Ideals, Varieties, and Algorithms

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The fun was out there | First Person | Johns Hopkins Magazine | Hub

Reposted The fun was out there (Johns Hopkins Magazine, Summer 2016)
For the first couple of months of freshman year, I spent my evenings breaking into buildings on campus.

Having just passed our 20th college reunion, an old friend starts spilling the beans…

Apparently the statute of limitations on college shenanigans has run out and one of my best friends has written a nice little essay about some of “our” adventures. Fortunately he has kindly left out the names of his co-conspirators, so I’ll also remain silent about who was responsible for which particular crimes. Like him, I will leave the numerous other crimes he redacted unsung.


For the first couple of months of freshman year, I spent my evenings breaking into buildings on campus. This began, naturally, because a few of us who lived in and around the Vincent-Willard dorm had mail ordered lock-picking kits, and, well, we needed something to practice on besides our own dorm rooms.

So down into the midnight bowels of Krieger we crept, sneaking deep underground into disused classrooms, mute hallways, and one strange lab whose floor was tight-knit mesh wiring with a Silence of the Lambs–esque chamber below. We touched little, took nothing (except, once, a jar of desiccant—sorry!), and were never caught.

Such was the state of fun at Johns Hopkins in the fall of 1992, an era when the administration seemed to have adopted a policy of benign neglect toward the extracurricular happiness of its undergraduate body. We had Spring Fair and the occasional bus trip to New York for the day. What more could we want?

For many—really, most—of my cutthroat classmates, this was reason to grumble. Why, they moaned from the depths of D-level, couldn’t school be more exciting? A student union, they pleaded. A bar. A café. Anything to make campus life more bearable.

But for my friends and me, the school’s DGAF attitude meant freedom: We could do whatever we wanted, on campus or off. When lock-picking grew old (quickly, I’m pleased to say), we began to roam, wandering among the half-abandoned industrial sites that lined the unreconstructed harbor, or driving (when someone happened to have a car) under the interstates that cut through and around the city. We were set loose upon Baltimore, and all we ever wanted was to go and see what there was.

Here’s what we found: A large yellow smiley face painted on the end of an oil-storage tank. The 16mm film collection at the Pratt Library. A man who claimed to have been hanging out with Mama Cass Elliot of the Mamas & the Papas the night she lost her virginity. The Baltimore Streetcar Museum. How to clear the dance floor at Club Midnite by playing the 1978 song “Fish Heads” (eat them up, yum!). The big slice at Angelo’s and the $4.95 crabcake subs at Sip & Bite. Smart drugs, Neal Stephenson, and 2600 magazine at Atomic Books. The indie movie screenings at Skizz Cyzyk’s funeral home “mansion.”

None of these alone was world-changing (okay, except maybe “Fish Heads”). Put together, though, they amounted to a constant stream of stimulation, novelty, and excitement, the discoveries that make new adulthood feel fresh and occasionally profound.

All the while, I heard the no-fun grumbling from around campus and failed to understand it. We had freedom—what more could we need? The world was all around us, begging to be explored. We didn’t even have to leave campus: One spring, my girlfriend and I simply stepped off the sidewalk next to Mudd Hall into a little dell—and discovered a stand of wild scallions. We picked a ton, brought them home, and feasted on our foraged bounty. All we’d had to do was to leave the asphalt path—no red brick in those days—behind.

Matt Gross, Johns Hopkins A&S ’96, ’98 (MA), is a food and travel writer/editor who’s worked for everyone from The New York Times and Bon Appétit to The Guardian, The Village Voice, and Saveur. He lives in Brooklyn with his wife, Jean Liu, A&S ’96, and their two daughters.

Incidentally he also had two other meaty pieces that came out yesterday as well:

Muhammad Ali Retrospective

Via @henryjameskorn: “Fortunately I spent a long time many years ago writing an entire book about “The Greatest” because today I’m not sure I’ve got the words.

Rest in peace…”

http://www.henryjameskorn.com/2016/06/04/the-greatest-of-all-time/

#muhammadali

Purple and brown sunset from the smoke out of the Calabassas fire today

Purple and brown sunset from the smoke out of the Calabassas fire today

Purple and brown sunset from the smoke out of the Calabassas fire today

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Photo taken at: Glendale, California

Feel the Bern California 2016

Almost as entertaining as the van itself, and particularly the front hood, was the entertained expressions of the passenger as I was taking photos! #bernievan

Feel the Bern California 2016

Instagram filter used: Clarendon

Photo taken at: 210 East

Webmention + Books = BookMention

Part of my plans to (remotely) devote the weekend to the IndieWeb Summit in Portland were hijacked by the passing of Muhammad Ali. Wait… What?! How does that happen?

igsyU1XmA year ago, I opened started a publishing company and we came out with our first book Amerikan Krazy in late February.  The author has a small backcatalogue that’s out of print, so in conjunction with his book launch, we’ve been slowly releasing ebook versions of his old titles. Coincidentally one of them was a fantastic little book about Ali entitled Muhammad Ali Retrospective, so I dropped everything I was doing to get it finished up and out as a quick way of honoring his passing.

But while I was working on some of the minutiae, I’ve been thinking in the back of my mind about the ideas of marginalia, commonplace books, and Amazon’s siloed community of highlights and notes. Is there a decentralized web-based way of creating a construct similar to webmention that will allow all readers worldwide to highlight, mark up and comment across electronic versions of texts so that they can share them in an open manner while still owning all of their own data? And possibly a way to aggregate them at the top for big data studies in the vein of corpus linguistics?

I think there is…

However it’ll take some effort, but effort that could have a worthwhile impact.

I have a few potential architectures in mind, but also want to keep online versions of books in the loop as well as potentially efforts like hypothes.is or even the academic portions of Genius.com which do web-based annotation.

If anyone in the IndieWeb, books, or online marginalia worlds has thought about this as well, I’d love to chat.

My Review Copy of The Big Picture by Sean Carroll

I’m already a major chunk of the way through the book, having had an early ebook version of the text prior to publication. This is the published first edition with all the diagrams which I wanted to have prior to finishing my full review, which is forthcoming.

One thing I will mention is that it’s got quite a bit more philosophy in it than most popular science books with such a physics bent. Those who aren’t already up to speed on the math and science of modern physics can certainly benefit from the book (like most popular science books of its stripe, it doesn’t have any equations — hairy or otherwise), and it’s certain to help many toward becoming members of both of C.P. Snow’s two cultures. It might not be the best place for mathematicians and physicists to start moving toward the humanities with the included philosophy as the philosophy is very light and spotty in places and the explanations of the portions they’re already aware of may put them out a bit.

I’m most interested to see how he views complexity and thinking in the final portion of the text.

More detail to come…

Bits from Brains for Biologically Inspired Computing | Computational Intelligence

Bookmarked Bits from Brains for Biologically Inspired Computing (Frontiers in Robotics and AI | Computational Intelligence journal.frontiersin.org)
Inspiration for artificial biologically inspired computing is often drawn from neural systems. This article shows how to analyze neural systems using information theory with the aim of obtaining constraints that help to identify the algorithms run by neural systems and the information they represent. Algorithms and representations identified this way may then guide the design of biologically inspired computing systems. The material covered includes the necessary introduction to information theory and to the estimation of information-theoretic quantities from neural recordings. We then show how to analyze the information encoded in a system about its environment, and also discuss recent methodological developments on the question of how much information each agent carries about the environment either uniquely or redundantly or synergistically together with others. Last, we introduce the framework of local information dynamics, where information processing is partitioned into component processes of information storage, transfer, and modification – locally in space and time. We close by discussing example applications of these measures to neural data and other complex systems.

16w5113: Stochastic and Deterministic Models for Evolutionary Biology | Banff International Research Station

Bookmarked Stochastic and Deterministic Models for Evolutionary Biology (Banff International Research Station)
A BIRS / Casa Matemática Oaxaca Workshop arriving in Oaxaca, Mexico Sunday, July 31 and departing Friday August 5, 2016

Evolutionary biology is a rapidly changing field, confronted to many societal problems of increasing importance: impact of global changes, emerging epidemics, antibiotic resistant bacteria… As a consequence, a number of new problematics have appeared over the last decade, challenging the existing mathematical models. There exists thus a demand in the biology community for new mathematical models allowing a qualitative or quantitative description of complex evolution problems. In particular, in the societal problems mentioned above, evolution is often interacting with phenomena of a different nature: interaction with other organisms, spatial dynamics, age structure, invasion processes, time/space heterogeneous environment… The development of mathematical models able to deal with those complex interactions is an ambitious task. Evolutionary biology is interested in the evolution of species. This process is a combination of several phenomena, some occurring at the individual level (e.g. mutations), others at the level of the entire population (competition for resources), often consisting of a very large number of individuals. the presence of very different scales is indeed at the core of theoretical evolutionary biology, and at the origin of many of the difficulties that biologists are facing. The development of new mathematical models thus requires a joint work of three different communities of researchers: specialists of partial differential equations, specialists of probability theory, and theoretical biologists. The goal of this workshop is to gather researchers from each of these communities, currently working on close problematics. Those communities have usually few interactions, and this meeting would give them the opportunity to discuss and work around a few biological thematics that are especially challenging mathematically, and play a crucial role for biological applications.

The role of a spatial structure in models for evolution: The introduction of a spatial structure in evolutionary biology models is often challenging. It is however well known that local adaptation is frequent in nature: field data show that the phenotypes of a given species change considerably across its range. The spatial dynamics of a population can also have a deep impact on its evolution. Assessing e.g. the impact of global changes on species requires the development of robust mathematical models for spatially structured populations.

The first type of models used by theoretical biologists for this type of problems are IBM (Individual Based Models), which describe the evolution of a finite number of individuals, characterized by their position and a phenotype. The mathematical analysis of IBM in spatially homogeneous situations has provided several methods that have been successful in the theoretical biology community (see the theory of Adaptive Dynamics). On the contrary, very few results exist so far on the qualitative properties of such models for spatially structured populations.

The second class of mathematical approach for this type of problem is based on ”infinite dimensional” reaction-diffusion: the population is structured by a continuous phenotypic trait, that affects its ability to disperse (diffusion), or to reproduce (reaction). This type of model can be obtained as a large population limit of IBM. The main difficulty of these models (in the simpler case of asexual populations) is the term modeling the competition from resources, that appears as a non local competition term. This term prevents the use of classical reaction diffusion tools such as the comparison principle and sliding methods. Recently, promising progress has been made, based on tools from elliptic equations and/or Hamilton-Jacobi equations. The effects of small populations can however not be observed on such models. The extension of these models and methods to include these effects will be discussed during the workshop.

Eco-evolution models for sexual populations:An essential question already stated by Darwin and Fisher and which stays for the moment without answer (although it continues to intrigue the evolutionary biologists) is: ”Why does sexual reproduction maintain?” Indeed this reproduction way is very costly since it implies a large number of gametes, the mating and the choice of a compatible partner. During the meiosis phasis, half of the genetical information is lost. Moreover, the males have to be fed and during the sexual mating, individual are easy preys for predators. A partial answer is that recombination plays a main role by better eliminating the deleterious mutations and by increasing the diversity. Nevertheless, this theory is not completely satisfying and many researches are devoted to understanding evolution of sexual populations and comparison between asexual and sexual reproduction. Several models exist to model the influence of sexual reproduction on evolving species. The difficulty compared to asexual populations is that a detailed description of the genetic basis of phenotypes is required, and in particular include recombinations. For sexual populations, recombination plays a main role and it is essential to understand. All models require strong biological simplifications, the development of relevant mathematical methods for such mechanisms then requires a joint work of mathematicians and biologists. This workshop will be an opportunity to set up such collaborations.

The first type of model considers a small number of diploid loci (typically one locus and two alleles), while the rest of the genome is considered as fixed. One can then define the fitness of every combination of alleles. While allowing the modeling of specific sexual effects (such as dominant/recessive alleles), this approach neglects the rest of the genome (and it is known that phenotypes are typically influenced by a large number of loci). An opposite approach is to consider a large number of loci, each locus having a small and additive impact on the considered phenotype. This approach then neglects many microscopic phenomena (epistasis, dominant/recessive alleles…), but allows the derivation of a deterministic model, called the infinitesimal model, in the case of a large population. The construction of a good mathematical framework for intermediate situation would be an important step forward.

The evolution of recombination and sex is very sensitive to the interaction between several evolutionary forces (selection, migration, genetic drift…). Modeling these interactions is particularly challenging and our understanding of the recombination evolution is often limited by strong assumptions regarding demography, the relative strength of these different evolutionary forces, the lack of spatial structure… The development of a more general theoretical framework based on new mathematical developments would be particularly valuable.

Another problem, that has received little attention so far and is worth addressing, is the modeling of the genetic material exchanges in asexual population. This phenomena is frequent in micro-organisms : horizontal gene transfers in bacteria, reassortment or recombination in viruses. These phenomena share some features with sexual reproduction. It would be interesting to see if the effect of this phenomena can be seen as a perturbation of existing asexual models. This would in particular be interesting in spatially structured populations (e.g. viral epidemics), since the the mathematical analysis of spatially structured asexual populations is improving rapidly.

Modeling in evolutionary epidemiology: Mathematical epidemiology has been developing since more than a century ago. Yet, the integration of population genetics phenomena to epidemiology is relatively recent. Microbial pathogens (bacteria and viruses) are particularly interesting organisms because their short generation times and large mutation rates allow them to adapt relatively fast to changing environments. As a consequence, ecological (demography) and evolutionary (population genetics) processes often occur at the same pace. This raises many interesting problems.

A first challenge is the modeling of the spatial dynamics of an epidemics. The parasites can evolve during the epidemics of a new host population, either to adapt to a heterogeneous environment, or because it will itself modify the environment as it invades. The applications of such studies are numerous: antibiotic management, agriculture… An aspect of this problem for which our workshop can bring a significant contribution (thanks to the diversity of its participants) is the evolution of the pathogen diversity. During the large expansion produced by an epidemics, there is a loss of diversity in the invading parasites, since most pathogens originate from a few parents. The development of mathematical models for those phenomena is challenging: only a small number of pathogens are present ahead of the epidemic front, while the number of parasites rapidly become very large after the infection. The interaction between a stochastic micro scale and a deterministic macro scale is apparent here, and deserves a rigorous mathematical analysis.

Another interesting phenomena is the effect of a sudden change of the environment on a population of pathogens. Examples of such situations are for instance the antibiotic treatment of an infected patients, or the transmission of a parasite to a new host species (transmission of the avian influenza to human beings, for instance). Related experiments are relatively easy to perform, and called evolutionary rescue experiments. So far, this question has received limited attention from the mathematical community. The key is to estimate the probability that a mutant well adapted to the new environment existed in the original population, or will appear soon after the environmental change. Interactions between biologists specialists of those questions and mathematicians should lead to new mathematical problems.

Workshop on Methods of Information Theory in Computational Neuroscience | CNS 2016

Bookmarked Workshop on Methods of Information Theory in Computational Neuroscience (CNS 2016) by Joseph T. Lizier (lizier.me)
Methods originally developed in Information Theory have found wide applicability in computational neuroscience. Beyond these original methods there is a need to develop novel tools and approaches that are driven by problems arising in neuroscience. A number of researchers in computational/systems neuroscience and in information/communication theory are investigating problems of information representation and processing. While the goals are often the same, these researchers bring different perspectives and points of view to a common set of neuroscience problems. Often they participate in different fora and their interaction is limited. The goal of the workshop is to bring some of these researchers together to discuss challenges posed by neuroscience and to exchange ideas and present their latest work. The workshop is targeted towards computational and systems neuroscientists with interest in methods of information theory as well as information/communication theorists with interest in neuroscience.