Biology Reference
In-Depth Information
where all molecules are the mirror-symmetry isomers of the molecules that do
constitute life on this planet. If one were to ask why this planet (probably)
harbors only the one form of life we know and not its mirrored analogue (life
based on d-enantiomers rather than l-enantiomers), the answer is likely to reside
in evolutionary biology. Systems biology does not need to ask this question for
it to be a complete science. Many areas of physics could discuss systems that
are not actually observed (such as a system identical to ours with all electric
charges inversed).
2. SYSTEMS BIOLOGICAL EXPLANATIONS ARE OFTEN
MECHANISTIC EXPLANATIONS
An important part of functional biology is about answering 'how' questions.
Answers to 'how' questions are usually phrased in causal mechanistic language.
One issue, therefore, that ought to be addressed by a philosophy of systems
biology is that it should analyze the types of explanations offered by systems
biologists and how their structure differs from explanations offered in other
sciences and biological disciplines. It can be argued that a philosophy of systems
biology should aim for a hybrid form of the unificationist and causal/mechanical
type of explanation. Some authors (Westerhoff & Kell; Schaffner, this volume)
have discussed the former kind of explanation, whereas several authors (Bechtel;
Fell; Richardson & Stephan; Schaffner; Shulman, this volume) have stressed the
importance of mechanistic explanations in systems biology. In fact, Westerhoff
& Kell engage in both.
In this topic, several authors have further argued that answers to 'how' ques-
tions are frequently given by discovering and articulating the organization and
inner workings of molecular mechanisms underlying behavior. The articula-
tion amounts to showing how the behavior is brought about by the parts when
engaging in interactions; this used to be done in terms of a graphical repre-
sentation of the mechanism (a network depiction of the molecular interactions);
more recently, detailed computer models for systems that have been character-
ized molecularly to a sufficient level of detail have been used for this purpose.
This kind of explanation belongs to the causal/mechanical type of explanations
in the philosophy of science (Bechtel & Richardson, 1993; Schaffner, 1994;
Woodward, 2005; Salmon, 2006) for the way individual macromolecules work,
but it rarely extends to the cellular level. An early example of a mechanistic
explanation covering systems phenomena is the analysis by Jacob and Monod
on how the molecular organization of the
lac
operon underlies diauxic growth in
Escherichia coli
. This example is discussed in depth by Stephan and Richardson
in this volume. A second early example was the chemiosmotic coupling hypoth-
esis of free-energy transduction (Mitchell, 1961). When molecular biology and
