The Hidden Algorithms Underlying Life | Quanta Magazine

Bookmarked Searching for the Algorithms Underlying Life by John Pavlus (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?”

Global Language Networks

Yesterday I ran across this nice little video explaining some recent research on global language networks. It’s not only interesting in its own right, but is a fantastic example of science communication as well.

I’m interested in some of the information theoretic aspects of this as well as the relation of this to the area of corpus linguistics. I’m also curious if one could build worthwhile datasets like this for the ancient world (cross reference some of the sources I touch on in relation to the Dickinson College Commentaries within Latin Pedagogy and the Digital Humanities) to see what influences different language cultures have had on each other. Perhaps the historical record could help to validate some of the predictions made in relation to the future?

The paper “Global distribution and drivers of language extinction risk” indicates that of all the variables tested, economic growth was most strongly linked to language loss.

This research also has some interesting relation to the concept of “Collective Learning” within the realm of a Big History framework via David Christian, Fred Spier, et al.  I’m curious to revisit my hypothesis: Collective learning has potentially been growing at the expense of a shrinking body of diverse language some of which was informed by the work of Jared Diamond.

Some of the discussion in the video is reminiscent to me of some of the work Stuart Kauffman lays out in At Home in the Universe: The Search for the Laws of Self-Organization and Complexity (Oxford, 1995). Particularly in chapter 3 in which Kauffman discusses the networks of life.  The analogy of this to the networks of language here indicate to me that some of Cesar Hidalgo’s recent work in Why Information Grows: The Evolution of Order, From Atoms to Economies (MIT Press, 2015) is even more interesting in helping to show the true value of links between people and firms (information sources which he measures as personbytes and firmbytes) within economies.

Finally, I can also only think about how this research may help to temper some of the xenophobic discussion that occurs in American political life with respect to fears relating to Mexican immigration issues as well as the position of China in the world economy.

Those intrigued by the video may find the website set up by the researchers very interesting. It contains links to the full paper as well as visualizations and links to the data used.

Abstract

Languages vary enormously in global importance because of historical, demographic, political, and technological forces. However, beyond simple measures of population and economic power, there has been no rigorous quantitative way to define the global influence of languages. Here we use the structure of the networks connecting multilingual speakers and translated texts, as expressed in book translations, multiple language editions of Wikipedia, and Twitter, to provide a concept of language importance that goes beyond simple economic or demographic measures. We find that the structure of these three global language networks (GLNs) is centered on English as a global hub and around a handful of intermediate hub languages, which include Spanish, German, French, Russian, Portuguese, and Chinese. We validate the measure of a language’s centrality in the three GLNs by showing that it exhibits a strong correlation with two independent measures of the number of famous people born in the countries associated with that language. These results suggest that the position of a language in the GLN contributes to the visibility of its speakers and the global popularity of the cultural content they produce.

Citation: Ronen S, Goncalves B, Hu KZ, Vespignani A, Pinker S, Hidalgo CA
Links that speak: the global language network and its association with global fame, Proceedings of the National Academy of Sciences (PNAS) (2014), 10.1073/pnas.1410931111

Related posts:

“A language like Dutch — spoken by 27 million people — can be a disproportionately large conduit, compared with a language like Arabic, which has a whopping 530 million native and second-language speakers,” Science reports. “This is because the Dutch are very multilingual and very online.”

What is Information? by Christoph Adami

Bookmarked What is Information? [1601.06176] by Christoph AdamiChristoph Adami (arxiv.org)

Information is a precise concept that can be defined mathematically, but its relationship to what we call "knowledge" is not always made clear. Furthermore, the concepts "entropy" and "information", while deeply related, are distinct and must be used with care, something that is not always achieved in the literature. In this elementary introduction, the concepts of entropy and information are laid out one by one, explained intuitively, but defined rigorously. I argue that a proper understanding of information in terms of prediction is key to a number of disciplines beyond engineering, such as physics and biology.

Comments: 19 pages, 2 figures. To appear in Philosophical Transaction of the Royal Society A
Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Information Theory (cs.IT); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)
Cite as:arXiv:1601.06176 [nlin.AO] (or arXiv:1601.06176v1 [nlin.AO] for this version)

From: Christoph Adami
[v1] Fri, 22 Jan 2016 21:35:44 GMT (151kb,D) [.pdf]

A proper understanding of information in terms of prediction is key to a number of disciplines beyond engineering, such as physics and biology.

Marvin Minsky, Pioneer in Artificial Intelligence, Dies at 88 | The New York Times

Professor Minsky laid the foundation for the field by demonstrating the possibilities of imparting common-sense reasoning to computers.

Source: Marvin Minsky, Pioneer in Artificial Intelligence, Dies at 88 – The New York Times

Forthcoming ITBio-related book from Sean Carroll: “The Big Picture: On the Origins of Life, Meaning, and the Universe Itself”

In catching up on blogs/reading from the holidays, I’ve noticed that physicist Sean Carroll has a forthcoming book entitled The Big Picture: On the Origins of Life, Meaning, and the Universe Itself (Dutton, May 10, 2016) that will be of interest to many of our readers. One can already pre-order the book via Amazon.

Prior to the holidays Sean wrote a blogpost that contains a full overview table of contents, which will give everyone a stronger idea of its contents. For convenience I’ll excerpt it below.

I’ll post a review as soon as a copy arrives, but it looks like a strong new entry in the category of popular science books on information theory, biology and complexity as well as potentially the areas of evolution, the origin of life, and physics in general.

As a side bonus, for those reading this today (1/15/16), I’ll note that Carroll’s 12 part lecture series from The Great Courses The Higgs Boson and Beyond (The Learning Company, February 2015) is 80% off.

The Big Picture

 

THE BIG PICTURE: ON THE ORIGINS OF LIFE, MEANING, AND THE UNIVERSE ITSELF

0. Prologue

* Part One: Cosmos

  • 1. The Fundamental Nature of Reality
  • 2. Poetic Naturalism
  • 3. The World Moves By Itself
  • 4. What Determines What Will Happen Next?
  • 5. Reasons Why
  • 6. Our Universe
  • 7. Time’s Arrow
  • 8. Memories and Causes

* Part Two: Understanding

  • 9. Learning About the World
  • 10. Updating Our Knowledge
  • 11. Is It Okay to Doubt Everything?
  • 12. Reality Emerges
  • 13. What Exists, and What Is Illusion?
  • 14. Planets of Belief
  • 15. Accepting Uncertainty
  • 16. What Can We Know About the Universe Without Looking at It?
  • 17. Who Am I?
  • 18. Abducting God

* Part Three: Essence

  • 19. How Much We Know
  • 20. The Quantum Realm
  • 21. Interpreting Quantum Mechanics
  • 22. The Core Theory
  • 23. The Stuff of Which We Are Made
  • 24. The Effective Theory of the Everyday World
  • 25. Why Does the Universe Exist?
  • 26. Body and Soul
  • 27. Death Is the End

* Part Four: Complexity

  • 28. The Universe in a Cup of Coffee
  • 29. Light and Life
  • 30. Funneling Energy
  • 31. Spontaneous Organization
  • 32. The Origin and Purpose of Life
  • 33. Evolution’s Bootstraps
  • 34. Searching Through the Landscape
  • 35. Emergent Purpose
  • 36. Are We the Point?

* Part Five: Thinking

  • 37. Crawling Into Consciousness
  • 38. The Babbling Brain
  • 39. What Thinks?
  • 40. The Hard Problem
  • 41. Zombies and Stories
  • 42. Are Photons Conscious?
  • 43. What Acts on What?
  • 44. Freedom to Choose

* Part Six: Caring

  • 45. Three Billion Heartbeats
  • 46. What Is and What Ought to Be
  • 47. Rules and Consequences
  • 48. Constructing Goodness
  • 49. Listening to the World
  • 50. Existential Therapy
  • Appendix: The Equation Underlying You and Me
  • Acknowledgments
  • Further Reading
  • References
  • Index

Source: Sean Carroll | The Big Picture: Table of Contents

Donald Forsdyke Indicates the Concept of Information in Biology Predates Claude Shannon

As it was published, I had read Kevin Hartnett’s article and interview with Christoph Adami The Information Theory of Life in Quanta Magazine. I recently revisited it and read through the commentary and stumbled upon an interesting quote relating to the history of information in biology:

Polymath Adami has ‘looked at so many fields of science’ and has correctly indicated the underlying importance of information theory, to which he has made important contributions. However, perhaps because the interview was concerned with the origin of life and was edited and condensed, many readers may get the impression that IT is only a few decades old. However, information ideas in biology can be traced back to at least 19th century sources. In the 1870s Ewald Hering in Prague and Samuel Butler in London laid the foundations. Butler’s work was later taken up by Richard Semon in Munich, whose writings inspired the young Erwin Schrodinger in the early decades of the 20th century. The emergence of his text – “What is Life” – from Dublin in the 1940s, inspired those who gave us DNA structure and the associated information concepts in “the classic period” of molecular biology. For more please see: Forsdyke, D. R. (2015) History of Psychiatry 26 (3), 270-287.

Donald Forsdyke, bioinformatician and theoretical biologist
in response to The Information Theory of Life in Quanta Magazine on

These two historical references predate Claude Shannon’s mathematical formalization of information in A Mathematical Theory of Communication (The Bell System Technical Journal, 1948) and even Erwin Schrödinger‘s lecture (1943) and subsequent book What is Life (1944).

For those interested in reading more on this historical tidbit, I’ve dug up a copy of the primary Forsdyke reference which first appeared on arXiv (prior to its ultimate publication in History of Psychiatry [.pdf]):

🔖 [1406.1391] ‘A Vehicle of Symbols and Nothing More.’ George Romanes, Theory of Mind, Information, and Samuel Butler by Donald R. Forsdyke  [1]
Submitted on 4 Jun 2014 (v1), last revised 13 Nov 2014 (this version, v2)

Abstract: Today’s ‘theory of mind’ (ToM) concept is rooted in the distinction of nineteenth century philosopher William Clifford between ‘objects’ that can be directly perceived, and ‘ejects,’ such as the mind of another person, which are inferred from one’s subjective knowledge of one’s own mind. A founder, with Charles Darwin, of the discipline of comparative psychology, George Romanes considered the minds of animals as ejects, an idea that could be generalized to ‘society as eject’ and, ultimately, ‘the world as an eject’ – mind in the universe. Yet, Romanes and Clifford only vaguely connected mind with the abstraction we call ‘information,’ which needs ‘a vehicle of symbols’ – a material transporting medium. However, Samuel Butler was able to address, in informational terms depleted of theological trappings, both organic evolution and mind in the universe. This view harmonizes with insights arising from modern DNA research, the relative immortality of ‘selfish’ genes, and some startling recent developments in brain research.

Comments: Accepted for publication in History of Psychiatry. 31 pages including 3 footnotes. Based on a lecture given at Santa Clara University, February 28th 2014, at a Bannan Institute Symposium on ‘Science and Seeking: Rethinking the God Question in the Lab, Cosmos, and Classroom.’

The original arXiv article also referenced two lectures which are appended below:

http://www.youtube.com/watch?v=a3yNbTUCPd4

[Original Draft of this was written on December 14, 2015.]

References

[1]
D. Forsdyke R., “‘A vehicle of symbols and nothing more’. George Romanes, theory of mind, information, and Samuel Butler,” History of Psychiatry, vol. 26, no. 3, Aug. 2015 [Online]. Available: http://journals.sagepub.com/doi/abs/10.1177/0957154X14562755

Quantum Biological Information Theory by Ivan B. Djordjevic | Springer

Bookmarked Quantum Biological Information Theory (Springer, 2015)
Springer recently announced the publication of the book Quantum Biological Information Theory by Ivan B. Djordjevic, in which I’m sure many readers here will have interest. I hope to have a review of it shortly after I’ve gotten a copy. Until then…

From the publisher’s website:

This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects.

  • Integrates quantum information and quantum biology concepts;
  • Assumes only knowledge of basic concepts of vector algebra at undergraduate level;
  • Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology;
  • Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models on tumor and cancer development, quantum modeling of bird navigation compass, quantum aspects of photosynthesis, quantum biological error correction.

Source: Quantum Biological Information Theory | Ivan B. Djordjevic | Springer

9783319228150I’ll note that it looks like it also assumes some reasonable facility with quantum mechanics in addition to the material listed above.

Springer also has a downloadable copy of the preface and a relatively extensive table of contents for those looking for a preview. Dr. Djordjevic has been added to the ever growing list of researchers doing work at the intersection of information theory and biology.

The Information Theory of Life | Quanta Magazine

Bookmarked The Information Theory of Life (Quanta Magazine)
The Information Theory of Life: The polymath Christoph Adami is investigating life’s origins by reimagining living things as self-perpetuating information strings.

Can computers help us read the mind of nature? by Paul Davies | The Guardian

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.”

Paul Davies, physicist, writer, and broadcaster
in Can computers help us read the mind of nature? in The Guardian

 

 ‘When we look at a plant or an animal we see the physical forms, not the swirling patterns of instructions inside them.’ Photograph: Abir Sultan/EPA
‘When we look at a plant or an animal we see the physical forms, not the swirling patterns of instructions inside them.’ Photograph: Abir Sultan/EPA

Stephen Hawking says he’s solved a black hole mystery, but physicists await the proof

Bookmarked Stephen Hawking says he's solved a black hole mystery, but physicists await the proof by Eryn BrownEryn Brown (latimes.com)
Physicist Stephen Hawking made a splash this week when he announced that he had solved a vexing conundrum that had puzzled generations of leading physicists -- including the 73-year-old scientific superstar himself -- for the better part of a half-century.

Breaking the code | The Economist

Bookmarked Breaking the code (The Economist)
Brief book overview of Matthew Cobb's "Life’s Greatest Secret" from The Economist.
For those interested in some of the history behind genetics, evolution, biology and information theory, the following book, which I just saw the attached review in The Economist, is likely to be of interest:

Life’s Greatest Secret: The Story of the Race to Crack the Genetic Code. By Matthew Cobb. Basic Books; 434 pages; $29.99. Profile Books; £25.

In 1953 James Watson and Francis Crick, with the help of Rosalind Franklin and Maurice Wilkins, described the structure of the molecule at the heart of life. Deoxyribonucleic acid, better known as DNA, was, they said, a double helix, two spirals joined across the middle by pairs of four chemical bases, like a twisted ladder. That work earned Messrs Crick, Watson and Wilkins a Nobel prize and a place in the history books. The image of the double helix now often stands for biology, or even science, itself.

But this was merely the most visible breakthrough in a long struggle to understand the engine of life—how traits are inherited, mutated and weeded out by natural selection, and how the whole mysterious process works at the biochemical level. It is that lesser-known history that Matthew Cobb, a professor of animal behaviour at the University of Manchester, aims to sketch in his book, which has been shortlisted for the Royal Society’s Winton prize for science writing.

The result is a fascinating reminder of just how hard-won are the seemingly obvious facts of modern biology. The development of genetics was a tale of confusion, accident, frustration and the occasional flash of insight. It was, says Dr Cobb, as important as the Manhattan or Apollo projects, but with no government support and little money, carried out by scientists interested in the question for its own sake.

The researchers started from almost total ignorance. William Harvey, better known for describing the circulation of the blood, wondered in the 17th century what could explain why children’s skin colour was often a blend of their parents’, whereas they share a sex with only one, and can have an eye colour different from either.

In the late 19th century a monk, Gregor Mendel, established, through experiments on pea plants, the basic rules of inherited traits. A Danish biologist, Wilhelm Johannsen, coined the term “gene” in 1909 to describe whatever it was that Mendel had found. But as late as 1933 scientists were still debating whether genes were physical things or just useful abstractions, and how they could transmit traits. Scientists knew that DNA existed, but many considered it a boring bit of scaffolding in the cell. Proteins, which come in zillions of different varieties, were seen by many as the only things exciting enough to account for all the diversity seen in life.

After the second world war, ideas from information theory, arising out of wartime work on computers and automation, percolated into biology. Once the structure of DNA had been established, those ideas helped crack the problem of how the four chemical bases do their job. Proteins are built by stringing together 20 different sorts of amino acid. Strings of three bases within a DNA molecule represent these amino acids, but with 64 such triplets, there is much redundancy which information theory alone could not fully explain. Years of painstaking lab-work were needed to reconcile theory with reality.

Dr Cobb is good on the human side of the story, showing science as fuelled by rivalry, jealousy, competitiveness and wonder. The only downside is that he must marshal hundreds of scientists across several disciplines into around 300 pages of narrative. The results can sometimes be dense, and readers without a command of biological jargon will frequently find themselves consulting the glossary for guidance. But the cracking of the code of life is a great story, of which this is an accomplished telling.

Source: Breaking the code | The Economist, 

 

Life’s Greatest Secret

César Hidalgo on Why Information Grows | The RSA

I’ve just recently finished the excellent book Why Information Grows by César Hidalgo. I hope to post a reasonable review soon, but the ideas in it are truly excellent and fit into a thesis I’ve been working on for a while. For those interested, he does a reasonable synopsis of some of his thought in the talk he gave the the RSA recently, the video can be found below.

The underlying mathematics of what he’s discussing are fantastic (though he doesn’t go into them in his book), but the overarching implications of his ideas with relation to the future of humankind as a function of our economic system and society could have some significant impact.

“César visits the RSA to present a new view of the relationship between individual and collective knowledge, linking information theory, economics and biology to explain the deep evolution of social and economic systems.

In a radical rethink of what an economy is, one of WIRED magazine’s 50 People Who Could Change the World, César Hidalgo argues that it is the measure of a nation’s cultural complexity – the nexus of people, ideas and invention – rather than its GDP or per-capita income, that explains the success or failure of its economic performance. To understand the growth of economies, Hidalgo argues, we first need to understand the growth of order itself.”

The Math That Connects Pluto to DNA — NOVA Next | PBS

Bookmarked The Math That Connects Pluto to DNA by Alex RileyAlex Riley (NOVA Next | PBS)
How a mathematical breakthrough from the 1960s now powers everything from spacecraft to cell phones.
Concurrent with the recent Pluto fly by, Alex Riley has a great popular science article on PBS that helps put the application of information theory and biology into perspective for the common person. Like a science version of “The Princess Bride”, this story has a little bit of everything that could be good and entertaining: information theory, biology, DNA, Reed-Solomon codes, fossils, interplanetary exploration, mathematics, music, genetics, computers, and even paleontology. Fans of Big History are sure to love the interconnections presented here.

Reed-Solomon codes correct for common transmission errors, including missing pixels (white), false signals (black), and paused transmissions (the white stripe).
Reed-Solomon codes correct for common transmission errors, including missing pixels (white), false signals (black), and paused transmissions (the white stripe).

Microscopic view of glass DNA storage beads

Why Information Grows: The Evolution of Order, from Atoms to Economies

I just ordered a copy of Why Information Grows: The Evolution of Order, from Atoms to Economies by Cesar Hidalgo. Although it seems more focused on economics, the base theory seems to fit right into some similar thoughts I’ve long held about biology.

Why Information Grows: The Evolutiion of Order from Atoms to Economies by Cesar Hidalgo
Why Information Grows: The Evolutiion of Order from Atoms to Economies by Cesar Hidalgo

 

From the book description:

“What is economic growth? And why, historically, has it occurred in only a few places? Previous efforts to answer these questions have focused on institutions, geography, finances, and psychology. But according to MIT’s antidisciplinarian César Hidalgo, understanding the nature of economic growth demands transcending the social sciences and including the natural sciences of information, networks, and complexity. To understand the growth of economies, Hidalgo argues, we first need to understand the growth of order.

At first glance, the universe seems hostile to order. Thermodynamics dictates that over time, order–or information–will disappear. Whispers vanish in the wind just like the beauty of swirling cigarette smoke collapses into disorderly clouds. But thermodynamics also has loopholes that promote the growth of information in pockets. Our cities are pockets where information grows, but they are not all the same. For every Silicon Valley, Tokyo, and Paris, there are dozens of places with economies that accomplish little more than pulling rocks off the ground. So, why does the US economy outstrip Brazil’s, and Brazil’s that of Chad? Why did the technology corridor along Boston’s Route 128 languish while Silicon Valley blossomed? In each case, the key is how people, firms, and the networks they form make use of information.

Seen from Hidalgo’s vantage, economies become distributed computers, made of networks of people, and the problem of economic development becomes the problem of making these computers more powerful. By uncovering the mechanisms that enable the growth of information in nature and society, Why Information Grows lays bear the origins of physical order and economic growth. Situated at the nexus of information theory, physics, sociology, and economics, this book propounds a new theory of how economies can do, not just more, but more interesting things.”

8th Annual North American School of Information Theory (NASIT)

Bookmarked 8th Annual North American School of Information Theory (NASIT) (nasit15.ucsd.edu)
August 10-13, 2015 – UC San Diego, La Jolla, California
Application deadline: June 7, 2015

The School of Information Theory will bring together over 100 graduate students, postdoctoral scholars, and leading researchers for four action-packed days of learning, stimulating discussions, professional networking and fun activities, all on the beautiful campus of the University of California, San Diego (UCSD) and in the nearby beach town of La Jolla.

  • Tutorials by some of the best known researchers in information theory and related fields
  • Poster presentations by student participants with feedback and discussion
  • Panel discussion on “IT: Academia vs. Industry Perspectives”
  • Social events and fun activities