👓 The First Species to Have Every Individual’s Genome Sequenced | The Atlantic

The First Species to Have Every Individual’s Genome Sequenced by Ed Yong (The Atlantic)
It’s an endearing, giant, flightless, New Zealand parrot, and it’s a poster child for the quantified-self movement.


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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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📺 A Universal Theory of Life: Math, Art & Information by Sara Walker

A Universal Theory of Life: Math, Art & Information by Sara Walker from TEDxASU
Dr. Walker introduces the concept of information, then proposes that information may be a necessity for biological complexity in this thought-provoking talk on the origins of life. Sara is a theoretical physicist and astrobiologist, researching the origins and nature of life. She is particularly interested in addressing the question of whether or not “other laws of physics” might govern life, as first posed by Erwin Schrodinger in his famous book What is life?. She is currently an Assistant Professor in the School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science at Arizona State University. She is also Fellow of the ASU -Santa Fe Institute Center for Biosocial Complex Systems, Founder of the astrobiology-themed social website SAGANet.org, and is a member of the Board of Directors of Blue Marble Space. She is active in public engagement in science, with recent appearances on “Through the Wormhole” and NPR’s Science Friday.

Admittedly, she only had a few short minutes, but it would have been nice if she’d started out with a precise definition of information. I suspect the majority of her audience didn’t know the definition with which she’s working and it would have helped focus the talk.

Her description of Speigelman’s Monster was relatively interesting and not very often seen in much of the literature that covers these areas.

I wouldn’t rate this very highly as a TED Talk as it wasn’t as condensed and simplistic as most, nor was it as hyper-focused, but then again condensing this area into 11 minutes is far from simple task. I do love that she’s excited enough about the topic that she almost sounds a little out of breath towards the end.

There’s an excellent Eddington quote I’ve mentioned before that would have been apropos to have opened up her presentation that might have brought things into higher relief given her talk title:

Suppose that we were asked to arrange the following in two categories–

distance, mass, electric force, entropy, beauty, melody.

I think there are the strongest grounds for placing entropy alongside beauty and melody and not with the first three.

Sir Arthur Stanley Eddington, OM, FRS (1882-1944), a British astronomer, physicist, and mathematician
in The Nature of the Physical World, 1927


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🔖 Origins of Life: A Problem for Physics

Origins of Life: A Problem for Physics by Sara I. Walker (arXiv)
The origins of life stands among the great open scientific questions of our time. While a number of proposals exist for possible starting points in the pathway from non-living to living matter, these have so far not achieved states of complexity that are anywhere near that of even the simplest living systems. A key challenge is identifying the properties of living matter that might distinguish living and non-living physical systems such that we might build new life in the lab. This review is geared towards covering major viewpoints on the origin of life for those new to the origin of life field, with a forward look towards considering what it might take for a physical theory that universally explains the phenomenon of life to arise from the seemingly disconnected array of ideas proposed thus far. The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins.
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👓 Can Darwinian Evolution Explain Lamarckism? | Quanta Magazine

Can Darwinian Evolution Explain Lamarckism? by Pradeep Mutalik (Quanta Magazine)
Answering three questions can help reveal how the “inheritance of acquired characteristic” fits into modern evolutionary theory.
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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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🔖 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.


E. Mayr, What Makes Biology Unique? Cambridge University Press, 2004.
A. Wissner-Gross and C. Freer, “Causal entropic forces.,” Phys Rev Lett, vol. 110, no. 16, p. 168702, Apr. 2013. [PubMed]
A. Barato and U. Seifert, “Thermodynamic uncertainty relation for biomolecular processes.,” Phys Rev Lett, vol. 114, no. 15, p. 158101, Apr. 2015. [PubMed]
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]
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
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]
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
C. Rovelli, “Meaning = Information + Evolution,” arXiv, Nov. 2006 [Online]. Available: https://arxiv.org/abs/1611.02420
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]
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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🔖 Human Evolution: Our Brains and Behavior by Robin Dunbar (Oxford University Press)

🔖 Human Evolution: Our Brains and Behavior by Robin Dunbar (Oxford University Press) marked as want to read.
Official release date: November 1, 2016
09/14/16: downloaded a review copy via NetGalley


The story of human evolution has fascinated us like no other: we seem to have an insatiable curiosity about who we are and where we have come from. Yet studying the “stones and bones” skirts around what is perhaps the realest, and most relatable, story of human evolution – the social and cognitive changes that gave rise to modern humans.

In Human Evolution: Our Brains and Behavior, Robin Dunbar appeals to the human aspects of every reader, as subjects of mating, friendship, and community are discussed from an evolutionary psychology perspective. With a table of contents ranging from prehistoric times to modern days, Human Evolution focuses on an aspect of evolution that has typically been overshadowed by the archaeological record: the biological, neurological, and genetic changes that occurred with each “transition” in the evolutionary narrative. Dunbar’s interdisciplinary approach – inspired by his background as both an anthropologist and accomplished psychologist – brings the reader into all aspects of the evolutionary process, which he describes as the “jigsaw puzzle” of evolution that he and the reader will help solve. In doing so, the book carefully maps out each stage of the evolutionary process, from anatomical changes such as bipedalism and increase in brain size, to cognitive and behavioral changes, such as the ability to cook, laugh, and use language to form communities through religion and story-telling. Most importantly and interestingly, Dunbar hypothesizes the order in which these evolutionary changes occurred-conclusions that are reached with the “time budget model” theory that Dunbar himself coined. As definitive as the “stones and bones” are for the hard dates of archaeological evidence, this book explores far more complex psychological questions that require a degree of intellectual speculation: What does it really mean to be human (as opposed to being an ape), and how did we come to be that way?

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NIMBioS Tutorial: Evolutionary Quantitative Genetics 2016

NIMBioS Tutorial: Evolutionary Quantitative Genetics 2016 by NIMBioS (nimbios.org)
This tutorial will review the basics of theory in the field of evolutionary quantitative genetics and its connections to evolution observed at various time scales. Quantitative genetics deals with the inheritance of measurements of traits that are affected by many genes. Quantitative genetic theory for natural populations was developed considerably in the period from 1970 to 1990 and up to the present, and it has been applied to a wide range of phenomena including the evolution of differences between the sexes, sexual preferences, life history traits, plasticity of traits, as well as the evolution of body size and other morphological measurements. Textbooks have not kept pace with these developments, and currently few universities offer courses in this subject aimed at evolutionary biologists. There is a need for evolutionary biologists to understand this field because of the ability to collect large amounts of data by computer, the development of statistical methods for changes of traits on evolutionary trees and for changes in a single species through time, and the realization that quantitative characters will not soon be fully explained by genomics. This tutorial aims to fill this need by reviewing basic aspects of theory and illustrating how that theory can be tested with data, both from single species and with multiple-species phylogenies. Participants will learn to use R, an open-source statistical programming language, to build and test evolutionary models. The intended participants for this tutorial are graduate students, postdocs, and junior faculty members in evolutionary biology.

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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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16w5113: Stochastic and Deterministic Models for Evolutionary Biology | Banff International Research Station

Stochastic and Deterministic Models for Evolutionary Biology (Banff International Research Station)
A BIRS / Casa Matemática Oaxaca Workshop arriving in Oaxaca, Mexico Sunday, July 31 and departing Friday August 5, 2016

Evolutionary biology is a rapidly changing field, confronted to many societal problems of increasing importance: impact of global changes, emerging epidemics, antibiotic resistant bacteria… As a consequence, a number of new problematics have appeared over the last decade, challenging the existing mathematical models. There exists thus a demand in the biology community for new mathematical models allowing a qualitative or quantitative description of complex evolution problems. In particular, in the societal problems mentioned above, evolution is often interacting with phenomena of a different nature: interaction with other organisms, spatial dynamics, age structure, invasion processes, time/space heterogeneous environment… The development of mathematical models able to deal with those complex interactions is an ambitious task. Evolutionary biology is interested in the evolution of species. This process is a combination of several phenomena, some occurring at the individual level (e.g. mutations), others at the level of the entire population (competition for resources), often consisting of a very large number of individuals. the presence of very different scales is indeed at the core of theoretical evolutionary biology, and at the origin of many of the difficulties that biologists are facing. The development of new mathematical models thus requires a joint work of three different communities of researchers: specialists of partial differential equations, specialists of probability theory, and theoretical biologists. The goal of this workshop is to gather researchers from each of these communities, currently working on close problematics. Those communities have usually few interactions, and this meeting would give them the opportunity to discuss and work around a few biological thematics that are especially challenging mathematically, and play a crucial role for biological applications.

The role of a spatial structure in models for evolution: The introduction of a spatial structure in evolutionary biology models is often challenging. It is however well known that local adaptation is frequent in nature: field data show that the phenotypes of a given species change considerably across its range. The spatial dynamics of a population can also have a deep impact on its evolution. Assessing e.g. the impact of global changes on species requires the development of robust mathematical models for spatially structured populations.

The first type of models used by theoretical biologists for this type of problems are IBM (Individual Based Models), which describe the evolution of a finite number of individuals, characterized by their position and a phenotype. The mathematical analysis of IBM in spatially homogeneous situations has provided several methods that have been successful in the theoretical biology community (see the theory of Adaptive Dynamics). On the contrary, very few results exist so far on the qualitative properties of such models for spatially structured populations.

The second class of mathematical approach for this type of problem is based on ”infinite dimensional” reaction-diffusion: the population is structured by a continuous phenotypic trait, that affects its ability to disperse (diffusion), or to reproduce (reaction). This type of model can be obtained as a large population limit of IBM. The main difficulty of these models (in the simpler case of asexual populations) is the term modeling the competition from resources, that appears as a non local competition term. This term prevents the use of classical reaction diffusion tools such as the comparison principle and sliding methods. Recently, promising progress has been made, based on tools from elliptic equations and/or Hamilton-Jacobi equations. The effects of small populations can however not be observed on such models. The extension of these models and methods to include these effects will be discussed during the workshop.

Eco-evolution models for sexual populations:An essential question already stated by Darwin and Fisher and which stays for the moment without answer (although it continues to intrigue the evolutionary biologists) is: ”Why does sexual reproduction maintain?” Indeed this reproduction way is very costly since it implies a large number of gametes, the mating and the choice of a compatible partner. During the meiosis phasis, half of the genetical information is lost. Moreover, the males have to be fed and during the sexual mating, individual are easy preys for predators. A partial answer is that recombination plays a main role by better eliminating the deleterious mutations and by increasing the diversity. Nevertheless, this theory is not completely satisfying and many researches are devoted to understanding evolution of sexual populations and comparison between asexual and sexual reproduction. Several models exist to model the influence of sexual reproduction on evolving species. The difficulty compared to asexual populations is that a detailed description of the genetic basis of phenotypes is required, and in particular include recombinations. For sexual populations, recombination plays a main role and it is essential to understand. All models require strong biological simplifications, the development of relevant mathematical methods for such mechanisms then requires a joint work of mathematicians and biologists. This workshop will be an opportunity to set up such collaborations.

The first type of model considers a small number of diploid loci (typically one locus and two alleles), while the rest of the genome is considered as fixed. One can then define the fitness of every combination of alleles. While allowing the modeling of specific sexual effects (such as dominant/recessive alleles), this approach neglects the rest of the genome (and it is known that phenotypes are typically influenced by a large number of loci). An opposite approach is to consider a large number of loci, each locus having a small and additive impact on the considered phenotype. This approach then neglects many microscopic phenomena (epistasis, dominant/recessive alleles…), but allows the derivation of a deterministic model, called the infinitesimal model, in the case of a large population. The construction of a good mathematical framework for intermediate situation would be an important step forward.

The evolution of recombination and sex is very sensitive to the interaction between several evolutionary forces (selection, migration, genetic drift…). Modeling these interactions is particularly challenging and our understanding of the recombination evolution is often limited by strong assumptions regarding demography, the relative strength of these different evolutionary forces, the lack of spatial structure… The development of a more general theoretical framework based on new mathematical developments would be particularly valuable.

Another problem, that has received little attention so far and is worth addressing, is the modeling of the genetic material exchanges in asexual population. This phenomena is frequent in micro-organisms : horizontal gene transfers in bacteria, reassortment or recombination in viruses. These phenomena share some features with sexual reproduction. It would be interesting to see if the effect of this phenomena can be seen as a perturbation of existing asexual models. This would in particular be interesting in spatially structured populations (e.g. viral epidemics), since the the mathematical analysis of spatially structured asexual populations is improving rapidly.

Modeling in evolutionary epidemiology: Mathematical epidemiology has been developing since more than a century ago. Yet, the integration of population genetics phenomena to epidemiology is relatively recent. Microbial pathogens (bacteria and viruses) are particularly interesting organisms because their short generation times and large mutation rates allow them to adapt relatively fast to changing environments. As a consequence, ecological (demography) and evolutionary (population genetics) processes often occur at the same pace. This raises many interesting problems.

A first challenge is the modeling of the spatial dynamics of an epidemics. The parasites can evolve during the epidemics of a new host population, either to adapt to a heterogeneous environment, or because it will itself modify the environment as it invades. The applications of such studies are numerous: antibiotic management, agriculture… An aspect of this problem for which our workshop can bring a significant contribution (thanks to the diversity of its participants) is the evolution of the pathogen diversity. During the large expansion produced by an epidemics, there is a loss of diversity in the invading parasites, since most pathogens originate from a few parents. The development of mathematical models for those phenomena is challenging: only a small number of pathogens are present ahead of the epidemic front, while the number of parasites rapidly become very large after the infection. The interaction between a stochastic micro scale and a deterministic macro scale is apparent here, and deserves a rigorous mathematical analysis.

Another interesting phenomena is the effect of a sudden change of the environment on a population of pathogens. Examples of such situations are for instance the antibiotic treatment of an infected patients, or the transmission of a parasite to a new host species (transmission of the avian influenza to human beings, for instance). Related experiments are relatively easy to perform, and called evolutionary rescue experiments. So far, this question has received limited attention from the mathematical community. The key is to estimate the probability that a mutant well adapted to the new environment existed in the original population, or will appear soon after the environmental change. Interactions between biologists specialists of those questions and mathematicians should lead to new mathematical problems.

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Nick Lane and Philip Ball Discuss Mitochondria, Sex, and How to Live Longer

Nick Lane and Philip Ball Discuss Mitochondria, Sex, and How to Live Longer by Philip Ball (Nautil.us)
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.

Read more

Books by Nick Lane

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A new view of the tree of life

A new view of the tree of life (Nature Microbiology)
An update to the €˜tree of life has revealed a dominance of bacterial diversity in many ecosystems and extensive evolution in some branches of the tree. It also highlights how few organisms we have been able to cultivate for further investigation.


The tree of life is one of the most important organizing principles in biology. Gene surveys suggest the existence of an enormous number of branches, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships or on the known, well-classified diversity of life with an emphasis on eukaryotes. These approaches overlook the dramatic change in our understanding of life’s diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

Laura A. Hug, Brett J. Baker, Karthik Anantharaman, Christopher T. Brown, Alexander J. Probst, Cindy J. Castelle, Cristina N. Butterfield, Alex W. Hernsdorf, Yuki Amano, Kotaro Ise, Yohey Suzuki, Natasha Dudek, David A. Relman, Kari M. Finstad, Ronald Amundson, Brian C. Thomas & Jillian F. Banfield in Nature Microbiology, Article number: 16048 (2016) doi:10.1038/nmicrobiol.2016.48


A reformatted view of the tree in Fig. 1in which each major lineage represents the same amount of evolutionary distance.
A reformatted view of the tree in Fig. 1in which each major lineage represents the same amount of evolutionary distance.

Carl Zimmer also has a nice little write up of the paper in today’s New York Times:

Carl Zimmer
in Scientists Unveil New ‘Tree of Life’ from The New York Times 4/11/16


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

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.

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



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

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

Paul Davies waxes poetic about the application of physics, chemistry, and information theory to biology, genetics, and the origin of life.

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
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