9 The Transformation Process
9.1 Experimental and Statistical Methods as Transformations
Biology experiments consist of performing complex recipes by which input
materials are ultimately transformed into output measurements. Research
papers specify the experiment in the Materials and Methods section. There
are two different types of information presented in a Materials and Methods
section. One is the list of initial materials used in the experiment. In other
words, these are the ingredients. They are the source materials of the experi-
ment. The second type of information in the Materials and Methods section
is the description of the processes. Processes consist of a sequence of steps
that transform input substances into output substances and measurements.
Consider the following excerpt from a Materials and Methods section in
a biology paper (Stock and Stock 1987): “Immunoaffinity chromatography.
IgG was purified from mouse ascites fluid by DEAE-Affi-Gel Blue (Bio-Rad)
chromatography (5) followed by precipitation in 50% ammonium sulfate at
0 ◦C. Purified IgG (5 mg/ml) was dialized against 0.1M sodium bicarbonate,
pH 8.5, mixed with Affi-Gel 10 (Bio-Rad) at a ratio of 10 mg of IgG per ml of
Affi-Gel 10, and incubated for 12 h at 40◦C....” The corresponding series of
steps performed in this procedure is shown in figure 9.1. For simplicity, not
all of the attributes of the actual procedure are shown. Note that materials
can be introduced at steps other than just the first one. Sometimes measure-
ments can occur at more than just the last step (although that does not occur
in this example).
The information transformation process is similar to the processing per-
formed during an experimental procedure. The ingredients are called the
sourceorcontent. This is the material that is processed and transformed into
the desired output information. As in experimental procedures, information
