Sunday 16 June 2013

PhD week 67: 15 Month Report

Diplacodes trivialis—Today's picture of the day on Wikimedia Commons. Licence: CC: BY-SA.

One of the more critical pieces of administration that Lincoln University requires of PhD students is that at around 15 months after starting their studies, the student gives a presentation to a select group of academics, including the student's supervisory team. This presentation explains what progress has been made to that point, what problems had been encountered, and what the plan is from that point onward. It's a process that is designed to identify problems fairly early in the piece and to revise the scope of the study where everyone has a bit more of a realistic view than in the proposal stage.

This past week, I had mine. I didn't find it particularly arduous, and the general consensus was that I was doing fairly well. A couple of concerns were raised, mainly around timing of certain aspects of my research, and encouraging that I clarify the exact questions in one of my objectives. I found it encouraging, looking back over the past 15 months, and comparing what I said I would do with what I've actually done. Happily enough, I wasn't too unrealistic in most of my proposals, but there are a few aspects which I haven't done to the extent that I would've liked. The timing of the report was a little annoying, as it took time away from other things that I would've liked to have done, but overall I found the process to be a valuable one.


Websites:
American Hardcore: A Tribal History

Saturday 8 June 2013

PhD week 66: LaTeX fonts

As part of my research, I will be making labels that indicate the type status of a number of weevil specimens. To create these, I have adapted my previous method of creating specimen labels in LaTeX to include a coloured background. The result of this is that I need to make the font on the labels bigger and bolder.

Unfortunately, because of the idiosyncratic way that I had established my fonts in the document, this ended up being not as trivial as checking out the TeX font catalogue. Instead I wanted to get an idea of what fonts were available on my system, and set about trying to create a font sampler of my very own.

While it wasn't difficult to get a list of the fonts on my computer (using the advice given at StackExchange), it became somewhat more tricky to get an idea of what they looked like. Attempting to compile a test document revealed two errors: The first was that some fonts could not be loaded:

"Font xxxx not loadable: Bad metric (TFM) file"
In addition, some that passed the first test, threw a second error when compiled by themselves:
"mktexpk: don't know how to create bitmap font for xxxx"

A quick email to the texhax mailing list quickly elicited some useful responses, including a very useful code fragment that gets around the first error. The second one was a little harder to overcome. Updating my map file (as suggested by another StackExchange post) didn't seem to do the trick, and messing around in the man pages of mktexpk and related programs didn't suggest any possibilities to one as unfamiliar with the programs as I am.

The breakthrough came when I had the realisation that I could extract the names of the fonts directly from the map file itself. Using this in conjunction with the code fragment mentioned above, I was able to get a document that compiled correctly when broken into three parts of c. 3000 fonts to get around size and space limitations.

I did encounter the error

"pdfTeX error: (file xxxxx.pfb): cannot open Type 1 font file for reading"
which I solved by manually removing the offending lines from the .tex document. There (thankfully!) weren't many of these, so this was not a particularly arduous step. If you try and replicate this though, you have been warned! If you figure out how to get around this, please let me know.

I used R (via Sweave) to extract the names of the fonts from the map file and to create the tex file. Undoubtedly other languages could do the same thing, but I chose to stick with what I'm familiar with. The file is available from gitHub


Websites:
PILN Soundbites
FAO report: Edible insects. Future prospects for food and feed security
Where to buy tango music
RSPB
NHBS: Relentless Evolution by John Thompson

Sunday 2 June 2013

PhD week 65: DMHF

Male (left) and female (right) weevil parts mounted in DMHF.

The internal morphology of insects is a veritable gold mine of interesting characters. Obviously, in order to find investigate these characters it is necessary to dissect specimens. Unfortunately, this results in disarticulated beetle bits that one needs to store somehow in order to look at them again in the future.

The classic method of storing dissected materials is in very small vials that can be kept on the pin that holds the remainder of the specimen. This can be useful, but is a bit fiddly to remove the pieces from the vial when one needs to look at them again. In addition, it's become difficult to buy smaller glass vials, and I'm not a fan of the polyurethane vials that are readily available.

An alternative method that I've been exploring this past week is using the mounting medium DMHF. This mountant is soluble in water and dries crystal clear. The method that I've been using is to put a drop of DMHF on a card, immediately place the parts into the medium, add sufficient DMHF to cover the parts entirely, and leave for a couple of days to set. The card is then pinned below the specimen, and the parts are both protected and readily viewable (see picture above). I haven't tried it yet, but I understand that removing the parts is as simple as placing the card in a small dish of water and waiting a few minutes for the DMHF to dissolve.

A frustrating part of working with DMHF is that it forms a skin soon after exposure to air (c. 30 seconds). This skin can make it a little tricky to manoeuver pieces after placing them into the medium. After a little bit of experience though, one can usually get pieces in without needing to do too much messing around with them after the fact. I've had a positive first experince with the stuff, and am intending to carry on using it for the time being at least.


Websites:
Logic Matters
NetKnots—Tautline Hitch
Arctic Terns breeding in Netherlands migrate via Australia
LaTeX Stack Exchange: What fonts are installed on my box?

Listened:
Norma Jean—Disconnecktie: The Faithful Vampire

Watched:
Star Trek (Original Series) Season One

Saturday 25 May 2013

PhD week 64: Canterbury Museum

Canterbury Museum. Image courtesy of acroamatic via Flickr. License: CC: BY-SA-NC.

One of the things that I love about doing what I do is going to insect collections I haven't been to before, and discovering what cool things they have in them. Last week I visited the Canterbury Museum to look through their weevil collection to see what specimens of Irenimus they had. In the process I was able to identify a number of previously unidentified specimens, as well as correcting a couple of errors that had been made previously. There's not many jobs that can make a priceless national treasure even more valuable. and I'm lucky enough to have one that does!


Websites:
Vatican Radio—Culture of Encounter is the Foundation of Peace

Watched:
Star Trek (Original Series) Season One

Monday 20 May 2013

PhD week 63: Geographic data extraction

A natural part of the taxonomic process is the collection of distribution data. These can be useful for figuring out species limits, and for determining geographical areas where some interesting biology may be found. They can also be used with other geographic data to get an idea of the spatial patterns of species diversity, or for inferring the environmental preferences of a species—the subject of a field called environmental niche modelling or species distribution modelling.

Some of the different data that can be used include climatic information such as that available from WorldClim, geological data (e.g. GNS' QMAP), or composite datasets such as the Land Environments of New Zealand (LENZ) dataset.

A nice little summary as to how one can do this sort of stuff in R is given on the The Molecular Ecologist blog.


Websites:
Zegrahm Expeditions review of journey to Melanesia

Watched:
Star Trek (Original Series) Season One

Twelve weeks of Star Trek:
Star Trek Into Darkness

Monday 13 May 2013

PhD week 62: Detective work

Sherlock Holmes and Dr Watson discuss the intricacies of type specimens.
Image courtesy of Wikimedia Commons, and is in the public domain.

The foundation of biological taxonomy is formed by the designation of type specimens. These are specimens that were examined by the person who described the species in question, and which bear the name they proposed. They are important in that, in the event of confusion regarding the status of the name, the species represented by the type specimen gets the name. For more information on the categories and establishment of type specimens, read the wikipedia page linked to above, or the ICZN.

On this last trip to NZAC, I had the excitement of discovering some previously undetected type specimens, and the pain of realising that some types that should've been deposited there were either not present, or not adequately labelled. This required a degree of detective work involving checking original descriptions and specimen label data. The process is not yet completed, but progress it being made.

While I was in Auckland (and truth be told, the reason for the timing of this visit) I was able to catch Norma Jean playing at the Kings Arms Tavern on Friday. Compared with the Sydney concert, this was a more intimate show, featuring support bands that I know and love, and attended by people whom I hadn't seen for some time. Antagonist A.D. played with an intensity that belied their arrival from the USA that morning, and one wouldn't have guessed that it was Cold by Winter's first show in a good many years. The quality of the support was such that Norma Jean did not stand out as prominently as in Sydney. They played an excellent set, and it was great seeing them in NZ. Discussions after the show suggested that they may try and get here again in the near future, which will be amazing. If they don't make it, however, Friday was a worthy show by which to remember Norma Jean's visit to God's own country.


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

Websites:
Fauna of Chile blog: Aegorhinus superciliosus

Watched:
Star Trek (Original Series) Season One

Twelve weeks of Star Trek:
Star Trek (2009)

Monday 6 May 2013

PhD week 61: Sydney

Norma Jean take the stage at the Hi Fi, Sydney, 3 May 2013.

I've been a fan of metalcore band Norma Jean for eight or so years; so when I learned that they were touring Australia, I wanted to make sure that I caught them while they were in this part of the world. In this way, I found myself in Sydney on Friday night enjoying one of the best concerts I have ever experienced. From the pre-set sound check, one knew that something special was about to happen; and from the moment the curtains opened, they played with an intensity that few other bands I've seen have been able to match. They played a good variety of songs from across their releases, including one from their upcoming album that is due to be released in a few months. Personal highlights were their opening song "Disconnecktie", "Bastardizer", crowd favourite "Memphis Will be Laid to Waste", and "Vipers, Snakes and Actors". I was impressed by the bands attitude, and have come away with a greater respect for the band and enjoyment for their music; something I hardly thought possible.

Check out the following links to see the setlist of the show, as well as photos from the night by Gwendolyn Lee and Rebecca Pacey.

In addition to the concert, I was also able to spend some time in the Australian Museum looking at broad-nosed weevils from Australia, walked through Royal National Park and Wolli Creek Regional Park, and enjoyed a milonga at Tango Pasión. I managed to pack a decent amount into a short visit. I liked Sydney, and would like to visit it again in the not-so-distant future.


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

Websites:
Geoscience Australia: Topographic mapping

Watched:
Star Trek (Original Series) Season One
Norma Jean Australian Tour Trailer

Twelve weeks of Star Trek:
Star Trek X: Nemesis

Thursday 25 April 2013

PhD week 60: ANZAC day

Hill 60 Commonwealth War Graves Commission Cemetery. Gallipoli.
Image courtesy of Wikimedia Commons. License: CC: BY-SA

Secret Music

I keep such music in my brain
No din this side of death can quell;
Glory exulting over pain,
And beauty, garlanded in hell.

My dreaming spirit will not heed
The roar of guns that would destroy
My life that on the gloom can read
Proud-surging melodies of joy.

To the world's end I went, and found
Death in his carnival of glare;
But in my torment I was crowned,
And music dawned above despair.

Siegfried Sassoon


Read:
    St Augustine, Betteson H (Translator). 2003. City of God. London: Penguin Classics

Websites:
Climate Change Ecology—Python complements R's shortcomings
Christopher Gandrud—Reinhart & Rogoff: Everyone makes mistakes
One Big Photo—Most Amazing Macro Insect Photography

Watched:
Star Trek (Original Series) Season One
Mr Pip Trailer

Twelve weeks of Star Trek:
Star Trek IX: Insurrection

Sunday 21 April 2013

PhD week 59: Disappointment

Tautuku Bay, Catlins, Southland.

The great thing about working in systematics and conservation is that there is often the opportunity to go to some really cool places.

Last week, the intention was to go to Pig Island, off the coast of Southland to assist a fellow student to a survey of the giant weta (Deinacrida carinata) that are found on the island. We were to be dropped off by the coastguard and spend three nights on the island looking for weta. To this end we drove down, staying in Owaka on Monday night, and driving through the Catlins on Tuesday morning. Not far out of Invercargill, we got a call from the coastguard informing us that the weather was not looking good and that the trip was cancelled. Disappointing!

Despite the change of plans, we did manage to salvage sufficient collecting in some cool places (such as Forest Hill and Trotters Gorge Scenic Reserves) to make the trip worthwhile. Also, getting home a couple of nights earlier than expected meant that I was able to do a few more things at work and socially that I would've missed if we had made it to the island.


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

Websites:
Bryce McQuillan macro photography—Weevils

Twelve weeks of Star Trek:
Star Trek VIII: First Contact

Saturday 13 April 2013

PhD week 58: Graduation

The graduation procession begins.

Friday was graduation day. Since the earthquakes, Lincoln University has moved their graduation ceremony from in Christchurch city where it was formerly held, to Lincoln township. This move means that graduands muster at the university before their march down the road to the Events Centre; with the result that the University is filled with a vibrancy and an air of celebration at a level that is rarely reached by other occasions. It is enjoyable to walk through the throng and see proud parents and supporters congratulating their person on a job well done. Seeing fellow students graduating is also a great encouragement, particularly when one knows the trials they had to undergo to get there.

To all who graduated yesterday, congratulations!


Websites:
NSW National Parks
GeoLabs Blog—Interactive WebGL plot exported from R

Watched:
Star Trek: Enterprise Season Four

Twelve weeks of Star Trek:
Star Trek VII: Generations

Monday 8 April 2013

PhD week 57: Entomological Society

Auckland Tree Weta (Hemideina thoracica).
Image courtesy of Jon Sullivan. Licence: CC: BY-NC.

Over the three days from 3 to 5 April was the 62nd annual conference of the Entomological Society of New Zealand, held at Massey University in Palmerston North. The conference was a typically enjoyable event, with a lot of catching up with old friends and meeting new ones, as well as a neat overview of some of the cool things that people are studying around the country. There were a large number of talks on various aspects of weta biology—unsurprising given that Massey is a hotbed of weta research; but great to see that New Zealand's most iconic insect is becoming better known.

After the conference, I spent three very pleasant days collecting in and around Wellington. I was looking two species of Irenimus that were described from the region; specifically Titahi Bay and Wadestown. Obtaining topotypic specimens (i.e. specimens collected from the same locality as the type specimen) is a useful exercise when sorting out taxonomic problems. As it is unlikely that several similar species live in the same spot, collecting fresh material from the type locality can help bring clarity as to what the species actually is. It so happened that I managed to find good numbers of both species that I hoped to find, so the trip was most definitely a good one!


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

Websites:
Stanley Hauerwas—Living well in ordinary time: A tribute to Rowan Williams
Alison Milbank—Christ is not divided: The Easter journey into paradox

Watched:
Star Trek: Enterprise Season Four

Twelve weeks of Star Trek:
Star Trek VI: The Undiscovered Country

Friday 29 March 2013

PhD week 56: Easter

The crucifixion of Christ. Icon by Dionisius (1500 AD). Image courtesy of WikiMedia Commons. Image is in the Public Domain.

When I Survey the Wondrous Cross

When I survey the wondrous cross
On which the Prince of glory died,
My richest gain I count but loss,
And pour contempt on all my pride.

Forbid it, Lord, that I should boast,
Save in the death of Christ my God!
All the vain things that charm me most,
I sacrifice them to His blood.

See from His head, His hands, His feet,
Sorrow and love flow mingled down!
Did e'er such love and sorrow meet,
Or thorns compose so rich a crown?

Were the whole realm of nature mine,
That were an offering far too small;
Love so amazing, so divine,
Demands my soul, my life, my all.

Isaac Watts, 1707. From the Open Hymnal.


Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward

Websites
Revista Chilena de Historia Natural online
GIMP contact sheet plugin

Watched:
Star Trek: Enterprise Season Four

Twelve weeks of Star Trek:
Star Trek V: The Final Frontier

Saturday 23 March 2013

PhD week 55: Outreach

Ivey Hall, Lincoln University

This year marks 150 years since the establishment of Lincoln township, and the occasion was marked by a range of activities and festivities held over the past week. On Thursday, the University welcomed the community onto the grounds and held tours around the campus, and had a bunch of stalls manned by enthusiastic people to show people a few of the things that happen at the university. I was one of these enthusiastic people, and my job was showing off the diversity of invertebrates that can be found in pasture.

I do enjoy talking to people about insects, and seeing their reactions to their encounters with them. It find it interesting how different age groups respond in different ways. Pre-school to early primary school age children show a great interest in things and will happily poke, prod and otherwise engage with insects. Late primary school kids start expressing fears and misgivings about various invertebrates, but usually end up interacting extensively with them. High school students loudly voice how gross and disgusting they find everything when they're with their peers, but if you get them by themselves they tend to show a lot more interest. Finally, adults take a very utilitarian view of things, asking what functions the organisms provide, and ask how to control particular species.

What I like most about this sort of outreach though is that most people, despite having a negative view of insects initially, tend to go away with at least a grudging respect for them. This, for me, makes it all worthwhile.


Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward
   Proverbs 22–24

Websites
Tortricids of agricultural importance

Watched:
Star Trek: Enterprise Season Three

Twelve weeks of Star Trek:
Star Trek IV: The Voyage Home

Saturday 16 March 2013

PhD week 54: Primers

A critical part of the process of sequencing DNA involves the development of primers. These are short stretches of DNA that bind to the gene of interest in the specimen DNA and provide a starting point to copy that gene. Two primers are required for amplication in PCR in order to amplify both strands of DNA and get the eponymous chain reaction. The easiest way of designing primers is to use ones that other researchers have used sucessfully for related organisms. Primer sequences are usually published in papers, and it is a simple matter to get them made. However, there is no standard convention to naming primers, which can be annoying at times. My preference is that the name include the name of the gene, the direction of the primer, and some measure of the position of where the primer binds to the gene. Unfortunately, many published primers lack some (or all!) of this information, which can make it tricky to make decisions as to which primers to try out. The primer numbering system of Simon et al is, in my opinion, a good model to follow.


Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward
   Proverbs 20–21

Watched:
Star Trek: Enterprise Season Three

Listened:
Vanna—And They Came Bearing Bones

Twelve weeks of Star Trek:
Star Trek III: The Search for Spock

Saturday 9 March 2013

PhD week 53: Auckland, second journey

Rangitoto Island from St Helier's Beach
Photo courtesy of Sandy Austin via Flickr. Licence: CC: BY-NC-ND.

I was in Auckland over the past week, looking at specimens held by NZAC. I was also able to visit Guillermo Kuschel and Beverley Holloway, who are both internationally respected weevil taxonomists, who have been retired for some time. I greatly enjoy their company, and learn a lot with each visit.

This time I showed them some of my illustrations made using Inkscape. I found their reaction very interesting. They did have a few concerns about the accuracy of the drawings, particularly with regard to the representation of fine detail. However, their main concern was that the process, which I think they perceived to be largely mechanical and automatic, did not respect the organisms involved. They felt that the slight imperfections in the lines of inked drawings expressed a humanity that the vector graphics lacked, and that the simplicity of the illustration process showed a certain callousness.

While the previous paragraph makes them sound overly negative. In our conversation, Beverley and Guillermo also spoke of the sense of discovery that they experienced as they sketched structures directly from the microscope, and the feelings of excitement as they observed aspects of insect morphology that had been rarely encountered. It was very cool to see their passion that extended beyond being an occupation to having emotional regard for their study subjects.

Will I change the way that I operate? Unlikely. The benefits of using tools like Inkscape are too great. However, it will make me think further regarding the philosophical implications of my methods of choice.


Read:
   Pine-Coffin RS (translator). 1961. The confessions of Saint Augustine Middlesex: Penguin
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward
   Howe JT. 2012. Affirmations after God: Friedrich Nietzsche and Richard Dawkins on Atheism. Zygon. 47(1) 140–155

Websites:
Nikon Travelite V Binoculars
Canadensys—Why we should publish our data under Creative Commons Zero (CC0)

Watched:
Star Trek: Enterprise Season Three

Twelve weeks of Star Trek:
Star Trek II: The Wrath of Khan

Saturday 2 March 2013

PhD week 52: One year in

Well. One year ago, I started my PhD. Since then I done some pretty cool things like attending a weevil taxonomy workshop in Arizona, going to the Southern Connections Congress in Dunedin, and collecting in Central Otago and the Two Thumb Range. I have also become better schooled in some of the key techniques of taxonomic research including sorting, dissecting, and slide-mounting. Overall, I've been enjoying it greatly.

How things go over the next 12 months will be in determining how close I will get to finishing on time. At this stage, everything is progressing nicely in the right direction. Long may it last.


Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward
    St Augustine, Betteson H (Translator). 2003. City of God. London: Penguin Classics
   Tolkien JRR. 1967. Smith of Wootton Major. London: HarperCollins
   Proverbs 17–19

Websites:
Breeding grounds of NZ Storm Petrel discovered
Super Rugby
Better View Desired—Binocular reviews

Listened:
Project 86—Numb

Twelve weeks of Star Trek:
Star Trek I: The motion picture

Tuesday 26 February 2013

PhD week 51: Corbels

A selection of corbels. For larger pictures and my interpretation of the structures, see the examples on my Flickr page.

The corbel is a character on the hind leg that is frequently used in the higher classification of broad-nosed weevils. It is a feature that is difficult to describe in words, and can be tricky to see at first. Unfortunately, there are few easily accessable pictures that show the different types of corbel. This post is an attempt to rectify the situation.

The corbel refers to the form of the apex of the hind tibia. An "Open" corbel has no particular modification to the apex. An "Enclosed" or "Closed" corbel has a flat area (often with scales or short setae) lying between two rows of setae on the outer edge of the tibial apex. When the corbel is large, such as in Leptopius and Cecyropa, it is easily seen. However, sometimes the corbel can be very slender, as shown by Naupactus leucoloma. In such casees, it can be difficult to determine whether the corbel is open or enclosed. A "Semi-enclosed" corbel has a concave area between the apex of the tibia and the insertion of the tarsus that is always bare. It is important to note that the semi-enclosed corbel is not homologous with the enclosed corbel.

An excellent discussion on the corbel, that goes into a lot more depth than I've covered here, can be found on the International Weevil Community Website.

References:
Thompson RT. 1992. Observations on the morphology and classification of weevils (Coleoptera, Curculionidae) with a key to major groups. Journal of Natural History 26: 835–891.


Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward
    St Augustine, Betteson H (Translator). 2003. City of God. London: Penguin Classics
   Proverbs 13–16

Watched:
Star Trek: Enterprise Season Two
National Geographic—Best videos of the Russian meteor strike

Saturday 16 February 2013

PhD week 50: Thomas Broun

Portrait of Thomas Broun. From Searell P, Watt JC. 1974. Science gallery: Thomas Broun (1838–1919). New Zealand's Natural Heritage. 3(37) via Bugz

The key figure in the study of New Zealand beetles is without a doubt Thomas Broun (1838–1919). Born in Scotland, he served in the British Army, seeing action in the Crimean War and the Indian Rebellion. He arrived in New Zealand in 1863, where he served in the New Zealand wars before becoming a school teacher on retirement from the army. While he had a strong interest in natural history from a young age, it was not until his arrival in New Zealand he began serious taxonomic research, describing insects in the evenings after work. Over the course of his 56 years in New Zealand, he described 3538 beetle species, covering all families.

While his work has not, in the words of Elwood Zimmerman "stood the test of time", it must be remembered that it was done in testing conditions and with the aid of substantially poorer optics than we have today. Being so distant from the centre of entomological research at the time, he had to rely on the literature he was able to obtain from European colleagues. His decision to bequeath his collection to the British Museum of Natural History has indeed limited further research into New Zealand beetles; but this decision was a prudent one in an age where New Zealand institutions were still very much in their infancy.

He described approximately 70 species of Irenimus, though he described them in the genus Catoptes. He recognised the difficulty of the group, and made the following comment in 1904:

[Catoptes (= Irenimus) duplex] is one of several species that do not accord exactly with Catoptes, Brachyolus or Inophloeus, but partake more or less the structure and appearence of all three. In order to avoid confusion it will be necessary before long to redescribe these genera and define their limits more accurately; when that is accomplished the aberrant species alluded to above may be referred to new but certainly very intermediate genera. As I have not seen some of these species as yet, and as very few examples of some others are possessed by me, the difficult task must be allowed to stand over at present
This "difficult task" has been left until now. Here's hoping that my contribution will finally make this group tractable.

References:
Crosby TK. 2012. 'Broun, Thomas - Broun, Thomas', from the Dictionary of New Zealand Biography. Te Ara—the Encyclopedia of New Zealand
Cheesman TF. 1920. Major Thomas Broun 1838–1919. Transactions and Proceedings of the New Zealand Institute 52: ix–x


Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward

Websites:
The Internet Bird Collection—Videos, photos and recordings of a number of birds around the world

Watched:
Project 86—Fall, Goliath, Fall music video
Open AIr Summer Shakespeare 2013—Twelfth Night
Star Trek: Enterprise Season Two

Saturday 9 February 2013

PhD week 49: Slide mounting

Weevils slide mounted in Euparal

If you look back over previous blogposts (such as this one and this one), you'll see that I've agonised over different microscope mounting media like I were a character from Twilight. Swayed by my colleague, Rich Leschen, I have thrown my lot in with Euparal, and have spent the past week dissecting and slide-mounting weevil specimens. I will be unable to see the results for another two weeks or so, but initial indications suggest that it will have been a worthwhile exercise. The features that I particularly hope to see are characters of the mouthparts, where I hope to see differences between species that suggest different food preferences. Determining these differences will require careful observation, and it is hoped that these slide mounts will make the task much easier.

While it seems that I am currently at peace with my decision of slide mountant, there remain some dark clouds on the horizon. I recently read a paper that states that Euparal is becoming difficult to source due to a combination of concerns over its toxicity, and its continued availability. This paper suggests dimethyl hydantoin formaldehyde (DMHF) or polyvinylpyrrolidone homopolymer (PVP) as possible substitutes. Maybe my slide mountant angst will continue for a little while yet.

References:
Leschen RAB. 2005. Erotylidae phylogeny and review (Insecta: Coleoptera: Cucujoidea). Fauna of New Zealand 47: 1–108
Liberti G. 2005. Improved solutions of two water-soluble media for mounting beetle genitalia. The Coleopterist 14(1): 29–35.


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

Websites:
DNA barcoding blog—Seven Deadly sins of DNA barcoding
Tom Robinson—Māori Macron Characters

Listened:
Angel D'Agostino—Adios Arrabel

Sunday 3 February 2013

PhD week 48: Alpine collecting

Camping at Round Hill Skifield.

I love skifields. Only at this time of year though. In a few months time they get covered with snow, and all the insects hide away making them not worth visiting in the slightest. In the past week, I had two very pleasant days in the Two Thumb Range at Round Hill and Mt Dobson Skifields. The point of the trip was to search for Haplolobus saevus, which was collected from the "mountains near Lake Tekapo" according to the original description. We managed to track some down in some spent flowers of Celmisia lyalli at Round Hill. We also found some specimens of Inophloeus in Aciphylla plants growing at the top of Mt Dobson skifield at an elevation of 1950 m. Pretty hardy organisms! The weather was perfect, the company was enjoyable, and the collecting was excellent. The total was one very succcessful field trip.


Read:
   Chesterton GK. 1908. Orthodoxy. Image, New York (2001 Edition)
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin

Listened:
Phantom Empire—If the World Burns
Blindside—The Great Depression
Norma Jean—Meridonal

Watched:
Star Trek: Enterprise Season One

Tuesday 29 January 2013

PhD week 47: VII Southern Connections Congress

The Otago University clock tower.
Photo courtesy of Velvet Android via Flickr. Licence: CC: BY-NC-SA.

Over the past week I had the priviledge of attending the 7th Southern Connections Congress, held this year at the University of Otago in Dunedin. This congress, held every three years, seeks to bring together scientists from a variety of disciplines including biology, climatology, palaeontology and geology to discuss factors which have influenced the distribution of plants and animals in the Southern Hemisphere. For me, the highlights of this conference included:

Microclimate: A number of talks highlighted the variation in environmental conditions that exist at very localised scales. For example, a rock may be heated up to 50°C, while a couple of metres away, it may be only 12°C in the shade of a plant. Alpine areas are particularly variable in this respect. This is somewhat intuitive, but it is worth being reminded about, particularly when regional-level climatic data is being used to try to infer the effect of climate change on species responses.

NZ in the Oligocene: It is well known in geological circles that the extent of New Zealand was much reduced during the Oligocene period, as much of the land was submerged below the ocean. A few years ago, some biologists and geologists questioned whether there any part of New Zealand was actually above the water, with the implication that all of NZ's biota got here from somewhere else after this time. This contention has spurred a significant amount of geological research to figure out where land may have been during this time. Evidence is appearing that there may have been islands north of New Zealand, and emergent land in the Otago and Catlins area during this time of maximum inundation.

Evolutionary Radiations: I had the priviledge of talking in a symposium of papers considering evolutionary radiations. All the talks were excellent, and included both conceptual overviews of the subject, as well as more in-depth case studies.

Overall, I had a great time. Many thanks to the organisers! The next congress is in 2016 and will be held in Chile. I hope to get there, depending on my situation at that time.


Read:
   Pine-Coffin RS (translator). 1961. The confessions of Saint Augustine Middlesex: Penguin
   Chesterton GK. 1908. Orthodoxy. Image, New York (2001 Edition)
   Proverbs 6–8, Romans 1–11

Websites:
Public access data for mapmaking
Norma Jean Australia Tour 2013 tickets

Sunday 20 January 2013

PhD week 46: The poetry of taxonomy

Not-so-gratuitous picture: My new favourite bird: the Fernbird Megalurus punctatus. Image out of copyright.

There is a poetry in the process of taxonomic description. Reducing an organism's appearence to a paragraph of characters requires a certain degree of creativity and wordsmithing. It it unfortunate, therefore that the end result should be somewhat unenthralling. Descriptions are useful though and writing them makes one appreciate good ones all the more.


Read:
   Pine-Coffin RS (translator). 1961. The confessions of Saint Augustine Middlesex: Penguin
   Chesterton GK. 1908. Orthodoxy. Image, New York (2001 Edition)
   Proverbs 6–8, Romans 1–11

Websites:
Dolph Schluter's Laboratory blog
geomorph R package
Spinnerette—A webcomic
ABC Religion and Ethics

Listened:
Antagonist A.D.—Nothing From No One

Watched:
Star Trek: Enterprise Season One

Tuesday 15 January 2013

PhD week 45: Back into it

Gratuitous picture: Stolas chalybaea (Germar, 1824) (Chrysomelidae) from Brazil. Courtesy of Udo Schmidt via Flickr. License: CC: BY-NC-SA.

The past week has been spent hanging out and relaxing into the new year. It involved a bit of lab work, a bit of looking at specimens, and a bit of sorting out my priorities for the next little while. I couldn't be too strategic unfortunately—dealing with immediate issues (in my case, a conference) took top priority over planning for the long term. Overall though, it's good to be back! (Though one could question if I ever really left...)


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

Websites:
Animal Genome Size Database

Watched:
Star Trek: Enterprise Season One