Physics of Life (2022) / Chapter Skim
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Pages 140-158
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From page 140... ...
As discussed in Chapter 5, active matter now is a lively field of physics independent of its origins in the physics of living systems.
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From page 141... ...
Rao, and R.A. Simha, 2013, Hydrodynamics of soft active matter, Reviews of Modern Physics 85:1143, copyright 2013 by the American Physical Society.
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From page 142... ...
Recently, quantitative theories and related experiments based on active matter ideas have addressed questions such as the size and shape of mitotic spindles and the cortical flow leading to polarization of worm embryos. Connecting to the World The cytoskeletal networks of filaments and motors inside the cell are linked to the environment outside the cell through integrin protein assemblies (see Figure 3.12)
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From page 143... ...
Perspective Active matter provides a perspective on the emergence of structure and function from interactions among motile components. From this perspective, in looking at the cytoskeleton the "particles" are molecules, while in tissues the particles are cells, but the physical principles are the same.
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From page 144... ...
Important successes often have become part of the mainstream of neuroscience, but the effort to understand collective behavior in networks of neurons continues to occupy a significant part of the biological physics community, as experimentalists develop new instruments for quantitative exploration of network dynamics and theorists use neural networks as a source of new problems in statistical mechanics. Observing the Human Brain Humans have a special interest in the dynamics of their own brains.
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From page 145... ...
Monitoring Many Single Neurons Simultaneously At the opposite extreme from measuring the EEG is the measurement of electrical activity of single neurons in laboratory animals. The first such experiments in the 1910s strained the sensitivity of instruments in the physics laboratory, and there is continuing input from the physics community into these measurement techniques.
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From page 146... ...
more slowly, calcium concentration is a signal that traces a temporally smoothed version of electrical activity. Animals genetically engineered to express calcium-sensitive fluorescent proteins in their neurons thus make it possible to visualize electrical activity as a flickering movie of fluorescent signals.
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From page 147... ...
To make progress, two extreme simplifications emerged from the biological physics community. As often the case in the physics of interacting many-body systems, neither of these simplifications are literally correct for networks of neurons in real brains, but both have been powerful sources of ideas.
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From page 148... ...
The second, alterna tive simplification is to imagine that all synaptic connections are symmetrical, in which case the dynamics of the network are equivalent to motion on an energy landscape. In both cases, ideas from statistical physics play a key role in the analysis; more deeply, these model neural networks have been the source of new statistical mechanics problems.
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From page 149... ...
An important challenge in searching for collective behavior in networks of neurons, as in many other living systems, is the absence of the usual macroscopic, thermodynamic probes. Even in models that map to well-defined statistical physics problems, order parameters are complex combinations of activity across the network; available experimental manipulations do not couple naturally to these order parameters (as with applying a magnetic field to a ferromagnet)
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From page 150... ...
Nonetheless, there is general agreement that the biological physics community has played, and will continue to play, a crucial role in the development of imaging techniques for the acquisition of data and in the devel opment of analysis techniques for image processing and the elucidation of neural circuits. Extensive challenges concern the successful visualization and tracing of trillions of axons and their synaptic connections, key constituents of a complete connectome, as illustrated in Figure 3.14.
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From page 151... ...
Complete maps of the connections among tens of thousands of neurons d z = 4,006have been 4,012 achieved 4,022 in4,030 the fly brain, and there is intense effort in other systems. Different organisms, from hydra to octopus, are emerging rapidly Brain as model systems 4,039 in which 4,054 to make 4,070 coordinated 4,086 explorations of neural networks and behavior.
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From page 152... ...
The hope for the coming decade is that there will be not only continued, parallel progress in theory and experiment, but new ideas about how to build bridges between the two. COLLECTIVE BEHAVIOR Collective behaviors in animal groups provide some of the most familiar ex amples of emergent phenomena in living systems.
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From page 153... ...
FIGURE 3.15 Collective behaviors in animal groups, such as the large construction projects of ter mite nests, provide examples of emergent phenomena in living systems. Three-dimensional structure, reconstructed via X-ray tomography of a Cubitermes nest, from a set collected in equatorial forest regions of the Central African Republic and Cameroon.
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From page 154... ...
Analysis of correlation functions in flocks of European starlings showed, sur prisingly, that correlations among velocity fluctuations are independent of scale (see Figure I.3)
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From page 155... ...
These also are social behaviors, but evidently this term covers a much wider range of possibilities. In some cases, the collective behavior is so compelling that what emerges is a "superorganism," as with social insects such as termites, ants, and social wasps.
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From page 156... ...
The biological physics community's understanding of flocks and swarms began with somewhat complicated agent-based models from the biological literature and went through phases of simplification and deeper theoretical analysis, followed by dramatic improvements in quantitative measurement that exposed new statistical physics problems. The understanding of social insects seems somewhere near the beginning of this process, and it is encouraging to see new experiments probing the collective behaviors of honeybees, ants, and others using modern physics-based ap proaches.
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From page 157... ...
In flocks and swarms, and with social insects, the search for theories proceeds in parallel with dramatic improvements in experimental observations, and there are opportunities for substantial leaps forward in the coming decade. The world of collective behaviors is much larger than described in this section, and it is possible that the deepest insights will come from taming an example that currently is only barely explored.
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From page 158... ...
As will be familiar from examples in previous chapters, the biological physics community has made progress on understanding adaptation, learning, and evolution by engaging with the myriad details of particular examples. But standing behind these details is an approach to living systems more generally.
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