Thursday, 16 December 2010

Setting up a mail server on Ubuntu

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.

Friday, 19 November 2010

Apodrosus revision and blog


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.

Thursday, 18 November 2010

HTML helps

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.

Monday, 15 November 2010

Asian Beetle Websites II


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.

Wednesday, 10 November 2010

Using pdfpages to rotate odd pages only

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.

Monday, 8 November 2010

South Pacific Study

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.

Sunday, 7 November 2010

"Kairos" and the universality of Christ

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.

Friday, 5 November 2010

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


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

Thursday, 4 November 2010

Insect farming

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.

Friday, 29 October 2010

"Scientist at Work" —NY Times blog

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

Thursday, 28 October 2010

Papua New Guinea plants


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.

Tuesday, 26 October 2010

Google maps latitude/longitude bookmarklet

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!

Sunday, 24 October 2010

Pacific Island Ecosystems at Risk (PIER)

Sphagneticola trilobata
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

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"

Monday, 18 October 2010

3 years on...

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?

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.

Friday, 15 October 2010

Google translate now translating Latin

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.

Thursday, 14 October 2010

Solomon Island Caddisflies

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

Thursday, 7 October 2010

Asian Beetle Websites

Sphenocorynes ocellatus
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.

Thursday, 30 September 2010

Featured insect: Oxymorostes riedeli (Coleoptera: Hybosoridae)

Oxymorostes riedeli Copyright Mario Toledo
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.

Eusphaeropeltis species


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

Wednesday, 22 September 2010

Microscope mounting media

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.

Thursday, 9 September 2010

Image-stacking software for Linux

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.

Wednesday, 8 September 2010

Canterbury Earthquakes part III

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.

Tuesday, 7 September 2010

Canterbury Earthquakes part II

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

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.

Monday, 6 September 2010

Less than negative?

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

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.

Wednesday, 1 September 2010

apply functions in R

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.

Monday, 30 August 2010

German Beetles

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

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

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.

Friday, 27 August 2010

Speech recognition in Linux

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.

Monday, 23 August 2010

Crosby Codes

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

Friday, 20 August 2010

Phylogenetic trees online

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

Buff-bellied Monarch Neolalage banksiana
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.

Monday, 16 August 2010

Featured insect: Pantorhytes plutus (Coleoptera: Curculionidae)


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.

Sunday, 15 August 2010

Downloading DNA sequences into R

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.

Saturday, 14 August 2010

Pacific Disaster Network

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).

Monday, 9 August 2010

Zookeys and Cybertaxonomy

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

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.

Wednesday, 4 August 2010

NZ Scholarships for Pacific Island Students

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.

Tuesday, 3 August 2010

Houseflies of New Caledonia and Vanuatu

Musca domestica
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

Thursday, 22 July 2010

New hemipteran species from New Caledonia


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:

A mystery... scale insects on European manuka

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:

Monday, 19 July 2010

PNG Entomology Textbook

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.

Friday, 16 July 2010

Blood parasites in Melanesian White-eyes

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.

Thursday, 15 July 2010

Australian weevil photos


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

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.

Monday, 12 July 2010

Smithsonian Contributions online

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

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.

Sunday, 11 July 2010

Featured insect: Ceresium tuberculatum (Coleoptera: Cerambycidae)

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).

Friday, 9 July 2010

Statio

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

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.

Wednesday, 7 July 2010

Proceedings of the Hawaiian Entomological Society

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

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:

Music. Lots of music

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...

Monday, 5 July 2010

South Pacific insects in a Russian Journal


The Russian Entomological Journal is not the usual outlet for taxonomic research on South Pacific insects. That said, it has published a number of papers over the last few years that are freely available to everyone on their website. For some reason, they all deal with the Hemiptera. So, if you ever wanted to know about Microveliines from Fiji, Maana emeljanovi (Lophopidae) from West Papua, or Nerthra kerzhneri (the first species of the Gelastocoridae found from New Caledonia, pictured), now you know where to look.

Tuesday, 29 June 2010

Act for the sake of Love

The Copenhagen summit on climate change in December last year promised much and delivered little. During the talk-fest, Archbishop of Canterbury Rowan Williams delivered a sermon entitled "Act for the sake of love". Unfortunately, this talk received very little publicity. This is a shame because I for one think that it details very elegantly why the push for action on climate change thus far has largely failed and turns the

A couple of (what I reckon are) the highlights of the talk:
Love casts out fear. If we begin from the belief that God wants us to rejoice and delight in the created world, our basic attitude to the environment will not be anxiety or the desperate search for ways of controlling it; it will be the excited and hopeful search for understanding it and honouring its goodness and its complex, interdependent beauty. If there is any 'fear' around here, it should be fear of spoiling the heritage given us, of forgetting the overwhelming scale and depth of the gift and of our responsibility and care for it, fear of forgetting that we are called to show consistent and sacrificial love for the created world as we must show towards our fellow-human beings.

The second sentence sums up in a nutshell my motivation for what I do and why I love science. The third sentence grounds this motivation in what really matters---Love.
We are afraid because we don't know how we can survive without the comforts of our existing lifestyle. We are afraid that new policies will be unpopular with a national electorate. We are afraid that younger and more vigorous economies will take advantage of us – or we are afraid that older, historically dominant economies will use the excuse of ecological responsibility to deny us our right to proper and just development.

I think that this is a very insightful quote that sums up exactly what happened in Copenhagen. Archbishop Williams does recognise that these fears may be justified:

There is, in a word, no shortage of excellent excuses for turning away from decisions that will mean real change. But at least let's be honest about where they come from: it is fear – not necessarily irrational fear, not even necessarily purely selfish fear, but fear all the same. And so long as that dominates our calculations, we are stepping back from love – love for the creation itself, which we must look at as God looks at it, love for one another and for the generations still unborn

Unfortunately, although Archbishop Williams outlines the principle, he does not give concrete guidelines as to how this works. He has a precedent for this: it tends to be the primary way God appears to operate. This means that it is up to us to work out how "Acting for the sake of Love" looks like. It's a bit easier at the personal level than at the governmental level---at the personal level you don't have angry constituents on your back if you decide something they don't agree with.

Acting out of Love always involves vulnerability, and making yourself vulnerable is NOT the aim of international relations. However, it is the model that Christ gives us and is what frees us from fear, greed and oppression. While it may have largely fallen under the radar, this speech by Archbishop Williams is a great reminder that Christ's redemption extends not only to us and our personal lives, but to the environment also.