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The Qur'an in ar-Ruum:30-31 says

فَأَقِمۡ وَجۡهَكَ لِلدِّينِ حَنِيفً۬ا‌ۚ فِطۡرَتَ ٱللَّهِ ٱلَّتِى فَطَرَ ٱلنَّاسَ عَلَيۡہَا‌ۚ لَا تَبۡدِيلَ لِخَلۡقِ ٱللَّهِ‌ۚ ذَٲلِكَ ٱلدِّينُ ٱلۡقَيِّمُ وَلَـٰكِنَّ أَڪۡثَرَ ٱلنَّاسِ لَا يَعۡلَمُونَ (٣٠).

مُنِيبِينَ إِلَيۡهِ وَٱتَّقُوهُ وَأَقِيمُواْ ٱلصَّلَوٰة وَلَا تَكُونُواْ مِنَ ٱلۡمُشۡرِڪِينَ (٣١)

translated as [1]

Set your face to religion as a hanif, in the primordial nature from God upon which he originated mankind...(30). turning unto Him...(31).

This is consistent with other descriptions of Fitrah elsewhere in the Qur'an that refers to this natural tendency to lean towards believing in the one God [2].

On the other hand, the Qur'an in Yusuf:53 says

وَمَآ أُبَرِّئُ نَفۡسِىٓ‌ۚ إِنَّ ٱلنَّفۡسَ لَأَمَّارَةُۢ بِٱلسُّوٓءِ إِلَّا مَا رَحِمَ رَبِّىٓ‌ۚ إِنَّ رَبِّى غَفُورٌ۬ رَّحِيمٌ۬ (٥٣)

translated as [1]

But I absolve not my own soul. Surely the soul commands to evil...(53).

My question is how are we to understand this seeming difference in the message of 30:30 vs 12:53? In the former, the fitrah, the primordial nature of man, is said to lean towards the one God (and so all that is against ألسوء/evil), and the latter says that the human soul tends to call/urge towards evil.

Can there ever be a soul that urges towards evil, who, at the same time has, a primordial nature to lean towards tawhid, or vice versa?

Please could you provide evidences based on the Qur'an and hadeeth that can help explain this seeming discrepancy?

I can think of several approaches to this: that one's nature or soul is indeed good, but that it nevertheless urges towards evil (of course, taking into account the remainder of 12:53:

Save whom my Lord may show mercy...)

; that the soul and the human nature (my shortening of the concept of 'the primordial nature, from God, upon which he originated mankind') are not entirely or necessarily the same thing; and others. But I am not familiar with the scholarly thoughts on this and would be grateful for any guidance.

Thank you and جزاك الله خيرا كثيرا.

Notes:
[1] from Nasr et al. The Study Quran. HarperCollins Publishers. 2015
[2] e.g. for Ibrahim: 2:135; and for Muhammad: 10:105

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Assalamu alaikum dear brother, Your question is very good.

There are three natures of human (Nafs) mentioned in the Quran. The first one as you mentioned in 12:53 is (نفس الأمارۃ) the one which commands to evil. Second one is mentioned in Surah Qiyamah 75:02 and that is (نفس اللوامۃ) the one which blames. And the third one is in Surah Fajr 89:27 and that is (نفس المطمئنۃ) the satisfied one.

Now we have only one نفس (soul) but it has three different conditions on three different times as ابلیس the devil was provoked to disobey Allah by his own soul (نفس) that was (نفس الأمارۃ) the one which commands us to evil the one which provokes us to disobey our Almighty God. Now if you've noticed that when we commit a sin their is voice in us that tells us that we are doing a wrong deed that is (نفس اللوامۃ) which kind of stops us sometimes from doing a sin and most of the time its an after thought which leads us to ask forgiveness from Allah Paak for that sin.

This was brief introduction of three different types of our one soul. Now coming towards the verse which you mentioned from Surah Room 30:30 that is using the word (فطرة) which is primordial nature, its clear and proven by several means that there is a built-in function in humans that leads them towards their One God and in this verse Allah Paak is mentioning that primordial nature. How did Ibrahim (A.S) find One God? That was this فطرة And how did our prophet صلی اللہ علیہ وسلم find Him? It was this فطرة

And there are a lot more detail. I hope I answered the question may it help you to clear the confusion. Thank you.

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