PhD week 29: Fieldwork aftermath

Trotter's Gorge, northeast of Palmerston. The real thing.

We returned home from the field trip earlier than expected due to my leaving a cheap and easily replaceable, but vital item on the side of the road. It was annoying at the time, but exactly the sort of thing that I had wanted to figure out on this trip. Aside from this ignoble end, the remainder of the trip was great. We found Irenimus in most locations, sometimes in quite high numbers. We also discovered some incredible places: Trotter's Gorge in particular was amazing. It's acessability and utter lack of publicity makes its beauty especially remarkable.

Upon our return, I had insect and soil samples to label and put into appropriate storage. As I have collecting events with a measure of collecting effort (namely, time), I also started a collecting events spreadsheet that contains a lot of additional information that can't be presented on an insect label. This information will be stored electronically, linked by a collection number to the specimen which will allow the data to be associated with the specimen in the future. Among the information which is included is a geomorphological description of the collection site. It has been great to learn the basics of this rich field, and it will be fun to learn more about describing landscapes, as well as applying it.

---

Read:
   Edwards AWF. 1972. Likelihood. An account of the statistical concept of likelihood and its application to scientific inference. Cambridge University Press, Cambridge.
   Borg MJ. 2001. Reading the Bible Again for the First Time. HarperOne, New York.
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 115–118

Websites:
andywibbels.com—How to add Google Analytics to your Blogger blog
Ubuntu Forums—Preserving filenames in ImageMagick
Beginner's guide to Police harassment
Clipartist.net—Aggregating, annotating and enhancing public domain and creative commons clipart

Listened:
A Game of Thrones audiobook read by Roy Dotrice

Watched:
Sifting—Animation showing the collecting process of the LLAMA expedition
Firefly

LaTeX command with more than 9 argments

Upon my return from my field trip over the weekend, I have a number of samples to deal to, including a bunch of soil samples. With these samples, the opportunity exists to give a substantial amount more information than is possible on insect labels. Some of this information includes details of the landform and management practises of the area that the sample was collected.

To create the labels, I have enlisted the power of LaTeX (as one would probably expect). As I want the same headings on all samples, I wanted to create a command that includes all these details. However, I want more than 9 arguments, which is not allowed in general LaTeX commands. Searching for options to get around this problem, I found that it was a FAQ on the UK TeX list: How to break the 9-argument limit. Their helpful suggestion of using keyval wasn't backed up by an explicit example of how to implement it. The following code shows how to implement their example:

\usepackage{keyval}

\newcommand{\flowerinstance}[1]{\setkeys{flwr}{#1}}

\makeatletter
\define@key{flwr}{species}{\textbf{Species:} \emph{#1}\\}
\define@key{flwr}{family}{\textbf{Family:} #1\\}
\define@key{flwr}{location}{\textbf{Location:} #1\\}
\define@key{flwr}{locationtype}{\textbf{Location type:} #1\\}
\define@key{flwr}{date}{\textbf{Date:} #1\\}
\define@key{flwr}{numplants}{\textbf{Number of plants:} #1\\}
\define@key{flwr}{soiltype}{\textbf{Soil type:} #1\\}
\makeatother

\begin{document}

\flowerinstance{species=Primula veris,
family=Primulaceae,
location=Coldham's Common,
locationtype=Common grazing land,
date=1995/04/24,
numplants=50,
soiltype=alkaline
}

\end{document}

For more details regarding soil sampling which can be easily extended to other sorts of samples, see the Soil Description Handbook published by Manaaki Whenua Press.

PhD week 28: Fieldwork preparation

Trotter's Gorge, northeast of Palmerston, showing the exent of Trotter's Gorge Scenic Reserve, location of the DOC campsite, and the track.

Spring has well and truly sprung here in Canterbury, with all the attendant signs such as lambs, daffodils and flowering magnolias that look magnificent for two days before the northwesterly wind picks up and blows all the flowers off.

Spring is also the time of year that Irenimus come out in force, making it a worthwhile time to get out and about to supplement my collections with fresh specimens and anecdotal knowledge of their biology and behaviour. It's also an excellent excuse to get outside, enjoy the lovely weather, and see more of the beautiful country I live in. The intention for this trip is to get a first taste of field work and work out the systems and equipment that I will need to put in place in the future. I'm hoping to collect four species that I haven't got many specimens of, and from which I can extract DNA.

To plan the field trips, I downloaded a bunch of GIS shapefiles showing areas of interest including the locations of DOC land and tracks, as well as the Topo50 series of topographic maps showing New Zealand (which are freely available online). I viewed these using Quantum GIS, overlaying all the data of interest, and printing off maps of areas that look to be particularly worth visiting.

I've also had to amass a bunch of collecting equipment. In particular, a departure from the norm for me is the extent of soil-sampling gear that I require. Irenimus larvae live in the soil, feeding on plant roots, and I am keen to find some. For this I've been able to borrow an array of corers, augers and spades to try and determine the best method of trying to get them. More standard equipment includes beating trays for sampling shrubs and trees, and a vacuum sampler for sucking weevils out of grass and low vegetation.

---

Read:
   Edwards AWF. 1972. Likelihood. An account of the statistical concept of likelihood and its application to scientific inference. Cambridge University Press, Cambridge.
   Borg MJ. 2001. Reading the Bible Again for the First Time. HarperOne, New York.
   Psalms 111–114

Websites:
Ubuntu GIS

Listened:
Project 86—Wait for the Siren
Project 86—XV
Lutri-Kriss—Throwing Myself
John Cage—Cartridge Music
Leo Tolstoy—War and Peace Book 2 LibriVox audiobook
A Game of Thrones audiobook read by Roy Dotrice

PhD week 27: Thoughts on specimen labels

Gratuitous image: Spectacular lightning as part of the thunderstorm that passed through Canterbury on Tuesday. From seabirdnz's Flickr Photostream. Licence: CC: BY-ND

The conversion between ornamental pinned insects and valuable scientific specimens occurs with the simple act of labelling. As well as locality information, two other critical pieces of information contained on standard insect labels are the date of collection, and the collector(s) of the specimen. This combination of time, place and personality makes reading the labels on a large collection a fascinating experience.

As part of the databasing that I've been doing over the past couple of weeks, I've had many of these encounters. Some examples include: looking at insects that are over 100 years old, specimens collected on my birthday 20 years before I was born; collections made by some of the pioneers of New Zealand insect collecting—C. E. Clarke, A.E. Brookes and P.S. Sandager—and the prolific collections of the 1970s and 80s made by John Dugdale, Charles Watt and Guillermo Kuschel.

This connection with the past is one of the aspects of taxonomic research that I find extremely enriching. Working with specimens that past entomologists collected and looked at is a great experience that gives my work a sense of continuity that fairly few other fields can boast.

---

Read:
   Edwards AWF. 1972. Likelihood. An account of the statistical concept of likelihood and its application to scientific inference. Cambridge University Press, Cambridge.
   Borg MJ. 2001. Reading the Bible Again for the First Time. HarperOne, New York.
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 108–110

Websites:
New Zealand Library Catalogue
Public Domain Review—Lewis Carroll and the Hunting of the Snark
Public Domain Review—Was Charles Darwin an atheist?
PhD comics:
  What you know vs. How much you know about it
  Staring Contest
  Grad Stereogram
  The Joy of Research

Watched:
Emirates Team New Zealand takes flight
Star Trek: Voyager

ICZN allows electronic publications

Today, in a paper published in Zootaxa, the International Commission on Zoological Nomenclature announced that it had amended the International Code of Zoological Nomenclature to allow the availability of scientific names published in exclusively online publications. There are a few conditions of publication namely: 1) that the date of publication be contained within the publication and 2) that the publication be registered in ZooBank.

This announcement ends a debate that has been happening over the past several years. The issues at hand have been the tension between the obviously superior form of distribution that electronic works have, versus the known permanence of printed publications. The requirement that the work be registered is, I think, a prudent one, and one that will encourage the use and extend the utility of ZooBank.

Zoological taxonomy has entered a new and exciting era, and it will be interesting to see how the field responds and develops as a result of this decision.

Update
The announcement was published simultaneously in both Zootaxa and ZooKeys.

References:
    International Commission on Zoological Nomenclature. 2012. Amendment of Articles 8,9,10,21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication. Zootaxa 3450: 1–7.
    International Commission on Zoological Nomenclature. 2012. Amendment of Articles 8,9,10,21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication. ZooKeys 219: 1–10.

Quote: A.W.F. Edwards on Scientists and Statisticians

The perpetual sniping which statisticians suffer at the hands of practising scientists is largely due to their collective arrogance in presuming to direct the scientist in his consideration of hypotheses; the best contribution they can make is to provide some measure of 'support', and the failure of all but a few to admit the weaknesses of the conventional approaches has not improved the scientists' opinion.

Edwards AWF. 1972. Likelihood. An account of the statistical concept of likelihood and its application to scientific inference. Cambridge University Press, Cambridge. Chapter 3: Support. Page 34.