Guinea Pigs fighting?

Question
I have 2 guinea pigs, about the same age, under 6 months.  One is large and the other has stayed small.  The big one (Princess) is picking on the little one (Midnight).  I know she has to be dominant, but it is so sad to hear the little one cry loudly.  I have never seen any blood, but have seen the big one bite the little one and chase her away from food, etc.  The big one seems to even lay in the food and go to the bathroom in the water.  They have a 40x18 inch cage. I have pellets and timothy hay available all the time. Twice a day I give them treats and I know I give them enough, because they usually leave some.  It was getting so bad a few days ago, I separated them.  Must of been the wrong thing to do, because the bigger on "pouted".  I put them in a playpen tonight and they are both doing Popcorning, however the big one still goes over and chases the little one and bites her.  Do I keep them separated?  Do I just try not to let the crying get to me? Will they grow out of this?  Thank You

Answer
This is not an uncommon problem. I am assuming you are certain they're both female. If they were both boars you would need to separate them, but being female it's handled a little differently.

A female dog is referred to as a bitch in the same way a guinea pig female is called a sow. But there's a reason females are often referred to by the female dog's identity. A female dog will always be the boss in a household of more than one dog. They get bossy, cranky, pushy and sometimes difficult to live with if you're a male dog.

Sows are much the same. In every herd of animals there is always an alpha and an omega. That's the way nature has intended it to be and in their lives they accept those roles without question. A pack of wolves are one of the best examples. The alpha male and female are the only ones allowed to breed. That prevents inbreeding. That's not the case with guinea pigs, but they're happiest when living in a communal environment. Even then there will be an alpha female and the omega, who is the lowest on the chain and the most submissive.

The omega will not be allowed to starve, she must simply eat last. In nature's wild environment they have no problem with that. It's their expected position in life and there's no argument.  With two sows who are living in a cage that is certainly large enough, they will have their squabbles now and then. Princess is the self proclaimed alpha pig, and little Midnight is accepting of her status and won't fight back.

That doesn't mean that she won't get to eat. Princess won't allow her to starve. She's just excercising her dominance. There's also the possibility that Princess is in heat and has become, for lack of a better description, a bitch. Fortunately this will pass and peace will reign again. As long as Midnight is not showing wounds that are open you can just leave them together and they'll work it out.

The down side is that they come into heat every two or three weeks for just a couple of days. Midnight will recognize when Lady Fido is in a hormonal rage and will leave her alone.

If you see blood drawn, that's a different thing. Then you need to separate them on a permanent basis. But it sounds to me like it's the typical "time of the month" that has the household upset.  

I hope this isn't a bigger answer than you needed. If so, please forgive me. Sometimes understanding the dynamics of the relationship sheds a little bit of light on why it's happening.  

I hope this helps you.