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.
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".
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
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
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]
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.
Our evolution certainly hasn’t been keeping up with our level of fear in the modern world. Even simple things like kids playing around their own neighborhood like I did as a kid in the 70’s and 80’s has changed drastically. How can we keep ourselves from being held back unnecessarily?
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.
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.
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.
Biochemist Nick Lane explains the elements of life, sex, and aging in an engaging popular science interview.
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.
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’sThe Big Picture, I can only imagine how well the two may go together despite being written nearly 60 years apart.
For too long, scientists focused on what we can see. Now they are at last starting to decode life’s software.
“A soup of chemicals may spontaneously form a reaction network, but what does it take for such a molecular muddle to begin coherently organising information flow and storage? Rather than looking to biology or chemistry, we can perhaps dream that advances in the mathematics of information theory hold the key.”
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):
“It is a truly impressive fact that, simply by knowing that if one can memorize and master about 250 words in Latin, it will allow them to read and understand 50% of most written Latin. Further, knowledge of 1,500 Latin words will put one at the 80% level of vocabulary mastery for most texts. Mastering even a very small list of vocabulary allows one to read a large variety of texts very comfortably.”
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.
“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.”
Yesterday, via a notification from Lanyard, I came across a notice for the upcoming conference “The Information Universe” which hits several of the sweet spots for areas involving information theory, physics, the origin of life, complexity, computer science, and microbiology. It is scheduled to occur from October 7-9, 2015 at the Infoversum Theater in Groningen, The Netherlands.
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
Infoversum Theater, The Netherlands
Conference synopsis from their homepage:
The main ambition of this conference is to explore the question “What is the role of information in the physics of our Universe?”. This intellectual pursuit may have a key role in improving our understanding of the Universe at a time when we “build technology to acquire and manage Big Data”, “discover highly organized information systems in nature” and “attempt to solve outstanding issues on the role of information in physics”. The conference intends to address the “in vivo” (role of information in nature) and “in vitro” (theory and models) aspects of the Information Universe.
The discussions about the role of information will include the views and thoughts of several disciplines: astronomy, physics, computer science, mathematics, life sciences, quantum computing, and neuroscience. Different scientific communities hold various and sometimes distinct formulations of the role of information in the Universe indicating we still lack understanding of its intrinsic nature. During this conference we will try to identify the right questions, which may lead us towards an answer.
Is the universe one big information processing machine?
Is there a deeper layer in quantum mechanics?
Is the universe a hologram?
Is there a deeper physical description of the world based on information?
How close/far are we from solving the black hole information paradox?
What is the role of information in highly organized complex life systems?
The Big Data Universe and the Universe : are our numerical simulations and Big Data repositories (in vitro) different from real natural system (in vivo)?
Is this the road to understanding dark matter, dark energy?
The conference will be held in the new 260 seats planetarium theatre in Groningen, which provides an inspiring immersive 3D full dome display, e.g. numerical simulations of the formation of our Universe, and anything else our presenters wish to bring in. The digital planetarium setting will be used to visualize the theme with modern media.
César A. Hidalgo (Applied Network Science | SpringerLink)
