Physics of Life (2022) / Chapter Skim
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Introduction and Overview
Introduction and Overview
Pages 5-44
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From page 5... ...
The physics community takes seriously the Galilean dictum that "the book of Nature is written in the language of mathematics," and searches for an understanding that is expressible in a compact and compelling mathematical structure. This understanding emerges through an intricate dialogue between theory and experiment.
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From page 6... ...
New science is fueled by new young people entering the field, and it matters how they are educated. Integration of biological physics into the physics curriculum, at all levels, can be synergistic with a broader modernization of physics teaching and the nurturing of a more quantitative biol ogy (Chapter 8)
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From page 7... ...
In this first attempt to survey biological physics as a part of physics, the committee has taken a broad view: Biological physics is the effort to understand the phenomena of life in ways that parallel the physicists' understanding of the inanimate world, prizing the search for new physics that does not have an obvious analog outside the living world. Even though physicists ask different questions, the biological physics community often builds on foundations laid by generations of biologists.
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From page 8... ...
This flow of ideas and methods across disciplinary boundaries speaks to the centrality of biological physics in the current scientific landscape. A Brief History For centuries, the phenomena of life were seen as fundamental challenges to human understanding of the physical world.
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Even chaos itself could be tamed. These successes certainly emboldened the physics community, providing examples where it was possible to "find the physics" in ever more complex systems.
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From page 10... ...
Beyond the electrical currents flowing through single ion channels, or the voltages generated by single cells, new methods make it possible to monitor, simultaneously, the electrical activity of hundreds or even thousands of individual neurons in the brain as an animal executes complex behaviors. Beyond the classic experiments of tracking the behavior of a single bacterium, experiments now monitor thousands of individual cells in a growing bacterial community, or thousands of individual birds in a flock, as they engage in collective behaviors.
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Condensed matter physics studies the unexpected behaviors that emerge when very many particles interact with one another. In this catalogue of extremes, biological physics is concerned with matter that is extremely organized, and organized in ways that make possible the remarkable functions that are the everyday business of life.
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From page 12... ...
(B) FIGURE I.1 Determining the structure of DNA was a seminal moment for nascent biological physics, as it captured the attention of the physics community.
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This is evident on very large scales, as with the ordered yet fluid behavior of birds in a flock, but also on very small scales, as protein structures emerge from interactions among many amino acids. It is an old dream of the physics community that such emergent phenomena in living systems could be described in the language of statistical mechanics.
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From page 14... ...
Statistical physics provides a unifying language, connecting phenomena across the full range of scales, identifying new kinds of order, and locating living systems in the phase diagram of possible systems. Searching for What Is Special About Living Systems Biological physics encourages us to view living systems as examples drawn from a much larger class of possible systems.
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From page 15... ...
This example connects otherwise arbitrary facts about the living world to basic physical principles, quantitatively, and is based on the idea that evolution can select for structures and mechanisms that come close to the physical limits on their performance at tasks crucial in the life of the organism. Ideas in this spirit now appear more widely, both in the abstract and in detailed partnership with experiment: Amino acid sequences could be selected to minimize the competing interactions that would frustrate protein folding; gene expression levels in bacteria could be tuned to maximize the conversion of nutrients into growth; the dynamics
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From page 16... ...
of immunological memory could be selected to optimize the response to the likely time course of antigenic challenges; neural codes could provide efficient representa tion of information in patterns of electrical activity, or efficient storage of memories in patterns of connections between neurons. Even if real organisms do not reach true optima, these theories provide useful idealizations and more precise ideas about what physics problems organisms need to solve in order to survive.
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From page 17... ...
Many crucial functions operate in a limit where information is scarce, creating pressure to represent and process this information efficiently; new physics emerges as mechanisms are selected to extract the maximum information from limited physical resources. Understanding the physics of living systems requires us to understand how information flows across many scales, from single molecules to groups of organisms, as described in Chapter 2.
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Many of the central questions in biological physics are aimed at understanding these emergent phenomena, as described in Chapter 3. How do living systems navigate parameter space?
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Along the way to realizing this promise, the biological physics community will develop new experimental methods that expand our ability to explore the living world, and new theories that expand the conceptual framework of physics. Success will lead to a redrawing of the intellectual landscape, likely in ways that will surprise us.
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From page 20... ...
Although many people have the sense that biological physics is a nascent or minor activity in the physics community, in fact the number of students receiving physics PhDs with a specialization in biological physics has grown, in just 15 years, to a volume comparable to that of well-established subfields (see Figure 8.1 in Chapter 8)
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From page 21... ...
Experiments from the biological physics community provide the most compelling measurements of the entropic elasticity of polymers, a problem that appears in almost all statistical physics textbooks. Polymers, membranes, and other materials inspired by biological molecules were at the origins of soft matter physics, while attempts to describe the collective behavior of flocks and swarms provided a foundation for the field of active matter; soft and active matter now are burgeoning fields of physics, independent of their connection to the phenomena of life.
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. Thinking about the dynamics of these biomolecules has been driven by the theoretical ideas about energy land scapes which emerged from the biological physics community.
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This report takes a broad view of the biological physics community, recognizing that many exciting developments also could be categorized as biophysics or quantitative biology. This in clusive view is used also in describing the historical development of the field, recognizing that early work by physicists who asked new questions and brought new tools to explore the phe nomena of life should be seen as continuous with the 21st-century version of biological physics.
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From page 24... ...
. This has involved a mix of theory and experiment, observing the dynamics of single channels but also building mathematical models that explain how these dynamics shape the computations done by neurons; making it possible to record, simultaneously, the electrical activity of thousands of neurons but also providing theoretical frameworks within which to search for meaningful collective dynamics in these large data sets.
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From page 25... ...
Prosthetic devices, from cochlear implants for the deaf to brain-computer interfaces for quadriplegics, depend on recording/stimulation methods that grow out of techniques developed in the biological physics community, and theoretical ideas about how information is represented in the brain. Tools and ideas developed in studying the physics of living systems provide a foundation for the design of new molecules with useful functions, and there is a particularly close connection between theoretical ideas about protein folding and the design of new proteins.
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From page 26... ...
The ease with which we walk or run through complex environments belies the enormously challenging physics problems that complicate efforts to build robots. There are clear paths from ideas in the biological physics community about the mechanics and neural control of movement to robots that implement a broad range of locomotion strategies, from insect-like hexapods to snake-like limbless robots.
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From page 27... ...
Ideas and results from the physics of living systems convey central ideas in physics: Flying, swimming, and walking provide an engaging universe of examples in classical mechanics; the dynamics of neurons provide examples of electric circuits and current flow; optical trapping and super-resolution microscopy illustrate deep principles of electromagnetism and optics; and the broad optical absorption bands of biological molecules, which literally provide color to much of our world, provide opportunities to build quantum mechanical intuition beyond the energy levels of isolated atoms. The concepts and methods of statistical physics, in particular, are illustrated by numerous phenomena from the living world, on all scales from protein folding to flocking and swarming.
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From page 28... ...
As in many fields, there is a challenge in maintaining a portfolio of mechanisms to fund the spontaneity of individual investigators, the supportive mentoring environ ments of research centers, and the ambitious projects requiring larger collabora tions. As biological physics matures, theory plays a more central role, not just as a tool for data analysis but as an independent activity, and there is an opportunity to develop programs that support this independence, as in other subfields of physics.
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From page 29... ...
The first such survey was released by the National Research Council in 1966.2 Twenty years later,3 Physics Through the 1990s divided physics into six subdisciplines, each described in a separate volume: elementary particle physics; nuclear physics; condensed matter physics; atomic, molecular, and optical physics; plasmas and fluids; and gravitation, cosmology, and cosmicray physics. There was, in addition, a volume devoted to "scientific interfaces and technological applications," and that volume contained a section about biophysics.
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From page 30... ...
Where the physicist's intel lectual style can seem demanding and inaccessible, taking inspiration from the phenomena of life connects these scientific ambitions to the imagination of a wider audience. Many members of the biological physics community see this as a special path to exciting the public about science more generally, to recruiting and retaining a more diverse community of students, and ultimately to shaping how we think of ourselves as humans.
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From page 31... ...
These disclosures are updated over the course of the committee's work, and the final editing of the report provided a chance to revisit these issues, which can be subtle. As an example, not only have all committee members been supported by one or more of the federal agencies and private foundations whose funding programs are described in Chapter 9, several committee members have provided advice to these agencies and foundations.
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From page 32... ...
This leads to the committee's first, overarching conclusion: Conclusion: Biological physics, or the physics of living systems, now has emerged fully as a field of physics, alongside more traditional fields of astro physics and cosmology; atomic, molecular, and optical physics; condensed matter physics; nuclear physics; particle physics; and plasma physics. At the same time that this report marks the emergence of biological physics as a distinct enterprise, it is essential to remember that all fields of physics have extensive connections to one another, and to other disciplines: Conclusion: Explorations in the physics of living systems have produced re sults, ideas, and methods that have had enormous impact on neighboring fields within physics, many fields of biology, on the sciences more generally, and on society through medicine and industry.
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Specific Recommendation: The biological physics community should sup port exploration of the full range of questions being addressed in the field, and assert its identity as a distinct and coherent subfield embedded in the larger physics community. Educating the Next Generation Establishing a new field and stretching the boundaries of well-established disciplines are multigenerational projects.
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Specific Recommendation: Physics faculty should modernize the presenta tion of statistical physics to undergraduates, find ways of moving at least parts of the subject earlier in the curriculum, and highlight connections to biological physics. Finding: Current treatment of optics in the undergraduate physics curriculum does not reflect modern developments, many of which have strong connections to biological physics.
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From page 35... ...
Twenty years ago, the BIO 2010 report brought attention to the educational challenges that follow from these developments, emphasizing that quantitative measurements and mathematical analyses would play a central role in the future of the biomedical sciences.7 The intervening decades have seen even more rapid progress, in directions that have strong overlap with the interests of the biological physics community. These developments underscore the continued relevance of the message in BIO 2010.
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From page 36... ...
Conclusion: The biological physics community has a central role to play in initiatives for multidisciplinary education in quantitative biology, bioengineer ing, and related directions. General Recommendation: University and college administrators should al locate resources to physics departments as part of their growing educational and research initiatives in quantitative biology and biological engineering, acknowledging the central role of biological physics in these fields.
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Finding: Department of Defense agencies have highlighted multiple areas where the interests of the biological physics community intersect their missions.
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As an alternative to looking at individual agencies, it also is useful to look at how funding is distributed across other dimensions of the scientific enterprise: Conclusion: As in many areas of science, there is a challenge in maintaining a portfolio of mechanisms to fund the spontaneity of individual investigators, the supportive mentoring environments of research centers, and the ambitious projects requiring larger collaborations. Finding: Physics programs do not have the stable, programmatic support for PhD students that is the norm in the biomedical sciences.
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From page 39... ...
Finding: Large-scale physical tools, particularly those for imaging and ad vanced computing and data, are an important part of the infrastructure sup porting thousands of researchers exploring the living world. Conclusion: There is an opportunity for Department of Defense agencies to use the Multidisciplinary University Research Initiatives Program to support biological physics, and for the National Science Foundation and the National Institutes of Health to expand their support of these mid-sized collaborations.
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From page 40... ...
Specific Recommendation: Federal agencies and private foundations should develop funding programs that recognize and support theory as an indepen dent activity in biological physics, as in other fields of physics. Finally, an essential part of the justification for federal support of science is that it generates useful products.
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From page 41... ...
Chapter 10 explores the human dimensions of science, focusing on international engagement and equality of opportunity. Many of the issues are immediately relevant to biological physics, but also much more general, and need to be addressed across science as a whole.
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From page 42... ...
policy toward international students and scientists are being driven by concerns about national and economic security. Conclusion: The open exchange of people and ideas is critical to the health of biological physics, physics, and the scientific enterprise generally.
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From page 43... ...
Although the experience of each group is unique, one can find related problems for all of the underrepresented groups in the biological physics community. Parallel to the role of Historically Black Colleges and Universities (HBCUs)
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From page 44... ...
There is a sense, however, that biological physics has a special role to play in welcoming a broader community. Conclusion: The biological physics community has a special opportunity to reach broader audiences, leveraging human fascination with the living world to create entrance points to physics for a more diverse population of students and for the general public.
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