The Role of Theory in Advancing 21st-Century Biology Catalyzing Transformative Research (2008) / Chapter Skim
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6 What Are the Engineering Principles of Life?
6 What Are the Engineering Principles of Life?
Pages 90-109
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From page 90... ...
The engineering principles that make possible a space shuttle can be encapsulated in an engineering textbook. Is it possible that there are similarly fundamental principles governing the organization of dynamic interacting systems that hold across all scales of biology?
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From page 91... ...
However described and however generalizable they may be, the phenomena of modular organization, complex ensemble behavior that might be called emergent behavior, and robustness in biological processes exist and can be described and measured. Whether the best approach will be classical, using existing tools, or whether an entirely new set of formalisms will be required, the problem remains that effective conceptual and theoretical treatment of those topics is not yet available.
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From page 92... ...
or Some neurons die and most brain activity external changes continues normally Swarm travels despite death of individual locusts or geographical barriers Communities continue despite extinction of some species of inheritance. Genetic units were defined by certain abstract properties such as segregation of phenotypes upon genetic segregation without knowledge of their physical embodiment.
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From page 93... ...
, biological function (e.g., cognitive processes) , component interactions (e.g., protein complexes)
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From page 94... ...
For example, during development, gene regulatory feedback loops that have the property of driving cells into a new developmental stage can, through evolution, be linked to other developmental modules to implement major phenotypic changes. In Box 6-1 an example is given of a regulatory loop preserved in star fish and sea urchins but which in sea urchins has evolved to link to another module that drives the development of a skeletal system.
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From page 95... ...
, competition or antagonistic interaction may also be an essential force. For example, many gene regulation processes within a cell involve antagonistic interaction of two regulatory proteins competing for the same space on the DNA.
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From page 96... ...
not present in the starfish, while the GataE gene is auto-activated in the starfish and not in the sea urchin. Also, the FoxA gene represses the GataE gene in starfish but not in sea urchins.
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From page 97... ...
. PMC-specific Eve Transcription factors Krox Otx Krox Otx Endo16 Tbr Tbr Lim Bra FoxA GataE Bra FoxA GataE Endomesoderm Endomesoderm Skeletogenic Specification Specification Structural Genes Sea Urchin evolution of network over ~ 500M yrs Starfish Figure and photos courtesy of David Galas.
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From page 98... ...
In a sense, the cooperation of individual slime mold cells produces a coherent higher-scale individual as a slug and a fruiting body. The slug-like assemblies have a definite anterior and posterior, respond to envi ronmental gradients, and have coordinated motility: that is, the complex internal interactions of the individual cells are hidden to produce a higher organization that has distinct interface with the external environment.
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From page 99... ...
The recent explosion of functional genomics data has led to unprecedented large-scale assays of biological component interaction such as gene regulatory interaction and protein-protein interaction. A natural representation of such interactions is as a graph where each node represents an interacting unit (e.g., a protein)
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From page 100... ...
Ideas of how some component interactions might give rise to emergent behaviors in biological systems can be deduced by analogy with engineered
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From page 101... ...
Some of these networks produce extremely stable overall behavior, such as the physiological regulatory mechanisms that maintain our body temperature and blood pH within very narrow ranges. Other networks are able to generate irreversible switch-like behaviors, as when different cell types within a developing multicellular organism become committed to particular cell fates (cf.
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From page 102... ...
The existence of message-sending and m essage-receiving capacity in diverse species of bacteria has been facilitated by the ability of these organisms to exchange genetic information through the transfer of plasmids and phages. Therefore, a key ingredient for interacting parts, such as different species of bacteria, to display emergent behavior seems to be the existence of some process to pass information, sense information, and react to information.
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From page 103... ...
How components interact locally to produce global patterns is at the heart of the matter of emergent properties. A fundamental problem is what type of information transfer is carried out and how individuals are equipped to sense the input and act on it appropriately to produce the global patterns (Box 6-3)
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From page 104... ...
Therefore, to achieve a conceptual understanding of emergent properties requires the development of a theory on the architecture of biological systems, a theory of the Bauplan applicable to scales from protein structure to ecosystems. ROBUSTNESS OF BIOLOGICAL PHENOMENA By technological standards, all organisms are highly complex, consisting of hundreds of thousands of interacting chemical species and thousands of regulated genetic elements.
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From page 105... ...
An individual displays robust function while its component cells are constantly undergoing birth and death. Individual neurons maintain relatively constant activity patterns for much of the lifetime of the animal, despite the fact that the ion channels and receptors that control excitability are constantly being replaced at time scales of hours or days.
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From page 106... ...
Loss of a key predator could lead to a qualitative reorganization of a community, changing the level of a key molecule could lead to a switch in metabolism from dormancy to active proliferation, and changing the right set of amino acids could change the structure of a protein from an alpha-helix to a fundamentally different beta-sheet. Therefore, a key conceptual challenge is to understand and develop a theory of how robustness is promoted in biological systems and how it interplays with the control of sensitivity of the same systems.
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From page 107... ...
How do these processes with high inherent variability achieve precise system-level function despite such noise? Synthetic gene regulatory circuits have been constructed in bacteria that display precise dynamic behavior such as an inducible bi-stable switch (Isaacs et al., 2003)
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From page 108... ...
Is modular architecture a necessary requirement for generating complex biological objects? Modular construction is a human engineering concept and need not be a characteristic of evolutionarily derived biological objects or ecological assemblies.
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From page 109... ...
A major area of biological theory will be developing a similar understanding of constructive principles of biological organizations.
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