Bookmark | Chris Aldrich

🔖 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]

🔖 Causal Entropic Forces, Phys. Rev. Lett. 110, 168702 (2013)

Bookmarked Causal Entropic Forces (Phys. Rev. Lett. 110, 168702 (2013) journals.aps.org )

Recent advances in fields ranging from cosmology to computer science have hinted at a possible deep connection between intelligence and entropy maximization, but no formal physical relationship between them has yet been established. Here, we explicitly propose a first step toward such a relationship in the form of a causal generalization of entropic forces that we find can cause two defining behaviors of the human “cognitive niche”—tool use and social cooperation—to spontaneously emerge in simple physical systems. Our results suggest a potentially general thermodynamic model of adaptive behavior as a nonequilibrium process in open systems.

[1]

A. D. Wissner-Gross and C. E. Freer, “Causal Entropic Forces,” Physical Review Letters, vol. 110, no. 16. American Physical Society (APS), 19-Apr-2013 [Online]. Available: http://dx.doi.org/10.1103/PhysRevLett.110.168702 [Source]

🔖 How Life (and Death) Spring From Disorder | Quanta Magazine

Bookmarked 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]

I can’t wait to try out Micropublish with WordPress

I can’t wait to try out Micropublish with WordPress.

🔖 A de Bruijn identity for discrete random variables by Oliver Johnson, Saikat Guha

Bookmarked 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.

Sage vs Underscores

Bookmarked Sage vs Underscores | WordPress Starter Themes (Roots)

Sage makes you a better developer. Modern build tooling, live reloading, modern PHP & requirements, DRY templates with template inheritance and more.

Modern front-end workflow

If Underscores is a “1,000 hour head start”, Sage is a 10,000 hour head start.

Write stylesheets with Sass, automatically check your JavaScript for errors, optimize images, enable synchronized browser testing, and more with our gulp setup.

🔖 Blockchain Revolution: How the Technology Behind Bitcoin Is Changing Money, Business, and the World by Don Tapscott, Alex Tapscott

Bookmarked Blockchain Revolution: How the Technology Behind Bitcoin Is Changing Money, Business, and the World by Don Tapscott, Alex Tapscott (Portfolio, May 10, 2016)

The first generation of the digital revolution brought us the Internet of information. The second generation—powered by blockchain technology—is bringing us the Internet of value: a new, distributed platform that can help us reshape the world of business and transform the old order of human affairs for the better.

Blockchain is the ingeniously simple, revolutionary protocol that allows transactions to be simultaneously anonymous and secure by maintaining a tamperproof public ledger of value. Though it’s the technology that drives bitcoin and other digital currencies, the underlying framework has the potential to go far beyond these and record virtually everything of value to humankind, from birth and death certificates to insurance claims and even votes.

Perhaps not necessarily this particular book which appears to be on the overview side, but sometime this year I’d like to delve more deeply into the concept of blockchain and the tech behind it.

Anyone have recommendations of books they liked?

Resilient Web Design

Bookmarked Resilient Web Design by Jeremy Keith (resilientwebdesign.com)

The World Wide Web has been around for long enough now that we can begin to evaluate the twists and turns of its evolution. I wrote this book to highlight some of the approaches to web design that have proven to be resilient. I didn’t do this purely out of historical interest (although I am fascinated by the already rich history of our young industry). In learning from the past, I believe we can better prepare for the future.

You won’t find any code in here to help you build better websites. But you will find ideas and approaches. Ideas are more resilient than code. I’ve tried to combine the most resilient ideas from the history of web design into an approach for building the websites of the future.

I hope you will join me in building a web that lasts; a web that’s resilient.

Walter B. Rudin: "Set Theory: An Offspring of Analysis"

Bookmarked Set Theory: An Offspring of Analysis (YouTube)

Prof. Walter B. Rudin presents the lecture, "Set Theory: An Offspring of Analysis." Prof. Jay Beder introduces Prof. Dattatraya J. Patil who introduces Prof....

A WordPress plugin for posting to IndieNews

Bookmarked WordPress IndieNews by Matthias Pfefferle (github.com)

Automatically send webmentions to IndieNews

I just noticed that Matthias Pfefferle has kindly created a little WordPress plugin for posting to IndieNews .

🔖 Green’s Dictionary of Slang

Bookmarked Green’s Dictionary of Slang (greensdictofslang.com)

h/t The Largest Historical Dictionary of English Slang Now Free Online: Covers 500 Years of the “Vulgar Tongue” | Open Culture.

“The three volumes of Green’s Dictionary of Slang demonstrate the sheer scope of a lifetime of research by Jonathon Green, the leading slang lexicographer of our time. A remarkable collection of this often reviled but endlessly fascinating area of the English language, it covers slang from the past five centuries right up to the present day, from all the different English-speaking countries and regions. Totaling 10.3 million words and over 53,000 entries, the collection provides the definitions of 100,000 words and over 413,000 citations. Every word and phrase is authenticated by genuine and fully-referenced citations of its use, giving the work a level of authority and scholarship unmatched by any other publication in this field.”

If you head over to Amazon.com, that’s how you will find Green’s Dictionary of Slang pitched to consumers. The dictionary is an attractive three-volume, hard-bound set. But it comes at a price. $264 for a used edition. $600 for a new one.

Now comes the good news. In October, Green’s Dictionary of Slang became available as a free website, giving you access to an even more updated version of the dictionary. Collectively, the website lets you trace the development of slang over the past 500 years. And, as Mental Floss notes, the site “allows lookups of word definitions and etymologies for free, and, for a well-worth-it subscription fee, it offers citations and more extensive search options.” If you’ve ever wondered about the meaning of words like kidlywink, gollier, and linthead, you now know where to begin.