The Gemarah (Bava Kama 83a) distinguishes between the Greek language and the Greek philosophy. The Greek language was considered very elegant and, based on a possuk in Chumash, the chachomim permitted a sefer Torah to be written in Greek (Megillah 9b). However, the chachomim frowned upon chochma Yevonis. The Gemarah (Bava Metzia 83b) has a comment that Olam Hazeh is compared to night time. The Mesilas Yesharim (perek 3) explains this Gemarah by pointing out that in the dark of the night people can make two typed of mistakes. Sometimes they can see a human being from a distance and think mistakenly that it is a lamppost; and sometimes they can see a lamppost from a distance and think that it is a human being. Similarly in this world, it is sometimes very difficult to distinguish between right and wrong. Sometimes we will be facing a mitzvah and think that it is an aveira and sometimes the reverse. Dovid Ha'melech says in Tehillim (119:105) that the words of the Torah are compared to a candle and a torch in that they give illumination. The Midrash (Yalkut Shimoni, ibid) explains that when one begins to learn, the Torah only illuminates like a candle, but the more one learns, the gates of learning open up before him, one thing leads to another, until all of the gates will open up and the Torah will illuminate like a torch. Knowledge is compared to a light that illuminates the darkness. We daven to Hashem every day v'hoer eininu b'sorosecha, i.e. that we should succeed in Torah learning to illuminate our lives. When the possuk says in Parshas Bereishis (1:2) that there was darkness all over the world, the Midrash has a comment that this is referring to the Greek philosophy. The Midrash (Eicha Rabbosi 2:13) has a famous statement that there is much chochma to be found amongst all of the nations of the world but not Torah. Torah means knowledge that guides us to know the difference between right and wrong, between mitzvah and aveira.
It is said over in the name of Rav Chaim Soloveitchik that in addition to the thirteen principles that guide us in deriving halochos by reading in between the lines in the chumash, there is a fourteenth middah, namely sevara - logical analysis (based on Bava Kama 46b). However, it is also recorded in the name of Rav Caim Soloveitchik that he instructed his sons that they should not dare to suggest a sevara in learning before they complete all of Talmud Bavli with Rashi[1]. Each discipline has its own self-contained logic. One cannot impose outside sevaras onto the Gemarah. The sevaras have to flow from within the sugya.
The Gemarah (Kiddushin 82a) tells us that Avraham Avinu volunteered to observe all of the mitzvos on his own even though he was never commanded to do so. The midrash (Bereishis Rabbah 95:3) elaborates on this idea and says that Avraham Avinu was able to understand on his own, intuitively, what the mitzvos were. Where did this intuition come from? It is traditionally understood based on the midrashim in Parshas Bereishis (Bereishis Rabbah 1:1, and others)which state that when Hashem created the world He looked into the Torah first and created the world accordingly. So in a certain sense, the Torah was the blueprint of the world, and therefore if one looks at the world he should be able to figure out what the blueprint was.
However, when looking at the world one has to take the correct approach to understanding it. The Greek philosophers did not believe in experimentation, since they felt that manual labor is only for slaves and free men should always be involved in thinking only. Instead of collecting the data from experimentation, they would philosophize about everything, even physical phenomena (see Nefesh Harav, p.17). But one cannot impose outside sevaras on science, and therefore this approach led them to incorrect understandings.
It is well known that Rav Chaim Soloveitchik developed a new analytic approach to Gemarah study. It is also well known that in order to answer many apparent contradictions in the Gemarah Rav Chaim would explain that the two Gemarahs that seem to be contradictory are dealing with two different halochos. Many students of Gemarah today imitate this style of Rav Chaim even when there are no contradictory passages in the Gemarah and they always will be splitting hairs in distinguishing between two dinim that seem to be identical. The Malbim in his commentary in Parshas Miketz points out that Pharoh had two different dreams and all of his advisors and scholars were explaining to him that the two dreams were "tzvei dinim" and contained two unrelated messages about the future. Yosef came and explained to Pharoh that even though they were two different dreams, they actually comprised one big dream with one overall interpretation. Logical sevaras are certainly valuable but they all have to flow from within the sugya and not to be imposed from without.
In the biography of Rav Kook[2] it is related that as a young boy his father would often take him to Dvinsk (across the river from the city where they lived) to speak in learning with Rav Reuveleh Deneburger (the German name for the city of Dvinsk was Deneberg.) Years later Rav Kook would say over in the name of that gaon that one ought not suggest an original sevara unless it is either explicit or almost explicit (in the Gemara or in the Rishonim).[3]
[1] Kuntres Limud haTorah, p. 46, found at the end of Sefer Toras Chaim, on Tanach
[2] Tal Haray"h, by Rav Moshe Tzvi Neriah, p. 18
[3] Ibid., pp. 66-67