The Praise of Insects

Featured insect: Polyrhanis dabraensis (Coleoptera: Cicindelidae)

2012-01-31T10:39:00.002+13:00

Tiger beetles (family Cicindelidae) are active predators as adults, pursuing their prey by running and flying. The larvae are bizarre looking things, and catch their prey by sitting and waiting in holes in clay banks and the like (such as one I found in my youth in the Solomon Islands that had taken up residence in a spent WWII rifle cartridge)

Polyrhanis dabraensis is a beautiful tiger beetle from Western New Guinea that was recently described by Andrey Matalin and Fabio Cassola. The insect fauna of this region is fairly poorly known, but the tiger beetles are doing fairly well for themselves. A total of 64 species are known from the region, though undoubtedly more are yet to be discovered. A list of the known species is available on the Website of the Papua Insects Foundation, which also includes images for a select number of species.

Picture courtesy of the Korean Society of Applied Entomology, Taiwan Entomological Society and the Malaysian Plant Protection Society.

References

Matalin AV, Cassola F. 2012. A new species of the genus Polyrhanis Rivalier, 1963 (Coleoptera: Cicindelidae) from Papua (New Guinea, Indonesia). Journal of Asia-Pacific Entomology 15(1): 196-199.

Bishop Museum Occasional Papers

2012-01-12T11:59:00.002+13:00

I thought that I had blogged here before regarding the availability of the Bishop Museum Occasional Papers; but it seems that I was mistaken. Suffice to say, the Bishop Museum is in the process of digitising the issues of BMOP and making them available online. It is actively occuring—today I was able to see a few articles that were unavailable previously. The Occasional Papers and pretty much everything published by the Bishop Museum form a immensely valuable body of knowledge for South Pacific biology; and it should be considered a first port-of-call for anyone keen on the fauna and flora of the region.

Moorean Insects on Flickr

2012-01-11T18:28:00.007+13:00

The Moorea Biocode is an ambitious project that aims to DNA barcode every organism on the island of Moorea in French Polynesia.The project has an online database with records of the specimens collected thus far, many of which contain photographs (e.g. the weevil gallery). There's also a Flickr stream that have a number of nice photos, including the beautiful Cranopoeus pictured above, and a cool-looking Proterhinus.

Unfortunately, it's still a little to early to really see the benefits of the project. The DNA sequences are not yet available (as far as I can tell); and many of the photos above are unidentified, or worse, misidentified at the family level. The project has great potential, but we'll have to wait a little while longer before the above resources become really useful for South Pacific zoology.

Picture courtesy of the Moorea Biocode Flickr stream

spider: an R package for species identity and evolution

2011-12-13T16:23:00.003+13:00

spider: Species identity and evolution is an R package developed by the Lincoln University molecular ecology lab group to do a range of analyses that various lab members wanted to run that were not yet implemented in R. In particular, the package provides functions for conducting sliding window analyses on DNA sequences, the calculation of identification efficacy of a library of reference DNA sequences, and the segregation of distance matrices into their inter- and intra-specific components.

The above are the main attractions, and the ones that we tend to write about when promoting it in places like the 4th International Barcode of Life Conference. There's a bunch of other neat utilities in there also though. A couple of the ones that I particularly enjoy are tiporder(), which returns the tip labels in the order in which they appear on the tree; paa() which conducts population aggregate analysis on a dataset; and rosenberg() which calculates Rosenberg's probability of monophyly for the nodes on a tree.

Spider is available on CRAN, and R-Forge, the latter providing opportunities to report bugs and to collaborate in the future development of the package should you desire to do so.

Vanuatu Caddisflies

2011-12-13T16:20:00.001+13:00

A recently published paper by Kjell Johanson revises the caddisfly fauna of Vanuatu, descibing 12 new species and providing a key to the species currently known from the archipelago. It is an important contribution to the knowledge of the caddisfly fauna of the region, as most of the previous work done on the fauna of the region is several decades old.

A couple of things stood out to me in this paper. The first is that Orthotricha has not been recorded from any other oceanic Pacific islands. These are small (2-3 mm wing length) creatures, and it is likely that they just haven't been collected elsewhere in the Pacific. The second was their discovery that a female of Triplectides australis had a large number of larvae inside her abdomen. While I was hitherto unaware that ovoviviparity occurred in caddisflies, it turns out that this has been known since 1890, the first instance of it being confirmed by Prof. Wood-Mason in the following manner:

I threw the insect alive into a liqueur-glass of whiskey that happened to be ready at hand.

Adult caddisflies tend to be overlooked by the general public, usually being confused as small, fairly dull-looking moths. Their larvae are aquatic where they form an important part of the macro-invertebrate fauna of streams, and can be useful as indicators of water quality and stream health. Unfortunately, very little biological information is recorded in the paper, and larvae are not considered. In part this is due to Malaise and light traps providing the bulk of the material that was considered in the revision. Discovering and describing larvae and their habitats is a natural application of the taxonomic effort of this paper.

References

Johanson KA, Wells A, Malm T, Espeland M. 2011. The Trichoptera of Vanuatu. Deutsche Entomologische Zeitschrift 58(2): 279-320.

Wood-Mason J. 1890. On a viviparous caddis fly. Annals and Magazine of Natural History 6th series, 6: 139-141.

TVNZ streaming America's Cup races live

2011-11-18T15:26:00.006+13:00

Good news for New Zealand sailing fans: TVNZ is now streaming the AC45 world series matches live. Check out the sailing news page of their website to be directed to the links. Replays can be accessed by clicking through their OnDemand links, but the price paid is having to endure a Microsoft ad before getting into the actual footage. Access to the full replays on YouTube is once again delayed for viewers from NZ, but hopefully will be available in a week or so.

Unfortunately, coverage of the San Diego races has been a bit of a debacle. A lack of communication regarding the course, time of live streams, and delays in the posting of full replays have left a fans with a sour taste in their mouths. I am personally annoyed that the full replays for Port Cities Challenge that kicks off the event are not available. Let us hope that the organisers are learning valuable lessons so they don't make these mistakes again.

Using Sweave with Beamer: A note on fonts

2011-11-02T19:47:00.002+13:00

Recently, I've been preparing a poster using the LaTeX packages Beamer and beamerposter. The poster discusses a bunch of R stuff that I've been doing lately, so I successfully used Sweave to incorporate R code into the poster. However, I had some trouble with package names that I wanted to typeset as small caps. The package names looked the same as the rest of the text. A bit of sleuthing around revealed Sweave as the culprit. In the Sweave.sty package, on line 20, it calls the deprecated LaTeX package "ae", which for some reason doesn't recognise small caps. Changing the package to "lmodern" made small caps turn up correctly within the text.

Unfortunately, my problems had not yet been solved completely. I had mentioned the package names in the titles which were set in bold. I thus had created a fairly commonly encountered bugbear with LaTeX—the non-compatibility of bold and small caps in computer modern font. While there are workarounds for this (see this Stack Exchange and TeX FAQ for more details), unfortunately these solutions did not work with Beamer.

So, I set about finding a font that both looked alright, and would accomodate bold and small caps. I found that using helvetica would be fine, but had to be loaded after Sweave to work. As my Sweave block kept placing the \usepackage{Sweave} immedediately before \begin{document}, I resorted to calling helvetica in the Sweave file itself.

The relevant lines in of the Sweave.sty (lines 18-21) file. Before:

\ifthenelse{\boolean{Sweave@ae}}{%
\RequirePackage[T1]{fontenc}
\RequirePackage{ae}
}{}%

After:

\ifthenelse{\boolean{Sweave@ae}}{%
\RequirePackage[T1]{fontenc}
\RequirePackage[scaled]{helvet}
}{}%

Microscopy mounting media II

2011-10-19T17:55:00.003+13:00

Today I found a brilliantly written, hugely informative, and well-illustrated guide to Safe Microscope Techniques for Amateurs, written by Walter Dioni. It is a series of four articles, originally published in Micscape, the magazine of the Microscopy UK organisation.

"Safe Microscope Techniques for Amateurs" discusses liquid media, solid media, mixed media and glycerin jellies. All techniques are explained clearly and several suggestions for equipment or readily available appropriate subsitutes are given. In summary, the series is an excellent introduction to microscope mounting techniques and gives some very useful tips for making good microscope mounts.

Old codes

2011-10-02T15:23:00.003+13:00

The International Code of Zoological Nomenclature is the document that details the rules of how the scientific names of animals are managed. It's a complex document with a rich history, and it is necessary to consult previous editions for correct knowledge as to the reasoning behind some of the provisions of the code. Old editions tend to be fairly hard to come by, but thankfully the Biodiversity Heritage Library has them digitised and on the interweb for all to enjoy. Thus, it holds copies of the first (1961), second (1964), third (1985), and fourth (current, 1999) editions are all available. The current edition is also available from the official website as an indexed html version.

Jetsetting Dragonflies

2011-09-28T18:04:00.004+13:00

Image: Muhammad Mahdi Karim

Not only not are dragonflies some of the best aeronauts of the insect world, some also have the greatest endurance. A couple of years ago, it was discovered that the globe skimmer dragonfly (Pantala flavescens) migrates from India to South East Africa via the Indian Ocean islands of the Maldives and the Seychelles, and back via East Africa. That's a grand total of around 18 000 km. That's a fair bit further than the 11 000 km I recently traveled from New Zealand to South Africa. It is considered that the round trip takes place over several generations, but it's still an amazing phenomenon.

For more information, there's news reports from Wildlife Extra and the Daily Mail; and a blog post from National Geographic. There's even a graphic on DeviantArt celebrating the journey. To hear it from the horse's mouth (so to speak) watch a video of Charles Anderson himself talking about his findings.

Beamer themes

2011-09-20T18:48:00.004+12:00

I enjoy using Beamer for my presentations. Initially, the limitations it imposes (particularly on graphics placement) are irksome, but after a while you realise that they actually help you create better presentations faster. I've tried 'quickly' putting together something in PowerPoint since starting to use Beamer and found it so fiddly that I went straight back and did it all in Beamer. However: I still find the themes and colour schemes provided in the base distribution of beamer to be less than ideal, and disobey the university's guidelines for presentations. As I garner the skills to start preparing my own themes, a list of customised Beamer themes will provide inspiration and guidance. In particular, I like the look of the Torino theme.

Extracting comments from PDFs

2011-09-15T16:25:00.003+12:00

I received a reviewer's response from one of my submitted papers a while ago, and have delayed working on it because they had written their comments in the PDF using "sticky notes". Unfortunately, these notes don't print very well. I like to be able to read things off the computer, so this presented a problem. Thankfully, PDFs encode their sticky note comments in ASCII-formatted text, which meant that I was able to extract the comments using the beautiful linux command line:

grep -o --text /Contents\([^/]* review.pdf | tee comments.txt

This single line resulted in a nice text file for me to print as I please.

1 2 3 steps to publishing a scientific comment

2011-09-14T13:42:00.003+12:00

For a humorous, yet ultimately disturbing tale, check out Rick Trebino's How to publish a scientific comment in 1 2 3 easy steps, then wonder how scientific journals managed to achieve the power over the research process that they currently have.

Quote: GK Chesterton from 'Orthodoxy'—Nature

2011-09-13T11:00:00.003+12:00

The essence of all pantheism, evolutionism and modern cosmic religion is really in this proposition: that Nature is our mother. Unfortunately, if you regard Nature as a mother, you discover that she is a step-mother. The main point of Christianity was this: that Nature is not our mother: Nature is our sister. We can be proud of her beauty, since we have the same father; but she has no authority over us; we have to admire, but not to imitate. This gives to the typically Christian pleasure in this earth a strange touch of lightness that is almost frivolity. Nature was a solemn mother to the worshippers of Isis and Cybele. Nature was a solemn mother to Wordsworth or to Emerson. But Nature is not solemn to Francis of Assisi or to George Herbert. To St. Francis, Nature is a sister, and even a younger sister: a little, dancing sister, to be laughed at as well as loved.

Chesterton GK. 1908. Orthodoxy. Image, New York (2001 Edition)
Chapter VII: The Eternal Revolution. Page 115.

post-installation script error solved

2011-09-12T18:52:00.004+12:00

Had some problems today with aptitude getting its knickers in a knot, returning the error

dpkg: error processing install-info (--configure):
subprocess installed post-installation script returned error exit status 1

. This blog post helped to solve the problem simply and easily with the commands:

sudo rm /var/lib/dpkg/install-info.postinst
sudo aptitude reinstall install-info

Many thanks to azimout!

Alternately coloured line environment with fancyvrb

2011-09-11T18:08:00.004+12:00

Recently, while typing up an R tutorial, I used the LaTeX fancyvrb package to create two environments—one coloured blue for R commands, and one coloured red to display R output. This worked well for large blocks of each type. Then I decided I wanted to display a number of one-line commands and output alternately. Looking up the fancyvrb package documentation, it was easy to get alternate colours. The problem was, it did it globally. My environments for input and output also went psychedelic.

After a bit of messing around, I discovered the following solution. My red environments remain red, my blue environments stay blue, and alternate colours only turn up when I want them to!

\documentclass{article}
\usepackage{fancyvrb}
\usepackage{color}

\newcommand{\ChangeLine}[1]{%
\ifodd\value{FancyVerbLine}%
\textcolor{blue}{#1}\else\textcolor{red}{#1}\fi}

\DefineVerbatimEnvironment{blueEnv}{Verbatim}{formatcom=\color{blue}}{}
\DefineVerbatimEnvironment{redEnv}{Verbatim}{formatcom=\color{red}}{}
\DefineVerbatimEnvironment{alternate}{Verbatim}{formatcom=\renewcommand{\FancyVerbFormatLine}{\ChangeLine}}{}

\begin{document}

\begin{Verbatim}
aaaaaaaaaaa
bbbbbbbbbb
cccccccccccc
ddddddddddddd
\end{Verbatim}

\begin{blueEnv}
aaaaaaaaaaa
bbbbbbbbbb
cccccccccccc
ddddddddddddd
\end{blueEnv}

\begin{redEnv}
aaaaaaaaaaa
bbbbbbbbbb
cccccccccccc
ddddddddddddd
\end{redEnv}

\begin{alternate}
aaaaaaaaaaa
bbbbbbbbbb
cccccccccccc
ddddddddddddd
\end{alternate}

\end{document}

Guardian article about academic publishing

2011-09-01T21:28:00.005+12:00

I agree with a lot of this article in the Guardian. Especially:

Reading a single article published by one of Elsevier's journals will cost you $31.50. Springer charges €34.95, Wiley-Blackwell, $42. Read 10 and you pay 10 times. And the journals retain perpetual copyright. You want to read a letter printed in 1981? That'll be $31.50.

I get especially annoyed with the said letter was published in 1881, and therefore out of copyright yet they still charge you for it.

Yet another estimate of the number of species on earth

2011-08-28T12:42:00.003+12:00

This week in PLoS Biology, paper was published that estimates the number of species on earth being around the 8 million mark (give or take 2 million). This study takes a rarefaction-type approach, seeing how the rate of discovery of higher taxa is decreasing, and extrapolating from that to the species level, resulting in the figure of 8.7 million with an error range of 1.3 million.

This study is nothing new—there's been a number of estimates published over the past two decades that attempt to give a number to the total diversity of life on earth. While this one does appear to be a bit more robust, all these studies are based on various assumptions, and have given some very different figures. There seems to be some sort of convergence on the 10 million mark, but at the end of the day, we just don't know.

I guess the value of these papers are that they make public how far we have to go before we know the most basic thing about the other organisms that share the world with us. I still surprise people when I tell them my tales of discovering new species, the general belief being that we know essentially all there is to know about biology. However, unless there are some useful outcomes (e.g. increased funding or employment) from them, I view these papers with a certain cynicism. We know the task ahead of us is huge. It'd be great to be able to dive into it whole-heartedly and without needing to worry about the finances.

The paper did alert me to the World Taxonomist Database, a register of taxonomists from around the world and encompassing all taxa. The register gives contact details for each of the researchers in the database, as well as their taxonomic and geographic interests. It's a very handy resource.

Harvard's Caribbean Insects

2011-08-26T18:26:00.002+12:00

Harvard University has has an interest and presence in the Caribbean for the past 150 years. As you can imagine, they've accumulated a lot of information on the biota of the region. They've made a sizable portion of their entomological knowledge available on the Caribbean Insects @ Harvard Entomology webpage, which is very nice of them. of particular interest are is the insect and plant database which you can search to find specimen information, or cool photos, like the image of Eurhinus festivus suturalis above. They've also made a whole lot of papers available through their taxonomic literature database, though unfortunately I was unable to access the database for some reason or another. Finally, they've made a number of posters of different taxa available, and very kindly sent me copies of their beautiful weevil and bark beetle ones. Good on them for creating all this cool stuff!

Mounting insect specimens in resin

2011-08-26T12:59:00.002+12:00

I do a number of school presentations throughout the year, and am frequently asked if I can bring a few specimens to show the students. I am usually fairly loathe to do so, because of the fragility of most specimens, and the fact that the majority of my specimens are fairly small and therefore not especially exciting. Getting into work today, I saw a couple of resin-encased beetles I have received as gifts and had a brainwave. A quick search for instructions for how to do it revealed a number of tutorials. The one by Dalchem is useful, as is the guide provided by Complete Paints.

Rings and starships: A new shark embraces pop culture

2011-08-24T10:03:00.008+12:00

I couldn't let this one go past without commenting on it. Today in Zootaxa, a description was published today that has references to two highly regarded elements of pop culture in the past 50 years. Gollum suluensis is a deep water shark from the Philippines whose name calls to mind Gollum from The Lord of the Rings, and Captain Sulu from Star Trek.

Before latin scholars point out that the -ensis suffix to the specific name refers to a place not to a person, I will clarify the specific name actually refers to the Sulu Sea. The generic name though is genuine. Established in 1973 by Leonard Compagno, the original description gives this explanation for the name:

Gollum (treated as a masculine noun), named for the antihero of J. R. R. Tolkien's Lord of the Rings trilogy, to whom this shark bears some resemblane in form and habits.

Appropriately enough, the type species lurks around New Zealand.

References
Compagno LJV. 1973. Ctenacis and Gollum, two new genera of sharks (Selachii: Carcharhinidae). Proceedings of the California Academy of Sciences 4(39): 257–272.

Last PR, Gaudiano JP. 2011. Gollum suluensis sp. nov. (Carcharhiniformes: Pseudotriakidae), a new gollumshark from the southern Philippines. Zootaxa 3002: 17-30.

Bohumiljania of New Caledonia

2011-08-22T22:08:00.004+12:00

Today in Zootaxa a paper was published describing a number of species in the leaf beetle genus Bohumiljania from New Caledonia. Unfortunately, these species aren't going to win many prizes in the beauty stakes—they're all pretty nondescript, generic looking chrysomelids (See the picture of Bohmiljania aoupinie above). However, it belongs to a group (the Spilopyrinae), that displays a classical Gondwanan distribution pattern so it will be of interest to those people who are interested in the biogeography of New Caledonia. These beetles tend to be found in mountainous areas, and all known hostplants are in the Myrtaceae.

Incidentally, this is Zootaxa's 3000th issue. Pretty good going for a journal that celebrated its 10th birthday on 28 May this year.

Reference:
Reid CAM, Beatson M. 2011. Revision of the New Caledonian endemic genus Bohumiljania Monrós (Coleoptera: Chrysomelidae: Spilopyrinae). Zootaxa 3000: 1-43. The full 6 MB article is here

Faraday Institute

2011-08-19T17:37:00.004+12:00

Today I went to a talk by John Wood, based on the question "Is Man a Machine?". The talk in a nutshell discussed the uncertainty inherent in scientific measurement and human perception, the difference between man and machine being freedom, and that Christ sets us free to question, to investigate and to think.

He also directed us to the Faraday Institute for Science and Religion, particularly the recently developed resource Test of Faith. This resource contains interviews with a number of leading scientists and theologians discussing the connections between the two fields and what they each can offer. In addition, the Faraday Institute website itself contains a large number of audio and video recordings of lectures discussing the interface between religion and science, and published documents on the subject also.

Invertebrate Macro Photography

2011-08-18T20:27:00.010+12:00

Earlier this year, I met up with up-and-coming New Zealand nature photography Bryce McQuillan, who specialises in macro photography of invertebrates, particularly spiders. He puts the majority of his photos on Flickr and are well worth checking out.

Nature photographers are uniquely able to capture and portray the beauty and wonder of the natural world, and communicate it to the public in a way that can be broadly appreciated. The photos of the chalcidoid wasp above and the entomobryoid springtail below demonstrate this. These invertebrates are minute and incredibly beautiful. They are common and widespread, but their small size means that most people are not aware of them. The adage of one picture being worth 1000 words is particularly relevant in this situation.

Bryce's favorite group are spiders, which are particularly needy in the PR department. His photographs are able to capture their beauty and personality in such a way that even those who have no natural fondness for spiders are able to see beyond their "creepy-crawly" facade.

And this is why nature photographers are so important. Photos are an acccessable medium that people are easily able to understand and relate to. They are vital in the communication of the importance of biodiversity to the general public.

Book review: "Every Living Thing" by Rob Dunn

2011-08-16T11:32:00.002+12:00

The subtitle of this book, "Man's Obsessive Quest to Catalog Life, from Nanobacteria to New Monkeys" caught my eye as I was looking through a book sale table. Being one of those who desires to contribute to this quest, I was delighted to find it. The book is an enjoyable overview of selected personalities whose lives and work define (for the author) the growth of our knowledge of biodiversity. Their stories are told with understanding and humour.

Starting with indigenous knowledge of biota, he introduces us to Linnaeus and Leeunwenhoek before describing modern scientists whose work has increased our appreciation for the diversity of life and expanded our understanding of its limits. The journey described is one that progresses from a focus on the species with greatest impact on daily life, to an understanding that "the rest of life does not revolve around us, nor is it like us (p. 247)". Comparing this discovery to the Copernican revolution, he argues that there remains the need for humility in assessing our knowledge and acheivements in discovering the natural world.

A major theme of the book is the obsessiveness that drives the scientists who are described. Being one who shares a similar outlook, I can sympathise with the men and women described. Indeed, I find myself wishing I could be (to a certain extent) in their shoes. However, I don't know if someone who doesn't have the same drive and desires would find the portrayals heroic or pathetic. As the author describes,

"If systematists are socializing, it means, to many of them, simply time they are not looking at the organisms they really love. The obscurity of the things on which taxonomists work does not lessen their focus. In fact, it may heighten it. To dig into their subject, they have to dig so far in, focus so intensely, that the rest of the world seems farther and farther away." (p. 101)

Balance is important, and many of the best taxonomists I've met understand that. But it is hard, when there's so many fascinating and beautiful creatures out there not to succumb to the temptation.

In summary, "Every Living Thing" is an accessible and enjoyable book that tells the story of a few of the personalities who have contributed to the classification and discovery of the organisms we share this world with.

Dunn, R. 2009. Every Living Thing. Man's Obsessive Quest to Catalog Life, from Nanobacteria to New Monkeys. HarperCollins, New York.

America's Cup revamped

2011-08-15T21:06:00.004+12:00

The America's Cup World Series had it's first winner today, and of course I'm happy because Team New Zealand won it. I've always been keen on the America's Cup, but I dare say that the latest revamp of the competition has me excited. The boats look cool, go fast, and having them essentially identical between competitors makes the competition less an arms race and more a test of sailing. The Russell Coutts/Dean Barker rivalry is still In addition, having a lead up to the main event with regattas in multiple locations will make the competition more accessable and will hopefully diminish the (valid) criticisms that the America's cup was becoming merely a distraction for the rich. Sure, there's still an awful amount of money being spent on the water there, but at least it looks cooler now... It's been in Portugal for the last week or so, and is moving to Plymouth, UK in mid-September.

Watch the replay of the 14 August fleet race here

tlmgr not available for Ubuntu

2011-08-08T19:58:00.003+12:00

One of the hardest things about LaTeX is the way it manages packages. Doing it manually is (in a word) annoying. When I was on windows I loved MikTeX for the ease by which it downloaded and installed extra packages, and I was disappointed when this functionality wasn't available on Ubuntu. Lately though I discovered that TeXlive had a similar package manager called tlmgr, and I started getting excited. When installing TeXlive though, I was dismayed to find that tlmgr did not work. A bit of a google search later I found that this was reason:

There is no way that a second package manager independent of the normal packaging infra structure (apt here, or rpm, or whatever) can work, because it will break the main system.

TeX Live Manager is currently only for system trees. THere is a patch in the dev repository for activating user mode, so that tlmgr can be used to manage TEXMFHOME, but it has not been worked on since quite some time (Norbert Preining on launchpad.net)

I take this to mean that there's only room in Ubuntu-town for one package manager, and synaptic is it. This is fair enough I guess, but it is still unfortunate.

Norbert goes on to say "get your hands dirty and help coding!" Unfortunately, my perl is non-existent, so I'll have to give it a miss until such a time as I actually have some idea what I'm doing.

Quote: James Hannam on science and religion

2011-08-07T20:51:00.003+12:00

One of the best quotes I've seen recently about the interface between science and religion. It's constructive and promotes dialogue, unlike a lot of the rhetoric that unfortunately gets more publicity.

"Nonetheless, today, science and religion are the two most powerful intellectual forces on the planet. Both are capable of doing enormous good, but their chances of doing so are much greater if they can work together. The award of the Templeton Prize to Lord Rees is a small step in the right direction."

James Hannam on the "Soapbox Science" blog.

Pressing plants

2011-08-07T20:00:00.003+12:00

Weevils feed on plants, with many species being very picky about the plants they eat. These host interactions are very important for understanding the ecology of both the weevils and the plants. When collecting therefore, it is important that the plants from which weevils have been collected are identified and noted. Therefore, as a weevil guy, it is important that I have a fair understanding of plant identification.

A key aspect of the process is knowing the proper way to collect, preserve and label plant specimens. Searching the internet has revealed good guides on the University of Florida Herbarium webpage and a PDF produced by the Herb Society of America.

It's not too arduous—pressing plant material can be done by placing the material under a few big books. Much more important is knowing what to put on the label. Plant specimens tend to be mounted on large (A3) sheets of paper, giving a lot of space to write pertinent information. Therefore, major additional categories from that on insect labels include its frequency (is it rare, common, or something in between?), and details of the plant's height, growth habit and description of aspects of the plant that disappear when pressed (e.g. colour of flowers, smell and sap). There's also the space and ability to provide exact locality data and more detailed habitat information than is possible with insect labels.

Quote: GK Chesterton from 'Orthodoxy'

2011-07-18T10:09:00.003+12:00

Let us suppose we are confronted with a desperate thing—say Pimlico. If we think what is really best for Pimlico we shall find the thread of thought leads to the throne or the mystic and the arbitrary. It is not enough for a man to disapprove of Pimlico: in that case he will merely cut his throat or move to Chelsea. Nor, certainly, is it enough for a man to approve of Pimlico, for then it will remain Pimlico, which would be awful. The only way out of it seems to be for somebody to love Pimlico: to love it with a transcendental tie and without any earthly reason. If there arose a man who loved Pimlico, then Pimlico would rise into ivory towers and golden pinnacles; Pimlico would attire herself as a woman does when she is loved. For decoration is not given to hide horrible things: but to decorate things already adorable. A mother does not give her child a blue bow because he is so ugly without it. A lover does not give a girl a necklace to hide her neck. If men loved Pimlico as mothers love children, arbitrarily, because it is theirs, Pimlico in a year or two might be fairer than Florence.

Chesterton GK. 1908. Orthodoxy. Image, New York (2001 Edition)
Chapter V: The Flag of the World. Page 66.

New Zealand Weevil Image Database now online

2011-07-16T09:39:00.008+12:00

In the last couple of days, the TFBIS funded New Zealand Weevil Image Database has been put online. The project involves taking high-quality photos of representatives of every weevil genus (including the Etheophanus sp. shown above) known from New Zealand. It is a great effort, and one that I will make full use of in my research. Not only will it help assisting others to identify NZ weevils, but it will also serve as a useful aid for overseas workers wanting to become familiar with the diversity of weevils in this country, and help in the efforts to produce a coherent classification of the world weevil fauna. Mainly though, it is a splendid showcase of the diversity and beauty of the weevils in NZ, and shows some of the extraordinary forms of many of our species. My picks for the most bizarre are Stephanorhynchus, Geochus, Ectopsis and Colabotelus.

Building R packages for Windows when you don't use it.

2011-05-02T18:47:00.000+12:00

Are you a non-windows user wanting to share your R package with others who do use windows? There's a handy utility (http://win-builder.r-project.org/)that allows you to upload your .tar.gz file and it checks it, builds it, and sends you a link to download a nice, shiny .zip file to give to your mates. Problem solved.

Subversion

2011-04-22T15:59:00.005+12:00

To start a new project on R-Forge, I've had to starting coming to grips with Subversion, the widely used program for source code versioning. To help me, I've found this tutorial very helpful for learning the "Subversion lifecycle" and the general use of the program. The Subversion book is a wonderful resource, but I'm currently not yet at the stage where my knowledge of the thing is at the level required to understand it properly.

Simplifying polygon shapefiles in R

2011-04-20T14:29:00.003+12:00

Recently I downloaded the Crosby Code shapefile from Landcare Research's LRIS server for use in some publications I'm preparing. This shapefile is incredibly detailed, far more so than what I require. This detail means that it takes a while for the map to be plotted each time. As detail is less important for me than speed of plotting, I decided to try and simplify the map.

The first thing we needed is to load the packages required and the shapefile itself:

library(maptools)
library(shapefiles)

CCBound <- readShapePoly("nz-area-codes-for-recording-specimen-localities")
CCBound2 <- CCBound

system.time(plot(CCBound2))
user system elapsed
9.537 14.789 142.760

I'm wanting to plot this map multiple times, so waiting 2.5 minutes each time is not at all desirable. The first thing to do was to check out the structure and composition of the object.

str(CCBound, max.level = 3)

sapply(CCBound@polygons, function(x) length(x@Polygons))
62 62 1 1 182 216 2332 81 158 2012 1 22 126 284 45 41 1 35 1 3 1 68 30 78 142 333 1 14 1070 1257 716

area <- lapply(CCBound@polygons, function(x) sapply(x@Polygons, function(y) y@area))

quantile(unlist(area))
0% 25% 50% 75% 100%
3.379739e-10 1.978036e-08 6.223511e-08 2.120671e-07 1.952179

Part of the reason why this is plotting so slowly is the enormous number of polygons to be plotted---9376 in total. We can also see that the majority of these polygons are very small. These polygons represent the myriad of small offshore islands around the NZ coast. As I'm wanting to look at NZ as a whole, these islands are not significant. If we can get rid of these, we will be a long way toward making a leaner, meaner version of the shapefile. We first need to find out what polygons within each larger group are large enough to be worth keeping, then remove them.

mainPolys <- lapply(area, function(x) which(x > 0.001))

CCBound@data <- CCBound@data[-c(1:2),]
CCBound@polygons <- CCBound@polygons[-c(1:2)]
CCBound@plotOrder <- 1:length(CCBound@polygons)
mainPolys <- mainPolys[-c(1:2)]

for(i in 1:length(mainPolys)){
  if(length(mainPolys[[i]]) >= 1 && mainPolys[[i]][1] >= 1){
    CCBound@polygons[[i]]@Polygons <- CCBound@polygons[[i]]@Polygons[mainPolys[[i]]]
    CCBound@polygons[[i]]@plotOrder <- 1:length(CCBound@polygons[[i]]@Polygons)
  }
}

When we look at mainPolys, we see the first two larger groupings of polygons have no significantly sized polygons in them. We get rid of these in the following block of data. @plotOrder needs to be the same length as @polygons or else the object will create an error. The second block of code crawls through the object retaining only those polygons we found in mainPolys.

When we plot the returned object:

system.time(plot(CCBound))
user system elapsed
2.536 0.292 3.211

We see that the plotting time is much more efficient. Depending on our requirements, we could leave it as it is. Being a devil for punishment however, 3 seconds is still a little too slow. There is still a lot of detail in the edges of the main polygons that is unecessary for my requirements. This detail can be simplified using the dp() function in the shapefiles package. Once again, we create a loop that goes through the object simplifying each of the polygons within it. dp() works only on dataframes, so we need to break each @coords matrix into a dataframe, run dp(), then convert it back into a matrix.

for(i in 1:length(CCBound@polygons)){
  for(j in 1:length(CCBound@polygons[[i]]@Polygons)){
    temp <- as.data.frame(CCBound@polygons[[i]]@Polygons[[j]]@coords)
    names(temp) <- c("x", "y")
    temp2 <- dp(temp, 0.01)
    CCBound@polygons[[i]]@Polygons[[j]]@coords <- as.matrix(cbind(temp2$x, temp2$y))
  }
}

WARNING: This code takes a while to run---around 5 minutes on my machine. The time increases as you decrease the threshold given to dp(). When I had it set to 0.001 it took 7 minutes. However, the time taken to plot the shapefile is now:

system.time(plot(CCBound))
user system elapsed
0.072 0.096 0.873

Much better! The final thing to do now is to compare the difference between the original and the final product.

png("comparison.png", width=800, height=500)
layout(matrix(1:2, ncol=2))
plot(CCBound2)
title(main="Original shapefile")
plot(CCBound)
title(main="Modified shapefile")
dev.off()

Looks pretty good to me! When looking at the two of them, you can tell that the modified version has been, well, modified. However, for the purposes I have in mind, the modified version is more than adequate.

Data is of course reproduced with the permission of Landcare Research New Zealand Limited. Get your own copy of it here.

Pseudoscorpions

2011-04-12T12:38:00.005+12:00

Pseudoscorpions are reasonably common, though inconspicuous, creatures that are found in a range of environments, particularly soil and leaf litter. They are predacious, feeding on things like springtails, bark lice and other invertebrates that they catch with their pedipalps.

I've been interested in pseudoscorpions for quite some time, though I have not yet deliberately retained specimens or allowed myself time to look at them. I recently stumbled across a site that contains a lot of useful information for the budding pseudoscorpion enthusiast. The pseudoscorpion site contains information on how to collect, preserve and identify these usually overlooked creatures.

For those interested in the New Zealand fauna, Max Beier published a key to the species of New Zealand and Norfolk Island in 1976 It is available online here on the Bugz Bibliography of New Zealand Insects Online. Beier also published on the pseudoscorpions of Micronesia, also available on Bugz.

NB: Bugz unfortunately does not provide completely stable URLs for the papers in the database. If the direct links to the papers do not work, search Bugz manually for access to the papers.

References:
Beier M. 1976. The pseudoscorpions of New Zealand, Norfolk and Lord Howe. New Zealand Journal of Zoology 3(3):199-246

Beier M. 1957. Pseudoscorpionida. Insects of Micronesia 3(1):1-64

Two R functions for working with DNA alignments

2011-03-29T17:26:00.005+13:00

Recently I wrote a couple of small functions as a result of work done by myself and others in my lab group. The first is a function that determines what sites in a sequence alignment are ambiguous (i.e. not A, G, C or T).

require(ape)
data(woodmouse)

is.ambig <- function(x){
   x <- as.matrix(x)
   bases <- c(136, 72, 40, 24)
   ambig <- apply(x, 2, FUN=function(x) sum(as.numeric(!as.numeric(x) %in% bases)))
   ambig > 0
}

is.ambig(woodmouse)

This function utilises the bit-level coding scheme that Emmanuel Paradis developed for encoding sequences in R. The unambiguous bases A, G, C and T have the numeric values 136, 72, 40 and 24 respectively. This function figures out which sites don't have these values and returns a vector of TRUEs and FALSEs, TRUEs being ambiguous bases.

The second function is an implementation of Tajima's K, published as equation A3 in Tajima 1983

tajima.K <- function(x, prop = TRUE){
   res <- mean(dist.dna(x, model="N"))
   if(prop) res <- res/dim(x)[2]
   res
}

tajima.K(woodmouse)

This function calculates the mean number of sites that are different between any two sequences. As a default, it returns the result as a proportion of the length of the alignment. Setting prop = FALSE will return the result as the actual number of sites.

References:
Tajmia F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.

Freely available Digital Elevation Models for New Zealand

2011-02-27T17:33:00.003+13:00

For people wanting to view aspects of New Zealand's amazing topography, a number of Digital Elevation Models are freely available from Geographx, a company specialising in producing New Zealand geographic information and atlases. Thanks Geographx!

Amphibious caterpillars in Hawaii

2011-02-17T10:18:00.010+13:00

The Hawaiian Islands are renowned for their unique biota that display a number of bizarre adaptations that do not appear elsewhere in the world. Widely known examples of these include the predacious caterpillars in the genus Eupithecia, and the wekiu bug (Nysius wekiuicola) that lives on Mauna Kea eating insects that are blown to them on the wind.

Recent work by Daniel Rubinoff and Patrick Schmitz have added another example to the list: amphibious caterpillars. In a paper published in March in PNAS they describe the ecology of some recently discovered 12 currently undescribed species of the moth genus Hyposmocoma that are able to develop equally well both in and out of water. Intriguingly, a phylogenetic tree hypothesizing the evolution of these insects suggest that this amphibious trait arose independently at least four times, an unexpected result for a specialised trait such as amphibiousness.

The major driving force for the development of this unique lifestyle in Hawaii is believed to be due primarily to a lack of competition. Hawaii lacks the major aquatic insect orders of the stoneflies, mayflies and caddisflies (the latter two represented by introduced species only), leaving Hawaii's freshwater environments unexploited. Hyposmocoma has stepped into the breech.

In addition to the written paper, the authors have provided movies showing the caterpillars moving in and out of the water. They are provided as supplementary information to the paper and available on the PNAS website here and here. Unfortunately, a David Attenborough documentary this isn't. There is no informative commentary spoken with a British accent, but it is an interesting watch nonetheless.

References:
Rubinoff D, Schmitz P. 2010. Multiple aquatic invasions by an endemic, terrestrial Hawaiian moth radiation. Proceedings of the National Academy of Sciences of the United States of America 107(13):5903-5906

Zimmerman EC. 1957. Insects of Hawaii. Volume 6, Ephemeroptera-Neuroptera-Trichoptera and Supplement to Volumes 1 to 5. University of Hawai'i Press.

GIS Shapefile of DOC-administered land

2011-01-24T20:47:00.012+13:00

The New Zealand Department of Conservation, fondly known as DOC is the department in charge of the bulk of New Zealand's publically owned land. Their best known pieces of real estate are the 14 national parks that conserve some of New Zealand's most iconic landscapes and least modified habitats. Less well known are the legion of scenic reserves and conservation areas that make up a substantial portion of our property. These smaller reserves are no less interesting, and tend to protect small but important areas of near-natural habitat, or intriguing aspects of New Zealand history. Until now, the main way of finding out about them is by stumbling across them while on a road trip, or by word-of-mouth. However, now DOC has released a GIS shapefile that shows the boundaries of all the conservation estate, along with information on what acts of parliament they're protected under and how large the reserve is.

It is important to note that this shapefile only shows those reserves in DOC's ownership and management. Thus, it does not show community-initiated reserves such as Maungatautari Ecological Island or QEII Covenants; nor does it show reserves owned by city councils, like the Auckland Regional Parks or Christchurch's Port Hills Reserves.

Koleopterologische Rundschau

2011-01-19T10:45:00.005+13:00

The Austrian entomological journal Koleopterologische Rundschau is an excellent serial that is focussed on beetle taxonomy. It publishes a single issue a year, but this issue is filled to the brim with interesting and informative papers on beetles of all families from Europe and the world. Issues prior to 1990 (Volumes 1-59) are freely available online. PDF versions of papers published since then are also available, but at a cost. Unlike some other outfits though, this cost is actually reasonable; being around 1 Euro per paper.

The Lay of Gudrún (stanzas 100–101)

2011-01-15T18:09:00.004+13:00

At the dark doorways
They dinned and hammered;
there was clang of swords
and crash of axes.
The smiths of battle
smote the anvils;
sparked and splintered
spears and helmets.

In they hacked them,
out they hurled them,
bears assailing,
boars defending.
Stones and stairways
streamed and darkened;
day came dimly —
the doors were held.

The Lay of Gudrún, stanzas 100–101.
JRR Tolkien and Christopher Tolkien. (2009). The Legend of Sigurd and Gudrún. Harper Collins.

Changing phylogeny tip labels in R

2011-01-14T20:39:00.004+13:00

During the process of molecular systematic research, specimens are given code names and numbers to keep track of data through the pipeline. These can contain a lot of information of relevance to the researcher, but unfortunately are meaningless to others who aren't as involved with the data. On publication, it is necessary to change the names from the code to a label that is more widely understood. This process can be tedious and fiddly, particularly when it needs to be done multiple times.

The following is a simple R-based solution for changing the tip labels of phylogenetic trees. First, we need to create a tree and a dataframe containing both the specimen codes and the ultimate labels.

library(ape)
tr <- rtree(5)
d1 <- c("t1","t2","t3","t4","t5")
d2 <- c( "paste(italic('Aus bus'), ' top')", "paste(italic('Aus bus'), ' bottom')", "paste(italic('Aus cus'), ' middle')", "paste(italic('Aus cus'), ' north')", "paste(italic('Dus gus'), ' south')" )
d <- as.data.frame(cbind(label=d1, nlabel=d2))

The code in the nlabel column contains code defining a plottable expression that enables scientific names to be formatted as italics. In my work, I saved this table as a separate file which I call with read.table("file.txt", header=TRUE, sep="\t", stringsAsFactors=FALSE, quote=""). The quote argument is important as it carries the nested quotes through into the dataframe properly.

The business of actually changing the tip labels is done with the following lines:

tr$tip.label<-d[[2]][match(tr$tip.label, d[[1]])]
tr$tip.label<-sapply(tr$tip.label, function(x) parse(text=x))

The first line enters the expressions for the new labels in the correct order. The second line converts the character string into a printable expression.

Plot the tree and voila!

Ubuntu translations

2011-01-13T10:04:00.000+13:00

A key part of the Ubuntu philosophy is their emphasis on making computers usable in one's language of choice:

We believe that every computer user should be able to use their software in the language of their choice.

The wiki page provides an entry point for those interested in contributing translations to the project. The process is managed through a project launchpad. Of most interest to me are the Samoan, Maori and Marshallese translations.

Origami

2011-01-11T13:04:00.006+13:00

Origami is pretty amazing. While my skills have never progressed beyond the traditional crane, I am always amazed at how people can make a square of paper into something amazing. This website shows a particularly spectacular gallery including the origami cicada pictured above. What's really cool is that it also includes a diagram of the folding patterns for each model. All that's needed is the interpretation of said diagrams, and the time to do it!

Setting up a mail server on Ubuntu

2010-12-16T19:57:00.002+13:00

Yesterday I bought a cheap computer as a phylogenetic workhorse. Today I installed PhyLiS, and have been working on getting a mail server configured so that I can get the thing to automatically send me results of analyses over the coming weeks. This blog post gave me the general gist of the commands required to send mail. After a few unsuccessful attempts at sending mail, I learned from this site that I needed to set myself up as a mail server. Thanks to the community documentation for Postfix, I was able to fairly painlessly it up and now have the ability to send messages from the linux command line.

Apodrosus revision and blog

2010-11-19T17:42:00.005+13:00

Apodrosus is a genus of broad-nosed weevil found in the isles of the Caribbean. Apodrosus wilcotti, pictured above, is from Puerto Rico. It has recently been revised in a well written and illustrated paper by Jennifer Girón and Nico Franz. This paper was part of Jennifer's Masters degree project, and the process of conducting the revision was chronicled on her blog, appropriately titled Apodrosus. It's a great insight into the taxonomic process, and the combination of scientific thought, careful observation and personal passion that it requires. Other valuable outputs from Jennifer's work include a poster and a presentation.

HTML helps

2010-11-18T19:49:00.002+13:00

I am not a particularly on-to-it web designer (as you can probably guess by my having a blogger blog), having a rudimentary knowledge of HTML and not having either the time or the incentive to enter the brave new world of cascading style sheets and the like. While there are a good many websites that help with learning and remembering HTML tags, I've found the w3schools.com page to be particularly useful. The categories are not always aligned with my intuition, but it's good nonetheless.

Asian Beetle Websites II

2010-11-15T19:56:00.005+13:00

In addition to the websites on Asian beetles mentioned previously, here's a couple more which are worth visiting.

The first is the Kisti website that provides online access to issues of Insecta Koreana and the Journal of Asia-Pacific Entomology, both of which have many articles written in English. In addition they have issues of the Korean Journal of Applied Entomology and the Proceedings of the Korean Society of Applied Entomology Conference which are in Korean.

The second site is the insect collection database of the Kyushu University Museum (English page). Many of the database entries have got habitus photographs including the Acallinus tuberculatus shown above. Unfortunately, the encoding seems to be incompatible with my font set, which makes it look ugly and hard to navigate on my machine.

Using pdfpages to rotate odd pages only

2010-11-10T18:21:00.004+13:00

Today I scanned a document to PDF. It was a large document, and I scanned it in stages. No worries about putting the pieces together—that's what the LaTeX package pdfpages is for. What did cause a bit of a problem was that the odd and even pages were oppositely orientated. When I scanned the pages I had to turn the book around, meaning that all the odd pages were upside down.

To rectify this problem I had to delve into the dark world of LaTeX programming. It was an adventure, but thankfully it wasn't too difficult. What I came up with was the following tex file:

\documentclass[a4paper,twoside]{memoir}

\newcounter{number@}

\usepackage{pdfpages}

\begin{document}

\setcounter{number@}{0}

\loop\ifnum \value{number@} < 6 %CHANGE for each document
\stepcounter{number@}
   \ifodd \value{number@}
      \includepdf[pages=\arabic{number@}, angle=180]{document}
   \else
      \includepdf[pages=\arabic{number@}]{document}
\fi
\repeat

\end{document}

To illustrate, I've made an example PDF file to test it on. This test file is an open access paper from Zootaxa, the original of which is available here.

Do remember to change the number that \value{number@} is being compared to. This number is the total pages in "document.pdf", and I haven't yet figured out how to automatically retrieve it. Doing so would've consumed more time than I can afford just now.

Particularly helpful in this adventure was the Tralics site that contains documentation on all TeX commands, and this site on counters.

South Pacific Study

2010-11-08T14:42:00.003+13:00

South Pacific Study is a Japanese periodical that publishes scholarly articles on a diverse range of subjects of relevance to the South Pacific in a very broad sense. The scope of the journal is extremely wide—you'll find articles ranging from analyses of Buddhist missionary activity, to measurements of volcanic SO₂, to the biology of pests, to taxonomic papers. The icing on top is that these articles are freely available online, back to around 2000. Tables of contents and some articles prior to then are also available.

"Kairos" and the universality of Christ

2010-11-07T19:41:00.001+13:00

A central Christian doctrine is the universality of Jesus' death and resurrection and Lordship. This means that the spiritual needs of all people—whether they originate from Europe, India, Saudi Arabia, Cameroon, PNG or Japan—can be fulfilled by following Jesus. Simeon, speaking over the newborn Jesus: "A light to bring revelation to the Gentiles and the glory of Your people Israel" (Luke 2:32 NKJV). Jesus himself: "If I am lifted up from the earth, I will draw all peoples to Myself" (John 12:32 NKJV).

Revolutionary stuff, particularly in this age of post-modern thought and the promotion of pluralism and tolerance. In actual fact, however, the above admission of the universal sufficiency of Christ can promote a love for others that is far greater and deeper than a live-and-let-live tolerance of those differences.

Modern mission training recognises the beauty and significance of different cultures and promotes the understanding of different cultures by all Christians. It also maintains that Christ should be seen as the fulfillment of the hopes and dreams of each culture, on the premise that every culture has legends, beliefs and traditions that point to the one true God. Examples of these can be found in Don Richardson's very interesting and inspiring book "Eternity in Their Hearts". Finally, current teaching on cross-cultural mission warns against the danger of confusing cultural tendencies with Christian truth, and encourages the moulding of methods of proclamation and forms of worship (NB: NOT core doctrine) to the pattern of what is natural, acceptable and God-glorifying in the culture being reached.

Recently, I participated in the Kairos course, which was developed by Living Springs International and is being run in about 50 countries throughout the world. Its emphasis is on the cross-cultural proclamation of Jesus' death and resurrection and the implications of this event for the lives of those who decide to follow Him. It is a great course and well worth doing if you have the chance. A particular highlight of the course was the video by J. Edwin Orr on the role of prayer in spiritual awakening.

Other useful internet resources for those interested in cross-cultural mission include the Joshua Project, and Wycliffe Bible Translators.

They don't publish papers like this anymore...

2010-11-05T18:11:00.004+13:00

Modern scientific writing is very detached and impersonal, a style which encourages objectivity but makes it somewhat difficult to read. This wasn't always the case. I came across a paper by Thomas Vernon Wollaston published in the periodical Annals and Magazine of Natural History, one of the top scientific journals of the time. The title is enough to make you want to take a second look: "On certain musical Curculionidae...."

His introduction goes:

Whilst residing in the remote and almost inaccessible village of Taganana (towards Point Anaga), in the north of Teneriffe ... my attention was called to a peculiarity in a beautiful species of Acalles ... which I do not remember to have seen recorded concerning any other Coleopterous insect whatsoever.

Without any further ado, he launches into the methods section:

It was on the 22nd of May that my Portuguese servant ... brought me home eleven specimens of a large Acalles which he had captured within the dried and hollow stems of a plant growing on the rocky slopes towards the sea ... he was about, in this instance, to throw away these rotten stems as worthless, when he was arrested by a loud grating, or almost chirping, noise, as of many creatures in concert ... On shaking the hollow stem, so as to arouse its inmates, and putting his ear alongside it, the whole plant appeared musical, as though enchanted ....

The methods continue:

So pleased was I with the accomplishments of these anomalous musicians, when brought to me, that I felt quite a reluctance (even though an entomologist) to put them to death. I therefore made a compromise with my feelings, and killed only eight of them.

The results of this investigation are that:

... in the case of the Acalles, the pygidium, although roughened, is not very sensibly so; whilst the small portion of the inner surface of the elytra against which (at each successive pulsation) it is brought to play is far less strictly file-like than was the triangular mesothoracic space of Deucalion [a genus of longhorn beetles that also make a noise] ... yet this is certainly the contrivance by means of which this little Curculionidous musician is enabled to perform its anal "song".

I don't think that Nature would appreciate a piece written in this style...

Reference:
Wollaston TV. 1860. On certain musical Curculionidae; with descriptions of two new Plinthi. Annals and Magazine of Natural History Series 3, 6:14-19

Insect farming

2010-11-04T14:02:00.003+13:00

Insect specimens can be big business. There are enough people out there with money to spare, and who find large and colourful insects such as butterflies, jewel beetles and certain scarab and longhorn beetles worth spending it on. As in all things, this offers both an opportunity and a challenge. Typically, countries with an abundance of desirable specimens are in the tropics and are classed as developing countries. The insect trade offers a high-value export product that can be sustainably produced and can give value to undisturbed habitats. The converse is the usual danger of unsustainable production and unscrupulous middlemen

The sites that follow are a selection of insect trading websites that I've found that are well illustrated, and have some sort of connection with the Pacific. I am not involved with any of these companies, and cannot vouch for the ethics of their trading practises.

Papua New Guinea company, The Insect Farming and Trading Agency, functions as a link between rural insect collectors and breeders and the trade, and sells a range of butterflies and beetles.

The Insect-Sale site is a Taiwan based outfit that exports insects collected from throughout the world, and particularly South East Asia. It boasts that it has the world's largest number of online insect photographs, and is also notable for its gallery of freak insect specimens.

Finally, InsectNet serves as a portal for a number of other sites that offer insect specimens for sale.

"Scientist at Work" —NY Times blog

2010-10-29T17:07:00.004+13:00

The New York Times website has been hosting a series devoted to scientific expeditions and activity—the "Scientist at Work" blog. Of particular interest are the articles by Chris Filardi. Chris is an ornithologist based at the American Museum of Natural History, but who has done a lot of work on the avifauna of Melanesia. He writes about a trip to Kolombangara Island in the Western Province of the Solomons.

Other contributors to the series are icthyologist Melanie Stiassny and mathematician Ron Eglash with current contributors ornithologist Douglas Stotz and botanist Nigel Pitman currently talking about a trip to South America

Papua New Guinea plants

2010-10-28T13:38:00.003+13:00

There is fairly little readily available information for the native flora of the South Pacific. Thankfully, this has started to change with the advent of the PNGPlants Project. This excellent website brings together descriptions, factsheets and photos of herbarium specimens (such as the specimen of Nothofagus pullei above) to provide a very accessible introduction to the plants of one of the most biodiverse regions in the world.

Google maps latitude/longitude bookmarklet

2010-10-26T16:49:00.002+13:00

Bookmarklets are little strings of JavaScript that reside in your internet bookmark list and can do useful things. In particular, the one I find most useful is this one that retrieves the coordinates of the point at the centre of a Google Maps window:

javascript:alert(window.gApplication.getMap().getCenter())

Thanks to liquidx for writing it!

Pacific Island Ecosystems at Risk (PIER)

2010-10-24T19:19:00.006+13:00

The Pacific Island Ecosystems at Risk (PIER) website is an excellent resource to the weeds of importance throughout the tropical Pacific region. The main strength of the site is the extensive list of species fact sheets (including Sphagneticola trilobata, an important lowland weed in Western Viti Levu, Fiji; pictured above) It also includes assessments of the weed fauna of several Pacific Islands, primarily within Micronesia and Polynesia.

While on the subject, SPREP has published some guidelines for the management of invasive species in the Pacific, an important document for those dealing with such things in the region.

Quote: Jules Verne

2010-10-24T19:05:00.008+13:00

Been reading Jules Verne's Twenty Thousand Leagues Under the Sea lately, and the following quote amused me somewhat:

Truly if this good fellow had had gills instead of lungs, I think he would have made a very good fish.—Chapter 19, "The Gulf Stream"

3 years on...

2010-10-18T17:40:00.002+13:00

Three years ago I started this blog to fulfill an assessment requirement for my MSc. It then languished for a while, before I realised it might be of use to me as a place to record interesting websites and to make publicly available any interesting software, R or LaTeX code, or anything else that I cared to post. I've found that this has been the best way for me to regularly post things, though it may not be as reader-focused as it could be. I apologise very insincerely, as though I feel for you, the fact is is that I'm not going to be changing the format anytime soon.

Thank you though, for visiting the site. If you've visited before, even greater thanks. And feel an overwhelming appreciation from me to you if you've commented here or have made other people aware of this blog. It would still happen without you, but its significance would be much diminished.

Cheers!

A Fading Field?

2010-10-18T10:14:00.001+13:00

A year or so ago, The Scientist published an article on "A Fading Field: Traditional taxonomists are an endangered species. Could their unique brand of knowledge disappear, too?". The authors talked to a number of leading taxonomists, including Anthony Cognato and Jiri Hulcr (always good to see the Curculionidae represented!), and have produced a very well-written piece on the lamentable state of taxonomy. There is little here that is new for those of us who follow these things, but unlike pieces, this is actually a good read.

The key issues in my view are jobs and communication. The lack of jobs discourage all interested students from pursuing a career in the field, prefering to become competent in other disciplines (often molecular systematics or bioinformatics) that has better employment opportunities. It would be hard enough if the jobs that were available were being replaced, but it is criminal when instutions of the calibre of the Kew Botanical Gardens do not hire new taxonomists when the previous generation retire. As a scientist-in-training I am experiencing this right now, desperately wanting to devote my time to taxonomic discovery, but having to be realistic enough to forsee that I probably won't be able to get work that is full-time taxonomic research. I also know a number of other students that would be extremely interested in taxonomy, if there was the possibility of getting jobs.

Communication is extremely important, but one that many taxonomists are not particularly proficient at. Taxonomy undergirds the remainder of biology, and the applicability of that biological research often stands or falls on how well the taxonomy that supports it has been done. However, you very rarely hear about it. Biosecurity, pest management, and conservation are all heavily dependant on taxonomic expertise. This needs to be publicised much more broadly. We taxonomists reguarly moan about how little we're valued. Possibly if we inspire others with the beauty and value of our work and how excited we are about it, we won't have to suffer our inferiority complex so much.

Google translate now translating Latin

2010-10-15T11:21:00.002+13:00

Google Translate is an excellent little tool for converting between languages. Until now though it has not had that mainstay of the early scientific period, latin. While being only an alpha version and therefore not being completely accurate, it still serves to make it much easier to read and understand the gist of old documents like one of Carl Johan Schoenherr's landmark monographs on weevils, Curculionidum dispositio methodica, cum generum characteribus, descriptionibus atque observationibus variis, seu Prodromus ad Synonymiae, insectorum partem IV.

Solomon Island Caddisflies

2010-10-14T20:17:00.005+13:00

Caddisflies (order Trichoptera) are one of the major groups of aquatic insects, well known for building cute cases out of sand, grit and other detritus.

While having a fair number of species, relatively little is known about the group in the Pacific, with the exception of some excellent work being done on the New Caledonian fauna. That being the case, it was excellent to see that nine species were described in a paper recently published in Zootaxa, authored by Kjell Arne Johansen, the man behind the current work on New Caledonian Trichoptera. With only 16 species previously described from the islands, this represents a fairly sizable addition to our knowledge of the caddisflies of the Solomon Islands.

References:

Johansen KA, Espeland M. 2010. Description of new Chimarra (Trichoptera: Philopotamidae) species from the Solomon Islands. Zootaxa 2638:25-43

Asian Beetle Websites

2010-10-07T16:12:00.005+13:00

Today, I came across a number of Asian-origin webpages that have many beautiful photos of beetles in general and weevils in particular.

The first, the 動物區 blog (which Google translates for me as "Animal Zone") is a photo diary focusing on invertebrates. The author has a keen eye and a good camera, and so manages to capture some excellent images of a wide variety of animals. Even better, they've taken the time to identify all the subjects, providing a very useful and informative site. As always, it pays to treat the identifications as tentative, but I haven't seen any grossly incorrect determinations thus far.

Another site has an excellent gallery of weevils. This site has the nice feature of providing photos of several different views of most species. Click on the picture in the gallery, and you get taken to another page that often has photos of the underside, lateral and dorsal aspects of the creature.

The last is the Taiwan Insect Wiki house, a wiki devoted to insects and insect photos. It has a page for their weevil photos, which has a number of very nice photos, including the photo of the beautiful Sphenocorynes ocellatus posted above.

Featured insect: Oxymorostes riedeli (Coleoptera: Hybosoridae)

2010-09-30T17:12:00.006+13:00

It's been an interesting month, and what better way to finish it off than with an interesting beetle! I present Oxymorostes riedeli, a bizarre leaf-litter inhabiting beetle from West Papua described in 2009 by Alberto Ballerio. Not only does this beetle look wierd with its out-of-proportion pronotum being wider than its elytra, but it also has several cavities in its mouthparts and underside the function of which is currently unknown. Several other beetles, most notably the bark beetles, have similar cavities known as mycangia in which they store the spores of their food fungus. This is unlikely to be the case in this beetle though, as fungal spores have not been found in them. They did however have an "unknown substance of uncertain origin" inside them, for which there was "an unsuccessful attempt was made to analyze the substance". Just adds to the wierdness really.

Oxymorostes is placed in the subfamily Ceratocanthinae of the Hybosoridae, a worldwide though little known family similar to the scarab beetles. The Ceratocanthinae in general are pretty cool, with some very beautiful species in it such as this currently unknown Eusphaeropeltis species from Malaysia.

References:

Ballerio A. 2009. Unusual morphology in a new genus and species of Ceratocanthinae from New Guinea (Coleoptera: Scarabaeoidea: Hybosoridae). The Coleopterists Bulletin 63(1):44-53

Ballerio A, Maruyama M. 2010. The Ceratocanthinae of Ulu Gombak: high species richness at a single site, with descriptions of three new species and an annotated checklist of the Ceratochanthinae of Western Malaysia and Sinagapore (Coleoptera, Scarabaeoidea, Hybsoridae). Zookeys 34:77-104

Grebennikov VV, Leschen RAB. 2010. External exoskeletal cavities in Coleoptera and their possible mycangial functions. Entomological Science 134:81-98

Microscope mounting media

2010-09-22T13:52:00.004+12:00

Currently for work, I'm starting to explore and become familiar with the Springtails (Collembola). They are fascinating little creatures, but are a bit hard to identify with any degree of certainty without mounting them on a microscope slide.

There are a number of different techniques of mounting specimens on a microscope slide. None are the best for all situations though. For quick, temporary mounts, liquids such as Glycerol and Lactic acid can be suitable. For longer-lasting mounts, more complex mixtures usually involving various hazardous substances are used. The Smithsonian Copepod Page and a guide to insect collection curation both give an excellent overview of the longer-term options available for slide mounting specimens, as well as recipes for the various fluids and mixtures. Additionally, the Natural History Museum has a page giving a summary of the results of a mailing list discussion on the subject.

It seems though that the general consensus is that the resin Canada Balsam is THE medium for long-term (i.e. greater than 20 years) mounting of specimens. Despite concerns about requiring Xylene in its preparation, the long time required to make the slides, and concerns that its refractive index is sometimes too high for some specimens, it remains the time-tested solution for microscope mounting of specimens that need to go the distance. A paper describing its use is available in the New Zealand Entomologist.

References:

Palma RL. 1978. Slide-mounting of lice: a detailed description of the Canada balsam technique. New Zealand Entomologist 6(4):432-436

Walker AK, Crosby TK. 1988. The preparation and curation of insects. DSIR Information Series 163. DSIR; Wellington.

Image-stacking software for Linux

2010-09-09T11:42:00.004+12:00

Back in the day, when I was still Windows-based, I was able to get some pretty decent focus-stacked ("automontage") photos of insects using the brilliant freeware programs DeepFocus and PrepareStack written by Stuart Ball. Unfortunately, I can't find the download anywhere, though his detailed manual is still available. While commercial applications are available, I have not yet found an open-source version that will suffice. Internet searches indicate that ImageMagick's "combine" might be suitable, when given a suitable stack of photos. Preparing that stack is a little trickier. There are suggestions that GIMP might be suitable, however as far as I can see, there are no published scripts or tutorials that make it easier beyond tedious manual adjustments. I will continue to look around and see if I can work out some sorta fix.

Canterbury Earthquakes part III

2010-09-08T19:24:00.009+12:00

As more people keep following the GeoNet website, they are starting to notice the seismic activity in areas other than Christchurch. A few people I've talked to have expressed concern that the Saturday 7-pointer has sparked earthquakes around the country. This is incorrect, as earthquakes below magnitude 3 are extremely common and as can be seen in the plot below, they occur throughout the country.

A closer look at the magnitude of these earthquakes shows their temporal distribution is fairly uniform. What is interesting is that prior to the time of the big one there appears to be a lull in the frequency of lower-level earthquakes nation-wide. Is this at all significant? I don't know.

The magnitude follow a right-skewed normal distribution with a mean of 2.47 and a standard deviation of 0.617, while their depth follows an approximate Poisson distribution with a mean of 44 km.

Looking at the seismic activity within the Canterbury region, we see that earthquakes appear to have been fairly randomly distributed throughout the region until the 4 September quake. Only a single tremor was detected from the vicinity of the recently revealed fault, an insignificant 2.31 that occurred on the 21st of March. That there weren't more tremors closer to the time would seem to count against the hypothesis of big earthquakes being preceeded by smaller ones.

As before, data was gained from the Quake Search data download query provided by GNS, and the data, R code and a file giving the location of Canterbury towns is available for all.

Canterbury Earthquakes part II

2010-09-07T21:25:00.001+12:00

Since posting last night, there's been several more aftershocks, including several big ones. The total now stands (at 7:00pm) at 304 aftershocks, 70 greater than 4 on the Richter scale, 29 greater than 4.5, and 10 greater than 5. A couple of the fives happened last night, waking us up, and causing more damage to several buildings around town.

This evening's installment is a map of the region of Canterbury where the earthquakes have been centred, showing the epicentre of all aftershocks and their magnitudes. It appears that while smaller tremours have been centred fairly widely, the larger magnitude earthquakes have been centred more around the epicentre of the initial 7.1 quake. As before, I've made the the data and R code available.

The region around the epicentre of the initial quake has been surveyed by GNS scientists. They've got some pretty awesome aerial photos showing the location of the fault on their webpage detailing their work.

Vanishing taxonomists

2010-09-07T16:50:00.002+12:00

A recent article published in the Canadian newspaper "The Globe and Mail" titled "The case of the vanishing taxonomists" is another article that again is lamenting the demise of taxonomists and highlighting the fact that more are dying than are being trained. Those of us who follow these things will learn nothing particularly new, as it has been repeated many times before.

The morphological taxonomist, engrossed in a single group and identifying its members by visual inspection, is increasingly an emeritus professor or someone near retirement. Younger scientists are drawn to molecular taxonomy, where powerful new techniques in the study of DNA have revealed interspecies connections never before suspected.

It's a little frustrating reading these sorts of articles, particularly as a young scientist who does want to be a taxonomist and get paid for doing so. Although the paragraph above makes it sound as if there's noone wanting to follow in their footsteps, in my experience I have come across a number of postgraduate science students who would love to get into taxonomy. The problem is that there is very little money in it, and that jobs with significant components of taxonomic research are few and far between. The "taxonomic impediment" could easily be solved if there were dedicated funding rounds for the employment of early-career taxonomists.

Less than negative?

2010-09-06T20:25:00.011+12:00

An interesting thing that I found while doing the analysis for my previous post on the Canterbury earthquakes, was the difficulty of constraining figures less than a negative number. For example:

a<-seq(1, 10, 1)
b<-a[a>3 & a<7]
c<-seq(-1, -10, -1)
d<-c[c<-3 & c>-7]

> a
[1] 1 2 3 4 5 6 7 8 9 10
> b
[1] 4 5 6
> c
[1] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE
> d
[1] -1 -2 -3 -4 -5 -6

The boolean operator for selecting a range less than a negative number ends up being the same as the assignment operator. To get around this I simply define the function neg()

neg<-function(x) -x
c<-seq(-1, -10, -1)
d<-c[c<neg(3) & c>neg(7)]

> c
[1] -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
> d
[1] -4 -5 -6

Canterbury Earthquake

2010-09-06T19:36:00.003+12:00

4:35 am on Saturday morning, I was woken up by a 7.1 magnitude earthquake, the epicentre being approximately 30 km west of where I live in Christchurch, New Zealand. The earthquake was one of the largest that New Zealand has experienced, and has been the most destructive one since the earthquake that struck Napier in 1931. Thankfully, the suburbs around the area that I live in suffered minimal damage, with most roads and houses essentially unscathed.

While the initial earthquake was fairly scary, it has been the aftershocks that have been the most unnerving. By this time we're starting to get fairly used to them, but they are still keeping all of us on edge. There's been a number, and now that I have access to the internet, I made it my mission to find out how many there's been thus far. The New Zealand Herald newspaper has published an online article showing the locations of all the aftershocks, but a bit scant on other details.

The New Zealand research institute Geological and Nuclear Sciences (GNS) is the primary monitor of New Zealand's earthquakes and makes all their data available online. In particular their Quake Search tool allows you to download CSV, KML and other files of any earthquakes that satisfy any given criteria. The GeoNet website in general is an excellent source of all sorts of information with regard to natural hazards in the New Zealand region.

I downloaded the data for the past week and started pulling out a bunch of trends. The two that I'll post here for now are the following:

Until 6 Sep 2010 19:03 NZST there has been 257 aftershocks, ranging between 2.4 and 5.4 on the Richter scale. Of these, there have been 64 with magnitudes above 4; 24 above 4.5; and 7 above 5. The average has been 3.6.

The comparison between the earthquakes recorded prior to and following the earthquake is remarkable. The four days prior to the earthquake there were no earthquakes originating within the Canterbury region (defined as being between 42--44 degrees S and 171--173 degrees E). Since Saturday morning, the region has been shaking like nothing else.

A line plot only of the Canterbury earthquakes does show that the aftershocks are lessening in frequency and intensity. Further playing around with the data and the plot might show this more effectively though.

A plot comparing the magnitude of each quake with its depth is quite interesting. The vast majority of the Canterbury earthquakes are fairly shallow (<20 km). Once again, further analysis will show if this is a significant thing or not, but it does explain why they've been so easily felt.

Feel free to look at the R code and the CSV file I used for the plots above.

apply functions in R

2010-09-01T11:35:00.004+12:00

Getting to know the "apply"s in R is extremely handy for using the language efficiently and effectively. Unfortunately, the help files tend to be rather information-dense and are fairly overwhelming for newcomers. A recent blog post by Neil Saunders provides a thorough overview and tutorial of the apply family, illustrated by simple and reproducible examples. I suspect I will refer to it frequently from here on in.

German Beetles

2010-08-30T18:12:00.002+12:00

In addition to having a superb gallery of photos of a huge number of weevils (see one of my previous posts), Christoph Benisch and colleagues have been displaying a featured beetle every week. In addition to having a typical beauful photo of the chosen insect, it is accompanied by a short note on its biology, distribution and lifecycle. Many of the species are endangered and rarely found, while others are strange or unusual in other respects.

Biomolecular Graphics

2010-08-30T18:02:00.003+12:00

A recently published article in PLoS Computational Biology is one by Cameron Mura and colleagues that discusses the great potential held by biomolecular graphics. It discusses the terminology, tools and how to go about teaching yourself the basics. While it is very biochemistry-focussed, the highlight of the paper "Box 2: Nine Simple Rules for Biomolecular Graphics" present some very useful hints to guide any scientific illustrator.

Reference:

Mura C, McCrimmon CM, Vertrees J, Sawaya MR. (2010). An Introduction to Biomolecular Graphics. PLoS Computational Biology 6(8): e1000918. doi:10.1371/journal.pcbi.1000918

Tijdschrift voor Entomologie

2010-08-30T17:12:00.002+12:00

Tijdschrift voor Entomologie is the Journal published by the Netherlands Entomological Society. The society has a bit of a heritage---it was founded in 1845, and has remained in action since. The Journal itself is has open access to PDFs of all papers published from 1998 until two years ago. Volumes published before 1923 are available at the Biodiversity Heritage Library.

This clearly illustrates what I think is a growing trend. Literature published since 2000 can generally be easily found online. The same goes for literature older than 1925---there's a good chance it's on BHL. However, it's actually fairly difficult to find the literature published in the period in between (i.e. 1925--2000). No doubt this will change as the sliding window of Copyright slowly moves over this time period. In addition, I think that some societies and publications are starting to fill this gap of their own goodwill, which is excellent also.

Speech recognition in Linux

2010-08-27T12:25:00.003+12:00

Whenever I'm looking at specimens under the microscope and noticing differences, I find it very difficult to stop what I'm doing, look at a bit of paper, and write it down. I'd much prefer to talk about it while looking at the specimen.

The first solution is to record yourself while talking. Audacity is a free, open-source music editing program that is pretty decent. I don't know how useful hard-core sound engineers would find it, but it's not bad for the application that I'm wanting to use it for, namely, recording my voice while I waffle on about what a specimen looks like. I could then listen to the recording repeatedly and transcribe what I say. More efficiently though, I'd be keen for some sorta sound recognition software a la Dragon NaturallySpeaking. NaturallySpeaking is the biggest-selling voice recognition software, and by all accounts it's pretty good. It does require some coin though, so I'm looking for less expensive, preferably open-source programs.

Unfortunately, it doesn't seem like there's much out there. A wikipedia page is a good entry point to the problem. Apparently one of the biggest issues is the lack of a voice database to test algorithms on. To solve this issue, VoxForge has been set up to encourage people to upload recordings and to work on the problem. The Ubuntu Wiki also has a page giving a bit of a road map of what Ubuntu want to see done. It looks like it might be a good project to start working on.

Crosby Codes

2010-08-23T10:28:00.002+12:00

Entomologists with any interest in the New Zealand fauna will no doubt have come across the two-letter codes affectionately known as "Crosby codes". These codes denote geographical regions in New Zealand and are used for the purposes of grouping and retrieving specimens. They are named after Trevor Crosby, the lead author of two papers in 1976 and 1998 where these codes were defined. The 1998 paper expanded the codes to include New Zealand's offshore islands, and includes written descriptions of the boundaries between each region.

The codes have proved to be very useful in the entomological context, and have also been used in many other fields where the distribution within New Zealand is important.

Reference:

Crosby TK, Dugdale JS, Watt JC. 1976. Recording specimen localities in New Zeland: an arbitrary system of areas and codes defined. New Zealand Journal of Zoology 3:69 + map.

Crosby TK, Dugdale JS, Watt JC. 1998. Area codes for recording specimen localities in the New Zealand subregion. New Zealand Journal of Zoology.25:175-183

Phylogenetic trees online

2010-08-20T18:09:00.005+12:00

The other day, an article was published in PLoS One describing a newly developed JavaScript library to visualise phylogenetic trees online: jsPhyloSVG. It's pretty nifty, and there's some pretty cool functionality that you can build into the trees. It's all based on the PhyloXML standard for describing phylogenetic trees and networks, but can display trees stored as other formats, in particular the common NEWICK format. The resulting files are viewable in any web browser, though Internet Explorer is dragging the chain a bit and does not yet support the full interactivity that other browsers are capable of.

It would be real cool to be able to export trees made and manipulated in R into PhyloXML format, and subsequent into PhyloSVG. Might be a fun project to work on when I've scraped some other things off my plate...

Reference:

Smits SA, Ouverney CC. (2010). jsPhyloSVG: A Javascript library for visualizing interactive and vector-based phylogenetic trees on the web. PLoS ONE 5(8): e12267. doi:10.1371/journal.pone.0012267

Vanuatu Birds Website

2010-08-20T14:58:00.005+12:00

While reading the paper on white-eye blood parasites, I noticed a link to the VanBirds website. It is an incredible website, and an excellent resource for both casual bird watchers and serious ornithologists. It has photos of many of the bird species found in the archipelago. In addition, it has recordings of the calls of many of the species also. Most importantly though, the website collates records of birds throughout the archipelago and displays them on a map as shown by this map of the distribution of the Vanuatu endemic flycatcher, the buff-bellied monarch (Neolalage banksiana, pictured above). It appears to be well-maintained, being last updated on the 25th of May this year.

This website is very impressive and is a highly valuable resource for the ornithology of Vanuatu. It is all the more remarkable, as it appears to be very much a grass-roots type effort and claims to have had no external funding thus far. It would be awesome to see more sites like this spring up for the other Melanesian island groups.

Featured insect: Pantorhytes plutus (Coleoptera: Curculionidae)

2010-08-16T12:12:00.012+12:00

The weevil genus Pantorhytes is a large genus placed in the tribe Pachyrhynchini in the subfamily Entiminae. It consists of over 74 species found primarily in New Guinea, but also being found in the Solomon Islands and Queensland. The species pictured here, P. plutus is found in the Bismarck Archipelago. A map showing the distribution of specimens in the Australian National Insect Collection (see here also) can be found here

Pantorhytes plutus and a number of other species in the genus have become major pests of cacao trees, particularly in PNG. All the species have fairly limited ranges, such that P. szentivanyi, P. albopunctulatus and P. healyi are pests in the Northern Province of PNG, P. torricellianus is a problem in the Sepik region, P. plutus through the Bismarcks, and P. biplagiatus through Bougainville and the Solomon Islands. The genus has had a surprisingly large amount of study done on their biology, including egg development, and control. A couple of studies have looked at their dispersal, including one study that used a radioactive isotope tracing technique, which provided theoretical insight into mathematical models of insect dispersal. A parasitic wasp, Pristocera rufa is known to parasitize P. szentivanyi, though not to such an extent as to be a reliable biological control agent.

They are such a threat, they have made it onto a page detailing the world's worst cocoa problems (though I cannot find any other evidence that Pantorhytes are in Tuvalu), and accordingly there's been a number of studies dealing to their control (such as this one and this one).Biopesticides, including Beauveria bassiana have also proved to be of use in their control. A photo of an infected beetle is shown above.

A circular detailing their control in the Solomon Islands recommends using ants as a form of biological control. Unfortunately, two of the species they recommend for this control are the yellow crazy ant (Anopolepis gracilipes) and the little fire ant (Wasmannia auropunctata). Both these species are highly invasive generalist predators and scavengers which have adverse effects on more than just Pantorhytes weevils in cacao plantations. Should they already be present in the area, their use as a control agent may be encouraged, but they should NOT be introduced anywhere for that purpose if they aren't already there.

References:
Gressitt JL. 1966. The weevil genus Pantorhytes (Coleoptera) involving cacao pests and epizoic symbiosis with cryptogamic plants and microfauna. Pacific Insects 8(4):915-965.
Setliff GP. 2007. Annotated checklist of weevils from the Papuan region (Coleoptera: Curculionoidea). Zootaxa 1536. 296pp.
Stibick JNL. 1978. The genus Pantorhytes (Coleoptera: Curculionidae) Division A. I Addistions and changes to the common and major cacao species. Pacific Insects 18(3&4):115-136.

Downloading DNA sequences into R

2010-08-15T23:20:00.008+12:00

A while ago, a friend of mine needed to download a number of different DNA sequences from Genbank, the online repository for the vast majority of DNA sequences read from all organisms by labs all over the world. This is not a problem. The "ape" package in R has a nifty function, read.GenBank(), that downloads the sequences identified by the accession numbers given to the function into a DNAbin object. Thus, read.GenBank("AY883003") downloads the sequence AY8833003, the internal transcribed spacer 2 gene for Anthonomus grandis, the cotton boll weevil. read.GenBank() is able to read a vector of accession numbers, making easy to download a lot of sequences if you're willing to give it the time.

All well and good. Unfortunately, the base function returns only the accession number as the name of the sequence. My friend was downloading sequences of many different genes from several different species. Understandably, mere accession numbers are not particularly helpful in this situation, and more information is helpful for processing datasets such as this. Thankfully, a quick hack of the function ensured that species and gene region info could be downloaded with the sequences, solving the problem. It also extended the function's utility significantly and in my opinion is now much more useful for phylogenetics-type work.

The resulting function is read.GB(). It currently reads the "ORGANISM", "DEFINITION", and "ACCESSION" fields of Genbank files which record the information regarding species identity, gene region and accession number respectively. These are stored in the resulting DNAbin object as an attribute, and can be returned in the following manner:

a<-read.GB("AY883003")
attr(a, "species")
attr(a, "gene")
attr(a, "accession_num")

The current default names for the sequences are returned in a standard format: accession number|scientific name.

Full credit goes to Emmanuel Paradis who wrote the original function, and who wrote it in such a way that it was fairly painless to extend it in the manner above.

Pacific Disaster Network

2010-08-14T16:52:00.009+12:00

The Pacific Disaster Network is a website devoted to the monitoring of natural disasters within the region and the dissemination of publications, reports and conference proceedings relevant to regional humanitarian efforts.

Its stated aim is to be:

the largest and most comprehensive information resource for Disaster Risk Management for the Pacific Island Countries.
...
The portal will provide a valuable resource to all Disaster Risk Management partners working in the Pacific region including government agencies, regional bodies, non-government organisations and international agencies.

The website displays alerts of natural disasters, has a LOT of publications and reports of relevant to natural disasters, public health and agricultural issues. It is a fairly exhaustive site, but unfortunately one that is fairly unintuitive to use(for me at least..) at first glance. Exploring it further reveals more of its power and utility. The homepage leads with a satellite map from Google and a box giving the latest alerts, giving the promise that the location of these alerts will be visualised. Unfortunately this is not the case; a pity for people like me who like to be able to see where events are occuring on a map.

The website is a collaboration between the South Pacific Applied Geosciences Commission (SOPAC), the United Nations Development Programme (UNDP), the International Red Cross and the UN Office for the Coordination of Humanitarian Affairs (OCHA).

Zookeys and Cybertaxonomy

2010-08-09T14:13:00.003+12:00

Taxonomy is changing... Rather, the way that taxonomy is done is undergoing large shifts from the traditional way thanks to the advent of the internet. A recent Zookeys special issue published a couple of forum papers showing how data presented online in Scratchpads can be nigh-on automatically converted into a publishable document in Zookeys.

While my previous comments on Scratchpads were less than complementary, this application of them is pretty cool. Whether or not it will completely streamline the process of publication more than the usual is another question, but it will be interesting to see.

Tonga Science Network

2010-08-09T12:05:00.003+12:00

In a collaboration between the University of Canterbury and the Tongan Ministry of Education, a new website has been launched: the Tonga Science Network. This website aims to promote and help disseminate science that is relevant to Tonga's environment and economy. Researchers are invited to register on the website and contribute content to smooth the flow of knowledge back to those who need to use it. Another cool feature is the "connections" that shows who has worked with who, and encourages the formation of new collaborations.

All in all, it's a neat initiative and hopefully will resolve one of the major issues I see with science in the Pacific, namely that most research is done by foreigners. This in turn means that relatively little of the results (despite the best intentions of most researchers) is returned to interested parties within the country, other than by laborious and ongoing literature searches. As with all community-type initiatives, it will only be as good as those who use it. It's made a good start though, and here's hoping that will continue.

NZ Scholarships for Pacific Island Students

2010-08-04T17:52:00.004+12:00

Good news for those Pacific Island students wanting to study in New Zealand. John Key has just announced that the number of scholarships available to Pacific Islanders will increase from 100 to 200 next year. These include full scholarships as well as a deal where students will be given a student loan that will be written off if they return to their country of origin. The scholarships will be administered by NZAID. Those currently offered can be seen on their scholarships page.

Read the article in the New Zealand Herald here.

Houseflies of New Caledonia and Vanuatu

2010-08-03T12:52:00.007+12:00

Over the past couple of months, Marcia Couri and colleagues have published two monographs on the Muscidae of New Caledonia and Vanuatu. These two papers describe six new species with nine other species recorded from the region for the first time. The world-wide house fly Musca domestica (pictured here) is newly recorded from a number of islands throughout Vanuatu.

These papers are important additions to our knowledge of Melanesian flies. They give keys and diagnoses for the genera and species found in each archipelago, and give comments on the wider distribution of the flies found. Unfortunately, there are few illustrations, limited to line drawings of taxonomically important structures of the newly described species. While this may limit their utility to users who don't already have some familiarity with the group, these paper effectively summarize the housefly fauna of the region and provide a good basis for the further study of this important group.

References:
Couri MS, Pont AC, Daugeron C. 2010. The Muscidae (Diptera) of Vanuatu. Zootaxa 2556: 1–39
Couri MS, Pont AC, Daugeron C. 2010. The Muscidae (Diptera) of New Caledonia. Zootaxa 2503: 1–61

New hemipteran species from New Caledonia

2010-07-22T18:55:00.004+12:00

In the same issue of Zootaxa describing the manuka scale insect, another hemipteran was described. Teabooma secunda is the second species of the genus (which is endemic to New Caledonia) to be described. It is in the family Cydnidae which are common and widespread. They are frequently mistaken for beetles, and it is usually only a careful look with some magnification that will reveal the mistake. It's a poorly known family, but they are thought to feed on roots, seeds and fallen branches. None are known for their economic importance.

References:

Lis JA, Lis B. 2010. Teabooma secunda (Hemiptera: Heteroptera: Cydnidae)---a new species of a New Caledonian endemic genus with a redescription of T. princeps Distant. Zootaxa 2543: 64-68.

A mystery... scale insects on European manuka

2010-07-22T17:59:00.009+12:00

Manuka (Leptospermum scoparium) is native to New Zealand and southeast Australia. It is common throughout New Zealand and is well known for being the source of manuka honey which is sought after for its healing properties, and for being a good source of firewood (particularly for smoking fish). Its trait of having numerous white flowers has also ensured that it is fairly commonly grown as a garden plant, and so has been exported around the world for this purpose.

So when a scale insect that apparently is specific to the plant is found in Italy and Corsica in 2004 and 2006, one would imagine that it came from New Zealand or Australia right?

Acanthococcus mariannae was described yesterday in a Zootaxa paper by Giuseppina Pellizzari and Jean-François Germain. The 30 or so specimens that went into the description were all collected from manuka from Italy and France. Surprisingly though, despite the author's (reasonable) assumption that the insect was introduced to these countries on the plants, this species has not (yet?) been found in either New Zealand or Australia. Moreover, specialists familiar with scale insects in these countries had not noticed it before. While it is likely that further searching will reveal it on manuka in NZ or Australia. However there is the lingering question: if it's not, where did it come from and how has it started attacking manuka?

Scale insects aren't glamorous. They are little more than a bag of fluid that get sap pumped into them. But they are important in a properly functioning ecosystem; and when they get out of control the consequences can be severe. This can be illustrated by an example that also involves manuka: the incidence of manuka blight in New Zealand in the 1940s and 1960s.

Manuka naturally harbours large numbers of the scale insect Coelostomidia wairoensis which produces a lot of honeydew. This in turn provides a food source for the sooty mould Capnodium walteri which covers the branches of manuka forming thick, black deposits.

In the late 1930s manuka in Canterbury (South Island of New Zealand) started to grow sick and die. By the late 1940s it was reported that it was hard to find living manuka in the region. Farmers assisted in the spread by moving infected manuka around the country to control what they viewed as a weed. The culprits were found to be two species of Eriococcus scale insect that presumably had been introduced from Australia. The effect on the plant appears to be due to nutrient stress from having large numbers of scale insects sucking on it as opposed to being a disease transmitted by the insects.

In 1957 it was discovered that a fungus was killing E. orariensis, the species that damaged manuka most severely. Subsequently, the numbers of this scale insect declined dramatically with a corresponding increase in manuka numbers. Manuka has also seen a rise in popularity and is no longer viewed as being as significant a weed.

References:

Epenjijsen CW, Henderson RC, Carpenter A, Burge GK. 2000. The rise and fall of manuka blight scale: a review of the distribution of Eriococcus orariensis (Hemiptera: Eriococcidae) in New Zealand. New Zealand Entomologist 23: 67-70.

Pellizzari G, Germain J-F. 2010. A new species of Acanthococcus (Hemiptera, Coccoidea, Eriococcidae) on Leptospermum scoparium (Myrtaceae) from Italy and France. Zootaxa 2543: 51-63

PNG Entomology Textbook

2010-07-19T14:16:00.003+12:00

Michael Schneider was a lecturer at the Bulolo University College in Morobe Provence, PNG from 1994 to 1999. As a result, he has produced both a key to the Insect Pects of PNG, and an entomology textbook for students and forestry. This last work is a particularly impressive effort, being a clear, informative and thorough textbook with a strong emphasis on the insect fauna of Papua New Guinea. For anyone with a developing interest in insects, it's well worth checking out. For those of us who are particularly fascinated with the insects of Melanesia though, it's a must-see.

Blood parasites in Melanesian White-eyes

2010-07-16T10:33:00.003+12:00

The white-eyes are a group of small birds in the genus Zosterops with an interest out of all proportion to their size. As a genus, they range from Africa, through Asia and Australia to many islands in the Pacific where they are fairly common. In the islands they have diversified to the extent that most archipelagos have at least one endemic species present. This is most impressive in the New Georgia group of the Solomon Islands, where six species are present over six different islands---many of which are separated only by a few kilometres of ocean. Additionally, one particular species, the silver-eye (Zosterops lateralis) has a wide range across Australia and into the central Pacific As such, there are many different questions regarding their dispersal, rate of speciation and the relationships between the different species.

In a paper by Farah Ishtiaq and coauthors, the birds themselves are not so much of interest. Rather, it's the prevalence of parasites in the blood of the birds found in Vanuatu and New Caledonia. More specifically, they look at the protozoans Plasmodium (more commonly known as avian malaria) and Haemoproteus that are spread from bird to bird by blood-sucking flies and mosquitoes. They took blood samples from a number of specimens, comprehensively sampling five different species of white-eye from Vanuatu (13 islands represented), mainland New Caledonia and the Loyalty Islands. Within these, they found seven different lineages of Haemoproteus and 14 lineages of Plasmodium. Most lineages were fairly scarce, with one lineage of each parasite genus being the most common and widespread.

When they looked at the number of parasite lineages on each island, they found that the larger islands had more lineages of Plasmodium than smaller islands. This trend was much less evident in Haemoproteus, being not statistically significant. The pattern of increasing numbers of lineages or species with increasing island area is a very well-known relationship that forms the basis of the Theory of Island Biogeography, first postulated by Robert MacArthur and EO Wilson in the 1960s. It is interesting that these parasites show the pattern also, despite the additional variables of requiring a host and a vector insect to be present.

Why is this of interest? Parasites have a huge effect on their hosts which is often invisible. They are also a part of the natural heritage of this world and so are worthy of study in their own right. These findings share a small glimpse into a world that is usually hidden, and increases our awareness of the biota of the Melanesian region. As with a lot of scientific research, progress is incremental with many small, initially insignificant findings building into a body of knowledge that can be extremely important for health, conservation, or technological impact.

References:
Ishtiaq F, Clegg SM, Phillimore AB, Black RA, Owens PF, Sheldon BC. 2010. Biogeographical patterns of blood parasite lineage diversity in avian hosts from southern Melanesian islands. Journal of Biogeography 37: 120-132.

Australian weevil photos

2010-07-15T14:00:00.006+12:00

Despite the legendary efforts of Elwood Zimmerman, our knowledge of the weevil fauna of Australia remains rudimentary. Guides to the identification of most species are non-existent and accordingly, very little is known about the life history of a vast proportion of the fauna. What's also interesting is how few people have become involved in the effort to discover more about them. It's not like they're unattractive either. Peter Lang has a number of photos of weevils, particularly the a number of South Australian representatives of the Belidae (including the unidentified specimen here).

There are also a number of photos of the weevils from Brisbane on this site. Take the identifications with a grain of salt though. The "attelabid" is a broad-nosed weevil of some sort, and the latter two species on the Apionidae page appear to be a cryptorhynchine and an attelabid respectively.

Agriculture in the Pacific

2010-07-15T13:12:00.004+12:00

Agriculture in developing countries is an area where a lot of international assistance and aid money goes. A lot of hard work, interesting information and useful resources are the fruits of these activities. Unfortunately though, this information can get easily lost in the morass of information that is the internet. The following is my humble attempt to promote a few of the sites I know that are relevant to Agriculture in the South Pacific, in addition to the ACIAR and SPC Forestry pamphlets I've talked about before.

Terracircle is an NGO that works primarily in Melanesia promoting sustainable agriculture through technical training, publications, consultancy and the provision of small grants for communities.

Working in close association with Terracircle is the Kastom Gaden Association (another website is under construction here) and the Planting Material Network, both based in the Solomon Islands. Both these organisations operate much more on the grass-roots level, connecting farmers within the Solomons to each other and encouraging communication at that level.

The Melanesian Farmer First Network is broader in scope than the two above, supporting farmers throughout PNG, the Solomons and Vanuatu. I liked the Innovations page on their site, though unfortunately it is only very infrequently updated.

OISAT (or the "Online Information Service for Non-Chemical Pest Management in the Tropics" in full) aims to detail control methods for tropical crops and pests. It seems to have more of a focus on Asia, but the information that is here will be of worth in most places with these crops and pests. It is currently fairly incomplete, with few of the insects in the Pest Management strategy having any information beyond a picture. However, there was a note saying the page had been updated in some form a day ago, so there is hope that this will change in the future.

Smithsonian Contributions online

2010-07-12T15:29:00.002+12:00

The Smithsonian Institute has published a lot of interesting and important stuff over the years. A lot of it is now available online here.

A miscellany including the beetles of Gibraltar and Libya

2010-07-12T12:51:00.004+12:00

In my continual meanderings through the wonders of the world-wide web, I have uncovered the following gems: A list to the beetles of Gibraltar, and a site on the Beetles and Rock Art of Libya which includes a list of the weevils found in that fair country.

If old entomological art is more your thing, this page showcasing the art of Edmund Reitter is both fascianting and beautiful. If you'd prefer to see a beetle walk, there's an animation of it here.

Featured insect: Ceresium tuberculatum (Coleoptera: Cerambycidae)

2010-07-11T19:16:00.008+12:00

One of the unfortunate aspects of South Pacific entomology is the lack of Pacific Islanders that are actually involved in the discovery and naming of their biota. Thankfully, there are signs that this situation is beginning to change. Last August on a trip to Fiji I had the immense privilege of meeting a number of young scientists from Fiji, the Solomon Islands and the Cook Islands. One of these was Hilda Waqa, the senior author of this paper describing two new Fijian longhorn beetles, one of which is the beetle pictured, Ceresium tuberculatum.

The Cerambycidae commonly known as the longhorn beetles tend to be wood borers in the larval stages. These larval stages can last for a long time---several years in some species. The larvae of some of the larger species are eaten occasionally and are considered delicacies in some areas. Unfortunately, very little is known about the biology of Ceresium tuberculatum specifically. It has been collected from the Fijian islands of Gau and Viti Levu, and have been collected from primary, undisturbed forest in the heart of Viti Levu as well as secondary, plantation forests in the vicinity of Suva.

The paper is well illustrated with some very clear photos of various characters that are useful for identification. Unfortunately though, there is little in the way of comparison with other species of Ceresium in Fiji and the South Pacific. This makes the paper less useful than it might have been. It remains a valuable addition to the literature, and it is well worth having a look at for the illustrations alone, whether or not you have any further interest in Cerambycidae.

References:
Waqa H, Lingafelter SW. 2009. New Fijian Callidiopini (Coleoptera: Cerambycidae). In: Fiji Arthropods XV. Edited by Neal L. Evenhuis & Daniel J. Bickel. Bishop Museum Occasional
Papers 106: 3–15 (2009).

Statio

2010-07-09T17:43:00.001+12:00

The Bible is an amazing book and one that I recommend to all. Heck, even Richard Dawkins at his recent talk here in Christchurch recommended that people read it. Yet when I came to deciding whether or not I should put a random Bible verse generator on this site, I realised that I was reluctant to do so. Fears that readers may feel that I'm ramming something down their throat, question my objectivity as a scientist, or that it's just plain too cheesy all led me to be somewhat wary of putting it up there.

It's up there though, and this is why. I blog for myself, and am slowly making this site a place that has links to everything that I need. One thing that I need an easy way to read a random bible verse and meditate on it briefly throughout the day. This sort of thing is rooted in a practice followed by Benedictine monks called "statio"; a standing still. I first came across it while reading "Reaching for the Invisible God" by Philip Yancey, but there's an outline of the practise in this article by a doctor. I'm hoping that having this bible verse up here will get me thinking more on Christ and His love and keep my perspective on things that matter.

Fauna Hawaiiensis

2010-07-09T14:12:00.002+12:00

I've always been surprised how hard it's been to find information on the beetles of Hawaii. Due to it being a state of the USA and the fascination for many other aspects of the fauna and flora of the islands I would've thought that it would be very easy to find out pretty much anything about the beetles of the area. This expectation for the most part has not been met.

Lately though, I've been having more luck. The other day I found the Proceedings of the Hawaiian Entomological Society, and today I found the website of Karl Magnacca. He's working on the Drosophila of Hawaii which form a very famous radiation with approximately 600 species found in Hawaii. A big task. He's also taken a number of photos of Hawaiian beetles, and has put online the masterpiece of early Hawaiian biological study: Fauna Hawaiiensis. This ambitious project details the entirety of the animals from Hawaii at that time. Vertebrates, insects, worms, springtails, molluscs: it's all here.

Proceedings of the Hawaiian Entomological Society

2010-07-07T14:26:00.002+12:00

The Proceedings of the Hawaiian Entomological Society is one of the key journals for South Pacific entomology, and now it is freely available online. There's a lot of very cool things in here, including a large number of papers by Elwood Zimmerman on weevils from throughout the South Pacific.

Beetles of Mauritius: Syzygops vinsoni

2010-07-07T14:05:00.005+12:00

A Scratchpad to promote the study of the beetles of Mauritius has been set up by Edward Baker. It's a reasonable site, with a number of photos of what look like heritage specimens. It's always good having more sites disseminating more information, particularly of interesting islands like Mauritius. However, I do always find Scratchpads to be fairly clunky and hard to get around and unfortunately this site continues that trend.

As mentioned before though, there are some pretty neat photos including the species pictured here which has the very cool name Syzygops vinsoni. The genus Syzygops is restricted to Mauritius and the nearby island of Réunion and is part of a group (the Ottistrini) that is otherwise found in Australia, New Guinea and the Pacific. These weevils have their eyes situated right on top of the head, and are so narrowly separated that they might as well be joined together. You can see them in this photo if you look carefully---the black things in the middle of its head. These weevils are also very sexually dimorphic. This specimen is a male as evidenced by the very boxy back-end of the creature. Females have the apex of the elytra more rounded and normal-looking. The adults are found commonly on tree ferns throughout the hot season (November-April), but unfortunately the larvae are currently unknown.

References:

Wiliams JR. 2000. A revision of the Mascarene weevil genus Syzygops Schönherr (Coleoptera : Curculionidae : Entiminae). Invertebrate Taxonomy 14: 411–432

Music. Lots of music

2010-07-07T11:04:00.002+12:00

The way music has changed in the past century is phenomenal. Where before you had to play it yourself or go to concerts, you now can immerse yourself in the stuff without knowing anything or going anywhere. A while ago I had so much music on my computer that if I wanted I could go for at least a week without hearing the same song twice if I didn't want to. And I'm not as obsessed as some people are. It's a rather massive shift if you ask me, and no doubt in years to come it will provide historians and social scientists with ample fodder for study.

If you want to get still more music and learn about yet more bands, a useful site to keep checking is the Hype Machine, an aggregator of music blogs. Updating frequently, it's a treasure trove of all things musical. If you want to sign up, it promises that you're able to customize what you see, presumably allowing you to keep tabs on the genres that you particularly enjoy. Otherwise, check it frequently to see what people are listening to and what they think of it...