Systems Biology - concepts, properties and insights

 Systems biology sees an organism as a living system and not as a machine. Living organisms, societies and ecosystems are all systems. Living systems form multi-leveled structures. Each level consists of several subsystems. The molecules in the subsystems combine to form organelles, which in turn combine to form cells. The cells form tissues and organs, which themselves form larger systems like digestive or nervous systems. They altogether present a ‘stratified order’ of organization from molecules to human beings. Then people form families, tribes, societies and nations.

What are natural systems?

All the natural systems are integrated wholes, whose specific structures arise from the interactions and interdependence of their parts. Most natural systems are hierarchical: they are composed of smaller sets of systems made up of smaller interacting parts. The properties of a system cannot be reduced to those of its parts. A living system is capable of adaptation and evolution. In the evolutionary process, there is a progressive increase of complexity, coordination and interdependence. The living systems exhibit self-maintenance which includes the processes of self-renewal, healing, homeostasis and adaptation. They also show self-transformation and self – transcendence, a phenomenon that expresses itself in the processes of learning, development and evolution.

The living organisms have an inherent potential for reaching out beyond themselves to create new structures and new patterns of behavior. The stability of a living system is continually tested by its fluctuations. When a system is disturbed, it has the tendency to maintain its stability by means of negative feedback mechanism. The stability of a living system is never absolute.

Example of a natural system

Planet earth is an integrated system consisting of 4 main subsystems. The lithosphere consists of rocks and minerals that form the solid body of the earth. The atmosphere has a layer of air surrounding the earth’s surface. The hydrosphere forms water on and near the earth’s surface. The biosphere is a layer of living organisms of which human beings form a part.

What is a system?

The word ‘system’ is defined as a group of interrelated, interacting or interdependent constituents forming a complex whole. The components work together to perform a function e.g., a computer.

There are three propositions in the definition: 1.the system is made up of component parts; 2.the parts work together; 3. The whole thing serves some purpose.

A system is a set elements that are orderly and interrelated to make a functional whole e.g., social system

Boundaries are the borders that separates one entity from another e.g., skin. Homeostasis is the tendency of a system to maintain a relatively stable, constant state of balance.

Systems view – looks at the world in terms of relationships and integration.

Systems thinking –it is process thinking.

Systems approach – emphasizes basic principles of organization.

Concept of holon and holarchy

Holon implies wholeness. A holon is something that is simultaneously a ‘part’ and a ‘whole’. The term holon was coined by Arthur Koestler from the Greek ‘holos’ meaning whole (all) and the suffix ‘-on’ meaning an individual part. This concept describes something that is whole in itself and, simultaneously a part of a larger system. So the main characteristic of a holon is the duality of being both an autonomous whole, while also being a part of a larger whole. This larger whole does only exist by the combination and the interactions of the composing parts holons. In other words a holon is a whole to those parts beneath it in a hierarchy but a part to those wholes above it. For example we can see an organization as a holon, because it is made up of smaller systems (e.g., people), but it is also a part of a larger system ( e.g., the community or economy).
A holarchy is conceived of as a hierarchical structure of holons. Our body, society, nature, the earth and the universe are all examples of so-called holarchies. The holarchy is the grouping of parts to create larger wholes where wholes are greater than the sum of the composing pats and each part in itself is also a whole.
                              Organisms-->organs-->tissues-->cells--->molecules.

Objective of systems biology

The world of nature is often very complex. To understand this complexity, scientists try to envisage ‘systems model’. Models in science tend to be simplified representations of reality that can be explained mathematically and through the use of graphics.

                                 Inputs----àSystem----àoutputs

Common characteristics of systems

1.    All systems have some structure and organization.

2.    They are all some extent generalizations, abstractions or idealizations of the real world.

3.    They all function in some way.

4.    There are, therefore functional as well as structural relationships between the units.

5.    Function implies the flow and transfer of some material.

6.    Function requires the presence of some driving force or source of energy.

7.    All systems show some degree of integration.

Properties of biological systems

1.    A biological/ natural system is intrinsically dynamic in nature. They show a high degree of internal flexibility and plasticity. It is this flexibility that enables living organisms to adapt to new circumstances.

2.    The functioning of organisms is guided by cyclical patterns of information flow known as feedback loops. When a system breaks down the break down is usually caused by multiple factors that may amplify each other through interdependent feedback loops.

3.    A living organism is a self-organizing system, which means that its order in structure and function is not imposed by the environment but is established by the system itself.

4.    Living organisms are open systems which mean that they have to maintain a continuous exchange of energy and matter with their environment to stay alive.

5.    Living organisms have a high degree of stability with dynamic properties. The stability consists in maintaining the same overall structure in spite of ongoing changes and replacements of its components.

6.    The phenomenon of self-organization is dynamic with self-renewal and self-transcendence. Self-renewal is the ability of living systems continuously to renew and recycle their components, while maintaining the integrity of their overall structure. Self-transcendence is the ability to reach out creatively beyond physical and mental boundaries in the process of learning, development and evolution.

7.    Fluctuations play a central role in the dynamics of self-maintenance. All variables of the system oscillate between a wide range of upper and lower limits so that the system is in a state of continual fluctuations, even when there is no disturbance. Such a state is known as homeostasis.  It is a state of dynamic and transactional balance. Negative feedback is only one aspect of self-organization through fluctuations.

Types of systems

Systems can be divided into open and closed systems depending on the inputs and outputs of energy.Traditionally systems can be 4 types like morphological, cascading, and input-output and control systems.

Black box system-we only understand inputs and outputs

Grey box system – we understand internal working

White box system – we understand individual components, their flows and storages.
Thermodynamic systems classification
An open system exchanges matter and energy with its environment.
A closed system exchanges only energy with its environment.
An isolated system exchanges neither matter nor energy with its environment.

Key traits of environmental systems

1.    Openness – it exchanges matter and or energy with other systems.

2.    Integration – refers to the strength of the interactions among the parts of the system and

3.    Complexity- how many kinds of parts a system has.

   Traits of an ecosystem

   An ecosystem is basically an energy processing and nutrient-regenerating system. Plants and animal populations within the system represent the subsystems. Inputs into the systems are both biotic and abiotic. The abiotic inputs are energy and inorganic matter. Radiant energy influences temperature, moisture, seasonality and photosynthesis. Inorganic matter consists of all nutrients like water, carbon dioxide, oxygen and so forth that affect the growth, reproduction and replacement of biotic material and maintenance of energy flow. The biotic inputs include other organisms that move into the ecosystem.