Biology Reference
In-Depth Information
in terms of biochemistry as we know it. I shall show how it is possible to com-
bine these two strands of thought into a relational model that commutes with
our current knowledge of cellular biochemical processes. This model, which I
call a metabolism-construction-assembly system, also makes explicit the role
of information, and identifies unassisted self-assembly as the process that ulti-
mately makes the system self-fabricating (or, using Rosen's words: 'closes the
system with respect to efficient causation'). What makes this model even more
interesting is that it is consistent with Barbieri's ribotype theory, and, through
that, with the body of thought known as biosemiotics.
1. HOW TO BE A SYSTEMS BIOLOGIST
The aim of this topic is to explore the possibility that systems biology may need
philosophical foundations of its own. I believe it does, and that systems biology
should aim to provide a way of thinking about living organisms that will allow
us to understand them as autonomous entities. At present the dominant views of
biology are through the glasses of evolutionary biology and of molecular biology.
Evolutionary biology seeks to understand life in terms of how natural selection
has moulded organisms through the millennia. The philosophy of molecular
biology is based on the idea that exhaustive knowledge of all the individual
molecular components of the cell will afford the best understanding of life. I
shall make a case for a philosophy of systems biology that is based on the
premise that the living state exists because of a particular organisation of the
internal components of cells.
What does systems biology actually entail in practice (Westerhoff & Hofmeyr,
2005)? If one listens to talks at conferences on systems biology (Cornish-
Bowden, 2005) or reads editorial introductions to special journal issues devoted
to systems biology (Russel & Superti-Furga, 2005), it becomes clear that
although many individual scientists who regard themselves as systems biologists
have very clear views on what they regard as the gist of their discipline, there
is no clear consensus. It also does not help that the phrase 'systems biology'
in a grant proposal has become, or is at least perceived as, a means for ensur-
ing funds. Be it as it may, the different views are all compatible and can be
consolidated into something along the lines of 'explaining or understanding
the emergence of systemic functional properties of the living cell as a result
of the interactions of its components'. How this is to be achieved is usually
seen to be by means of two approaches, either on their own or in combination
(Chapter 2). Both approaches espouse what I would call the 'system-wide' view:
the conviction that one cannot understand the cell if one does not consider it
as a whole. One approach comes from the age of 'omics' and proposes that,
now that the new high-throughput techniques have made it possible, we should
