Hartley and Shannon's Information

"Shannon spent much of his life working with the conceptual tools that Hartley built, and for the better part of his life, much of his public identity—'Claude Shannon, Father of Information Theory'—was bound up in having been the one who extended Hartley’s ideas far beyond what Hartley, or anyone, could have imagined. In the 1939 letter in which Shannon first laid out the study of communications that he would complete nine years later, he used Nyquist’s 'intelligence.' By the time the work was finished, he used Hartley’s crisper term: 'information.' While an engineer like Shannon would not have needed the reminder, it was Hartley who made meaning’s irrelevance to information clearer than ever." Full article @ Nautilus.



Quantum teleportation is even weirder than you think

(Via Thiago Carvalho)"Then what is it information about, exactly? That issue, at the heart of quantum information theory, has not been resolved. Is it, for example, information about some underlying reality, or about the effects of our intervention in it? Information universal to all observers, or personal to each? And can it be meaningful to speak of quantum information as something that flows, like liquid in a pipe, from place to place? No one knows (despite what they might tell you). If we can answer these questions, we might be close finally to grasping what quantum mechanics means." Full column @ Nature News.



Claude Shannon’s New York Years

"By day, Claude Shannon labored on top-secret war projects at Bell Labs. By night, he worked out the details of information theory." Full article @ IEEE Spectrum.



Kenneth J. Arrow (1921–2017)

Kenneth Arrow was the doyen of economic theory during the second half of the twentieth century. His fundamental and diverse contributions — to fields including welfare economics, which aims to evaluate social welfare on the basis of individual choices or preferences — were founded on abstract reasoning and remarkably few elementary mathematical concepts. [...]The crown jewel of mathematical politics is Arrow's impossibility theorem — the demonstration that collective decision-making based on the choices of individuals cannot produce results that reflect the preferences of society as a whole." Full obituary @ Nature.



From Bone to Computer via Music

"Necessity is the mother of invention, right? Well, not always. Steven Johnson shows us how some of the most transformative ideas and technologies, like the computer, didn't emerge out of necessity at all but instead from the strange delight of play. Share this captivating, illustrated exploration of the history of invention. Turns out, you'll find the future wherever people are having the most fun." Full Video: Steven Johnson: The playful wonderland behind great inventions | TED Talk. Thanks Al Abi-Haidar!



Could a Neuroscientist Understand a Microprocessor?

I like the conclusion: "we argue for scientists using complex non-linear dynamical systems with known ground truth." I certainly think is a great way to test theories indeed.

"We show that the approaches reveal interesting structure in the data but do not meaningfully describe the hierarchy of information processing in the microprocessor. This suggests current analytic approaches in neuroscience may fall short of producing meaningful understanding of neural systems, regardless of the amount of data. Additionally, we argue for scientists using complex non-linear dynamical systems with known ground truth, such as the microprocessor as a validation platform for time-series and structure discovery methods." Full article @ PLOS Computational Biology



Big data: are we making a big mistake?

Worth revisiting again and again (thank you Thiago): 'As for the idea that “with enough data, the numbers speak for themselves” – that seems hopelessly naive in data sets where spurious patterns vastly outnumber genuine discoveries. “Big data” has arrived, but big insights have not. The challenge now is to solve new problems and gain new answers – without making the same old statistical mistakes on a grander scale than ever'. Full article at Financial Times.

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The Cybernetic Humanities

'For cybernetics, the digital brain completed the picture. Animals were machines, communication was control, and information processing was the principle, not just an element, of the new science. Wiener would not shy away from the philosophical consequences, claiming that “information is information, not energy or matter. No materialism which does not admit this can survive at the present day.”' Full review @ The Cybernetic Humanities - Los Angeles Review of Books

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Turing Tape Neural architecture

"Although there are clear parallels between human reasoning and the running of computer programs, we lack an understanding of how either of them could be implemented in biological or artificial neural networks. Graves and colleagues take a substantial step forward in this quest by presenting a neuro-computational system that shows striking similarities to a digital computer." Full news article @ Nature; target article "Hybrid computing using a neural network with dynamic external memory" also at Nature.

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How the Soviets invented the internet and why it didn't work

"Soviet scientists tried for decades to network their nation. What stalemated them is now fracturing the global internet." Full article @ Aeon Essays



Update Science's structure

Sure, I share Popkin's call to Update the Nobel Prizes, but that is just the tip of the iceberg (or the ivory tower). In truth, from universities, to funding bodies and even to the top journals that dictate impact, science has not updated itself to the changing reality. Even Popkin's article fails to discuss the lack of Nobel recognition for Computer Science/Informatics, when this has been the field that most dramatically changed society in the last century. As I like to say, Turing and Von Neumann had much greater impact in the lives of people than Darwin, yet recognition of the field is lacking not only at the Nobel level. You will very rarely see a computer scientist in the top scientific advising bodies in any country (those are typically reserved for Nobel categories). Same is true for editors and thus papers in Nature and Science. But beyond discipline, what is truly lacking is support and recognition for interdisciplinary research, which is needed to actually solve problems---something that both Turing and Von Neumann already excelled at. Nobel's main sin is to actually award prizes per discipline, rather than unconstrained advance. But this is also the sin of most national funding agencies who organize calls within disciplinary walls and prefer to fund the agendas of lead principal investigators from a discipline (props to NIH and somewhat NSF for actually making measurable advances to try to counter this, despite the conservative, disciplinary disposition of universities and scientists alike). Universities too, remain largely organized by traditional disciplines as they were in Mr. Nobel's days. This makes it very hard for teams of scientists to escape the silos of disciplinary training and be collectively rewarded, rather than made to follow the single agenda of a lead investigator---even though we know that no single lab can address the complex challenges of the 21st century.

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first ever computer music recording generated on Alan Turing's computer

New Zealand researchers have restored the first recording of computer-generated music, created in 1951 on a gigantic contraption built by British genius Alan Turing. See article @ Australian Broadcasting Corporation and music @ Thump. Thank you Nathan Ratkiewicz for sharing.

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first ever computer music recording generated on Alan Turing's computer

New Zealand researchers have restored the first recording of computer-generated music, created in 1951 on a gigantic contraption built by British genius Alan Turing. See article @ Australian Broadcasting Corporation and music @ Thump.

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The end of Moore's law

"The observations in the chip manufacturing industry and the shifting demands of the chip market are a strong indication that Moore's law is indeed coming to an end and future increases in computer power will be more punctual than systematic as it has been in the past 50 years. Even if there would be no progress in hardware performance at all—what is, of course, very unlikely—we can expect substantial further progress in numerical mathematics and new algorithms, which will render computation in the future more efficient than today. Indeed there is no need to be pessimistic." Full article @



Making RNA in the prebiotic world

"The RNA World hypothesis posits that RNA was one of the first self-replicating molecules leading to the origin of life. The nucleotide bases of RNA—A, U, C, and G—are chemically complex, and it has been unclear how the large purine bases A and G might have arisen on prebiotic Earth. Becker et al. show that the A and G bases can be synthesized easily and in high yield from prebiotically reasonable precursors, lending further support to the RNA World hypothesis." Full paper: A high-yielding, strictly regioselective prebiotic purine nucleoside formation pathway | Science



How Can We Apply Physics to Biology?

"Physics is not just what happens in the Department of Physics. [...] Scientific ideas developed in one field can turn out to be relevant in another"How Can We Apply Physics to Biology?



The multifaceted impact of Ada Lovelace in the digital age

"Ada Lovelace (1815–1852), the Victorian-era mathematician daughter of the Romantic poet Lord Byron, is famous for her work with Charles Babbage on the Analytic Engine and is widely celebrated as the first computer programmer. [...] The book [an interdisciplinary collection of papers inspired by Ada's life, work, and legacy] covers Ada's collaboration with Babbage, her position in the Victorian and steampunk literature, her representation in contemporary art and comics, and her increasing relevance in promoting women in science and technology. [This book] review [focuses] in particular on Ada's visionary ideas of software, on her relation with Alan Turing and the inception of Artificial Intelligence." Full review @ The multifaceted impact of Ada Lovelace in the digital age



Design and synthesis of a minimal bacterial genome

Absolutely loving this paper! Some highlights: "During the process of genome minimization, there is a trade-off between genome size and growth rate. JCVI-syn3.0 is a working approximation of a minimal cellular genome, a compromise between small genome size and a workable growth rate for an experimental organism. [...] To obtain a viable genome, avoid deleting pairs of redundant genes for essential functions. [...] Unexpectedly, it also contains 149 genes with unknown biological functions. JCVI-syn3.0 is a versatile platform for investigating the core functions of life and for exploring whole-genome design."

"A goal in biology is to understand the molecular and biological function of every gene in a cell. One way to approach this is to build a minimal genome that includes only the genes essential for life. In 2010, a 1079-kb genome based on the genome of Mycoplasma mycoides (JCV-syn1.0) was chemically synthesized and supported cell growth when transplanted into cytoplasm. Hutchison III et al. used a design, build, and test cycle to reduce this genome to 531 kb (473 genes). The resulting JCV-syn3.0 retains genes involved in key processes such as transcription and translation, but also contains 149 genes of unknown function." Full paper @ Design and synthesis of a minimal bacterial genome | Science

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Donald Hoffman: Do we see reality as it is? | TED Talk | TED.com

"Cognitive scientist Donald Hoffman is trying to answer a big question: Do we experience the world as it really is ... or as we need it to be? In this ever so slightly mind-blowing talk, he ponders how our minds construct reality for us."Donald Hoffman: Do we see reality as it is? | TED Talk | TED.com




Wolfram: AI & The Future Of Civilization

"What makes us different from all these things? What makes us different is the particulars of our history, which gives us our notions of purpose and goals. That's a long way of saying when we have the box on the desk that thinks as well as any brain does, the thing it doesn't have, intrinsically, is the goals and purposes that we have. Those are defined by our particulars—our particular biology, our particular psychology, our particular cultural history." Full conversation @ Edge.org



How the Brain Is Computing the Mind

"The history of science has shown us that you need the tools first. Then you get the data. Then you can make the theory. Then you can achieve understanding." Interview with Ed Boyden @ Edge.org



Physicists Detect Gravitational Waves, Proving Einstein Right

"Scientists say they heard the faint chirp of two black holes colliding a billion light-years away, fulfilling Einstein’s general theory of relativity." Full news article @ The New York Times



complexity theory and everything

"In complexity theory, physicists try to understand economics while sociologists think like biologists. Can they bring us any closer to universal knowledge?" News article @ Slate



Ingenious: David Krakauer

"The systems theorist David Krakauer explains what’s wrong with standard models of intelligence". Full interview @ Nautilus



Physical and Mathematical Modeling in Experimental Papers

Pay special attention to the Null Models and “Black Box” Approaches for Prediction section... "An increasing number of publications include modeling. Often, such studies help us to gain a deeper insight into the phenomena studied and break down barriers between experimental and theoretical communities. However, combining experimental and theoretical work is challenging for authors, reviewers, and readers. To help maximize the usefulness and impact of combined theoretical and experimental research, this Primer describes the purpose, usefulness, and different types of models and addresses the practical aspect of integrated publications by outlining characteristics of good modeling, presentation, and fruitful collaborations." Full paper @



Jorge Luis Borges, Information and messages

Some pointers to the Jorge Luis Borges stories we discussed in class.

The Library of Babel
The Garden of Forking Paths
Interview with Jorge Luis Borges Borges' biography.

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DNA memory: What’s Old Is New Again

"Revolutionary new methods for extracting, purifying, and sequencing ever-more-ancient DNA have opened an unprecedented window into the history of life on Earth. In just a few decades, the study of ancient DNA has gone from a scientific curiosity to an extremely powerful method for reconstructing past biological phenomena." News article @ The Scientist Magazine®

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Ada ovelace: Enchantress of abstraction

"The bicentenary of Augusta Ada King, Countess of Lovelace, heralds the critical reassessment of a remarkable figure in the history of Victorian science. Ada Lovelace (as she is now known) was 27 years old and married with 3 children when she published the first account of a prototype computer and its possible applications in 1843. Her 20,000-word paper was appended as seven Notes to a translation of a descriptive article, Sketch of the Analytical Engine Invented by Charles Babbage." Book review @ Nature : Nature

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Tara Oceans science

"The scientific activities of the Tara Oceans expedition, led by EMBL senior scientist Eric Karsenti, present an unprecedented effort that resulted in 35,000 samples containing millions of small organism collected in more than 210 ocean stations, chosen for their climatic significance or biodiversity. Putting to work its extremely advanced microscopy facility, analysing the genetic sequences of all organism with sophisticated bioinformatics tools, and explaining the story of life through surprising opportunities in evolutionary biology, EMBL is putting the crowning analysis on top of one of the most ambitious projects of our time". More @ EMBL


Mysterious Statistical Law May Finally Have an Explanation

"In general, Majumdar and Schehr believe, systems in the Tracy-Widom universality class exhibit one phase in which all components act in concert and another phase in which the components act alone." News article @ WIRED



Biologists trace how human innovation impacts tool evolution

"Professor Marcus Feldman's lab has devised a computer model that could help solve a long-standing mystery over why the introduction of new tools in prehistoric societies sometimes comes in periodic bursts."Biologists trace how human innovation impacts tool evolution


Remote Mind Control

"Using chemogenetic tools to spur the brain into action. [...] Less than a decade ago, such precise control over neuronal activity in a dish, let alone in a living brain, was impossible. "Remote Mind Control | The Scientist Magazine®



Mathematics: Logic and Lewis Carroll

In 1855, Charles L. Dodgson became the mathematical lecturer at Christ Church College in the University of Oxford, UK. His job was to prepare Christ Church men (for it was all men) to pass examinations in mathematics. Dodgson (1832–98) would go on to publish Alice's Adventures in Wonderland (1865) and Through the Looking-Glass (1871) under the pen name Lewis Carroll, but he also produced many pamphlets and ten books on mathematical topics. In some of these, he exhibited unusual methods — for rapid arithmetic, for example. Others featured innovative ideas that foreshadowed developments in the twentieth century, for instance in voting theory". Full review @ Nature



Why significant variables aren’t automatically good predictors

recent puzzle in the big data scientific literature is that an increase in explanatory variables found to be significantly correlated with an outcome variable does not necessarily lead to improvements in prediction. This problem occurs in both simple and complex data. We offer explanations and statistical insights into why higher significance does not automatically imply stronger predictivity and why variables with strong predictivity sometimes fail to be significant. We suggest shifting the research agenda toward searching for a criterion to locate highly predictive variables rather than highly significant variables. We offer an alternative approach, the partition retention method, which was effective in reducing prediction error from 30% to 8% on a long-studied breast cancer data set. Full paper @ PNAS



Interdisciplinarity: Topping the charts

"We offer ideas on why India ranks highest and Brazil fifth — above the United States and Europe — in terms of the numbers of interdisciplinary research papers that they publish in Elsevier journals "Interdisciplinarity: Topping the charts : Nature : Nature Publishing Group


GEPHI - Introduction to Network Analysis and Visualization

Modelling with networks. Gephi is an easy access and powerful network analysis tool. See tutorial designed to allow everyone to try a couple of first experiments on two complementary datasets.GEPHI - Introduction to Network Analysis and Visualization

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