text:
12777
A Novel Nonparametric Approach for Neural Encoding and Decoding Models of Multimodal Receptive Fields
"Pyramidal neurons recorded from the rat hippocampus and entorhinal cortex, such as place and grid cells, have diverse receptive fields, which are either unimodal or multimodal. Spiking activity from these cells encodes information about the spatial position of a freely foraging rat. At fine timescales, a neuron’s spike activity also depends significantly on its own spike history. However, due to limitations of current parametric modeling approaches, it remains a challenge to estimate complex, multimodal neuronal receptive fields while incorporating spike history dependence. Furthermore, efforts to decode the rat’s trajectory in one- or two-dimensional space from hippocampal ensemble spiking activity have mainly focused on spike history–independent neuronal encoding models. In this letter, we address these two important issues by extending a recently introduced nonparametric neural encoding framework that allows modeling both complex spatial receptive fields and spike history dependencies. Using this extended nonparametric approach, we develop novel algorithms for decoding a rat’s trajectory based on recordings of hippocampal place cells and entorhinal grid cells. Results show that both encoding and decoding models derived from our new method performed significantly better than state-of-the-art encoding and decoding models on 6 minutes of test data. In addition, our model’s performance remains invariant to the apparent modality of the neuron’s receptive field."
to:NB  neuroscience  neural_coding_and_decoding  neural_data_analysis  statistics  nonparametrics
yesterday
A Single Hidden Layer Feedforward Network with Only One Neuron in the Hidden Layer Can Approximate Any Univariate Function
"The possibility of approximating a continuous function on a compact subset of the real line by a feedforward single hidden layer neural network with a sigmoidal activation function has been studied in many papers. Such networks can approximate an arbitrary continuous function provided that an unlimited number of neurons in a hidden layer is permitted. In this note, we consider constructive approximation on any finite interval of $\mathbb{R}$ by neural networks with only one neuron in the hidden layer. We construct algorithmically a smooth, sigmoidal, almost monotone activation function $\sigma$ providing approximation to an arbitrary continuous function within any degree of accuracy. This algorithm is implemented in a computer program, which computes the value of $\sigma$ at any reasonable point of the real axis."
to:NB  to_read  neural_networks  approximation
yesterday
Mastering Feature Engineering - O'Reilly Media
"Feature engineering is essential to applied machine learning, but using domain knowledge to strengthen your predictive models can be difficult and expensive. To help fill the information gap on feature engineering, this complete hands-on guide teaches beginning-to-intermediate data scientists how to work with this widely practiced but little discussed topic."

Author Alice Zheng explains common practices and mathematical principles to help engineer features for new data and tasks. If you understand basic machine learning concepts like supervised and unsupervised learning, you’re ready to get started. Not only will you learn how to implement feature engineering in a systematic and principled way, you’ll also learn how to practice better data science.
to:NB  books:noted  data_mining  statistics  data_analysis  to_teach:data-mining  kith_and_kin  zheng.alice
5 days ago
Have human societies evolved? Evidence from history and pre-history - Springer
"I ask whether social evolutionary theories found in sociology, archaeology, and anthropology are useful in explaining human development from the Stone Age to the present-day. My data are partly derived from the four volumes of The Sources of Social Power, but I add statistical data on the growth of complexity and power in human groups. I distinguish three levels of evolutionary theory. The first level offers a minimalist definition of evolution in terms of social groups responding and adapting to changes in their social and natural environment. This is acceptable but trivial. The hard part is to elucidate what kinds of response are drawn from what changes, and all sociology shares in this difficulty. This model also tends to over-emphasize external pressures and neglect human inventiveness. The second level of theory is “multilineal” evolution in which various paths of endogenous development, aided by diffusion of practices between societies, dominate the historical and pre-historical record. This is acceptable as a model applied to some times, places, and practices, but when applied more generally it slides into a multi-causal analysis that is also conventional in the social sciences. The third level is a theory of general evolution for the entire human experience. Here materialist theories are dominant but they are stymied by their neglect of ideological, military, and political power relations. There is no acceptable theory of general social evolution. Thus the contribution of social evolutionary theory to the social sciences has been limited."
to:NB  social_evolution  cultural_evolution  mann.michael  re:do-institutions-evolve
6 days ago
Expectations of brilliance underlie gender distributions across academic disciplines | Science
"The gender imbalance in STEM subjects dominates current debates about women’s underrepresentation in academia. However, women are well represented at the Ph.D. level in some sciences and poorly represented in some humanities (e.g., in 2011, 54% of U.S. Ph.D.’s in molecular biology were women versus only 31% in philosophy). We hypothesize that, across the academic spectrum, women are underrepresented in fields whose practitioners believe that raw, innate talent is the main requirement for success, because women are stereotyped as not possessing such talent. This hypothesis extends to African Americans’ underrepresentation as well, as this group is subject to similar stereotypes. Results from a nationwide survey of academics support our hypothesis (termed the field-specific ability beliefs hypothesis) over three competing hypotheses."
to:NB  education  academia  sexism  racism  to_be_shot_after_a_fair_trial
7 days ago
Lowes, J.L.: The Road to Xanadu: A Study in the Ways of the Imagination. (eBook, Paperback and Hardcover)
"John Livingston Lowes's classic work shows how various images from Coleridge's extensive reading, particularly in travel literature, coalesced to form the imagistic texture of his two most famous poems, The Rime of the Ancient Mariner" and "Kubla Khan.""
books:recommended  books:owned  creativity  imagination  psychology  literary_history  literary_criticism  romanticism  poetry
7 days ago
Dupree, L.: Afghanistan (eBook, Paperback and Hardcover).
"The ancient land and the modern nation of Afghanistan are the subject of Louis Dupree's book. Both in the text and in over a hundred illustrations, he identifies the major patterns of Afghan history, society, and culture as they have developed from the Stone Age to the present.
"Originally published in 1973."

--- A classic, but now only historical.
books:recommended  in_NB  afghanistan  anthropology  20th_century_history  19th_century_history
7 days ago
Vartanian, A.: Diderot and Descartes (eBook, Paperback and Hardcover).
"A study of scientific naturalism in the Enlightenment. In tracing the materialism of Diderot, La Mettrie, Buffon, and D’Holbach to its sources, it offers a fresh appraisal of the total influence of Descartes on the Enlightenment."
in_NB  books:recommended  coveted  history_of_ideas  philosophy  enlightenment  vartanian.aram  de_la_mettrie.julian_offray  descartes.rene  diderot.denis
7 days ago
Vartanian, A.: LaMettrie's L'Homme Machine (eBook, Paperback and Hardcover).
"As a classic of the French Enlightenment, L’Homme Machine has in the past been of equal interest to students of philosophy, science, and literature. The present edition offers the first established text, with extensive notes. In his introduction, Dr. Vartanian discusses La Mettrie’s thesis, its sources, the place of the man-machine idea in the development of La Mettrie’s materialism, and its critical impact on the intellectual struggles of the eighteenth century."
books:recommended  in_NB  history_of_ideas  history_of_science  materialism  man_a_machine  philosophy  de_la_mettrie.julien_offray  vartanian.aram
7 days ago
Swerdlow, N.M.: The Babylonian Theory of the Planets (eBook, Paperback and Hardcover).
"In the second millennium b.c., Babylonian scribes assembled a vast collection of astrological omens, believed to be signs from the gods concerning the kingdom's political, military, and agricultural fortunes. The importance of these omens was such that from the eighth or seventh until the first century, the scribes observed the heavens nightly and recorded the dates and locations of ominous phenomena of the moon and planets in relation to stars and constellations. The observations were arranged in monthly reports along with notable events and prices of agricultural commodities, the object being to find correlations between phenomena in the heavens and conditions on earth. These collections of omens and observations form the first empirical science of antiquity and were the basis of the first mathematical science, astronomy. For it was discovered that planetary phenomena, although irregular and sometimes concealed by bad weather, recur in limited periods within cycles in which they are repeated on nearly the same dates and in nearly the same locations.
"N. M. Swerdlow's book is a study of the collection and observation of ominous celestial phenomena and of how intervals of time, locations by zodiacal sign, and cycles in which the phenomena recur were used to reduce them to purely arithmetical computation, thereby surmounting the greatest obstacle to observation, bad weather. The work marks a striking advance in our understanding of both the origin of scientific astronomy and the astrological divination through which the kingdoms of ancient Mesopotamia were governed."
to:NB  books:noted  ancient_history  history_of_science  mesopotamia
7 days ago
Hildenbrand, W.: Market Demand: Theory and Empirical Evidence. (eBook, Paperback and Hardcover)
"In a major work that is the culmination of over a decade of intensive research, Werner Hildenbrand presents a new theory of market demand, the principal aim of which is to identify the conditions under which the Law of Demand holds true. Hildenbrand argues that the Law of Demand is due mainly to the "heterogeneity" of the population of households. In his view, "rationality" of individual behavior plays only a minor role. While the traditional approach to the theory of market demand is to analyze the question, To what extent are the postulated properties of individual behavior preserved by going from individual to market demand?, this book asks the question, Which properties of the market demand function are created by the aggregation process?.
"Two hypotheses on the population of households play a key role in Hilden-brand's thinking. The first is the "increasing dispersion" and the second the "increasing spread" of households' demand. These hypotheses can easily be interpreted and are a priori plausible. For a positive theory of market demand, according to Hildenbrand, it is more important that the hypotheses are well supported by empirical evidence. His claims in this important new book are based on a nonparametric statistical data analysis of the U.K. Family Expenditure Survey and the French Enquête Budget de Famille.
"Originally published in 1994."

- An elaboration of Becker?
to:NB  books:noted  economics
7 days ago
Berkey, J.P.: The Transmission of Knowledge in Medieval Cairo: A Social History of Islamic Education. (eBook, Paperback and Hardcover)
"In rich detail Jonathan Berkey interprets the social and cultural consequences of Islam's regard for knowledge, showing how education in the Middle Ages played a central part in the religious experience of nearly all Muslims. Focusing on Cairo, which under Mamluk rule (1250-1517) was a vital intellectual center with a complex social system, the author describes the transmission of religious knowledge there as a highly personal process, one dependent on the relationships between individual scholars and students. The great variety of institutional structures, he argues, supported educational efforts without ever becoming essential to them. By not being locked into formal channels, religious education was never exclusively for the elite but was open to all. Berkey explores the varying educational opportunities offered to the full run of the Muslim population--including Mamluks, women, and the "common people." Drawing on medieval chronicles, biographical dictionaries, and treatises on education, as well as the deeds of endowment that established many of Cairo's schools, he explains how education drew groups of outsiders into the cultural center and forged a common Muslim cultural identity."
to:NB  books:noted  education  social_life_of_the_mind  islamic_civilization
7 days ago
Reardon, B.: The Form of Greek Romance (eBook, Paperback and Hardcover).
"In the early Roman Empire a new literary genre began to flourish, mainly in the Greek world: prose fiction, or romance. Broadly defined as a love story that offers adventure and a romantic vision of life, this form of literature emerged long after the other genres and, until recently, seemed hardly worthy of critical attention. Here B. P. Reardon addresses the growing interest in ancient fiction by providing a literary and cultural framework in which to understand Greek romance, and by demonstrating its importance as an artistic and social phenomenon. Beginning with a discussion of Chariton's Chaereas and Callirhoe, Reardon sets out the generic characteristics of the romance. He then moves through a wide range of works, including those of Longus and Heliodorus, and reveals their sophistication in terms of social observation, technique within a convention, and the stance adopted by the authors toward their own creations. Although antiquity left behind little discussion of the genre, Reardon shows how romance can be assessed within its time period by considering the practice of narrative in other Greek literature and the concept of fiction in antiquity."
to:NB  books:noted  ancient_history  literary_history  novels
7 days ago
Henderson, J.B.: Scripture, Canon and Commentary: A Comparison of Confucian and Western Exegesis. (eBook, Paperback and Hardcover)
"In this major contribution to the study of the Chinese classics and comparative religion, John Henderson uses the history of exegesis to illuminate mental patterns that have universal and perennial significance for intellectual history. Henderson relates the Confucian commentarial tradition to other primary exegetical traditions, particularly the Homeric tradition, Vedanta, rabbinic Judaism, ancient and medieval Christian biblical exegesis, and Qur'anic exegesis. In making such comparisons, he discusses some basic assumptions common to all these traditions--such as that the classics or scriptures are comprehensive or that they contain all significant knowledge or truth and analyzes the strategies deployed to support these presuppositions. As shown here, primary differences among commentarial or exegetical traditions arose from variations in their emphasis on one or another of these assumptions and strategies. Henderson demonstrates that exegetical modes of thought were far from arcane: they dominated the post-classical/premodern intellectual world. Some have persisted or re-emerged in modern times, particularly in ideologies such as Marxism. Written in an engaging and accessible style, Scripture, Canon, and Commentary is not only a challenging interpretation of comparative scriptural traditions but also an excellent introduction to the study of the Confucian classics."
to:NB  books:noted  history_of_ideas  interpretation  social_life_of_the_mind  confucianism  comparative_history
7 days ago
Watkins, S.C.: From Provinces into Nations: Demographic Integration in Western Europe, 1870-1960. (eBook, Paperback and Hardcover)
"Between 1870 and 1960, national boundaries became more evident on the demographic map of Western Europe. In most of the fifteen countries examined here, differences in marital fertility, illegitimacy, and marriage from one province (counties, cantons, arrondissements) to another diminished considerably. From Provinces into Nations describes this shift to greater national demographic homogeneity and places it in the context of a parallel decline in linguistic diversity, as well as in the context of increases in national market integration, the expansion of state activities, and nation-building.
"The book interprets the shift as evidence of the influence of communities on demographic behavior, and as an indication of the growing predominance of national over local communities. The author uses demographic data, too often the property of specialists, to examine themes of interest to historians, sociologists, economists, and political scientists interested in the integration of modern societies."
to:NB  books:noted  nationalism  peasants_into_frenchmen  demography  19th_century_history  20th_century_history  european_history
7 days ago
Brandon, R.N.: Adaptation and Environment (eBook, Paperback and Hardcover).
"By focusing on the crucial role of environment in the process of adaptation, Robert Brandon clarifies definitions and principles so as to help make the argument of evolution by natural selection empirically testable. He proposes that natural selection is the process of differential reproduction resulting from differential adaptedness to a common selective environment."
to:NB  books:noted  adaptation  evolutionary_biology  philosophy_of_science
7 days ago
Shafer, D.M.: Deadly Paradigms: The Failure of U.S. Counterinsurgency Policy. (eBook, Paperback and Hardcover)
"Michael Shafer argues that American policymakers have fundamentally misperceived the political context of revolutionary wars directed against American clients and that because American attempts at counterinsurgency were based on faulty premises, these efforts have failed in virtually every instance.
"Originally published in 1988."
to:NB  books:noted  us_military  american_hegemony  counter-insurgency
7 days ago
Quality in the Undergraduate Experience: What Is It? How Is It Measured? Who Decides? Summary of a Workshop | The National Academies Press
"Students, parents, and government agencies need as much information as possible about the outcomes of the higher education experience and the extent to which they can expect a fair return on their investment in higher education.In order to better understand the concept of quality - enabling students to acquire knowledge in a variety of disciplines and deep knowledge in at least one discipline, as well as to develop a range of skills and habits of mind that prepare them for career success, engaged citizenship, intercultural competence, social responsibility, and continued intellectual growth - an ad hoc planning committee of the National Academies of Sciences, Engineering, and Medicine Board on Higher Education and Workforce, with funding from the Lumina Foundation, organized a workshop in Washington, D.C., on December 14-15, 2015.This report summarizes the presentations and discussion of that event."

--- Did they _really_ do something like this without involving either (on the left hand) anyone from the humanities, or (on the right hand) any experts in social measurement?
to:NB  education  academia  social_measurement  to_be_shot_after_a_fair_trial
8 days ago
[1606.05340] Exponential expressivity in deep neural networks through transient chaos
"We combine Riemannian geometry with the mean field theory of high dimensional chaos to study the nature of signal propagation in generic, deep neural networks with random weights. Our results reveal an order-to-chaos expressivity phase transition, with networks in the chaotic phase computing nonlinear functions whose global curvature grows exponentially with depth but not width. We prove this generic class of deep random functions cannot be efficiently computed by any shallow network, going beyond prior work restricted to the analysis of single functions. Moreover, we formalize and quantitatively demonstrate the long conjectured idea that deep networks can disentangle highly curved manifolds in input space into flat manifolds in hidden space. Our theoretical analysis of the expressive power of deep networks broadly applies to arbitrary nonlinearities, and provides a quantitative underpinning for previously abstract notions about the geometry of deep functions."

--- I am very skeptical, because (1) we know single-laye neural networks are universal approximators, so I don't see how we can get an increase in expressivity, and (2) I don't see how dynamical systems (about mapping a state space into itself) can tell us about _feed-forward_ networks. So either I'll learn a lot or absolutely nothing, i.e., last tag applies.
to:NB  to_read  neural_networks  chaos  via:sifu_tweety  to_be_shot_after_a_fair_trial
8 days ago
Networking on the Network: A Guide to Professional Skills for PhD Students
This was a huge influence on me when I read it 20 years ago, and I think it still holds up (modulo little mechanical details). Strongly recommended.
13 days ago
Algorithms and Models for Network Data and Link Analysis | Knowledge Management Databases and Data Mining | Cambridge University Press
"Network data are produced automatically by everyday interactions - social networks, power grids, and links between data sets are a few examples. Such data capture social and economic behavior in a form that can be analyzed using powerful computational tools. This book is a guide to both basic and advanced techniques and algorithms for extracting useful information from network data. The content is organized around 'tasks', grouping the algorithms needed to gather specific types of information and thus answer specific types of questions. Examples include similarity between nodes in a network, prestige or centrality of individual nodes, and dense regions or communities in a network. Algorithms are derived in detail and summarized in pseudo-code. The book is intended primarily for computer scientists, engineers, statisticians and physicists, but it is also accessible to network scientists based in the social sciences. Matlab/Octave code illustrating some of the algorithms will be available at: http://www.cambridge.org/9781107125773."
in_NB  books:noted  network_data_analysis
14 days ago
Sociology as a Population Science | Research Methods Sociology and Criminology | Cambridge University Press
"John Goldthorpe is one of Britain's most eminent sociologists and a strong advocate of quantitative sociology. In this concise and accessible book, he provides a new rationale for recent developments in sociology which focus on establishing and explaining probabilistic regularities in human populations. Through these developments, Goldthorpe shows how sociology has become more securely placed within the 'probabilistic revolution' that has occurred over the last century in the natural and social sciences alike. The central arguments of the book are illustrated with examples from different areas of sociology, ranging from social stratification and the sociology of the family to the sociology of revolutions. He concludes by considering the implications of these arguments for the proper boundaries of sociology, for its relations with other disciplines, and for its public role."
in_NB  books:noted  sociology  probability
14 days ago
Imagined Futures: Fictional Expectations and Capitalist Dynamics — Jens Beckert | Harvard University Press
"In a capitalist system, consumers, investors, and corporations orient their activities toward a future that contains opportunities and risks. How actors assess uncertainty is a problem that economists have tried to solve through general equilibrium and rational expectations theory. Powerful as these analytical tools are, they underestimate the future’s unknowability by assuming that markets, in the aggregate, correctly forecast what is to come."

Jens Beckert adds a new chapter to the theory of capitalism by demonstrating how fictional expectations drive modern economies—or throw them into crisis when the imagined futures fail to materialize. Collectively held images of how the future will unfold are critical because they free economic actors from paralyzing doubt, enabling them to commit resources and coordinate decisions even if those expectations prove inaccurate. Beckert distinguishes fictional expectations from performativity theory, which holds that predictions tend to become self-fulfilling prophecies. Economic forecasts are important not because they produce the futures they envision but because they create the expectations that generate economic activity in the first place. Actors pursue money, investments, innovations, and consumption only if they believe the objects obtained through market exchanges will retain value. We accept money because we believe in its future purchasing power. We accept the risk of capital investments and innovation because we expect profit. And we purchase consumer goods based on dreams of satisfaction.
to:NB  books:noted  economics  psychology  cultural_criticism  rhetoric  to_be_shot_after_a_fair_trial
14 days ago
The Matrix Cookbook
"Matrix identities, relations and approximations. A desktop reference for quick overview of mathematics of matrices."

--- The canonical version.
linear_algebra  reference  to_teach:modreg
19 days ago
Luckiness and Regret in Minimum Description Length Inference
"Minimum Description Length (MDL) inference is based on the intuition that understanding the available data can be defined in terms of the ability to compress the data, i.e. to describe it in full using a shorter representation. This brief introduction discusses the design of the various codes used to implement MDL, focusing on the philosophically intriguing concepts of luckiness and regret: a good MDL code exhibits good performance in the worst case over all possible data sets, but achieves even better performance when the data turn out to be simple (although we suggest making no a priori assumptions to that effect). We then discuss how data compression relates to performance in various learning tasks, including parameter estimation, parametric and nonparametric model selection and sequential prediction of outcomes from an unknown source. Last, we briefly outline the history of MDL and its technical and philosophical relationship to other approaches to learning such as Bayesian, frequentist and prequential statistics."
to:NB  have_skimmed  statistics  information_theory  mdl  grunwald.peter  low-regret_learning
19 days ago
Review of Cultural Evolution: Society, Technology, Language, and Religion Edited by Peter J. Richerson and Morten H. Christiansen
"Peter J. Richerson and Morten H. Christiansen have assembled a compelling picture of the evolution of societies, technology, language, and religion--with culture at the epicenter. The book is a must-have for economists and any other social scientists interested in the evolution of behavior. Using the book as a starting point, this article sums up what cultural evolution can teach us about these four major aspects of human behavior. Each topic is also linked to the relevant empirical research in economics. Directions for future research integrating cultural evolution into an economic framework are also explored."
to:NB  books:noted  cultural_evolution  evolutionary_economics  book_reviews  re:do-institutions-evolve
23 days ago
Complexity and Economic Policy: A Paradigm Shift or a Change in Perspective? A Review Essay on David Colander and Roland Kupers's Complexity and the Art of Public Policy
"In their recent book, Colander and Kupers (2014) argue that viewing the economy as a complex adaptive system should change the way in which we make economic policy. This would necessitate a paradigm shift. Economics has, over time, tried to produce a coherent model to underpin the dominant laissez-faire liberal approach. But we have never proved, in that model, that left to their own devices, the participants in an economy will self-organize into a satisfactory state. This is an assumption. Complex interactive systems with direct interaction between heterogeneous agents may show no tendency to self-equilibrate and will undergo endogenous crises. Economists should concentrate on the emergence of certain patterns. Colander and Kupers suggest that we may be able to nudge the system into "good" basins of attraction. A more radical view is that there are no fixed basins of attraction; these change with the evolution of the system and it is illusory to believe that we can choose good basins. We may be able to recognize and influence the emergence of certain states of the economy, but we are far from Leon Walras's dream of economics as a science like astrophysics."
to:NB  books:noted  book_reviews  economics  economic_policy  complexity  kirman.alan  macroeconomics
23 days ago
The Rapid Adoption of Data-Driven Decision-Making
"We provide a systematic empirical study of the diffusion and adoption patterns of data-driven decision making (DDD) in the U.S. Using data collected by the Census Bureau for a large representative sample of manufacturing plants, we find that DDD rates nearly tripled (11%-30%) between 2005 and 2010. This rapid diffusion, along with results from a companion paper, are consistent with case-based evidence that DDD tends to be productivity-enhancing. Yet certain plants are significantly more likely to adopt than others. Key correlates of adoption are size, presence of potential complements such as information technology and educated workers, and firm learning."
to:NB  economics  diffusion_of_innovations  data_mining
23 days ago
SFIHMM (Estimating Hidden Markov Models)
"high-speed C code for the estimation of Hidden Markov Models (finite state machines) on arbitrary time-series, for Viterbi Path Reconstruction, and for the generation of simulated data from HMMs."
to:NB  markov_models  state-space_models  kith_and_kin  dedeo.simon
25 days ago
Moral Economy | Yale University Press
"Should the idea of economic man—the amoral and self-interested Homo economicus—determine how we expect people to respond to monetary rewards, punishments, and other incentives? Samuel Bowles answers with a resounding “no.” Policies that follow from this paradigm, he shows, may “crowd out” ethical and generous motives and thus backfire.
"But incentives per se are not really the culprit. Bowles shows that crowding out occurs when the message conveyed by fines and rewards is that self-interest is expected, that the employer thinks the workforce is lazy, or that the citizen cannot otherwise be trusted to contribute to the public good. Using historical and recent case studies as well as behavioral experiments, Bowles shows how well-designed incentives can crowd in the civic motives on which good governance depends."
to:NB  books:noted  political_economy  institutions  moral_psychology  moral_philosophy  kith_and_kin  bowles.samuel
26 days ago
Cause and Correlation in Biology: A User's Guide to Path Analysis, Structural Equations and Causal Inference with R | Ecology and Conservation | Cambridge University Press
"Many problems in biology require an understanding of the relationships among variables in a multivariate causal context. Exploring such cause-effect relationships through a series of statistical methods, this book explains how to test causal hypotheses when randomised experiments cannot be performed. This completely revised and updated edition features detailed explanations for carrying out statistical methods using the popular and freely available R statistical language. Sections on d-sep tests, latent constructs that are common in biology, missing values, phylogenetic constraints, and multilevel models are also an important feature of this new edition. Written for biologists and using a minimum of statistical jargon, the concept of testing multivariate causal hypotheses using structural equations and path analysis is demystified. Assuming only a basic understanding of statistical analysis, this new edition is a valuable resource for both students and practising biologists."
to:NB  books:noted  causal_inference  graphical_models  statistics  re:ADAfaEPoV
26 days ago
Water splitting–biosynthetic system with CO2 reduction efficiencies exceeding photosynthesis | Science
"Photosynthesis fixes CO2 from the air by using sunlight. Industrial mimics of photosynthesis seek to convert CO2 directly into biomass, fuels, or other useful products. Improving on a previous artificial photosynthesis design, Liu et al. combined the hydrogen-oxidizing bacterium Raistonia eutropha with a cobalt-phosphorus water-splitting catalyst. This biocompatible self-healing electrode circumvented the toxicity challenges of previous designs and allowed it to operate aerobically. When combined with solar photovoltaic cells, solar-to-chemical conversion rates should become nearly an order of magnitude more efficient than natural photosynthesis.
"Abstract: Artificial photosynthetic systems can store solar energy and chemically reduce CO2. We developed a hybrid water splitting–biosynthetic system based on a biocompatible Earth-abundant inorganic catalyst system to split water into molecular hydrogen and oxygen (H2 and O2) at low driving voltages. When grown in contact with these catalysts, Ralstonia eutropha consumed the produced H2 to synthesize biomass and fuels or chemical products from low CO2 concentration in the presence of O2. This scalable system has a CO2 reduction energy efficiency of ~50% when producing bacterial biomass and liquid fusel alcohols, scrubbing 180 grams of CO2 per kilowatt-hour of electricity. Coupling this hybrid device to existing photovoltaic systems would yield a CO2 reduction energy efficiency of ~10%, exceeding that of natural photosynthetic systems."

--- I realize there're a lot of steps between showing this in the lab and an industrial technology, but how is increasing the efficiency of photosynthesis by an order of magnitude not a huge fucking deal?
26 days ago
A kriging procedure for processes indexed by graphs - Springer
"We provide a new kriging procedure of processes on graphs. Based on the construction of Gaussian random processes indexed by graphs, we extend to this framework the usual linear prediction method for spatial random fields, known as kriging. We provide the expression of the estimator of such a random field at unobserved locations as well as a control for the prediction error."

--- Errr, why is there anything special about linear prediction on graphs? Once you know (excuse me, "posit") the covariance function, everything falls in to place, and there's no need to assume Gaussian fluctuations...
to:NB  network_data_analysis  smoothing  prediction
26 days ago
A Little Primer of Tu Fu – New York Review Books
"The deepest and most varied of the Tang Dynasty poets, Tu Fu (Du Fu) is, in the words of David Hinton, the “first complete poetic sensibility in Chinese literature.” Tu Fu merged the public and the private, often in the same poem, as his subjects ranged from the horrors of war to the delights of friendship, from closely observed landscapes to remembered dreams, from the evocation of historical moments to a wry lament over his own thinning hair.
"Although Tu Fu has been translated often, and often brilliantly, David Hawkes’s classic study, first published in 1967, is the only book that demonstrates in depth how his poems were written. Hawkes presents thirty-five poems in the original Chinese, with a pinyin transliteration, a character-by-character translation, and a commentary on the subject, the form, the historical background, and the individual lines. There is no other book quite like it for any language: a nuts-and-bolts account of how Chinese poems in general, and specifically the poems of one of the world’s greatest poets, are constructed. It’s an irresistible challenge for readers to invent their own translations."
books:recommended  have_read  poetry  tang  du.fu
27 days ago
The End of Ownership: Personal Property in the Digital Economy | The MIT Press
"If you buy a book at the bookstore, you own it. You can take it home, scribble in the margins, put in on the shelf, lend it to a friend, sell it at a garage sale. But is the same thing true for the ebooks or other digital goods you buy? Retailers and copyright holders argue that you don’t own those purchases, you merely license them. That means your ebook vendor can delete the book from your device without warning or explanation—as Amazon deleted Orwell’s 1984 from the Kindles of surprised readers several years ago. These readers thought they owned their copies of 1984. Until, it turned out, they didn’t. In The End of Ownership, Aaron Perzanowski and Jason Schultz explore how notions of ownership have shifted in the digital marketplace, and make an argument for the benefits of personal property.
"Of course, ebooks, cloud storage, streaming, and other digital goods offer users convenience and flexibility. But, Perzanowski and Schultz warn, consumers should be aware of the tradeoffs involving user constraints, permanence, and privacy. The rights of private property are clear, but few people manage to read their end user agreements. Perzanowski and Schultz argue that introducing aspects of private property and ownership into the digital marketplace would offer both legal and economic benefits. But, most important, it would affirm our sense of self-direction and autonomy. If we own our purchases, we are free to make whatever lawful use of them we please. Technology need not constrain our freedom; it can also empower us."

--- When we used to talk how the capitalist system would itself produce something that transcended capitalist private property, this was _not_ what we had in mind.
to:NB  books:noted  intellectual_property  networked_life
27 days ago
What a City Is For | The MIT Press
"Portland, Oregon, is one of the most beautiful, livable cities in the United States. It has walkable neighborhoods, bike lanes, low-density housing, public transportation, and significant green space—not to mention craft-beer bars and locavore food trucks. But liberal Portland is also the whitest city in the country. This is not circumstance; the city has a long history of officially sanctioned racialized displacement that continues today.
"Over the last two and half decades, Albina—the one major Black neighborhood in Portland—has been systematically uprooted by market-driven gentrification and city-renewal policies. African Americans in Portland were first pushed into Albina and then contained there through exclusionary zoning, predatory lending, and racist real estate practices. Since the 1990s, they’ve been aggressively displaced—by rising housing costs, developers eager to get rid of low-income residents, and overt city policies of gentrification.
"Displacement and dispossessions are convulsing cities across the globe, becoming the dominant urban narratives of our time. In What a City Is For, Matt Hern uses the case of Albina, as well as similar instances in New Orleans and Vancouver, to investigate gentrification in the twenty-first century. In an engaging narrative, effortlessly mixing anecdote and theory, Hern questions the notions of development, private property, and ownership. Arguing that home ownership drives inequality, he wants us to disown ownership. How can we reimagine the city as a post-ownership, post-sovereign space? Drawing on solidarity economics, cooperative movements, community land trusts, indigenous conceptions of alternative sovereignty, the global commons movement, and much else, Hern suggests repudiating development in favor of an incrementalist, non-market-driven unfolding of the city."

--- I am speculating in advance of actually reading the evidence, but from the description it sounds like the problem with displacement arises not so much because the housing stock in these neighborhoods is _privately owned_, but because it's _owned by non-residents_. So why isn't the solution, as in a developing country, enacting land reform by transferring ownership to the occupants?
tl;dr: last tag applies.
to:NB  books:noted  cities  economics  gentrification  portland  class_struggles_in_america  to_be_shot_after_a_fair_trial
27 days ago
What Is the Argument? | The MIT Press
"The best way to introduce students to philosophy and philosophical discourse is to have them read and wrestle with original sources. This textbook explores philosophy through detailed argument analyses of texts by philosophers from Plato to Strawson. It presents a novel and transparent method of analysis that will teach students not only how to understand and evaluate philosophers’ arguments but also how to construct such arguments themselves. Students will learn to read a text and discover what the philosopher thinks, why the philosopher thinks it, and whether the suporting argument is good.
"Students learn argument analysis through argument diagrams, with color-coding of the argument’s various elements—conclusion, claims, and “indicator phrases.” (An online “mini-course” in argument diagramming and argument diagramming software are both freely available online.) The original text and the analysis appear side by side, so the student can easily follow the analysis of the argument. Each chapter ends with exercises and reading questions.
"After a general introduction to philosophy and logic and an explanation of argument analysis, the book presents selections from primary sources, arranged by topics that correspond to contemporary debates, with detailed analysis and evaluation. These topics include philosophy of religion, epistemology, theory of mind, free will and determinism, and ethics; authors include Aristotle, Aquinas, Descartes, Hume, Kant, Ryle, Fodor, Dennett, Searle, and others. What Is the Argument? not only introduces students to great philosophical thinkers, it also teaches them the essential skill of critical thinking."

--- I am, like a grown-up, resisting the temptation to send various stats. & ML graduate students down the stairs and to the left to sit in on this course.
to:NB  books:noted  rhetoric  logic  philosophy
27 days ago
The Wild and the Wicked | The MIT Press
"Most of us think that in order to be environmentalists, we have to love nature. Essentially, we should be tree huggers—embracing majestic redwoods, mighty oaks, graceful birches, etc. We ought to eat granola, drive hybrids, cook tofu, and write our appointments in Sierra Club calendars. Nature’s splendor, in other words, justifies our protection of it. But, asks Benjamin Hale in this provocative book, what about tsunamis, earthquakes, cancer, bird flu, killer asteroids? They are nature, too.
"For years, environmentalists have insisted that nature is fundamentally good. In The Wild and the Wicked, Benjamin Hale adopts the opposite position—that much of the time nature can be bad—in order to show that even if nature is cruel, we still need to be environmentally conscientious. Hale argues that environmentalists needn’t feel compelled to defend the value of nature, or even to adopt the attitudes of tree-hugging nature lovers. We can acknowledge nature’s indifference and periodic hostility. Deftly weaving anecdote and philosophy, he shows that we don’t need to love nature to be green. What really ought to be driving our environmentalism is our humanity, not nature’s value.
"Hale argues that our unique burden as human beings is that we can act for reasons, good or bad. He claims that we should be environmentalists because environmentalism is right, because we humans have the capacity to be better than nature. As humans, we fail to live up to our moral potential if we act as brutally as nature. Hale argues that despite nature’s indifference to the plight of humanity, humanity cannot be indifferent to the plight of nature."
to:NB  books:noted  environmentalism  environmental_management  moral_philosophy  heaven_and_earth_are_not_benevolent
27 days ago
The Systemic Image: A New Theory of Interactive Real-Time Simulations | The MIT Press
"Computer simulations conceive objects and situations dynamically, in their changes and progressions. In The Systemic Image, Inge Hinterwaldner considers not only the technical components of dynamic computer simulations but also the sensory aspects of the realization. Examining the optic, the acoustic, the tactile, and the sensorimotor impressions that interactive real-time simulations provide, she finds that iconicity plays a dominant yet unexpected role. Based on this, and close readings of a series of example works, Hinterwaldner offers a new conceptualization of the relationship between systemic configuration and the iconic aspects in these calculated complexes.
"Hinterwaldner discusses specifications of sensorialization, necessary to make the simulation dynamic perceivable. Interweaving iconicity with simulation, she explores the expressive possibilities that can be achieved under the condition of continuously calculated explicit changes. She distinguishes among four levels of forming: the systems perspective, as a process and schema that establishes the most general framework of simulations; the mathematical model, which marks off the boundaries of the simulation’s actualization; the iconization and its orientation toward the user; and interaction design, necessary for the full unfolding of the simulation. The user makes manifest what is initially latent. Viewing the simulation as an interface, Hinterwaldner argues that not only does the sensorially designed aspect of the simulation seduce the user but the user also makes an impact on the simulation—on the dynamic and perhaps on the iconization, although not on the perspectivation. The influence is reciprocal."

--- This sounds like it's talking about interesting things, but if the text is anything like this description, I rather doubt I'll be up to the effort of mental translation / editing.
to:NB  books:noted  simulation
27 days ago
Bibliometrics and Research Evaluation | The MIT Press
"The research evaluation market is booming. “Ranking,” “metrics,” “h-index,” and “impact factors” are reigning buzzwords. Government and research administrators want to evaluate everything—teachers, professors, training programs, universities—using quantitative indicators. Among the tools used to measure “research excellence,” bibliometrics—aggregate data on publications and citations—has become dominant. Bibliometrics is hailed as an “objective” measure of research quality, a quantitative measure more useful than “subjective” and intuitive evaluation methods such as peer review that have been used since scientific papers were first published in the seventeenth century. In this book, Yves Gingras offers a spirited argument against an unquestioning reliance on bibliometrics as an indicator of research quality. Gingras shows that bibliometric rankings have no real scientific validity, rarely measuring what they pretend to.
"Although the study of publication and citation patterns, at the proper scales, can yield insights on the global dynamics of science over time, ill-defined quantitative indicators often generate perverse and unintended effects on the direction of research. Moreover, abuse of bibliometrics occurs when data is manipulated to boost rankings. Gingras looks at the politics of evaluation and argues that using numbers can be a way to control scientists and diminish their autonomy in the evaluation process. Proposing precise criteria for establishing the validity of indicators at a given scale of analysis, Gingras questions why universities are so eager to let invalid indicators influence their research strategy."
in_NB  books:noted  bibliometry  academia
27 days ago
Actual Causality | The MIT Press
"Causality plays a central role in the way people structure the world; we constantly seek causal explanations for our observations. But what does it even mean that an event C “actually caused” event E? The problem of defining actual causation goes beyond mere philosophical speculation. For example, in many legal arguments, it is precisely what needs to be established in order to determine responsibility. The philosophy literature has been struggling with the problem of defining causality since Hume.
"In this book, Joseph Halpern explores actual causality, and such related notions as degree of responsibility, degree of blame, and causal explanation. The goal is to arrive at a definition of causality that matches our natural language usage and is helpful, for example, to a jury deciding a legal case, a programmer looking for the line of code that cause some software to fail, or an economist trying to determine whether austerity caused a subsequent depression.
"Halpern applies and expands an approach to causality that he and Judea Pearl developed, based on structural equations. He carefully formulates a definition of causality, and building on this, defines degree of responsibility, degree of blame, and causal explanation. He concludes by discussing how these ideas can be applied to such practical problems as accountability and program verification. Technical details are generally confined to the final section of each chapter and can be skipped by non-mathematical readers."
to:NB  books:noted  causality  halpern.joseph_y.
27 days ago
System | The MIT Press
"A system can describe what we see (the solar system), operate a computer (Windows 10), or be made on a page (the fourteen engineered lines of a sonnet). In this book, Clifford Siskin shows that system is best understood as a genre—a form that works physically in the world to mediate our efforts to understand it. Indeed, many Enlightenment authors published works they called “system” to compete with the essay and the treatise. Drawing on the history of system from Galileo’s “message from the stars” and Newton’s “system of the world” to today’s “computational universe,” Siskin illuminates the role that the genre of system has played in the shaping and reshaping of modern knowledge.
"Previous engagements with systems have involved making them, using them, or imagining better ones. Siskin offers an innovative perspective by investigating system itself. He considers the past and present, moving from the “system of the world” to “a world full of systems.” He traces the turn to system in the seventeenth and eighteenth centuries, and describes this primary form of Enlightenment as a mediator of political, cultural, and social modernity—pointing to the moment when people began to “blame the system” for working both too well (“you can’t beat the system”) and not well enough (it always seems to “break down”). Throughout, his touchstones are: what system is and how it has changed; how it has mediated knowledge; and how it has worked in the world."

--- The alternative would be that "system" is now a word too vague to be of much use, except for sounding more dignified than "thing'. (I admit that, e.g., "theory of dynamical things" is more awkward than "dynamical systems theory", but deny that it's any less precise.)
to:NB  books:noted  rhetoric  systems  history_of_science  history_of_ideas  to_be_shot_after_a_fair_trial
27 days ago
Ebola's Message: Public Health and Medicine in the Twenty-First Century | The MIT Press
"The 2013–2015 outbreak of the Ebola virus disease (EVD) was a public health disaster: 28,575 infections and 11,313 deaths (as of October 2015), devastating the countries of Guinea, Liberia, and Sierra Leone; a slow and mismanaged international response; and sensationalistic media coverage, seized upon by politicians to justify wrongheaded policy. And yet there were also promising developments that may improve future responses to infectious disease epidemics: the UN Security Council’s first involvement in a public health event; a series of promising clinical treatments and vaccines for EVD; and recognition of the need for a global public health system to deal with epidemics that cross national borders. This volume offers a range of perspectives on these and other lessons learned, with essays on the science, politics, and ethics of the Ebola outbreak.
"The contributors discuss topics including the virology and management of EVD in both rich and poor nations; the spread of the disease (with an essay by a leader of Médecins Sans Frontières); racist perceptions of West Africa; mainstream and social media responses to Ebola; and the ethical issue of whether to run clinical trials of experimental treatments during an outbreak. "
to:NB  books:noted  plagues_and_peoples  ebola  moral_responsibility
27 days ago
Rebel Genius: Warren S. McCulloch's Transdisciplinary Life in Science | The MIT Press
"Warren S. McCulloch (1898–1969) adopted many identities in his scientific life—among them philosopher, poet, neurologist, neurophysiologist, neuropsychiatrist, collaborator, theorist, cybernetician, mentor, engineer. He was, writes Tara Abraham in this account of McCulloch’s life and work, “an intellectual showman,” and performed this part throughout his career. While McCulloch claimed a common thread in his work was the problem of mind and its relationship to the brain, there was much more to him than that. In Rebel Genius, Abraham uses McCulloch’s life as a window on a past scientific age, showing the complex transformations that took place in American brain and mind science in the twentieth century—particularly those surrounding the cybernetics movement.
"Abraham describes McCulloch’s early work in neuropsychiatry, and his emerging identity as a neurophysiologist. She explores his transformative years at the Illinois Neuropsychiatric Institute and his work with Walter Pitts—often seen as the first iteration of “artificial intelligence” but here described as stemming from the new tradition of mathematical treatments of biological problems. Abraham argues that McCulloch’s dual identities as neuropsychiatrist and cybernetician are inseparable. He used the authority he gained in traditional disciplinary roles as a basis for posing big questions about the brain and mind as a cybernetician. When McCulloch moved to the Research Laboratory of Electronics at MIT, new practices for studying the brain, grounded in mathematics, philosophy, and theoretical modeling, expanded the relevance and ramifications of his work. McCulloch’s transdisciplinary legacies anticipated today’s multidisciplinary field of cognitive science."

--- McCulloch was one of the greats, so it's exciting to see a biography, along with a reprinting of his paper collection _Embodiments of Mind_ (http://mitpress.mit.edu/9780262529617).
to:NB  books:noted  coveted  lives_of_the_scientists  neuroscience  cybernetics  psychology  cognitive_science  mcculloch.warren_s.  rhetorical_self-fashioning  history_of_science  neural_networks
27 days ago
Windows into the Soul: Surveillance and Society in an Age of High Technology, Marx
"We live in an age saturated with surveillance. Our personal and public lives are increasingly on display for governments, merchants, employers, hackers—and the merely curious—to see. In Windows into the Soul, Gary T. Marx, a central figure in the rapidly expanding field of surveillance studies, argues that surveillance itself is neither good nor bad, but that context and comportment make it so.
"In this landmark book, Marx sums up a lifetime of work on issues of surveillance and social control by disentangling and parsing the empirical richness of watching and being watched. Using fictional narratives as well as the findings of social science, Marx draws on decades of studies of covert policing, computer profiling, location and work monitoring, drug testing, caller identification, and much more, Marx gives us a conceptual language to understand the new realities and his work clearly emphasizes the paradoxes, trade-offs, and confusion enveloping the field. Windows into the Soul shows how surveillance can penetrate our social and personal lives in profound, and sometimes harrowing, ways. Ultimately, Marx argues, recognizing complexity and asking the right questions is essential to bringing light and accountability to the darker, more iniquitous corners of our emerging surveillance society."

--- Some of the chapter titles make me suspect an insufferably self-indulugent scholar. (Takes one to know one, I realize.)
to:NB  books:noted  surveillance  national_surveillance_state  networked_life
28 days ago
The Dancing Bees: Karl von Frisch and the Discovery of the Honeybee Language, Munz
"We think of bees as being among the busiest workers in the garden, admiring them for their productivity. But amid their buzzing, they are also great communicators—and unusual dancers. As Karl von Frisch (1886–1982) discovered during World War II, bees communicate the location of food sources to each other through complex circle and waggle dances. For centuries, beekeepers had observed these curious movements in hives, and others had speculated about the possibility of a bee language used to manage the work of the hive. But it took von Frisch to determine that the bees’ dances communicated precise information about the distance and direction of food sources. As Tania Munz shows in this exploration of von Frisch’s life and research, this important discovery came amid the tense circumstances of the Third Reich.
"The Dancing Bees draws on previously unexplored archival sources in order to reveal von Frisch’s full story, including how the Nazi government in 1940 determined that he was one-quarter Jewish, revoked his teaching privileges, and sought to prevent him from working altogether until circumstances intervened. In the 1940s, bee populations throughout Europe were facing the devastating effects of a plague (just as they are today), and because the bees were essential to the pollination of crops, von Frisch’s research was deemed critical to maintaining the food supply of a nation at war. The bees, as von Frisch put it years later, saved his life. Munz not only explores von Frisch’s complicated career in the Third Reich, she looks closely at the legacy of his work and the later debates about the significance of the bee language and the science of animal communication."
to:NB  books:noted  history_of_science  lives_of_the_scientists  bees  insects  ethology
28 days ago
The Experimental Self: Humphry Davy and the Making of a Man of Science, Golinski
"What did it mean to be a scientist before the profession itself existed? Jan Golinski finds an answer in the remarkable career of Humphry Davy, the foremost chemist of his day and one of the most distinguished British men of science of the nineteenth century. Originally a country boy from a modest background, Davy was propelled by his scientific accomplishments to a knighthood and the presidency of the Royal Society. An enigmatic figure to his contemporaries, Davy has continued to elude the efforts of biographers to classify him: poet, friend to Coleridge and Wordsworth, author of travel narratives and a book on fishing, chemist and inventor of the miners’ safety lamp. What are we to make of such a man?
"In The Experimental Self, Golinski argues that Davy’s life is best understood as a prolonged process of self-experimentation. He follows Davy from his youthful enthusiasm for physiological experiment through his self-fashioning as a man of science in a period when the path to a scientific career was not as well-trodden as it is today. What emerges is a portrait of Davy as a creative fashioner of his own identity through a lifelong series of experiments in selfhood."
to:NB  books:noted  lives_of_the_scientists  history_of_science  rhetorical_self-fashioning
28 days ago
From Notes to Narrative: Writing Ethnographies That Everyone Can Read, Ghodsee
"Ethnography centers on the culture of everyday life. So it is ironic that most scholars who do research on the intimate experiences of ordinary people write their books in a style that those people cannot understand. In recent years, the ethnographic method has spread from its original home in cultural anthropology to fields such as sociology, marketing, media studies, law, criminology, education, cultural studies, history, geography, and political science. Yet, while more and more students and practitioners are learning how to write ethnographies, there is little or no training on how to write ethnographies well.
"From Notes to Narrative picks up where methodological training leaves off.  Kristen Ghodsee, an award-winning ethnographer, addresses common issues that arise in ethnographic writing. Ghodsee works through sentence-level details, such as word choice and structure. She also tackles bigger-picture elements, such as how to incorporate theory and ethnographic details, how to effectively deploy dialogue, and how to avoid distracting elements such as long block quotations and in-text citations. She includes excerpts and examples from model ethnographies. The book concludes with a bibliography of other useful writing guides and nearly one hundred examples of eminently readable ethnographic books."
to:NB  books:noted  ethnography  writing_advice
28 days ago
Plotinus: Myth, Metaphor, and Philosophical Practice, Clark
"Plotinus, the Roman philosopher (c. 204-270 CE) who is widely regarded as the founder of Neoplatonism, was also the creator of numerous myths, images, and metaphors. They have influenced both secular philosophers and Christian and Muslim theologians, but have frequently been dismissed by modern scholars as merely ornamental. In this book, distinguished philosopher Stephen R. L. Clark shows that they form a vital set of spiritual exercises by which individuals can achieve one of Plotinus’s most important goals: self-transformation through contemplation.
"Clark examines a variety of Plotinus’s myths and metaphors within the cultural and philosophical context of his time, asking probing questions about their contemplative effects. What is it, for example, to “think away the spatiality” of material things? What state of mind is Plotinus recommending when he speaks of love, or drunkenness, or nakedness? What star-like consciousness is intended when he declares that we were once stars or are stars eternally? What does it mean to say that the soul goes around God? And how are we supposed to “bring the god in us back to the god in all”? Through these rich images and structures, Clark casts Plotinus as a philosopher deeply concerned with philosophy as a way of life. "
to:NB  books:noted  lives_of_the_scholars  history_of_ideas  barely-comprehensible_metaphysics  ancient_history
28 days ago
History Within: The Science, Culture, and Politics of Bones, Organisms, and Molecules, Sommer
"Personal genomics services such as 23andMe and Ancestry.com now offer what once was science fiction: the ability to sequence and analyze an individual’s entire genetic code—promising, in some cases, facts about that individual’s ancestry that may have remained otherwise lost. Such services draw on and contribute to the science of human population genetics that attempts to reconstruct the history of humankind, including the origin and movement of specific populations. Is it true, though, that who we are and where we come from is written into the sequence of our genomes? Are genes better documents for determining our histories and identities than fossils or other historical sources?
"Our interpretation of gene sequences, like our interpretation of other historical evidence, inevitably tells a story laden with political and moral values. Focusing on the work of Henry Fairfield Osborn, Julian Sorell Huxley, and Luigi Luca Cavalli-Sforza in paleoanthropology, evolutionary biology, and human population genetics, History Within asks how the sciences of human origins, whether through the museum, the zoo, or the genetics lab, have shaped our idea of what it means to be human. How have these biologically based histories influenced our ideas about nature, society, and culture? As Marianne Sommer shows, the stories we tell about bones, organisms, and molecules often change the world."
to:NB  books:noted  genomics  human_genetics  historical_genetics  history_of_science  human_evolution
28 days ago
Macroeconomics: A Critical Companion, Fine, Dimakou
"Macroeconomics is fundamental to our understanding of how the world functions today. But too often our understanding is based on orthodox, canonized analysis. In this rule-breaking book, Ben Fine and Ourania Dimakou provides an engaging, heterodox primer for those interested in an alternative to mainstream macroeconomic theory and history. From classical theory to the Keynesian revolution and more modern forms including the Monetarist counterrevolution, New Classical Fundamentalism, and New Consensus Macroeconomics, Fine and Dimakou rigorously and comprehensively lay out the theories of mainstream economists, warts and all."
to:NB  books:noted  economics  macroeconomics
28 days ago
Microeconomics: A Critical Companion, Fine
"The culmination of forty years of teaching, researching, and advising on political economy, Ben Fine’s Microeconomics offers a clear and concise exposition of mainstream microeconomics from a heterodox perspective. Covering topics from consumer and producer theory to general equilibrium to perfect competition, it sets the emergence and evolution of microeconomics in both its historical and interdisciplinary context. Fine critically exposes the methodological and conceptual content of dominant microeconomic models without sacrificing the technical detail required for those completing a first degree in economics or entering postgraduate study. The result is a book which is sure to establish a strong presence on undergraduate reading lists and in comparative literature on the subject."
to:NB  books:noted  economics  market_failures_in_everything  imperfect_competition
28 days ago
Meanwhile, Back on Most Campuses
"The focus on extreme political correctness at Oberlin and other elite colleges risks obscuring what less privileged undergraduates are dealing with."
education  academia  class_struggles_in_america  press.eyal
29 days ago
[1411.4686] Community detection in sparse networks via Grothendieck's inequality
"We present a simple and flexible method to prove consistency of semidefinite optimization problems on random graphs. The method is based on Grothendieck's inequality. Unlike the previous uses of this inequality that lead to constant relative accuracy, we achieve any given relative accuracy by leveraging randomness. We illustrate the method with the problem of community detection in sparse networks, those with bounded average degrees. We demonstrate that even in this regime, various simple and natural semidefinite programs can be used to recover the community structure up to an arbitrarily small fraction of misclassified vertices. The method is general; it can be applied to a variety of stochastic models of networks and semidefinite programs."
in_NB  community_discovery  optimization
29 days ago
Separating Homophily and Peer Influence with Latent Space by Joseph P Davin, Sunil Gupta, Mikolaj Jan Piskorski :: SSRN
"We study the impact of peer behavior on the adoption of mobile apps in a social network. To identify social influence properly, we introduce latent space as an approach to control for latent homophily, the idea that “birds of a feather flock together.” In a series of simulations, we show that latent space coordinates significantly reduce bias in the estimate of social influence. The intuition is that latent coordinates act as proxy variables for hidden traits that give rise to latent homophily. The approach outperforms existing methods such as including observed covariates, random effects, or fixed effects. We then apply the latent space approach to identify social influence on installation of mobile apps in a social network. We find that peer influence account for 27% of mobile app adoptions, and that latent homophily inflates this estimate by 40% (to 38%). In some samples, ignoring latent homophily can result in overestimation of social effects by over 100%."
to:NB  have_read  causal_inference  network_data_analysis  statistics  homophily  re:homophily_and_confounding  scooped?
29 days ago
Minimizing regret in dynamic decision problems - Springer
"The menu-dependent nature of regret minimization creates subtleties when it is applied to dynamic decision problems. It is not clear whether forgone opportunities should be included in the menu. We explain commonly observed behavioral patterns as minimizing regret when forgone opportunities are present. If forgone opportunities are included, we can characterize when a form of dynamic consistency is guaranteed."
in_NB  decision_theory  low-regret_learning  halpern.joseph_y.
29 days ago
Good manners: signaling social preferences - Springer
"Certain messages, even when not directly payoff relevant, can be a credible form of communication in light of natural social preferences. Social image concerns and other-regarding preferences interact to create incentives to communicate about how one feels about other people. Recognizing the prevalence of the incentive to communicate about one’s social preferences suggests that many social and economic phenomena—from norms of etiquette to cooperation to gift exchange—should be seen, in part, as forms of signaling. These behaviors may be surprisingly robust to material costs, yet sensitive to context."
to:NB  etiquette  game_theory
29 days ago
EconPapers: Is the market really a good teacher ?
"This paper proposes to model market mechanisms as a collective learning process for firms in a complex adaptive system, namely Jamel, an agent-based, stock-flow consistent macroeconomic model. Inspired by Alchian's (1950) " blanketing shotgun process " idea, our learning model is an ever-adapting process that puts a significant weight on exploration vis-à-vis exploitation. We show that decentralized market selection allows firms to collectively adapt their overall debt strategies to the changes in the macroeconomic environment so that the system sustains itself, but at the cost of recurrent deep downturns. We conclude that, in complex evolving economies, market processes do not lead to the selection of optimal behaviors, as the characterization of successful behaviors itself constantly evolves as a result of the market conditions that these behaviors contribute to shape. Heterogeneity in behavior remains essential to adaptation in such an ever-changing environment. We come to an evolutionary characterization of a crisis, as the point where the evolution of the macroeconomic system becomes faster than the adaptation capabilities of the agents that populate it, and the so far selected performing behaviors suddenly cease to be, and become instead undesirable."
to:NB  to_read  evolutionary_economics  economics  via:jbdelong
4 weeks ago
On The So-Called “Huber Sandwich Estimator” and “Robust Standard Errors”
"The “Huber Sandwich Estimator” can be used to estimate the variance of the MLE when the underlying model is incorrect. If the model is nearly correct, so are the usual standard errors, and robustification is unlikely to help much. On the other hand, if the model is seriously in error, the sandwich may help on the variance side, but the parameters being estimated by the MLE are likely to be meaningless—except perhaps as descriptive statistics."
to:NB  have_read  statistics  estimation  misspecification  freedman.david  to_teach:linear_models
4 weeks ago
Could a neuroscientist understand a microprocessor? | bioRxiv
"There is a popular belief in neuroscience that we are primarily data limited, that producing large, multimodal, and complex datasets will, enabled by data analysis algorithms, lead to fundamental insights into the way the brain processes information. Microprocessors are among those artificial information processing systems that are both complex and that we understand at all levels, from the overall logical flow, via logical gates, to the dynamics of transistors. Here we take a simulated classical microprocessor as a model organism, and use our ability to perform arbitrary experiments on it to see if popular data analysis methods from neuroscience can elucidate the way it processes information. We show that the approaches reveal interesting structure in the data but do not meaningfully describe the hierarchy of information processing in the processor. This suggests that current approaches in neuroscience may fall short of producing meaningful models of the brain."
to:NB  neuroscience  have_read  neural_data_analysis  via:arthegall  satire
4 weeks ago
PLOS ONE: Trickle-Down Preferences: Preferential Conformity to High Status Peers in Fashion Choices
On first skim, they don't really seem to consider that women who move from low to high status locations are probably _already different_ from those who don't...
I can't believe I'm writing this, but this might really be a job for propensity-score matching.
to:NB  to_be_shot_after_a_fair_trial  social_influence  economics  shoes  re:homophily_and_confounding  to_teach:undergrad-ADA
4 weeks ago
KONECT - The Koblenz Network Collection
"KONECT contains over a hundred network datasets of various types, including directed, undirected, bipartite, weighted, unweighted, signed and rating networks. The networks of KONECT are collected from many diverse areas such as social networks, hyperlink networks, authorship networks, physical networks, interaction networks and communication networks. The KONECT project has developed network analysis tools which are used to compute network statistics, to draw plots and to implement various link prediction algorithms. The result of these analyses are presented on these pages. Whenever we are allowed to do so, we provide a download of the networks."
to:NB  to_teach:baby-nets  data_sets  networks  network_data_analysis  social_networks  via:BenjaminLind
4 weeks ago
The Political Legacy of American Slavery: The Journal of Politics: Vol 0, No 0
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The Inner Workings of Life | Genomics Bioinformatics and Systems Biology | Cambridge University Press
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 Title: Modeling of generation and transport of particles in low pressure glow discharges and contamination of wafers Author(s): Choi, Seung Jin Doctoral Committee Chair(s): Kushner, Mark J. Department / Program: Electrical and Computer Engineering Discipline: Electrical Engineering Degree Granting Institution: University of Illinois at Urbana-Champaign Degree: Ph.D. Genre: Dissertation Subject(s): Engineering, Electronics and Electrical Physics, General Physics, Fluid and Plasma Abstract: Large particles (tens of nm to tens of $\mu$m in diameter) are problematic in low pressure ($<$1 Torr) plasma processing (etching, deposition) discharges because they can contaminate the product and can perturb electron transport. The role of negative ions in the formation of large clusters, the precursors to particles, in low pressure plasmas is theoretically investigated. We find that the formation of particles requires a critically large cluster. We propose that negatively charged intermediates, which are trapped in electropositive plasmas, increase the average residence time of clusters to allow the growth of critically large clusters.Particulates (or "dust") preferentially accumulate near the cathode sheath-plasma boundary where energetic electrons accelerated in the cathode fall emanate into the negative glow. We theoretically investigate the penetration of the electron flux generated in dc cathode falls through the particulate "barriers" formed by dust contamination. We find that at constant current densities, the plasma responds to the reduction in ionization rate coefficients caused by the particulates by increasing the electric field in the cathode fall.The dynamics of the shielding of particulates in low pressure glow discharge has also been investigated with a pseudoparticle-in-cell simulation (PICs) for electrons and ions in the vicinity of a dust particle. We find that the shielding distance around the dust particle is well-characterized by the ion Debye length. Collisions of orbiting ions effectively decrease the ion temperature, thereby increasing its potential to more negative values. Electron and ion momentum transfer and collection cross sections for scattering from the dust particle are calculated. We also report on results of PICs of the mutual shielding of two adjacent dust particles. We found that two closely spaced particles not only shield each other but can shadow their partner, thereby resulting in asymmetric charging of otherwise identical particles.The distribution of dust particles in plasma processing reactors is determined by a variety of forces, the most important being electrostatic, viscous ion drag, gravitational, thermophoretic and neutral fluid drag. We find that the spatial distribution of dust depends on the spatial dependence of the sheaths and plasma potential in bulk plasma which in turn depend upon the electrical topography of the surfaces. Experimentally observed "dome" and "ring" distributions of dust particles are computationally reproduced for specific combinations of discharge power particle size and substrate topography. Issue Date: 1993 Type: Text Language: English URI: http://hdl.handle.net/2142/20486 Rights Information: Copyright 1993 Choi, Seung Jin Date Available in IDEALS: 2011-05-07 Identifier in Online Catalog: AAI9411590 OCLC Identifier: (UMI)AAI9411590

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This Title All WIREs
How to cite this WIREs title:
WIREs RNA
Impact Factor: 4.838

# Physics‐based all‐atom modeling of RNA energetics and structure

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The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All‐atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x‐ray structures, but are ‘unreliable’ for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x‐ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA. WIREs RNA 2017, 8:e1422. doi: 10.1002/wrna.1422

Umbrella sampling can sample across barriers in landscapes. The x‐axis of these plots is a reaction coordinate, which can be any quantity that describes progress along the conformational change pathway, such as a distance, angle, or dihedral angle. The y‐axis is the Gibbs free energy change. In panel (a), a molecular landscape is shown, where there are two low free energy basins and a barrier between them. If this barrier is much larger than thermal energy, then molecular dynamics will be slow to cross it. In panel (b), a restraint energy (red) is added to the landscape to lower the barrier between the two low free energy states. In this way, the barrier can be easily crossed, as shown in the final landscape (green). Although in theory this would work to enable sampling, in practice the determination of the height and shape of the barrier is the goal of the simulations, hence it is not clear what potential would suffice to use as the restraint. Panel (c) shows that a series of umbrella potentials (red) can be used to guide the molecule across the barrier. Each restraint is used in a separate, equilibrium simulation, and therefore each independent equilibrium simulation will sample a distinct region of the reaction coordinate. In panel (d), each simulation has been analyzed to determine the free energy for each equilibrium simulation, but an arbitrary offset results for each. To recover the original landscape (panel a), the free energies are ‘stitched’ together using the weighted histogram analysis method.
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This figure shows the refinement process that RNA force fields have undergone from the early 1990s to the present. The black bars show these connections as a cladistic tree would, and their length is proportional to the number of years between publications. AMBER FF94, FF99, Parmbsc0, and FF10 are described in Refs , , , and , respectively. These record the development of the standard AMBER force field for RNA (note that more recent standard AMBER force fields for RNA are identical to FF10). χ Yildirim and ParmTor are described in Refs and , respectively. Chen and Garcia's force field is described in Ref , and is based on the hypothesis that FF99 overemphasizes stacking which they reduce by scaling down van der Waals (VDW) radii and well depths to 95 and 80%, respectively, to agree with quantum mechanics (QM) (CCSD(T)) calculations. Cheatham's group hypothesized that phosphate oxygens might be incorrectly sized, based on work from the Case group, and produced Amber + vdW BB and Amber + vdW. All use parameters described in Ref . AmberPDB is the result of a new approach for force‐field fitting, described in Ref , where targeted metadynamics (TMD) simulations enforce a free energy curve along degrees of freedom explicitly parameterized by the force field, whereupon those parameters are fit to the TMD free energy curve. In this case the enforced free energy curve was the log‐odds of dihedral angles for α, β, ε, and from dinucleotides in the PDB. Amber + Aytenfisu is a refit of the dihedral parameters using a simultaneous linear regression to match QM energies calculated for an ensemble of dinucleotides amassed from the PDB and sampled from simulations, described in Ref . CHARMM has also offered force fields tuned for nucleic acids, with CHARMM22, 27, and 36 described in Refs , and , and , respectively.
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Geometry and partial charges of TIP3P water model, rO − H is bond length, θ is bond angle, rvdW is van der Waals radius of oxygen atom, qH is partial charge of each H atom, and qO is partial charge of an O atom.
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An example of RNA sequence (left), secondary structure (middle), and tertiary structure (right). The secondary structure records base‐pairing associations for the sequence which, being mostly more favorable than other contacts, constrain tertiary structure. This is what is meant by the observation that RNA structure is hierarchical. One goal of computational methods is to accurately predict 3D structure from sequence.
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Two structures commonly generated in molecular dynamics simulations of 5’GACC. (Left) An A‐form like structure consistent with nuclear magnetic resonance (NMR) spectra. (Right) A structure with G1 intercalated between C3 and C4; NMR does not detect this structure.
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Results from tests of different force fields used to predict structure of UUCG tetraloop. Cluster 5 agrees best with the nuclear magnetic resonance structure, which is shown in green. (Reprinted with permission from Ref . Copyright 2015 Cold Spring Harbor Laboratory Press for the RNA Society)
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Nuclear magnetic resonance (NMR) structures and free energy increments at 37°C for internal loops in $5′GCUGA¯GGCU2$, $5′GCGGA¯UGCU2$, $5′GCGGA¯CGC2$, and $5′GGCGA¯GCC2$. Note that the NMR spectra do not eliminate the possibility of up to 10% of a minor structure. Values for loop ΔG are modified from previously published values because nonloop nearest neighbors were subtracted using parameters from Xia et al. and Chen et al.
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Comparison between experimental and predicted change in ΔG (kcal/mol) at 300 K for duplex formation when GC pairs are replaced by iGiC. The thermodynamic cycle requires that $ΔG4∘−ΔG2∘−ΔG1∘+2ΔG3∘=0$ so that $ΔG4∘−ΔG1∘=ΔG2∘−2ΔG3∘$. Revisions to FF99 for parameters of torsions, χ, α, γ, ε, ζ, and β increased agreement between experiment and prediction by about 10 kcal/mol.
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(a, b) GU pairs with two and one hydrogen bond. (c, d) Sheared (trans Hoogsteen/Sugar edge A–G) and imino (cis Watson‐Crick/Watson‐Crick A–G) GA pairs, respectively. (e) Watson‐Crick AU pair. (f) Hairpin used for umbrella sampling to predict change in ΔG° when one or both of circled GC pairs are changed to AU.
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Free energy integration. This example shows the alchemical transformation of a G–C pair to an iG–iC pair, where the amino and carbonyl groups are transposed relative to G and C. In free energy integration, the system is transformed from one molecule to another, where λ indicates the progress. In this example, λ = 0 is the G–C pair and λ = 1 is the iG–iC pair. For intermediate values of λ, the pair is partially G–C and partially iG–iC.
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# Why the resistor is not considered?

Why in the following solution the 6Ω resistor is not considered?

• I suggest you do the calculation twice: 1) without the 6 ohms resistor in place (replace it with a wire) 2) with the 6 ohm resistor in place. Then compare the answers. – Bimpelrekkie Feb 8 '16 at 15:56
• Your sample calculation is wrong. KCL sums currents into a node. The value 2v0 is not a current term. – Michael Karas Feb 8 '16 at 16:25
• @MichaelKaras - if you bothered to look at the diagram you would see that there is a voltage dependent current source whose value is 2Vo, so there is nothing wrong with its use in the equation – I. Wolfe Feb 8 '16 at 16:30
• @MichaelKaras Yes it is. Look to the right of the schematic. Don't confuse him/her more. – Asmyldof Feb 8 '16 at 16:31
• You found out that in order to calculate V0, the 6 ohm resistor does nothing. Why is that so ? It is because what you're interested in is the current through the 4 ohm resistor. As that current is defined by 2 current sources in parallel (so you can sum their values) the value of the 6 ohm resistor is irrelevant. It could be any value because that would not change the current as that current is set by the 2 sources. If Vo is the voltage across the 6 ohm resistor then indeed the value of the 4 ohm resistor does not matter for the same reasons. – Bimpelrekkie Feb 9 '16 at 9:53

The amount of current flowing from the 6-ohm branch into the node can be determined without considering the 6-ohm resistor in the circuit. The current in that branch is easily obtained by dividing the potential difference across any component in the branch by the impedance of that component.

So the current in the 6-ohm branch is simply $I = v_0/4$. And this can be added to other currents flowing into the node ($10 A$ and $2v_0$) to get a node equation according to KCL.

• So if Vo were the voltage of the 6Ω resistor the solution would be this: Vo/6 + 10 + 2Vo = 0 ⇒ Vo + 60 + 12Vo = 0 ⇒ 13 Vo = -60 ⇒ Vo = -4.615. It's right? – ᴜsᴇʀ Feb 9 '16 at 9:25
• Yes, if Vo was the voltage across the 6-ohm resistor – TisteAndii Feb 9 '16 at 9:30

This is simply because the variable of interest is Vo.

There is only one current running through a branch. The current through the 6 ohm is the same current running through the 4 ohm, which is the current through the branch. Since KCL deals with currents leaving or entering a node from its branches and the current through the 4 ohm is the same as the current through the branch, we don't have to include the 6 ohm resistor and the equation solves directly for V0.

• it's not that the 6ohm resistor isn't connected to the node, that phrase is very misleading. You could very easily make V0 the voltage across both 4ohm and 6ohm resistors, which would make both relevant. the only reason 6ohm is not relevant is because V0 is defined as the voltage across the 4ohm resistor. likewise you could make V1 the voltage across the 6ohm reistor and use it, ignoring the 4ohm resistor (of course this would cause issues with the dep current source, but you see my point) – I. Wolfe Feb 8 '16 at 16:35
• That's true, but in that case, the resistors would have to be combined, then the equivalent resistor would be connected. I guess I wasn't sure if the question was in reference to the use of KCL, or calculating V0. – JosephQ Feb 8 '16 at 16:40
• It is most likely a school problem to calculate Vo using KCL. The 6 ohm resistance is completely dismiss-able, and OP was wondering why that is. The answer is not that the 6 ohm resistance isn't connected to the right node, as it is in series with the 4 ohm and between the same two nodes. The reason is because the problem is an arbitrary school problem, and all you care about is the current in the branch, which does not require the 6ohm to compute. I could swap the positions of the two resistors and get the same answer, making your comment of nodes irrelevant. – I. Wolfe Feb 8 '16 at 16:50
• I see your point. Let me know if my edited answer is better. – JosephQ Feb 8 '16 at 17:00
• Yup, much better answer now. – I. Wolfe Feb 8 '16 at 17:22

KCL only depends on the sum of the currents flowing into any particular node. Taking the top node, you have three branches of current:

The 10A source and the variable 2*Vo source are pretty much given to us. In the remaining branch, we are given a 4 ohm resistor with a voltage difference across it. V=IR will allow us to find the current in that one branch, which would be the same at ANY point in that one branch.

That being said there should be ways of calculating this with the 4 ohm resistor but it would simply add extra complication for no reason.

The 4$\Omega$ resistor is in series with a current source (actually a parallel combination of two current sources).
Therefore the current through the 4$\Omega$ resistor must be the same as the current through the current source (actually sum currents through both current souces), no matter what other components (6$\Omega$ resistors or any other resistor or voltage source) are also in series.

If you care only for currents you can ignore resistors in series with current sources just as you can ignore resistors in parallel with voltage sources if you care only for voltages (the dual case).

Let's take a look at this. I'll name the currents to make the math clearer:

simulate this circuit – Schematic created using CircuitLab

$I_i$ and $I_d$ both flow from ground to node A. $I_0$ flows from node A to ground through the resistors. So our KCL equation for node A is:

$$I_i + I_d = I_0$$

$I_i$ is an independent current source, and we already know its current, so we're done there. $I_d$ is a voltage-controlled current source. Its controlling voltage is the voltage across the $4\ \Omega$ resistor. Note that I've (arbitrarily) made $I_0$ flow into the negative terminal of this resistor. The dependent source's current is thus given by:

$$I_d = 2 \cdot -I_0 \cdot 4 \Omega = -8I_0$$

Now we have two equations with two unknown variables:

$$I_0 = I_d + 10 \mathrm A$$ $$I_d = -8I_0$$

Note that the $6\ \Omega$ resistor does not appear in either of these equations. That's because our sources are all current sources, and the one control voltage depends only on the sum of the two source currents. The absolute voltage is irrelevant.

Let's finish this off. Substituting the second equation into the first gives:

$$I_0 = -8I_0 + 10 \mathrm A$$ $$9I_0 = 10 \mathrm A$$ $$I_0 = \frac {10} {9} \mathrm A \approx 1.111 \mathrm A$$

Since we know $I_0$, we can calculate $I_d$:

$$I_d = -8I_0 = -\frac {80} 9 \mathrm A \approx -8.889 \mathrm A$$

The current through $I_d$ is negative, which makes sense given the polarity of $V_0$. Let's double-check our result using the original KVL equation:

$$10 \mathrm A - 8.889 \mathrm A = 1.111 \mathrm A$$ $$10 \mathrm A = 10 \mathrm A$$


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Can -num_alignments influence the outfmt 6 blast output format?
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Entering edit mode
3.0 years ago

Hello guys, I was reading about the basic parameters of BLAST+, I used to set the parameters -outfmt 6 to return a tabular file as output with 12 columns.

But I have one question about the parameter -num_aligments.

If, for example, I set -num_aligments 5, in my tabular output only 5 lines per query will be written? or this parameter only works for the output in formats =< 4?

Best.

blast parameters • 2.1k views
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Entering edit mode
3.0 years ago
GenoMax 123k

Correct. You actually get n+1 alignments. If you select less than 5 blastn will give you a warning

Warning: [blastn] Examining 5 or more matches is recommended

This has to do with a bug that was fixed in blast+ package.

That said you may want to control the number by using -max_target_seqs instead.

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Entering edit mode

Thanks genomax,

I was reading and making some tests, the -num_alignments will show N alignments per HSPS between query-subject right?

So can I combine -num_alignments 5 with -max_hsps 1, for example, to recovery only 5 lines per query?