The hearing loss issue is a real one, and one that's going to start weighing on LEOs who issue M-4 type carbines as well as civilians. If you're going to use an AR as a primary home defense weapon (and I agree 100% with Rob on the Hornady TAPS as the round of choice), you must have a set of electronic ear protection for each member of your family and a plan on using them.
An expensive alternative but one that I plan to execute in 2009 is fitting the home defense AR with a suppressor. I'm leaning toward SureFire, but that's not a "for sure." Suppressors solve the noise problem, minimizes flash (which is another seldom-mentioned issue on short-barreled ARs in closed spaces) and reduces even more the 5.56's minimal recoil. Yes, you have to get a tax stamp and pony up the $200, but I believe 35 some-odd states allow civilians to have suppressors, and this situation is an excellent and intelligent use of the technology.
There has been a lot written about the potential dangers of using Class III weaponry for self-defense, but I would feel in a very strong position walking into court with the rationale for a suppressed AR for home use.
1) The 5.56 is proven to be less of a penetrator then the typical home defense pistol rounds (you saw the video on TBD, so you know this for a fact).
2) A rifle is demonstrably easier to shoot than a handgun.
3) The 5.56 when fired in a closed room will result in damage on unprotected ears.
4) Even the best headphones can be knocked off in the heat of an armed encounter, while a suppressor is attached to firmly to the rifle.
5) In my absence, I would much rather my loved ones had at least 30 rounds of 5.56 in one of the easiest guns to fire ever manufactured than 8 rounds of .45 or 17 rounds of 9mm.
Michael B
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