<?xml version="1.0" encoding="UTF-8"?>
 <rdf:RDF xmlns="http://purl.org/rss/1.0/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:taxo="http://purl.org/rss/1.0/modules/taxonomy/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://web.resource.org/cc/" xmlns:syn="http://purl.org/rss/1.0/modules/syndication/" xmlns:admin="http://webns.net/mvcb/">
  <channel rdf:about="http://pinboard.in">
    <title>Pinboard (Vaguery)</title>
    <link>https://pinboard.in/u:Vaguery/public/</link>
    <description>recent bookmarks from Vaguery</description>
    <items>
      <rdf:Seq>	<rdf:li rdf:resource="https://arxiv.org/abs/2103.14000"/>
	<rdf:li rdf:resource="https://unrealnature.wordpress.com/2020/11/14/utterly-absent-from-textbooks/"/>
	<rdf:li rdf:resource="https://understandingsociety.blogspot.com/2021/03/wickham-on-feudalism.html"/>
	<rdf:li rdf:resource="https://www.biorxiv.org/content/10.1101/320481v1?rss=1"/>
	<rdf:li rdf:resource="https://venturebeat.com/2020/04/29/ruha-benjamin-on-deep-learning-computational-depth-without-sociological-depth-is-superficial-learning/"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1506.04349"/>
	<rdf:li rdf:resource="http://advances.sciencemag.org/content/5/2/eaat1328"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1802.06764"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1808.05875"/>
	<rdf:li rdf:resource="http://www.mdpi.com/2073-4425/9/2/61/htm"/>
	<rdf:li rdf:resource="https://tedunderwood.com/2017/07/13/were-probably-due-for-another-discussion-of-stanley-fish/"/>
	<rdf:li rdf:resource="http://www.themathcitadel.com/2017/09/08/the-central-limit-theorem-isnt-a-statistical-silver-bullet/"/>
	<rdf:li rdf:resource="https://www.quora.com/Why-is-the-paper-%E2%80%9CUnderstanding-Deep-Learning-Requires-Rethinking-Generalization%E2%80%9D-important/answer/Eric-Jang?share=ad0453e3"/>
	<rdf:li rdf:resource="https://www.theatlantic.com/magazine/archive/2017/09/how-america-lost-its-mind/534231/"/>
	<rdf:li rdf:resource="https://www.edge.org/response-detail/27168"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1704.01565"/>
	<rdf:li rdf:resource="https://arxiv.org/abs/1507.05249"/>
	<rdf:li rdf:resource="https://radicalscholarship.wordpress.com/2016/12/08/on-education-and-credentialing-making-a-straight-cut-ditch-of-a-free-meandering-brook/"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1605.08682"/>
	<rdf:li rdf:resource="http://biorxiv.org/content/early/2016/04/25/050146?rss=1%2522"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1509.04145"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1511.00039"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1512.00268"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1510.05574"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1511.03652"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1411.6756"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1503.00687"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1502.01602"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1502.00664"/>
	<rdf:li rdf:resource="http://biorxiv.org/content/early/2015/08/04/016840"/>
	<rdf:li rdf:resource="http://hackeducation.com/2015/04/25/factory-model/"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1410.4465"/>
	<rdf:li rdf:resource="http://biorxiv.org/content/early/2014/11/10/011288"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1402.4648"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1411.0944"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1401.0207"/>
	<rdf:li rdf:resource="http://aeon.co/magazine/nature-and-cosmos/why-its-time-to-lay-the-selfish-gene-to-rest/"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1210.6156"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1211.1144"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1112.0665"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1208.3334"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1008.1846"/>
	<rdf:li rdf:resource="http://www.ssireview.org/articles/entry/measuring_social_value/"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1007.4113"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1007.3424"/>
	<rdf:li rdf:resource="http://arxiv.org/abs/1007.3964"/>
	<rdf:li rdf:resource="http://seekingalpha.com/article/207889-naive-thinking-about-sovereign-risk?source=feed"/>
	<rdf:li rdf:resource="http://zenpundit.com/?p=3348"/>
	<rdf:li rdf:resource="http://www.calculatedriskblog.com/2010/02/shadow-rental-market-pushing-down-rents.html?utm_source=feedburner&amp;utm_medium=feed&amp;utm_campaign=Feed%3A+CalculatedRisk+(Calculated+Risk)"/>
	<rdf:li rdf:resource="http://www.garyjones.org/mt/archives/001193.html"/>
	<rdf:li rdf:resource="http://www.phdcomics.com/comics/archive.php?comicid=1174"/>
      </rdf:Seq>
    </items>
  </channel><item rdf:about="https://arxiv.org/abs/2103.14000">
    <title>[2103.14000] Fairness in Ranking: A Survey</title>
    <dc:date>2022-04-19T10:28:14+00:00</dc:date>
    <link>https://arxiv.org/abs/2103.14000</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In the past few years, there has been much work on incorporating fairness requirements into algorithmic rankers, with contributions coming from the data management, algorithms, information retrieval, and recommender systems communities. In this survey we give a systematic overview of this work, offering a broad perspective that connects formalizations and algorithmic approaches across subfields. An important contribution of our work is in developing a common narrative around the value frameworks that motivate specific fairness-enhancing interventions in ranking. This allows us to unify the presentation of mitigation objectives and of algorithmic techniques to help meet those objectives or identify trade-offs.
]]></description>
<dc:subject>machine-learning fairness rather-interesting ethics it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e96c4423254a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:machine-learning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:fairness"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ethics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://unrealnature.wordpress.com/2020/11/14/utterly-absent-from-textbooks/">
    <title>Utterly Absent from Textbooks | Unreal Nature</title>
    <dc:date>2022-02-14T15:03:53+00:00</dc:date>
    <link>https://unrealnature.wordpress.com/2020/11/14/utterly-absent-from-textbooks/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[… Four gray squirrels loaf in the bright upper branches of a dead shagbark hickory tree fifty meters down slope. I watch them for an hour, and mostly they loll in the sun, limbs sprawled. They seem companionable, sporadically nibbling the fur on one another’s hind legs or tails. Occasionally one will break from sunbathing and chew the fungus-encrusted dead branches, then return to sit silently with the other squirrels.

This scene of sciurid tranquility makes me unaccountably delighted. Perhaps I so often see and hear squabbling among the squirrels that today’s ease seems particularly sweet. But something more is behind my delight; I feel freed from some burden carried by my overtrained mind. Wild animals enjoying one another and taking pleasure in their world is so immediate and so real, yet this reality is utterly absent from textbooks and academic papers about animals and ecology. There is a truth revealed here, absurd in its simplicity.

This insight is not that science is wrong or bad. On the contrary: science, done well, deepens our intimacy with the world. But there is a danger in an exclusively scientific way of thinking. The forest is turned into a diagram; animals become mere mechanisms; nature’s workings become clever graphs. Today’s conviviality of squirrels seems a refutation of such narrowness. Nature is not a machine. These animals feel. They are alive; they are our cousins, with the shared experience that kinship implies.

]]></description>
<dc:subject>scientism the-mechanistic-world natural-philosophy learning-by-watching the-mangle-in-practice it's-more-complicated-than-you-think natural-history</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:38acbf47f415/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:scientism"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:the-mechanistic-world"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:natural-philosophy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:learning-by-watching"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:the-mangle-in-practice"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:natural-history"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://understandingsociety.blogspot.com/2021/03/wickham-on-feudalism.html">
    <title>Understanding Society: Wickham on &quot;feudalism&quot;</title>
    <dc:date>2021-06-05T10:29:57+00:00</dc:date>
    <link>https://understandingsociety.blogspot.com/2021/03/wickham-on-feudalism.html</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Rather than looking for a single all-embracing concept of the "social and political system of the medieval period", Markham insists on recognizing the diversity of arrangements found throughout the period, and the parallel importance of detailed historical investigation of various sub-regions. Franks, Magyars, Bulgars, Visigoths, Vandals, Lombards, Danes, Khazars, Anglo-Saxons, and Andalusian Muslims -- the populations of various regions of Europe possessed their own histories and social arrangements, with influences flowing in all directions over time. Attempting to capture the social system of much of this map in terms of an abstract concept of "feudalism" is an error of historiography. There are commonalities across the regions and populations of the face of Europe, created by the fundamental existential circumstances of life in an environment with limited technology, communication, and travel. But the problems of material life, and the political and coercive arrangements through which groups of people were coordinated and controlled, varied across time and space. This critique can be put in terms of Weber's idea of ideal types as well (link): the concept of feudalism is an ideal type, that accentuates some features of the social order and minimizes others, in order to capture a broad social reality in a compact description. But for Wickham the historian, this attempt is wrong-headed. We do not gain anything of intellectual value by asserting that rural England, Saxony, and the territory of the Khazars were all "feudal" in their fundamental social relations. 
]]></description>
<dc:subject>political-economy history it's-more-complicated-than-you-think rather-interesting theory-and-practice-sitting-in-a-tree</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:d929c214783d/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:political-economy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:history"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theory-and-practice-sitting-in-a-tree"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.1101/320481v1?rss=1">
    <title>RNA polymerase organizes into distinct spatial clusters independent of ribosomal RNA transcription in E. coli | bioRxiv</title>
    <dc:date>2020-07-11T18:58:21+00:00</dc:date>
    <link>https://www.biorxiv.org/content/10.1101/320481v1?rss=1</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Recent studies have shown that RNA polymerase (RNAP) is spatially organized into distinct clusters in E. coli and B. subtilis cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use of membranes, which may offer new insights into pertinent functions and regulations. However, the function of RNAP clusters and whether its formation is driven by active ribosomal RNA (rRNA) transcription remain elusive. In this work, we investigated the spatial organization of RNAP in E. coli cells using quantitative superresolution imaging. We observed that RNAP formed large, distinct clusters under a rich medium growth condition and preferentially located in the center of the nucleoid. Two-color superresolution colocalization imaging showed that under the rich medium growth condition, nearly all RNAP clusters were active in synthesizing rRNA, suggesting that rRNA synthesis may be spatially separated from mRNA synthesis that most likely occurs at the nucleoid periphery. Surprisingly, a large fraction of RNAP clusters persisted under conditions in which rRNA synthesis was reduced or abolished, or when only one out of the seven rRNA operons (rrn) remained. Furthermore, when gyrase activity was inhibited, we observed a similar rRNA synthesis level, but multiple dispersed, smaller rRNA and RNAP clusters occupying not only the center but also the periphery of the nucleoid, comparable to an expanded nucleoid. These results suggested that RNAP was organized into active transcription centers for rRNA synthesis under the rich medium growth condition; their presence and spatial organization, however, were independent of rRNA synthesis activity under the conditions used but were instead influenced by the structure and characteristics of the underlying nucleoid. Our work opens the door for further investigations of the function and molecular nature of RNAP clusters and points to a potentially new mechanism of transcription regulation by the spatial organization of individual molecular components.

]]></description>
<dc:subject>cell-biology structural-biology ultrastructure supramolecular-complexes cytoskeleton but-in-bacteria??? it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:b2578693849a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cell-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:structural-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ultrastructure"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:supramolecular-complexes"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cytoskeleton"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:but-in-bacteria???"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://venturebeat.com/2020/04/29/ruha-benjamin-on-deep-learning-computational-depth-without-sociological-depth-is-superficial-learning/">
    <title>Ruha Benjamin on deep learning: Computational depth without sociological depth is 'superficial learning’ | VentureBeat</title>
    <dc:date>2020-05-02T11:13:54+00:00</dc:date>
    <link>https://venturebeat.com/2020/04/29/ruha-benjamin-on-deep-learning-computational-depth-without-sociological-depth-is-superficial-learning/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[“We should acknowledge that most people are forced to live inside someone else’s imagination, and one of the things we have to come to grips with is how the nightmares that many people are forced to endure are really the underside of elite fantasies about efficiency, profit, safety, and social control,” she said. “Racism, among other axes of domination, helps to produce this fragmented imagination, so we have misery for some and monopoly for others.”

Answering questions Tuesday in a live conversation with members of the machine learning community, Benjamin said her next book and work at the Just Data Lab will focus on matters related to race and tech during the COVID-19 global pandemic. Among recent examples at the intersection of these issues, Benjamin points to the Department of Justice’s use of a PATTERN algorithm to reduce prison populations during the pandemic. An analysis found that the algorithm is more than 4 times as likely to label white inmates low risk as black inmates.

]]></description>
<dc:subject>ethics machine-learning philosophy-of-engineering representation equality algorithms warm-data it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:dccf7b2c2ff2/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ethics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:machine-learning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-engineering"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:equality"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:algorithms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:warm-data"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1506.04349">
    <title>[1506.04349] Rare Speed-up in Automatic Theorem Proving Reveals Tradeoff Between Computational Time and Information Value</title>
    <dc:date>2019-03-02T13:05:58+00:00</dc:date>
    <link>https://arxiv.org/abs/1506.04349</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We show that strategies implemented in automatic theorem proving involve an interesting tradeoff between execution speed, proving speedup/computational time and usefulness of information. We advance formal definitions for these concepts by way of a notion of normality related to an expected (optimal) theoretical speedup when adding useful information (other theorems as axioms), as compared with actual strategies that can be effectively and efficiently implemented. We propose the existence of an ineluctable tradeoff between this normality and computational time complexity. The argument quantifies the usefulness of information in terms of (positive) speed-up. The results disclose a kind of no-free-lunch scenario and a tradeoff of a fundamental nature. The main theorem in this paper together with the numerical experiment---undertaken using two different automatic theorem provers AProS and Prover9 on random theorems of propositional logic---provide strong theoretical and empirical arguments for the fact that finding new useful information for solving a specific problem (theorem) is, in general, as hard as the problem (theorem) itself.]]></description>
<dc:subject>computer-science theorem-provers no-free-lunch performance-measure looking-to-see rather-interesting multiobjective-optimization it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:c2a1f0c0837d/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:computer-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theorem-provers"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:no-free-lunch"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:performance-measure"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:multiobjective-optimization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://advances.sciencemag.org/content/5/2/eaat1328">
    <title>Best reply structure and equilibrium convergence in generic games | Science Advances</title>
    <dc:date>2019-02-23T13:31:36+00:00</dc:date>
    <link>http://advances.sciencemag.org/content/5/2/eaat1328</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Game theory is widely used to model interacting biological and social systems. In some situations, players may converge to an equilibrium, e.g., a Nash equilibrium, but in other situations their strategic dynamics oscillate endogenously. If the system is not designed to encourage convergence, which of these two behaviors can we expect a priori? To address this question, we follow an approach that is popular in theoretical ecology to study the stability of ecosystems: We generate payoff matrices at random, subject to constraints that may represent properties of real-world games. We show that best reply cycles, basic topological structures in games, predict nonconvergence of six well-known learning algorithms that are used in biology or have support from experiments with human players. Best reply cycles are dominant in complicated and competitive games, indicating that in this case equilibrium is typically an unrealistic assumption, and one must explicitly model the dynamics of learning.
]]></description>
<dc:subject>game-theory dynamical-systems complexology it's-more-complicated-than-you-think simulation to-write-about rather-interesting nudge-targets collective-behavior</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:4297fe75f59b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:game-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:dynamical-systems"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-behavior"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1802.06764">
    <title>[1802.06764] Stability of items: an experimental test</title>
    <dc:date>2018-10-20T11:10:15+00:00</dc:date>
    <link>https://arxiv.org/abs/1802.06764</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The words of a language are randomly replaced in time by new ones, but long since it was observed that words corresponding to some items (meanings) are less frequently replaced then others. Usually, the rate of replacement for a given item is not directly observable, but it is inferred by the estimated stability which, on the contrary, is observable. This idea goes back a long way in the lexicostatistical literature, nevertheless nothing ensures that it gives the correct answer. The family of Romance languages allows for a direct test of the estimated stabilities against the replacement rates since the protolanguage (Latin) is known and the replacement rates can be explicitly computed. The output of the test is threefold: first, we prove that the standard approach which tries to infer the replacement rates trough the estimated stabilities is sound; second, we are able to rewrite the fundamental formula of Glottochronology for a non universal replacement rate (a rate which depends on the item), third, we give indisputable evidence that the stability ranking is far to be the same for different families of languages. This last result is also supported by comparison with the Malagasy family of dialects. As a side result we also provide some evidence that Vulgar Latin and not Late Classical Latin is at the root of modern Romance languages.]]></description>
<dc:subject>linguistics chronology rather-interesting simulation statistics heterogeneity it's-more-complicated-than-you-think to-write-about cladistics</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:d17322757572/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:linguistics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:chronology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:statistics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:heterogeneity"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cladistics"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1808.05875">
    <title>[1808.05875] Co-evolution of nodes and links: diversity driven coexistence in cyclic competition of three species</title>
    <dc:date>2018-08-20T11:35:14+00:00</dc:date>
    <link>https://arxiv.org/abs/1808.05875</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[When three species compete cyclically in a well-mixed, stochastic system of N individuals, extinction is known to typically occur at times scaling as the system size N. This happens, for example, in rock-paper-scissors games or conserved Lotka-Volterra models in which every pair of individuals can interact on a complete graph. Here we show that if the competing individuals also have a "social temperament" to be either introverted or extroverted, leading them to cut or add links respectively, then long-living state in which all species coexist can occur when both introverts and extroverts are present. These states are non-equilibrium quasi-steady states, maintained by a subtle balance between species competition and network dynamcis. Remarkably, much of the phenomena is embodied in a mean-field description. However, an intuitive understanding of why diversity stabilizes the co-evolving node and link dynamics remains an open issue.]]></description>
<dc:subject>coevolution theoretical-biology rather-interesting population-biology social-norms to-write-about to-simulate artificial-life it's-more-complicated-than-you-think complexology agent-based</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f60dbf50ce32/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coevolution"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:population-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:social-norms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-simulate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.mdpi.com/2073-4425/9/2/61/htm">
    <title>Genes | Free Full-Text | Another Round of “Clue” to Uncover the Mystery of Complex Traits | HTML</title>
    <dc:date>2018-02-27T12:43:44+00:00</dc:date>
    <link>http://www.mdpi.com/2073-4425/9/2/61/htm</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Abstract: A plethora of genetic association analyses have identified several genetic risk loci. Technological and statistical advancements have now led to the identification of not only common genetic variants, but also low-frequency variants, structural variants, and environmental factors, as well as multi-omics variations that affect the phenotypic variance of complex traits in a population, thus referred to as complex trait architecture. The concept of heritability, or the proportion of phenotypic variance due to genetic inheritance, has been studied for several decades, but its application is mainly in addressing the narrow sense heritability (or additive genetic component) from Genome-Wide Association Studies (GWAS). In this commentary, we reflect on our perspective on the complexity of understanding heritability for human traits in comparison to model organisms, highlighting another round of clues beyond GWAS and an alternative approach, investigating these clues comprehensively to help in elucidating the genetic architecture of complex traits.]]></description>
<dc:subject>GWAS bioinformatics medicine machine-learning epistasis it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:d478a0f637e2/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:GWAS"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:medicine"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:machine-learning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:epistasis"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://tedunderwood.com/2017/07/13/were-probably-due-for-another-discussion-of-stanley-fish/">
    <title>We’re probably due for another discussion of Stanley Fish | The Stone and the Shell</title>
    <dc:date>2017-10-08T01:49:25+00:00</dc:date>
    <link>https://tedunderwood.com/2017/07/13/were-probably-due-for-another-discussion-of-stanley-fish/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Of course, if you pursue that approach systematically enough, it will lead you away from topic modeling toward methods that rely more explicitly on human judgment. I have been leaning on supervised algorithms a lot lately—not because they’re easier to test or more reliable than unsupervised ones—but because they explicitly acknowledge that interpretation has to be anchored in human history.

At a first glance, this may seem to make progress impossible. “All we can ever discover is which books resemble these other books selected by a particular group of readers. The algorithm can only reproduce a category someone else already defined!” And yes, supervised modeling is circular. But this is a circularity shared by all interpretation of history, and it never merely reproduces its starting point. You can discover that books resemble each other to different degrees. You can discover that models defined by the responses of one interpretive community do or don’t align with models of another. And often you can, carefully, provisionally, draw explanatory inferences from the model itself, assisted perhaps by a bit of close reading.

]]></description>
<dc:subject>digital-humanities machine-learning reasonableness it's-more-complicated-than-you-think modeling philosophy criticism to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:df931316753a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:digital-humanities"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:machine-learning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:reasonableness"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:modeling"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:criticism"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.themathcitadel.com/2017/09/08/the-central-limit-theorem-isnt-a-statistical-silver-bullet/">
    <title>The Central Limit Theorem isn’t a Statistical Silver Bullet – The Math Citadel</title>
    <dc:date>2017-09-26T23:16:37+00:00</dc:date>
    <link>http://www.themathcitadel.com/2017/09/08/the-central-limit-theorem-isnt-a-statistical-silver-bullet/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Chances are, if you took anything away from that high school or college statistics class you were dragged into, you remember some vague notion about the Central Limit Theorem. It’s likely the most famous theorem in statistics, and the most widely used. Most introductory statistics textbooks state the theorem in broad terms, that as the sample size increases, the sample distribution of the sum of the sample elements will be approximately normally distributed, regardless of the underlying distribution. Many things used in statistical inference as justification in a broad variety of fields, such as the classical z-test, rely on this theorem. Many conclusions in science, economics, public policy, and social studies have been drawn with tests that rely on the Central Limit Theorem as justification. We’re going to dive into this theorem a bit more formally, and discuss some counterexamples to this theorem. Not every sequence of random variables will obey the conditions of theorem, and the assumptions are a bit more strict than are used in practice.

]]></description>
<dc:subject>probability-theory statistics it's-more-complicated-than-you-think rather-interesting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a30374553eb7/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:probability-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:statistics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://www.quora.com/Why-is-the-paper-%E2%80%9CUnderstanding-Deep-Learning-Requires-Rethinking-Generalization%E2%80%9D-important/answer/Eric-Jang?share=ad0453e3">
    <title>Eric Jang's answer to Why is the paper “Understanding Deep Learning Requires Rethinking Generalization” important? - Quora</title>
    <dc:date>2017-09-25T11:11:57+00:00</dc:date>
    <link>https://www.quora.com/Why-is-the-paper-%E2%80%9CUnderstanding-Deep-Learning-Requires-Rethinking-Generalization%E2%80%9D-important/answer/Eric-Jang?share=ad0453e3</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Succinctly, this paper is considered important because it shows that deep nets learn random datasets by memorizing them (zero generalization). This then begs the question of how it learns non-random datasets.

My own opinion on this generalization business:

It’s not altogether surprising that a high-capacity parametric model with a well-conditioned optimization objective (ReLUs, Batchnorm, high-dimensional spaces) will just soak up the input data like some kind of data sponge. I think of Deep Nets optimization objectives as an extremely “lazy” but powerful optimizer: it will discover semantically meaningful feature hierarchies if the right model biases are present and compatible with the input data, but if it isn’t convenient to optimize that solution, the network is perfectly happy to optimize in a way that just memorizes the data. Right now we just lack the means to control the degree of memorization vs. generalization, short of using blunt tools like weight norm regularization and dropout.
]]></description>
<dc:subject>deep-learning neural-networks review rather-interesting to-write-about the-mangle-in-practice it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:b5edd034dadc/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:deep-learning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:neural-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:review"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:the-mangle-in-practice"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://www.theatlantic.com/magazine/archive/2017/09/how-america-lost-its-mind/534231/">
    <title>How America Went Haywire - The Atlantic</title>
    <dc:date>2017-08-27T13:41:20+00:00</dc:date>
    <link>https://www.theatlantic.com/magazine/archive/2017/09/how-america-lost-its-mind/534231/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The great unbalancing and descent into full Fantasyland was the product of two momentous changes. The first was a profound shift in thinking that swelled up in the ’60s; since then, Americans have had a new rule written into their mental operating systems: Do your own thing, find your own reality, it’s all relative.

The second change was the onset of the new era of information. Digital technology empowers real-seeming fictions of the ideological and religious and scientific kinds. Among the web’s 1 billion sites, believers in anything and everything can find thousands of fellow fantasists, with collages of facts and “facts” to support them. Before the internet, crackpots were mostly isolated, and surely had a harder time remaining convinced of their alternate realities. Now their devoutly believed opinions are all over the airwaves and the web, just like actual news. Now all of the fantasies look real.

]]></description>
<dc:subject>cultural-dynamics politics philosophy cultural-criticism to-write-about it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f792b4dbcf93/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cultural-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:politics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cultural-criticism"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://www.edge.org/response-detail/27168">
    <title>Edge.org</title>
    <dc:date>2017-08-27T12:50:10+00:00</dc:date>
    <link>https://www.edge.org/response-detail/27168</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[This raises a problem for scientists: Coalition-mindedness makes everyone, including scientists, far stupider in coalitional collectivities than as individuals. Paradoxically, a political party united by supernatural beliefs can revise its beliefs about economics or climate without revisers being bad coalition members. But people whose coalitional membership is constituted by their shared adherence to “rational,” scientific propositions have a problem when—as is generally the case—new information arises which requires belief revision. To question or disagree with coalitional precepts, even for rational reasons, makes one a bad and immoral coalition member—at risk of losing job offers, one's friends, and one's cherished group identity. This freezes belief revision.  

Forming coalitions around scientific or factual questions is disastrous, because it pits our urge for scientific truth-seeking against the nearly insuperable human appetite to be a good coalition member. Once scientific propositions are moralized, the scientific process is wounded, often fatally.  No one is behaving either ethically or scientifically who does not make the best case possible for rival theories with which one disagrees. 

]]></description>
<dc:subject>psychology tribalism via:??? system-of-professions academic-culture rather-interesting to-write-about it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8a39544a1f13/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:psychology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:tribalism"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:via:???"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:system-of-professions"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:academic-culture"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1704.01565">
    <title>[1704.01565] Charging changes contact composition in binary sphere packings</title>
    <dc:date>2017-08-13T14:03:58+00:00</dc:date>
    <link>https://arxiv.org/abs/1704.01565</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Equal volume mixtures of small and large polytetrafluorethylene (PTFE) spheres are shaken in an atmosphere of controlled humidity which allows to also control their tribo-charging. We find that the contact numbers are charge-dependent: as the charge density of the beads increases, the number of same-type contacts decreases and the number of opposite-type contacts increases. This change is not caused by a global segregation of the sample. Hence, tribo-charging can be a way to tune the local composition of a granular material.
]]></description>
<dc:subject>packing condensed-matter looking-to-see experiment rather-interesting granular-materials to-write-about it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1bd0c0af7328/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:packing"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:condensed-matter"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:looking-to-see"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:granular-materials"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://arxiv.org/abs/1507.05249">
    <title>[1507.05249] Diversity improves performance in excitable networks</title>
    <dc:date>2017-05-09T11:37:55+00:00</dc:date>
    <link>https://arxiv.org/abs/1507.05249</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[As few real systems comprise indistinguishable units, diversity is a hallmark of nature. Diversity among interacting units shapes properties of collective behavior such as synchronization and information transmission. However, the benefits of diversity on information processing at the edge of a phase transition, ordinarily assumed to emerge from identical elements, remain largely unexplored. Analyzing a general model of excitable systems with heterogeneous excitability, we find that diversity can greatly enhance optimal performance (by two orders of magnitude) when distinguishing incoming inputs. Heterogeneous systems possess a subset of specialized elements whose capability greatly exceeds that of the nonspecialized elements. Nonetheless, the behavior of the whole network can outperform all subgroups. We also find that diversity can yield multiple percolation, with performance optimized at tricriticality. Our results are robust in specific and more realistic neuronal systems comprising a combination of excitatory and inhibitory units, and indicate that diversity-induced amplification can be harnessed by neuronal systems for evaluating stimulus intensities.
]]></description>
<dc:subject>network-theory collective-behavior physics! coupled-oscillators simulation it's-more-complicated-than-you-think to-write-about nudge-targets consider:engineering-design</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:83e12270f733/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:collective-behavior"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:physics!"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:coupled-oscillators"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:engineering-design"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="https://radicalscholarship.wordpress.com/2016/12/08/on-education-and-credentialing-making-a-straight-cut-ditch-of-a-free-meandering-brook/">
    <title>On Education and Credentialing: “Mak[ing] a Straight-cut Ditch of a Free, Meandering Brook” | the becoming radical</title>
    <dc:date>2016-12-21T12:58:42+00:00</dc:date>
    <link>https://radicalscholarship.wordpress.com/2016/12/08/on-education-and-credentialing-making-a-straight-cut-ditch-of-a-free-meandering-brook/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Education and teacher education are trapped in a very long technocratic nightmare bound to a reductive behaviorism and positivism.

These false gods are useful for control and compliance, but are in no way supportive of educating everyone in a free society.

Technocrats and bureaucrats cut straight ditches; teaching and learning are meandering brooks.

]]></description>
<dc:subject>education what-gets-measured-gets-fudged performance-measure rubrics academic-culture social-norms pedagogy it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:5e2f2d2049b7/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:education"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:what-gets-measured-gets-fudged"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:performance-measure"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rubrics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:academic-culture"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:social-norms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pedagogy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1605.08682">
    <title>[1605.08682] The Dose Makes The Cooperation</title>
    <dc:date>2016-06-28T22:35:17+00:00</dc:date>
    <link>http://arxiv.org/abs/1605.08682</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Explaining cooperation is one of the greatest challenges for basic scientific research. We proposed an agent-based model to study co-evolution of memory and cooperation. In our model, reciprocal agents with limited memory size play Prisoner's Dilemma Game iteratively. The characteristic of the environment, whether it is threatening or not, is embedded in the payoff matrix. Our findings are as follows. (i) Memory plays a critical role in the protection of cooperation. (ii) In the absence of threat, subsequent generations loose their memory and are consequently invaded by defectors. (iii) In contrast, the presence of an appropriate level of threat triggers the emergence of a self-protection mechanism for cooperation within subsequent generations. On the evolutionary level, memory size acts like an immune response of the population against aggressive defection. (iv) Even more extreme threat results again in defection. Our findings boil down to the following: The dose of the threat makes the cooperation.
]]></description>
<dc:subject>evolutionary-economics prisoners'-dilemma game-theory agent-based artificial-life it's-more-complicated-than-you-think nudge-targets consider:looking-to-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8c63c84ae2d9/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:evolutionary-economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:prisoners'-dilemma"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:game-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:artificial-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:looking-to-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://biorxiv.org/content/early/2016/04/25/050146?rss=1%2522">
    <title>Chromatin structure shapes the search process of transcription factors | bioRxiv</title>
    <dc:date>2016-05-01T11:57:47+00:00</dc:date>
    <link>http://biorxiv.org/content/early/2016/04/25/050146?rss=1%2522</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The diffusion of regulatory proteins within the nucleus plays a crucial role in the dynamics of transcriptional regulation. The standard model assumes a 3D plus 1D diffusion process: regulatory proteins either move freely in solution or slide on DNA. This model however does not considered the 3D structure of chromatin. Here we proposed a multi-scale stochastic model that integrates, for the first time, high-resolution information on chromatin structure as well as DNA-protein interactions. The dynamics of transcription factors was modeled as a slide plus jump diffusion process on a chromatin network based on pair-wise contact maps obtained from high-resolution Hi-C experiments. Our model allowed us to uncover the effects of chromatin structure on transcription factor occupancy profiles and target search times. Finally, we showed that binding sites clustered on few topological associated domains leading to a higher local concentration of transcription factors which could reflect an optimal strategy to efficiently use limited transcriptional resources.

]]></description>
<dc:subject>structural-biology molecular-design molecular-biology systems-biology bioinformatics it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f151d98280fe/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:structural-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:molecular-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:molecular-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:systems-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1509.04145">
    <title>[1509.04145] The physics of epigenetics</title>
    <dc:date>2016-02-25T11:54:51+00:00</dc:date>
    <link>http://arxiv.org/abs/1509.04145</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the daughter cells. This intriguing phenomenon is achieved by a variety of processes that have been collectively termed epigenetics: the stable and inheritable changes in gene expression patterns. This article reviews the extremely rich and exquisitely multi-scale physical mechanisms that govern the biological processes behind the initiation, spreading and inheritance of epigenetic states. These include not only the change in the molecular properties associated with the chemical modifications of DNA and histone proteins - such as methylation and acetylation - but also less conventional ones, such as the physics that governs the three-dimensional organization of the genome in cell nuclei. Strikingly, to achieve stability and heritability of epigenetic states, cells take advantage of many different physical principles, such as the universal behavior of polymers and copolymers, the general features of non-equilibrium dynamical systems, and the electrostatic and mechanical properties related to chemical modifications of DNA and histones. By putting the complex biological literature under this new light, the emerging picture is that a limited set of general physical rules play a key role in initiating, shaping and transmitting this crucial "epigenetic landscape". This new perspective not only allows to rationalize the normal cellular functions, but also helps to understand the emergence of pathological states, in which the epigenetic landscape becomes dysfunctional.
]]></description>
<dc:subject>epigenetic review biophysics supramolecular-complexes it's-more-complicated-than-you-think molecular-machinery complexology theory-and-practice-sitting-in-a-tree</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e502aa78093a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:epigenetic"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:review"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biophysics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:supramolecular-complexes"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:molecular-machinery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theory-and-practice-sitting-in-a-tree"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1511.00039">
    <title>[1511.00039] Theory of diffusion-influenced reactions in complex geometries</title>
    <dc:date>2016-02-25T11:50:53+00:00</dc:date>
    <link>http://arxiv.org/abs/1511.00039</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Chemical reactions involving diffusion of reactants and subsequent chemical fixation steps are generally termed "diffusion-influenced" (DI). Virtually all biochemical processes in living media can be counted among them, together with those occurring in an ever-growing number of emerging nano-technologies. The role of the environment's geometry (obstacles, compartmentalization) and distributed reactivity (competitive reactants, traps) is key in modulating the rate constants of DI reactions, and is therefore a prime design parameter. Yet, it is a formidable challenge to build a comprehensive theory able to describe the environment's "reactive geometry". Here we show that such a theory can be built by unfolding this many-body problem through addition theorems for special functions. Our method is powerful and general and allows one to study a given DI reaction occurring in arbitrary "reactive landscapes", made of multiple spherical boundaries of given size and reactivity. Importantly, ready-to-use analytical formulas can be derived easily in most cases.
]]></description>
<dc:subject>biophysics diffusion it's-more-complicated-than-you-think crowding nanotechnology complexology contingent-dynamics to-write-about consider:simulation</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a60a17588bef/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biophysics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:diffusion"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:crowding"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nanotechnology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:contingent-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:simulation"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1512.00268">
    <title>[1512.00268] Chromatin assortativity: integrating epigenomic data and 3D genomic structure</title>
    <dc:date>2016-02-25T11:23:58+00:00</dc:date>
    <link>http://arxiv.org/abs/1512.00268</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Background: The field of 3D chromatin interaction mapping is changing our point of view on the genome, paving the way for new insights into its organization. Network analysis is a natural and powerful way of modelling chromatin interactions. Assortativity is a network property that has been widely used in the social sciences to measure the probability of nodes with similar values of a specific feature to interact preferentially. We propose a new approach, using Chromatin feature Assortativity (ChAs), to integrate the epigenomic landscape of a specific cell type with its chromatin interaction network. Results: We use high-resolution Promoter Capture Hi-C and Hi-Cap data as well as ChIA-PET data from embryonic stem cells to generate promoter-centered interaction networks. We calculate the presence of a collection of 78 chromatin features in the chromatin fragments constituting the nodes of the network. Based on the ChAs of these epigenomic features calculated in 4 different interaction networks, we find Polycomb Group proteins and associated histone marks to play a prominent role. Remarkably, in promoter-centered networks, we observe higher ChAs of the actively elongating form of RNA Polymerase 2 compared to inactive forms in interactions between promoters and other elements. Conclusions: Contacts amongst promoters and between promoters and other elements have different characteristic epigenomic features. Using ChAs we identify a possible role of the elongating form of RNAPII in enhancer activity. Our approach facilitates the study of multiple genome-wide epigenomic profiles, considering network topology and allowing for the comparison of any number of chromatin interaction networks.
]]></description>
<dc:subject>bioinformatics structural-biology it's-more-complicated-than-you-think supramolecular-complex cell-biology molecular-machinery experiment</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:d7eadedfcdd2/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:structural-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:supramolecular-complex"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cell-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:molecular-machinery"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1510.05574">
    <title>[1510.05574] Physics of base-pairing dynamics in DNA</title>
    <dc:date>2016-02-24T12:45:28+00:00</dc:date>
    <link>http://arxiv.org/abs/1510.05574</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque- driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain degrees of freedom can be integrated out, and the quasi- static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.]]></description>
<dc:subject>biophysics Peyrard-Bishoqp-Dauxois it's-more-complicated-than-you-think bioinformatics-ain't-databases models-and-modes to-write-about</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1b0caba0bd0b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biophysics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Peyrard-Bishoqp-Dauxois"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics-ain't-databases"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:models-and-modes"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:to-write-about"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1511.03652">
    <title>[1511.03652] Linear response to leadership, effective temperature and decision making in flocks</title>
    <dc:date>2015-11-20T11:04:03+00:00</dc:date>
    <link>http://arxiv.org/abs/1511.03652</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Large collections of autonomously moving agents, such as animals or micro-organisms, are able to "flock" coherently in space even in the absence of a central control mechanism. While the direction of the flock resulting form this critical behavior is random, this can be controlled by a small subset of informed individuals acting as leaders of the group. In this article we use the Vicsek model to investigate how flocks respond to leadership and make decisions. Using numerical simulations, we demonstrate that flocks display a linear response to leadership that can be cast in the framework of the fluctuation-dissipation theorem, identifying an "effective temperature" reflecting how promptly the flock reacts to the initiative of the leaders. The linear response to leadership also holds in the presence of two groups of informed individuals with competing interests, indicating that the flock's behavioral decision is determined by both the number of leaders and their degree of influence.
]]></description>
<dc:subject>ethology swarms flocks self-organization experiment rather-interesting it's-more-complicated-than-you-think nudge-targets consider:parameter-sweep</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a62c955362e0/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ethology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:swarms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:flocks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:self-organization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:parameter-sweep"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1411.6756">
    <title>[1411.6756] Fast Algorithms for Parameterized Problems with Relaxed Disjointness Constraints</title>
    <dc:date>2015-11-04T11:27:50+00:00</dc:date>
    <link>http://arxiv.org/abs/1411.6756</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In parameterized complexity, it is a natural idea to consider different generalizations of classic problems. Usually, such generalization are obtained by introducing a "relaxation" variable, where the original problem corresponds to setting this variable to a constant value. For instance, the problem of packing sets of size at most p into a given universe generalizes the Maximum Matching problem, which is recovered by taking p=2. Most often, the complexity of the problem increases with the relaxation variable, but very recently Abasi et al. have given a surprising example of a problem --- r-Simple k-Path --- that can be solved by a randomized algorithm with running time O∗(2O(klogrr)). That is, the complexity of the problem decreases with r. In this paper we pursue further the direction sketched by Abasi et al. Our main contribution is a derandomization tool that provides a deterministic counterpart of the main technical result of Abasi et al.: the O∗(2O(klogrr)) algorithm for (r,k)-Monomial Detection, which is the problem of finding a monomial of total degree k and individual degrees at most r in a polynomial given as an arithmetic circuit. Our technique works for a large class of circuits, and in particular it can be used to derandomize the result of Abasi et al. for r-Simple k-Path. On our way to this result we introduce the notion of representative sets for multisets, which may be of independent interest. Finally, we give two more examples of problems that were already studied in the literature, where the same relaxation phenomenon happens. The first one is a natural relaxation of the Set Packing problem, where we allow the packed sets to overlap at each element at most r times. The second one is Degree Bounded Spanning Tree, where we seek for a spanning tree of the graph with a small maximum degree.]]></description>
<dc:subject>graph-theory computational-complexity it's-more-complicated-than-you-think algorithms nudge-targets generalization rather-interesting counterintuitive-means-interesting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e029a6b7c35f/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:graph-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:computational-complexity"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:algorithms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:generalization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:counterintuitive-means-interesting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1503.00687">
    <title>[1503.00687] A review of mean-shift algorithms for clustering</title>
    <dc:date>2015-09-27T12:47:05+00:00</dc:date>
    <link>http://arxiv.org/abs/1503.00687</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[A natural way to characterize the cluster structure of a dataset is by finding regions containing a high density of data. This can be done in a nonparametric way with a kernel density estimate, whose modes and hence clusters can be found using mean-shift algorithms. We describe the theory and practice behind clustering based on kernel density estimates and mean-shift algorithms. We discuss the blurring and non-blurring versions of mean-shift; theoretical results about mean-shift algorithms and Gaussian mixtures; relations with scale-space theory, spectral clustering and other algorithms; extensions to tracking, to manifold and graph data, and to manifold denoising; K-modes and Laplacian K-modes algorithms; acceleration strategies for large datasets; and applications to image segmentation, manifold denoising and multivalued regression.
]]></description>
<dc:subject>clustering review it's-more-complicated-than-you-think rather-interesting performance-measure nudge-targets detailed-narrative the-right-tool-for-the-job consider:rediscovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:87dc84d7006b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:clustering"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:review"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:performance-measure"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:detailed-narrative"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:the-right-tool-for-the-job"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:rediscovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1502.01602">
    <title>[1502.01602] Phantom cascades: The effect of hidden nodes on information diffusion</title>
    <dc:date>2015-09-18T22:22:06+00:00</dc:date>
    <link>http://arxiv.org/abs/1502.01602</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Research on information diffusion generally assumes complete knowledge of the underlying network. However, in the presence of factors such as increasing privacy awareness, restrictions on application programming interfaces (APIs) and sampling strategies, this assumption rarely holds in the real world which in turn leads to an underestimation of the size of information cascades. In this work we study the effect of hidden network structure on information diffusion processes. We characterise information cascades through activation paths traversing visible and hidden parts of the network. We quantify diffusion estimation error while varying the amount of hidden structure in five empirical and synthetic network datasets and demonstrate the effect of topological properties on this error. Finally, we suggest practical recommendations for practitioners and propose a model to predict the cascade size with minimal information regarding the underlying network.
]]></description>
<dc:subject>social-networks statistics models inference social-norms communication rather-interesting it's-more-complicated-than-you-think nudge-targets look-and-see</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f8dad810fed8/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:social-networks"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:statistics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:models"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:inference"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:social-norms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:communication"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:look-and-see"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1502.00664">
    <title>[1502.00664] Analytical description of the structure of chaos</title>
    <dc:date>2015-09-13T22:01:34+00:00</dc:date>
    <link>http://arxiv.org/abs/1502.00664</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We consider analytical formulae that describe the chaotic regions around the main periodic orbit (x=y=0) of the H\'{e}non map. Following our previous paper (Efthymiopoulos, Contopoulos, Katsanikas 2014) we introduce new variables (ξ,η) in which the product ξη=c (constant) gives hyperbolic invariant curves. These hyperbolae are mapped by a canonical transformation Φ to the plane (x,y), giving "Moser invariant curves". We find that the series Φ are convergent up to a maximum value of c=cmax. We give estimates of the errors due to the finite truncation of the series and discuss how these errors affect the applicability of analytical computations. For values of the basic parameter κ of the H\'{e}non map smaller than a critical value, there is an island of stability, around a stable periodic orbit S, containing KAM invariant curves. The Moser curves for c≤0.32 are completely outside the last KAM curve around S, the curves with 0.32<c<0.41 intersect the last KAM curve and the curves with 0.41≤c<cmax≃0.49 are completely inside the last KAM curve. All orbits in the chaotic region around the periodic orbit (x=y=0), although they seem random, belong to Moser invariant curves, which, therefore define a "structure of chaos". Orbits starting close and outside the last KAM curve remain close to it for a stickiness time that is estimated analytically using the series Φ. We finally calculate the periodic orbits that accumulate close to the homoclinic points, i.e. the points of intersection of the asymptotic curves from x=y=0, exploiting a method based on the self-intersections of the invariant Moser curves. We find that all the computed periodic orbits are generated from the stable orbit S for smaller values of the H\'{e}non parameter κ, i.e. they are all regular periodic orbits.
]]></description>
<dc:subject>rather-interesting nonlinear-dynamics chaos analytics it's-more-complicated-than-you-think nudge-targets consider:feature-discovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2ee9f1c4637b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nonlinear-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:chaos"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:analytics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:consider:feature-discovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://biorxiv.org/content/early/2015/08/04/016840">
    <title>A General Theory of Differentiated Multicellularity | bioRxiv</title>
    <dc:date>2015-09-11T23:48:10+00:00</dc:date>
    <link>http://biorxiv.org/content/early/2015/08/04/016840</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Scientists agree that changes in the levels of gene expression are important for the cell differentiation process. Research in the field has customarily assumed that such changes regulate this process when they interconnect in space and time by means of complex epigenetic mechanisms. In fundamental terms, however, this assumed regulation refers only to the intricate propagation of changes in gene expression or else leads to logical inconsistencies. The evolution and intrinsic regulatory dynamics of differentiated multicellularity also lack a unified and falsifiable description. To fill this gap, I analyzed publicly available high-throughput data of histone H3 post-translational modifications and mRNA abundance for different Homo sapiens, Mus musculus, and Drosophila melanogaster cell-type/developmental-period samples. An analysis of genomic regions adjacent to transcription start sites generated for each cell-type/developmental-period dataset a profile from pairwise partial correlations between histone modifications controlling for the respective mRNA levels. Here I report that these profiles, while explicitly uncorrelated to transcript abundance by construction, associate strongly with cell differentiation states. This association is not expected if cell differentiation is, in effect, regulated by epigenetic mechanisms. Based on these results, I propose a theory of differentiated multicellularity, which relies on the synergistic coupling across the extracellular space of two stochastically independent "self-organizing" systems constraining histone modification states at the same sites. This theory describes how the differentiated multicellular organism—understood as an intrinsic, higher-order, self-sufficient, self-repairing, self-replicating, and self-regulating constraint—emerges from proliferating undifferentiated cells. If it resists falsification, this theory will explain the intrinsic regulation of gene transcriptional changes during cell differentiation and the emergence of differentiated multicellular lineages throughout evolution.

]]></description>
<dc:subject>theoretical-biology no-really-theoretical multicellularity theories-of-life formalization it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:09eb4d008fcb/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:no-really-theoretical"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:multicellularity"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theories-of-life"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:formalization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://hackeducation.com/2015/04/25/factory-model/">
    <title>The Invented History of 'The Factory Model of Education'</title>
    <dc:date>2015-04-26T12:46:02+00:00</dc:date>
    <link>http://hackeducation.com/2015/04/25/factory-model/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[As Dorn notes, phrases like “the industrial model of education,” “the factory model of education,” and “the Prussian model of education” are used as a “rhetorical foil” in order make a particular political point – not so much to explain the history of education, as to try to shape its future.
]]></description>
<dc:subject>history education public-policy disintermediation-in-action the-unshared-narrative it's-more-complicated-than-you-think solutionism</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2493446a8f2a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:history"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:education"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:public-policy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:disintermediation-in-action"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:the-unshared-narrative"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:solutionism"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1410.4465">
    <title>[1410.4465] On the abundance of intrinsically disordered proteins in the human proteome and its relation to diseases: there is no enrichment</title>
    <dc:date>2015-03-15T20:39:42+00:00</dc:date>
    <link>http://arxiv.org/abs/1410.4465</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Intrinsically disordered proteins are fascinating the community of protein science since the last decade, at least. There is a well-established line of research that intends to reveal the crucial role played by intrinsically disordered proteins (IDPs) in the development of human diseases. The main argument is that IDPs are differentially more present in groups of disease-related proteins. In this note we compare the frequency of disorder in human proteins, both disease-related and not. The frequency of disorder is comparable in the two sub-groups of proteins. Disorder is widespread in human proteins, but it is not a specific pre-requisite of proteins involved in the development of cancer, cardiovascular diseases, diabetes and neurodegenerative diseases. A tendency of cancer-related proteins to be statistically more disordered than the rest of human proteins is confirmed.
]]></description>
<dc:subject>bioinformatics biochemistry structural-biology protein-folding Thom-LaBean's-thesis it's-more-complicated-than-you-think Oh Science.</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e941d1fa5934/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biochemistry"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:structural-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:protein-folding"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Thom-LaBean's-thesis"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Oh"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Science."/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://biorxiv.org/content/early/2014/11/10/011288">
    <title>Modes of interaction between individuals dominate the topologies of real world networks | bioRxiv</title>
    <dc:date>2014-12-28T13:20:47+00:00</dc:date>
    <link>http://biorxiv.org/content/early/2014/11/10/011288</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We find that the topologies of real world networks, such as those formed within human societies, by the Internet, or among cellular proteins, are dominated by the mode of the interactions considered among the individuals. Consequently, a major dichotomy in previously studied networks arises from modeling networks in terms of pairwise versus group tasks. The former often intrinsically give rise to scale-free, disassortative, hierarchical networks, whereas the latter often give rise to broad-scale, assortative, nonhierarchical networks. These dependencies explain contrasting observations among previous topological analyses of real world complex systems. We also observe this trend in systems with natural hierarchies, in which alternate representations of the same networks, but which capture different levels of the hierarchy, manifest these signature topological differences. For example, in both the Internet and cellular proteomes, networks of lower-level system components (routers within domains or proteins within biological processes) are assortative and nonhierarchical, whereas networks of upper-level system components (internet domains or biological processes) are disassortative and hierarchical. Our results demonstrate that network topologies of complex systems must be interpreted in light of their hierarchical natures and interaction types.

]]></description>
<dc:subject>network-theory it's-more-complicated-than-you-think theoretical-biology philosophy-of-science pattern-discovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:3c3d09dc53d3/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:theoretical-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:philosophy-of-science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pattern-discovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1402.4648">
    <title>[1402.4648] Natural statistics of binaural sounds</title>
    <dc:date>2014-12-14T13:45:04+00:00</dc:date>
    <link>http://arxiv.org/abs/1402.4648</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Binaural sound localization is usually considered a discrimination task, where interaural time (ITD) and level (ILD) disparities at pure frequency channels are utilized to identify a position of a sound source. In natural conditions binaural circuits are exposed to a stimulation by sound waves originating from multiple, often moving and overlapping sources. Therefore statistics of binaural cues depend on acoustic properties and the spatial configuration of the environment. In order to process binaural sounds efficiently, the auditory system should be adapted to naturally encountered cue distributions. Statistics of cues encountered naturally and their dependence on the physical properties of an auditory scene have not been studied before. Here, we performed binaural recordings of three auditory scenes with varying spatial properties. We have analyzed empirical cue distributions from each scene by fitting them with parametric probability density functions which allowed for an easy comparison of different scenes. Higher order statistics of binaural waveforms were analyzed by performing Independent Component Analysis (ICA) and studying properties of learned basis functions. Obtained results can be related to known neuronal mechanisms and suggest how binaural hearing can be understood in terms of adaptation to the natural signal statistics.
]]></description>
<dc:subject>it's-more-complicated-than-you-think sensory-perception biology experiment rather-interesting machine-learning nudge-targets signal-processing feature-extraction</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:a52b45b6bb8b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:sensory-perception"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:machine-learning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:signal-processing"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:feature-extraction"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1411.0944">
    <title>[1411.0944] The cost of getting local monotonicity</title>
    <dc:date>2014-11-08T12:54:55+00:00</dc:date>
    <link>http://arxiv.org/abs/1411.0944</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Manfred Holler introduced the Public Good index as a proposal to divide a public good among players. In its unnormalized version, i.e., the raw measure, it counts the number of times that a player belongs to a minimal winning coalition. Unlike the Banzhaf index, it does not count the remaining winning coalitions in which the player is crucial. Holler noticed that his index does not satisfy local monotonicity, a fact that can be seen either as a major drawback or as an advantage.
]]></description>
<dc:subject>public-policy it's-more-complicated-than-you-think trade-offs multiobjective-optimization optimization solutionism rather-interesting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e7a6661135a8/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:public-policy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:trade-offs"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:multiobjective-optimization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:optimization"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:solutionism"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rather-interesting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1401.0207">
    <title>[1401.0207] Urban Mobility Scaling: Lessons from `Little Data'</title>
    <dc:date>2014-08-09T12:04:14+00:00</dc:date>
    <link>http://arxiv.org/abs/1401.0207</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Recent mobility scaling research, using new data sources, often relies on aggregated data alone. Hence, these studies face difficulties characterizing the influence of factors such as transportation mode on mobility patterns. This paper attempts to complement this research by looking at a category-rich mobility data set. In order to shed light on the impact of categories, as a case study, we use conventionally collected German mobility data. In contrast to `check-in'-based data, our results are not biased by Euclidean distance approximations. In our analysis, we show that aggregation can hide crucial differences between trip length distributions, when subdivided by categories. For example, we see that on an urban scale (0 to ~15 km), walking, versus driving, exhibits a highly different scaling exponent, thus universality class. Moreover, mode share and trip length are responsive to day-of-week and time-of-day. For example, in Germany, although driving is relatively less frequent on Sundays than on Wednesdays, trips seem to be longer. In addition, our work may shed new light on the debate between distance-based and intervening-opportunity mechanisms affecting mobility patterns, since mode may be chosen both according to trip length and urban form.
]]></description>
<dc:subject>aggregation statistics it's-more-complicated-than-you-think models diversity experiment interesting</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:9fc92fff755b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:aggregation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:statistics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:models"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:diversity"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:experiment"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:interesting"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://aeon.co/magazine/nature-and-cosmos/why-its-time-to-lay-the-selfish-gene-to-rest/">
    <title>Why it's time to lay the selfish gene to rest – David Dobbs – Aeon</title>
    <dc:date>2013-12-14T22:45:07+00:00</dc:date>
    <link>http://aeon.co/magazine/nature-and-cosmos/why-its-time-to-lay-the-selfish-gene-to-rest/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[It’s a gorgeous story. Along with its beauty and other advantageous traits, it is amenable to maths and, at its core, wonderfully simple. It has inspired countless biologists and geneticists to plumb the gene’s wonders and do brilliant work. Unfortunately, say Wray, West-Eberhard and many others, the selfish-gene story is so focused on the gene’s singular role in natural selection that in an age when it’s ever more clear that evolution works in ways far more clever and complex than we realise, the selfish-gene model increasingly impoverishes both scientific and popular views of genetics and evolution. As both conceptual framework and metaphor, the selfish-gene has helped us see the gene as it revealed itself over the 20th century. But as a new age and new tools reveal a more complicated genome, the selfish-gene is blinding us.

]]></description>
<dc:subject>models-and-modes biology selfish-genes operational-conditioning systems-biology it's-more-complicated-than-you-think nice also-about-damned-time</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:dcaebfd561f8/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:models-and-modes"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:selfish-genes"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:operational-conditioning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:systems-biology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nice"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:also-about-damned-time"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1210.6156">
    <title>[1210.6156] Non-Ideality of a DNA Strand Displacement AND Gate Studied with a Dynamic Bonded DNA Model</title>
    <dc:date>2013-03-18T20:12:03+00:00</dc:date>
    <link>http://arxiv.org/abs/1210.6156</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement using several lengths of the toehold and the adjacent domains. DNA strands are modelled using a coarse-grained dynamic bonding model {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. We observe a complex transition path from the initial state to the final state of the AND gate. This path is strongly influenced by non-ideal effects due to transient bubbles revealing undesired toeholds and thermal melting of whole strands. We have also characterized the bound and unbound kinetics of single strands, and in particular the kinetics of the total AND operation and the three distinct distinct DNA transitions that it is based on. We observe a exponential kinetic dependence on the toehold length of the competitive displacement operation, but that the gate operation time is only weakly dependent on both the toehold and adjacent domain length. Our gate displays excellent logical fidelity in three input states, and quite poor fidelity in the fourth input state. This illustrates how non-ideality can have very selective effects on fidelity. Simulations and detailed analysis such as those presented here provide molecular insights into strand displacement computation, that can be also be expected in chemical implementations.]]></description>
<dc:subject>simulation DNA-computing engineering-design it's-more-complicated-than-you-think</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:e916d8ec558b/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:simulation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:DNA-computing"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:engineering-design"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1211.1144">
    <title>[1211.1144] Genome-wide association studies with high-dimensional phenotypes</title>
    <dc:date>2013-03-09T00:49:16+00:00</dc:date>
    <link>http://arxiv.org/abs/1211.1144</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been proposed for testing jointly all traits in a high-dimensional vector of phenotypes, with prospect of increased power to detect small effects that would be missed if tested individually. However, the methods have rarely been compared to the extent of enabling assessment of their relative merits and setting up guidelines on which method to use, and how to use it. We compare the methods on simulated data and with a real metabolomics data set comprising 137 highly correlated variables and approximately 550,000 SNPs. Applying the methods to genome-wide data with hundreds of thousands of markers inevitably requires division of the problem into manageable parts facilitating parallel processing, parts corresponding to individual genetic variants, pathways, or genes, for example. Here we utilize a straightforward formulation according to which the genome is divided into blocks of nearby correlated genetic markers, tested jointly for association with the phenotypes. This formulation is computationally feasible, reduces the number of tests, and lets the methods take advantage of combining information over several correlated variables not only on the phenotype side, but also on the genotype side. Our experiments show that canonical correlation analysis has higher power than alternative methods, while remaining computationally tractable for routine use in the GWAS setting, provided the number of samples is sufficient compared to the numbers of phenotype and genotype variables tested. Regression models with latent confounding factors show promising performance when the number of samples is small compared to the dimensionality of the data.]]></description>
<dc:subject>finally representation genetics GWAS bioinformatics it's-more-complicated-than-you-think nudge-targets measurement ontology methods-of-discovery</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:f538f40b6bf3/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:finally"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:genetics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:GWAS"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:measurement"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ontology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:methods-of-discovery"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1112.0665">
    <title>[1112.0665] Generalized Thresholding and Online Sparsity-Aware Learning in a Union of Subspaces</title>
    <dc:date>2013-03-09T00:47:31+00:00</dc:date>
    <link>http://arxiv.org/abs/1112.0665</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[This paper studies a sparse signal recovery task in time-varying (time-adaptive) environments. The contribution of the paper to sparsity-aware online learning is threefold; first, a Generalized Thresholding (GT) operator, which relates to both convex and non-convex penalty functions, is introduced. This operator embodies, in a unified way, the majority of well-known thresholding rules which promote sparsity. Second, a non-convexly constrained, sparsity-promoting, online learning scheme, namely the Adaptive Projection-based Generalized Thresholding (APGT), is developed that incorporates the GT operator with a computational complexity that scales linearly to the number of unknowns. Third, the novel family of partially quasi-nonexpansive mappings is introduced as a functional analytic tool for treating the GT operator. By building upon the rich fixed point theory, the previous class of mappings helps us, also, to establish a link between the GT operator and a union of linear subspaces; a non-convex object which lies at the heart of any sparsity promoting technique, batch or online. Based on such a functional analytic framework, a convergence analysis of the APGT is provided. Furthermore, extensive experiments suggest that the APGT exhibits competitive performance when compared to computationally more demanding alternatives, such as the sparsity-promoting Affine Projection Algorithm (APA)- and Recursive Least Squares (RLS)-based techniques.]]></description>
<dc:subject>signal-processing thresholding algorithms it's-more-complicated-than-you-think mathy statistics representation nudge-targets adaptive-control</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:8f3e7a1aa68c/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:signal-processing"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:thresholding"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:algorithms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:mathy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:statistics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:adaptive-control"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1208.3334">
    <title>[1208.3334] Computational Complexity in Electronic Structure</title>
    <dc:date>2012-08-29T11:41:11+00:00</dc:date>
    <link>http://arxiv.org/abs/1208.3334</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In quantum chemistry, the price paid by all known efficient model chemistries is either the truncation of the Hilbert space or uncontrolled approximations. Theoretical computer science suggests that these restrictions are not mere shortcomings of the algorithm designers and programmers but could stem from the inherent difficulty of simulating quantum systems. Extensions of computer science and information processing exploiting quantum mechanics has led to new ways of understanding the ultimate limitations of computational power. Interestingly, this perspective helps us understand widely used model chemistries in a new light. In this article, the fundamentals of computational complexity will be reviewed and motivated from the vantage point of chemistry. Then recent results from the computational complexity literature regarding common model chemistries including Hartree-Fock and density functional theory are discussed.]]></description>
<dc:subject>quantums modeling chemistry it's-more-complicated-than-you-think a-heuristic-old-world representation analytics</dc:subject>
<dc:source>https://pinboard.in/</dc:source>
<dc:identifier>https://pinboard.in/u:Vaguery/b:b7af9b575d07/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:quantums"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:modeling"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:chemistry"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:a-heuristic-old-world"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:representation"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:analytics"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1008.1846">
    <title>[1008.1846] An algorithmic information-theoretic approach to the behavior of financial markets</title>
    <dc:date>2010-08-15T13:08:51+00:00</dc:date>
    <link>http://arxiv.org/abs/1008.1846</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["Using frequency distributions of daily closing price sequences of several stock markets, we investigate whether the bias away from an equiprobable sequence distribution, predicted by algorithmic probability, may account for some of the deviation of financial markets from log-normal, and if so for how much of said deviation and over what sequence lengths. Our discussion might constitute a potential starting point for a further investigation of the market as a rule-based system with an 'algorithmic' component, despite its apparent randomness. The use of the theory of algorithmic complexity may supply a set of probing new tools that can be applied to the study of the market price phenomenon. Moreover, the main discussion is cast in terms of assumptions common to areas of economics consistent with an algorithmic view of the market."
]]></description>
<dc:subject>it's-more-complicated-than-you-think economics complexology information-theory Platonism</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:24b718d2dbea/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:information-theory"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:Platonism"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.ssireview.org/articles/entry/measuring_social_value/">
    <title>Measuring Social Value (August 5, 2010) | Stanford Social Innovation Review</title>
    <dc:date>2010-08-15T12:17:16+00:00</dc:date>
    <link>http://www.ssireview.org/articles/entry/measuring_social_value/</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["We started by scanning existing social value metrics, such as the ones described in the table “10 Ways to Measure Social Value” on page 41. We found hundreds of competing tools, of which foundations and NGOs generally use one set, governments another, and academics yet another. In addition to discovering this segmentation, our survey suggested two more reasons why so few metrics guide real decisions. First, most metrics assume that value is objective, and therefore discoverable through analysis. Yet as most modern economists now agree, value is not an objective fact. Instead, value emerges from the interaction of supply and demand, and ultimately reflects what people or organizations are willing to pay. Because so few of the tools reflect this, they are inevitably misaligned with an organization’s strategic and operational priorities."
]]></description>
<dc:subject>public-policy social-entrepreneurship decision-making benchmarking it's-more-complicated-than-you-think pragmatism</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:1a7609432291/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:public-policy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:social-entrepreneurship"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:decision-making"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:benchmarking"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:pragmatism"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1007.4113">
    <title>[1007.4113] Aspiring to the fittest and promotion of cooperation in the prisoner's dilemma game</title>
    <dc:date>2010-07-30T12:43:58+00:00</dc:date>
    <link>http://arxiv.org/abs/1007.4113</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["Strategy changes are an essential part of evolutionary games. Here we introduce a simple rule that, depending on the value of a single parameter $w$, influences the selection of players that are considered as potential sources of the new strategy. For positive $w$ players with high payoffs will be considered more likely, while for negative $w$ the opposite holds. Setting $w$ equal to zero returns the frequently adopted random selection of the opponent. We find that increasing the probability of adopting the strategy from the fittest player within reach, i.e. setting $w$ positive, promotes the evolution of cooperation. The robustness of this observation is tested against different levels of uncertainty in the strategy adoption process and for different interaction network. Since the evolution to widespread defection is tightly associated with cooperators having a lower fitness than defectors, the fact that positive values of $w$ facilitate cooperation is quite surprising. …"
]]></description>
<dc:subject>agent-based prisoner's-dilemma it's-more-complicated-than-you-think complexology evolutionary-economics nudge-targets</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2185a3acd4b1/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:agent-based"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:prisoner's-dilemma"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:evolutionary-economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1007.3424">
    <title>[1007.3424] Bacterial Community Reconstruction Using A Single Sequencing Reaction</title>
    <dc:date>2010-07-28T12:05:19+00:00</dc:date>
    <link>http://arxiv.org/abs/1007.3424</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. While current methods enable in-depth study of a small number of communities, a simple tool for breadth studies of bacterial population composition in a large number of samples is lacking. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. This method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of the known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture.…"
]]></description>
<dc:subject>bacteria community-assembly microbiology bioinformatics sequenomics ecology complexology datasets it's-more-complicated-than-you-think stuff-I-wish-we-had-20-years-ago-DAMMIT</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:6509886d8e75/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bacteria"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:community-assembly"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:microbiology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:sequenomics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:ecology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:complexology"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:datasets"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:stuff-I-wish-we-had-20-years-ago-DAMMIT"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://arxiv.org/abs/1007.3964">
    <title>[1007.3964] Non-hereditary maximum parsimony trees</title>
    <dc:date>2010-07-28T11:46:07+00:00</dc:date>
    <link>http://arxiv.org/abs/1007.3964</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary. The conjecture suggests that a Maximum Parsimony tree for a particular (DNA) alignment necessarily has subtrees of all possible sizes which are most parsimonious for the corresponding subalignments. We answer the conjecture affirmatively for binary alignments on five taxa but also show how to construct examples for which Maximum Parsimony trees are not hereditary. …we also show that compatible most parsimonious quartets do not have to provide a most parsimonious supertree. Last, we show that our results can be generalized to Maximum Likelihood for certain nucleotide substitution models."
]]></description>
<dc:subject>cladistics sequences bioinformatics modeling algorithms modeling-is-not-mathematics it's-more-complicated-than-you-think nudge-targets</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:2a9a8aa310b9/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:cladistics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:sequences"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bioinformatics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:modeling"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:algorithms"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:modeling-is-not-mathematics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:nudge-targets"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://seekingalpha.com/article/207889-naive-thinking-about-sovereign-risk?source=feed">
    <title>Naive Thinking About Sovereign Risk -- Seeking Alpha</title>
    <dc:date>2010-06-07T12:20:21+00:00</dc:date>
    <link>http://seekingalpha.com/article/207889-naive-thinking-about-sovereign-risk?source=feed</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["The folks at CreditSuisse have created a new figure making this point by re-ranking sovereigns according to credit risk based on this multifactor model. The upshot is that China, Germany, Switzerland, the U.S., Australia, Japan, and Canada lead the way in terms of least sovereign credit risk. Agree or disagree with the absolute levels from the model, the point stands that naive models of sovereign risk are mostly fodder for idiotic headline writers, not helpful standalone measures for assessing real risk."
]]></description>
<dc:subject>it's-more-complicated-than-you-think economics debt deficit public-policy government the-idea-of-debt-raises-the-question-of-boundaries</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:125fe6672cb2/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:debt"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:deficit"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:public-policy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:government"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:the-idea-of-debt-raises-the-question-of-boundaries"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://zenpundit.com/?p=3348">
    <title>zenpundit.com » Blog Archive » Arquilla on the New Rules of War</title>
    <dc:date>2010-02-25T23:20:11+00:00</dc:date>
    <link>http://zenpundit.com/?p=3348</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA['These developments suggest that the United States is spending huge amounts of money in ways that are actually making Americans less secure, not only against irregular insurgents, but also against smart countries building different sorts of militaries. And the problem goes well beyond weapons and other high-tech items. What’s missing most of all from the U.S. military’s arsenal is a deep understanding of networking, the loose but lively interconnection between people that creates and brings a new kind of collective intelligence, power, and purpose to bear — for good and ill…..”'
]]></description>
<dc:subject>war social-dynamics military tactics planning strategy it's-more-complicated-than-you-think network-culture network-thinking American-cultural-assumptions</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:599aa972df7a/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:war"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:social-dynamics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:military"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:tactics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:planning"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:strategy"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-culture"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:network-thinking"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:American-cultural-assumptions"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.calculatedriskblog.com/2010/02/shadow-rental-market-pushing-down-rents.html?utm_source=feedburner&amp;utm_medium=feed&amp;utm_campaign=Feed%3A+CalculatedRisk+(Calculated+Risk)">
    <title>Calculated Risk: Shadow Rental Market Pushing down Rents</title>
    <dc:date>2010-02-24T13:53:43+00:00</dc:date>
    <link>http://www.calculatedriskblog.com/2010/02/shadow-rental-market-pushing-down-rents.html?utm_source=feedburner&amp;utm_medium=feed&amp;utm_campaign=Feed%3A+CalculatedRisk+(Calculated+Risk)</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["These could be investors buying REOs for cash flow, condo "reconversions", builders changing the intent of new construction (started as condos but became rentals), flippers becoming landlords, or homeowners renting their previous homes instead of selling.

As Scott Monroe noted, this huge surge in rental supply - what he calls the "gray or shadow market" - has pushed down rents, and pushed the rental vacancy rate to record levels. Yes, people are doubling up with friends and family during the recession, and some renters are now buying again, but the main reason for the record vacancy rate is the surge in supply. Eventually many of these "gray market" rentals will be sold as homes again - keeping the existing home supply elevated for years."
]]></description>
<dc:subject>economics it's-more-complicated-than-you-think financial-crisis real-estate renting-is-not-buying rentals building supply-and-demand</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:eae50f39f8ed/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:economics"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:financial-crisis"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:real-estate"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:renting-is-not-buying"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:rentals"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:building"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:supply-and-demand"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.garyjones.org/mt/archives/001193.html">
    <title>Muck and Mystery: Bacon Butter</title>
    <dc:date>2009-06-06T19:48:14+00:00</dc:date>
    <link>http://www.garyjones.org/mt/archives/001193.html</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["All true, but it's useful to also remember that fat was a rare and valuable commodity in the day, and so was not consumed in large quantities. It also wasn't wasted. In my grandmother's kitchen it was saved after use as a cooking oil for later use. Any fat that cooked out of meats was also saved for later use. It wasn't a disposal problem, something that was difficult to compost or a threat to plumbing."
]]></description>
<dc:subject>food bad-for-you-no-more lard olives it's-more-complicated-than-you-think</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:adb39ebac58d/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:food"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:bad-for-you-no-more"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:lard"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:olives"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
<item rdf:about="http://www.phdcomics.com/comics/archive.php?comicid=1174">
    <title>PHD Comics: Science News Cycle</title>
    <dc:date>2009-05-20T12:04:21+00:00</dc:date>
    <link>http://www.phdcomics.com/comics/archive.php?comicid=1174</link>
    <dc:creator>Vaguery</dc:creator><dc:subject>science media academia communication it's-more-complicated-than-you-think</dc:subject>
<dc:identifier>https://pinboard.in/u:Vaguery/b:ab874bdbf866/</dc:identifier>
<taxo:topics><rdf:Bag>	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:science"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:media"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:academia"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:communication"/>
	<rdf:li rdf:resource="https://pinboard.in/u:Vaguery/t:it's-more-complicated-than-you-think"/>
</rdf:Bag></taxo:topics>
</item>
</rdf:RDF>