Information Technology Reference
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autonomous, adaptive agents (e.g., Devine and Paton [5]). They have been
used to model the dynamics of population interaction over time in ecological
systems, but IBMs can equally be applied to biological systems at other levels
of scale. The IBM approach can be used to simulate the emergence of global
information processing from individual, local interactions in a population of
agents.
When it is sensible and appropriate, we seek to incorporate an ecological and
social view of inter-agent interactions to all scales of the biological hierarchy
[6, 12, 13]. In this case we distinguish among individual “devices” (agents),
networks (societies or communities), and networks in habitats (ecologies). In
that they are able to interact with other molecules in subtle and varied ways, we
may say that many proteins have social abilities [22, 25]. This social dimension
to protein agency also presupposes that proteins have an underlying ecology in
that they interact with other molecules including substrates, products, regula-
tors, cytoskeleton, membranes, water, and local electric fields. The metaphor
also facilitates a richer understanding of the information-processing capacities
of cells [11, 12, 24]. This can be characterized as an ability to act in a flexible,
unscripted manner—another feature of adaptive agents.
SCOPE FOR MICROPHYSICAL INFORMATION PROCESSING
IN PROTEINS
Following an established tradition that can be traced back to Rosen [17], we
support the view that information is generated at the quantum level and man-
ifested at mesoscopic and macroscopic levels within molecular and cellular
systems. Quantum effects can be related to many biological processes. Clearly,
interactions between photons and matter are quantum-mechanical in nature,
and so we may think about “biophotons,” bioluminescence, photosynthesis,
and photodetection. When molecular interactions occur in proteins and polynu-
cleotides, quantum processes are taking place; these can be related to shape-
based interactions and molecular recognition as well as to more long-range
phenomena. Cellular microenvironments are very far removed from
in vitro
homogeneous high-dilution experimental systems. They are highly structured,
with (relatively) low local water content and complex microarchitectures. A
number of molecules and molecular systems that could form part of cellular
quantum information-processing systems may be described. Components for
biological quantum information processing could include wiring (e.g., conduc-
tive biopolymers); storage (e.g., photosystem II reaction centers, cytochromes,
blue proteins, ferritin); and gates and switches such as bacteriorhodopsin, cell
receptors, and ATPase. Solitonlike mechanisms may result in the conduction
of electrons and bond vibrations along sections of alpha-helices, and Ciblis and
