1. Universities are a Christian Invention
That’s right, Christian Scholastics invented the university.
“We can trace the birth of universities to the magnetism of single teachers, whose skill and enthusiasm for learning attracted students wherever they happened to be”
From influential visionaries such as St. Augustine, bishop of Hippo (AD 353-430), Flavius Magnus Aurelius Cassidorus (AD 40-585), and Ancius Manlius Severinus Boethius (AD 480-524), some monasteries and cathedral schools grew into universities.
The development of schools can be traced back much further to the ancient world of Greece where other individuals in Athens or Alexandria, ran schools. But we are talking about the university that during the middle ages had developed into “corporations.” 
Universities unlike schools were not dependent on a few individuals and could survive long after the death of influential people.
These “Dark Age” universities were not as many of thought, pathetic places where Christians argued over, “how many angels could dance on the head of a needle”. Instead medieval scholastics;
“reviewed past authorities and current opinions, giving analysis of them and reasons for rejecting some and accepting others. Altogether, the methodology already in place by the early twelfth century shows the scholastics’ willingness, and readiness, to criticize the foundation documents of their perspective fields. More than simply receiving and expanding these traditions deemed to have outlived their usefulness. They also freely realigned the authorities they retained to defend positions that these authorities might well have thought strange and novel.”
“The early Scholastic scientists did not just sit in their studies and think about the world; they increasingly relied on careful observation of the matters involved, that is, on empiricism. For example, the Greeks, Romans, Muslims, Chinese mostly based their “knowledge” of physiology on philosophy and introspection, and some dissections of animals, but they rejected and condemned cutting up humans. Christian Scholastics were the first scholars to build their anatomical knowledge on human dissection!”
This was done for the first time in 1315 by Mondino de’Luzzi in front of an audience of students and faculty of the University of Bologna.
Most common histories will be very quite with regards to the Christian origins of university. It is typically said to have been developed out of Greek and Roman learning, brought about by help from Muslim lands, and the few who in Europe were brave enough to oppose the authority of the church. These ideas can be traced to men like Edward Grant, or A.D. White. In reality universities was like a child of the Papacy. This does not mean that papal control over universities existed. There was as I have already said, freedom to explore and expound theories because issues of theological orthodoxy was fixed.
It may help quite a bit to know while attending university as a Christian that scholarly empiricism, the sciences, history, grammar, and logic are actually what have brought students to the door of spiritual wisdom as well as what we deem sacred study.
The chief aim in the middle ages was the search for spiritual wisdom. But their approach to such wisdom was not confined only to the bible. The bible held each field in check. A beautiful union had taken place between religion and liberal arts. Many make this union out to be a bloody battle in which science and intellectual freedom finally broke free from when we reach the enlightenment. But this is not complete reality. Just as in any loving union, there is to be tension. So in this union of church and scholastic education which became university was an ongoing healthy tension where church orthodoxy was at times stretched or readdressed and new theories had to be put in check with Christian orthodoxy.
Your struggles as a university student are nothing new. In fact there is a wonderful heritage you are walking into. The bible remains key to education simply because it is a library. A unique collection of books selected with extreme care. Sixty-six books, forty plus authors, sixteen-hundred years, three different languages, all telling a single story. Beginning with creation and ending with recreation. Offering students a expanding, progressive, and yet coherent view of life and the world. 
Just as monks did not study scripture because they were looking for a job, we are not simply attending university because we are seeking a job but the knowledge of truth.
Even the historical critic of the Catholic church, H. G. Wells admitted,
“The Catholic Church provided what the Roman Empire had lacked, a system of popular teaching, a number of universities and methods of intellectual communication. By this achievement it opened the way to new possibilities of human government… possibilities that are still being apprehended and worked out.” 
These institutions, unlike Chinese academies for training Mandarins of a Zen masters school, were not content to settle for repeating the wisdom of the Greeks. They were fully prepared to criticize and correct the ancients. Something that scholars of Islam were unwilling to do, though translation of the works of Aristotle and Plato took place in Arab lands. 
A final testimony to the willingness within these scholastic communities to adjust theological views was the development of the rise of Capitalism. Not something simply invented in Venetian countinghouses, or protestant banks in Holland, but within the ninth century monastic communities. Monks found it necessary to adjust their view, that “money and pleasure is the root of all evil”. They were able to see the blessing in well managed finances, mix that with their value for hard work and entrepreneurship and a perfect environment for the rise of capitalism was given to the western world.  This was not the same corrupted capitalism one might explore today but one based on principles of moderate living, value in work, and community building. Medieval monks were not concerned with consuming capital gains but with learning to value wealth for its proper use in community building. Monks were able to re-evaluate the passage, “the love of money is the root of all evil” and began to see the value of wealth as a service to God.
In conclusion; there is no need to feel like a fish out of water when stepping onto campus of secular universities. Though there is a real challenge facing you, it is not a challenge that the church is not familiar with. It is a challenge that needs really, to be meet head-on. Literally and figuratively. That brings me to theology. It is essential that for Christians we know that reason, and intellect are not something to be detached from the spiritual wisdom we claim to have gained by our faith in Christ, and scriptures.
2. More Knowledge does not need to make your Faith Smaller
A Passage for expounding Knowledge
According to Genesis 1-2, man is made in the image of God. Keep in mind the intricacies of creation. God is without any doubt an intelligent creator, far beyond what we can comprehend. However, if we are in Gods image we may begin to comprehend all that God wishes us to in this life. In other words, we are creative, intellectual, beyond what realize. Man is always pushing the limits, and finding new things. It seems there is endless potential for the human intellect. Maybe that is true, maybe that is because we are made in the image of an immensely intelligent God.
A passage “against” expounding Knowledge
According to Corinthians 1:18-31, it would seem to some that Paul is discouraging knowledge, or the pursuit of it beyond the pursuit of Christ and the foolishness of the cross. I do not however, believe this passage is meant to discourage 21st Century Christians from going beyond knowledge of the cross. Paul himself, in order to write so eloquently and convincingly for both Jews and Greeks had a large knowledge of Jewish culture, scripture, language, as well as Greek culture, language, literature, and Greek rhetoric in particular. Scholars of the Middles ages grew quite adept at understanding Greek rhetoric of masters like Cicero because Paul’s style is almost identical.
Beyond that, a full observation of this passage and you will find verses like, The foolishness of God is wiser than the wisdom of Man (v25). All the wisdom of Jews and Greeks may have pointed to a messiah, but all pale in comparison to the revelation of Christ and his work. So it is not that God wishes man to be foolish, ignorant, intellectually lazy. In fact quite the opposite is obvious. It is considered foolishness, but it should never be considered foolishness by those who believe. It is to be considered the power of God, and the wisdom of God (v18 & 24).
A final exhortation from this passage, and something that I’m sure will prove very useful for those in university. Because your views will be considered foolish by worldly standards, the best way to move forward is in humility. We don’t get to boast before God or man because of our power and wisdom. Its been revealed to us. We did not earn it. Through humility and intellect God will reveal himself to others around you.
C.S. Lewis is a powerful reminder of what that can look like. His ‘Mere Christianity’ on display during his career at Oxford University was not just a book he wrote, it was his constant way of life among intellectuals who deemed his wisdom as foolishness. But very few today would call him foolish, or unintellectual, or unchristian.
 Church History in Plane Language; 3rd Edition: Bruce L. Shelley. 2008 – Thomas Nelsons Publishers (Ch 12 pg 196)
 The Genesis of Science: James Hannam, 2011 – Regenery Publishing (ch4 pg66)
 Medieval Foundations of Western Intellectual Tradition: Marcia L. Colish, 1997 – Yale University Press
 Triumph of Christianity; Rodney Stark, 2011 – HarperCollins Publisher (ch16 pg281)
 The Book that made your World – Vishal Mangalwadi, 2011 – Thomas Nelsons Press (ch12 pg211)
 The Outline of History; H.G. Wells, 1961 – Garden City Books (pg 587-88)
, The Victory of Reason; Rodent Stark, 2005 – Random House Publishers, (pg 52-53 & 55-56)
Disclaimer: I have not yet been to university, hopefully sometime in the next couple years. This post is for friends who are in University right now. Some at secular schools and some are in bible seminaries. I want to offer what I think will help these friends and anyone else who is facing years of study before you can get on with whatever is next. The post is particularly in mind for those attending secular universities. However, I think the principles can apply to many attending Christian Seminaries. Faith is endangered in both environments. Perhaps a follow up to this post will specifically for Christian Seminaries.