PhD week 56: Easter

The crucifixion of Christ. Icon by Dionisius (1500 AD). Image courtesy of WikiMedia Commons. Image is in the Public Domain.

When I Survey the Wondrous Cross

When I survey the wondrous cross
On which the Prince of glory died,
My richest gain I count but loss,
And pour contempt on all my pride.

Forbid it, Lord, that I should boast,
Save in the death of Christ my God!
All the vain things that charm me most,
I sacrifice them to His blood.

See from His head, His hands, His feet,
Sorrow and love flow mingled down!
Did e'er such love and sorrow meet,
Or thorns compose so rich a crown?

Were the whole realm of nature mine,
That were an offering far too small;
Love so amazing, so divine,
Demands my soul, my life, my all.

Isaac Watts, 1707. From the Open Hymnal.

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Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward

Websites
Revista Chilena de Historia Natural online
GIMP contact sheet plugin

Watched:
Star Trek: Enterprise Season Four

Twelve weeks of Star Trek:
Star Trek V: The Final Frontier

PhD week 55: Outreach

Ivey Hall, Lincoln University

This year marks 150 years since the establishment of Lincoln township, and the occasion was marked by a range of activities and festivities held over the past week. On Thursday, the University welcomed the community onto the grounds and held tours around the campus, and had a bunch of stalls manned by enthusiastic people to show people a few of the things that happen at the university. I was one of these enthusiastic people, and my job was showing off the diversity of invertebrates that can be found in pasture.

I do enjoy talking to people about insects, and seeing their reactions to their encounters with them. It find it interesting how different age groups respond in different ways. Pre-school to early primary school age children show a great interest in things and will happily poke, prod and otherwise engage with insects. Late primary school kids start expressing fears and misgivings about various invertebrates, but usually end up interacting extensively with them. High school students loudly voice how gross and disgusting they find everything when they're with their peers, but if you get them by themselves they tend to show a lot more interest. Finally, adults take a very utilitarian view of things, asking what functions the organisms provide, and ask how to control particular species.

What I like most about this sort of outreach though is that most people, despite having a negative view of insects initially, tend to go away with at least a grudging respect for them. This, for me, makes it all worthwhile.

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Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward
   Proverbs 22–24

Websites
Tortricids of agricultural importance

Watched:
Star Trek: Enterprise Season Three

Twelve weeks of Star Trek:
Star Trek IV: The Voyage Home

PhD week 54: Primers

A critical part of the process of sequencing DNA involves the development of primers. These are short stretches of DNA that bind to the gene of interest in the specimen DNA and provide a starting point to copy that gene. Two primers are required for amplication in PCR in order to amplify both strands of DNA and get the eponymous chain reaction. The easiest way of designing primers is to use ones that other researchers have used sucessfully for related organisms. Primer sequences are usually published in papers, and it is a simple matter to get them made. However, there is no standard convention to naming primers, which can be annoying at times. My preference is that the name include the name of the gene, the direction of the primer, and some measure of the position of where the primer binds to the gene. Unfortunately, many published primers lack some (or all!) of this information, which can make it tricky to make decisions as to which primers to try out. The primer numbering system of Simon et al is, in my opinion, a good model to follow.

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Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward
   Proverbs 20–21

Watched:
Star Trek: Enterprise Season Three

Listened:
Vanna—And They Came Bearing Bones

Twelve weeks of Star Trek:
Star Trek III: The Search for Spock

PhD week 53: Auckland, second journey

Rangitoto Island from St Helier's Beach
Photo courtesy of Sandy Austin via Flickr. Licence: CC: BY-NC-ND.

I was in Auckland over the past week, looking at specimens held by NZAC. I was also able to visit Guillermo Kuschel and Beverley Holloway, who are both internationally respected weevil taxonomists, who have been retired for some time. I greatly enjoy their company, and learn a lot with each visit.

This time I showed them some of my illustrations made using Inkscape. I found their reaction very interesting. They did have a few concerns about the accuracy of the drawings, particularly with regard to the representation of fine detail. However, their main concern was that the process, which I think they perceived to be largely mechanical and automatic, did not respect the organisms involved. They felt that the slight imperfections in the lines of inked drawings expressed a humanity that the vector graphics lacked, and that the simplicity of the illustration process showed a certain callousness.

While the previous paragraph makes them sound overly negative. In our conversation, Beverley and Guillermo also spoke of the sense of discovery that they experienced as they sketched structures directly from the microscope, and the feelings of excitement as they observed aspects of insect morphology that had been rarely encountered. It was very cool to see their passion that extended beyond being an occupation to having emotional regard for their study subjects.

Will I change the way that I operate? Unlikely. The benefits of using tools like Inkscape are too great. However, it will make me think further regarding the philosophical implications of my methods of choice.

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Read:
   Pine-Coffin RS (translator). 1961. The confessions of Saint Augustine Middlesex: Penguin
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward
   Howe JT. 2012. Affirmations after God: Friedrich Nietzsche and Richard Dawkins on Atheism. Zygon. 47(1) 140–155

Websites:
Nikon Travelite V Binoculars
Canadensys—Why we should publish our data under Creative Commons Zero (CC0)

Watched:
Star Trek: Enterprise Season Three

Twelve weeks of Star Trek:
Star Trek II: The Wrath of Khan

PhD week 52: One year in

Well. One year ago, I started my PhD. Since then I done some pretty cool things like attending a weevil taxonomy workshop in Arizona, going to the Southern Connections Congress in Dunedin, and collecting in Central Otago and the Two Thumb Range. I have also become better schooled in some of the key techniques of taxonomic research including sorting, dissecting, and slide-mounting. Overall, I've been enjoying it greatly.

How things go over the next 12 months will be in determining how close I will get to finishing on time. At this stage, everything is progressing nicely in the right direction. Long may it last.

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Read:
   Ferngren GB (Editor). 2002. Science and Religion. A Historical Introduction Baltimore: The John Hopkins University Press
   Hughes P (Translator). 1937. Meditations for Lent from St. Thomas Aquinas. London: Sheed and Ward
    St Augustine, Betteson H (Translator). 2003. City of God. London: Penguin Classics
   Tolkien JRR. 1967. Smith of Wootton Major. London: HarperCollins
   Proverbs 17–19

Websites:
Breeding grounds of NZ Storm Petrel discovered
Super Rugby
Better View Desired—Binocular reviews

Listened:
Project 86—Numb

Twelve weeks of Star Trek:
Star Trek I: The motion picture