Biology Reference
In-Depth Information
biochemistry and molecular biology study all the molecules that occur in organ-
isms, but they refrain from addressing the life that is embodied by all those
molecules. Although this claim of insufficiency of biochemistry and molecular
biology has often been made by physiologists and other organismal biologists,
it is not immediately appreciated by all, and certainly its remedy is not. There
is indeed a paradox: if biochemistry and molecular biology were to continue
to study and establish the structure and the mechanisms of action of every
macromolecule of a living organism, then they should ultimately understand that
whole living cell. For what else is there in a living cell than its molecules? This
contention is the most common version of the reductionist agenda: dissect any
system into its elements, study all those elements individually, and then just
understand the system. Technically, the 'just understand the system', implies
that system's behaviour can be understood as a superposition of how all its
components behave individually. The organismal biologists often observe that
when a living system is taken apart, it loses much of the essential behaviour of
living systems. This makes some of them turn to the holist agenda, which studies
only intact systems. This then makes them subject to much of the limitations
noted above for organismal biology, and more importantly, it implies that those
limitations will stay forever, independently of the progress of science.
The reductionist and holist paradigms seem to be irreconcilable, but below
we shall propose that through systems biology and the silicon-cell approach they
may not be. Here we shall first indicate why the 'just understand the system'
methodology does not work, i.e. why by themselves biochemistry and molecular
biology cannot produce biology. The reason is again the essential nonlinearities
of biological systems. Much of biology depends on dynamic phenomena that
emerge in nonlinear interactions. These cannot be understood by the simple
addition of the behaviour of the components in isolation. This is one reason
why biology lies outside the realm of biochemistry and molecular biology
sensu
stricto
. In other words, what makes a system different from its parts list is the
non-linear interactions between those parts, and these are changed or lost upon
disassembly.
2.4. Irreducibility
A third limitation is again related to the cartoon aspect of biochemistry and
molecular biology: in these new disciplines molecules are not drawn in terms
of their structure or chemical equation, but by coloured balls with short, non-
chemical names, such as hexokinase, HXK, Ras or wnt. These names serve
reasonably well as mnemonics. Attempts to give enzymes systematic names pro-
duced names that referred to their activity rather than to their chemical formula
or structure. The reason was that for many enzymes the chemical structure could
not be established, whereas at least some of the catalytic activities could be. The
