Systems biology

Systems biology is a term used to describe an emerging approach applied to biomedical and biological scientific research. Systems biology is a biology-based inter-disciplinary field of study that focuses on complex interactions within biological systems, using a more holistic perspective (holism instead of the more traditional reductionism) approach to biological and biomedical research. Particularly from year 2000 onwards, the term systems biology has been used widely in the biosciences in a variety of contexts. One of the outreaching aims of systems biology is to model and discover emergent properties, properties of cells, tissues and organisms functioning as a system whose theoretical description is only possible using techniques which fall under the remit of systems biology. These typically involve metabolic networks or cell signaling networks.

Predicate calculus

Note: The following section was taken from "Systems Biology: Principles, Methods, and Concepts".

Deduction, induction, and pragmatic inference

Forming conclusions from premises is called inference. One can distinguish several types (modes) of systematic inference. Their non-exhaustive list includes:

1. Deduction (from general to specific;
2. Induction (from specific to general); and
3. Pragmatic inference
   • Abduction (finding the most plausible explanation available)
   • Consilience (transcending different sequences of inferences)

Formal logic, as we know it today, can only deal with deductive inferences and to some extent with induction (such as inductive proofs of properties of integers). All other types of systematic inference that appear similar to an intricate (i.e., not simple) induction are often referred to collectively as pragmatic inference. They cannot be easily formalized and thereby require language and domain-of-application-dependent conventions that would define their semantics (syntax alone will not suffice).

Inference via deduction always leads to specific conclusions from general premises. For instance, the implication: "every man is mortal, I am a man, and therefore I am mortal" is an example of deduction. The general scheme of deduction is:

1. Every object A has a property B.
2. Therefore, a given specific individual object A has a property B.

Induction is a derivation of a general conclusion from specific premises. The scheme of inductive inference is:

1. Every individual object A observed thus far has a property B
2. Therefore every A has property B

The question of what the phrase "thus far" should exactly mean has been hotly debated for centuries and is known under the name the Problem of Induction. If we see the night following the day, say 1000 times, does it mean that the night always follows the day? Or perhaps, in order to decide that it is always a case, we need to see that happening 10,000 times instead of 1000? What about 10,000,000 observations? Will we be more certain of the outcome than we would have been with only 1000 events?

Consilience, as we understand it today, is a synergistic combination of two or more (originally unrelated) sequences of inferences that can be transcended into a useful new concept or hypothesis.