Veyavinu BeMikra is a booklet written to explain why Peshuto Shel Mikra had to be banned. The very first example that it brings is the explanation of the illumination of the Ark. As you will recall, Chazal gave two explanations - one was that it was a window, and the second was that it was a gemstone or crystal that radiated light. In discussing the second view, Peshuto Shel Mikra says as follows:
"והדעת נוטה, שהאבנים הטובות המאירות אין להן אור מעצמן, כי בכוחן רק להגביר את האור מחמת המאור הנמצא בקרבתן ולהפיצו ביותר, כדוגמאות המראות המבריקים מאוד. וא"כ, גם לדעה זו הֻצרך נח לנרות דולקים, שעל ידם יפיצו המרגליות את אורן בתבה".
"Reason indicates that because precious stones do not emit their own light, but rather refract the light emitted from other sources, like very shiny mirrors, then Noah must have also been burning candles, the light of which would be reflected around the Ark by these precious stones."
Veyavinu BeMikra explains that this heretical for two reasons. First is that the Rishonim who discuss this approach are clearly of the view that the stone emitted its own light. Second is that the authors preference for that which makes sense according to "reason" means that he only accepts that which the human mind can rationally grasp and rejects the supernatural.
I think that it's easy to understand the concern. One minute you're rejecting the traditional view about how Noah's crystal worked, and before you know it, you're asking how kangaroos got to the Ark. And trying to make the story of Noah's Ark fit with science is indeed a recipe for leading someone away from conventional Torah thought and risks opening a Pandora's Box. Indeed, Rabbi Moshe Meiselman goes to great lengths to explain why the account of Noah's Ark cannot be reconciled with science in any way, as a sort of bizarre purging effort to make people reject rationalism.And yet, the desire to make Torah conform with reason and science has long been a mainstream approach in rabbinic thought. Rambam wrote this explicitly:
"…Our efforts, and the efforts of select individuals, are in contrast to the efforts of the masses. For with the masses who are people of the Torah, that which is beloved to them and tasty to their folly is that they should place Torah and rational thinking as two opposite extremes, and will derive everything impossible as distinct from that which is reasonable, and they say that it is a miracle, and they flee from something being in accordance with natural law, whether with something recounted from past events, with something that is in the present, or with something which is said to happen in the future. But we shall endeavor to integrate the Torah with rational thought, leading events according to the natural order wherever possible; only with something that is clarified to be a miracle and cannot be otherwise explained at all will we say that it is a miracle." (Rambam, Treatise Concerning the Resurrection of the Dead)
The Rishonim who spoke about Noah's crystal emitting light were not trying to describe a miracle - they explained it in this way because until recently it was standard belief that certain precious stones do indeed emit light (which actually isn't so far from the truth). And if you're going to start heresy-hunting over this, then you're also going have to burn goodness knows how many Stone Chumashim, which describes the crystal view as meaning that Noah placed a prism in the wall of the Ark that refracted the outside light around the Ark. ArtScroll is clearly taking this approach in order to make it conform to the scientifically possible, even though it is not the traditional explanation of the crystal view.
Yes, reason and rationalism have their risks. But they are nevertheless a traditional part of Judaism, and it is both wrong and dangerous to ban them as being outside the scope of Jewish thought. Over 25 years ago I was tortured by the question of how the kangaroos got to the Ark, and so I went to ask Rav Aharon Feldman, with whom I was quite close at the time. He kindly but sternly suggested that I shouldn't be interested in such questions. Well, naturally, that didn't do anything to satisfy my distress, but fortunatel I was able to go down the block and discuss it with Rav Aryeh Carmell ztz"l instead. He gave me an answer that Rav Feldman would consider heresy, but which is consistent with the approach of Rambam and many other greats throughout history.
Personally, notwithstanding the dangers of trying to make Torah fit with reason wherever possible, I think it's an approach whose legitimacy is worth defending.
(On a related note, if you can bring a suitcase from Teaneck containing a deck prism and other Ark-related materials for our exhibit, please be in touch!)