🔖 Why Boltzmann Brains Are Bad by Sean M. Carroll

Why Boltzmann Brains Are Bad by Sean M. Carroll (arxiv.org)
Some modern cosmological models predict the appearance of Boltzmann Brains: observers who randomly fluctuate out of a thermal bath rather than naturally evolving from a low-entropy Big Bang. A theory in which most observers are of the Boltzmann Brain type is generally thought to be unacceptable, although opinions differ. I argue that such theories are indeed unacceptable: the real problem is with fluctuations into observers who are locally identical to ordinary observers, and their existence cannot be swept under the rug by a choice of probability distributions over observers. The issue is not that the existence of such observers is ruled out by data, but that the theories that predict them are cognitively unstable: they cannot simultaneously be true and justifiably believed.
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🔖 How Life (and Death) Spring From Disorder | Quanta Magazine

How Life (and Death) Spring From Disorder by Philip Ball (Quanta Magazine)
Life was long thought to obey its own set of rules. But as simple systems show signs of lifelike behavior, scientists are arguing about whether this apparent complexity is all a consequence of thermodynamics.

This is a nice little general interest article by Philip Ball that does a relatively good job of covering several of my favorite topics (information theory, biology, complexity) for the layperson. While it stays relatively basic, it links to a handful of really great references, many of which I’ve already read, though several appear to be new to me. [1][2][3][4][5][6][7][8][9][10]

While Ball has a broad area of interests and coverage in his work, he’s certainly one of the best journalists working in this subarea of interests today. I highly recommend his work to those who find this area interesting.

References

[1]
E. Mayr, What Makes Biology Unique? Cambridge University Press, 2004.
[2]
A. Wissner-Gross and C. Freer, “Causal entropic forces.,” Phys Rev Lett, vol. 110, no. 16, p. 168702, Apr. 2013. [PubMed]
[3]
A. Barato and U. Seifert, “Thermodynamic uncertainty relation for biomolecular processes.,” Phys Rev Lett, vol. 114, no. 15, p. 158101, Apr. 2015. [PubMed]
[4]
J. Shay and W. Wright, “Hayflick, his limit, and cellular ageing.,” Nat Rev Mol Cell Biol, vol. 1, no. 1, pp. 72–6, Oct. 2000. [PubMed]
[5]
X. Dong, B. Milholland, and J. Vijg, “Evidence for a limit to human lifespan,” Nature, vol. 538, no. 7624. Springer Nature, pp. 257–259, 05-Oct-2016 [Online]. Available: http://dx.doi.org/10.1038/nature19793
[6]
H. Morowitz and E. Smith, “Energy Flow and the Organization of Life,” Santa Fe Institute, 07-Aug-2006. [Online]. Available: http://samoa.santafe.edu/media/workingpapers/06-08-029.pdf. [Accessed: 03-Feb-2017]
[7]
R. Landauer, “Irreversibility and Heat Generation in the Computing Process,” IBM Journal of Research and Development, vol. 5, no. 3. IBM, pp. 183–191, Jul-1961 [Online]. Available: http://dx.doi.org/10.1147/rd.53.0183
[8]
C. Rovelli, “Meaning = Information + Evolution,” arXiv, Nov. 2006 [Online]. Available: https://arxiv.org/abs/1611.02420
[9]
N. Perunov, R. A. Marsland, and J. L. England, “Statistical Physics of Adaptation,” Physical Review X, vol. 6, no. 2. American Physical Society (APS), 16-Jun-2016 [Online]. Available: http://dx.doi.org/10.1103/PhysRevX.6.021036 [Source]
[10]
S. Still, D. A. Sivak, A. J. Bell, and G. E. Crooks, “Thermodynamics of Prediction,” Physical Review Letters, vol. 109, no. 12. American Physical Society (APS), 19-Sep-2012 [Online]. Available: http://dx.doi.org/10.1103/PhysRevLett.109.120604 [Source]
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🔖 A de Bruijn identity for discrete random variables by Oliver Johnson, Saikat Guha

A de Bruijn identity for discrete random variables by Oliver Johnson, Saikat Guha (arxiv.org)
We discuss properties of the "beamsplitter addition" operation, which provides a non-standard scaled convolution of random variables supported on the non-negative integers. We give a simple expression for the action of beamsplitter addition using generating functions. We use this to give a self-contained and purely classical proof of a heat equation and de Bruijn identity, satisfied when one of the variables is geometric.
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🔖 Information theory, predictability, and the emergence of complex life

Information theory, predictability, and the emergence of complex life by Luís F. Seoane and Ricard Solé (arxiv.org)
Abstract: Despite the obvious advantage of simple life forms capable of fast replication, different levels of cognitive complexity have been achieved by living systems in terms of their potential to cope with environmental uncertainty. Against the inevitable cost associated to detecting environmental cues and responding to them in adaptive ways, we conjecture that the potential for predicting the environment can overcome the expenses associated to maintaining costly, complex structures. We present a minimal formal model grounded in information theory and selection, in which successive generations of agents are mapped into transmitters and receivers of a coded message. Our agents are guessing machines and their capacity to deal with environments of different complexity defines the conditions to sustain more complex agents.
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🔖 Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity

Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity by Danielle S. Bassett, Ankit N. Khambhati, Scott T. Grafton (arxiv.org)
Neuroengineering is faced with unique challenges in repairing or replacing complex neural systems that are composed of many interacting parts. These interactions form intricate patterns over large spatiotemporal scales, and produce emergent behaviors that are difficult to predict from individual elements. Network science provides a particularly appropriate framework in which to study and intervene in such systems, by treating neural elements (cells, volumes) as nodes in a graph and neural interactions (synapses, white matter tracts) as edges in that graph. Here, we review the emerging discipline of network neuroscience, which uses and develops tools from graph theory to better understand and manipulate neural systems, from micro- to macroscales. We present examples of how human brain imaging data is being modeled with network analysis and underscore potential pitfalls. We then highlight current computational and theoretical frontiers, and emphasize their utility in informing diagnosis and monitoring, brain-machine interfaces, and brain stimulation. A flexible and rapidly evolving enterprise, network neuroscience provides a set of powerful approaches and fundamental insights critical to the neuroengineer's toolkit.

17 pages, 6 figures. Manuscript accepted to the journal Annual Review of Biomedical Engineering [1]

References

[1]
D. Bassett S., A. Khambhati N., and S. Grafton T., “Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity,” arXiv, 23-Dec-2016. [Online]. Available: https://arxiv.org/abs/1612.08059. [Accessed: 03-Jan-2017]
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🔖 A Physical Basis for the Second Law of Thermodynamics: Quantum Nonunitarity

A Physical Basis for the Second Law of Thermodynamics: Quantum Nonunitarity by R. E. Kastner (arxiv.org)
It is argued that if the non-unitary measurement transition, as codified by Von Neumann, is a real physical process, then the "probability assumption" needed to derive the Second Law of Thermodynamics naturally enters at that point. The existence of a real, indeterministic physical process underlying the measurement transition would therefore provide an ontological basis for Boltzmann's Stosszahlansatz and thereby explain the unidirectional increase of entropy against a backdrop of otherwise time-reversible laws. It is noted that the Transactional Interpretation (TI) of quantum mechanics provides such a physical account of the non-unitary measurement transition, and TI is brought to bear in finding a physically complete, non-ad hoc grounding for the Second Law.

Download .pdf copy

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🔖 100 years after Smoluchowski: stochastic processes in cell biology

100 years after Smoluchowski: stochastic processes in cell biology by David Holcman and Zeev Schuss (arxiv.org)
100 years after Smoluchowski introduces his approach to stochastic processes, they are now at the basis of mathematical and physical modeling in cellular biology: they are used for example to analyse and to extract features from large number (tens of thousands) of single molecular trajectories or to study the diffusive motion of molecules, proteins or receptors. Stochastic modeling is a new step in large data analysis that serves extracting cell biology concepts. We review here the Smoluchowski's approach to stochastic processes and provide several applications for coarse-graining diffusion, studying polymer models for understanding nuclear organization and finally, we discuss the stochastic jump dynamics of telomeres across cell division and stochastic gene regulation.

65 pages, J. Phys A 2016 [1]

References

[1]
D. Holcman and Z. Schuss, “100 years after Smoluchowski: stochastic processes in cell biology,” arXiv, 26-Dec-2016. [Online]. Available: https://arxiv.org/abs/1612.08381. [Accessed: 03-Jan-2017]
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🔖 H-theorem in quantum physics by G. B. Lesovik, et al.

H-theorem in quantum physics by G. B. Lesovik, A. V. Lebedev, I. A. Sadovskyy, M. V. Suslov & V. M. Vinokur (Nature.com)

Abstract

Remarkable progress of quantum information theory (QIT) allowed to formulate mathematical theorems for conditions that data-transmitting or data-processing occurs with a non-negative entropy gain. However, relation of these results formulated in terms of entropy gain in quantum channels to temporal evolution of real physical systems is not thoroughly understood. Here we build on the mathematical formalism provided by QIT to formulate the quantum H-theorem in terms of physical observables. We discuss the manifestation of the second law of thermodynamics in quantum physics and uncover special situations where the second law can be violated. We further demonstrate that the typical evolution of energy-isolated quantum systems occurs with non-diminishing entropy. [1]

Footnotes

[1]
G. B. Lesovik, A. V. Lebedev, I. A. Sadovskyy, M. V. Suslov, and V. M. Vinokur, “H-theorem in quantum physics,” Scientific Reports, vol. 6. Springer Nature, p. 32815, 12-Sep-2016 [Online]. Available: http://dx.doi.org/10.1038/srep32815
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Statistical Physics, Information Processing, and Biology Workshop at Santa Fe Institute

Information Processing and Biology by John Carlos Baez (Azimuth)
The Santa Fe Institute, in New Mexico, is a place for studying complex systems. I’ve never been there! Next week I’ll go there to give a colloquium on network theory, and also to participate in this workshop.

I just found out about this from John Carlos Baez and wish I could go! How have I not managed to have heard about it?

Stastical Physics, Information Processing, and Biology

Workshop

November 16, 2016 – November 18, 2016
9:00 AM
Noyce Conference Room

Abstract.
This workshop will address a fundamental question in theoretical biology: Does the relationship between statistical physics and the need of biological systems to process information underpin some of their deepest features? It recognizes that a core feature of biological systems is that they acquire, store and process information (i.e., perform computation). However to manipulate information in this way they require a steady flux of free energy from their environments. These two, inter-related attributes of biological systems are often taken for granted; they are not part of standard analyses of either the homeostasis or the evolution of biological systems. In this workshop we aim to fill in this major gap in our understanding of biological systems, by gaining deeper insight in the relation between the need for biological systems to process information and the free energy they need to pay for that processing.

The goal of this workshop is to address these issues by focusing on a set three specific question:

  1. How has the fraction of free energy flux on earth that is used by biological computation changed with time?;
  2. What is the free energy cost of biological computation / function?;
  3. What is the free energy cost of the evolution of biological computation / function.

In all of these cases we are interested in the fundamental limits that the laws of physics impose on various aspects of living systems as expressed by these three questions.

Purpose: Research Collaboration
SFI Host: David Krakauer, Michael Lachmann, Manfred Laubichler, Peter Stadler, and David Wolpert

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🔖 Free download of Quantum Theory, Groups and Representations: An Introduction by Peter Woit

Final Draft of Quantum Theory, Groups and Representations: An Introduction by Peter Woit (Not Even Wrong | math.columbia.edu)

Peter Woit has just made the final draft (dated 10/25/16) of his new textbook Quantum Theory, Groups and Representations: An Introduction freely available for download from his website. It covers quantum theory with a heavy emphasis on groups and representation theory and “contains significant amounts of material not well-explained elsewhere.” He expects to finish up the diagrams and publish it next year some time, potentially through Springer.

I finally have finished a draft version of the book that I’ve been working on for the past four years or so. This version will remain freely available on my website here. The plan is to get professional illustrations done and have the book published by Springer, presumably appearing in print sometime next year. By now it’s too late for any significant changes, but comments, especially corrections and typos, are welcome.

At this point I’m very happy with how the book has turned out, since I think it provides a valuable point of view on the relation between quantum mechanics and mathematics, and contains significant amounts of material not well-explained elsewhere.

Peter Woit (), theoretical physicist, mathematician, professor Department of Mathematics, Columbia University
in Final Draft Version | Not Even Wrong

 

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My Review Copy of The Big Picture by Sean Carroll

On the Origins of Life, Meaning, and the Universe Itself

I’m already a major chunk of the way through the book, having had an early ebook version of the text prior to publication. This is the published first edition with all the diagrams which I wanted to have prior to finishing my full review, which is forthcoming.

One thing I will mention is that it’s got quite a bit more philosophy in it than most popular science books with such a physics bent. Those who aren’t already up to speed on the math and science of modern physics can certainly benefit from the book (like most popular science books of its stripe, it doesn’t have any equations — hairy or otherwise), and it’s certain to help many toward becoming members of both of C.P. Snow’s two cultures. It might not be the best place for mathematicians and physicists to start moving toward the humanities with the included philosophy as the philosophy is very light and spotty in places and the explanations of the portions they’re already aware of may put them out a bit.

I’m most interested to see how he views complexity and thinking in the final portion of the text.

More detail to come…

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Quantum Information Meets Quantum Matter

Quantum Information Meets Quantum Matter -- From Quantum Entanglement to Topological Phase in Many-Body Systems by Bei Zeng, Xie Chen, Duan-Lu Zhou, Xiao-Gang Wen (arxiv.org)
This is the draft version of a textbook, which aims to introduce the quantum information science viewpoints on condensed matter physics to graduate students in physics (or interested researchers). We keep the writing in a self-consistent way, requiring minimum background in quantum information science. Basic knowledge in undergraduate quantum physics and condensed matter physics is assumed. We start slowly from the basic ideas in quantum information theory, but wish to eventually bring the readers to the frontiers of research in condensed matter physics, including topological phases of matter, tensor networks, and symmetry-protected topological phases.
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Matter, energy… knowledge: How to harness physics’ demonic power | New Scientist

Matter, energy… knowledge: How to harness physics' demonic power by Stephen Battersby (New Scientist)
Running a brain-twisting thought experiment for real shows that information is a physical thing – so can we now harness the most elusive entity in the cosmos?

This is a nice little overview article of some of the history of thermodynamics relating to information in physics and includes some recent physics advances as well. There are a few references to applications in biology at the micro level as well.

References

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How Can We Apply Physics to Biology?

How Can We Apply Physics to Biology? by Philip Ball (nautil.us)
We don’t yet know quite what a physics of biology will consist of. But we won’t understand life without it.

This is an awesome little article with some interesting thought and philosophy on the current state of physics within biology and other related areas of study. It’s also got some snippets of history which aren’t frequently discussed in longer form texts.

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