This is an interesting experiment, and one that should be really applicable to our every day lives.
The way your daughter has planned the experiment, by comparing one type of food to another, i.e. McD's vs fresh, she has already established one control. The fresh food would be the control to which she will compare the results of the McDs food.
You have a key idea about the controlled atmosphere. It is important to control as many variables as possible. To do this properly, she should monitor the temperature and humidity under each glass jar, and perhaps establish one other type of "control". If she could put one food item under each jar that was the same, like a piece of apple or some other food that is not in either of the test sample, then if the environments were controlled the same she should observe the same deterioration in the "control" food substance. If the control sample does not decompose in the same way, either the environments were not really the same, or something inside the glass dome affected the way the control food sample deteriorated.
One other thing to consider is that this experiment needs to be repeated multiple times. We can never form a valid conclusion from an experiment if we doi it just once.
And be sure she does some basic research. I did a quick scan of the internet and have a couple sites she should study:http://science.howstuffworks.com/innova ... vation.htmhttp://www.juliantrubin.com/fairproject ... ation.html
Good luck helping your daughter with this great project, and HAVE FUN!