📗 Started reading The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane

📗 Started reading pages 1-18 Introduction: Why is Life the Way it is in The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane

A quick, but interesting peek into where he intends to go. He lays out some quick background here in the opening. He’s generally a very lucid writer so far. Can’t wait to get in further.

Some may feel like some of the terminology is a hurdle in the opening, so I hope he circles around to define some of his terms a bit better for the audience I suspect he’s trying to reach.

book cover of Nick Lane's The Vital Question
The Vital Question: Energy, Evolution and the Origins of Complex Life by Nick Lane
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📕 Read pages 381-461 of Origin by Dan Brown

📕 Read pages 381-461 to finish reading Origin: A Novel by Dan Brown

This last section got pretty heavy into evolution and touched on ideas of information theory applied to biology and complexity, but didn’t actually mention them. Surprisingly he mentioned Jeremy England by name! He nibbled around the edges of the field to tie up the plot, but there’s some reasonable philosophical questions hiding here in the end of the book that I’ll have to pull into a more lengthy review.

🎧 Antibiotics and agriculture | Eat This Podcast

Antibiotics and agriculture by Jeremy Cherfas from Eat This Podcast
Tackling the problem of antibiotic resistance at (one) source In the past year or so there has been a slew of high-level meetings pointing to antibiotic resistance as a growing threat to human well-being. But then, resistance was always an inevitable, Darwinian consequence of antibiotic use. Well before penicillin was widely available, Ernst Chain, who went on to win a Nobel Prize for his work on penicillin, noted that some bacteria were capable of neutralising the antibiotic. What is new about the recent pronouncements and decisions is that the use of antibiotics in agriculture is being recognised, somewhat belatedly, as a major source of resistance. Antibiotic manufacturers and the animal health industry have, since the start, done everything they can to deny that. Indeed, the history of efforts to regulate the use of antibiotics in agriculture reveals a pretty sordid approach to public health. But while it can be hard to prove the connection between agriculture and a specific case of antibiotic resistance, a look at hundreds of recent academic studies showed that almost three quarters of them did demonstrate a conclusive link. Antibiotic resistance – whether it originates with agriculture or inappropriate medical use – takes us back almost 100 years, when infectious diseases we now consider trivial could, and did, kill. It reduces the effectiveness of other procedures too, such as surgery and chemotherapy, by making it more likely that a subsequent infection will wreck the patient’s prospects. So it imposes huge costs on society as a whole. Maybe society as a whole needs to tackle the problem. The Oxford Martin School, which supports a portfolio of highly interdisciplinary research groups at Oxford University, has a Programme on Collective Responsibility for Infectious Disease. They recently published a paper proposing a tax on animal products produced with antibiotics. Could that possibly work?

Here’s another great example of a negative externality. Too often capitalism brushes over these and creates a larger longer term cost by not taking these into account. It’s almost assuredly the case that taxing the use of these types of antibiotics across the broadest base of users (eaters) (thereby minimizing the overall marginal cost), would help to minimize the use of these or at least we’d have the funding for improving the base issue in the future. In some sense, the additional cost of eating organic meat is similar to this type of “tax”, but the money is allocated in a different way.

Not covered here are some of the economic problems of developing future antibiotics when our current ones have ceased to function as the result of increased resistance over time. This additional problem is an even bigger worry for the longer term. In some sense, it’s all akin to the cost of smoking and second hand smoke–the present day marginal cost to the smoker of cigarettes and taxes is idiotically low in comparison to the massive future cost of their overall health as well as that of the society surrounding them. Better to put that cost upfront for those who really prefer to smoke so that the actual externalities are taken into account from the start.

This excellent story reminds me of a great series of stories that PBS NewsHour did on the general topic earlier this year.

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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:

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🎧 Why save seeds? | Eat This Podcast

Why save seeds? by Jeremy Cherfas from Eat This Podcast
What, really, is the point of conserving agricultural biodiversity? The formal sector, genebanks and the like, will say it is about genetic resources and having on hand the traits to breed varieties that will solve the challenges tomorrow might throw up. Thousands of seed savers around the world might well agree with that, at least partially. I suspect, though, that for most seed savers the primary reason is surely more about food, about having the varieties they want to eat. David Cavagnaro has always championed that view. David’s is a fascinating personal history, which currently sees him working on the Pepperfield Project, “A Non-Profit Organization Located in Decorah, IA Promoting and Teaching Hands-On Cooking, Gardening and Agrarian Life Skills”. I first met David 15 or 20 years ago at Seed Savers Exchange in Decorah. This year, I was lucky enough to be invited there again, and I lost no time in finding time for a chat. David pointed out that immigrants are often keen gardeners and, perforce, seed savers as they struggle to maintain their distinctive food culture in a new land. That’s true for the Hmong in Minneapolis, Asian communities in England and, I’m sure, many others elsewhere. What happens as those communities assimilate? The children and grandchildren of the immigrant gardeners are unlikely to feel the same connection to their original food culture, and may well look down on growing food as an unsuitable occupation. Is immigrant agricultural biodiversity liable to be lost too? Efforts to preserve it don’t seem to be flourishing. Seed saving for its own sake, rather than purely as a route to sustenance, does seem to be both a bit of a luxury and to require a rather special kind of personality. John Withee, whose bean collection brought David Cavagnaro to Seed Savers Exchange and people like Russ Crow, another of his spritual heirs, collect and create stories as much as they do agricultural biodiversity. And that’s something formal genebanks never seem to document.

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There’s a lot to unpack here with respect to agricultural diversity and evolution. Mass food manufacture is a boon for the world, but this type of industrial process should be working on ways to keep some programmed diversity in the process as well. I would have been perfectly happy for this interview to have gone on for several hours and in greater depth.

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👓 Why Facts Don’t Change Our Minds | The New Yorker

Why Facts Don’t Change Our Minds by Elizabeth Kolbert (The New Yorker)
New discoveries about the human mind show the limitations of reason.

The vaunted human capacity for reason may have more to do with winning arguments than with thinking straight.
The vaunted human capacity for reason may have more to do with winning arguments than with thinking straight. Credit Illustration by Gérard DuBois
Continue reading “👓 Why Facts Don’t Change Our Minds | The New Yorker”
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🔖 Want to read: From Bacteria to Bach and Back: The Evolution of Minds by Daniel C. Dennett

From Bacteria to Bach and Back: The Evolution of Minds by Daniel C. Dennett (W. W. Norton & Company; 1 edition, 496 pages (February 7, 2017))
One of America’s foremost philosophers offers a major new account of the origins of the conscious mind.

How did we come to have minds?

For centuries, this question has intrigued psychologists, physicists, poets, and philosophers, who have wondered how the human mind developed its unrivaled ability to create, imagine, and explain. Disciples of Darwin have long aspired to explain how consciousness, language, and culture could have appeared through natural selection, blazing promising trails that tend, however, to end in confusion and controversy. Even though our understanding of the inner workings of proteins, neurons, and DNA is deeper than ever before, the matter of how our minds came to be has largely remained a mystery.

That is now changing, says Daniel C. Dennett. In From Bacteria to Bach and Back, his most comprehensive exploration of evolutionary thinking yet, he builds on ideas from computer science and biology to show how a comprehending mind could in fact have arisen from a mindless process of natural selection. Part philosophical whodunit, part bold scientific conjecture, this landmark work enlarges themes that have sustained Dennett’s legendary career at the forefront of philosophical thought.

In his inimitable style―laced with wit and arresting thought experiments―Dennett explains that a crucial shift occurred when humans developed the ability to share memes, or ways of doing things not based in genetic instinct. Language, itself composed of memes, turbocharged this interplay. Competition among memes―a form of natural selection―produced thinking tools so well-designed that they gave us the power to design our own memes. The result, a mind that not only perceives and controls but can create and comprehend, was thus largely shaped by the process of cultural evolution.

An agenda-setting book for a new generation of philosophers, scientists, and thinkers, From Bacteria to Bach and Back will delight and entertain anyone eager to make sense of how the mind works and how it came about.

4 color, 18 black-and-white illustrations

🔖 Want to read: From Bacteria to Bach and Back: The Evolution of Minds by Daniel C. Dennett

 

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IPAM Workshop on Regulatory and Epigenetic Stochasticity in Development and Disease, March 1-3

IPAM Workshop on Regulatory and Epigenetic Stochasticity in Development and Disease (Institute for Pure and Applied Mathematics, UCLA | March 1-3, 2017)
Epigenetics refers to information transmitted during cell division other than the DNA sequence per se, and it is the language that distinguishes stem cells from somatic cells, one organ from another, and even identical twins from each other. In contrast to the DNA sequence, the epigenome is relatively susceptible to modification by the environment as well as stochastic perturbations over time, adding to phenotypic diversity in the population. Despite its strong ties to the environment, epigenetics has never been well reconciled to evolutionary thinking, and in fact there is now strong evidence against the transmission of so-called “epi-alleles,” i.e. epigenetic modifications that pass through the germline.

However, genetic variants that regulate stochastic fluctuation of gene expression and phenotypes in the offspring appear to be transmitted as an epigenetic or even Lamarckian trait. Furthermore, even the normal process of cellular differentiation from a single cell to a complex organism is not understood well from a mathematical point of view. There is increasingly strong evidence that stem cells are highly heterogeneous and in fact stochasticity is necessary for pluripotency. This process appears to be tightly regulated through the epigenome in development. Moreover, in these biological contexts, “stochasticity” is hardly synonymous with “noise”, which often refers to variation which obscures a “true signal” (e.g., measurement error) or which is structural, as in physics (e.g., quantum noise). In contrast, “stochastic regulation” refers to purposeful, programmed variation; the fluctuations are random but there is no true signal to mask.

This workshop will serve as a forum for scientists and engineers with an interest in computational biology to explore the role of stochasticity in regulation, development and evolution, and its epigenetic basis. Just as thinking about stochasticity was transformative in physics and in some areas of biology, it promises to fundamentally transform modern genetics and help to explain phase transitions such as differentiation and cancer.

This workshop will include a poster session; a request for poster titles will be sent to registered participants in advance of the workshop.

Speaker List:
Adam Arkin (Lawrence Berkeley Laboratory)
Gábor Balázsi (SUNY Stony Brook)
Domitilla Del Vecchio (Massachusetts Institute of Technology)
Michael Elowitz (California Institute of Technology)
Andrew Feinberg (Johns Hopkins University)
Don Geman (Johns Hopkins University)
Anita Göndör (Karolinska Institutet)
John Goutsias (Johns Hopkins University)
Garrett Jenkinson (Johns Hopkins University)
Andre Levchenko (Yale University)
Olgica Milenkovic (University of Illinois)
Johan Paulsson (Harvard University)
Leor Weinberger (University of California, San Francisco (UCSF))

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🔖 Statistical Physics of Adaptation

Statistical Physics of Adaptation by Nikolay Perunov, Robert A. Marsland, and Jeremy L. England (journals.aps.org Phys. Rev. X 6, 021036 (2016))
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.
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🔖 Meaning = Information + Evolution by Carlo Rovelli

Meaning = Information + Evolution by Carlo Rovelli (arxiv.org)
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".
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🔖 How Life (and Death) Spring From Disorder | Quanta Magazine

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]
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🎧 Fearless | Invisibilia (NPR)

Fearless by Lulu Miller and Alix Spiegel from Invisibilia | NPR.org
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?

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Disconnected, Fragmented, or United? A Trans-disciplinary Review of Network Science

Disconnected, Fragmented, or United? A Trans-disciplinary Review of Network Science by César A. HidalgoCésar A. Hidalgo (Applied Network Science | SpringerLink)

Abstract

Applied Network Science

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.

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Weekly Recap: Interesting Articles 7/24-7/31 2016

Some of the interesting things I saw and read this week

Went on vacation or fell asleep at the internet wheel this week? Here’s some of the interesting stuff you missed.

Science & Math

Publishing

Indieweb, Internet, Identity, Blogging, Social Media

General

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Penguin Revives Decades-Old Software for 30th Anniversary Edition of “The Blind Watchmaker” | The Digital Reader

Penguin Revives Decades-Old Software for 30th Anniversary Edition of "The Blind Watchmaker" by Nate Hoffelder (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.

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