Biology Reference
In-Depth Information
a generic concept of phenotype there can be no context for
a deep, predictive understanding of the relationship between
genotype and phenotype. This chapter will address this issue
and its importance for revealing the system design principles
arrived at by the operation of natural selection. But first some
background will be provided to set the stage.
Systems
There is no universally accepted, unambiguous definition
for what we mean by a 'system'. Any dictionary typically
has dozens of definitions. I have previously formulated the
following
[2]
, which will be helpful for my purposes here:
A system can be defined as a collection of interacting parts that in
some sense constitutes a whole. Everything excluded from the
collection is considered the environment of the system. It is
immediately obvious that if the parts mentioned in the above
definition are also made up of interacting parts, then they too fit
the definition and could therefore be considered as subsystems.
BACKGROUND
The experimental study of specific systems by molecular
biologists has revealed an immense variety of molecular
mechanisms that are combined into complex networks, and
the patterns of gene expression observed in response to
environmental and developmental signals are equally
diverse. Despite this impressive progress we are at a loss to
understand the integrated behavior of most cell and molec-
ular systems. Even in the best-studied organisms we are
unable to predict the response to a specific change in its
genome or its response to a novel compound in the envi-
ronment. In short, our knowledge is still fragmented and
descriptive: we have almost no understanding of the 'design
principles' that govern cell and molecular systems. Uncov-
ering these design principles will be important not only for
understanding the normal function of cell and molecular
systems but also for developing judicious methods to redi-
rect normal expression for biotechnological purposes or to
correct pathological expression for therapeutic purposes.
If there is to be an understanding based on design
principles, then it must integrate the principles of physics,
chemistry and biological organization. Although organisms
must deal with many forms of energy, the basic unit of
exchange is chemical. All other types of energy are inter-
convertible with the chemical form by means of specialized
energy-transduction processes. Electromagnetic energy is
converted to chemical energy in photosynthesis, whereas
chemical energy is converted to mechanical energy in
muscle contraction. Aside from such specialized energy
conversions, the overwhelming majority of cellular func-
tions are of a strictly chemical nature.
Although chemical change can be described in a variety of
ways, the most fruitful in dealing with large systems are
quantitative: to what extent a reaction normally takes place,
and how fast it proceeds. These thermodynamic and kinetic
aspects have had extensive development. The conventional
representation in dealing with chemical kinetics is the mass-
action formalism, whereas that in dealing with biochemical
kinetics is the rational-function formalism, which results from
mass action with constraints. Both of these formalisms can be
considered special cases of the generalized mass-action
formalism that will be discussed in detail later in this chapter.
In this way a description of nature in terms of a hierarchy of
systems is produced. For example, cells could be considered
the subsystems of a tissue, tissues the subsystems of an
organ, and organs the subsystems of an organism. This
hierarchy could be greatly extended in both directions.
One does not study the universe but only some portion
or level within its total hierarchical representation. In the
selection of a system as a subject for investigation two
conflicting demands are encountered: (a) the need to
maintain wholeness, and (b)
the need to limit
the
complexity of the problem.
Wholeness and Open Systems
The idea of wholeness connotes a complete or closed
system, an idealization that is approached to varying
extents in different cases. Many examples of close
approximation to a closed system can be found among
technological systems in which the concept of modularity
originated. However, one of the most characteristic features
of biological systems is that they are open, i.e., they are
characterized by a high degree of interaction with their
environment.
Biological systems seldom present themselves as well
defined or closed: the investigator must make choices. This
is an art, not a mechanical process, and the importance of
intimate familiarity with the system should not be over-
looked. Nevertheless, the choice for delineation of a system
must be made according to some criterion such as the
following: Let systems be selected so as to maximize the
numerical ratio of internal interactions to external inter-
actions. In this way the resulting system will tend to have
a minimal number of interactions with its environment, but
at the same time a maximum number of interactions will be
included within the system. This choice will tend to
preserve the integrity of critical functional groupings,
which is important because certain phenomena cannot be
adequately understood by simply analyzing the component
parts of a system. At certain levels of organization new
properties emerge that can be understood only at these
levels; such phenomena must be treated as a whole.
Nothing in biology makes sense except in the light of systems.
with apologies to Dobzhansky
