209
evolutionary selection pressures? What do these details mean for ecosystem dynamics and larger ocean processes now and in the future?
These and other important questions are now theoretically addressable through
(a) well-reasoned scientific thinking and experimentation, (b) collection of relevant
comprehensive molecular data (genomes, transcriptomes, proteomes, metabolomes), and (c) systematic, robust, and scientific methods of data interpretation,
aggregation, analysis, modeling, prediction, and validation.
10.2 Systems Biology
The specific organization and intrinsic biological programs operating within living
cells in their environments define their functional and ecological roles. Cast about
randomly in a marine environment, the millions of highly specialized biomolecules
inside a cell would accomplish very little, fail to self-replicate, and quickly cease to
exist. Simply cataloging their presence individually in that case would mean equally
little: it is the programmed and compartmentalised coordination of these biomolecules that govern their existence and functions. The systematic co-organization of
nucleic acids, proteins, metabolites, and systems by millions of years of evolutionary selection results in irreducible and interconnected processes. This integrative
nature is essential to their functions and relevance, and this thinking motivates and
defines “systems biology” as a scientific discipline (Ideker et al. 2001). It is not
simple however to accurately, rigorously, and scientifically measure, model, and
study biological systems in an integrative or exhaustively detailed manner.
Biological systems can be defined at many levels: a single metabolic pathway,
signaling cascade, or set of coevolving gene functions; each operates as a molecular
system. The outward functions of these systems are defined (and selected upon) as
much by their coalescent properties as a whole, as by the functions of their individual components. These small systems do not function or make sense except in
the context of the additional information contained within their coevolving properties and interactions. No protein, gene, or environmental response mechanism operates in isolation; the operation of one biomolecule, phenotype, or gene depends on
the functions and identities of others. Viruses, organelles, cells and tissues, organisms, populations, and ecosystems are all complex biological systems, whose relevance and operation similarly cannot be reduced to individual parts without missing
critical information. Likewise, the relevance and specific effect or response of any
single environmental variable can only be understood or predicted in the context of
co-varying conditions. The unique and irreducible information stored within the
context and arrangement of a biological system in its dynamic environment is essential to understanding its nature and operation—and the principles and theories
therein are as important to study, measure, model, and predict as the properties of
single genes, proteins, or metabolic components.
The importance of this “systems-level” thinking has long been recognized (von
Bertalanffy 1968) but seldom easily or scientifically addressed. Billions of
10 Marine Microalgae: Systems Biology from ‘Omics’
evolutionary selection pressures? What do these details mean for ecosystem dynamics and larger ocean processes now and in the future?
These and other important questions are now theoretically addressable through
(a) well-reasoned scientific thinking and experimentation, (b) collection of relevant
comprehensive molecular data (genomes, transcriptomes, proteomes, metabolomes), and (c) systematic, robust, and scientific methods of data interpretation,
aggregation, analysis, modeling, prediction, and validation.
10.2 Systems Biology
The specific organization and intrinsic biological programs operating within living
cells in their environments define their functional and ecological roles. Cast about
randomly in a marine environment, the millions of highly specialized biomolecules
inside a cell would accomplish very little, fail to self-replicate, and quickly cease to
exist. Simply cataloging their presence individually in that case would mean equally
little: it is the programmed and compartmentalised coordination of these biomolecules that govern their existence and functions. The systematic co-organization of
nucleic acids, proteins, metabolites, and systems by millions of years of evolutionary selection results in irreducible and interconnected processes. This integrative
nature is essential to their functions and relevance, and this thinking motivates and
defines “systems biology” as a scientific discipline (Ideker et al. 2001). It is not
simple however to accurately, rigorously, and scientifically measure, model, and
study biological systems in an integrative or exhaustively detailed manner.
Biological systems can be defined at many levels: a single metabolic pathway,
signaling cascade, or set of coevolving gene functions; each operates as a molecular
system. The outward functions of these systems are defined (and selected upon) as
much by their coalescent properties as a whole, as by the functions of their individual components. These small systems do not function or make sense except in
the context of the additional information contained within their coevolving properties and interactions. No protein, gene, or environmental response mechanism operates in isolation; the operation of one biomolecule, phenotype, or gene depends on
the functions and identities of others. Viruses, organelles, cells and tissues, organisms, populations, and ecosystems are all complex biological systems, whose relevance and operation similarly cannot be reduced to individual parts without missing
critical information. Likewise, the relevance and specific effect or response of any
single environmental variable can only be understood or predicted in the context of
co-varying conditions. The unique and irreducible information stored within the
context and arrangement of a biological system in its dynamic environment is essential to understanding its nature and operation—and the principles and theories
therein are as important to study, measure, model, and predict as the properties of
single genes, proteins, or metabolic components.
The importance of this “systems-level” thinking has long been recognized (von
Bertalanffy 1968) but seldom easily or scientifically addressed. Billions of
10 Marine Microalgae: Systems Biology from ‘Omics’