The butter is still bubling from the water in it when the color goes from golden yellow to brown. How do you achieve a golden color?? Should you take the ghee of the stove when the bubbles are still coming up and you still hear the noises? But that means there will be water in it?
Mine is always brown, but smells really nice, like candy caramel. Does that mean its oxidized and bad?
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When making clarified butter ghee you part the foam you will see golden yellow color ghee (changes from creamy yellow to transparent yellow color) and it now slowly changes to very light brown color and the milk solids settle at the bottom changes to slight brown color. Switch of the flame. Keep the pan aside.
Pure ghee contains no lactose or oxidized cholesterol
Weird, mine is always a bright yellow Ghee color. I'm thinking it's discoloration from your pot + uneven temp / overcooking. I usually do mine in a borosilicate jar that sits in a hot water bath (the same way I melt down dark chocolate bars, but with a little more heat.) It doesn't take too much heat to start the separation if it's able to sit steady for a bit, just a light simmer for 20m or so, then spoon off the top froth, pour out and store the liquid gold middle fraction, then discard the bottom protein layer. You don't want the temp of the ghee going too much higher than 212F.
From my understanding it is desired to cook it until it begins to brown to add the nutty flavor.
What happens when making ghee is the proteins in butter ( The 'impurities' ) that can cause it to burn when cooking at higher temps are seperated from the fat in the butter. The proteins sink to the bottom or foam to the top, as the ghee cooks longer and longer the proteins that sink to the bottom begin to brown and let off a nuttier flavoring to the ghee. You are probably overcooking it, you wan't to stop right after the proteins at the bottom of the pot go from white to brownish, you shouldn't be letting it go for too long after that. ( IMO )
Now the paleo question is, is whatever those proteins are leaching into the fat bad? Should we just aim for full seperation and then remove before the protein browns? If you would like to expirement with this you can just stop cooking it when the foaming stops before the protein at the bottom browns.
TL:DR - Who knows, just cut down your cook time.
I have never made ghee, but I wonder if a double boiler would help here? This is how I mix sugar free sweetener into 100% cacao baking bars, and that works great. The one I bought on Amazon is fantastic: http://www.amazon.com/gp/product/B0000DE0PF
i prefer the taste of clarified butter. just cook it less, or not as hot. the amount of milk solids left in it will be negligible enough to not notice them at high heat. But the brown colour should be coming from the caramelization of the milk solids(same idea as making browned butter, or how a roux should turn red). Im not certain on the science behind it, but butter is so high in saturated fat that i wouldn't worry to much about oxidizing when at the fairly low temps used for making ghee.