Chows

Chows are made from mixed ingredients like corn, soy, alfalfa, dried
milk, bone meal etc. Each chow ingredient has many different nutrients,
each inseparable from the others. So there is no way to modify chows to
study a single nutrient alone and separate from the others. Chow
formulas are generally kept as trade secrets and thus can not be
reported accurately. These closed formulas may be further obscured as
they may be changed from batch to batch to make up for acknowledged
batch to batch differences in the nutrient composition of the raw
materials. In addition to these issues regarding known nutrients in
chows, there are unknown and varying amounts of other unknown and
interesting plant compounds such as phytoestrogens.

OpenSource Diets

OpenSource Diets differ from chows in several ways. They are formulated from purified ingredients (protein from casein, carbohydrate from corn starch/sucrose, etc.). Purified ingredients theoretically each have one and only one nutrient. Thus each nutrient is added separately by a single ingredient and can be varied alone while all else remains unchanged. This is theoretically wonderful and laudable. They are easy to report, repeat and revise. They are infinitely and intentionally variable. We can modify an OpenSource Diet in just about any way (remove/decrease a nutrient) while this is not possible with a chow-based diet.

Hence when animals on chow are compared to animals on an OpenSource Diet, (even one that may have the same overall level of protein, carbohydrate and fat), there are going to be differences in the phenotype that will be difficult, if not impossible to attribute to any one nutrient difference.

Interesting Reading

Ricci, Matthew R., Ulman, Edward A., Laboratory Animal Diets: A Critical Part of Your In Vivo Research. Animal Lab News, Sep-Oct 2005 Vol. 4, No. 6. View (PDF)