Last year when I was treating my main tanks for ich, things went nuts, so I had to do a large water change. The result of all the chaos was black splotches all over my clowns. I documented this semi-disaster here:
http://forums.loaches.com/viewtopic.php?f=1&t=24777
Here's some before and after pics:
After this, I ran activated carbon in my filters for a few days and the splotches completely disappeared.
There any many theories as to why to this happens.
Some people have even claimed that the dust from fresh activated carbon, which wasn't pre-rinsed properly, causes the spots. I'm not so sure about that, as in the past I've seen the spots crop up without using activated carbon.
I think the answer is all of the above. It's pH, it's chlorine, it's ammonia, it's activated carbon dust, it's leaching rocks, it's brass leaching pipes, it's large water changes, it's poor water quality, it's an old water heater, and it's TDS changes. It's something that causes clown loaches (pituitary gland?) to send melanin or black pigment to the wrong areas of their body. It's some kind of panic response. Maybe it's connected as to why they have black stripes? Maybe it's why some clowns have darker black stripes than others? Maybe it's why those black stripes sometimes fade during loach battles? Maybe it's why older fatter clowns have their stripes separate?
That black pigment is not permanent, as I've seen clowns completely lose their ability to produce the melanin, and turn albino shortly after. Here's an example:
http://forums.loaches.com/viewtopic.php ... 8&p=199444
Normally, clowns are constantly producing the melanin or black pigment, and it usually goes to where their stripes are, but sometimes when they are stressed it ends up someplace else. At least that's what I think.