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Something that has really bothered me in The Walking Dead was the part in the first season when Merle Dixon, after being handcuffed to some ducting on top of the building, uses a hacksaw to cut off his hand.

He had a hacksaw! Why didn't he cut through the handcuff chain? Or the metal rod the other cuff was attached to?

Has there ever been a reason given as to why he had to cut off his hand instead of the handcuff? Maybe in the comics or commentary or something?

From the script of season one, episode four, Vatos, in the scene where Daryl, T-Dog, and Rick find the severed hand:

Daryl [to T-Dog]: "You got a do-rag or something?"

T-Dog hands him one.

Daryl: (sighs) "I guess the saw blade was too dull for the handcuffs."

Daryl gingerly picks Merle’s hand up by a finger and examines the cut.

Daryl: "Ain’t that a bitch."

The hacksaw blade was too dull to cut through metal, so Merle cut through flesh and bone, which are much softer. Better to cut off a hand than die of thirst, exposed on a scorching rooftop in Atlanta, during the summer.

In real life, handcuffs are (unsurprisingly) designed to be difficult to remove without the key, so it is entirely plausible that a dull hacksaw would be unable to cut off a pair of police cuffs.

It would be extremely difficult even for a person using both hands and a sharp hacksaw; Merle is limited to using one hand to operate the saw. If we assume he's a righty, he is even worse off, because it is his right hand that is chained to the roof - he can only use his weak hand to try to cut through hardened steel with a dull saw.

You've never used a hacksaw on hardened steel have you? I cut soft steel once as a tween, cutting a 2" steel pipe so I could make a periscope. It took me the better part of an hour. The steel on handcuffs is much stronger than that, and deliberately polished to make it even harder to get the blade set. He'd be long eaten by the time he got through it.