How do we explain the theological shift in the mainline? How do we explain the movement of major conservative universities, seminaries and churches away from a conservative view of Scripture that believes it to be the inerrant and infallible word of God into a much more novel and liberal view which makes it subject to human criticism and interpretation? John Frame speaks of one major underlying theological factor in this shift in his new book The Doctrine of the Word of God, namely, the presupposition of intellectual autonomy. His explanation is so helpful I will quote him at length:
Conservative scholars and churchmen did take issue with this principle, or at least they refused to accept it. But within the liberal movement itself, there was no consideration of the alternative. Intellectual autonomy was accepted as a presupposition, as something fundamental, not to be argued about. It was thought that anyone who disagreed was simply not a scholar, not qualified to do serious research.
Many did disagree and therefore maintained the authority of Scripture as the church had always done before Spinoza. We recall in this connection the names of biblical scholars E. W. Hengstenberg, J. F. K. Keil, Franz Delitzsch… Certainly these men qualify as scholars…
But the major university faculties were nonetheless dominated by those who embraced the principle of intellectual autonomy. It all happened very quickly. There was no academic debate on whether it is right for human beings to exercise reason without the authority of God’s revelation. There was not much argument about whether the universities should change their time-honored commitments to divine revelation. Rather, major figures simply began teaching from the new point of view, and there was no significant resistance. They accepted the assumption of autonomy and saw to it that their successors accepted it too. Campus politics certainly played a major role in this development. The conservatives did not know what hit them.
Soon, because pastors were trained in universities [at that time], the liberal view spread to the churches, so that by the late nineteenth century most mainstream denominations in America were tolerating that approach. In 1924, 1,274 ministers of the Presbyterian Church USA signed a document called the Auburn Affirmation [read at http://www.covenantnetwork.org/sermon&papers/aubaff.html], which denied that the inerrancy of Scripture, the virgin birth of Christ, the substitutionary atonement, the resurrection of Christ, and his miracles should be tests of orthodoxy in the denomination. In the 1930’s, ministers in the denomination were disciplined for insisting that the church’s missionaries believe in the above-listed doctrines. The liberal commitment to intellectual autonomy had made these doctrines optional, and many church leaders regarded them as literally untrue. Those who objected to these developments (contrary to liberal claims of “tolerance”) were given no respect or power in the councils of the church.
This change was astonishing. The adoption of intellectual autonomy as a theological principle was certainly at least as important as the church’s adoption of the Nicene doctrine of the Trinity in 381, or the doctrine of the two natures of Christ in 451. Yet without any council, without any significant debate, much of the church during the period of 1650 to the present came to adopt the principle of intellectual autonomy in place of the authority of God’s personal words. But this new doctrine changed everything. Given intellectual autonomy, there is no reason to accept supernatural biblical teachings such as the doctrine of the Trinity and the two natures of Christ. The virgin birth, miracles, atonement, resurrection, and glorious return of Jesus are on this basis no longer defensible. J. Gresham Machen showed, in Christianity and Liberalism, that liberalism rejected the historic Christian teachings about the Bible, God, Christ, the atonement, salvation, and the church. Some thinkers rejected these traditional doctrines outright. Other reinterpreted them in some symbolic fashion. In both cases, these doctrines had to meet the criteria of autonomous human reason.
If these doctrines are true, they must be true because of God’s personal testimony. There is no way that they can be validated on the authority of autonomous reason. Indeed, if human reason is autonomous, the God of the Bible does not exist, for his very nature as the Creator excludes the autonomy of his creatures. And in fact nothing at all can be validated by autonomous reason… such reasoning leads to a rationalist-irrationalist dialectic, which destroys all knowledge. For that pottage, much of the church has forsaken its birthright, God’s personal word.
Don Cupitt wrote in Taking Leave of God: “The church is a museum.” In other words, the church’s role in society lies in the past; it is nothing but old bricks and artwork to be admired by the progressive culture that has left it behind. Divine revelation (the counterpart to human intellectual autonomy) to people like Cupitt, is a relic hanging in a gallery somewhere in the museum that is orthodox Christian theism.
Those in the church who embrace the principle of intellectual autonomy have essentially silenced the very thing that would define them as Christian, the Bible. They have done like Cupitt and many others—assigned orthodox, conservative Christianity the task of “guarding tradition and being the repository of admittedly obsolete but deeply cherished beliefs and images.” “Tradition” (the word typically assigned to those things we want little to do with now-a-days) is valuable as long as it remains on the shelf or hanging in a gallery where it has little influence over how I spend my time and money.
When God’s Word becomes merely a “tradition” nothing is sure and all is up for grabs. This phenomenon has been on stage for all to see in so many denominations today. With their ever-changing ideas and standards for the Christian faith, what is “Christian” is an increasingly fluid and malleable concept that has in recent decades come to look more and more like the world. And not surprisingly, for this is exactly what the apostle Paul predicted would happen in the last days. James Boice writes: “the problem Paul is describing [in 2 Timothy 3:5] is not that the world will be evil in the final days before Christ’s return but that the church will be like the world, as it is today. The church will be indistinguishable from the world and will be equally corrupt…”
So what has happened? To use D. A. Carson’s words, we have gagged God.
 R. C. Sproul writes: “Infallibility refers to [the Bible’s] indefectibility or the impossibility of its being in error. That which is infallible is incapable of failing” (What is Reformed Theology: Understanding the Basics [Grand Rapids: Baker, 1997), 45.). He writes of inerrancy saying, “Infallibility means that something cannot err, while inerrancy means that it does not err. Infallibility describes the ability or potential. It describes something that cannot happen. Inerrancy describes actuality” (What is Reformed Theology, 48).
 James Tunstead Burtchaell wrote a book about this very phenomenon that was published in 1998. He speaks primarily to the College and University shift away from Christian associations. The opening line of the preface reads: “Countless colleges and universities in the history of the United States were founded under some sort of Christian patronage, but many which still survive do not claim any relationship with a church or denomination. Even on most of the campuses which are still listed by churches as their affiliates, there is usually some concern expressed today about how authentic or how enduring that tie really is; and often wistful concern is all that remains” (The Dying of the Light: The Disengagement of Colleges & Universities from their Christian Churches [Grand Rapids: Eerdman’s, 1998], ix.).
 Intellectual autonomy is, in John Frame’s words, “the view that human beings have the right to seek knowledge of God’s world without being subject to God’s revelation. It first appears in the history of thought in Genesis 3’s narrative of the fall, in which Adam and Eve make their decision to disobey God’s personal word to them. In their decision, they affirm their right to think autonomously, even to the point of contradicting God himself” (John Frame, The Doctrine of the Word of God: A Theology of Lordship [Phillipsburg, P&R, 2010], 15-16.).
 John Frame, The Doctrine of the Word of God, 19-20.
 Don Cupitt, Taking Leave of God (SCM Press, 1980), 168.
 Cupitt, Taking Leave, 168.
 James Montgomery Boice, Whatever Happened to the Gospel of Grace: Rediscovering the Doctrines that Shook the World (Wheaton: Crossway, 2009), 74.