Emergence - A System's elusive property

Systems Theory of Biology is a relatively new approach to how scientists once viewed having to explain phenomena. With a purely reductionist methodology, a given system was broken down into individual components and the complete knowledge of these components was additively thought to explain the behavior of the "whole". It was evident however that this was not the case. Use of computational tools and mathematical models to simulate biological systems in silico based on experimental data further reinforced this purview. Thus Systems Biology was born. Unlike the traditional reductionism, systems biology is an interdisciplinary approach that employs holism by considering not only components of a system but other attributes such as the complexity of interactions between components, environmental perturbations, subsystems, boundaries, etc. One of the more interesting of its considerations is a property called Emergence.

What exactly is Emergence?
For an understanding, emergent properties were thought to be irreducible, non- functionalizable fundamental properties exhibited by systems/sub-systems that could not be deduced from the properties of the systems/sub-systems components. In other words, the systems showed novel behavior that could not be explained by the properties of its components.

                   Fig1: A simplified look at emergent properties of a system (eg. Formation of water) 

Emergentist theorists, systems philosophers and biologists tread carefully even today to explain emergent properties in its entirety. This is primarily because although emergence is observationally intuitive, for it to be useful in scientific application its definition must encompass all its aspects some of which are still under debate. In most current applications, its presence is either taken for granted or adjusted for numerically.
Defining what counts as an emergent property has gone through a variety of views. Early 20th century saw Emergence as a vital force which meant it was treated as a non-physical property. Other philosophers conjectured that emergence would disappear as the tools to study systems improved. One of the earliest comprehensive views on emergence came from C.D. Broad. He went a step further to say that "complete knowledge" about components both in isolation and in "other wholes" were insufficient to predict the system's behavior. Although he was vague about what "other wholes" meant, a simple example of a chemical A (component) in 2 different environments XA and YA illustrates that properties exhibited by A in both environments will be different. Therefore we may infer that information about A from YA (other whole) and A in isolation are both insufficient to help predict A's properties in System X.
Down the line more clarity on the topic led to classifying emergence based on 2 notions. Strong emergence is when system level phenomena are dependent on properties of its components but not determined by it. It remains non deducible from lower level rules. Weak emergence on the other hand is when higher level phenomena is deducible from lower level rules but the phenomena is unexpected. Although both are important to biological systems, strong emergence is of greater interest at a fundamental level. This is because of the nature of its definition. Strongly emergent properties cannot be deduced by complete knowledge of lower level phenomena which means the fundamental principles of lower level domains need to be expanded upon to provide a mechanistic explanation of the higher level phenomena in question. This explains why science is more interested in strong compared to weak emergence.

Emergent properties in Biological systems
At the level of tissues and cells, many system level properties such as homeostasis, regulation, plasticity appear to be emergent. One of the simpler cases where emergence is evident is in the dogma of molecular biology (DNA->RNA->Protein). While it is true that genes determine the amino acid sequence of a protein, these gene level rules are not sufficient to describe the properties of proteins as there are many other processes involved such as mRNA regulation and protein folding which appear only at those levels. 

Fig2: Biochemical network with nodes representing metabolites and connections representing enzyme catalyzed interconversions.

In more recent years, study of dynamic properties of biochemical and genetic networks with respect to internal/external conditions and time has unearthed plenty about the intrinsic behavior of sub systems, their energetics and interactions with their parent system. Let us take up the example of the cell (System) and its organelles (subsystems). It was observed under specific cases of modeling that the properties of the cell was in part a function of its organelle as a "whole" which meant that, studying the components of the organelles themselves could not explain the cell's behavior. This was a key point presented by the case studies of F.G. Bruggeman and team. Another avenue in which emergent properties play a significant role is in genetic networks and gene expression shifts. Precisely speaking, properties such as critical dynamics of transitions in gene expression. To maintain genetic stability and aid evolvability, it is important for genetic networks to have an optimal robustness (resistance to external perturbations) and flexibility (degree of freedom). This optimal state is an emergent property called "Criticality" and it operates in and around phase transitions. There are many other emergent levels of regulation based on other contexts such as transcriptional or protein regulation such as mRNA degradation, protein folding and ubiquitination. 
In conclusion, while we have begun to account for the effects of emergence, we still continue to grapple with what it is and the extent of its role in systems biology. To quote anti-reductionist Karl Popper,
" life itself may be viewed as an emergent property of matter"

Sanjay Narayanaswamy

References:
1. Boogerd FC et al., 2005. 'Emergence and its place in nature: A case study of Biochemical networks' Synthese 145: 131-164.
2. Christian TS et al., 2012. 'Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability'  PLoS Computational Biology 9: e1002669.
3. Pepper S. 1926. 'Emergence' Journal of Philosophy 23: 241-245.
4. Srdjan K. 2015. 'Systems biology, Emergence and antireductionism' Saudi Journal of Biological Sciences 23: 584-591.
5. Schoen EL. 2007. 'The Re-emergence of Emergence: The Emergentist hypothesis from Science to religion' International Journal for Philosophy of Religion 62: 119.

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