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Last Updated: 2014/04/21
Summary of question
What is the reason behind the impurity of semen and urine?
Why semen and urine are impure? Semen is a combination of sperm and sugars that we are just supposed to maintain cleanness somewhat, but can you please tell us why it is impure? Urine has the same combination as sweat which contains much ammonia. You certainly tell us this rule (being impure) is Ta\'abbodi (which means there is no reason for being impure and we must obey the rules that Allah the Almighty order us), whereas it is not the real reason! Can you please tell us these are just dirty but don’t say they are Najis (impure)? This means we should only observe cleanness. Moreover, by this approach the new generation ought to accept it better. So, why don't you reconsider your opinion in this regard?
Concise answer
We must keep in mind that all of the divine laws are based upon securing the interests of mankind and keeping them away from harms. This means that nothing is lawful and unlawful without reason and it is not the case that things have been applied without any rhyme or reason, but either many of them may haven’t explained, yet or we still haven’t gotten them. However, maintaining cleanness and healthy practices is one of the moral recommendation and the wisdom of rules concerning purity and impurity in Islam, but since there are many reasons behind cleanness, it is not correct to limit it to the health matters, only. So, we couldn’t treat the thing which it becomes impure by urine or semen as Tahir (pure) upon maintaining cleanness and healthy practices. It should be noted that the circumstances of being an obedient worshipper is to obey Allah, only. Because, Allah the Most High who created all things, definitely knows better what is the best interest and good for His creatures. He always bid the people what is right and forbid them what is wrong.
Detailed Answer
According to the Shia scholars, the divine rulings such as the lawful and unlawful acts are based upon securing the interests of mankind and keeping them away from harms. This means that nothing is lawful and unlawful without reason and it is not the case that things have been applied without any rhyme or reason. Mukallaf (who is religiously responsible or accountable) in some cases, can access some of these interests of rulings by using his own intellect and knowledge, while the others are explained to him by the infallible Imams (a.s).[1]
Since the reason of many rulings still haven’t explained by the Infallible Imams (a,s) or they are explained but we haven’t received yet, the intellect and religious law order us to follow the religious rules, only. Because, there are many unknown things which the mankind knowledge has never answered yet. All people acknowledge that the human ignorance is actually greater than his knowledge. So, according to our own intellect, we must obey and follow the divine rulings and laws. When the existence of the Holy Prophets and the infallible Imams (a.s) have been proven by the intellectual and narrative reasons, undoubtedly all things which have been received by the devoted friends of Allah are correct and based upon securing the interests of mankind and the humane society, though they won't be able to comprehend it.
We mustn’t obey Allah's orders as it is based upon securing interests but as it is His commend. Otherwise, Allah is dismissed from being the Creator and Nurture. If one obeys Allah as He should be obeyed, the one would be considered as a good servant. Because, if one who denied Allah finds the interests of rulings out and acts upon it, there is no difference between him and the believer who just acts so.[2] In any case, Allah the Most High who created all things knows better what is the best interest and good for His creatures. He always bid the people what is right and forbid them what is wrong.
Being pure is the primary basis of everything in Islam. Which means, everything is treated as clean in Islam unless we find its uncleanness out by the religious law. The impurity of subjects may have many reasons such as health losses or being impure in its essence and etc. however, some of these reasons have been stated in Islam but others not yet. It may be said that why Allah stated something as being impure is to lay stress on avoiding them. So, we endeavor to avoid such that things very much.
As a result, we can neither to say the health matters is the reason of Najasat (impurity) in any cases nor to conclude changing the rules if we want to observe the health matter.
If the reason of why something is impure has been clearly stated in the Holy Quran or the traditions (ahadith) it would be considered as the real reason for its ruling. Otherwise, if we infer it by analogy and act upon our own guess and apprehension it would be regarded as contrary to the intellectual reason. Moreover, it is an absolutely materialistic approach if we restrict the reason of rulings solely for health matters and the evolution and perfection of the human to the material dimension.
What the reason of impurity of semen and urine is as follows:
The Shia scholars pass a verdict in which the semen and urine treated as impure, according to the verses of the Holy Quran and traditions. "[O, believers! Remember] When Allah covered you with a slumber To bestow you rest from His Presence And He caused rain to descend on You from the sky, to clean you thereby And to remove from you the impurity From Satan and to strengthen your Hearts and to keep your feet firm Therewith." Allah the Almighty said.
"إِذْ یُغَشِّیکُمُ النُّعَاسَ أَمَنَةً مِّنْهُ وَ یُنزَِّلُ عَلَیْکُم مِّنَ السَّمَاءِ مَاءً لِّیُطَهِّرَکُم بِهِ وَ یُذْهِبَ عَنکمُ‏ْ رِجْزَ الشَّیْطَانِ وَ لِیرَْبِطَ عَلىَ‏ قُلُوبِکُمْ وَ یُثَبِّتَ بِهِ الْأَقْدَام‏"[3]
It is narrated -regarding the above-mentioned verse- that what does Allah mean by the impurity from Satan is the semen.[4] It should be noted that those traditions which have been mentioned in Feqh and Hadith books are also supporting the idea of the impurity of semen.
It should be noted that firstly the further researches may reject the primary view concerning the composition of semen, urine or the like and also add newest composition to them, secondly the experimental science is only evaluate the material dimension too limited, so we have no choice, but obedience to the religious laws that Allah the All-merciful sent them to us.

[1] . For further information in this regard, please refer to answer 3448 (Site: 4057) in this Website.
[2] . Ibid.
[3] . Anfal, verse 11. "Idh  yoghash­shêkomonno’asa  amanatam  men­hô  wa  yonazzelo  ‘alay­kom  menassamââ­e  mââ­alleyoṭah­herakom  behê  wa  yodh­heba  ‘ankom  rej­zash­shay­ṭâne  waleyar­beṭa  ‘alâ  qolôbekom  wa  yothabbeta  behel­aq­dâm"
[4]  . Alamul Huda, Sharif Murtadha, al-Intisar, pg. 96, the Islamic publication Institution, Qom, 1415 A.H.
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