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.
Tag: evolution
🔖 Meaning = Information + Evolution by Carlo Rovelli
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".
🔖 How Life (and Death) Spring From Disorder | 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.
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
🎧 Fearless | Invisibilia (NPR)
In "Fearless," co-hosts Alix Spiegel and Lulu Miller explore what would happen if you could disappear fear. A group of scientists believe that people no longer need fear — at least not the kind we live with — to navigate the modern world. We'll hear about the striking (and rare) case of a woman with no fear. The second half of the show explores how the rest of us might "turn off" fear.
Disconnected, Fragmented, or United? A Trans-disciplinary Review of Network Science
Abstract
During decades the study of networks has been divided between the efforts of social scientists and natural scientists, two groups of scholars who often do not see eye to eye. In this review I present an effort to mutually translate the work conducted by scholars from both of these academic fronts hoping to continue to unify what has become a diverging body of literature. I argue that social and natural scientists fail to see eye to eye because they have diverging academic goals. Social scientists focus on explaining how context specific social and economic mechanisms drive the structure of networks and on how networks shape social and economic outcomes. By contrast, natural scientists focus primarily on modeling network characteristics that are independent of context, since their focus is to identify universal characteristics of systems instead of context specific mechanisms. In the following pages I discuss the differences between both of these literatures by summarizing the parallel theories advanced to explain link formation and the applications used by scholars in each field to justify their approach to network science. I conclude by providing an outlook on how these literatures can be further unified.
Weekly Recap: Interesting Articles 7/24-7/31 2016
Science & Math
- Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering | PLOS Computational Biology
- The Competing Incentives of Academic Research in Mathematics
- [1607.08473] Quantum circuits and low-degree polynomials over F_2
- This Physics Pioneer Walked Away from it All | Nautilus
- Monumental proof to torment mathematicians for years to come: Conference on Shinichi Mochizuki’s work inspires cautious optimism. | Nature
- What Your Brain Looks Like When It Solves a Math Problem | New York Times
- Habits of Highly Mathematical People
- Why You Should Care About High-Dimensional Sphere Packing | Roots of Unity
- Initial steps toward reproducible research
- Bridging the Curation Gap between Research and Libraries – A Case Study
- Quantum steampunk: Quantum information applied to thermodynamics
- How Vector Space Mathematics Reveals the Hidden Sexism in Language
- How Sound Can Make Food Taste Better | Nautilus
- Top 10 algorithms of 20th century numerical analysis, from a talk by Alex Townsend
- UK vs. US: Who’s got the right way to teach math(s)? | Math with Bad Drawin
- Physics & Caffeine: Stop Motion Film Uses a Cup of Coffee to Explain Key Co
- The Water Kingdom: A Secret History of China by Philip Ball (review)
- The master of them all: Book review for”Leonhard Euler: Mathematical Genius in the Enlightenment” | The Economist
- Biologists Search for New Model Organisms: The bulk of biological research is centered on a handful of species. Are we missing a huge chunk of life’s secrets?
- One-sentence proof of Fermat’s theorem on sums of two squares | Fermat’s Library
- This protein designer aims to revolutionize medicines and materials
- Our last common ancestor inhaled hydrogen from underwater volcanoes
- Meet Luca, The Ancestor of All Living Things | New York Times
- *Disconnected, fragmented, or united? a trans-disciplinary review of network
- What’s Behind A Science vs. Philosophy Fight? | Big Think
- What is a “Neutral Network” Anyway? An Exploration and Rediscovery of the Aims of Net Neutrality in Theory and Practice
- The Brachistochrone Curve: The Problem of Quickest Descent | Fermat’s Library
- In what sense is Quantum Mechanics a theory of information? | Quora
- Major transitions in information technology | Philosophical Transactions of
- Human brain mapped in unprecedented detail: Nearly 100 previously unidentified brain areas revealed by examination of the cerebral cortex. | Nature
- Cell biologists should specialize, not hybridize: Dry cell biologists, who bridge computer science and cell biology, should have a pivotal role in driving effective team science, says Assaf Zaritsky | Nature
- Internet 3.0: How we take back control from the giants | New Scientist
- How a Guy From a Montana Trailer Park Overturned 150 Years of Biology | The Atlantic
- People can sense single photons | Nature News & Comment
- Defining synergy thermodynamically using quantitative measurements of entropy and free energy
- A Prime Case of Chaos | AMS.org
- Murray Gell-Mann (video interviews) – YouTube
- Mathematics & Chalk: A teary goodbye to Hagomoro | Jeremy Kun
Publishing
- Want to Change Academic Publishing? Just Say No | Chronicle
- Textbooks Show Aging Signs: Curated Guides Are Next – 10+ Disruptive Factors Transforming the World of Education and Learning — Consequences, Opportunities, Tools
- Simon & Schuster, Penguin, Random House Don’t Want to Talk About Their Ebook Sales
- Amazon Sales Rank: Taming the Algorithm | Self-Publishing Author Advice
- What Authors Should Know About Advance Review Copies
- Ingram Launches Ingram Academic Services
- How a Publishing House Designs a Book Cover
- How Indie Bookstores Help Drive Book Discoverability
- How to Grow Your Email List
- 3 Ways Indie Publishers Sell Books | Digital Book World
- 10 Self-Publishing Trends to Watch
- Ingram Launches Academic Services for University Presses and Academic Publishers
- Indigo Goes Where Amazon, B&N, Goodreads, and a Dozen Publishers and Startus Have Dared to Tread
- How To Make An Ebook Feel More Like A Real Book
- Looking for open digital collections – Wynken de Worde
Indieweb, Internet, Identity, Blogging, Social Media
- What is Open Source?
- Microformats with Tantek Çelik | tlks.io https://www.youtube.com/watch?v=kDQigkxyiqE
- My Text Editor is Absolutely Sublime | Devon Zuegel
- My zsh aliases | Devon Zuegel
- XOXO Festival
- Web Design in 4 minutes
- Custom Elements
- Design Principles
- Infographic: The Optimal Length for Every Social Media Update
- Notes For New (and Potential) Twitter Followers | Whatever
- How Blogs Work Today – Whatever
- My reply to: How Blogs Work Today | Whatever
- Unicode Character ‘ZERO WIDTH SPACE’ (U 200B)
- A Book Apart, Practical SVG
- Gillmor Gang Trumpathon
- The best news aggregation service – The Sweet Setup
- Social Startup Sprinklr Is Now Valued At $1.8 Billion After $105 Million Raise | Forbes
- Epeus’ epigone: Digital publics, Conversations and Twitter
General
- The New Meaning of Success
- 7 Lessons from the Future of Content: Part One — Tools Are Cheap, Time Is Expensive
- 7 Lessons from the Future of Content: Part Two — Let’s Play Risk
- Aron Pilhofer Joining Temple University School of Media and Communication
- Secrets and agents: George Akerlof’s 1970 paper, “The Market for Lemons”, is a foundation stone of information economics. The first in our series on seminal economic ideas | The Economist
- John Oliver has the takedown of Donald Trump’s Republican convention
- Reference: New Interactive Map Of 100,000 Photos and Videos Reveal “Lost London in the Victorian Era”
- “better modifiers than “insane(ly)” (Grammar and Usage)
- A lesson in the errors of statistical thinking: Nate Silver on Trump
- Trump & Putin. Yes, It’s Really a Thing
- Charlie Parker Plays with Dizzy Gillespie in Only Footage Capturing the “Bird” in True Live Performance
- Let Me Remind You Fuckers Who I Am (Shit HRC Can’t Say/satire)
Penguin Revives Decades-Old Software for 30th Anniversary Edition of “The Blind Watchmaker” | The Digital Reader
Even in 2016, publishers and authors are still struggling when it comes to re-releasing decades-old books, but Penguin had a unique problem when it set out to publish a 30th anniversary edition of Richard Dawkin's The Blind Watchmaker.<br /><br />The Bookseller reports that Penguin decided to revive four programs Dawkins wrote in 1986. Written in Pascal for the Mac, The Watchmaker Suite was an experiment in algorithmic evolution. Users could run the programs and create a biomorph, and then watch it evolve across the generations.<br /><br />And now you can do the same in your web browser.<br /><br />A website, MountImprobable.com, was built by the publisher’s in-house Creative Technology team—comprising community manager Claudia Toia, creative developer Mathieu Triay and cover designer Matthew Young—who resuscitated and redeployed code Dawkins wrote in the 1980s and ’90s to enable users to create unique, “evolutionary” imprints. The images will be used as cover imagery on Dawkins’ trio to grant users an entirely individual, personalised print copy.
A New Thermodynamics Theory of the Origin of Life | Quanta Magazine
Jeremy England, a 31-year-old physicist at MIT, thinks he has found the underlying physics driving the origin and evolution of life.
- Jeremy L. England Lab
- Talks
- Statistical physics of self-replication, Jeremy L. England; J. Chem. Phys. 139, 121923 (2013); doi: 10.1063/1.4818538
- Statistical Physics of Adaptation, Nikolai Perunov, Robert Marsland, and Jeremy England, arXiv, December 8, 2014
- Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences, Gavin E. Crooks, arXiv, February 1, 2008
- Life as a manifestation of the second law of thermodynamics, E.D. Schneider, J.J. Kay, doi:10.1016/0895-7177(94)90188-0, Mathematical and Computer Modelling, Volume 19, Issues 6–8, March–April 1994, Pages 25-48
Hypothesis annotations
Nick Lane and Philip Ball Discuss Mitochondria, Sex, and How to Live Longer
In his 2010 book, Life Ascending: The Ten Great Inventions of Evolution, Nick Lane, a biochemist at University College London, explores with eloquence and clarity the big questions of life: how it began, why we age and die, and why we have sex. Lane been steadily constructing an alternative view of evolution to the one in which genes explain it all. He argues that some of the major events during evolutionary history, including the origin of life itself, are best understood by considering where the energy comes from and how it is used. Lane describes these ideas in his 2015 book, The Vital Question: Why Is Life the Way It Is?. Recently Bill Gates called it “an amazing inquiry into the origins of life,” adding, Lane “is one of those original thinkers who make you say: More people should know about this guy’s work.” Nautilus caught up with Lane in his laboratory in London and asked him about his ideas on aging, sex, and death.
Read more
Devourer of Encyclopedias: Stanislaw Lem’s “Summa Technologiae”
A review of Summa Technologiae by Stanislaw Lem by David Auerbach from the Los Angeles Review of Books.
Summa Technologiae
AT LAST WE have it in English. Summa Technologiae, originally published in Polish in 1964, is the cornerstone of Stanislaw Lem’s oeuvre, his consummate work of speculative nonfiction. Trained in medicine and biology, Lem synthesizes the current science of the day in ways far ahead of most science fiction of the time.
His subjects, among others, include:
- Virtual reality
- Artificial intelligence
- Nanotechnology and biotechnology
- Evolutionary biology and evolutionary psychology
- Artificial life
- Information theory
- Entropy and thermodynamics
- Complexity theory, probability, and chaos
- Population and ecological catastrophe
- The “singularity” and “transhumanism”
Source: Devourer of Encyclopedias: Stanislaw Lem’s “Summa Technologiae” – The Los Angeles Review of Books
I came across this book review quite serendipitously today via an Auerbach article in Slate, which I’ve bookmarked. I found a copy of the book and have added it to the top of my reading pile. As I’m currently reading an advance reader edition of Sean Carroll’s The Big Picture, I can only imagine how well the two may go together despite being written nearly 60 years apart.
The Hidden Algorithms Underlying Life | Quanta Magazine
The biological world is computational at its core, argues computer scientist Leslie Valiant.
I did expect something more entertaining from Google when I searched for “what will happen if I squeeze a paper cup full of hot coffee?”
Can computers help us read the mind of nature? by Paul Davies | The Guardian
Collective learning has potentially been growing at the expense of a shrinking body of diverse language
I have to imagine that once the conceptualization of language and some basic grammar existed, word generation was a much more common thing than it is now. It’s only been since the time of Noah Webster that humans have been actively standardizing things like spelling. If we can use Papua New Guinea as a model of pre-agrarian society and consider that almost 12% of extant languages on the Earth are spoken in an area about the size of Texas (and with about 1/5th the population of Texas too), then modern societies are actually severely limiting language (creation, growth, diversity, creativity, etc.) [cross reference: A World of Languages – and How Many Speak Them (Infographic)]
Consider that the current extinction of languages is about one every 14 weeks, which puts us on a course to loose about half of the 7,100 languages on the planet right now before the end of the century. Collective learning has potentially been growing at the expense of a shrinking body of diverse language! In the paper “Global distribution and drivers of language extinction risk” the authors indicate that of all the variables tested, economic growth was most strongly linked to language loss.
To help put this exercise into perspective, we can look at the corpus of extant written Latin (a technically dead language):
These numbers become even smaller when considering ancient Greek texts.
Another interesting measurement is the vocabulary of a modern 2 year old who typically has a 50-75 word vocabulary while a 4 year old has 250-500 words, which is about the level of the exercise.
As a contrast, consider the message in this TED Youth Talk from last year by Erin McKean, which students should be able to relate to:
[ted id=2158]
And of course, there’s the dog Chaser, which 60 minutes recently reported has a vocabulary of over 1,000 words. (Are we now destroying variants of “dog language” for English too?!)
Hopefully the evolutionary value of the loss of the multiple languages will be more than balanced out by the power of collective learning in the long run.
Molecular Programming Project
“The Molecular Programming Project aims to develop computer science principles for programming information-bearing molecules like DNA and RNA to create artificial biomolecular programs of similar complexity. Our long-term vision is to establish molecular programming as a subdiscipline of computer science — one that will enable a yet-to-be imagined array of applications from chemical circuitry for interacting with biological molecules to nanoscale computing and molecular robotics.”
Source: MPP: Home
The Information Universe Conference
I’ll let their site speak for itself below, but they already have an interesting line up of speakers including:
Keynote speakers
- Erik Verlinde, Professor Theoretical Physics, University of Amsterdam, Netherlands
- Alex Szalay, Alumni Centennial Professor of Astronomy, The Johns Hopkins University, USA
- Gerard ‘t Hooft, Professor Theoretical Physics, University of Utrecht, Netherlands
- Gregory Chaitin, Professor Mathematics and Computer Science, Federal University of Rio de Janeiro, Brasil
- Charley Lineweaver, Professor Astronomy and Astrophysics, Australian National University, Australia
- Lude Franke, Professor System Genetics, University Medical Center Groningen, Netherlands
Conference synopsis from their homepage:
Additional details about the conference including the participants, program, venue, and registration can also be found at their website.