May 18, 2015

DevoWorm presentation, Indiana University


Last September, I gave a presentation on the DevoWorm project to the OpenWorm group. On May 20, I will be presenting another version of this talk to the Biocomplexity Institute at Indiana University.


Here is the abstract:
The nematode C. elegans provides a unique opportunity for developmental computational biology. The relatively small and invariant number of cells in the C. elegans adult (959 in males, 1031 in hermaphrodites) provides a means to build tractable representations of the entire organism. The deterministic nature of C. elegans embryogenesis itself allows for complete cell lineages to be constructed. This affords us an opportunity to approximate developmental processes without model underspecification. The unique biology of C. elegans also enables the discovery of fundamental statistical signatures that define non-regulative (mosaic) development and cellular differentiation more broadly. As the OpenWorm bioinformatics project (http://www.openworm.org/) is an attempt to emulate the whole organism (C. elegans), DevoWorm is an attempt to emulate developmental processes that lead to the adult C. elegans. Such a meta-emulation is useful in a number of ways, from providing crucial information about development itself to providing a combinatorial source of developmental outcomes for evaluating the potential functional roles of phenotypic variation.

In this talk, we will discuss not only how emulation of C. elegans development can proceed, but also how this is relevant to a broader developmental perspective. The talk will also highlight a few examples of what can be extracted from secondary data and computational representations. One involves the extraction and characterization of uniquely informative parameters. Another is application of the differentiation tree approach for purposes of providing multi-axial resolution to the process of cell division and differentiation in mosaic development. When combined with models of development physics, our two examples could help clarify the relationships between regulative and mosaic development. These examples can be augmented through the use of both computational representation and multiple datatypes such as gene expression, microscopy, and semantic metadata. To conclude, we will consider the limitations of developmental simulations and how they can be useful heuristics for enabling better cell, molecular, and computational biology.  
References:  
Alicea, B., McGrew, S., Gordon, R., Larson, S., Warrington, T., and Watts, M.   DevoWorm: differentiation waves and computation in C. elegans embryogenesis. bioRxiv, http://dx.doi.org/10.1101/009993  
Alicea, B.   Now Announcing the DevoWorm project. Synthetic Daisies blog, June 3 (2014).http://syntheticdaisies.blogspot.com/2014/06/now-announcing-devoworm-project.html  
Szigeti, B., Gleeson, P., Vella, M., Khayrulin, S., Palyanov, A., Hokanson, J., Currie, M., Cantrelli, M., Idili, G., and Larson, S.   OpenWorm: an open-science approach to modelling Caenorhabditis elegans. Frontiers in Computational Neuroscience, 8, 137 (2014).

May 12, 2015

Social Capital Meets Social Media in the Service of Peer Review

What is the proper reward for serving as a peer reviewer? Until now, the reward has been increased social capital [1] in the academic community. Yet like everything else, social media has served to quantify and formalize these relationships.

Regardless of their potential for success [2 3], two new services have attempted to "give credit" for the act of peer reviewing. While not explicity monetary, the idea is to formalize credit for an often thankless task that is a vital part of the academic community.

The first of these services is Publons. Named after the "least publishable unit", Publons allows you to formally publish and cite your peer reviews [4]. While the most prolific reviewers seem to be doing their work purely for within-site prestige, treating peer reviews like published manuscripts is an intriguing idea. Publons is also integrated with select proprietary and open-access publishers, making the service most than merely a self-contained curiosity.


The second is Academic Karma. As with Publons, peer reviews are made to be creditable and archivable. In addition, reviewers are unbundled from specific journals, which can either be a good thing or a bad thing depending on the context. The accounting system is linked to your ORCID account (almost every University-based academic is likely to have one), which makes the crediting system portable.

UPDATE (5-19): In keeping with the theme (in an appropriately timely manner), I was mentioned in a new PLoS One feature [5] as one of many reviewers who kept PLoS One publishing for the year of 2014.

NOTES:
[1] Social capital can be defined as social benefits derived from one's social network. Units of social capital are often derived from providing public goods, gifting, or the exchange of favors. However, social capital accumulation can also be an indicator of reputation (e.g. the more social capital one holds, the greater their reputation).

For a less-than-idyllic example from an academic context, please see: Graur, D.   Payback time for referee refusal. Nature, 505, 483 (2014).

[2] Hossenfelder, S.   Publons. Backreaction blog, April 17 (2015).

[3] Saunders, N.   Academic Karma: a case study in how not to use open data. What You're Doing is Rather Desperate blog, February 19 (2015).

[4] Van Noorden, R.   The Scientist Who Get Credit for Peer Review. Nature News, October 9 (2014).

[5] PLOS ONE 2014 Reviewer Thank You. PLoS One, 10(2), e0121093 doi:10.1371/journal. pone.0121093 (2015).

April 30, 2015

Talk to UIUC Fly/Worm Club

Here is a link to the slides (short, 20 minute talk) I presented last week to the Fly/Worm Club [1] at the University of Illinois Urbana-Champaign. The talk (an evo-devo perspective on Nematode life-history) is entitled "Natural Variation, Development, and Adaptive Phenotypes in C. elegans".


[1] the Fly/Worm club is hosted by the Smith-Bolton lab in the Department of Cell and Developmental Biology, and includes people interested in flies (Drosophila) and worms (Nematodes, Planaria) from across campus. It meets occasionally.

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).

April 22, 2015

Earth Day 2015 Links

Happy Earth Day 2015, by way of Google's Doodle series.


Here are some Earth Day Doodles of years past. And here is an op-ed piece on how the transition from fossil fuels is closer than the pundits believe. Then, enjoy the pale blue dot.

Earth from a slightly different perspective. You are somewhere in "there". COURTESY: Planetary society.



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