Friday, 25 May 2012

PhD week 12: Bits and pieces

This week was eclectic, and found me dabbling in a number of different areas. For example, on Monday I entered the locality and collection details for a number of Irenimus specimens into a spreadsheet, which will allow me to keep track of what I look at and what collections they came from. On Tuesday, I designed and ordered primers for PCR, which will enable me to sequence short strands of DNA from my weevils. On Wednesday, I wrestled with details of georeferencing. In particular I had to convert some coordinates from the old New Zealand Yard Grid (NZYG) projection that went out of general use around 1980, to latitudes and longitudes based on the WGS84 datum. Thursday found me looking at Irenimus specimens, contemplating details of their morphology and how best to communicate certain subtleties that I suspect will actually turn out to be rather important. Finally, today I updated my draft PhD proposal for my supervisors to read over before it's due in a couple of weeks.

So this week I have been an artist, an author, a data entry clerk, a geographer, a molecular biologist, and a programmer! This sort of variety is why I love science.

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.
    Rosas MV, Morrone JJ, Guadalupe del Rio M, Lanteri AA. 2011. Phylogenetic analysis of the Pantomorus-Naupactus complex (Coleoptera: Curculionidae: Entiminae) from North and Central America. Zootaxa 2780:1–19
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 60–62, Colossians 1:15–18

Plotting Brownian Motion and Orstein-Uhlenbeck models in R
Drosophila yakuba complete mitochondrial genome
Naupactus xanthographus complete mitochondrial genome
IDT Oligoanalyser
LINZ online coordinate conversion utility

The Simpsons Season 10

Tuesday, 22 May 2012

Book review: "The People's Bible" by Derek Wilson

The People's Bible book cover
2011 was the 400th anniversary of the first publication of the King James Bible. As a result, a number of books detailing the history of The Book were published to commemorate the occasion. The one I read was The People's Bible. The Remarkable History of the King James Version by Derek Wilson. I found it to be an insightful and enjoyable read. Wilson looks at the history of the KJV from the century before its publication to today, charting the changing religous and cultural climate that lead to its publication, and analysing its enduring influence.

Two aspects of the book particularly stood out for me. First, his portrayal of the situation prior to 1611 is vivid and memorable. The description of religious ritual in the setting of a primarily illiterate rural population evokes images of a way of 'doing' Christianity that is very different from the way it tend to be done in the Western world in this day and age. Furthermore, while the distribution of contraband bibles to believers desperate to read the Word of God in their own language is still a reality for many people in many countries, it is incredible to think that English speakers were in this very situation five centuries ago.

The second aspect that stood out was Wilson's discussion of the lasting influence of the King James Version of the Bible, and the questions that are still very relevant today. Should everybody be able to read and interpret the bible? Or should it be reserved for those who have undergone the training necessary to understand it deeply? How does the process of translation link into the belief that the Bible is the inspired Word of God, and the authority that belief engenders? He contends that the increasing number of English translations of the Bible hinders the memorisation of scripture. While this may not be true at an individual level, in the community of faith generally, the lack of a single standard translation makes it more difficult to build "religous currency" that "strengthen[s] fellowship and reaffirm[s] belief" (pg 197). This hindrance though is tempered by the impression one gets that Wilson considers the ideal of a single most accurate English translation that all parties agree upon to be something of a chasing of the wind.

Readers of this blog will know that I like my software to be open-source. I like my religion to be open-source too. It is a bold statement by the Bible to claim to be the Word of God, and a bold statement by the Church to claim to point to the Saviour of humanity. The Church has devoted considerable energy to ensuring that these claims can be evaluated by people for themselves. Not only does this include the translation of the Bible into as many languages as possible, but also the publication of the Bible in Greek and Hebrew. The result being that the Bible is probably the most scrutinised and studied document in the world. The Bible has a significance about that few other pieces of literature possess, and which demands careful consideration of its contents. It is well worth a read.

   McGrath A. 2001. In the Beginning: The Story of the King James Bible. London
   Wilson D. 2010. The People's Bible. The Remarkable History of the King James Version. Lion: Oxford.

Monday, 21 May 2012

Alternate way of plotting means and errors

Last month, I wrote a post discussing dynamite plots, noting that they're not considered to be especially good at presenting information. I got a little bit of flak for it, from people for and against dynamite plots. This post shows a different method of showing a point and an error bar. If you're going to do it, why not make it look like something cool. A TIE fighter maybe?
Values <- c(1,2,5,4)
Errors <- c(0.25, 0.5, 0.33, 0.12)
dummyNames <- paste("Trial", 1:4)

TIEplot(1:4, Values, Errors, names = dummyNames, ylim = c(0,6))

How much cooler is that?
TIE fighter plot

The code for TIEplot() is available on gitHub. Remember to acknowledge me when you use in all your papers/books/theses.

Friday, 18 May 2012

PhD week 11: Mouthparts

Face of Irenimus
Face of an unidentified Irenimus species.
Mouthparts are important. They are the entry point for the energy required by animals, and their form and structure can tell us something about the life and habitat of the creature in question. Insects have amazing mouthparts: consider the straw-like tube possessed by butterflies, the spongy pad used by blowflies, and the stilettos used by mosquitoes. What's even more incredible, is that it is modifications to the same four main structures that make up these very different structures. These structures are most easily seen in insects with biting mouthparts, such as grasshoppers or beetles. Their names and functions are as follows:
  • The topmost structure is the labrum. This structure is a plate that prevents food from escaping out the top. Human analogy: upper lip or palate.
  • The second strucure are the mandibles. These are a pair of large, strong, hardened plates that crush food into small particles that can be easily digested. Human analogy: teeth.
  • The third structure are termed the maxillae (singular: maxilla). These are paired structures (like the mandibles) that help manipulate food, and also possess palps that contain banks of hairs and sensors that help the insect make sure that it's eating what it's supposed to. Human analogy: tongue.
  • The fourth and final structure is the labium. This is a plate that stops food escaping out of the bottom of the mouth, similar to the labrum (notice the "R"), except that it also possessed palps like the maxillae. Human analogy: lower lip or lower jaw.
Weevil mouthparts
Maxilla (left) and labium (right) of Apotomoderes lateralis. Scale bars 0.2 mm and 0.1 mm respectively. Courtesy of Franz 2010. License: CC: BY

Weevils have their mouthparts at the end of the rostrum, and can just be seen in the photo at the top of the page. The structures listed above are possessed by weevils, with the exception of the labrum which is fused with the rest of the rostrum. In the picture above (taken from Franz 2010) you can see a maxilla on the left, and the labium on the right. They have not illustrated the mandibles, which can be pretty beefy in some species (such as Irenimus), but you can just see them at the tip of the rostrum in the photo above.

One of the question I hope to answer as part of my PhD is: do the mouthparts of Irenimus species reflect their environmental preferences? A reasonably straightforward question. Unfortunately, in order to look at their mouthparts, they need to be dissected out. This is easier said than done, as the mouthparts of weevils are very small and it takes a bit of fiddly microscope work to dissect them out. I tried my hand at it this week, following the methods used by Steve Davis in his work on baridine weevils, and successfully managed to get my first glimpse of weevil mouthparts. It will take a lot more dissecting to get to grips with some of the details, but the ice has been broken!

   Davis SR. 2009. Morphology of Baridinae and related groups (Coleoptera, Curculionidae). ZooKeys 10: 1–136.
   Franz NM. 2010. Revision and phylogeny of the Caribbean weevil genus Apotomoderes Dejean, 1834 (Coleoptera, Curculionidae, Entiminae). ZooKeys 49: 33–75.

   Wilson D. 2010. The People's Bible. The Remarkable History of the King James Version. Oxford: Lion
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 55–59, Genesis 1:2

Deep Thoughts and Silliness—a nature network blog by Bob O'Hara
Ubuntu 12.04 screensavers
Changing default applications

Astor Piazzolla—Octeto Buenos Aires

Star Trek: Deep Space Nine Season 3
Norma Jean—Kill More Presidents Music video

Friday, 11 May 2012

PhD week 10: First gel

agarose gel
This week's milestone is pictured above. It is a picture of an agarose electrophoresis gel. These gels are made from a seaweed derivative, and are used to separate DNA of different lengths. Samples of DNA are placed into holes in the gel, and an electric current is passed through it. The DNA moves through the gel towards the positive electrode, but longer pieces move more slowly than shorter pieces. The gel is then stained with a chemical that binds to the DNA and fluoresces under UV light, allowing one to see the result. The white dashes in the picture above show where DNA has ended up. The obvious ones at either side are the DNA ladder, a mixture of DNA of known lengths, which allows one to figure out the lengths of DNA in the samples.

It so happens that this particular gel is the first one of many that I will run over the course of my PhD. It is the result of a PCR amplification of a specific fragment of DNA for a number of weevil specimens. The reason you can tell that it is genuine is that it is hideous as far as agarose gel pictures go, and the only reasons for showing anyone a picture of this quality is to point out the problems with it, or for sentimental reasons. It is shown here for both purposes. For starters, I left it running for too long, and the ladder has run off the end. Secondly, only two of eighteen samples actually worked (the ones that have been ringed). One of these is a positive control, a DNA sample that is known to have worked under the same conditions previously.

So, all in all, it's a somewhat disappointing result. However, optimising PCR protocols is a routine (though annoying) part of getting DNA sequences from a number of specimens. What this gel does show clearly is that I shall have to go through that process before I can routinely sequence DNA from my weevils.

   Posadas P. 2012. Species composition and geographic distribution of Fuegian Curculionidae (Coleoptera: Curculionoidea). Zootaxa 3303: 1–36
   Wilson D. 2010. The People's Bible. The Remarkable History of the King James Version. Oxford: Lion
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 52–54

Marcus Ardern's blog and website
gitHub smart HTTP support details
gitHub: Forking repositories
Geographx free downloads
Using near IR in microscopy
Setting up screensavers in Precise Pangolin

Kevin Johansen—Sur O No Sur
Color Tango—Con Estilo Para Bailar

Wallace's standardwing (Semioptera wallacei) mating dance
National Geographic TV Profile of Jim Frazier
Star Trek: Deep Space Nine Season 3

Friday, 4 May 2012

PhD week 9: I have become precise

Ubuntu logo
This week, I gave my laptop a complete overhaul by deleting the Windows Vista partition I still had from when I purchased the thing, and upgrading my operating system to Ubuntu 12.04 Precise Pangolin. It was a straightforward, painless process that went very smoothly. The only niggles are those things that you don't do very often, but would've been easier had you remembered backing them up. Backing up the .bash-history file is one such example.

The big change that I have encountered, coming from Ubuntu 10.04 Lucid Lynx, is the Unity desktop environment. I'm actually rather enjoying it, actually. I find the behaviour of Alt + Tab takes a bit of getting used to (and the icons could be smaller), but generally I am happy with the changeover.

One of the things that took me the most time though, was setting up a keyboard shortcut to my text editor. I was easily able to make my way to System settings > Keyboard > Shortcuts and create a new shortcut, but to my dismay it told me it was disabled. After far too long searching on the internet and getting confused about the gconf editor, I finally find a bug that seems to deal with the issue. I prepare to comment on it, and then read the workaround proposed.

Click the + button and add a name to remember the shortcut and the specific command you want to execute. Click Apply. Find the name in the list and click the RIGHT HALF of the row. "Disabled" should change to "New accelerator". (My emphasis)
Man, I felt stupid.

All in all, it's been a great week. As well as the successful computer cleanup, I learned this week that two papers on which I am an author have been accepted! Always good news to receive, and it's handy heading into a PhD with a few publications up one's sleeve. I also had a pleasant afternoon on Tuesday looking at a number of Irenimus specimens, and starting to think carefully about useful anatomical features for their identification, and how might be best to record them.

   Fleming CA. 1962. New Zealand biogeography—A paleontologist's approach. Tuatara 10(2): 53–108
   Ray ET. 2003. Learning XML. Cambridge, Mass.: O'Reilly
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 48–51

Marcus Brown's blog
Entrez Programming utilities help
Ubuntu's #1 priority for bug fixing
APE website

21 Guns—Friends and Family
The Devil Wears Prada—With Roots Above and Branches Below

Brick vs Face—Warriors Live at Hamtown Smakdown 2007
Stavesacre—It's Beautiful (Once You're Out Here) Music Video

Wednesday, 2 May 2012

Rapid dispersal of Tahitian biological control agents

Glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae)
Gonatocerus ashmeadi (Hymenoptera: Mymaridae)
The glassy-winged sharpshooter (above) and its parasitoid (below). Pictures courtesy of the Center for Invasive Species Research. License: CC: BY-NC-ND

In 1999, Tahiti was invaded by the glassy-winged sharpshooter (Homalodisca vitripennis, a sap-sucking bug that feeds on a huge variety of plants. In the absence of its natural predators, the bug became extremely numerous. This was of concern for two reasons. The first was that the sharpshooter had the potential to spread bacteria that kill plants. The second was more aesthetic. The sharpshooter feeds on the xlyem fluid of plants, which is high in water and low in nutrients. The result is that the insect needs to drink a lot to get the nutrition it needs. In doing so, it excretes the excess water. When sharpshooter numbers get high, the result can be fairly unpleasant as this video shows. The "rain" in the video is actually water secreted by hundreds of glassy-winged sharpshooters.

Something had to be done, and it was. After pre-release testing, a minute parasitic wasp Gonatocerus ashmeadi (pictured above) was released on the island in 2005. This wasp parasitises the eggs of the sharpshooter. It rapidly became established, and glassy-winged sharpshooter numbers plunged dramatically. When I visited Tahiti in 2008, I found very few sharpshooters despite extensive collecting on the island.

A paper by Petit and co-authors investigated the dispersal of the wasp from two release sites on the island. Sites up to 5 km away were regularly monitored after the wasps were released, to determine how quickly they were moving around. They found that the wasps only took 50 days to be collected 1 km away, and were first collected from the 5 km sites 106 days after the initial release. The team calculated that this insects that is less than 2 mm in length was travelling at around 40 m/day.

This biological control scheme has been especially effective, and will (or should) become a textbook example of successful biological control introductions. Results have been clearly recognised within a short time period, thanks to this parasitoid which has managed to disperse rapidly despite its size.

Petit JN, Hoddle MS, Grandgirard J, Roderick GK, Davies N. 2008. Short-distance dispersal behaviour and establishment of the parasitoid Gonatocerus ashmeadi (Hymenoptera: Mymaridae) in Tahiti: Implications for its use as a biological control agent against Homalodisca vitripennis (Hemiptera: Cicadellidae). Biological Control 45: 344-352