Physics of Life (2022) / Chapter Skim
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From page 172... ...
The biological physics community has played a key role in recent efforts to understand these dynamics of stochastic evolutionary processes and the limits they place on optimization arguments in living systems. An important contribution from the biological physics community has been the calibration of ideas about evolutionary dynamics through the study of simplified models.
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Creative Commons License Attribution 4.0 International (CC BY 4.0)
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for the broader community, and biological physicists have played a key role in analyzing these data and making connections to theory. While the LTEE is a remarkably rich resource, it involves only 12 replicate populations of a single organism evolving in response to a single selective pres sure.
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. This combination of theory and experiment in the study of evolution is an example of how the intellectual scope of biological physics has expanded in the 21st century.
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The two strains of E coli were grown The biological physics community pioneered these separateexperiments, (identified here for E
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As discussed in Chapter 7, input from the biological physics community played an important role in realizing that HIV evolves rapidly, even over the lifetime of a single patient, and that effective treatments should take this into account. More recently, it has become possible to sequence samples from the population of viruses over time in many individual patients, sometimes in conjunction with surveys of the patient's antibody reper toire.
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FIGURE 4.8 The biological physics community pioneered DNA sequencing experiments that revo lutionized the exploration of antibody diversity. Statistical physics models provide a framework for inferring the parameters of recombination, deletion, and insertion events.
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H o w D o L i v i n g S y s t e m s N av i g at e P a r a m e t e r S pa c e ? 179 contributions to understanding the evolutionary process itself, particularly in re cent years.
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While biological physics has an independent existence, many of these new developments are deeply connected to progress in other fields, and this is part of the beauty of physics. This chapter surveys, briefly, some of the many points of contact between biological physics and the broader physics community, summarized even more briefly in Table 5.1.
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Conversely, the machine learning methods that are used today in the analysis of raw data from particle physics have their roots in models of brain func tion that began in the biological physics community. On the theoretical side, ideas from quantum field theory are central to thinking about the collective behavior of flocks and swarms, for example, but this reflects the merging of field theory and statistical physics that occurred in the 1970s, in the wake of the renormalization group.
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From page 184... ...
Similarly, although it was known in the 19th century that beams of light can apply forces to objects, it would take until the late 20th century to understand the conditions under which these forces could trap neutral particles. Crucially, optical traps or tweezers can produce forces on the scale of those generated by single biological molecules, which opened a whole genera tion of new experiments in the biological physics community (Chapters 1 and 2)
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The soft matter community has substantial overlap with the biological physics community, and many soft matter problems are interesting in part because they capture some aspects of living systems in simpler and more easily controlled contexts. As noted in Chapter 3, ideas from polymer physics also have been important in thinking about the structure and dynamics of chromosomes.
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From page 186... ...
Although the structures are intricate, there is no blueprint. Self-assembly is an important meeting ground for the biological physics and soft matter physics communities.
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Understanding of glassiness in random heteropolymers provides a benchmark for thinking about protein folding, ultimately leading to the view that amino acid sequences must be selected by evolution to avoid the glass transition (Chapter 3)
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As discussed in Part I of this report, the identification of these functions as physics problems, and understanding how they emerge, are central to biological physics. But the past two decades also have seen an explosion of activity in the statistical physics of small, non-equilibrium systems, more gener ally, often taking inspiration from the phenomena of life.
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(C) FIGURE 5.4 Testing the principles of non-equilibrium statistical mechanics with single biological molecules.
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This is generating a productive dialogue between the biological physics and active/soft matter communities, even driving the development of synthetic active systems. Understanding animal movement depends on understanding the environment in which this movement happens.
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There has been a productive interplay between nonlinear dynamics 3 2 8 | NaT U R E | VO L 5 4 5 | 1 8 m ay 2 0 1 7 and biological physics ©ever 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
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