Book review: Beyond Science by John Polkinghorne

Beyond Science is a series of nine essays by John Polkinghorne that examines a range of scientific and theological topics. The chapters progress from a discussion of the nature of scientific knowledge, through the process of scientific discovery, to the mystery of the human mind. From this foundation, Polkinghorne offers an argument for a reasonable acceptance of a Creator, and how this revelation influences one's outlook on a range of social and ethical issues. I found it to be a satisfying and enjoyable read, albeit one that is unlikely to be accessible to a wide audience. The themes discussed are thought-provoking, and Polkinghorne delivers them with clarity and a gentle humour. However, their juxaposition tends not to be especially fashionable, and Polkinghorne's scholarly writing does not lend itself easily to readers outside of academia.

PhD week 27: Thoughts on specimen labels

Gratuitous image: Spectacular lightning as part of the thunderstorm that passed through Canterbury on Tuesday. From seabirdnz's Flickr Photostream. Licence: CC: BY-ND

The conversion between ornamental pinned insects and valuable scientific specimens occurs with the simple act of labelling. As well as locality information, two other critical pieces of information contained on standard insect labels are the date of collection, and the collector(s) of the specimen. This combination of time, place and personality makes reading the labels on a large collection a fascinating experience.

As part of the databasing that I've been doing over the past couple of weeks, I've had many of these encounters. Some examples include: looking at insects that are over 100 years old, specimens collected on my birthday 20 years before I was born; collections made by some of the pioneers of New Zealand insect collecting—C. E. Clarke, A.E. Brookes and P.S. Sandager—and the prolific collections of the 1970s and 80s made by John Dugdale, Charles Watt and Guillermo Kuschel.

This connection with the past is one of the aspects of taxonomic research that I find extremely enriching. Working with specimens that past entomologists collected and looked at is a great experience that gives my work a sense of continuity that fairly few other fields can boast.

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Read:
   Edwards AWF. 1972. Likelihood. An account of the statistical concept of likelihood and its application to scientific inference. Cambridge University Press, Cambridge.
   Borg MJ. 2001. Reading the Bible Again for the First Time. HarperOne, New York.
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 108–110

Websites:
New Zealand Library Catalogue
Public Domain Review—Lewis Carroll and the Hunting of the Snark
Public Domain Review—Was Charles Darwin an atheist?
PhD comics:
  What you know vs. How much you know about it
  Staring Contest
  Grad Stereogram
  The Joy of Research

Watched:
Emirates Team New Zealand takes flight
Star Trek: Voyager

Quote: A.W.F. Edwards on Scientists and Statisticians

The perpetual sniping which statisticians suffer at the hands of practising scientists is largely due to their collective arrogance in presuming to direct the scientist in his consideration of hypotheses; the best contribution they can make is to provide some measure of 'support', and the failure of all but a few to admit the weaknesses of the conventional approaches has not improved the scientists' opinion.

Edwards AWF. 1972. Likelihood. An account of the statistical concept of likelihood and its application to scientific inference. Cambridge University Press, Cambridge. Chapter 3: Support. Page 34.

PhD week 12: Bits and pieces

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

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

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Read:
Thompson RT. 1992. Observations on the morphology and classification of weevils (Coleoptera, Curculionidae) with a key to major groups. Journal of Natural History 26: 835–891.
    Rosas MV, Morrone JJ, Guadalupe del Rio M, Lanteri AA. 2011. Phylogenetic analysis of the Pantomorus-Naupactus complex (Coleoptera: Curculionidae: Entiminae) from North and Central America. Zootaxa 2780:1–19
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 60–62, Colossians 1:15–18

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

Watched:
The Simpsons Season 10

PhD week 4: Publications and World Cups

Something exciting arrived in the university library this week. And no, it wasn't something geeky like a new book on weevils or phylogenetics. No, this was something other people could get excited about, and they sure did:

Yes indeed, that is the Web Ellis Trophy, the Rugby World Cup, of which New Zealand is currently the proud holder (not to crow about it though...).

There's a maxim in the academic world: "Publish or perish". Publication is essential for communicating the discoveries that you've made and the bit of the world that you've had a bit of insight into. There is also a lot of emphasis on using publications and the venues they're published in as a measure of your quality of the research you do and are carefully considered in hiring, firing, promoting and receiving grants. Publications are important.

They also take up a lot of time. Most of this week was spent dealing with various aspects of the publication process; from finishing and submitting a manuscript dealing some of my own research from before starting this PhD, to discussing our response to the reviews of a second manuscript on which I am a coauthor, to reviewing a third at the request of a publisher to give my opinion on how the paper may be improved before publication. There's a fourth manuscript that I need to have a look at for another journal that is lying on my desk, and which I won't get around to this week too.

While it occasionally feels like a waste of time, this process is what keeps science going. And with everybody doing their bit of the work, it gets spread fairly well. So, although this week was taken up with this aspect of doing science, I should be able to spend the next few weeks looking at some weevils, and doing some lab work which will get me going towards the next publication.

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Read:
Garonna AP, Dole SA, Saracino A, Mazzoleni S, Cristinzio G. 2012. First record of the black twig borer Xylosandrus compactus (Eichoff) (Coleoptera: Curculionidae, Scolytinae) from Europe. Zootaxa 3251: 64–68

Fletcher AC, Bourne PE. 2012. Ten Simple Rules for Starting a Company. PLoS Computational Biology 8(3): e1002439.

Wilkins JS. 2009. Defining Species. A Sourcebook from Antiquity to Today. New York: Peter Lang

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

Kirkpatrick R. 2009. Beyond the Wall of Time. Sydney: Voyager

Psalms 28–32

Listened:
National Geographic Music

Watched:
Dropkick Murphys—I'm Shipping Up to Boston

Star Trek: Deep Space Nine Season 1

2nd Fiji Conservation Science Forum

I had the privilege of attending the 1st Fiji Conservation Science Forum in 2009, and greatly enjoyed the quality of the talks and science presented, and the enthusiasm of the attendees. Unfortunately, I was unable to get along to the 2nd meeting, held 14–16 September 2011, but I gather that it likewise was an informative and exciting meeting. The abstracts are available at the Wildlife Conservation Society website, and show the breadth of territory covered by the forum.

The Fiji Conservation Science Forums are an excellent initiative that have and will continue to inspire science in the South Pacific. I wish the organisers all the best in their preparations for a third forum in the next couple of years.

South Pacific Biodiversity Science funders

The following is a list of organisations that provide funding for biodiversity and conservation science, whose scope includes the South Pacific region.

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American Museum of Natural History: Research and Fellowships

The American Museum of Natural History offers academic fellowships and research grants in biology, ecology, zoology, wildlife conservation, paleontology, anthropology, and some fields of the physical sciences.

Moorean Insects on Flickr

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

1 2 3 steps to publishing a scientific comment

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.

Faraday Institute

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.

Quote: James Hannam on science and religion

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.

Two R functions for working with DNA alignments

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.

"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

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.

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.

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

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.

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.

Conservation Biology papers with a Pacific focus

The most recent (April 2010) issue of Conservation Biology has a number of papers which focus on the fauna, flora and environment of the South Pacific.

The issue starts off with an editorial by David Melick on economic schemes to negate carbon emissions. In particular he deals with the scheme to compensate landowners for NOT cutting down forests on their land (REDD) and the way this has played out thus far in the Papua New Guinea scene. He ends with this very pertinent statement:

... REDD will come to nothing if the system is not supported by the people who own and live in the forests. If the process is not rushed (it may take years, not months) and the PNG government is willing to accept international scrutiny and advice, forest governance and communitybenefits for the rural poor may finally be improved significantly...

Highly relevant for all who work in the South Pacific, particularly those of us with a western, productivity-based mindset. As the Mainland cheese ads say---Good things take time.

William Laurance and others discuss the impact of Oil Palm cultivation and some of the issues and opportunities surrounding it. In particular, they discuss the Roundtable on Sustainable Palm Oil (RSPO) a nonprofit organisation that hopes to promote and market sustainably grown palm oil. Unfortunately, its track record appears to be fairly poor. The seeming blind eye the organisation has taken toward the destruction caused by growing oil palm in peat swamps is singled out as being a major failing of the RSPO. however Laurance et al. refuse to be pessimistic about the situation and make some recommendations, most of which involve fairly major restructuring of the RSPO and developments in its monitoring and enforcement policies. However, the real problem in the situation is the lack of market demand for sustainably grown palm oil, meaning that the RSPO has little clout.

Alison Boyer revisits the very high extinction rate of Pacific Island birds, this time investigating what ecological traits seem to have an influence on extinction rate. She concludes that differences in endemism, body size and diet influence the potential for extinction and gives a list of bird species that may be worthy of a higher threat category than currently given.

Shankar Aswani and Armagan Sabetian look at the impact that urbanisation has had on the parrotfish population around Gizo and Munda, in the Western Province of the Solomon Islands. Not surprisingly, they found that over the period 2004--2005 parrotfish numbers decreased around Gizo. However, they did find that some customary management systems were effectively preserving larger and greater numbers of parrotfish. The most effective systems were those that prevented all fishing in certain areas.

Mayeul Dalleau and team looked at shallow marine habitats around Wallis Island and used digital imagery and habitat maps as surrogates for biodiversity in the proposal of marine protected areas. While they promote this method as being an effective and efficient of surveying large areas, they do recognise that it is very desirable to do some actual field work to complement the habitat data, particularly in regions such as the Red Sea which has a very different environment from the oceanic Pacific islands.

It's a good issue. Well worth a read, certainly if any of the above issues pique your interest.

References:

Aswani S, Sabetian A. 2010. Implications of Urbanization for Artisanal Parrotfish Fisheries in the Western Solomon Islands. Conservation Biology 24(2): 520-530

Boyer AG. 2010. Consistent Ecological Selectivity through Time in Pacific Island Avian Extinctions Conservation Biology 24(2): 511-519

Dalleau M, Andréfouët S, Wabnitz CCC, Payri C, Wantiez L, Pichon M, Friedman K, Vigliola L, Benzoni F. 2010. Use of Habitats as Surrogates of Biodiversity for Efficient Coral Reef Conservation Planning in Pacific Ocean Islands. Conservation Biology 24(2): 541-552

Laurance WF, Koh LP, Butler R, Sodhi NS, Bradshaw CJA, Neidel JD, Consunji H, Vega JM. 2010. Improving the Performance of the Roundtable on Sustainable Palm Oil for Nature Conservation. Conservation Biology 24(2): p 377-381

Melick, D. 2010. Credibility of REDD and Experiences from Papua New Guinea. Conservation Biology 24(2): 359-361

Molecular identification of New Guinea mammal poo

The use of environmental DNA samples for identification and monitoring of animals has been increasingly widely used over the past five years or so. This essentially involves extracting DNA from non-tissue materials and analysing it in such a way as to discover the creatures that produced/lived in/ate/passed by the material. For example, pond water has been analysed to discover what frog species were present in the area and faecal matter has been analysed to figure out both what was eaten and who was the eater.

This last scenario has been played out on the Huon Peninsula in Papua New Guinea. Research has begun on the endangered Matschie's tree kangaroo (Dendrolagus matschiei) looking into its population structure and genetics. This research has applications to help direct the future conservation of the species by giving an indication as to how many individuals there are and how much they move around. However, the capture and collection of tissues from a rare, endangered animal that spends the majority of its time in montane rainforest canopies present both logistic and ethical concerns which are alleviated by the collection of DNA from their faeces. Finding poo is sometimes a lot easier than the beast itself!

Unfortunately, poo from one marsupial often looks the same as poo from another and so faeces were mistakenly collected from an additional two species the New Guinea pademelon (Thylogale browni) and the small dorcopsis (Dorcopsulus vanheurni). A recent paper published in Molecular Ecology Resources by Thomas McGreevy and coauthors give a method for determining which species of marsupial produced the poo of interest. The primer set they've developed amplifies a portion of DNA that is a different length in each species---making it easy to distinguish which came from what and making sure that time is not spent looking at the wrong ones.

References:
McGreevy TJ Jr, Dabek L, Husband TP. (2010). A multiplex PCR assay to distinguish among three sympatric marsupial taxa from Huon Peninsula, Papua New Guinea, using the mitochondrial control region. Molecular Ecology Resources. 10(2): 397-400.