Arrival of the fittest : solving evolution's greatest puzzle

Wagner, Andreas
Current, 2014

Publisher's Summary:

“Natural selection can preserve innovations, but it cannot create them. Nature’s many innovations—some uncannily perfect—call for natural principles that accelerate life’s ability to innovate.”

Darwin’s theory of natural selection explains how useful adaptations are preserved over time. But the biggest mystery about evolution eluded him. As genetics pioneer Hugo de Vries put it, “natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest.”

Can random mutations over a mere 3.8 billion years really be responsible for wings, eyeballs, knees, camouflage, lactose digestion, photosynthesis, and the rest of nature’s creative marvels? And if the answer is no, what is the mechanism that explains evolution’s speed and efficiency?

In Arrival of the Fittest, renowned evolutionary biologist Andreas Wagner draws on over fifteen years of research to present the missing piece in Darwin's theory. Using experimental and computational technologies that were heretofore unimagined, he has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.

Consider the Arctic cod, a fish that lives and thrives within six degrees of the North Pole, in waters that regularly fall below 0 degrees. At that temperature, the internal fluids of most organisms turn into ice crystals. And yet, the arctic cod survives by producing proteins that lower the freezing temperature of its body fluids, much like antifreeze does for a car’s engine coolant. The invention of those proteins is an archetypal example of nature’s enormous powers of creativity.

Meticulously researched, carefully argued, evocatively written, and full of fascinating examples from the animal kingdom, Arrival of the Fittest offers up the final puzzle piece in the mystery of life’s rich diversity.

Reality mining : using big data to engineer a better world

Nathan. Eagle; Kate Greene
The MIT Press, 2014

Publisher's Summary:

A look at how Big Data can be put to positive use, from helping users break bad habits to tracking the global spread of disease.

Big Data is made up of lots of little data: numbers entered into cell phones, addresses entered into GPS devices, visits to websites, online purchases, ATM transactions, and any other activity that leaves a digital trail. Although the abuse of Big Data -- surveillance, spying, hacking -- has made headlines, it shouldn't overshadow the abundant positive applications of Big Data. In Reality Mining, Nathan Eagle and Kate Greene cut through the hype and the headlines to explore the positive potential of Big Data, showing the ways in which the analysis of Big Data ("Reality Mining") can be used to improve human systems as varied as political polling and disease tracking, while considering user privacy.

Eagle, a recognized expert in the field, and Greene, an experienced technology journalist, describe Reality Mining at five different levels: the individual, the neighborhood and organization, the city, the nation, and the world. For each level, they first offer a nontechnical explanation of data collection methods and then describe applications and systems that have been or could be built. These include a mobile app that helps smokers quit smoking; a workplace "knowledge system"; the use of GPS, Wi-Fi, and mobile phone data to manage and predict traffic flows; and the analysis of social media to track the spread of disease. Eagle and Greene argue that Big Data, used respectfully and responsibly, can help people live better, healthier, and happier lives.

 

Decision making and imperfection

Tatiana V. Guy; Miroslav Kárný; David Wolpert
Springer, 2013

Publisher's Summary:

Decision making (DM) is ubiquitous in both natural and artificial systems. The decisions made often differ from those recommended by the axiomatically well-grounded normative Bayesian decision theory, in a large part due to limited cognitive and computational resources of decision makers (either artificial units or humans). This state of a airs is often described by saying that decision makers are imperfect and exhibit bounded rationality. The neglected influence of emotional state and personality traits is an additional reason why normative theory fails to model human DM process. The book is a joint effort of the top researchers from different disciplines to identify sources of imperfection and ways how to decrease discrepancies between the prescriptive theory and real-life DM. The contributions consider: · how a crowd of imperfect decision makers outperforms experts' decisions; · how to decrease decision makers' imperfection by reducing knowledge available; · how to decrease imperfection via automated elicitation of DM preferences; · a human's limited willingness to master the available decision-support tools as an additional source of imperfection; · how the decision maker's emotional state influences the rationality; a DM support of edutainment robot based on its system of values and respecting emotions. The book will appeal to anyone interested in the challenging topic of DM theory and its applications.

The Cambrian explosion: the construction of animal biodiversity

Douglas Erwin, James Valentine
Roberts and Company, 2013

Publishers Summary:

The Cambrian Period records one of the most extraordinary transitions in the history of life. Although animals may have first appeared nearly 700 million years ago, with the earliest sponges, their initial diversifications appear to have been modest until a richly diverse fossil fauna appeared abruptly about 170 million years later. In The Cambrian Explosion, Erwin and Valentine synthesize research from many fields to explain why there was such remarkable novelty of animal forms.

Metabolic ecology: a scaling approach

Richard M. Sibly, James H. Brown, and Astrid Kodric-Brown
Wiley-Blackwell, 2012

Publisher's Summary:

Most of ecology is about metabolism: the ways that organisms use energy and materials. The energy requirements of individuals - their metabolic rates - vary predictably with their body size and temperature. Ecological interactions are exchanges of energy and materials between organisms and their environments. So metabolic rate affects ecological processes at all levels: individuals, populations, communities and ecosystems. Each chapter focuses on a different process, level of organization, or kind of organism. It lays a conceptual foundation and presents empirical examples. Together, the chapters provide an integrated framework that holds the promise for a unified theory of ecology. The book is intended to be accessible to upper-level undergraduate, and graduate students, but also of interest to senior scientists. Its easy-to-read chapters and clear illustrations can be used in lecture and seminar courses. Together they make for an authoritative treatment that will inspire future generations to study metabolic ecology.

The new economics of inequality and redistribution

Samuel Bowles
Cambridge University Press, 2012

Publisher's Summary:

Economists warn that policies to level the economic playing field come with a hefty price tag. But this so-called 'equality-efficiency trade-off' has proven difficult to document. The data suggest, instead, that the extraordinary levels of economic inequality now experienced in many economies are detrimental to the economy. Moreover, recent economic experiments and other evidence confirm that most citizens are committed to fairness and are willing to sacrifice to help those less fortunate than themselves. Incorporating the latest results from behavioral economics and the new microeconomics of credit and labor markets, Bowles shows that escalating economic disparity is not the unavoidable price of progress. Rather it is policy choice - often a very costly one. Here drawing on his experience both as a policy advisor and an academic economist, he offers an alternative direction, a novel and optimistic account of a more just and better working economy.

The emergence of organizations and markets

John F. Padgett and Walter W. Powell
Princeton University Press, 2012

Publisher's Summary:

The social sciences have sophisticated models of choice and equilibrium but little understanding of the emergence of novelty. Where do new alternatives, new organizational forms, and new types of people come from? Combining biochemical insights about the origin of life with innovative and historically oriented social network analyses, John Padgett and Walter Powell develop a theory about the emergence of organizational, market, and biographical novelty from the coevolution of multiple social networks. They demonstrate that novelty arises from spillovers across intertwined networks in different domains. In the short run actors make relations, but in the long run relations make actors.

This theory of novelty emerging from intersecting production and biographical flows is developed through formal deductive modeling and through a wide range of original historical case studies. Padgett and Powell build on the biochemical concept of autocatalysis--the chemical definition of life--and then extend this autocatalytic reasoning to social processes of production and communication. Padgett and Powell, along with other colleagues, analyze a very wide range of cases of emergence. They look at the emergence of organizational novelty in early capitalism and state formation; they examine the transformation of communism; and they analyze with detailed network data contemporary science-based capitalism: the biotechnology industry, regional high-tech clusters, and the open source community.

 

Signals and boundaries; building blocks for complex adaptive systems

John H. Holland
MIT Press, 2012

Publisher's Summary:

Complex adaptive systems (cas), including ecosystems, governments, biological cells, and markets, are characterized by intricate hierarchical arrangements of boundaries and signals. In ecosystems, for example, niches act as semi-permeable boundaries, and smells and visual patterns serve as signals; governments have departmental hierarchies with memoranda acting as signals; and so it is with other cas. Despite a wealth of data and descriptions concerning different cas, there remain many unanswered questions about "steering" these systems. In Signals and Boundaries, John Holland argues that understanding the origin of the intricate signal/border hierarchies of these systems is the key to answering such questions. He develops an overarching framework for comparing and steering cas through the mechanisms that generate their signal/boundary hierarchies. Holland lays out a path for developing the framework that emphasizes agents, niches, theory, and mathematical models. He discusses, among other topics, theory construction; signal-processing agents; networks as representations of signal/boundary interaction; adaptation; recombination and reproduction; the use of tagged urn models (adapted from elementary probability theory) to represent boundary hierarchies; finitely generated systems as a way to tie the models examined into a single framework; the framework itself, illustrated by a simple finitely generated version of the development of a multi-celled organism; and Markov processes.

Chaos and fractals; an elementary introduction

David P. Feldman
Oxford University Press, 2012

Publisher's Summary:

This book provides the reader with an elementary introduction to chaos and fractals, suitable for students with a background in elementary algebra, without assuming prior coursework in calculus or physics. It introduces the key phenomena of chaos - aperiodicity, sensitive dependence on initial conditions, bifurcations - via simple iterated functions. Fractals are introduced as self-similar geometric objects and analyzed with the self-similarity and box-counting dimensions. After a brief discussion of power laws, subsequent chapters explore Julia Sets and the Mandelbrot Set. The last part of the book examines two-dimensional dynamical systems, strange attractors, cellular automata, and chaotic differential equations.

Mapping Mongolia: situating Mongolia in the world from geologic time to the present

Paula L.W. Sabloff
University of Pennsylvania Museum of Archaeology and Anthropology, 2011

Publisher's Summary:

Would marginalized countries such as Mongolia benefit from a reconfiguration of area studies programs or even from another way of thinking about grouping nations? This book uses Mongolia as a case study to critique the area studies methodology and test the efficacy of another grouping methodology, the "-scapes" method proposed by Arjun Appadurai. Could the application of this approach for tracing individuals' social networks by theme (finance, ethnicity, ideology, media, and technology) be applied to nation-states or peoples? Could it then prevent Mongolia from slipping through the cracks of academia and international diplomacy? Experts from ecology, genetics, archaeology, history, anthropology, and international diplomacy contemplate these issues in their chapters on Mongolia through the ages. Their work includes over 30 maps to help situate Mongolia in its geologic, geographic, economic, and cultural matrix. By comparing maps of different time periods and intellectual orientations, readers can consider for themselves the place of Mongolia in the world community and the relative benefits of these and other grouping methodologies.

Principles of evolution : from the Planck epoch to complex multicellular life

Hildegard. Meyer-Ortmanns; Stefan Thurner
Springer, 2011

Publisher's Summary:

With contributions from a team of leading experts, this volume provides a comprehensive survey of recent achievements in our scientific understanding of evolution. The questions it asks concern the beginnings of the universe, the origin of life and the chances of its arising at all, the role of contingency, and the search for universal features in the plethora of evolutionary phenomena. Rather than oversimplified or premature answers, the chapters provide a clear picture of how these essential problems are being tackled, enabling the reader to understand current thinking and open questions. The tools employed stem from a range of disciplines including mathematics, physics, biochemistry and cell biology. Self-organization as an overarching concept is demonstrated in the most diverse areas: from galaxy formation in the universe to spindle and aster formation in the cell. Chemical master equations, population dynamics, and evolutionary game theory are presented as suitable frameworks for understanding the universal mechanisms and organizational principles observed in a wide range of living units, ranging from cells to societies. This book will provide engaging reading and food for thought for all those seeking a deeper understanding of the science of evolution.

The nature of computation

Cristopher. Moore; Stephan. Mertens
Oxford University Press, 2011

Publisher's Summary:

Computational complexity is one of the most beautiful fields of modern mathematics, and it is increasingly relevant to other sciences ranging from physics to biology. But this beauty is often buried underneath layers of unnecessary formalism, and exciting recent results like interactive proofs, cryptography, and quantum computing are usually considered too "advanced" to show to the typical student. The aim of this book is to bridge both gaps by explaining the deep ideas of theoretical computer science in a clear and enjoyable fashion, making them accessible to non computer scientists and to computer scientists who finally want to understand what their formalisms are actually telling. This book gives a lucid and playful explanation of the field, starting with P and NP-completeness. The authors explain why the P vs. NP problem is so fundamental, and why it is so hard to resolve. They then lead the reader through the complexity of mazes and games; optimization in theory and practice; randomized algorithms, interactive proofs, and pseudorandomness; Markov chains and phase transitions; and the outer reaches of quantum computing. At every turn, they use a minimum of formalism, providing explanations that are both deep and accessible. The book is intended for graduates and undergraduates, scientists from other areas who have long wanted to understand this subject, and experts who want to fall in love with this field all over again.

Networks: an introduction

Mark E.J. Newman
Oxford University Press, 2010

Publisher's Summary:

The scientific study of networks, including computer networks, social networks, and biological networks, has received an enormous amount of interest in the last few years. The rise of the Internet and the wide availability of inexpensive computers have made it possible to gather and analyze network data on a large scale, and the development of a variety of new theoretical tools has allowed us to extract new knowledge from many different kinds of networks.

The study of networks is broadly interdisciplinary and important developments have occurred in many fields, including mathematics, physics, computer and information sciences, biology, and the social sciences. This book brings together for the first time the most important breakthroughs in each of these fields and presents them in a coherent fashion, highlighting the strong interconnections between work in different areas.

Subjects covered include the measurement and structure of networks in many branches of science, methods for analyzing network data, including methods developed in physics, statistics, and sociology, the fundamentals of graph theory, computer algorithms, and spectral methods, mathematical models of networks, including random graph models and generative models, and theories of dynamical processes taking place on networks.

 

Meaning and the lexicon: the parallel architecture, 1975-2010

Ray Jackendoff
Oxford University Press, 2010

Publisher's Summary:

Meaning and the Lexicon brings together 35 years of path-breaking work on language by Ray Jackendoff. It traces the development of his Parallel Architecture, in which phonology, syntax, and semantics are independent generative components, and in which knowledge of language consists of a repertoire of stored structures. Some of these structures, such as words and morphemes, are idiosyncratic mappings between phonology, syntax, and meaning; some, such as idioms, attach meaning to larger syntactic structures; other structures are purely syntactic or morphosyntactic; and yet others are pieces of meaning with no syntactic or phonological form. The Parallel Architecture also seeks to explain and understand how language is integrated with human cognition, particularly with vision.

Professor Jackendoff examines inherently meaningful syntactic constructions, incorporating insights from Construction Grammar; and he looks at how aspects of meaning can be unexpressed but nevertheless understood, integrating approaches from Generative Lexicon theory. A recurring focus is the balance in grammar between idiosyncrasy, regularity, and semiregularity. The chapters cover a wide range of phenomena, from well-studied domains such as the mass-count distinction, event structure, resultatives, and noun-noun compounds, to offbeat aspects of English grammar such as the time-away construction (We're twistin' the night away), contrastive focus reduplication (Do you LIKE-him-like him?) and the noun-preposition-noun construction (week after week).

Ray Jackendoff draws on work in a wide range of fields, including linguistics, cognitive science, and philosophy. His writing combines depth of thought with clarity and wit. Meaning and the Lexicon will be read and enjoyed by linguists of all theoretical persuasions, and will be of great interest to cognitive scientists, philosophers, and anyone interested in how language operates in the mind, brain, and human communication.

Shadows in the valley : a cultural history of illness, death, and loss in New England, 1840-1916

Alan C. Swedlund
University of Massachusetts Press, 2010

Publisher's Summary:

How does the experience of sickness, death, and loss change over time? We know that the incidence and virulence of particular diseases have varied from one period to another, as has their medical treatment. But what was it like for the individuals who suffered and died from those illnesses, for the health practitioners and institutions that attended to them, and for the families who buried and mourned them?

In Shadows in the Valley, Alan Swedlund addresses these questions by closely examining the history of mortality in several small communities in western Massachusetts from the mid-nineteenth to the early twentieth century―from just before the acceptance of the germ theory of disease through the early days of public health reform in the United States. This was a time when most Americans lived in rural areas or small towns rather than large cities. It was also a time when a wide range of healing practices was available to the American public, and when the modern form of Western medicine was striving for dominance and authority. As Swedlund shows, this juncture of competing practices and ideologies provides a rich opportunity for exploring the rise of modern medicine and its impact on the everyday lives of ordinary Americans.

To indicate how individuals in different stages of their lives were exposed to varying assaults on their health, the book is structured in a way that superimposes what the author calls "life-course time" onto chronological time. Thus the early chapters look at issues of infancy and childhood in the 1840s and 1850s and the last chapters at the problems of old age after 1900. The reader becomes familiar with specific individuals and families as they cope with the recurrent loss of children, struggle to understand the causes of new contagions, and seek to find meaning in untimely death. By using a broad time frame and a narrow geographical lens, Swedlund is able to engage with both the particularities and generalities of evolving medical knowledge and changing practice, and to highlight the differences in personal as well as collective responses to illness and loss.

In praise of science: curiosity, understanding, and progress

Sander Bais
MIT Press, 2010

Publisher's Summary:

A virtuoso introduction to the field of science, the most democratic of human endeavors.

In this engaging, lyrical book, physicist Sander Bais shows how science can liberate us from our cultural straitjacket of prejudice and intolerance. We're living in a time in which technology is taken for granted, yet belief in such standard scientific facts as evolution is actually decreasing. How is it possible for cell phones and Creationism to coexist? Science -- fundamental, fact-based knowledge, not the latest technological gadget -- can give us the global and local perspectives we need to make the world a better place.

Bais argues that turning points in the history of science have been accompanied by similar milestones in social change, deeply affecting our view of nature, our perception of the human condition, and our understanding of the universe and our place in it. After a lively description of how curiosity trumps prejudice and pseudoscience in matters ranging from lightning rods to the transmission of HIV, Bais considers what drives science and scientists, a quest that culminates in that miraculous mixture of creativity and ingenuity found in the greatest scientists. He describes what he calls the "circle of science" -- the microcosm and the macrocosm as mirror images -- and demonstrates unity in a dazzling sequence of topics, including the hierarchy of structures, the forces of nature, cosmological evolution, and the challenge of complexity. Finally, Bais takes on the obstacles science encounters in a world dominated by short-term political and economic interests.

Science, he says, needs to get its message out. Drawing on sources that range from Charles Darwin and Karl Popper to Herbert Marcuse and Richard Feynman, with In Praise of Science, Bais does just that.

 

Transistor rodeo: poems

Jon Wilkins
University of Utah Press, 2010

Publisher's Summary:

The annual Agha Shahid Ali Prize in Poetry was inaugurated in 2003 to honor the late poet, a nationally recognized writer and former professor at the University of Utah, and is sponsored by the University of Utah Press and the University of Utah Department of English. Transistor Rodeo was selected as the 2009 prize-winning volume by judge Ander Monson, poet, essayist, author of The Available World and Vanishing Point, and editor of DIAGRAM.

Manhattan Project to the Santa Fe Institute: the memoirs of George A. Cowan

George A. Cowan
University of New Mexico Press, 2010

Publisher's Summary:

The telephone lay in pieces on George Cowan's office desk in the basement of Princeton's physics building. It was his first day as a graduate student in the fall of 1941. Down the hall, on the door of the cyclotron control room, a sign warned, "Don't let Dick Feynman in. He takes tools." On that day, the future Nobel Prize winner Richard Feynman needed a piece from his new office mate's phone, so he borrowed it without even introducing himself.

Cowan's memoir is an engaging eyewitness account of how science works and how scientists, as human beings, work as well. In discussing his career in nuclear physics from the 1940s into the 1980s, Cowan weaves in intriguing anecdotes about a large cast of distinguished scientists--all related in his wry, self-deprecating manner.

Besides his nearly forty-year career at Los Alamos National Laboratory, Cowan also helped establish banks in Los Alamos and Santa Fe, served as treasurer of the group that created the Santa Fe Opera, and in the late 1980s participated in founding the Santa Fe Institute and served as its first president. He anchored its interdisciplinary work in his quest to find "common ground between the relatively simple world of natural science and the daily, messy world of human affairs."

Since the early 1990s Cowan has pursued a new interest in psychology and neuroscience to gain a deeper understanding of patterns of human behavior.

This autobiography will appeal to anyone interested in a concise, intellectually engaged account of science and its place in society and public policy over the past seventy years.

 

Complexity: a guided tour

Melanie Mitchell
Oxford University Press, 2009

Publisher's Summary:

What enables individually simple insects like ants to act with such precision and purpose as a group? How do trillions of neurons produce something as extraordinarily complex as consciousness? In this remarkably clear and companionable book, leading complex systems scientist Melanie Mitchell provides an intimate tour of the sciences of complexity, a broad set of efforts that seek to explain how large-scale complex, organized, and adaptive behavior can emerge from simple interactions among myriad individuals. Based on her work at the Santa Fe Institute and drawing on its interdisciplinary strategies, Mitchell brings clarity to the workings of complexity across a broad range of biological, technological, and social phenomena, seeking out the general principles or laws that apply to all of them. Richly illustrated, Complexity: A Guided Tour--winner of the 2010 Phi Beta Kappa Book Award in Science--offers a wide-ranging overview of the ideas underlying complex systems science, the current research at the forefront of this field, and the prospects for its contribution to solving some of the most important scientific questions of our time.

The nature and timing of the neolithic demographic transition in the North American Southwest

[Chapter in] The Neolithic demographic transition and its consequences

Timothy A. Kohler, Matt Glaude
Springer, 2008

Publisher's Summary:

Maize agriculture was practiced in the US Southwest slightly before 2000 BC, but had a negligible impact on population growth rates until it was coupled with other innovations in subsistence and social practice. These include the development or introduction of more productive landraces; the ability to successfully cultivate maize under a greater variety of conditions, with dry farming especially important; the addition of beans, squash, and eventually turkey to the diet; and what we infer to be the remapping of exchange networks and the development of efficient exchange strategies in first-millennium-AD villages. Our tabulations of the P(5-19) proportion emphasize the heartlands of the Chaco and Mesa Verde Anasazi (prehispanic Pueblo) populations. We find that this measure is somewhat affected by warfare in our region. Nevertheless, there is a strong identifiable Neolithic Demographic Transition signal in the US Southwest in the mid-first-millennium AD in most sub-regions, visible a few hundred years after the introduction of well-fired ceramic containers, and more or less contemporaneous with the first appearance of villages.