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Here's the context.

Blushing from embarrassment is governed by the same system that activates your fight-or-flight response: the sympathetic nervous system.

And I'd like to know the difference between that and as here.

  1. Blushing from embarrassment is governed by the same system that activates your fight-or-flight response.

The system that governs the blushing from embarrassment

The system that activates your fight or flight response

are exactly the same thing, right? but, when it comes to using 'as' like #2,

  1. Blushing from embarrassment is governed by the same system as activates your fight-or-flight response

The system that governs the blushing from embarrassment

The system that activates your fight or flight response

are similar.

From the context, the two system is referring to the exact same thing "the sympathetic nervous system", and that's why the author used that rather than as. Am I right to think this way?

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No, your two examples 1 and 2 are identical in meaning.

Example 2 is a shortened form of the sentence

Blushing from embarrassment is governed by the same system as [that which] activates your fight-or-flight response.

"That which" is understood, meaning it is assumed to be present without being spoken (or written). The example is an unusual and less-standard way of constructing the thought, but not unknown.

In general, there is no parallelism between two constructions, "same as" and "same that." As you can see, the underlying grammar differs between the two. Furthermore, the meaning of "similarity" in the two examples comes entirely from the word "same," and is not modified by auxiliaries like "as," "that," etc.

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