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A Glossary for Systems Biology
Contents
Index - Glossary -
Model
A Closer
Systems Biology
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System
One term of central importance in systems biology clearly is system. Its central position is obvious by its frequency of use; it appears in every other sentence written about research in this field, either as the subject of research (a system of proteins/genes/...), as part of other terms of interest (systemic properties, ...) or even in the name of the field itself: systems biology.
It is good to see that a term as central to a topic as system in the case of systems biology is understood by everybody involved in mostly the same or at least very similar ways. Still, there are a few different aspects to the various uses of this term.
Etymology
The origin of the word system is Greek; two etymological explanations can be found, probably going back to a common root.
The first derives system from 'synthithemi' (I put together) [27], the second gives a direct meaning for system as 'a new and structured whole, put together out of distinct parts' or 'something that is put together from multiple different parts in an ordered way' [46]. All these explanations have the common denominator of 'putting something together'.
A more modern formulation could be that it ``represents a set of components together with the relations connecting them to form a whole unity'' [36].
This is a definition that everybody seems to agree on.
Still, the term system is used by different fields of research
in different ways.
It is not just used in biology and systems theory, either, though
the latter probably has the most general definition, as most other
fields' definitions can be expressed in terms of systems theory's
definition of system.
Systems Theory
Even the term 'systems theory' is ambivalent, though, as there are 'systems theories' in a number of sciences, like psychology, sociology, educational theory, or economy, to name just a few. For the purpose of systems biology - and thus for the purpose of this paper as well - 'systems theory' refers to a field of research in its own right, that has developed from network theory in electronics.
Definitions
There exist a number of definitions of what a system is, all slightly different, but mostly consistent in the major points (system, illustrations):
- Defining a system divides reality into the system itself and its environment.
- As a rule of thumb, the number of interconnections within a system is greater than the number of connections with the environment.
- Systems can include other systems as parts of their construction. This simple point has enormous implications, since it allows complex systems to be put together from known simple ones (system of systems), thus making it easier to research the former once the latter are understood. This concept of modularity is an important one in biology as well as systems theory.
Systems in Biology
Biologists use system as another word for 'organism', or to describe a part of an organism. They also use terms derived from the same roots, like 'systemic' for 'system-wide' or 'belonging to a system' and like 'systematic' referring to the sub-field of taxonomy. Some of these terms can again be found in other fields of science, with similar, but not quite identical, meanings.
As can be seen from these examples, a lot of other terms are based on, or derived from, system. This fact adds to its weight and makes a clear definition of the way it should be used in such an interdisciplinary field all the more important.
Systems in Systems Theory
Systems theory has a more abstract understanding of the term system. Here a system is an entity distinct from its environment (system), with certain special properties. The most important of those is that signals are only propagated in one direction within each of the system's components; feedback is only possible through interconnections between components [20].
For the purposes of systems theory, a system can be characterized by its input/output relationship (transduction function) alone. The physical implementation of a system is not important.
This is a viewpoint of systems theory that is not realistic in most other fields, since they mostly define themselves by the distinct physical form of implementation or by the characteristics of the kinds of system they are interested in: biological systems for biology, chemical systems for chemistry, electrical systems in electronics, and so on. But it is one of the central ideas in systems theory that enables it to treat physically different systems, as e.g. chemical and electrical systems, with the same theoretic framework and set of methods, providing a larger scope of systems properties.
Systems in Systems Biology
Something very similar is a goal in systems biology: there are subsystems (like metabolic pathways), which serve very different purposes, but nevertheless are built and behave in very similar ways. Examples are the module for bacterial chemotaxis, or the MAP kinase cascade [39].
One big step would be to be able to characterize those subsystems by their systemic behavior alone, to be able to describe distinct classes of systems and then to classify such metabolic pathways as instances of a certain type of pathway (or system) for a special substrate. This could prove that there are an ``evolutionary family of circuits as well as a periodic table for functional regulatory circuits'' [34].
This shows that systems biology and systems theory share some fundamental concepts and hopes. These include modular (sub)systems, classes of systems independent of physical implementation, directed signal propagation, and modularity, as shown above.
For the purpose of systems biology, the definition and concepts of systems originating in systems theory are probably most relevant.
The concept of systems also is closely related to that of model, even to the point that the two terms are often used interchangeably - something which should be avoided to keep mutual understanding from getting more complicated than it already is.
All in all, the concept of systems, especially with its connotations of modularity and abstraction through classes, is a major factor in the hopes and concepts at the heart of the systems-oriented branch of systems biology.
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University of Liège