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William Bialek
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Theoretical physics is the search for simple and universal mathematical descriptions of the natural world. In contrast, much of modern biology is an exploration of the complexity and diversity of life. For many, this contrast is prima facie evidence that theory, in the sense that physicists use the word, is impossible in a biological context. For others, this contrast serves to highlight a grand challenge. Im an optimist, and believe (along with many colleagues) that the time is ripe for the emergence of a more unified theoretical physics of biological systems, building on successes in thinking about particular phenomena. In this essay I try to explain the reasons for my optimism, through a combination of historical and modern examples.
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Life is characterized by a myriad of complex dynamic processes allowing organisms to grow, reproduce, and evolve. Physical approaches for describing systems out of thermodynamic equilibrium have been increasingly applied to living systems, which often exhibit phenomena unknown from those traditionally studied in physics. Spectacular advances in experimentation during the last decade or two, for example, in microscopy, single cell dynamics, in the reconstruction of sub- and multicellular systems outside of living organisms, or in high throughput data acquisition have yielded an unprecedented wealth of data about cell dynamics, genetic regulation, and organismal development. These data have motivated the development and refinement of concepts and tools to dissect the physical mechanisms underlying biological processes. Notably, the landscape and flux theory as well as active hydrodynamic gel theory have proven very useful in this endeavour. Together with concepts and tools developed in other areas of nonequilibrium physics, significant progresses have been made in unraveling the principles underlying efficient energy transport in photosynthesis, cellular regulatory networks, cellular movements and organization, embryonic development and cancer, neural network dynamics, population dynamics and ecology, as well as ageing, immune responses and evolution. Here, we review recent advances in nonequilibrium physics and survey their application to biological systems. We expect many of these results to be important cornerstones as the field continues to build our understanding of life.
If the results of the first LHC run are not betraying us, many decades of particle physics are culminating in a complete and consistent theory for all non-gravitational physics: the Standard Model. But despite this monumental achievement there is a clear sense of disappointment: many questions remain unanswered. Remarkably, most unanswered questions could just be environmental, and disturbingly (to some) the existence of life may depend on that environment. Meanwhile there has been increasing evidence that the seemingly ideal candidate for answering these questions, String Theory, gives an answer few people initially expected: a huge landscape of possibilities, that can be realized in a multiverse and populated by eternal inflation. At the interface of bottom-up and top-down physics, a discussion of anthropic arguments becomes unavoidable. We review developments in this area, focusing especially on the last decade.
In this paper I am presenting an overview on several topics related to nonequilibrium fluctuations in small systems. I start with a general discussion about fluctuation theorems and applications to physical examples extracted from physics and biology: a bead in an optical trap and single molecule force experiments. Next I present a general discussion on path thermodynamics and consider distributions of work/heat fluctuations as large deviation functions. Then I address the topic of glassy dynamics from the perspective of nonequilibrium fluctuations due to small cooperatively rearranging regions. Finally, I conclude with a brief digression on future perspectives.
Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental assumptions and questions in the field, identify basic design principles and develop a key underlying theme -- the dynamics of quantum dynamical networks in the presence of an environment and the fruitful interplay that the two may enter. At the hand of three biological phenomena whose understanding is held to require quantum mechanical processes, namely excitation and charge transfer in photosynthetic complexes, magneto-reception in birds and the olfactory sense, we demonstrate that this underlying theme encompasses them all, thus suggesting its wider relevance as an archetypical framework for quantum biology.
We extend the Hopf algebra description of a simple quantum system given previously, to a more elaborate Hopf algebra, which is rich enough to encompass that related to a description of perturbative quantum field theory (pQFT). This provides a {em mathematical} route from an algebraic description of non-relativistic, non-field theoretic quantum statistical mechanics to one of relativistic quantum field theory. Such a description necessarily involves treating the algebra of polyzeta functions, extensions of the Riemann Zeta function, since these occur naturally in pQFT. This provides a link between physics, algebra and number theory. As a by-product of this approach, we are led to indicate {it inter alia} a basis for concluding that the Euler gamma constant $gamma$ may be rational.
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