🔖 Statistical Physics of Adaptation

Bookmarked Statistical Physics of Adaptation (journals.aps.org Phys. Rev. X 6, 021036 (2016))
Whether by virtue of being prepared in a slowly relaxing, high-free energy initial condition, or because they are constantly dissipating energy absorbed from a strong external drive, many systems subject to thermal fluctuations are not expected to behave in the way they would at thermal equilibrium. Rather, the probability of finding such a system in a given microscopic arrangement may deviate strongly from the Boltzmann distribution, raising the question of whether thermodynamics still has anything to tell us about which arrangements are the most likely to be observed. In this work, we build on past results governing nonequilibrium thermodynamics and define a generalized Helmholtz free energy that exactly delineates the various factors that quantitatively contribute to the relative probabilities of different outcomes in far-from-equilibrium stochastic dynamics. By applying this expression to the analysis of two examples—namely, a particle hopping in an oscillating energy landscape and a population composed of two types of exponentially growing self-replicators—we illustrate a simple relationship between outcome-likelihood and dissipative history. In closing, we discuss the possible relevance of such a thermodynamic principle for our understanding of self-organization in complex systems, paying particular attention to a possible analogy to the way evolutionary adaptations emerge in living things.

🔖 Meaning = Information + Evolution by Carlo Rovelli

Bookmarked Meaning = Information + Evolution (arxiv.org)
Notions like meaning, signal, intentionality, are difficult to relate to a physical word. I study a purely physical definition of "meaningful information", from which these notions can be derived. It is inspired by a model recently illustrated by Kolchinsky and Wolpert, and improves on Dretske classic work on the relation between knowledge and information. I discuss what makes a physical process into a "signal".

🔖 Irreversibility and Heat Generation in the Computing Process by R. Landauer

Bookmarked Irreversibility and Heat Generation in the Computing Process (ieeexplore.ieee.org)
It is argued that computing machines inevitably involve devices which perform logical functions that do not have a single-valued inverse. This logical irreversibility is associated with physical irreversibility and requires a minimal heat generation, per machine cycle, typically of the order of kT for each irreversible function. This dissipation serves the purpose of standardizing signals and making them independent of their exact logical history. Two simple, but representative, models of bistable devices are subjected to a more detailed analysis of switching kinetics to yield the relationship between speed and energy dissipation, and to estimate the effects of errors induced by thermal fluctuations.
A classical paper in the history of entropy.

The Map of Mathematics: Animation Shows How All the Different Fields in Math Fit Together | Open Culture

Read The Map of Mathematics: Animation Shows How All the Different Fields in Math Fit Together Open Culture (openculture.com)
Continue reading The Map of Mathematics: Animation Shows How All the Different Fields in Math Fit Together | Open Culture

George Harrison Explains Why Everyone Should Play the Ukulele, With Words and Music | Open Culture

Read George Harrison Explains Why Everyone Should Play the Ukulele, With Words and Music Open Culture (openculture.com)
Continue reading George Harrison Explains Why Everyone Should Play the Ukulele, With Words and Music | Open Culture

Betsy DeVos’s confirmation is suddenly on thin ice. Her defeat would be almost unprecedented. | The Washington Post

Read Betsy DeVos’s confirmation is suddenly on thin ice. Her defeat would be almost unprecedented. by Aaron Blake (Washington Post)
The last time a president who had a Senate majority saw his Cabinet nominee defeated: 1925.
Sadly I’ve just heard that she was confirmed… blech.
Continue reading Betsy DeVos’s confirmation is suddenly on thin ice. Her defeat would be almost unprecedented. | The Washington Post

Lost Bob Marley Tapes Are Restored After 40 Years in a Basement | The New York Times

Read Lost Bob Marley Tapes Are Restored After 40 Years in a Basement (nytimes.com)
The recordings, of concerts between 1974 and 1978, were found badly damaged in a London hotel and painstakingly restored.
Continue reading Lost Bob Marley Tapes Are Restored After 40 Years in a Basement | The New York Times

How Sean Spicer Wins by Losing | POLITICO Magazine

Read How Sean Spicer Wins by Losing (POLITICO Magazine)
He's only broadcast from the White House briefing room three times, but on each occasion presidential press secretary Sean Spicer has been asked to do the impossible.
Continue reading How Sean Spicer Wins by Losing | POLITICO Magazine

State Dept. Dissent Cable on Trump’s Ban Draws 1,000 Signatures | The New York Times

Read State Dept. Dissent Cable on Trump’s Ban Draws 1,000 Signatures (nytimes.com)
The cable, asserting that the president’s order on immigration will not make the nation safer, has wended through dozens of embassies and is still spreading.
Continue reading State Dept. Dissent Cable on Trump’s Ban Draws 1,000 Signatures | The New York Times

Gorsuch and the Senate — and the ghost of Garland | Medium

Read Gorsuch and the Senate — and the ghost of Garland (Medium)
In normal times, with a normal (right wing) president, Neil Gorsuch would be a fine nominee for the Supreme Court. One can disagree with…
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Meet Ben! – A Matter-Driven Narrative | Medium

Read Meet Ben! – A Matter-Driven Narrative (Medium)
I remember when I first walked through the garage door on Bryant St, to see Corey and Lara’s smiling faces, welcoming us in.
Continue reading Meet Ben! – A Matter-Driven Narrative | Medium

🔖 Energy flow and the organization of life | Complexity

Bookmarked Energy flow and the organization of life (Complexity, September 2007)
Understanding the emergence and robustness of life requires accounting for both chemical specificity and statistical generality. We argue that the reverse of a common observation—that life requires a source of free energy to persist—provides an appropriate principle to understand the emergence, organization, and persistence of life on earth. Life, and in particular core biochemistry, has many properties of a relaxation channel that was driven into existence by free energy stresses from the earth's geochemistry. Like lightning or convective storms, the carbon, nitrogen, and phosphorus fluxes through core anabolic pathways make sense as the order parameters in a phase transition from an abiotic to a living state of the geosphere. Interpreting core pathways as order parameters would both explain their stability over billions of years, and perhaps predict the uniqueness of specific optimal chemical pathways.
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[1]
H. Morowitz and E. Smith, “Energy flow and the organization of life,” Complexity, vol. 13, no. 1. Wiley-Blackwell, pp. 51–59, 2007 [Online]. Available: http://dx.doi.org/10.1002/cplx.20191

🔖 Evidence for a limit to human lifespan | Nature Research

Bookmarked Evidence for a limit to human lifespan (nature.com)
Driven by technological progress, human life expectancy has increased greatly since the nineteenth century. Demographic evidence has revealed an ongoing reduction in old-age mortality and a rise of the maximum age at death, which may gradually extend human longevity. Together with observations that lifespan in various animal species is flexible and can be increased by genetic or pharmaceutical intervention, these results have led to suggestions that longevity may not be subject to strict, species-specific genetic constraints. Here, by analysing global demographic data, we show that improvements in survival with age tend to decline after age 100, and that the age at death of the world’s oldest person has not increased since the 1990s. Our results strongly suggest that the maximum lifespan of humans is fixed and subject to natural constraints.
[1]
X. Dong, B. Milholland, and J. Vijg, “Evidence for a limit to human lifespan.,” Nature, vol. 538, no. 7624, pp. 257–259, Oct. 2016. [PubMed]

🔖 Hayflick, his limit, and cellular ageing | Nature Reviews Molecular Cell Biology

Bookmarked Hayflick, his limit, and cellular ageing ( Nature Reviews Molecular Cell Biology)
Almost 40 years ago, Leonard Hayflick discovered that cultured normal human cells have limited capacity to divide, after which they become senescent — a phenomenon now known as the ‘Hayflick limit’. Hayflick's findings were strongly challenged at the time, and continue to be questioned in a few circles, but his achievements have enabled others to make considerable progress towards understanding and manipulating the molecular mechanisms of ageing.
[1]
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]

🔖 Thermodynamic Uncertainty Relation for Biomolecular Processes, Phys. Rev. Lett. 114, 158101 (2015)

Bookmarked Thermodynamic Uncertainty Relation for Biomolecular Processes (Phys. Rev. Lett. 114, 158101 (2015) - journals.aps.org)
Biomolecular systems like molecular motors or pumps, transcription and translation machinery, and other enzymatic reactions, can be described as Markov processes on a suitable network. We show quite generally that, in a steady state, the dispersion of observables, like the number of consumed or produced molecules or the number of steps of a motor, is constrained by the thermodynamic cost of generating it. An uncertainty ε requires at least a cost of 2k_B T/ε^2 independent of the time required to generate the output.
[1]
A. C. Barato and U. Seifert, “Thermodynamic Uncertainty Relation for Biomolecular Processes,” Physical Review Letters, vol. 114, no. 15. American Physical Society (APS), 15-Apr-2015 [Online]. Available: http://dx.doi.org/10.1103/PhysRevLett.114.158101 [Source]