Dry Hopping Question

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I had seen someone hang the muslin bag inside the carboy and gripping at the stopper and did that to my IPA batch. but the next day the outer bag turned brown and I am now worried that bacteria might pass thru the gap of the muslin bag at the stopper. Am I worrying unnecessarily or should I sanitize and drop the entire bag inside the carboy? Thank you.

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I don't know why the color changed like that, but I'm pretty sure you're going to be fine. Nowadays I dry hop in the keg but when I was doing it in carboys, I would tie a piece of unscented dental floss to the bag and drop the whole thing in, then I would pass the other end of the line through my 3 piece airlock and tie it off on the stem of the airlock and put it back together. It was overkill but it worked. You could always just do the same trick, but instead of going through the airlock, pull it slightly out of the carboy and "Squish" it with the rubber stopper.
 
I just dump the hops in and let them swim around unfettered.

+1
Just let them swim. The color change is probably due to the trub, etc and I really wouldn't worry about it. The presence of alcohol would pretty much prevent anything from growing and hops prevent issues to some degree as well.
 
It's beer that turned it brown. This happened due to capillary action

Capillary action (sometimes capillarity, capillary motion, or wicking) is the ability of a liquid to flow in narrow spaces without the assistance of, and in opposition to, external forces like gravity. The effect can be seen in the drawing up of liquids between the hairs of a paint-brush, in a thin tube, in porous materials such as paper, in some non-porous materials such as liquified carbon fiber, or in a cell.

Same reason why kerosene lamps work despite the fuel being separate from the flame. As everyone already said though, you should be safe. If you decide to let the hops go free though, I'd suggest cutting off the part of the bag that was exposed and just let the muslin bag hang about inside the carboy along with the hops.
 
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