April 25, 2015

Reading Carnival, April Edition

A new feature here on Synthetic Daisies, which features a variety of readings from blogs, the popular press, and journals of both immediate and long-term interest. This edition features six pieces ranging topically from intellectual property and data analysis to evolutionary biology and complexity theory.

Haydari, S. and Smead, R.   Does Longer Copyright Protection Help of Hurt Scientific Knowledge Creation? JASSS, 18(2), 23 (2015).

An agent-based modeling approach (featuring a type of spatial lattice called an epistemic plane) is used to better understand how copyright protections can both enable and hinder knowledge creation. The model represents knowledge creation in two ways: knowledge can either either "discovered" by agents or remain "undiscovered". Discovered knowledge can be disseminated in either a high-access (proprietary) or open-access (freely-distributable) fashion. This distributed model of scholar behavior has revealed that extended periods of intellectual property protection can act to hinder innovation. While open-access can serve the public good, there is also a role for individual incentives which are served by limited periods of proprietary protection. Whether these returns are served through monetary compensation or social capital accumulation go unexplored.

Lind, P.A., Farr, A.D., and Rainey, P.B.   Experimental evolution reveals hidden diversity in evolutionary pathways. eLife, 10.7554/eLife.07074 (2015).

By examining 28 morphs of the wrinkly spreader phenotype in Pseudomonas fluorescens (a gram-negative bacterium), the authors were able to discover a number of new pathways through which diversity is generated. These unique pathways involved unique, uncharacterized mutations that provided variation to the existing taxonomic group. As instances of parallel evolution, they provided a means to suggest a set of principles that involve changing the regulation of genes followed by a change of function for those genes.

Kiers, E.T. and West, S.A.   Evolving new organisms via symbiosis. Science, 348(6233), 392-394 (2015).

A mini-review on the evolution of symbiont species and how it may account for major transitions in the tree of life.

Dennett, D. and Roy, D.   Our Transparent Future: No secret is safe in the digital age. Scientific American, 312(3), 32-27 (2015).

This essay compares the rise of information transparency, enabled through internet technologies, to the explosion of life's complexity as it occurred during the Cambrian explosion. As a result, the practice of information-handling by individuals and organizations will change due to key innovations. These innovations are analogous to the camera-like retinas, claws, jaws, and shells that emerged amongst animals during the Cambrian. A very Rodney Brooks-esque style argument for internet-enabled (or -forced, depending on your point of view) cultural evolution.

Ellenburg, J.   The Amazing, Autotuning Sandpile. Nautil.us, 23(1) (2015).

A popular science take on the Abelian Sandpile model and its role in pattern formation. The beginning of the article presents a neccessary contrast with the domino model of causality. Unlike a linear model of system dynamics (one event leads to another with a predictable timing), the sanpile model produces nonlinear dynamics with unpredictable timing. While both models involve a simplistic physical structure, but only one produces a highly complex output. Latter portions of the article focus on geometric abstractions (cellular automata) which produce self-organizing and "life-like" behavior.

Brown, C.T.   Cultural confusions about data - the intertidal zone between two styles of biology. Living in an Ivory Basement blog, April 2 (2015).

An interesting blog post (with links and comments) on the cultural meaning of data and what constitutes useful datasets when comparing both academic fields (e.g. computational biology vs. molecular biology) and research outputs (e.g. genome sequences vs. experimental outcomes).

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