Where is the autonomy when more than half your body is not human?

'"Prof Sarkis Mazmanian, a microbiologist from Caltech, argues: "We don't have just one genome, the genes of our microbiome present essentially a second genome which augment the activity of our own."What makes us human is, in my opinion, the combination of our own DNA, plus the DNA of our gut microbes."' Full news article @ BBC News.

This new understanding of the organization of vertebrates really highlights the external nature of DNA qua Turing tape. Notice that the microbes in us do not strictly reproduce with us; some may, but the majority enters us via the environment---which often explains that certain conditions run in families, and often disappear (or appear) when we leave home. Since some of this microbiome actually controls host behavior (as shown in drosophila experiments), our decision processes (e.g. what we like to eat and mating behavior) can change depending on the external DNA that gets into our guts. So the idea of a self or identity that is self-producing or self-reproducing becomes greatly challenged.

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The Scientific Paper Is Obsolete

"When you improve the praxis of science, the dream is that you’ll improve its products, too. Leibniz’s notation, by making it easier to do calculus, expanded the space of what it was possible to think. The grand scientific challenges of our day are as often as not computational puzzles: How to integrate billions of base pairs of genomic data, and 10 times that amount of proteomic data, and historical patient data, and the results of pharmacological screens into a coherent account of how somebody got sick and what to do to make them better? How to make actionable an endless stream of new temperature and precipitation data, and oceanographic and volcanic and seismic data? How to build, and make sense of, a neuron-by-neuron map of a thinking brain? Equipping scientists with computational notebooks, or some evolved form of them, might bring their minds to a level with problems now out of reach."

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The Mind-Expanding Ideas of Andy Clark

"Clark says that our minds extend out into the world, incorporating tools and other minds in order to think. The tools we use to help us think—from language to smartphones—may be part of thought itself. [...]. The idea of an extended mind has itself extended far beyond philosophy, which is why Clark is now, in his early sixties, one of the most-cited philosophers alive. His idea has inspired research in the various disciplines in the area of cognitive science (neuroscience, psychology, linguistics, A.I., robotics) and in distant fields beyond. Some archeologists now say that when they dig up the remains of lost civilizations they are not just reconstructing objects but reconstructing minds. Some musicologists say that playing an instrument involves incorporating an object into thought and emotion, and that to listen to music is to enter into a larger cognitive system comprised of many objects and many people." Full article @ the New Yorker

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Evolution is the New Deep Learning

"There is significant momentum building in this area; indeed, we believe evolutionary computation may well be the next big thing in AI technology." Full post at Sentient.

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Higher Education Is Drowning in BS

Pointed self-criticism of BS in academia by Christian Smith. Well done, it matches my experience with academia's rewards, as well as the frustration of both contributing to this same BS and agreeing with how difficult it is to change it, except, perhaps, via long-term strategies like demanding and interdisciplinary training of graduate students. Thanks to Erik Stolterman for the pointer.

"BS is the farce of what are actually 'fragmentversities' claiming to be universities, of hyperspecialization and academic disciplines unable to talk with each other about obvious shared concerns. [...] BS is the institutional reward system that coerces graduate students and faculty to "get published" as soon and as much as possible, rather than to take the time to mature intellectually and produce scholarship of real importance. [...] BS is the grossly lopsided political ideology of the faculty of many disciplines, especially in the humanities and social sciences, creating a homogeneity of worldview to which those faculties are themselves oblivious, despite claiming to champion difference, diversity, and tolerance. [...] the idea of tragedy is incomprehensible in institutions drifting in a Bermuda Triangle marked by the external-funding addictions of the STEM fields, the obsequious scientism of the social sciences, and the intellectual fads, ideological doctrines, and science-envy that captivate and enervate the humanities. And when the protagonists and victims of such a tragedy cannot even recognize their own tragic condition, the situation is even more dreadful and pathetic."




How to avoid glib interdisciplinarity

"The gains from interdisciplinary research are essential, especially in addressing grand challenges such as sustainability; together we must take on the tough challenge of not being glib. [...]To make progress on the grand challenges, authors, reviewers and editors must take the time to respect each others’ expertise and blind spots." Full Editorial @ Nature.




On data dredging

From A Failure to Heal By SIDDHARTHA MUKHERJEE. Thank you to Thiago Carvalho for the link.

"Perhaps the most stinging reminder of these pitfalls comes from a timeless paper published by the statistician Richard Peto. In 1988, Peto and colleagues had finished an enormous randomized trial on 17,000 patients that proved the benefit of aspirin after a heart attack. The Lancet agreed to publish the data, but with a catch: The editors wanted to determine which patients had benefited the most. Older or younger subjects? Men or women?

Peto, a statistical rigorist, refused — such analyses would inevitably lead to artifactual conclusions — but the editors persisted, declining to advance the paper otherwise. Peto sent the paper back, but with a prank buried inside. The clinical subgroups were there, as requested — but he had inserted an additional one: “The patients were subdivided into 12 ... groups according to their medieval astrological birth signs.” When the tongue-in-cheek zodiac subgroups were analyzed, Geminis and Libras were found to have no benefit from aspirin, but the drug “produced halving of risk if you were born under Capricorn.” Peto now insisted that the “astrological subgroups” also be included in the paper — in part to serve as a moral lesson for posterity. I’ve often thought of Peto’s paper as required reading for every medical student".

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Laptops hinder performance

Looks like I am right to ban laptops in my classes... "By the end of the semester, students in the classrooms with laptops or tablets had performed substantially worse than those in the sections where electronics were banned."

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Alien AI

DeepMind’s new self-taught Go-playing program is making moves that other players describe as “alien” and “from an alternate dimension.” Full article @ the Atlantic.

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Information Theory:
Entropy Applet
Letter frequency in English
Word and Letter Frequency in English
Entropy of English
Text Mechanic - Text Manipulation Tools
1952 – “Theseus” Maze-Solving Mouse @ cyberneticzoo.com

From At&T Archives:

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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.



3,700-year-old Babylonian tablet rewrites the history of math

"A 3,700-year-old clay tablet has proven that the Babylonians developed trigonometry 1,500 years before the Greeks and were using a sophisticated method of mathematics which could change how we calculate today". Full news article @ The Telegraph
. See also the response by Evelyn Lamb (Thanks Johan Bollen).

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Collection of letters by Alan Turing found in filing cabinet

"A lost collection of nearly 150 letters from the codebreaker Alan Turing has been uncovered in an old filing cabinet at the University of Manchester. The correspondence, which has not seen the light of day for at least 30 years, contains very little about Turing’s tortured personal life. It does, however, give an intriguing insight into his views on America. In response to an invitation to speak at a conference in the US in April 1953, Turing replied that he would rather not attend: 'I would not like the journey, and I detest America.' The collection focuses mainly on Turing’s academic research, including his work on groundbreaking areas in AI, computing and mathematics, and invitations to lecture at some of America’s best-known universities including the Massachusetts Institute of Technology". Full news article @
The Guardian.




From Bones to Turing and Cybernetics

The Lebombo Bone and Other Ancient Mathematical Objects

  The Ishango Bone

Turing Machine Simulator
Turing Machine Simulator 2

A Turing Machine Overview

BTW, my thoughts on the recent Turing Biopic and a related news article.

"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!

1952 – “Theseus” Maze-Solving Mouse @ cyberneticzoo.com

From At&T Archives:

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Digital Library of Babel

Very cool algorithmic exploration of Borges' Library of Babel submitted by Stephen Sher (thanks!) "The Library of Babel is a place for scholars to do research, for artists and writers to seek inspiration, for anyone with curiosity or a sense of humor to reflect on the weirdness of existence - in short, it’s just like any other library. If completed, it would contain every possible combination of 1,312,000 characters, including lower case letters, space, comma, and period. Thus, it would contain every book that ever has been written, and every book that ever could be - including every play, every song, every scientific paper, every legal decision, every constitution, every piece of scripture, and so on. At present it contains all possible pages of 3200 characters, about 10^4677 books."

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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


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