Essentially, a preserved specimen is placed in a solution that stains cartilage, then is bleached and placed in a sodium borate/trypsin solution to clear pigments from the tissue, and finally is placed in a solution that stains bone. The result is an excellent model for studying the (skeletal) anatomy of the specimen:
|E. sorosum salamander|
|I don't know why this frog has so many limbs....but for more cool clear and stain images, visit: http://theboneroomberkeley.tumblr.com/post/91417577277/check-out-these-clear-and-stained-specimens-of|
Alizarin is used to stain the bones red, and alcian blue is used to stain cartilage. The specimens are stored in glycerol (rather than ethanol).
This is an old paper (1952) regarding the methods of clear and stain, by Margaret Green from Ohio State University...it's pretty short, if you're interested:
p.s. if you just google "stain and clear" instead of "clear and stain" google will give a list of links about wood finishing techniques.
Complete tangent: If any of you are interested in evolutionary biology and are looking for a summer opportunity, you should check out the NSF REU for the California Academy of Sciences....http://www.nsf.gov/crssprgm/reu/list_result.jsp?unitid=5047