PhDs and an unsteady relationship with sanity

With a mid-candidature review coming up in a few weeks, I have been busy ensuring that I look as organised and in-control as possible to my readers for the day. My document is still very much a draft, but I am sure I will have that done in time for hand-in at the end of next week. Fingers crossed. As I have left a draft with my supervisor for a few days, I have been spending time trying to regain what was left of my sanity before I started intense writing over a month ago. I have found that clouds of words eases my tension - which is very unusual, I know - so I have been happily picking a topic and forming word clouds on an awesome site called Wordle.

For those of you who have already endured the loss of sanity through writing or academic life in general, I applaud you if you are currently not in a psychiatric ward. For those of you who have not reached this point yet, I wish you luck when it comes your time. Those of you who are currently at the same stage as me - I'm sure you have found solace in a video game, TV show, or random activity that will help you survive this experience. If not, go out and find one before your thesis sucks out your soul! I have a feeling I will look back in a few months at these blogs and say "sheesh, I was sure a whiny and negative person back then". C'est la vie, I'll survive! What doesn't kill you makes you stronger, right? Right?!?

Flies, food and pooters

It's official: I can now tell the sex of flies. Not without a couple of hours of getting my eye in for the task, but now I can add to my growing list of "skills of the universe". Even better, I have learnt the revered art of pootering. Which involves a pooter. You make "poot" sounds when you use it. Very glamorous. Essentially, when you are sexing flies or transferring flies to a new "cage", you can transport flies by sucking them up into a tube, and exhaling through the tube to shoot the flies to their destination (there is, of course, a filter between your mouth and the flies). The tube itself is referred to as a pooter by those who work with fruit flies. I have also witnessed someone cooking a special food mix for encouraging flies to lay eggs. It requires a level of precision that perhaps pastry chefs spend years developing, and I know that when it comes my turn it will be a very sad ending. Hopefully I will get the skills I need quickly so I don't waste too many ingredients.

My finger points...

The last few days have been spent writing a paper on the evolution of reptile metabolic rate. For those who have experienced the joys of writing up their results, I'm sure you understand the mental anguish that accompanies this activity. This time round, my writing-stress has expressed itself in the form of  unkemptness and spontaneous self-depreciation. I have also come to realise that having a shirt tucked in at the front, drawstring of my pants undone, and having food stains on my clothes constitutes my current becoming of a dag. Progress is slow, but it is being made. I have also learnt how to make requisitions using the university finance e-forms, which is a much bigger achievement than it sounds (for some reason the logic of finance is unobtainable to me).

My super-awesome poem on writing:

Words on the page are a mess

Probably the cause of my distress

I wish I had a published paper to caress

I need to work harder, I must confess

The effort won't kill me I guess

The best thing about a day of hard work is the satisfaction of coming home and kicking back, knowing you've done good work for the day. I haven't had that in a while, most days I come into uni just in time for lunch, have an extended lunch, procrastinate for as long as possible, then maybe find something more constructive to do for about 40 mins until I give up and go home for dinner. But I have just started a bio-statistics course which might give me some structural backbone to re-construct my weekly schedule. I am going to do a uni work-ethic makeover (amidst writing, I know). This is it people, before I'm tossed like chaff in the wind, I'm gonna re-take my position as a steady-going researcher!

Science: a many-flavoured thing

It is normal to expect researchers to be comfortable when handling their study organisms, but where do you draw the line in terms of 'familiarity'? Personally, I would draw the line at basic handling and post-mortem dissections. Valerie Clark, a herpetologist studying frog toxins, has a different level of familiarity with her study organisms: back-licking! By licking frogs she can determine whether they are poisonous by the taste of their skin secretions. (Note: I do not recommend non-experts pick up frogs and lick them to see if they are poisonous). Most skin secretions of poisonous frogs can't kill a human, but it can cause throat burning and constriction, but when in the field with limited equipment, often the only way to tell whether you've found a poisonous frog is to give it a hearty lick on the back.

Poisonous Mantella frogs from Madagascar taste bitter-sweet

In a recent study, Clark used electrical stimulation to extract skin secretions from some poisonous frogs found in Madagascar. Apparently, licking these study frogs leaves a bitter-sweet taste. The reason for this taste is revealed by mass spectrometry of the secretion products: sucrose and a new bile (or stomach) acid called tauromantellic acid. Frogs typically don't generate their own poison, their guts actually sequester and remove it from insects that they eat so they themselves are not poisoned. Clark believes that the bile acid on the skin is involved in transporting toxins from the frog's gut to its skin. FYI: this does not happen in humans, if you eat something particularly nasty and don't seek medical help, it is likely you will just die. On that happy note, frogs are cute anyway, so who wouldn't want to lick them?!

Original article via National Geographic News.

I want free bee metabolic rates!

I've spent the last week compiling a datasheet on the measured metabolic rates of insects from around the world since the 1940s. Tedious? You bet. I need this database so that I can perform what is called a Phylogenetic Generalised Least Squares (PGLS) analysis using data on not just the metabolic rates of insects, but also phylogeny. The question I am asking is: how and what levels of rainfall and ranges in temperatures can influence the evolution of metabolic rate in insects? The problems with this type of analysis are many, yet in evolutionary physiology there is no better way to look at the data as yet. The biggest problem of all is that there is no resolved phylogeny for insects, and we aren't as close as we'd like to be either. Not that it helps that a couple thousand new species are discovered every year, but all I can do at this stage is analyse the data based on the best phylogeny available, and wait until an improved version comes out in the future.

At this stage, I am having difficulty getting enough data on flies and bees. There have been many measures of their metabolic rate, but few papers have specified where the animals were caught, and if they do, the flies and bees have been kept in the laboratory for so long it is pointless using their data to assess the influence of environmental variables I'm interested in on their metabolism.

Free the bees! I need data from bees OUTSIDE of cages! (Nick Cage would also appreciate bee-freeing)

Despite these minor hiccups and tedium associated with sitting at a computer, I actually am looking forward to staring at a computer screen and writing up a paper (I have mid-term review coming up!) on one of my earlier PGLS analyses on the evolution of reptile metabolic rate. Watch this space for my post of paper submission success!

Image: http://i3.kym-cdn.com/entries/icons/original/000/002/910/not-the-bees.jpg

The dwarf of Nosy Hara

While constructing a timetable of sorts on how to manage selection experiments and ensuing measures of fecundity and metabolic rate, I realised that the updates for PLoS ONEs releases from yesterday had not been checked in my emails' inbox. While scanning through the journicle titles, the key words "dwarf", "chameleon" and "Madagascar" captured my interest. It's always a pleasure to read about the new and interesting fauna being discovered in Madagascar, and even moreso when the alternative is to frown and fret over mistakes in ones' timetabling of experiments.

The newly discovered leaf chameleon has been declared as "an extreme example of island dwarfism".  For the record, island dwarfism is common; the limited space on islands typically place pressures on its' inhabitants to reproduce faster and deal with limitations in resources in order to survive as a species. The new miniature leaf chameleon was found on a very small islet called Nosy Hara in the north of Madagascar. The animal, endowed with the name Brookesia micra, has a total length in both sexes that is less than 30 mm, making it the tiniest amniote vertebrate in the world. Thankyou, says the Guiness Book of Records.

The tiniest amniote vertebrate in the world is incidentally the cutest as well.

It also turned out that once I had finished my timetabling of my experiment plans, I had also mixed up my fertility and metabolic rate experiments with the wrong generations. I had a very busy afternoon and am at least glad for the chameleons that they never have to endure the self-induced torture of a PhD.

Citation: Glaw F, Köhler J, Townsend TM, Vences M. (2012). Rivaling the world's smallest reptiles: discovery of miniaturized and microendemic new species of leaf chameleons (Brookesia) from northern Madagascar. PLoS ONE 7(2). doi:10.1371/journal.pone.0031314.

Image: Glaw F, et al. (2012). PLoS ONE. (A) Adult Brookesia micra, (B) and (C) are juvenile B. micra, and (D) is typical habitat on Nosy Hara, Madagascar.

Loose ends are tied!

Loose ends always need tying-up. Not that I have any serious loose ends, unless you call a $35, 000 HECS debt a loose end, but since the annual biosafety test for our school has become available, I've been meaning to complete the online assessment. And register for the Evolution conference that is being held in July. Not to mention all the administration forms I have yet to complete, and replying to multiple people about availabilities for tutoring this semester.... ok, so I have had a lot of small things building up over the last 4 months that needed to be done. But today I did it all, and I feel very relieved and happy. Seriously, if you're having a bad or unproductive day, tie-up those loose ends and you will have achieved something for the day and feel a lot better for it.

I also met up with another person who works with Drosophila fruit flies, to see what feeding protocols are used and how to distinguish between different larval stages. Conveniently, larval development is divided into four logical stages: L1, L2, L3, and L4. That much was easy to understand. I was surprised to learn just how fast generation time was in these guys; in 10 days an egg will become a sexually mature adult fly, given it was reared at 25 degrees C. To encourage females to lay their eggs, simply dye an apple juice-based medium blue, introduce to the female fly, then lo and behold, little white eggs will appear. Apparently, this only works for Drosophila melanogaster, not for other species like D. simulans.

Imagine little white eggs on a blue (in this case purple) medium. At least, I hope the eggs are actually white, because if they are clear I'm in trouble!

Now that I am officially registered for it, I am really excited about the Evolution conference to be held this year! It is going to be in Ottawa, Canada, and runs from 6-10th of July. My supervisor and I haven't really been to an international evolution conference before, so we aren't sure what to expect, and whether my research thus far is even worthy of presentation, seeing as we aren't even sure if it suits the draw crowd for the talk sessions. To spare the on-lookers the pain of being told what they already know, we agreed that I will just present a poster for this conference, and focus on learning and getting ideas for my own research. What am I most excited about for this conference? Definitely the networking!

Image: http://browse.deviantart.com/?qh=&section=&q=drosophila+melanogaster#/d148ear