Rebbe Nachman's understanding of our system of site works like this:
1. We direct our gaze to something, light leaves our eye and heads towards that thing.
2. The light reaches the object and returns back to our eye.
The light that travels outwards from our eye is called אור הישר - straight light. The light that travels back to our eye is called אור החוזר - returning light.
Now, Rebbe Nachman's straight light clearly differs from modern scientific light (ie. comprised of photons) otherwise we would expect that Rebbe Nachman believed people's eyes glow in the dark--something trivial to disprove. (Not necesarily trivial actually, but let's say it's observationally trivial to disprove to the modern mindset.)
In modern science, light is always radiated and richocheting all around us, when we open our eyes we gather this ambient light and observe whatever scene is reflected in that light. Essentially, the scientific model only acknowledges the returning light. There's no equivalent to Rebbe Nachman's straight light in modern science.
The modern scientific model began to break down with the discovery of light's wave/particle duality, and further broke down with Quantum Mechanics proving that observation can even retroactively affect the outcome of our observations.
If the scientific model of light included Rebbe Nachman's straight light, although it might create other problems, they would no longer be stymied at why observations affect results. Of course observing something affects the object observed, it's being bombarded by straight light.
[Note that the Quantum Mechanics equivalent of observation doesn't mean a human being looking at something, but Rebbe Nachman didn't say that people are the only source of straight light either.]