Thursday, 12 February 2015

Stereo microscope stage for insects made out of LEGO®

The IMps. Photo courtesy of Dupont et al via ZooKeys. Licence: CC: BY.

I loved LEGO® as a child. It's been a long, long time since I last played with it, but I think I've just found a project that will encourage me back into it. A group of entomologists at the Natural History Museum have developed some designs to create microscope stages (dubbed IMps) with two axes of movement out of LEGO pieces, and have released them to the world in a paper published in Zookeys. These microscope stages allow fine movement of specimens under the microscope, allowing one to precisely manoeuvre the specimen in order to see or photograph particular structures. The designs published by Dupont et al are an elegant, portable and cheap solution; with the added benefit of playing with LEGO.

Dupont S, Price B, Blagoderov V. 2015. IMp: The customizable LEGO® Pinned Insect Manipulator. ZooKeys 481: 131–138.

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.

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

PILN Soundbites
FAO report: Edible insects. Future prospects for food and feed security
Where to buy tango music
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.

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

Norma Jean—Disconnecktie: The Faithful Vampire

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!

Vatican Radio—Culture of Encounter is the Foundation of Peace

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.

Zegrahm Expeditions review of journey to Melanesia

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.

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

Fauna of Chile blog: Aegorhinus superciliosus

Star Trek (Original Series) Season One

Twelve weeks of Star Trek:
Star Trek (2009)