PhD week 43: Merry Christmas!

Nativity and Adoration of the Shepherds, with Irenimus. With apologies to Bartolo di Fredi.

Savior of the Nations Come

Savior of the nations, come;
Virgin's Son, here make Thy home!
Marvel now, O heav'n and earth,
That the Lord chose such a birth.

Not by human flesh and blood;
By the Spirit of our God
Was the Word of God made flesh,
Woman's offspring, pure and fresh.

Wondrous birth! O wondrous Child
Of the virgin undefiled!
Though by all the world disowned,
Still to be in heaven enthroned.

From the Father forth He came
And returneth to the same,
Captive leading death and hell
High the song of triumph swell!

Thou, the Father's only Son,
Hast o'er sin the vict'ry won.
Boundless shall Thy kingdom be;
When shall we its glories see?

Brightly doth Thy manger shine,
Glorious is its light divine.
Let not sin o'ercloud this light;
Ever be our faith thus bright.

Praise to God the Father sing,
Praise to God the Son, our King,
Praise to God the Spirit be
Ever and eternally.

Ambrose of Milan, c. 397. Translated to German by Martin Luther, 1524. Translated from German to English by William M. Reynolds, 1851. From the Open Hymnal.

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Read:
   Tolkien JRR. 1937. The Hobbit. Harper Collins, London.
   Salmond A. 2009. Aphrodite's Island. The European Discovery of Tahiti. Viking, Auckland.

Listened:
Phantom Empire—If the World Burns

Watched:
Star Trek: Deep Space Nine Season 7

PhD week 42: Winding down

Gratuitous photo: A beautiful summer day at Cook's Beach, Coromandel Peninsula.

I have a saying that I repeat ad nauseum to anyone who asks me about holidays:

As a postgraduate student, you have a choice of two ways of looking at the world: you're either ALWAYS on holiday, or you're NEVER on holiday.

This week I've been operating in the latter part of the above statement. The university officially closed on Tuesday evening, and I'm still here doing various tasks.

Strangely though, it's actually rather enjoyable. There are fewer people around, meaning less distractions and allowing me to turn up the music and sing loudly (and badly) while editing DNA sequence data. Also, the mere effort of arriving at the university means that any work done is a bonus, which makes the day immensely satisfying.

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Read:
   Psalm 147–150

Listened:
Phantom Empire—If the World Burns
August Burns Red—Sleddin' Hill: A Holiday Album

Watched:
Star Trek: Into Darkness trailer
Star Trek: Deep Space Nine Season 7
John Hinton—The Type

PhD week 41: Success

Successful COI gel. All samples worked nicely
(including the negative control, precisely because it didn't).

Last week was a good week, on two counts. First, I managed to get consistent amplification of the cytochrome c oxidase region for my weevils. As I've previously written, this has been trickier than I originally thought. In the end it came down to a very simple fix, which in hindsight I should've figured out much earlier than now. However, the relief of getting it sorted compensates for the silliness I feel that I didn't click to it earlier.

Lateral view of Irenimus parilis Pascoe

The second success of the week was finding Irenimus parilis. This was important because this species is the type species of Irenimus. This means that to be included in the genus Irenimus, species have to be similar to I. parilis. This makes it an important species to obtain DNA sequence data for. A year ago I saw a specimen collected from a market garden north of Christchurch. I managed to get in touch with the owner of the place and visited it on Thursday. There, in a uninspiring, weedy corner of the property, we managed to find three specimens of I. parilis. Valuable, not only for their DNA, but also to get an idea of their habitat and biology.

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Read:
   Psalm 146

Watched:
The Hobbit: An Unexpected Journey
VESTAS Sailrocket 2 sails breaks 60 knot speed record
Frogs of the Marovo Lagoon, Solomon Islands
Star Trek: Deep Space Nine Season 7

PhD week 40: Societies

Not-so-gratuitous picture: Gull-billed Terns Gelochelidon nilotica.
Courtesy of Gossamer1013. Licence: CC: BY-NC-ND.

Last week, I talked about conferences being an important part of the world of science. Another major aspect is the role of scientific societies where professional scientists join together to promote and support their field of research through publishing scientific journals and hosting conferences, among others. Like every group, they require a corpus of people to ensure that everything runs smoothly. Somehow, I've managed to make my way into this esteemed circle in two of the societies that I am a member—namely as website editor for the Entomological Society of New Zealand and as newsletter editor for the Society of Australian Systematic Biologists. Neither of these roles take up copious amounts of time, but occasionally they require some action on my part. When those times do occur, it does feel a little like a distraction from the "real work" and requires a small reminder that it's all part of making the wider scientific community continue to function.

The week was ended by two very enjoyable experiences. The first was being present while a friend's song for their upcoming CD was being mixed, before watching the said friend's band perform live. The second was a sail on Lyttleton Harbour with another couple of friends on a spectacular Sunday afternoon.

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

Websites:
Discover Magazine—The Priest-Physicist Who Would Marry Science to Religion
Kill Your Stereo—Norma Jean to tour Australia 2013

Watched:
Norma Jean—Bayonetwork (Live at Reggie's)

Loading all installed R packages

The other day I was trying to set up an R for Windows installation on a USB drive. As I don't have a Windows machine, I had to use the university computer to do this task. However, for some reason, they've blocked R from downloading and installing packages using the install.packages() command. This required that I download the zip files and manually install them. No problem with that, until packages require the installation of dependencies. To ensure that I got all the packages I needed, I wanted a function that would load all of the packages locally installed on my machine. To my surprise, I didn't find a straight-forward solution, so I came up with the following kludge:

lapply(.packages(all.available = TRUE), function(xx) library(xx,     character.only = TRUE))

There may be a more elegant way to do the above, but it worked. Elegance is occasionally overrated.

PhD week 39: Conferences

Not-so-gratuitous picture: Bats that walk—Humeri of Icarops aenae (A–E), Mystacina robusta (F–H), M. tuberculata (I–L). M–O are schematics showing the morphological features of interest.

A big part of the social aspect of scientific research are conferences. These provide opportunities for scientists to present their research, learn what their colleagues are up to and offer and accept (ideally) useful criticism of their research. They also provide the opportunity to discuss problems and ideas and form long-lasting collaborations and friendships.

Over the past week Lincoln University has hosted two conferences, the New Zealand Ecological Society Conference, and the New Zealand Molecular Ecology Conference. The scope of these conferences broadly overlap, but are very different in execution. The EcoSoc conference was a moderately large conference of around 300 people, with several sessions happening concurrently over three days, and talks by some of the big names in New Zealand ecology. The Molecular Ecology Conference was much smaller with around 40 attendees, had a strong student focus, and was held in the Wainui YMCA campground. Both were valuable conferences to attend, and I learned a lot the speakers at from formal and informal discussions.

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Read:
   Borg MJ. 2001. Reading the Bible Again for the First Time. HarperOne, New York.

Watched:
Star Trek: Deep Space Nine Season 6

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.