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Fundamentally, Catholics and Protestants read Scripture differently.

Catholics believe that any private interpretation of Scripture is subject to the teachings of the church, whereas Protestants, subscribing to the priesthood of all believers, afford more latitude for private interpretation. Within that "private interpretation," however, is the doctrine of persecpecuity a term that ironically means that Scripture is always clear. (Ask any congregation to define it, and I'll bet 75% can't!)

The question, however, is how this doctrine developed. Is it Scriptural, for example, to say that the Bible proclaims itself as having obvious application? (The Gospel is veilied to those who are perishing) Or - is it more of a historical reaction (The answer to Pope is not to install a new Pope.)

In other words, where does this doctrine come from?

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Is it the case that this doctrine says "scripture is always clear" or that "the essential message of scripture is always clear"? There might be thing written in scripture that are not clear, but are not necessary to salvation. –  DJClayworth Oct 22 '12 at 17:04
    
If you click through on persepecuity, you'll see. –  Affable Geek Oct 22 '12 at 17:19

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This concept originated with Martin Luther. In his 1525 treatise On the Bondage of the Will—a response to Desiderius Erasmus' On Free Will—Luther makes the case that God has made the message of Scripture plain for all to understand, and has given us the Holy Spirit to guide our understanding. According to Luther, if anyone does not understand, it is a failure on their part and not a lack of the Scripture's clarity.

All the things, therefore, contained in the Scriptures; are made manifest, although some places, from the words not being understood, are yet obscure. But to know that all things in the Scriptures are set in the clearest light, and then, because a few words are obscure, to report that the things are obscure, is absurd and impious. And, if the words are obscure in one place, yet they are clear in another. But, however, the same thing, which has been most openly declared to the whole world, is both spoken of in the Scriptures in plain words, and also still lies hidden in obscure words. Now, therefore, it matters not if the thing be in the light, whether any certain representations of it be in obscurity or not, if, in the mean while, many other representations of the same thing be in the light. For who would say that the public fountain is not in the light, because those who are in some dark narrow lane do not see it, when all those who are in the Open market place can see it plainly?

Luther explains that God has provided everything we need in order to understand.

WHAT you adduce, therefore, about the darkness of the Corycian cavern, amounts to nothing; matters are not so in the Scriptures. For those things which are of the greatest majesty, and the most abstruse mysteries, are no longer in the dark corner, but before the very doors, nay, brought forth and manifested openly. For Christ has opened our understanding to understand the Scriptures, Luke xxiv. 45. And the Gospel is preached to every creature. (Mark xvi. 15, Col. i. 23.) “Their sound is gone out into all the earth.” (Psalm xix. 4.) And “All things that are written, are written for our instruction.” (Rom. xv. 4.) And again, “All Scripture is inspired from above, and is profitable for instruction.” (2 Tim. iii. 16.)

This is a building block for Luther's claim about God's sovereignty. Luther states that our sinfulness utterly prevents us from seeking God on our own.

The will of God, nevertheless, which rules over our mutable will, is immutable and infallible; as Boëtius sings, “Immovable Thyself, Thou movement giv’st to all.” And our own will, especially our corrupt will, cannot of itself do good;

And that God works things out according to his own will.

THIS, therefore, is also essentially necessary and wholesome for Christians to know: That God foreknows nothing by contingency, but that He foresees, purposes, and does all things according to His immutable, eternal, and infallible will.

One of the ways God accomplishes this is by making the message of the Scriptures as clear as possible, and by providing us with everything we need in order to understand that message.

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