beepr

A new performance by Irene Moon uses R software programming language to make music.  As quoted from the beepr documentation: "beepr is an R package that contains one function, beep(), with one purpose: To make it easy to play notification sounds on whatever platform you are on. It is intended to be useful, for example, if you are running a long analysis in the background and want to know when it is ready."

It is ready!

Media Arts and Entomology

Notes from Nature article about Scientifically Speaking with Irene Moon was published in promotion of the upcoming WeDigBio museum curation events.  This is a reposting of that original article.

Irene Moon and NFN

The University of California Santa Barbara Cheadle Center for Biodiversity and Ecological Restoration Director has an alter ego. She goes by the name Irene Moon, and she came into being decades ago when Katja Seltmann first started creating science-inspired performance art. Some of the performances are artier, but many of them are specifically created to Perform Science!

This intersection of science and art opens up interesting ways to communicate about natural history collections and science in popular culture. Seltmann and her partner, Yon Visell, have a weekly radio show called “Unknown Territories”, a hour-long cultural arts program on the UCSB campus radio station, KCSB 91.9fm. The show airs on Monday 9-1000am PT and streams online at kcsb.org.

Several of her recordings of science inspired radio shows are available online. You can listen to interviews with researchers about various topics including rust, evolution and field recordings through the Let’s Talk Scienceseries. Recent shows are archived through the Internet Archive and found on the Unknown Territories website. Just like with the collection data she puts online, all of these recordings are all released under Creative Common licenses for reuse, or put into the Public Domain.

Natural history collections work has inspired much of the music, and Irene has several pieces for radio that are specifically about natural history collections. “Curator Bill” is a fictional character that appears throughout the radio pieces, and the audio introduction to Bill.

So next time you need perk up a boring lecture for that intro bio class, think about singing songs in a gold jacket, or create music about the topic. She has performed absurd Scientifically Speaking with Irene Moon musical lectures where collections are highlighted as the character of one of her personal heroes, EO Wilson. “Most of the lectures are done in late night musical venues, rock clubs, and raves. The information is factual, inspired by research, and people do learn when they least expect it.”

Find out more at begoniasociety.org

Check out some of her performances at the links below.

My Queen and I

Sneaky Little Sneak

EO Wilson Song

Meditation on Odonata

Beautifully Uninformative

Part of my scientific research is to evaluate and visualize large biodiversity datasets around a type of insect commonly known as Plant Bugs (Miridae). The dataset is big, comprising of around 1.5 million specimen records from Natural History collections (tcn.amnh.org).

These visualizations can easily take on a life of their own leaving their descriptive and scientific nature behind, transforming into objects of beauty and disinformation rather than clarification. The illustrations are not random nor imaginative as each of them is powered by the same dataset of Plant Bugs - where the insects were collected, their food plants, and dates of that collection event. These simply exist as an alternative representation of a highly complex natural ecosystem as we have recorded and translated into discrete pieces of information.

Histogram 1 & 2: Collecting event based on plant family with
mixed up columns and rows.

Histogram 3: Plant diversity for every
insect species. The graph is so dense many of the 
columns just appear black.

Network graphs are some of the most striking on the Web and found in publication. Outside of demonstrating that a network is complex, it is very difficult to make them visually informative but fairly easy to make them striking. This is demonstrated with Host Network Graph 1, which is the product of using only the defaults of the R igraph package.

Host Network Graph 1: Default color scheme with all nodes arranged circularly. Only a few of the most numerous edges are visible. 

Art remains interrelated with the possibility of scientific discovery or description since the dataset originates from actual ecosystem observation. Highlights of information can be found in graphs simply made for visual pleasure. The two network graphs below are an example of graphs that convey some truth about Plant Bugs and the way they function in complex ecosystems. In Host Network Graph 2, the plants that the bugs eat tend to be the nodes that have several edges coming from them like fireworks scattering. Reminiscent of constellations, the pattern indicates that many plant bugs are fairly plant food specific. In other words, plant bugs are very selective about what they eat, leading toward isolated groupings of nodes and edges.

In Host Network Graph 3, green nodes are plants eaten by Plant Bugs. The large green circle indicates that more plant bugs like to eat this plant than any other. This network graph, with its giant green node, makes it clear that plant bugs like to eat pine trees.

Host Network Graph 2: Insect and plant interaction are rather isolated.

Host Network Graph 3: A host plant network for Plant Bugs with one favorite plant.

Ontology Matters

Ontology Does Matter for Biology

Ontology Matters is the first of a series of lectures by Irene Moon introducing you to the world of modern entomological research. This piece relates recent work with an ontology (Hymenoptera Anatomy Ontology) which describes and illustrates the vast terminology we use to describe bees, wasps, and ants. Additionally, Irene explains superficially how we perform research on model organisms and describe new species in publications.

The assumption in the 'Matters' series is that people would be interested in all the gritty details of the science of Entomology; not only a superficial impression. It is not important to understand all of the complexity of a 'Matters' lecture. It is more important to begin a dialog of intrigue and mystery into the world of modern science of insects.

mx multi-entry key. a self review from a recent web publication

Recently we published an example of an MX generated multi-entry key as part of the publication and review Revision of the Oriental genera of Agathidinae (Hymenoptera, Braconidae) with an emphasis on Thailand and interactive keys to genera published in three different formats authored by Michael J. Sharkey, Dicky S. Yu, Simon van Noort, yours truly, and Lyubomir Penev. The revision was part of a series in ZooKeys reviewing multi-key creation practices, including some suggestions for publishers of open-access journals.

heres the key online.

The publication was good as a nice real world example. It highlighted some strong points in the system (multi-use matrices, auto linker to the Hymenoptera Anatomical Ontology, ability to import/export Nexus files, link to Morphbank images using Morphbank web services) and how we can expose these views as public (ie matrix view can be public [no-edit] or private [edit]). But more importantly it showed me a few things that could be done to improve it particularly in archiving the key version for future use:



1. We expose the nexus file for the key and a character list but need a format to contain all of the key annotations for export (including image and specimen data). We have character lists with image and specimen information attached for download---enough information to recreate the key. BUT best to do this how? SDD? or NeXML? or Other?

2. Also wouldn't it be grand to add a public comment section to the key itself? So while a user is working through the key they could add comments that would be archived for the key author.

3. Greater focus on images as primary language...continue to move further away from the words.

4. Encourage the use of tags. To show confidences and quality of characters.