The Amplified Bible makes these verses clearer:
O Timothy, guard and keep the deposit entrusted [to you]! Turn away from the irreverent babble and godless chatter, with the vain and empty and worldly phrases, and the subtleties and the contradictions in what is falsely called knowledge and spiritual illumination. [For] by making such profession some have erred (missed the mark) as regards the faith. . . .
Paul warns Timothy about "the subtleties and contradictions of what is falsely called knowledge and spiritual illumination." The word translated "knowledge" in most translations ("science" in the King James Version) is the Greek gnosis. Literally meaning "to know," it forms the root of the word Gnosticism. It is possible, even probable, that Paul refers to Gnosticism here, since both of his letters to Timothy contain warnings against false teachers bringing in foreign concepts that were undermining the faith of church members.
Remember, however, that his warning is against a particular type of knowledge that induced some members to stray from the faith, knowledge that was subtle and yet contradictory. That it was contradictory is interesting because Gnosticism not only contradicts the truth, but within Gnostic beliefs there are also many contradictions.
Recently, the newly-discovered Gospel of Judas, an example of what is called a "Gnostic gospel," has made headlines worldwide. It was not written at the same time as the four canonical gospels - Matthew, Mark, Luke, and John - but appeared a couple of centuries later. The Gospel of Judas contradicts the true gospel accounts by asserting that Judas Iscariot was actually the hero, who had been given secret knowledge that the other disciples did not possess.
The opening line of the Gospel of Judas demonstrates this secret knowledge: "The secret account of the revelation that Jesus spoke in conversation with Judas Iscariot during a week, three days before he celebrated Passover." This so-called gospel gives a quite different view of the relationship between Jesus Christ and Judas, and its defenders say that it offers "new insights" into Jesus' betrayal, and the nature and character of Judas. "New insights" is another common theme of Gnosticism.
Several years ago, another Gnostic gospel, the Gospel of Thomas, was all the rage in the scholarly community. Its opening lines also emphasize this secret knowledge: "These are the secret sayings that the living Jesus spoke and Didymos Judas Thomas recorded. And [Jesus] said, 'Whoever discovers the interpretation of these sayings will not taste death.'" Notice that the emphasis is immediately on discovering an interpretation and on increasing knowledge as a way to eternal life. It contains nothing about salvation coming through one's relationship with God or even about living a godly life. In this Gnostic gospel, eternal life comes from the secret knowledge that will explain the obscure sayings.
Not only were the Gnostic gospels written long after the fact, but they are also full of statements that oppose the text of the Bible. For example, in the Gospel of Thomas, Jesus allegedly says, "If you fast, you will bring sin upon yourselves, and if you pray, you will be condemned, and if you give to charity, you will harm your spirits." Scholars say that Jesus is advocating "fitting in" and "being true to oneself," phrases often repeated these days.
In another place in the Gospel of Thomas, Jesus is quoted as saying, "[Blessed is] the one who came into being before coming into being." This makes absolutely no sense to us, but it does make a kind of sense to Gnostics, who believe in a dualism of flesh and spirit. Thus, they understand that "Jesus" implies that the spirit could come into being before the flesh. Many Gnostics were followers of docetism, the belief that Jesus and Christ were two separate beings in one body. Docetists believed that the man Jesus was born, and that the pre-existing god Christ entered into Him when He was baptized and left again before He was crucified. This, then, is an example of coming into being before coming into being.
Also in the Gospel of Thomas,
The disciples said to Jesus, "Tell us, how will our end come?" Jesus said, "Have you found the beginning, then, that you are looking for the end? You see, the end will be where the beginning is. [Blessed is] the one who stands at the beginning: that one will know the end and will not taste death.
Again, knowing something is shown as the antidote of death. In this case, another element of dualism is that every person has a little spark of God in him or her, and that we have an eternal spirit (or soul) that is trapped or imprisoned within a body of flesh.
Gnostics generally believed that all spirit was inherently stable and good (overlooking the fact that Satan and his demons are spirit and yet also unstable and evil), while all matter and flesh was inherently evil (contradicting God's statement in Genesis 1:31 that everything God had made was "very good"). Plato reinforced this belief, writing, "The soul is the very likeness of the divine - immortal, and intelligible, and uniform, and indissoluble, and unchangeable." He also declared, viewing the body as a temporary house in which the soul is imprisoned, "The soul goes away to the pure, the eternal, the immortal and unchangeable to which she is kin."
The Gnostic goal was to learn the secret knowledge that would allow the inner spirit to be released from the confines of the flesh, enabling it to rejoin God in the spirit realm. Thus, the Gnostics linked the beginning and end (often depicted in the figure of a snake swallowing its tail), because if a person could figure out how the divine spark was infused into the flesh in the first place, he could then reverse it and release the spirit. We find the same basic tenet in the modern doctrine of the immortality of the soul, and the widespread belief that our "home" is in heaven, and that we go to this home when we die.