Chapter 1: Section 7: Page 58: Line 27 (1008)

 "You're quite right, of course, the Æther has always been a religious question.

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"a religious question"
I suppose all scientific theory must be born from faith or we would ultimately learn nothing. If we only believe what we see evidence of without somebody extrapolating further on their observations, then nobody would ever come up with theories to test. At what point does a scientific theory go from the religious to the scientific? It seems to me what's most religious in the arena of science is when the evidence has stacked up against a long-held theory and yet adherents continue to cling to it.
    Here Heino agrees with Merle that Æther has been a religious question because it has merely been theorized as something needed to uphold scientists' views on light and its properties. Kind of like how String Theory's multiple dimensions haven't been proved in any actual way but are only theorized because of the math. Or maybe dark matter is a closer comparison, pretty much being the modern day equivalent of Æther in that it seems to be needed for the current model of the universe and general relativity to work.

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 They strolled among the elm-shadows, eating sandwiches and apples out of paper bags, "a peripatetic picnic," as the Professor called it, slipping thereupon into his lecture-hall style.

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"elm-shadows"
Elm trees create plenty of shade and are one of the most popular trees to be used in public landscaping, often planted as boundary markers for paths, creating tunnel-like effects when planted to either side of a path. The elm is both a symbol of pastoral peace and death. Perhaps Heino and Merle are walking in the shadows of these border trees because they are, technologically speaking, crossing from a time of pastoral peace, where technology has begun to make impacts in our lives and seen as improving them, toward a time when technology will begin its decent from the peak of improvement, hurtling toward the ground as it becomes destructive and deadly, until it finally crashes beyond the zero into nuclear annihilation.
    Or maybe its just a bit of descriptive tat.

"eating sandwiches and apples"
Apples being the symbolic fruit of which Eve partook. Yeah, I know the fruit is never actually described but instead of being a pedantic nerd on the Internet, how about understanding the cultural symbols all around you. There's a reason the Apple logo is that of an apple with one bite taken out of it. And it's not because it's the mark of the beast and an indication of man's inability to resist temptation! It's about gaining knowledge! Maybe those are the same things though. See my comments on "elm-shadows."

"out of paper bags"
They didn't have plastic bags yet! If you want to learn more about the history of plastics, Pynchon covers that topic in Gravity's Rainbow.

"a peripatetic picnic"
This is a pun. The Professor is commenting on how the picnic is a traveling picnic but also it's a picnic where they discuss philosophical matters as they eat. So peripatetic as the adjective in that they're traveling but also as in The Peripatetic school founded by Aristotle, as we see Heino begins to lecture Merle as they walk.

Chapter 1: Section 7: Page 58: Lines 24-25 (1005-1006)

 "Guess I'd better go take a look. Probably that gear train again."

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The guy just came out with singed hair and smelling of burning flesh and cleaning products. I don't think it was the gear train. I think the Professor decided to try holding the Leyden Jar in his non-cranking hand. He may also have been re-attempting the "What happens if the jar is down my pants?" experiment. Maybe he was rubbing the glass spheres against his scrotum to generate the static electricity? Am I projecting too many of my own kinks onto the Professor? Although his name is Heino Vanderjuice. There's got to be a semen joke in their somewhere.

Maybe the more important part of Merle's response is for the reader to understand that Merle has the know-how to build and fix an electrostatic generator!