The forgotten and ultimate survival tip for PhD

It's been a while since I've posted anything, and it is mostly due to me taking two months' leave from PhD. As such I have had literally nothing to comment on relating to my research. This post is in honour of someone who pointed out to me the key flaw in my "survival guide to PhD" post, that is, I didn't mention that a PhD student should never give up (although, life circumstance or job opportunity or any preferable change of direction in life are good reasons to quit). But for all of those out there with a general feeling of intellectual or motivational inadequacy, and are languishing over their PhD being a disaster and a dog's breakfast, you are not alone. Myself and so many others I know doing a PhD feel the same way. With the realisation that my PhD is likely to go for four years instead of three, I am currently coming to terms with a sense of failure, to myself and my supervisor, which is most likely unwarranted. I suspect it has a lot to do with high expectations for myself. This guilt and feeling of inadequacy and the fear of a sheer mountain of research and writing that has yet to be done, on top of a relationship breakdown and poor health, has literally caused me to breakdown. I've taken a break from PhD, but I won't give up. I know I shouldn't feel guilt at not being able to finish my PhD in three years, after all, if the government only wants to fund me for three years, that doesn't mean a PhD absolutely must be done in three years. Things take time, there's lots of waiting, and life happens. I've promised myself I'll get this PhD, and I'm going to do it. A close friend of mine has a great (and aptly Australian) definition for tenacity: "holding on for dear life, even when your dead", and I'll do my best to stick to that definition.
If you have a PhD story of dread or let-downs, feel free to share it in comments, after all, sharing the pain helps with the healing.

Alas! Poor Yorick

Homo sapiens (Cro-Magnon, 10000-30000 YA)

The primates include apes, monkeys and prosimians (bushbabies and lemurs). The main features that unite this group include a proportionately large brain, an opposable thumb on the hand, five fingers and toes, a long heel, nails instead of claws and forward facing eyes that provide binocular vision and good depth perception. Yes, this is obviously the group we (Homo sapiens) belong to. Specifically, humans (or Homo) belong to a tribe known as the Hominini, and within that, the subtribe Hominina. The reason I have bothered to mention all this information is because I want to share with the world the Bone clones rotational series, which gives you free access to a set of 3D and rotatable images of selected hominin skulls. It even has the fake "fossil" skull of Piltdown Man that was "found" in 1912 at Piltdown in Sussex, England that was hailed as the "missing link" between apes and humans (it wasn't until 1953 that it was proven to be fake). I have just spent the last half hour playing with the different skulls, so for those of you who are interested - Enjoy!

PhDs: a survival guide

 A five-step survival guide for all those who are about to start a PhD.

1. Eat healthily and exercise regularly. I know this sounds kind of intuitive, but your mental health is likely to take a beating throughout your PhD, so you might as well ensure you are at least physically healthy. Regular exercise is always a pain and a struggle, so perhaps consider joining a club so that the exercise is regular and there are people motivating you to push on. Also, don't fall into the trap of eating junk food because it is convenient, plan ahead so that when you are about to collapse after a long day at uni there is already a frozen meal ready to re-heat. Trust me, sitting behind a computer or a microscope all day, you will put on the pounds if you don't look after yourself.
2. Make time for social events. Without your mates you will have no one to bounce ideas off and just let off some steam with. During your PhD, it is likely your friends become your surrogate family, but to have friends you have to be a friend. So, try your best to turn up to events.
3. Organisation from the beginning. You've all heard it before and I reiterate: if you fall behind due to unforeseen problems, prior planning and staying on top of things will likely help you to meet that deadline or give you some time to come up with a contingency plan.
4. Choose a supervisory team and your readers wisely. So often I have seen students who have supervisors that are too busy, or just plain too scary to talk to. Furthermore, a friend of mine was dragged over the coals by an annoying reader for no apparent reason, there were no criticisms or feedback, just contradictions to the other readers because he/she could. If someone gives you a tip-off that a potential reader or supervisor is busy or unlikely to give you good feedback, can them. Don't waste your time.



If something doesn't seem right, it probably isn't...

5. If something doesn't feel right, stop, and reconsider your options. We've all heard a story about someone who did something in their PhD because their supervisor wanted them too, even though the student didn't feel it was right, then 3 years later the student finds out their gut feeling was right and they wasted 3 years doing something fruitless. IT'S TRUE. I know eight people where this has happened to them. If you feel uneasy or there are too many gaps in your experiment or model, sort the problem out immediately. Don't wait it out just because your supervisor says it will be fine. Time is a precious, precious commodity.

Spring cleaning

Ah Spring, how I love thee! The smell of flowers, the warmth of the sun, the displays of reproductive prowess in animals of all kinds.... and then to be stuck in an office. To address this issue, I've been dragging out some journal articles and highlighters to find an excuse to sit guilty-free on the grass outside. My excuse is that I need to brush-up on what I call "old knowledge" - the things that you should know, and did know, but have forgotten as they fell in line behind all the other things you should know. I'm calling it my "mental spring cleaning", dusting off old knowledge and putting it, nice and fresh, back where it belongs.

I've been working on fixing up my files of data (so that I can run better models) while I wait (still!) for equipment that I need to run my selection experiments with Drosophila serrata. It's been a long and tedious process, and I still have plenty data to go through. I keep telling myself that no matter what, I can only improve the quality of my research through repeatedly re-doing it. The only problem is pushing through the boredom and the lack of motivation. I always complain about it, but writing is not so bad, and I look forward to getting back to the stage I was at a few months ago where I was writing. My motivation at this point is derived from small self-rewards for reaching a "mini-goal", rewards such as a can of coke, or a walk through a park. My first mini-goal for today was to make a list of mini-goals. Check. I got a can of coke. I am winning!

Progress Report August 2012

1.            PROJECT AND RESEARCHER IN QUESTION         

1.1	Happiness-O-meter	No comment
1.2	Administering Organisation:	The University of Queensland
1.3	Project Title:	The evolution of terrestrial ectotherm metabolic rate
1.4	Project Leader:	Taryn Crispin

2.            PROJECT SUMMARY

2.1     100 word Project summary (as indicated in the original proposal)

The project focuses on (a) detecting and modelling major environmental factors that directly or indirectly affect the metabolic rate and scaling of terrestrial ectotherms (reptiles, amphibians, insects), (b) identifying the effect of selection for tolerance to environental change on the metabolic rate and scaling of terrestrial ectotherms.

3.            PROGRESS OF PROJECT

3.1     Have there been changes to or problems with the project?      YES

If No, please move on to section 4.  If Yes, please complete the remainder of section 3.

          If Yes, provide details

Not sure where to begin..... definitely both problems and changes. Also, I have been gaining weight, was this supposed to happen to researchers? And when am I supposed to submit a thesis again? Does not meeting a deadline count as a problem?

4.            ACHIEVEMENTS AND MILESTONES

4.1     What are your achievements and any research findings to date?

Milestones: successful confirmation and scraping through mid-candidature.

Research findings: N/A as of 2 weeks ago LOL

4.2     What are your research milestones for the coming year?

          FINISH THIS PHD AND GET A LIFE

The mutants of Fukushima

And suddenly being cross-eyed is not such a problem....

A month after the Fukushima nuclear power plant accident in Japan, scientists collected 144 pale grass blue butterflies, Zizeeria maha, near the plant. What they found was that the butterflies were starting to show mutations like deformed wings and dented eyes. Six months later another lot of butterflies were collected near the plant and, disturbingly, it was found that the incidence of these mutations had doubled. Lab-based exposure of butterflies to similar levels of radiation to that around Fukushima plant induced similar mutations, strengthening the link between the radiation and mutations butterflies on-site were displaying. Most worrying of all, is that there is an apparent accumulation of mutations down through the butterfly generations. This is likely a result of damage to the butterflies' germ line (cells that become sperm and eggs).

Having said all that, bear in mind that these butterflies are known as indicator species (meaning they are often used by scientists to assess impacts of, say, a nuclear power plant accident on the environment, as the butterflies are quite sensitive to small environmental changes). That means that all the important animals, like birds and other vertebrates, are OK (*prepares self for the onslaught from entomologists everywhere*).

Image courtesy of Hiyama et al. / Scientific Reports
Full paper available: http://www.nature.com/srep/2012/120809/srep00570/full/srep00570.html

Paper FAIL

Not surprisingly, my latest submission to Oikos was rejected. It's funny, I don't actually care... possibly because the weather outside at the time was so gorgeous that I just frolicked about in the grass and sun. Much more enjoyable than grimacing over each and every comment. Having said that, I spent the last hour grimacing over each and every comment, but at least the comments are useful. My paper will be accepted next time, next time for sure!

What will inevitably happen to users of R

As per usual, most of what is wrong has everything to do with my lack of statistical know-how. There appears to be a flaw in my approach to thermal effects on metabolic rate in my model, so I will spend the next few months (probably) re-doing what I spent the last two years doing in my PhD. For the first few minutes with this realisation I was more than a little enraged. Am I depressed by this now? Not as much as I probably should be, I think that a PhD has made me incredibly resilient to absolute FAILs, I take everything with a grain of salt and move on.

Why I can't have a dog

MegaDeath and Meister

If I wanted my pets to love me, I wouldn't have got lizards. Introducing my two Pogona henrylawsoni, MegaDeath (gender: male; the bottom lizard) and Meister (gender: ??).

Honestly, I originally did want a dog, or a cat, ANYTHING that I could come home to and cuddle up with at night while watching a movie. Basically, what I wanted was quiet company. Realistically, I knew it wasn't the right thing to do; I've seen far too many bored and lonely dogs and cats with owners who have full-time jobs and no energy at the end of the day. Knowing my PhD is so time- and mind-consuming, I sadly decided not to get a dog/cat. I didn't want to have an unhappy pet.

"Meister, it's time for cuddles!"

But, you can cuddle lizards. And they are quiet. Although MegaDeath treats me with mild indifference, and Meister regards me as one would regard a real-life "Alien" skulking in the shadows, that suits me fine, doing a PhD I'm hardly ever home, and it's a fair compromise to an energetic mammal.
I've learnt to relish the fact that my lizards would rather I was not home. As long as they are healthy and happy, I am thoroughly entertained by their shenanigans, however detached they seem from me.

Oh Canada!

I am returned from the first Joint Congress on Evolutionary Biology held in Ottawa from the 6th to 10th July. It was.... huge. 2500 attendees and 16 separate talk sessions, two poster evenings and one food-less banquet. The highlights? Meeting and making friends with many like-minded people, humble scientific geniuses and putting faces to all the names I've seen in the evolution papers I've read. All the talks I attended were fantastic and of high quality, and the ones I understood even more so (seriously, when there is such a wide variety of fields -within fields - it is pretty hard to understand everyone's research unless you are a scientific jack-of-all-trades).

The lowlight was the banquet: thrusting 1500 people into a - granted, enormous - room and then provide 50 seats, and have the small appetisers - oh sorry, dinner - run out for the evening before you even see the table where they (supposedly) were. Epic. Fail. On the brighter side, MacDonald's has no concept of a "small meal" in Canada, so there were plenty of satisfied customers after the "banquet".

For the Australians, yes, I did see squirrels and chipmunks. No, I did not see a moose. One day, one day....

Achievement for the week and now sleep...

Crazy week, absolutely nuts. But in a good way; I submitted two papers and finished a poster for the Evolution conference to be held in Ottawa in July. To clarify, I did not write those two papers in the last week (I wish!), these ones have been sitting on my desk waiting to be submitted for the last.... year? Yep, the last year. It feels good to knock a few things off my "to do" list. My self-reward? Sleep and a sense of satisfaction. The first paper is my honours work from two years ago, I sent that off to Physiological and Biochemical Zoology, and my second is on my first PhD chapter, which I sent to Oikos. Finger's crossed they get accepted, that would be very nice.

Self-castrating spiders

Do you fear for your life during pairing? Maybe not if you're a human, but for the male spider Nephilengys malabarensis, there's a 75% chance that he will fall victim to a females' penchant for cannibalism during sex. Unfortunately, this can also mean that the male may be killed before he has dispensed all his sperm, and to make matters worse (given the circumstances), his chances of fathering the next generation may be displaced by the sperm of the next successful male snack - er, suitor.

Male: "I didn't choose this life"

The address to this problem? The male snaps off his penis inside his partner while they have sex. Without his bulky sperm pump, the newly-lightened male can now fend off other males wanting to mate with his partner for longer without tiring, with an increase in stamina of up to 80%! And while defending his female, his detached genitals continue to pump sperm into the female.

Stupid nematodes II: a resolution

To avoid what would potentially be a nightmarish experience, I decided to autoclave all of my fly stocks. It is ok though, I have formulated a plan B. I will just change my model fly species and use a population stock that is already existing in another lab, one that has no diseases. The Blows lab in our biology school was kind enough to help me out of this awkward situation, probably out of sheer pity, nonetheless thanks so much guys! I guess now I have no excuse not to write up my papers (which I greatly despise doing), now that I have no need to maintain any stocks until I return from the Evolution conference in Ottawa in mid-July. Still, what a drama.

On a happier note, YAY for the transit of Venus eclipsing the sun, which happened between 0800 and 1500 today. Won't see anything like that again for a while. The University of Queensland astrophysicists had set up 4 telescopes for people to line up and view Venus eclipsing the sun, which was a real treat to peer through because you could see all the sunspots as well. There were also some special glasses being passed around that could be worn to look directly at the sun and view the eclipse, though everyone, including myself, using them had a nasty habit of looking to where the sun was and blinding themselves before putting the glasses on. Sometimes the obvious just isn't. Perhaps a warning should have been attached to the glasses "WARNING: Do not stare directly at the sun until after the glasses are placed in front of your eyes". And that's why they give me a scholarship to do a PhD.

Transit of Venus, 6/06/2012

Stupid nematodes

Sometimes working with animals, no matter how relatively simple their husbandry, can be a real trial, or reveal some completely unforeseeable problem. The plan for the last few months was to collect 40-60 female Drosophila melanogaster to kick-start a population to work with for a selection experiment. The recipe: catch flies, separate out females, keep the right species. Here's how I went:

Round 1, late April: Early AM, day 1. Collected 200-250 flies. Am confident most, if not all, are the right species based on a previous tip-off for the collection site.
Early PM, day 1. Most flies are not right species, but still have 67 "potentials".
Day 10. Only 27 are the right species. It is now too cold to catch more flies, but will try anyway. Time to start again.

Round 2, early May: Early AM, day 1. About 20 flies in total caught. Am not confident of species. Will leave traps out and return 2 hours before sundown.
2 hours before sundown, day 1. Catch 600 or more flies. Considered a successful trip. Return to lab to sort flies.
Day 10. Of 250, only 82 are the right species. That's ok, have more than enough females to start up a population.
Day 20. What's that strange stuff on the side of the population bottles? Looks like moisture, whatever.
Day 21. Did I see a small drop wriggle? I'm seeing things.
Day 24. Oh?! A nematode. Well, I don't want the spread of a pathogen, so I'll segregate this bottle from all the others.
Day 26. Oh wow, all the bottles have a few nematodes. I wonder if they are bad?
Day 26, 10 mins after previous observation. Oh wow, these nematodes are bad. Huh? Some nematodes use fruit flies as a vector, the target: human eyes!?! I don't think I've touched my eyes after contacting the bottles.... and I'm sure there is some research that has a way to kill off the nematodes but not the flies....

It turns out that nematode infestations in laboratory Drosophila cultures is quite rare, and there is no readily found preventative or killer of nematodes that doesn't affect their hosts. Unless I get rid of these swarming nematodes, I can kiss my populations (and a PhD chapter) goodbye, and I am limited in how much time I can spend on solving this problem as I only have about 9 months left of my PhD (in theory anyway). Oh, and my own health is a concern too. I'm seeing an optometrist to check my (and my partner's eyes) for nematode infection tomorrow. It's sad when I realise my health is my second, not my first, thought after reading about nematodes and how they like peoples' eyes. My first thought was "Oh no! My poor flies are living with nematodes, and it is going to screw up my experiment!". I'm going to call this the third symptom of PhD-induced insanity: "PhD comes before personal health". The first two symptoms is (1) The feeling that you are the unwelcome outlier, and, (2) I would rather eat a piece of poo than write that document.

In most cultures there exists tales of a trickster deity or spirit that is responsible for sowing discord in the universe as it is known. The Norse have Loki, a famously malicious and unconventional trickster god, the Japanese have Kappa, apparently responsible for both kidnapping and drowning people, the Greeks have Eris, Africans have Ekwensu, and the Irish, leprechauns. If my lab has a malicious trickster spirit that is distributing nematodes and screwing with our experiments, I would just like to say, "I don't like you" (that is re-phrased politely from what I would actually like to say). I am considering acknowledging that each lab may have a special little sprite that just wants to cause trouble when not doing something tedious, like, I don't know, cleaning the receiver on antique radios. In my lab's case, probably cleaning the insides of tygon tubing or computer screens. If you can relate to this, or have any suggestions on killing nematodes but not fruit flies, please post your comments!

Mid-candidature completion = back to the PhD

Achievement. Finally I can move on and actually get back to my PhD without worrying about proving that I can write and talk effectively. I have also noticed over the past few weeks that all my tutoring commitments are starting to build up and I have little patience for mediating between the inconsistencies in the material provided to the students and myself during my tutoring sessions. These little things, and many more, are slowly building up and causing me to plan two drastic future actions if I want to actually finish my PhD on time. Firstly, I will sacrifice the convenience of extra pocket money and refuse to tutor any more university courses for the remainder of my PhD. Second, I will publish everything I have data for before the end of the year so I don't have to stress about the write-up of my thesis. I know that the first plan is easily achievable, but I hope I can fulfill my second action plan. Fingers crossed I can still keep and have a life outside of my PhD.

Image: http://permanentstressrelief.com/wp-content/uploads/2011/11/Stress-Relief1.jpg

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

Timing is everything, or, Just ask

Today is Friday, the 10th of February, 2012 AD, Epoch: Holocene. I have spent the last few days planning what methodology to employ in my selection experiments, and how best to manage time. Timing is everything. In the past I would have not bothered trying to timetable specifics for lab experiments, I would have just winged it and see how I fit everything in given 24 hrs in a day. That was part of the adventure in research, cramming an immense amount of work into the space of just 2 days due to poor planning. Ultimately, this led to disaster as organisms were forced to adapt to different conditions within stringent timeframes, giving me dicey data at best. Nature will always refuse to cooperate with my planning, so I need to change the way I think and cooperate with nature. Thankfully, that happened in Honours research, and now I am in my PhD with just a little more wisdom in my belt.

Drosophila kicking back and enjoying a cold one: nature's suggestion for Friday afternoon activities

I have never worked with Drosophila, so when I read papers about the types of correlates used to assess fitness in different lines of selection, I imagine that the work and time involved in performing these assessments is relatively easy and short. I mean, the methods section is easy and short to read, and Drosophila are small animals, so the process is likely to be easy, right? But, knowing my usual 'flawless' train of logic, I thought that this assumption is potentially detrimental to my research and it was time to talk to people who actually do this kind of stuff, to get a real answer. Lucky I did. Apparently, the logistics associated with what I was planning to do were insane - too much work for one person with time constraints. Even better: the people in this lab were very helpful and gave me some great suggestions for time-managing my experiments. I now have contacts who are also happy to train me in Drosophila husbandry and managing lines of selection. By simply asking people with experience, I have saved myself a lot of time and heartache. Drosophila, you guys are crazy!

Image: http://browse.deviantart.com/?q=drosophila&order=9&offset=24#/d2ynv1p

Glorious technology

Breakfast: a crumbed sausage and coke. I know that deep-fried food is probably not the best way to start the day but I could not help the food-urge. I had to indulge. On other news, in my quest to understand selection and what words like "isofemale" mean, I wondered at the simple yet effective piece of equipment I frequently read about that can be used to separate out fruit flies that have different tolerances to heat or the cold: the Weber column. Put simply, flies are dumped into the top of a tube, and water that is either heated or cooled to a desired temperature is pumped into a jacket surrounding the tube to control the air temperature experienced by the flies. As flies are KO'd by extremes in temperature, they fall out the bottom, meaning the last flies to fall out the bottom are the most tolerant to the temperature. Brilliant. If only all the equipment I have used in the past were that simple. 

Weber's gift to science: a column of awesomeness. Image based on that of Huey et al. (1992)

Apart from admiring simple technology, I found most of the afternoon drift along as I mined Google Scholar for journal articles (which I lovingly refer to as "journicles"). I am looking for what are worthy correlates for fruit flies that are selected for cold tolerance. So far, it seems the classic life-history angles of fecundity, development time, egg viability, and ageing, are the reasonable options. When it comes to physiological correlates, there is chill-coma recovery time and tolerances to heat (which would also involve using Weber's column!), but some measure of "willingness" to be active is, according to a paper by Latimer et al. (2011), probably worth my time as well. Because most people could not be bothered sitting around watching fruit flies walk around, there's some sexy "laser" technology on the block that can determine activity of fruit flies, referred to as DAMs (Drosophila Activity Monitors). I know that there is one of these DAMs in the biology school, so it would be cool to examine differences in activity in selected lines of fruit flies versus control lines. If I am able to play with these bits of equipment, then at this point in time lab work is going to be fun!

References:

Huey RB, Crill WD, Kingsolver JG, and Weber KE. (1992). A method for rapid measurement of heat or cold resistance of small insects. Functional Ecology 6:489-494.

Latimer CAL, Wilson RS, Chenoweth SF. (2011). Quantitative genetic variation for thermal performance curves within and among natural populations of Drosophila serrata. Journal of Evolutionary Biology 24:965-975.