Rapid response to change driven by cross-species gene exchanges

"Gulf killifish have made a stunning comeback in Houston with the help of genetic mutations imported from interspecies mating with Atlantic killifish Scientists have suspected that mixing genes through hybridization 'can benefit populations experiencing rapid environmental change,' Clint Muhlfeld, an aquatic ecologist with the United States Geological Survey (USGS) who was not involved in the study, tells The Scientist in an email. 'But to my knowledge this is the first comprehensive study to directly and scientifically support this prediction." The paper itself is another nice example of bioinformatics methods helping understand bioloigy and new phenomena caused by human impact: "Given the limited migration of killifish, recent adaptive introgression was likely mediated by human-assisted transport. We suggest that interspecies connectivity may be an important source of adaptive variation during extreme environmental change." Full news article @ The Scientist and Original Article in Science.

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AI Uses Images and Omics to Decode Cancer

Machine learning can analyze photographs of cancer, tumor pathology slides, and genomes. Now, scientists are poised to integrate that information into cancer uber-models. Full article @ The Scientist.

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CRISPR Computer in Human Cells

A CRISPR/Cas9-based core processor that enables different sets of user-defined guide RNA inputs to program a single transcriptional regulator (dCas9-KRAB) to perform a wide range of bitwise computations, from simple Boolean logic gates to arithmetic operations such as the half adder. [...] In principle, human cells integrating multiple orthogonal CRISPR/Cas9-based core processors could offer enormous computational capacity. Full article @ PNAS

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AI, DDI, and Chat Bots

"Adapting chatbots to medicine has the potential to help millions, if not billions, of people around the world, right when they most need it. If you have a mobile phone, you have access to a doctor. Imagine the positive effect on people's lives with this equalising force. Especially in developing countries where doctors can be few and far between, or in developed countries where health care can be expensive and not immediate. Even if we can help to reduce people's anxiety about something going wrong with their body (or the body of someone in their care) until they can get to a doctor, that can be an immense relief of global suffering. Medical chatbots can offer relevant high-quality information, reassurance, answers, and ways of thinking about the situation that might be more useful. They would not replace human doctors, but they could help to set a new, increased standard of care. [...] A retrospective review in Geriatric Oncology found that 75% of [Cancer] patients had a potential drug–drug interaction. Pharmaceutial chatbots can be a resource for physicians, preventing these unintentional drug–drug interactions. Chatbots can also be useful as diagnosticians." Full article at The Lancet.

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DNA Computer executes six-bit algorithms

"A general-purpose, reprogrammable molecular computer has been constructed from DNA by a team of researchers in the US and Ireland. The system can execute different algorithms ranging from copying and sorting processes, generating random walks and executing cellular automata. It works by the self-assembly of DNA strands or ‘tiles’ into helices that form tubular structures by complementary base pairing. The emerging patterns on the tubes encode the output from the algorithm, and can be read out mechanically using an atomic force microscope (AFM) to inspect the molecular structures." News Article @ Chemical World and Full research paper @ Nature. (Thanks to Thiago Carvalho for link)

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genetic Memory can have More symbols

"The DNA of life on Earth naturally stores its information in just four key chemicals — guanine, cytosine, adenine and thymine, commonly referred to as G, C, A and T, respectively. Now scientists have doubled this number of life’s building blocks, creating for the first time a synthetic, eight-letter genetic language that seems to store and transcribe information just like natural DNA. Synthetic DNA seems to behave like the natural variety, suggesting that chemicals beyond nature’s four familiar bases could support life on Earth." Full news article @ Nature News, scientific article @ Science.

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Manfred Eigen: Steps Towards Life (and Information)

"Manfred Eigen, who shared the 1967 Nobel Prize in Chemistry for devising a method to time chemical reactions that had been thought too swift to measure, died on Feb. 6 in at his home in Göttingen, Germany. He was 91." Obituary @ NYTimes. Anyone who has taken my courses knows how much I admire his work, and has certainly seen images from his wonderful little book "Steps Towards Life"; a must for anyone interested in understanding how the concept of information is fundamental to understand life and evolution. A giant of Science.

Great interview from a series where his thinking is explored at length.

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How Alan Turing Deciphered Shark Skin

"[Turing's] theory outlined how endless varieties of stripes, spots, and scales could emerge from the interaction of two simple, hypothetical chemical agents, or 'morphogens.' Decades passed before biologists seriously considered that this mathematical theory could in fact explain myriad biological patterns. The development of mammalian hair, the feathers of birds, and even those ridges on the roof of your mouth all stem from Turing-like mechanisms." News article @ Nautilus, full research article @ Science Advances

The arrangement of denticles on a stained shark embryo (left) closely mirrors the pattern produced by researchers’ mathematical Turing model.

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Optical Neural Nets Reborn

Lin et al "have created a 3D-printed artificial neural network that uses light photons to rapidly process information." This very cool device reminds me of  Weston and Von Foerster's Numa-Rete device from the 1960s at the BCL in Urbana (which Von Foerster told me was a favorite of John Von Neumann because it could even count doughnut-shape objects without error). News article @TheScientist and paper in Science.

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The quantified heart

"In September 2017, a screenshot of a simple conversation went viral on the Russian-speaking segment of the internet. It showed the same phrase addressed to two conversational agents: the English-speaking Google Assistant, and the Russian-speaking Alisa, developed by the popular Russian search engine Yandex. The phrase was straightforward: ‘I feel sad.’ The responses to it, however, couldn’t be more different. ‘I wish I had arms so I could give you a hug,’ said Google. ‘No one said life was about having fun,’ replied Alisa." Full article @ Aeon. Thanks Thiago for link.

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Social biases in AI

The Hippocratic oath for data scientists would be a good start, though I am sure greater regulation is needed. There needs to be government agencies (NIST?) who query commercial and government AI systems with blackbox system identification techniques. They would statistically test against non-biased response distributions; If public systems fail hypothesis testing (e.g. chi-square) against fair distributions, they should be further investigated, their algorithms subpoenaed, and prosecuted if need be---same for data scientists shown to fail any future oath. See book reviews @ The New York Review of Books. (Thank you Thiago for link)

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Genetic adaptation in Humans helps deep divers

"The indigenous Bajau people (“Sea Nomads”) of Southeast Asia live a subsistence lifestyle based on breath-hold diving and are renowned for their extraordinary breath-holding abilities. However, it is unknown whether this has a genetic basis. Using a comparative genomic study, we show that natural selection on genetic variants in the PDE10A gene have increased spleen size in the Bajau, providing them with a larger reservoir of oxygenated red blood cells. We also find evidence of strong selection specific to the Bajau on BDKRB2, a gene affecting the human diving reflex. Thus, the Bajau, and possibly other diving populations, provide a new opportunity to study human adaptation to hypoxia tolerance." Full article @ Cell.

News Article from CNN: Diving deep on one breath could be in a 'sea nomad's' DNA

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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

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