🔖 Spontaneous fine-tuning to environment in many-species chemical reaction networks | PNAS

Bookmarked Spontaneous fine-tuning to environment in many-species chemical reaction networks (Proceedings of the National Academy of Sciences)
Significance A qualitatively more diverse range of possible behaviors emerge in many-particle systems once external drives are allowed to push the system far from equilibrium; nonetheless, general thermodynamic principles governing nonequilibrium pattern formation and self-assembly have remained elusive, despite intense interest from researchers across disciplines. Here, we use the example of a randomly wired driven chemical reaction network to identify a key thermodynamic feature of a complex, driven system that characterizes the “specialness” of its dynamical attractor behavior. We show that the network’s fixed points are biased toward the extremization of external forcing, causing them to become kinetically stabilized in rare corners of chemical space that are either atypically weakly or strongly coupled to external environmental drives. Abstract A chemical mixture that continually absorbs work from its environment may exhibit steady-state chemical concentrations that deviate from their equilibrium values. Such behavior is particularly interesting in a scenario where the environmental work sources are relatively difficult to access, so that only the proper orchestration of many distinct catalytic actors can power the dissipative flux required to maintain a stable, far-from-equilibrium steady state. In this article, we study the dynamics of an in silico chemical network with random connectivity in an environment that makes strong thermodynamic forcing available only to rare combinations of chemical concentrations. We find that the long-time dynamics of such systems are biased toward states that exhibit a fine-tuned extremization of environmental forcing.
Suggested by First Support for a Physics Theory of Life in Quanta Magazine.

👓 Big names in statistics want to shake up much-maligned P value | Nature

Read Big names in statistics want to shake up much-maligned P value by Dalmeet Singh Chawla (Nature)
One of scientists’ favourite statistics — the P value — should face tougher standards, say leading researchers.
The related articles listed at the bottom, many of which I’d previously read, also give some great additional background.

👓 EXCLUSIVE: First human embryos edited in U.S., using CRISPR | MIT Technology Review

Read EXCLUSIVE: First human embryos edited in U.S., using CRISPR by Steve Connor (MIT Technology Review)
Researchers have demonstrated they can efficiently improve the DNA of human embryos.

👓 First Support for a Physics Theory of Life | Quanta Magazine

Read First Support for a Physics Theory of Life by Natalie Wolchover (Quanta Magazine)
Take chemistry, add energy, get life. The first tests of Jeremy England’s provocative origin-of-life hypothesis are in, and they appear to show how order can arise from nothing.
Interesting article with some great references I’ll need to delve into and read.


The situation changed in the late 1990s, when the physicists Gavin Crooks and Chris Jarzynski derived “fluctuation theorems” that can be used to quantify how much more often certain physical processes happen than reverse processes. These theorems allow researchers to study how systems evolve — even far from equilibrium.

I want to take a look at these papers as well as several about which the article is directly about.


Any claims that it has to do with biology or the origins of life, he added, are “pure and shameless speculations.”

Some truly harsh words from his former supervisor? Wow!


maybe there’s more that you can get for free

Most of what’s here in this article (and likely in the underlying papers) sounds to me to have been heavily influenced by the writings of W. Loewenstein and S. Kauffman. They’ve laid out some models/ideas that need more rigorous testing and work, and this seems like a reasonable start to the process. The “get for free” phrase itself is very S. Kauffman in my mind. I’m curious how many times it appears in his work?

📅 Entropy 2018: From Physics to Information Sciences and Geometry

RSVPed Might be attending Entropy 2018: From Physics to Information Sciences and Geometry
14-16 May 2018; Auditorium Enric Casassas, Faculty of Chemistry, University of Barcelona, Barcelona, Spain

One of the most frequently used scientific words, is the word “Entropy”. The reason is that it is related to two main scientific domains: physics and information theory. Its origin goes back to the start of physics (thermodynamics), but since Shannon, it has become related to information theory. This conference is an opportunity to bring researchers of these two communities together and create a synergy. The main topics and sessions of the conference cover:

  • Physics: classical Thermodynamics and Quantum
  • Statistical physics and Bayesian computation
  • Geometrical science of information, topology and metrics
  • Maximum entropy principle and inference
  • Kullback and Bayes or information theory and Bayesian inference
  • Entropy in action (applications)

The inter-disciplinary nature of contributions from both theoretical and applied perspectives are very welcome, including papers addressing conceptual and methodological developments, as well as new applications of entropy and information theory.

All accepted papers will be published in the proceedings of the conference. A selection of invited and contributed talks presented during the conference will be invited to submit an extended version of their paper for a special issue of the open access Journal Entropy. 

Entropy 2018 Conference

An Information Theory Playlist on Spotify

In honor of tomorrow’s release of Jimmy Soni and Rob Goodman’s book A Mind at Play: How Claude Shannon Invented the Information Age, I’ve created an Information Theory playlist on Spotify.

Songs about communication, telephones, conversation, satellites, love, auto-tune and even one about a typewriter! They all relate at least tangentially to the topic at hand. To up the ante, everyone should realize that digital music would be impossible without Shannon’s seminal work.

Let me know in the comments or by replying to one of the syndicated copies listed below if there are any great tunes that the list is missing.

Enjoy the list and the book!

👓 Meet the Authors of a Mind at Play: How Claude Shannon Invented the Information Age | IEEE Spectrum

Read Meet the Authors of a Mind at Play: How Claude Shannon Invented the Information Age (IEEE Spectrum)
Jimmy Soni and Rob Goodman wrote the first biography of the digital pioneer

📖 Read pages 16-55 of A Mind at Play by Jimmy Soni & Rob Goodman

📖 Read pages 16-55 of A Mind at Play: How Claude Shannon Invented the Information Age by Jimmy Soni & Rob Goodman

Knowing that I’ve read a lot about Shannon and even Vannevar Bush over the years, I’m pleasantly surprised to read some interesting tidbits about them that I’ve not previously come across.  I was a bit worried that this text wouldn’t provide me with much or anything new on the subjects at hand.

I’m really appreciating some of the prose and writing structure, particularly given that it’s a collaborative work between two authors. At times there are some really nonstandard sentence structures, but they’re wonderful in their rule breaking.

They’re doing an excellent job so far of explaining the more difficult pieces of science relating to information theory. In fact, some of the intro was as good as I think I’ve ever seen simple explanations of what is going on within the topic. I’m also pleased that they’ve made some interesting forays into topics like eugenics and the background role it played in the story for Shannon.

They had a chance to do a broader view of the history of computing, but opted against it, or at least must have made a conscious choice to leave out Babbage/Lovelace within the greater pantheon. I can see narratively why they may have done this knowing what is to come later in the text, but a few sentences as a nod would have been welcome.

The book does, however, get on my nerves with one of my personal pet peeves in popular science and biographical works like this: while there are reasonable notes at the end, absolutely no proper footnotes appear at the bottoms of pages or even indicators within the text other than pieces of text with quotation marks. I’m glad the notes even exist in the back, but it just drives me crazy that publishers blatantly hide them this way. The text could at least have had markers indicating where to find the notes. What are we? Animals?

Nota bene: I’m currently reading an advanced reader copy of this; the book won’t be out until mid-July 2017.

The quintessential poolside summer reading: A Mind at Play

The quintessential poolside summer reading: A Mind at Play

The quintessential poolside summer reading: A Mind at Play

Instagram filter used: Clarendon

Photo taken at: Gerrish Swim & Tennis Club

📗 Started reading A Mind at Play by Jimmy Soni & Rob Goodman

📖 Read pages i-16 of A Mind at Play: How Claude Shannon Invented the Information Age by Jimmy Soni & Rob Goodman

A great little introduction and start to what portends to be the science biography of the year. The book opens up with a story I’d heard Sol Golomb tell several times. It was actually a bittersweet memory as the last time I heard a recounting, it appeared on the occasion of Shannon’s 100th Birthday celebration in the New Yorker:

In 1985, at the International Symposium in Brighton, England, the Shannon Award went to the University of Southern California’s Solomon Golomb. As the story goes, Golomb began his lecture by recounting a terrifying nightmare from the night before: he’d dreamed that he was about deliver his presentation, and who should turn up in the front row but Claude Shannon. And then, there before Golomb in the flesh, and in the front row, was Shannon. His reappearance (including a bit of juggling at the banquet) was the talk of the symposium, but he never attended again.

I had emailed Sol about the story, and became concerned when I didn’t hear back. I discovered shortly after that he had passed away the following day.

nota bene: I’m currently reading an advanced reader copy of this; the book won’t be out until mid-July 2017.

Valerie Alexander on How Women Can Succeed in the Workplace (Despite Having “Female Brains”)

This morning, at the Friday morning coffee meetup of Innovate Pasadena held at Cross Campus, I saw one of the singularly best and most valuable talks I’ve heard in a long time. Many of these types of speakers, while engaging or even entertaining, are telling the same tired stories and at best you learn one sentence’s worth of value. Definitively not the case this morning!!!

How Women Can Succeed in the Workplace (Despite Having “Female Brains”) by Valerie Alexander

Entitled How Women Can Succeed in the Workplace (Despite Having “Female Brains”) writer and speaker Valerie Alexander presented a brief discussion of human evolutionary history (a topic I’ve studied closely for several decades) that featured the difference in development of male and female human brains. Based on this and with a clearer picture of what broadly differentiates the sexes, Valerie then gave a multitude of highly relate-able examples from her professional life highlighting how women can simply take back control in the workplace to not only better succeed for themselves, but to also help their companies see their true value and succeed simultaneously.

Further, she also included some simple and very actionable advice (for men and women) to be able to make a better space within corporations so that they’re able to extract more of the value women bring to the workplace. Hint: Women bring a HUGE amount of value, and a majority of companies are not only undervaluing it, but they are literally throwing it away.

Not only were the messages tremendously valuable and imminently actionable by both women AND men, but she delivered it with fantastic confidence, grace, wit, charm, and warmth. In fact, I’d say it was not only strikingly informative, but it was also very entertaining. If you’re in the corporate space and looking to turn around your antediluvian or even pre-historic work culture (I’m looking ominously at you Uber and similar Silicon Valley brogrammer cultures), then jump in line as quickly as you can to book up what I can only expect is the diminishing time in her speaking and travel schedule.

Innovate Pasadena recorded the talk and I’ll try to post it here as soon as it’s available. Until then I will highly recommend purchasing her book How Women Can Succeed in the Workplace (Despite Having “Female Brains”), which I’m sure has not only the content of her lecture, but assuredly includes a whole lot more detail and additional examples than one could fit into such a short time frame. I also suspect it’s the type of book one would want to refer back to frequently as well. I’ve already got a half a dozen copies of it on their way to me to share with friends and family. I’m willing to make a substantial bet that for uncovering inherent value, this book and her overall message will eventually stand in the pantheon of texts and work of those like those of Frederick Winslow Taylor, Lillian Gilbreth, Frank Gilbreth, Dale Carnegie, Napoleon Hill, J.M. Juran, and W. Edwards Deming.


Psst… If the good folks at TED need some fantastic content, I saw a shortened 25 minute version of her hour-long talk. It could be tightened a hair for content and length, but it’s got exactly the tone, tempo and has the high level of presentation skills for which you’re known. Most importantly, it’s definitively an “Idea worth spreading.”

Innovate Pasadena has finally uploaded a copy of the video of Valerie Alexander’s talk:

https://www.youtube.com/watch?v=ySO1s4WMMkg

🔖 A Mind at Play: How Claude Shannon Invented the Information Age by Jimmy Soni, Rob Goodman

Bookmarked A Mind at Play: How Claude Shannon Invented the Information Age (Simon & Schuster)
The life and times of one of the foremost intellects of the twentieth century: Claude Shannon—the neglected architect of the Information Age, whose insights stand behind every computer built, email sent, video streamed, and webpage loaded. Claude Shannon was a groundbreaking polymath, a brilliant tinkerer, and a digital pioneer. He constructed a fleet of customized unicycles and a flamethrowing trumpet, outfoxed Vegas casinos, and built juggling robots. He also wrote the seminal text of the digital revolution, which has been called “the Magna Carta of the Information Age.” His discoveries would lead contemporaries to compare him to Albert Einstein and Isaac Newton. His work anticipated by decades the world we’d be living in today—and gave mathematicians and engineers the tools to bring that world to pass. In this elegantly written, exhaustively researched biography, Jimmy Soni and Rob Goodman reveal Claude Shannon’s full story for the first time. It’s the story of a small-town Michigan boy whose career stretched from the era of room-sized computers powered by gears and string to the age of Apple. It’s the story of the origins of our digital world in the tunnels of MIT and the “idea factory” of Bell Labs, in the “scientists’ war” with Nazi Germany, and in the work of Shannon’s collaborators and rivals, thinkers like Alan Turing, John von Neumann, Vannevar Bush, and Norbert Wiener. And it’s the story of Shannon’s life as an often reclusive, always playful genius. With access to Shannon’s family and friends, A Mind at Play brings this singular innovator and creative genius to life.
I can’t wait to read this new biography about Claude Shannon! The bio/summer read I’ve been waiting for.

With any luck an advanced reader copy is speeding it way to me! (Sorry you can’t surprise me with a belated copy for my birthday.) A review is forthcoming.

You have to love the cover art by Lauren Peters-Collaer.

📺 Scientific Studies: Last Week Tonight with John Oliver (HBO)

Watched Scientific Studies: Last Week Tonight from HBO
John Oliver discusses how and why media outlets so often report untrue or incomplete information as science.
This episode reminds me a bit about a short snippet I wrote in 2015 about the Evolution of a Scientific Journal Article Title (from Nature to TMZ)

https://www.youtube.com/watch?v=0Rnq1NpHdmw

📺 Paris Agreement: Last Week Tonight with John Oliver (HBO)

Watched Paris Agreement: Last Week Tonight from HBO
Donald Trump plans to withdraw the United States from the Paris agreement on climate change. That's bad news for anyone who happens to live on this planet.
https://www.youtube.com/watch?v=5scez5dqtAc