as we have been led to believe.

So where in the Qur'an does it state that alcohol is haraam or forbidden? Here is a reply on a QA site written by Muslims to the question: Why is alcohol forbidden in Islam?

Intoxicants were forbidden in the Qur'an through several separate verses revealed at different times over a period of years. At first, it was forbidden for Muslims to attend to prayers while intoxicated (4:43). Then a later verse was revealed which said that alcohol contains some good and some evil, but the evil is greater than the good (2:219). This was the next step in turning people away from consumption of it. Finally, "intoxicants and games of chance" were called "abominations of Satan's handiwork," intended to turn people away from God and forget about prayer, and Muslims were ordered to abstain (5:90-91). (Note - the Qur'an is not arranged chronologically, so later verses of the book were not necessarily revealed after earlier verses.)

This seems to be a full and reasonable answer and I'm sure many Muslims reading this would be reassured. Nonetheless, those who know their Qur'an well will immediately realise that an important verse has been omitted from the seemingly authoritative explanation.
Surah 16 (Nahl) has many verses describing the beneficence of Allah which enumerate what He has provided for us.
From water:
Allah sendeth down water from the sky and therewith revives the earth after her death! Lo! herein is indeed a portent for a folk who hear. 16:65
..to milk:
And lo! in the cattle there is a lesson for you. We give you to drink of that which is in their bellies, from betwixt the refuse and the blood, pure milk palatable to the drinkers. 16:66
and honey:
And thy Lord inspired the bee, saying: Choose thou habitations in the hills and in the trees and in that which they thatch;
Then eat of all fruits, and follow the ways of thy Lord, made smooth (for thee). There cometh forth from their bellies a drink diverse of hues, wherein is healing for mankind. Lo! herein is indeed a portent for people who reflect. 16: 68-69

...and in the very middle of this list of the wonderful things which Allah has provided for us comes...ALCOHOL:
And of the fruits of the date palm, and grapes, whence ye derive strong drink and (also) good nourishment. Lo! therein, is indeed a sign for people who have sense.

Isn't it strange how the good people at about.islam.com neglected to mention this verse? Perhaps it was an oversight and other Islamic sites do better. Here's another one which mentions the many verses which tell Muslims how angry Allah will be if they drink or gamble but signally fails to give their readers the full picture.
Why is this do you think?

Might it be that the doctrine of abrogation begins to look a little desperate when the verses stand in such blatant contradiction to each other? How can Allah on the one hand say alcohol is a gift to humanity in the same way as water, milk and honey are, and then later perform a complete volt-face so that it is utterly forbidden. Are the keepers of the mysteries of Islam worried that if they allow the full picture to emerge, Muslims will start to question the whole dubious doctrine of abrogation?

Now before I go any further I perhaps need to mention that there are some Islamic sites (such as the despicable quranandscience.com) which mention 16:67. But strangely enough the translations they give leave out any suggestion that the verse refers to alcoholic drink. Here's a typical example:
"And from the fruit of the date-palm and the vine ye get out wholesome drink and food: behold in this also is a Sign for those who are wise."

Why should such sites feel the need to change or interpret the words of Allah, do you think? 

One last thing. Some Muslims have taken the final words of the verse (Therein is a sign for people who have sense) as an indication  that we are supposed to view the fact that we can get both  liquor and nourishment as an example of how we can choose to make both good and bad use of Allah's gifts.  This might hold water were it not for the CONTEXT of the verse. You will have noticed that ALL the other verses in this section of Nahl also have similar words about signs, portents or lessons:

verse 65: Lo! herein is indeed a portent for a folk who hear (about water)

verse 66: And lo! in the cattle there is a lesson for you (about milk)

verse 67: Therein is a sign/portent for people who have sense (about alcohol)

verse 69: Lo! herein is indeed a portent for people who reflect (about honey)

We thus have a very clear series of gifts that Allah has given us and upon which we are to supposed to reflect. Nothing more, nothing less.

For those who read the Qur'an with an open mind without the weight of scholarly "wisdom" to hamstring our interpretation, it is clear that the author of the Qur'an meant for his followers to treat alcohol as a gift from God - just like the Jews and Christians did  (whom Muhammad was so keen to attract when he was writing the early surahs. Is it too much to suppose that Muhammad, in saying that alcohol was an important gift from God in the new religion was trying to attract the Jews and Christians who he knew used alcohol in their ceremonies? It is perhaps worth reminding readers how Jerusalem was the direction of prayer in the early surahs before this was abrogated as well and the followers were told to pray to Mecca.)

He then changed his mind. Just like a human author is want to do.

Note: Before any Muslim tells me that they AREN'T allowed to drink alcohol...I know. It was meant to be nothing more than a thought-provoking title...and I hope readers HAVE thought a little more about the issue of alcohol and how and when it came to be haraam.

What if you lose Pascal's wager?

A little while back I posited the theory that Pascal's Wager - the idea that it makes more sense to spend your life as a believer than not, since if  you're wrong you lose nothing, and if you're right you win everything - in fact made more sense for Muslims than anyone else, since the threats and promises made by Allah are that much more ... extreme than those made by the woolly liberal, C of E, post enlightenment, post-modern, Christian God. I then came across this nasty, life-denying little quote from the Ayatollah Khomeini:

"Allah did not create man so that he could have fun. The aim of creation was for mankind to be put to the test through hardship and prayer. An Islamic regime must be serious in every field. There are no jokes in Islam. There is no humor in Islam. There is no fun in Islam. There can be no fun and joy in whatever is serious." 

...and decided the wager didn't make as much sense for Muslims after all. Apart from the immediate reaction that this must...surely...be a quote made up by some loony-tunes Islamophobe (it's not, I checked),  it strikes me that this vicious, vacuous denial of everything that makes life worth living has at its heart a kernel of truth about Islam. It's that word "test". It's a word that has cropped up many times in my discussions with my convert friend: "This life is just a test", he'll say... as I slap my forehead in frustration. And so to the big question: What if it's not? What if this life is all we have, Mr Khomeini? Suddenly the wager doesn't seem like such a no-brainer. What if you go through this life, denying yourself the earthly pleasures of laughter, joy, jokes, booze, gay sex (if that's your thing) and FUN ... only to discover that that was it? To paraphrase Basil Fawlty:

Whoosh! "What was that?" "That was your life, mate." "That was quick. What about the after-life?" "Sorry, mate - that's your lot!"

Of course I'm not suggesting that the majority of Muslims, like the sour-faced loon Khomeini, live their lives perversely relishing the rashes induced by their proverbial hair shirts. But hair shirts, like tests, come in all shapes and sizes. Fasting from sunrise to sunset in the middle of summer...not drinking...praying five times a day... covering yourself from head to foot in case a man sees your flesh...forcing yourself to deny evolution despite the evidence...eating only animals killed by having their throats slit while still alive..Muslims will say that all this gives them a feeling of peace and spirituality. But at what cost? Wouldn't the one life we all get be so much pleasanter and joyful if we knew that this was it? Enjoy this life and do good for goodness' sake instead of in the hope of winning the celestial lottery or out of a constant fear of the fiery pit.What must it be like to be constantly wondering how you're doing in the test?

I'm your creator - worship me!

A Muslim recently asked why non-believers should be concerned about Allah torturing them for an eternity:

If you do not believe in something, why do you take exception to a condition that is implied by not believing in that thing? Take a hypothetical situation where a human creates a ‘universe’ wherein he creates robotic beings with need and wants, and he also fulfills those needs and wants. In addition, he gives these beings the capacity to comprehend and understand him and assigns them the task of recognising him as a means of evaluating each being’s validity. The basic requirement he places on these robots is that in the very least they accept and acknowledge their creators (sic) existence. Now if some of these beings do not, does the human not have a right to punish these robots as he sees fit? Will the human not expect his creation to understand the feeling of betrayal (from not recognising their creator) if these robots are capable of this feeling?

Why do you find it difficult to understand non-believers’ concerns over a large proportion of humanity (1.6 billion Muslims at last count, I think) firmly believing that the rest of humanity (over 5 billion souls), will be roasted for an eternity? 
We don’t believe it for one minute. But we do find it disturbing, to say the least, that so many apparently rational and intelligent people are happy to worship a deity who does such appallingly sadistic things. 
Can you not understand our concerns? 
For if you are happy to worship a deity of such mind-blowing cruelty, then that in turn says something about you, doesn't it? About how you view non-believers for a start…
Personally, I can’t conceive, nor would I want to, the agony suffered by someone being burned for an hour, let alone for an eternity. And yet you are happy not just to accept that your God inflicts this torture on countless people whose only fault is not to believe in such a sadistic creation, but to worship Him  (and this really gets me) as “the most merciful of all who are merciful”!
Your metaphor of robots is interesting since it takes away the horror of torturing people. But let’s stick with a similar analogy.
I create a world of little creatures.  I then ensure their world is full of clues to strongly suggest that I DIDN’T create it, such a fossils, evolution theory, junk DNA, a universe of unimaginable wastefulness, etc etc. I also make sure that my message to the little creatures, explaining it was me who created them and that their most important task is to worship me, is in a language only a small minority of them can understand. (I have also, of course, sent down previous messages to other groups of the creatures but I allowed these to get corrupted, so they're basically useless)  I then sadistically torture any of the little creatures who use the intelligence that I gave them to question my existence. 
What do you think that says about me?
I'd say the men in white coats ought to be along to put me in a nice, safe, padded cell. 
Wouldn't you?

(Oh - and by the way, isn't "betrayal" a very human emotion?)

Should the Qur'an be read "in context"?

If you are a liberal it must be hard being a Muslim. How, for example, do you square your desire for humane and  just treatment of criminals with the shariah requirement of chopping the hands off thieves, or the whipping of adulterers, or the crucifiction of those whose spread sedition. How do you look your gay friends in the eye, knowing that your god has decreed that the punishment meted out to the inhabitants of Sodom and Gomorrah, is a valid response to those who indulge their natural sexual desires?
One way of dealing with this apparent insurmountable clash of ideologies is to read the Qur'an "contextually".
I have been having an interesting debate with a Muslim convert over at New Muslim(ah) Walking Around - a thoughtful Islamic blog by an American female convert to Islam. This blogger, and I'm sure she is not alone, believes the message contained in the Qur'an can be "re-interpreted" and that it "isn't static".
This is, of course, what Christian liberals have been doing for hundreds of years.
"Oh, we don't take the Old Testament literally anymore! No-one is suggesting that we should stone people to death for working on the Sabbath or that you should kill your children if they cheek you...for goodness sake!"
So the Christians (and Jews) pick and choose which rules to follow and which to quietly ignore and brush under the carpet. Indeed, so successful has the Church been in re-interpreting the Bible, that the vast majority of Christians now have no idea that their holy book contains such blood-curdling exhortations to infanticide and murder.

The trouble with the Qur'an is that no Muslim can (or would want to?) deny one iota of its content and this is for two important reasons:
i. it is a fundamental tenet of Islam that the Qur'an is the uncreated word of God. That is to say that every word, every letter has come direct from God (via the Angel Gabriel and Muhammad of course).
and
ii. not a word or letter has been changed in the 1,400 odd years since the Prophet received the revelation.
Thus, for most Muslims, to say (as Christians do) that no-one believes such-and-such a part of the revelation nowadays is tantamount to apostasy (and we all know what dire retribution God has ordained for Muslims who apostise...)

Hence my difficulty with the Muslim blogger mentioned earlier. I have a sneaking admiration for anyone who has the balls to stand up in the 21st century and tell me they believe that evolution is a lie, that it's right and proper to give a hundred lashes to adulterers and that Heaven is an endless, drunken orgy. At least they stand by their peculiar convictions. I think I have less time for the apparent liberal Muslim who tries to accommodate a plainly medieval belief system by cherry-picking the Meccan verses (those "revealed" when Muhammad was in Mecca and conscious of the need not to upset putative followers) whilst ignoring the Medinan verses (those from the time when Muhammad had moved to Medina and had established a power base and was less interested in sounding understanding of non-believers)

Why follow a religion if you feel the need to reinterpret what your god has told you is the law? Why not try a dangerous but thrilling thought experiment ... and imagine, for a moment, if you feel such laws and views are plainly anachronistic and inhumane that perhaps then so is your god...and if your god is such then perhaps, just perhaps, he doesn't exist.

Now go and marvel at what science has achieved in the last few days and take a look at the pictures being beamed back from Mars (and wait for the first Muslim miracle seeker to claim he can see the word Allah written in the Martian dust...)

Why are you a Muslim?

A Muslim asked the following question on an Islamic site (islamweb.net):

I had a debate with a Christian man and he asked me ‘why are you a Muslim?’, and ‘what did you gain from Islam?’

Please give me a decisive and convincing answer.

The answer:

A Muslim’s belief in his religion must be from a complete rational conviction that cannot be subjected to doubt, because Islam is not simply a blind imitation like the case of some religions which says (sic) to its followers: ‘close your eyes and follow me’. Indeed Islam gave its followers the tranquillity of the heart, inner peace, and a rational conviction that it is the true religion from Allaah which falsehood cannot approach from before it or from behind it.

Leaving aside the depressing fact that this Muslim is incapable of explaining for himself why he has devoted his life to worshiping a deity who promises to torture the vast majority of humanity* (for no other reason than they have failed to recognise that He is "the most merciful of all who are merciful"), the immam's answer is shocking in its oxymoronic duplicity.

Belief must come, he says, from a "rational conviction that cannot be subjected to doubt". There in a nut-shell is all that is hateful in religion, and in Islam in particular: the arrogance that comes from utter certainty that your god is better than anyone else's, the denial of intellectual inquiry, the pretence of logic and rationality and the ever-present implied threat. 

The "explanation" continues by enumerating the reasons why Muslims are "convinced and content with their religion"

The Muslims are convinced and content with their religion because of the following:

1-    It is the religion of Allaah to which all the Prophets of Allaah successively called, starting from the father of humanity –Prophet Aadam  –all the way until the last Prophet, Muhammad  . This was after the human mind became mature from the succession of Prophets who were sent to the people with the same call.

2-    This great religion corresponds to the Fitrah (natural disposition upon which Allaah created mankind) of the human being. Islam fulfils both man’s intellectual and material needs. This religion also harmonizes with his mind in regard to his belief, acts of worship, morals, dealings, and rulings in every field.  

3-    This religion only brings what can be conceived and accepted by the sane mind. It [religion] never brings something that is judged by the mind to be impossible to achieve, contrarily to other religions which are full of falsehood, superstitions, illusions and nonsense.

Don't you just love the way that this immam accuses"other religions" of containing "falsehood, superstitions, illusions and nonsense"? Let's not forget that this poor Muslim is asked to accept, inter alia, that desert sprites made of smokeless fire exist (although we can't see them because they are invisible), that the devil resides in your nostrils and you must therefore clean your nose every morning, that Heaven consists of a bachinalean orgy where men get to endlessly shag 90 foot magically rejuvenating virgins whilst drinking magic wine that never gives you a hang-over, that Adam and Eve and Noah and Jonah and the whale REALLY existed, that hell is a place where the fires are eight times hotter than fire on earth, and that God turned some Jews into pigs and monkeys.

How dare this old fool accuse anyone of believing nonsense when he follows the dictates of such a puerile fantasy.

*there are 2 billion Muslims out of a global population of 7 billion. Non-Muslims are destined for Hell, according to Islam, where Allah, in his divine wisdom and mercy has devised unspeakable torments which he will inflict on everyone for an eternity.

Shaherkani - one small step for a woman

one giant leap forward for womankind.

Muhammad and the torture of the camel thieves

We know that Muslims regard Muhammad, "the last Prophet of God", as the best example of humanity. My Muslim convert friend refers to Muhammad as "the best human being ever", and his is the accepted, required doctrine: no-one has ever been, or ever will be, better than Muhammad. 
That is quite a reputation to live up to. It's also one that has led many non-believers to question how such a supposed moral giant can have done the things that he did...like, for example, torturing people to death as a punishment.
Let's look at the evidence.
This hadith is repeated several times in Bukhari from many different sources. It also appears in several guises in the other most trusted collection of hadith - Sahih Muslim. It is thus considered beyond doubt by Sunni Muslims to be the authentic words and actions of the Prophet

volume 8, Book 82, Number 796:Narrated Anas:
A group of people from 'Ukl (tribe) came to the Prophet and they were living with the people of As-Suffa, but they became ill as the climate of Medina did not suit them, so they said, "O Allah's Apostle! Provide us with milk." The Prophet said, I see no other way for you than to use the camels of Allah's Apostle." So they went and drank the milk and urine of the camels, (as medicine) and became healthy and fat. Then they killed the shepherd and took the camels away. When a help-seeker came to Allah's Apostle, he sent some men in their pursuit, and they were captured and brought before mid day. The Prophet ordered for some iron pieces to be made red hot, and their eyes were branded with them and their hands and feet were cut off and were not cauterized. Then they were put at a place called Al-Harra, and when they asked for water to drink they were not given till they died. (Abu Qilaba said, "Those people committed theft and murder and fought against Allah and His Apostle.")

Now we need to reflect upon this for the full import of what we have just read to sink in. God's best effort at creating a moral hero, who is to act as a role model for humanity until the end of time, whose tiniest actions and sayings will be pored over and from which laws and codes of behaviour will be derived which billions will have to follow (sometimes on pain of death)... thinks torture as a means of retributive punishment is acceptable.
It is interesting that even some Muslims apparently believe that Muhammad's actions were so extreme on this occasion that he was chastised by God for over-stepping the mark:

When the Apostle of Allah . . . cut off (the hands and feet of) those who had stolen his camels and he had their eyes put out by fire (heated nails), Allah reprimanded him on that(action), and Allah, the Exalted, revealed: "The punishment of those who wage war against Allah and His Apostle and strive with might and main for mischief through the land is execution or crucifixion."(Abu Dawud, no. 4357)

Hence it seems that the infamous verse 5:33...

The punishment of those who wage war against Allah and His Messenger, and strive with might and main for mischief through the land is: execution, or crucifixion, or the cutting off of hands and feet from opposite sides, or exile from the land: that is their disgrace in this world, and a heavy punishment is theirs in the Hereafter;

... was actually revealed to temper the barbarous actions of the Prophet after he had tortured the thieves. Which of course begs the question: How can it be that the best human acted so badly that God himself needed to intervene? (Even if it was only to say, "On reflection, oh Prophet of mine, I think crucifying someone or chopping off their hands and feet is probably better that gouging their eyes out, don't you?") 

And let's not forget of course (just out of academic interest) that the punishment of crucifiction and chopping off hands and feet from opposite sides was Pharaoh's preferred means of discouragement, as revealed in this verse from the Qur'an:

"Be sure I will cut off your hands and your feet on apposite sides, and I will cause you all to die on the cross." 

That would be the same wicked, degenerate Pharaoh whom God punished for being a cruel tyrant to the Jews, by drowning him in the Red Sea would it? Yup. (Am I alone in finding the logic of the moral lessons we are being asked to learn here a little ambiguous?)

Little wonder then perhaps that the Shias have rejected this story and others narrated by Bukhari

"He has transmitted strange and even abominable tales unsuitable even for the minds of superstitious Berbers and old Sudani women." (Taht Rayah al-Haqq) .

Strange and abominable tales indeed. But if you're a Sunni (majority) Muslim I'm afraid you just have to swallow it.

Or, of course, you could ask your Immam how he explains the apparent contradictions highlighted above.

So how do Muslims who know about the torturing of the camel raiders justify the actions of Muhammad?
Rather confusingly one explanation seems to rely upon the very verse that Abu Dawad (quoted above) said was revealed to chastise the Prophet.
Muhammad, they say, was simply following the advice given in the Qur'an in verse 5:33. Since the camel raiders had apparently tortured the shepherd, Muhammad was doing what he had to do by punishing them in the same manner: they poked thorns into the eyes of the shepherd so Muhammad branded their eyes in turn. The problem, of course, with this explanation (apart from Abu Dawad saying the verse that Muhammad was following was revealed AFTER he tortured the thieves to chastise him!) is that the sahih hadiths don't mention the fact that the camel raiders tortured the shepherd. Is it not strange, to say the least, that the hadiths which mention (in stomach churning detail) what Muhammad did to the thieves, fail to mention the fact that the thieves tortured the shepherd and that all the Prophet was doing was paying them back? So where then does the story of the thieves torturing the shepherd come from? www.islamiclife.com refers mysteriously to "other sources" in its explanation (reproduced below). In fact, the story appears in the Islamic biographies of Muhammad, the authenticity and reliability of which Muslims have been keen to question since they also contain many stories that they would rather were not regarded as true*.

It is clear that the Prophet Muhammad (peace be upon him) prescribed the hands and feet to be cut off in accordance with the Islamic laws concerning hiraabah (armed robbery). What doesn't appear in this narration is the reason for branding their eyes with heated pieces of iron. This is explained in other narrations where it states that this was the punishment because they had done the same thing to the sheperd whom they killed. As Shaykh Abdul Khaliq Hasan Ash-Shareef states about this narration:

It should be made clear that those people who came to the Prophet (peace and blessings be upon him) were Muslims and they were sick. The Prophet advised them to go to the herd of camels and to drink their milk and urine (as a medicine). When they became healthy, they killed the herder of the Prophet and drove away all the camels that were allocated for sadaqah (charity). When the Prophet (peace and blessings be upon him) came to know about this, he applied the punishment for Hirabah on them. Hiraba means killing people, robbing their money or raping women by an armed group of people. The punishment for Hirabah is mentioned in the Qur’an. Allah says:

“The only reward of those who make war upon Allah and His Messenger and strive after corruption in the land will be that they will be killed or crucified, or have their hands and feet on alternate sides cut off, or will be expelled out of the land. Such will be their degradation in the world, and in the Hereafter theirs will be an awful doom” (Al-Ma’idah: 33). 

As for branding their eyes, the Prophet (peace and blessings be upon him) branded the eyes of the people of `Ukl or `Uraina with iron because they killed the herder and branded his eyes with iron. Imam Ibn Hajar stated the differences of opinions among scholars and he said, “The killing that took place (that is, in reference to the above hadith) was in retaliation and Allah Almighty says, 

‘And one who attacketh you, attack him in like manner as he attacked you’ (Al-Baqarah: 194).”

All in all, using this story as evidence in favor of the permissibility of torturing people in Islam is refuted by the fact that the Prophet (peace and blessings be upon him) applied the punishment for Hirabah on them and that he did not do so for personal vengeance. 

As an example of tortuous semiotics and logic chopping this takes some beating. We can't take the example of Muhammad torturing the camel thieves as suggesting that Islam regards such actions as permissible because Muhammad didn't torture them out of personal vengeance. No, that's right... he did it because he was simply following the rules as clearly stated in the Qur'an. Forgive me if I'm being dense here, but doesn't that mean the Qur'an DOES permit torture? 

Another justification some Muslims seem  to think acceptable is that Prophets in the Old Testament were violent and sadistic so what right has anyone got to criticise Muhammad? Answering Christianity does this rather spectacularly. See here. This works only if  debating with a believer in the literal truth of the Bible, of course...and even then it seems a strange justification: "OK, our Prophet was cruel on occasions , but then so were yours". Think that's bad? A Muslim acquaintance once tried to justify Muhammad's torture by asking if it was any worse than the carpet bombing of Dresden....I'm serious.)

*This is how islamgreatreligion describes the difficulty of believing the autobiographies (where we find the references to the camel raiders torturing the shepherd)

There are about 600 Hadiths in Ibn Ishaq’s book “Sirat Rasullah” and most of them have what appears to be questionable (at best) isnads (chains of transmissions) . But the later hadith collectors (Bukhari, Muslim, etc) rarely used any material from the Sira (because of the lack of quality and authentic isnads). It is important to note that Muslims follow the Quran and the Hadith 100% only. Not the Sira. There are almost as many poems as hadiths in Ibn Ishaq, but later commentaries tend to view them as worthless because they feel so many of them were forged (by Muslims). Alfred Guillaumme, translated it in English in his own monumental work “The Life of Muhammad”.

So Muslims follow the Qur'an and hadith 100% only. Except, that is, when some other source contains something to make Muhammad seem slightly less cruel or hypocritical....