The Signs and Proofs as mentioned in the Holy Quran and also what is meant by the Book of Allah (according to their inner meaning) are the Holy Imams (a.s.)
Ali bin Ibrahim has, narrated with reliable chains of narrators that Imam Baqir (a.s.) had said, while explaining the verse:
وَالَّذِينَ كَذَّبُوا بِآيَاتِنَا صُمٌّ وَبُكْمٌ فِي الظُّلُمَاتِ مَنْ يَشَأْ اللَّهُ يُضْلِلْهُ وَمَنْ يَشَأْ يَجْعَلْهُ عَلَى صِرَاطٍ مُسْتَقِيمٍ.
And they who reject Our communications are deaf and dumb, in utter darkness; whom Allah pleases He causes to err and whom He pleases He puts on the right way. (Sura Anam 6:39)
The apparent meaning of which is: Those who belied our verses are such deaf that they do not hear the verses as they should be heard so that they may benefit by them and who are so dumb that they do not speak the true word. They are groping restlessly in the darkness of blasphemy and waywardness. Allah deviates whom He wants to deviate, that is He leaves the one who is not capable of Divine Mercy to Himself and He guides to the right path one whom He wants.
The Imam (a.s.) said that this verse has been revealed for the group which belied messengers and their legatees and it is only those who are deaf and dumb. As Allah says, they are surrounded by darkness. The one who is an offspring of Satan does not testify the legatees and does not put faith in them. They are those whom Allah deviates. The one who is from the progeny of Adam (a.s.) and in whose seed Satan has not participated, puts faith in messengers and their legatees and he is on the right path.
The narrator says that he heard the Hazrat saying that wherever the words: who reject Our communications are mentioned what is meant is the belying of all the legatees.1
Similarly in the explanation of the verse:
وَالَّذِينَ هُمْ عَنْ آيَاتِنَا غَافِلُونَ.
And those who are heedless of Our communications. (Sura Yunus 10:7)
It is narrated that here ‘communications’ means Amirul Momineen (a.s.) and the Infallible Imams (a.s.) and that the evidence of this statement is the word of Imam Ali (a.s.): No sign of Allah is greater than I am.
Likewise, according to reliable chains of narrators, Imam Sadiq (a.s.) is reported to have said, in the explanation of the verse:
وَمَا تُغْنِي الْآيَاتُ وَالنُّذُرُ عَنْ قَوْمٍ لَا يُؤْمِنُونَ.
The verses and the warners do not give any benefit to those waywards who have no Faith. (Sura Yunus 10:101)
‘Ayaat’, here, means Imams (a.s.) and ‘Nuzur’ (warners) means the messengers. Then in further explanation he added that:
وَالَّذِينَ كَفَرُوا وَكَذَّبُوا بِآيَاتِنَا فَأُوْلَئِكَ لَهُمْ عَذَابٌ مُهِينٌ.
And (as for) those who disbelieve in and reject Our communications, these it is who shall have a disgraceful chastisement. (Sura Muminoon 23:57)
This verse refers to those people who became disbelievers and who belied our signs. So for them is the humiliating chastisement. It means the group which did not put faith in the Wilayat of Amirul Momineen and the Holy Imams (a.s.). Then added that the Divine words: “Very soon Allah will show you His signs (ayats) and that at that time you will recognize them.” Here ‘them’ means Amirul Momineen and the Holy Imams (a.s.) when they will return in Raja’t (Second coming). Then their enemies will recognize them when they see them.
Again with a good chain of narrators Imam Sadiq (a.s.) is reported to have said, in explanation of the verse:
إِنْ نَشَأْ نُنَزِّلْ عَلَيْهِمْ مِنْ السَّمَاءِ آيَةً فَظَلَّتْ أَعْنَاقُهُمْ لَهَا خَاضِعِينَ.
If We wish We may send down from sky an ayat which may make them bow before it (Sura Shuraa 42:4)
Here the meaning of ‘those who will bow down’ is the ‘necks of proud Bani Umayyah’. They will bow when a voice from sky will be heard in the name of Sahibul Amr (a.s.). At that time they will have to obey.
Similarly, it has been mentioned in the explanation of the divine commandment: “No one denies our verses but the disbelievers” that ‘who do not deny’ means Amirul Momineen (a.s.).
Likewise, according to trustworthy chains of narrators, Imam Kazim (a.s.) is reported to have said, while explaining the verse:
ذَلِكَ بِأَنَّهُمْ كَانَتْ تَأْتِيهِمْ رُسُلُهُمْ بِالْبَيِّنَاتِ فَكَفَرُوا فَأَخَذَهُمْ اللَّهُ إِنَّهُ قَوِيٌّ شَدِيدُ الْعِقَابِ.
That was because there came to them their apostles with clear arguments. (Sura Ghafir 40:22)
“Clear arguments” means Imams (a.s.).
According to Kulaini, while explaining the verse:
وَإِذَا تُتْلَى عَلَيْهِمْ آيَاتُنَا بَيِّنَاتٍ قَالَ الَّذِينَ لَا يَرْجُونَ لِقَاءَنَا ائْتِ بِقُرْآنٍ غَيْرِ هَذَا أَوْ بَدِّلْهُ.
And when Our clear communications are recited to them, those who hope not for Our meeting say: Bring a Quran other than this or change it. (Sura Yunus 10:15)
Imam Sadiq (a.s.) is reported to have said that it means bring a Quran in which there is no mention of the Wilayat of Ali or make, in this Quran, mention of those other than Ali (a.s.).
In many traditions from Ibne Mahyar and others, Imam Sadiq and Imam Ridha (a.s.) are reported to have said, while explaining the verse that it implies that the Quran in the protected tablet is with Us. It is protected from any changes or alterations and it is the highest in rank among all Divine scriptures and it is full of wisdom, that is, it contains many words of wisdom or it is Mohkam (clear) and it is not cancelled or amended but by itself.
These gentleman have said that it means that Ali (a.s.) is mentioned in Surah Fatiha which is Ummul-Kitab (Mother of the Book) who is both wise and intelligent. And it depends upon the fact that Imam Ali (a.s.) is the straight path in the path of guardianship and following. Hence it is said that when people asked Imam Ridha (a.s.) as to where Imam Ali Ibne Abi Talib has been mentioned in Ummul-Kitab. He replied: in “Guide us” because Ali (a.s.) is the Sirate Mustaqeem and it is mentioned in the prayer of the day of Ghadeer that: I give witness that Ali (a.s.) is the guiding Imam and that he is the Master of the Believers whose mention has been made by Allah in His book, saying:
وَإِنَّهُ فِي أُمِّ الْكِتَابِ لَدَيْنَا لَعَلِيٌّ حَكِيمٌ.
And surely it is in the original of the Book with Us, truly elevated, full of wisdom. (Sura Zukhruf 43:4)