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How to understand the per-gate computation overhead of the FHE scheme?

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In BGV12(Fully Homomorphic Encryption without bootstapping), they investigate the efficiency of a FHE scheme by considering the per-gate computation overhead of the FHE scheme, defined as the ratio between the time it takes to compute a circuit homomorphically to the time it takes to compute it in the clear. I wanna know what means compute a circuit homomorphically and compute it in clear?

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One spends an addition time to evaluate circuit homomorphically because of scaling and modulus switching (in the case of BGV scheme). In general case, one also spends an addition time because of similar reasons.

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