"He very much denigrated philosophers and scientists and he said that there is not in it any intelligence like in any saying of Maharsho or Maharam Shif...Happy he is who knows naught of their books but walks in simplicity...(Sichos Haran,5)
R. Nachman prescribed to his folowers nothing but simple faith. He believed that reading books of inquiry strengthens the powers of denial within oneself. "For we do not find that anyone became a decent person by reading the books of speculation, even though one can find in them something about good behavior and the like. Still they are nonsense for they confuse the mind...and look elsewhere about how great is the sin to study these books, God Forbid" (ibid)
Denying science is of course not popular for it invites contradictions. How can one derive benefits from the developments in medicine, technology and engineering and at the same time claim that they are impure and heretical. R. Nachman was too much of a sophisticated thinker to propose that. Instead, R. Nachman evolved an interesting justification for rejecting philosophy and science. In brief, he posited two types of scientific questions, both bad, but one that can be redeemed and the other beyond Redemption.
In Likkutei Moharan 64 he writes that after God's self-withrawal,(tsimtsum) there remained an empty space (chalal). Inside this empty space some Godliness remained so as to enable farther unfolding of the world. In effect, there remained in existence two entities; there was emptiness and there was Godliness that filled it.
Two types of heresy corrrespond to these two factors. One comes from the kelipos, shells that came into being from the breaking of the vessels (at the subsequent word of Nekudim). This kind of heresy has real substance because it ultimately springs from Godliness, albeit concealed and captive to the 'outside' forces. It is therefore included in the Sages admonistion, "know what to answer to a heretic", for these questions are capable of being answered, or should we say reconciled? Technological advances ("such as amazing war machines and other wondrous inventions... that come from Above") fall into this category. "Even though one must escape and run away from these, one who falls into them is able to go out from them, for he can find Hashem there and let him seek and search for Him there...therefore he can find there Godliness and knowledge with which to answer heresies". In other words, delving into these sciencies is not recommended but one can theoretically find God in them and resolve contradictions between these sciences and religion.
So far it is standard Hassidic teaching found in many other primary works, for example in Chapter 8 of Tanya, where it says: "
מה שאין כן בחכמת האומות הוא מלביש ומטמא בחינות חב״ד שבנפשו האלקית, בטומאת קליפת נוגה שבחכמות אלו
Not so in the case of the science of the nations; thereby one clothes and defiles his divine soul’s faculties of ChaBaD (intellect) with the impurity of the kelipat nogah contained in those sciences,
שנפלו שמה בשבירת הכלים מבחינת אחוריים של חכמה דקדושה, כידוע ליודעי ח״ן
whither they (the sciences) have fallen, through the “shattering of the vessels,” out of the “hinder-part” of Chochmah of holiness, as is known to those familiar with the Esoteric Wisdom.
Thus the study of these sciences contaminates the intellectual faculties of the G‑dly soul, and it is therefore much worse than idle speech, which contaminates only the emotional faculties,
אלא אם כן עושה אותן קרדום לחתוך בה, דהיינו כדי להתפרנס מהן בריוח לעבוד ה׳
unless one employs them (these sciences) as a useful instrument, viz., as a means of earning a more affluent livelihood with which to be able to serve G‑d,
או שיודע להשתמש בהן לעבודת ה׳ או לתורתו
or unless he knows how to apply them (the sciences) in the service of G‑d or to his better understanding of His Torah; e.g., he utilizes mathematics to better understand the laws of the Sanctification of the New Moon.
וזהו טעמו של הרמב״ם ורמב״ן ז״ל וסיעתן שעסקו בהן
This is the reason why Maimonides and Nachmanides, of blessed memory, and their peers, engaged in them (in the sciences — since they were able to utilize this knowledge in the service of G‑d and Torah).
This is how R. Nachman expresses this thought.
And this is as brought in the Yerushalmi Talmud (Ta'anit chapter 1): "If someone asks you, 'Where is your God?,' you shall say to him, 'In a great book in Rome,' as it is written, 'My God calls out from Se'ir.'" We see that this person who asked 'Where is your God?' must obviously be immersed in the realm of the "shells" (kelipot), for he has removed himself completely from the community, as he says: 'Where is your God?' - it appears to him that in the place where he is, there is no God. And so you should tell him: 'Even in the place where you are, immersed in the realm of the kelipot - even there you may find Divinity. For He gives life to everything, as it is written, "And You give life to all." And from that place you can bring yourself closer to the blessed God, and return to him in complete repentance. For it [repentance] is not far removed from you; only in your place its [concealing] garments are many. And as man climbs from one level to the next, he approaches nearer and nearer to the blessed God, and may come to know Hashem with a great understanding. For the higher his level, the fewer the garments, and the less the constriction, and then he may approach nearer to Hashem and may bring himself to love Hashem with a great love. (Likutei Moharan Kama 33:2).
The second kind of science, however, is beyond redemption, for it comes from the void. In Likutei Moharan 64 R. Nachman posits a type of heresy, which he identifies with questions which ontologically cannot be answered. Here is a quote from R. Nachman about how to deal with this kind of question.
"And I have found nothing better for the physical welfare of man than silence," because there, in the empty space, there is nothing better than silence, as stated above, for entry is permitted there only for one who is the aspect of silence, the aspect of Moshe (note: a messianic figure as found in the Zohar), as stated above. And that which he said: "All my days I have grown up between the Sages and have found nothing, etc," for by grabbing hold of this level, the aspect of silence, as he said that there is nothing better than silence, he therefore caused his days and middot to grow there in the empty space, for entry is permitted there only to one who has the aspect of silence, as stated above."
As best as I can understand it, such questions and inquiries are based on basic deficiencies in reasoning, whereby there is really no question to begin with. There is an inapparent internal flaw or contradiction within the logical chain of reasoning that produces a question that has no reasonable answer. This kind of question or heresy is by definition unanswerable because it derives from the Empty Space, where God is absent. The Empty Space is in itself a logical inpossibility for it posits the existence of something that is empty of Divinity and that is impossible. Yet, it exists; so also certain irresolvable scientific questions that deny God paradoxically exist. If the question comes from this empty space, it possesses no Godliness within and it cannot be anwered. Only when the Messiah arrives and the Empty Space is flooded with Divine Light, will such questons become resolved. For us, for now, there is no response but silence. In his other writings it is apparent that by this he means a retreat into emunah, or belief, despite and in spite of questions.