PhD week 43: Merry Christmas!

Nativity and Adoration of the Shepherds, with Irenimus. With apologies to Bartolo di Fredi.

Savior of the Nations Come

Savior of the nations, come;
Virgin's Son, here make Thy home!
Marvel now, O heav'n and earth,
That the Lord chose such a birth.

Not by human flesh and blood;
By the Spirit of our God
Was the Word of God made flesh,
Woman's offspring, pure and fresh.

Wondrous birth! O wondrous Child
Of the virgin undefiled!
Though by all the world disowned,
Still to be in heaven enthroned.

From the Father forth He came
And returneth to the same,
Captive leading death and hell
High the song of triumph swell!

Thou, the Father's only Son,
Hast o'er sin the vict'ry won.
Boundless shall Thy kingdom be;
When shall we its glories see?

Brightly doth Thy manger shine,
Glorious is its light divine.
Let not sin o'ercloud this light;
Ever be our faith thus bright.

Praise to God the Father sing,
Praise to God the Son, our King,
Praise to God the Spirit be
Ever and eternally.

Ambrose of Milan, c. 397. Translated to German by Martin Luther, 1524. Translated from German to English by William M. Reynolds, 1851. From the Open Hymnal.

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Read:
   Tolkien JRR. 1937. The Hobbit. Harper Collins, London.
   Salmond A. 2009. Aphrodite's Island. The European Discovery of Tahiti. Viking, Auckland.

Listened:
Phantom Empire—If the World Burns

Watched:
Star Trek: Deep Space Nine Season 7

PhD week 42: Winding down

Gratuitous photo: A beautiful summer day at Cook's Beach, Coromandel Peninsula.

I have a saying that I repeat ad nauseum to anyone who asks me about holidays:

As a postgraduate student, you have a choice of two ways of looking at the world: you're either ALWAYS on holiday, or you're NEVER on holiday.

This week I've been operating in the latter part of the above statement. The university officially closed on Tuesday evening, and I'm still here doing various tasks.

Strangely though, it's actually rather enjoyable. There are fewer people around, meaning less distractions and allowing me to turn up the music and sing loudly (and badly) while editing DNA sequence data. Also, the mere effort of arriving at the university means that any work done is a bonus, which makes the day immensely satisfying.

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Read:
   Psalm 147–150

Listened:
Phantom Empire—If the World Burns
August Burns Red—Sleddin' Hill: A Holiday Album

Watched:
Star Trek: Into Darkness trailer
Star Trek: Deep Space Nine Season 7
John Hinton—The Type

PhD week 41: Success

Successful COI gel. All samples worked nicely
(including the negative control, precisely because it didn't).

Last week was a good week, on two counts. First, I managed to get consistent amplification of the cytochrome c oxidase region for my weevils. As I've previously written, this has been trickier than I originally thought. In the end it came down to a very simple fix, which in hindsight I should've figured out much earlier than now. However, the relief of getting it sorted compensates for the silliness I feel that I didn't click to it earlier.

Lateral view of Irenimus parilis Pascoe

The second success of the week was finding Irenimus parilis. This was important because this species is the type species of Irenimus. This means that to be included in the genus Irenimus, species have to be similar to I. parilis. This makes it an important species to obtain DNA sequence data for. A year ago I saw a specimen collected from a market garden north of Christchurch. I managed to get in touch with the owner of the place and visited it on Thursday. There, in a uninspiring, weedy corner of the property, we managed to find three specimens of I. parilis. Valuable, not only for their DNA, but also to get an idea of their habitat and biology.

---

Read:
   Psalm 146

Watched:
The Hobbit: An Unexpected Journey
VESTAS Sailrocket 2 sails breaks 60 knot speed record
Frogs of the Marovo Lagoon, Solomon Islands
Star Trek: Deep Space Nine Season 7

PhD week 40: Societies

Not-so-gratuitous picture: Gull-billed Terns Gelochelidon nilotica.
Courtesy of Gossamer1013. Licence: CC: BY-NC-ND.

Last week, I talked about conferences being an important part of the world of science. Another major aspect is the role of scientific societies where professional scientists join together to promote and support their field of research through publishing scientific journals and hosting conferences, among others. Like every group, they require a corpus of people to ensure that everything runs smoothly. Somehow, I've managed to make my way into this esteemed circle in two of the societies that I am a member—namely as website editor for the Entomological Society of New Zealand and as newsletter editor for the Society of Australian Systematic Biologists. Neither of these roles take up copious amounts of time, but occasionally they require some action on my part. When those times do occur, it does feel a little like a distraction from the "real work" and requires a small reminder that it's all part of making the wider scientific community continue to function.

The week was ended by two very enjoyable experiences. The first was being present while a friend's song for their upcoming CD was being mixed, before watching the said friend's band perform live. The second was a sail on Lyttleton Harbour with another couple of friends on a spectacular Sunday afternoon.

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Read:
   Pine-Coffin RS (translator). 1961. The confessions of Saint Augustine Middlesex: Penguin

Websites:
Discover Magazine—The Priest-Physicist Who Would Marry Science to Religion
Kill Your Stereo—Norma Jean to tour Australia 2013

Watched:
Norma Jean—Bayonetwork (Live at Reggie's)

Loading all installed R packages

The other day I was trying to set up an R for Windows installation on a USB drive. As I don't have a Windows machine, I had to use the university computer to do this task. However, for some reason, they've blocked R from downloading and installing packages using the install.packages() command. This required that I download the zip files and manually install them. No problem with that, until packages require the installation of dependencies. To ensure that I got all the packages I needed, I wanted a function that would load all of the packages locally installed on my machine. To my surprise, I didn't find a straight-forward solution, so I came up with the following kludge:

lapply(.packages(all.available = TRUE), function(xx) library(xx,     character.only = TRUE))

There may be a more elegant way to do the above, but it worked. Elegance is occasionally overrated.

PhD week 39: Conferences

Not-so-gratuitous picture: Bats that walk—Humeri of Icarops aenae (A–E), Mystacina robusta (F–H), M. tuberculata (I–L). M–O are schematics showing the morphological features of interest.

A big part of the social aspect of scientific research are conferences. These provide opportunities for scientists to present their research, learn what their colleagues are up to and offer and accept (ideally) useful criticism of their research. They also provide the opportunity to discuss problems and ideas and form long-lasting collaborations and friendships.

Over the past week Lincoln University has hosted two conferences, the New Zealand Ecological Society Conference, and the New Zealand Molecular Ecology Conference. The scope of these conferences broadly overlap, but are very different in execution. The EcoSoc conference was a moderately large conference of around 300 people, with several sessions happening concurrently over three days, and talks by some of the big names in New Zealand ecology. The Molecular Ecology Conference was much smaller with around 40 attendees, had a strong student focus, and was held in the Wainui YMCA campground. Both were valuable conferences to attend, and I learned a lot the speakers at from formal and informal discussions.

---

Read:
   Borg MJ. 2001. Reading the Bible Again for the First Time. HarperOne, New York.

Watched:
Star Trek: Deep Space Nine Season 6

Book review: Beyond Science by John Polkinghorne

Beyond Science is a series of nine essays by John Polkinghorne that examines a range of scientific and theological topics. The chapters progress from a discussion of the nature of scientific knowledge, through the process of scientific discovery, to the mystery of the human mind. From this foundation, Polkinghorne offers an argument for a reasonable acceptance of a Creator, and how this revelation influences one's outlook on a range of social and ethical issues. I found it to be a satisfying and enjoyable read, albeit one that is unlikely to be accessible to a wide audience. The themes discussed are thought-provoking, and Polkinghorne delivers them with clarity and a gentle humour. However, their juxaposition tends not to be especially fashionable, and Polkinghorne's scholarly writing does not lend itself easily to readers outside of academia.

Japanese Journal of Systematic Entomology

I've just recently stumbled across the website for the Japanese Journal of Systematic Entomology, the new name for what was previously known as the Transactions of the Shikoku Entomological Society. I've encountered references to this journal before, but they've only recently made a home for themselves on the internet. They promise that older issues will become freely available, but it's a little early in the piece just yet. Here's hoping they're not too far away, because the contents look rather exciting!

PhD week 38: Otago Museum

Loganburn Reservoir, Otago, New Zealand

Last week I had the opportunity to visit Otago Museum. This was something of an achievement, as the museum has a reputation for being difficult to access. I had two days in their collection, looking through the weevil material primarily. I found a good number of Irenimus specimens, including some from some rather exciting and remote locations. However, it was a case of quality over quantity, with most specimens being represented by fairly small series.

While I was in Dunedin I also had the opportunity to go out collecting with a bunch of the AgResearch Invermay crew. We had a very pleasant morning up on the Rock and Pillar plateau, in the vicinity of Loganburn Reservoir. We did a combination of vacuum sampling and soil turves for extraction in the lab. It was a beautiful morning, as well as being a valuable experience for me, experiencing how AgResearch go about their sampling.

I returned from Dunedin in time to catch the big Christchurch Tango weekend, with six milongas over three days, organised by Tangovibe and La Luna. Once it was over, we worked out that we spent 16 hours dancing over the course of the weekend. An excellent way to round off an enjoyable week.

---

Read:
   Brown CG. 2010. What was the Religious Crisis of the 1960s? Journal of Religious History 34(4): 468–479

Websites:
Ubuntu Forums—Create ISO from USB drive
B & F Papers—Goatskin Parchment

Listened:
Martin GRR. A Clash of Kings audiobook read by Roy Dotrice

PhD week 37: Cup and Show Week

Not-so-gratuitous picture: The holotype of Sminthurus multidentatus Salmon 1943. Courtesy of the Museum of New Zealand Te Papa Tongarewa. License: BY-NC-ND.

This past Friday was Canterbury Provincial Anniversary day, better known as Show Day. It is the culmination of a week of festivities, including horse racing events and the Christchurch Agricultural and Pastoral (A & P) show.

All of which passed me by. I keep meaning to attend these exciting events, but each year I manage to find other things to occupy my time more pleasantly or productively. In this case it was spending Wednesday collecting weevils at Lake Coleridge, sorting out insect diets on Thursday, and spending a very enjoyable morning watching birds at Lake Ellesmere on Friday. My obligation to attend these quintessential Cantabrian events shall have to wait until next year (at least).

---

Read:
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 138

Websites:
Cowon Portable Music Players
Mozai.com—How my Mom can make DVDs

Watched:
Star Trek: Deep Space Nine Season 6

PhD week 36: Summer scholar

Not-so-gratuitous picture: Ngutuparore (Wrybill) Anarhynchus frontalis.
Courtesy of the Biodiversity Heritage Library. Licence: CC: BY-SA-NC.

This week I had the pleasure of hanging out with an enthusiastic undergraduate entomologist who will be working with me over the summer. Lincoln University offers a number of promising undergraduate students employment over the summer, allowing them to gain experience of the research environment. Together, we've worked out a little research project that will involve him attempting to rear the larvae of Irenimus on artificial diets. This is something that I have been rather keen to give a go, but have been unable to devote the time needed to do it, so it will be very interesting to see how it goes.

The first obstacle that we've got to overcome is where to get the larvae. We will be attempting to get them using two methods. The first will be to keep adults in captivity, and hope that the females will eventually lay some eggs. The second will be to get into the field and start digging. This latter task sounds like a job for next week.

---

Read:
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 135–137

Websites:
University of Otago Marine Science—Coordinate transforms
OSGeo.org Nabble Forum—NZGD2000 to NZGD49
StackExchange—Calculate area of intersecting polygons in QGIS
StackExchange—Using R to calculate area of intersecting polygons
R-sig-Geo—Merging polygons
AntKey
Pirate Science—Meaningful clusters in trees
Science Daily—World's rarest whale seen for the first time

Watched:
Star Trek: Deep Space Nine Season 6

PhD week 35: Central Otago

Top: Cecil Peak and Queenstown Hill from Coronet Peak. Bottom: Mt David from the summit of Danseys Pass.

Irenimus find their greatest diversity in the rugged landscape of Central Otago, so it was inevitable that I would spend a fair amount of time down those ways over the course of this PhD. This past week I did exactly that—seven days of collecting on the mountains and in the valleys surrounding the towns of Queenstown and Alexandra. We enjoyed beautiful weather, spectacular scenery, warm friendship, and managed to catch a few beetles in between. Everything needed for a most agreeable and memorable week.

---

Websites:
StackOverflow—How to tell lapply to ignore an error?

Watched:
Star Trek: Deep Space Nine Season 6

PhD week 34: Meetings, meetings, meetings

It was a short week, thanks to Labour Day on Monday. While it was nice to have a day off, it did make the rest of the week rather hectic. The frentic pace was not helped by my plans to be in the field all of next week. The trickiest part of the week was sorting out meetings with a number of different people. Figuring out a time that suited without interfering with plans to get some actual work done was a difficult task. However, I think I (largely) managed to do it, and had the privilege of having good talks with people on a range of subjects including website design, collecting localities in Central Otago, the need for students to understand data management, what to get a student to do over summer, and how my PhD is going.They haven't been as significant as the conference pictured above (The 1st Solvay Conference), but they've each been helpful and enjoyable in their own way.

---

Read:
   Polkinghorne J. 1996. Beyond Science. The Wider Human Context.Cambridge University Press, Cambridge
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 132–134

Websites:
Natural History Museum—Beetle Blog
Papers Past—Tour of the Hon. W. J. Hall-Jones

PhD week 33: Going long

Diagram showing the arrangement of genes in the mitochondrial genome of Drosophila yakuba. This is the typical arrangement for insects.

Mitochondria are organelles in the cell that provide energy-carrying molecules that are used in other cell functions. They do this in a manner somewhat analogous to a hydroelectric power station by creating an electrochemical gradient across a membrane, then using this gradient to power a turbine that produces the molecules. It's a place where a lot of activity is happening, and it needs a repair crew immediately on hand to keep it running. For this reason, there is a small amount of DNA inside the mitochondrion that contains the vital proteins and RNA units that are required for optimal performance.

Because there are a lot of mitochondria in each cell, mitochondrial DNA tends to be easily amplified from a range of organisms, making mitochondrial genes the regions of choice for phylogenetic analyses. One gene in particular, cytochrome c oxidase subunit 1 (COI), has been earmarked as being the gene of choice for specimen identification or DNA barcoding as it is otherwise known. For both these reasons, I am keen to use this gene in my analyses of Irenimus relationships. However, I'm finding that this is more easily said than done. It seems that entimine weevils have a lot of variation in these genes, which makes them hard to amplify. One idea that I will be trying involves trying to amplify the 5000 base pair region between the 12S gene (which is often less variable between species) and COI. A schematic is shown above.

To assist in planning this endeavour, I am able to make use of the resources available on Genbank. Genbank is a repository for DNA sequence data collected by scientists around the world. One can use this data to get an idea of where might be good places to position PCR primers, which provide the starting points for amplification. Unfortunately, there are only two complete weevil mitochondrial genomes available on Genbank—For Naupactus xanthographus and an unidentified Sphenophorus species. In addition, there are partial genomes available for 26 other species. However, these partial genomes cover everything but the region that I'm wanting to use, so are rather uninformative for my purposes. It looks like my plan going forward is just going to have to involve going in blind.

---

Read:
   Mazur MA. 2012. First record of the tribe Eugnomini Lacordaire 1863 (Coleoptera: Curculionidae) from Fiji, with description of Pactola fiji sp. n.Zootaxa 3517: 63–70
   Psalms 130–131

Websites:
Renaming files in Linux
Inkscape Manual—Patterns along paths
Wikipedia—The Planets
Half of all wetlands destroyed since 1900

PhD week 32: Steady as she goes

Royal Spoonbill Platalea regia. From igor_nz's flickr photostream. License: CC: BY-NC-SA

The PhD journey involves boldly entering new and exciting territory, and discovering new techniques and methods of analysis. It also involves doing the same thing over and over again. This past week has involved more of the latter. Dissections, databasing and communication with colleagues—this week has had all three with abundance.

The above does not mean that the week was somewhat ho-hum. On the contrary, many of the dissections I made this week were on species and genera that I have little familiarity with, and it was great seeing the results and thinking about what it all means in the greater context.

---

Read:
   Polkinghorne J. 1996. Beyond Science. The Wider Human Context.Cambridge University Press, Cambridge
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Teilhard de Chardin P. 1955. The Phenomenon of Man London: Fountain
   The Qur'an Surat 5: Al-Maaida via Zekr
   Psalms 127–129

Websites:
Boops Boops—Self publishing "failed" thesis chapters on Figshare
Ask Ubuntu: Convert PDF to image

PhD week 31: Sorting

A bench of Irenimus. A portion of the specimens available to me.

One of the tricky parts of taxonomic research is to go from a mass of unsorted specimens to a nicely curated collection of putative species. When confronted by a collection of well over 1000 specimens, this task can be somewhat intimidating.

André Larochelle and Marie-Claude Larivière in their Fauna of New Zealand volume to the ground beetle tribe Harpalini present a helpful outline of the process they took in revising the group. In summary, it goes as follows:

1. Borrow as many specimens as possible.
2. Label the borrowed specimens with their collection of origin.
3. Roughly group similar-looking specimens.
4. Within these groups, subdivide further by geography
5. Dissect a number of specimens from each of these geographic/morphological groups.
6. Identify putative species and make drawings of dissection results.
7. Make correlations between the results of the dissections and the external morphology.
8. Photograph specimens.
9. Describe the taxa
10. Compare putative species with the type specimens of previously described species.
11. Construct identification key

This list gives a handy guide to the way ahead. When broken down into jobs described above, the effort becomes somewhat less herculean.

References:
Larochelle A, Larivière M-C. 2005. Harpalini (Insecta: Coleoptera: Carabidae: Harpalinae). Fauna of New Zealand 53: 1–160

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Read:
   Polkinghorne J. 1996. Beyond Science. The Wider Human Context.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
   Teilhard de Chardin P. 1955. The Phenomenon of Man London: Fountain
   Psalms 123–127

Websites:
Ubuntu Community Help Forum—Webcams

Watched:
Star Trek: Deep Space Nine Season 6

SPIDER makes the top 10 barcoding publications of 2012

In the recent Barcode Bulletin published by iBoL, our humble paper announcing the R package spider: Species identity and evolution made second on their list of the top 10 publications of 2012. Not bad for a side project!

Spider is available for download from CRAN, and R-Forge. Be sure to check out the spider website as well for a tutorial on the use of the package.

References:
Brown SDJ, Collins RA, Boyer S, Lefort M-C, Malumbres-Olarte J, Vink CJ, Cruickshank RH. 2012. Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding.Molecular Ecology Resources 12: 562–565.

PhD week 30: Epitimetes lutosus

Epitimetes lutosus Pascoe (Coleoptera: Curculionidae: Entiminae)

The best things always happen serendipitously. Over the past week I got asked to identify some weevils that had turned up in some pitfall traps set by one of the research institutes on the Canterbury Plains. They were Epitimetes lutosus Pascoe, a weevil that was described from Christchurch and by all accounts is endemic to the plains. It is represented in national insect collections by less than 30 species, and its larvae and biology are unknown.

A jar full of Epitimetes lutosus

I was pretty excited by this find and asked for more, if they managed to get some. I got a call a few days later saying they got some others, and if I could come and pick them up. I arrived to find the container pictured above—literally hundreds of specimens from a single agricultural field. Plenty enough for pinning, dissecting, extracting DNA, and generally essentially anything else one would require specimens for!

---

Read:
   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 119–122

Websites:
Huffington Post—Reef fishes of the East Indies Book release
XKCD—Click and Drag

Listened:
Project 86—Wait for the Siren

Watched:
Firefly

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.

PhD week 26: Half a year gone

Unidentified Irenimus species.

Well... six months ago I started my PhD. It's been a busy few months, writing my proposal, visiting to insect collections around the country, and going to Arizona to attend a workshop on weevil taxonomy. Happily, everything seems to be going to plan. I feel that I'm starting to have an idea as to what morphological characters I should be looking at in order to differentiate between species. I've got a feel for what the valid, previously described species look like. And I'm close to having most of my techniques sorted.

What will the next six months look like? I'll be doing field work over the next few months, focusing on the type localities of the previously described species. This will result in a large number of specimens which I'll be able to look at morphologically, as well as providing material for DNA sequencing. Work on both these aspects will hopefully continue progressing as well as they've begun, with the common species (at least) well characterised by the end of the year. I will have to start on an identification key to the species of Irenimus, though it will only be a rough draft at this stage of the game. I may also have a student help me with some behavioural/biological research that is related but secondary to the core questions of my PhD.

I won't need to be bored!

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Read:
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 105–107

Websites:
David Winter—Code for Evolutionary Biology
OpenOffice community forum—File locked for editing
VII Southern Connection Congress
New Zealand Herald—Yachting: Only four challengers enter America's Cup

Watched:
America's Cup World Series—San Fransisco 23–26 August 2012

PhD week 25: Databasing

Gratuitous image: Bizarre oriental brentid weevils. From left to right:
Arrenodes xiphias, Calodromus mellyi female, C. mellyi male, Ceocephalus forcipatus.
Modified from BioDivLibrary's Flickr Photostream.

The raw data for taxonomic research comes from specimens—parts of individual organisms preserved and held in collections as a perpetual record. In the case of entomological taxonomy, we tend to deal with whole organisms. This is not the case for everyone. It is not particularly convenient to preserve whole whales or trees, for example. Also, because insects are small, common and don't have vertebrae, large numbers can be collected and stored. This means that I am in the fortunate position of having many hundreds of specimens to look at, which will give me an appreciation of the variation that exists within and between species. The downside is that I have many hundreds of specimens to look at and manage.

A range of data can be obtained from these specimens, including geographic coordinates, details of morphological features and DNA sequences. To manage everything, I've given each specimen a unique number which serves as a data identifier. I have a spreadsheet into which I enter the geographic and morphological data for each specimen; and the DNA sequences are stored as a FASTA formatted file.

While some might argue that a relational database may be more suited for this sort of thing, I am content with the system at present. Because the focus is on specimens, as opposed to collecting events or other aspects involving multiple specimens, the spreadsheet is suitable. Having the unique specimen number also means that it should be fairly straightforward to migrate the data into a relational database if necessary.

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Read:
Psalms 102–104

Websites:
Public Domain Review
Inkscape books
A guide to Inkscape
Geometry and Postscript

Listened:
Leo Tolstoy—War and Peace Book 2 LibriVox audiobook

Watched:
Star Trek: Deep Space Nine Season 5

PhD week 24: Back home

Gratuitous image: New Zealand weevils. From left to right:
Stephanorhynchus crassus, Ancistropterus prasinus, Rhicnobelus rubicundus, Novitas nigricans.
Modified from images on BioDivLibrary's Flickr Photostream.

As enjoyable as my Arizona trip was, it's great to be home in every way with one exception. The weather. The past week in Canterbury has consisted of cold and foggy, overcast days with very little sunshine or clear skies, and the horrible Christchurch drizzle or 'chizzle' as we've begun to call it—light rain that's accompanied by a breeze that whips it into your face and cuts through your clothing—has never been too far away. A far cry from the hot, dry, sunny days that I had started getting used to in Arizona.

Thanks to the workshop and my visit to Auckland, I've been inspired to start doing more dissections, and to try and slide-mount whole specimens of disarticulated weevils. Thus, a lot of the week was spent organising laboratory space to do such things, and ordering appropriate tools for the job. It'll be a couple of weeks before I'm able to start actually doing making slide mounts or using my fancy new tools, but I'm looking forward to it.

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Read:
   Fitzhugh K . 2006. The philosophical basis of character coding for the inference of phylogenetic hypotheses. Zoologica Scripta 261–286
   Vanin SA, Guerra TJ. 2012. A remarkable new species of flesh-fly mimicking weevil (Coleoptera: Curculionidae: Conoderinae) from Southeastern Brazil. Zootaxa 3413: 55–63
   Vanin SA, Bená DC, Albertoni FF. 2012. Description of immature stages of Phelypera shuppeli (Boheman, 1834) with comments on natural history (Coleoptera: Curculionidae: Hyperinae). Zootaxa 3423: 45–60
   Psalms 100–101

Websites:
Smithsonian guide to North American Mammals
Wikipedia—List of mammals of North America
Page ranges in awk
The Atavism—Measuring population differentiation in R

A method for subsetting FASTA files

I got back my first sequences for various Irenimus specimens this past week, and have created nice, clean contigs from the forward and reverse sequences. I've done this using FinchTV and Seaview, saving the results as a FASTA file with all of forward, reverse and consensus sequences for each specimen. Saving the data in this format has the benefit of being suitable for tracking through version control software, which means that every change I make to the file can be recalled. I'm only using one file for creating the contigs, but I'm using three gene regions, which will then need to be aligned with each other in the future. Thus, I need to have a method for subsetting my master document into smaller files with only those sequences from the same gene regions.

To do this, I have come up with a convention for naming the sequences I wish to use down the line:

>geneRegion|specimenNumber|speciesCode|otherInformation

From here, all sequences from a certain gene region can be retrieved using a little piece of awk magic. For example, all sequences from the 28S ribosomal RNA region (i.e. those starting with the line >28S|....) can be obtained by running the following code in the terminal:

awk '/>/{p=0};/>28S/{p=1} p' raw_sequences > 28S.fasta

A big thanks to backreference.org for pointing out how this might be achieved.

PhD week 23: Arizona continued

An unidentified baridine weevil from Fiji

I returned to Chirstchurch yesterday morning, after two very pleasant weeks in Arizona. One of the things that really struck me during my trip was how globalised the world is. Particularly pertinent examples include: Australian and New Zealand plants being the first things I saw when I arrived in Los Angeles; the apples we had for our lunches at the research station were from New Zealand, and looking at Fijian weevil specimens at Arizona State University.

A few of the other things that I learned in Arizona were:

• Tell a good story with your research. Encourage people to want to become more interested in the group by revealing interesting biology, morphology, distributions etc.
• Characters useful for identification may not be good for revealing relationships and vice versa
• Get some good dissecting gear. I'll be doing a lot, so I shouldn't mess around with cheap alternatives when I have the option of buying better stuff. Fine Science Tools has been recommended to me as being a supplier of quality dissecting equipment.
• Squirrels can be a lot bigger than I had realised

Overall, my time in the States was very enjoyable. I saw some amazing plants, animals and landscapes; and it was great hanging out with others who were enthusiastic and knowledgeable about beetles and the world in general. I have returned inspired and with new ideas and methods to try out. It was well worth the trip.

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Read:
   Pine-Coffin RS (translator). 1961. The confessions of Saint Augustine Middlesex: Penguin
   Psalms 90–99

Websites:
TangoArizona
Hangman in R
Manu—Birds of Polynesia

Listened:
Leo Tolstoy—War and Peace Book 2 LibriVox audiobook
Coldplay—Mylo Xyloto

Watched:
The Hunger Games
The Billy T James Show

PhD week 22: Arizona

The entrance to Cave Creek Canyon, Chiricahua Mountains, Arizona, USA.

Getting formal training in weevil systematics is rather rare. To date, most of my knowledge of weevils has been self-taught, or gleaned through discussions with other weevil people. So it happened, that when I heard that a workshop on weevil taxonomy was going to be held this month, I signed up like a shot.

Thus, I now find myself in southeastern Arizona, halfway through a week of learning about the weevil diversity of North America in the company of over 20 other keen people. These people include some of the most respected names in weevil taxonomy, the course being tutored by Bob Anderson, Nico Franz, Gregory Setliff, Anthony Cognato and Charles O'Brien. The workshop has involved a formal talks and demonstrations, field collections, and plenty of specimen identification and informal discussions about weevil biology, morphology and relationships.

The workshop is being held at the American Museum of Natural History's Southwestern Research Station, situated in the Chiricahua Mountains of Arizona. The station is surrounded by oak/juniper woodland, and all sorts of amazing plants and animals are abundant within close proximity of the station. Thus far, I have seen squirrels, rattlesnakes, deer, bombardier beetles, tarantulas, solifuges, woodpeckers, and hummingbirds, all without trying too hard.

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Read:
   Pine-Coffin RS (translator). 1961. The confessions of Saint Augustine Middlesex: Penguin
   Pratchett T. 2011. Snuff London: Corgi
   Psalms 90–95

Listened:
Rise Against—Endgame
Sufjan Stevens—The Age of Adz

Watched:
Star Trek: Deep Space Nine Season 5

PhD week 21: Farewells

Not-so-gratuitous picture: cyprinid fishes in the genus Danio from India. Courtesy of the Biodiversity Heritage Library. Licence: CC: BY-SA-NC.

It is a sad fact of the academic life that one has to be a mercenary to one extent or another. Jobs tend to be few and far between, particularly when one becomes extremely specialised in a particular field. This requires that if you're wanting to work as a scientist, you need to be willing to move to where the jobs are.

This week we farewelled two people who had done their PhDs here at Lincoln and who are starting postdoctorate positions in two very different parts of the world. One is heading to the Czech republic to study weeds, while the other is heading to Manaus in Brazil to study fish. Both have been good people to have around, and they will be missed.

Of course, one of the benefits of this diaspora is that one ends up knowing people in all sorts of places. Brazil and the Czech republic have just become that much higher on our list of places to visit sometime.

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Read:
   Morin A, Urban J, Sliz P. 2012. A quick guide to software licensing for the scientist-programmer. PLoS Computational Biology 8(7): e1002598
   Pratchett T. 2011. Snuff London: Corgi
   Psalms 86–89

Websites:
E-utilities Quick Start
Bug report on Clementine interfacing with iPods
Psychological Statistics—The aesthetics of error bars

Listened:
Leo Tolstoy—War and Peace Book 1 LibriVox audiobook
Per Landgren—Natural History: from Aristotle to Linnaeus - Influences on the Early Modern Relation between the Bible and Science
William Carrol—Creation and Contemporary Science: The Legacy of Thomas Aquinas

Watched:
Star Trek: Deep Space Nine Season 5

Systematics of South Pacific sap beetles

The species of Carpophilus of particular interest: dorsal habitus above, male parameres below.

Two and a half years ago, I completed my MSc looking at the sap beetles in the genus Carpophilus. In particular, I looked at the C. oculatus species complex from the South Pacific. The species was first described in 1864, before it settled into obscurity. It was only mentioned a few times in the literature until 1993, when Ron Dobson published the results of a study where he looked at a large series of the species. He described three subspecies, two of which were widespread and sympatric, while the third was confined to Vanuatu. Another species, C. maculatus is rather similar in appearance, to the extent that questions were being raised as to the validity of the taxon complex.

My task was to look at this group using molecular methods. In particular, I used three genes to investigate the relationships between these four taxa, and any other species of Carpophilus I could get my grubby hands on. I found that C. maculatus is indeed a distinct species from C. oculatus, and also found sufficient evidence to warrant raising the subspecies from Vanuatu to a full species. The other two subspecies, while being somewhat distinct, did not form entirely separate groups, which suggests that something interesting has happened in the genetic history of these taxa. It was a successful and enjoyable project, and I am proud to say that I completed my MSc with first class honours.

So far, so good. However, the currency of modern academia is peer-reviewed publications. The preparation of manuscripts is an arduous process, and over the past two years the one describing the aforementioned research has been languishing on various people's desks (mine, mainly). In the past month though, it been brought into the light of day and has been published in Molecular Phylogenetics and Evolution. Check it out! If you don't have access to it, feel free to email the author.

References:
Brown SDJ, Armstrong KF, Cruickshank RH. 2012. Molecular phylogenetics of a South Pacific sap beetle species complex (Carpophilus spp., Coleoptera: Nitidulidae). Molecular Phylogenetics and Evolution, 64(3), 428–440

PhD week 20: Auckland

The Auckland War Memorial Museum (top) and Landcare Research (bottom)

I spent the past week in Auckland visiting two of the major insect collections in New Zealand, namely the New Zealand Arthropod Collection (affectionately known as NZAC) housed by Landcare Research, and the Auckland Museum. Both these collections are nationally important, and a visit to these insitutions is vitally important for anyone studying the insects of New Zealand in any depth. I spent five happy days immersing myself in getting a better understanding of the genera of NZ's broad-nosed weevils and going through the unsorted Irenimus in the collections. A bigger job than it sounds! I returned to Christchurch with just short of 1000 specimens to look at over the next few years. That should keep me occupied for a decent amount of time. My time up there coincided with the arrival of Steve Davis, a fellow weevil-man who is visiting NZAC for a time. It was great meeting him, and discussing methods, characters and aspects of the New Zealand weevil fauna.

In addition to spending time doing work, I was also able to enjoy spending time with family, viewing the Wildlife Photographer of the Year Exhibition at Auckland Museum, going to a hardcore show featuring Terror and Antagonist A.D., dancing tango at Cafe Limon, and having dinner at Father Ted's Irish Bar with Steve. A good balance, methinks.

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Read:
   Pratchett T. 2011. Snuff. London: Corgi
   Psalms 81–85

PhD week 19: Dissections

Image of Rhabdoscelus obscurus male genitalia, from Sharp and Muir (1912). Courtesy of the Biodiversity Heritage Library. Licence: CC: BY-SA-NC.

As part of the process of undergoing a taxonomic revision of an insect group, it is important to consider the internal anatomy of the organisms in question. In particular, characteristics of the male genitalia are especially useful for differentiating between species, and for ascertaining relationships between species. For an example of how differences in genitalia can be more obvious than external characters, check out the beautiful leaf beetles Spilopyra sterlingi and S. sumptuosa (compare figures 5 vs 6 and 82 vs 84).

One of the pioneers who investigated insect genitalia in a taxonomic context was David Sharp, who in conjunction with his son-in-law Frederick Muir, published a nearly 200 page monograph that spanned the breadth of beetle diversity. It took several decades for the technique to take hold, but these days, if you have a look at any of the insect taxonomy papers in Zootaxa or Zookeys, it is likely that you will find that these characters have been used in that research. The problem with the technique is that is holds no relevance to readers who are not familiar with the taxon, but for those who are these drawings are frequently the most useful part of the paper.

The process of insect dissection is fairly straightforward—soften the insect, remove the abdomen, open it up to reveal the structures of interest, and then tease them out. Doing it on a creature that is around 3 mm can be a bit challenging. Like everything, the process is fairly intimidating at first but as one becomes more comfortable and skillful at the technique, it quickly becomes a simple routine that is done rapidly and easily. Of course, once the data is collected, it then has to be interpreted! However, that is a story for another time.

References:
Reid CAM, Beatson M. 2010. Revision of the Australo-Papuan genus Spilopyra Baly (Coleoptera: Chrysomelidae: Spilopyrinae). Zootaxa 2692: 1–32
Sharp D, Muir F. 1912. The comparative anatomy of the male genital tube in Coleoptera. Transactions of the Entomological Society of London (3) 477–642

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Read:
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 77–80

Websites:
Fitting models to discrete characters
Wikipedia—Vernier scale
Wikipedia—Gloria Patri
Systematics and Biogeography— the blog of David Williams and Malte Ebach

Watched:
Star Trek: Deep Space Nine Season 4

PhD week 18: Sickness and admin stuff

Gratuitous picture: illustrations of paussine beetles from the
Biodiversity Heritage Library Flickr Photostream. License: CC: BY-SA-NC

The start of this week was disrupted by both me and my wife being somewhat ill. Thus, Monday and Tuesday was spent at home, convalescing over multiple hot drinks, keeping warm, generally trying to keep each other's spirits up, and watching far too much trashy TV. Started coming back into work on Wednesday, but didn't really manage to get much momentum, instead spending time doing various administration-type things. I did manage to spend some time in the collection this afternoon, which was useful for clarifying some ideas about morphological characters, but in terms of hard-core research, unfortunately that's been it for this week.

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Read:
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 73–76

Websites:
CERN press release regarding the Higg's boson
Rule of St Benedict
Wikipedia—Andrei Rublev, Iconographer
Commentary on Rublev's Icon of the Trinity

Listened:
A Game of Thrones audiobook read by Roy Dotrice

Watched:
PhD comics—The Higgs Boson explained
Evolution according to Prometheus
Planet Dinosaur
Star Trek: Deep Space Nine Season 4

PhD week 17: A tutorial on shading curves in Inkscape

As part of my research, I will need to illustrate anatomical structures that are useful for the identification of the weevils that I will be working with. I intend to use a combination of photographs and line drawings, using the different formats in different situations. Photos will be used in some instances (i.e. habitus images) to give a realistic idea of what the creatures look like. In some cases though, photographs give too much information, and line drawings are the way to go. To create my line drawings, I will be using the free and open-source vector graphics program Inkscape.

As the structures I will be working with are 3-dimensional, I want to convey that (to a degree) in my illustrations. Traditional line drawings would depict this by using the method of stippling. If this is replicated in Inkscape, the resulting file becomes massive and unwieldly, due to the huge number of dots that it has to handle. The digital way of doing this it to use gradients. Unfortunately, curved gradients are not supported in the SVG specifications, which means we have to fake it. A method for doing this is presented below.