Next year...spread the spider love

It's New Year's Eve, and I'm writing a chapter of my thesis. A close (probably closest) relative of the Cantuaria genus is the Misgolas genus, so I looked it up on Wikipedia to make sure of its distribution.

This is what Wikipedia has to say about Misgolas:

The origin of the name Misgolas is unclear, but may have come from the prosecution of Timarchos by Aeschines in ancient Greece. In it, a particularly unsavory and disrespected individual is named Misgolas, possible prompting the naming of the species.

What? Why? What has Misgolas done to deserve that? Reading that short paragraph cut me deep. It's bad enough that the Maori call almost all spiders "pungawerewere", Punga being the ancestor of all ugly things and "werewere" meaning "hanging". Throughout history, even in taxonomy where people should really know better, spiders have been unfairly represented as ugly, horrible, or disgusting. Why are we so nasty about creatures which have no way of taking on board our criticisms, or of fighting back?

The only way that spiders can improve their image is by proving us wrong, which they have done since prehistoric times, but we have ignored their usefulness, beauty, cleverness and wonder and preferred to keep our heads in the sand and call them ugly.

In 2015, I am going to try a lot harder to make people appreciate spiders. They are important, and they do not deserve our disgust. I urge you to do the same. If we even change one person's mind about spiders, that is an improvement; if we change a few, all the better.

Here are some reasons to love spiders:

• Spiders are useful. Everyone knows that spiders catch flies, but they don't quite seem to consider the implications of that. Spiders also catch other insects, including pests, and even if the spider isn't hungry her web is there to ensnare things that fly past. Each spider web is an extremely good insect trap, and you don't need to buy them, look after them, or even see most of them. Also, spiders are more than just pest control - their silk is useful in medicine, fabric design, physics (including space) research, and other things besides. Their venom is useful in pest control and medicine. Many larger species are edible, and provide nutrition in countries where people really, really need it.
• Spiders are beautiful. Instinctively we think of them as ugly. On the surface, many spiders that we come across look ugly. But what about the gooty ornamental, the peacock jumping spider, or the ladybird spider? Many spiders are brightly coloured, unusually shaped, or have big, soulful eyes. Even very common spiders are only ugly because traditionally we think of spiders as ugly. The long, slender legs of the cellar spider are elegant, not creepy. The furry Tegenaria bodies are soft and endearing, not scary. Beauty is in the eye of the beholder. Look closely at the intricate body parts of spiders - their eyes, their feet, their genitalia - and every spider has a beauty of its own.
• Spiders are clever. Well, not all spiders. Although one has to admire the clever life history strategies that they have evolved. Some spiders are quite adorably dumb. But others, particularly jumping spiders, are surprisingly smart. They can plan hunting trips, outsmart other spiders, and navigate mazes. Their eyesight is good and they can be trained to perform simple tasks.
• Spiders are wonderful. These are creatures that have existed for over 300 million years. Silk comes out of them. They are master architects, songsters, and dancers. They court their mates, fight for them, and guard them. They live on the highest mountains, and in the deepest caves, and even underwater. They have colonised the vast majority of land on this planet. And what's more, they keep out of our way for the most part, and we hardly notice their existence.

So, happy new year to you all, and I hope 2015 is a good one, and that maybe we can change a mind or two about spiders.

Routine

Two nights ago, at 2am, the peaceful village of Prebbleton was shaken by a blast of rock music roaring from the windows of a bashed up Toyota Levin. Houses shook with the racket, dogs barked, and people probably woke up a little bit annoyed.

Sorry, Prebbleton. It was me. I was trying to keep myself awake, because for the first time in my PhD I had to work into the night. I'm not very good at working into the night.

PhD students are expected to work pretty much constantly, including nights and weekends. Most of my friends do that; they wake up some time in the late morning or afternoon, then do science until the wee hours the next morning. They procrastinate during this time too - go for coffee, check facebook, check email, look at the news, go for coffee, chat to friends, check facebook, go for coffee. Their day is homogenous - they spend the entire time doing a mixture of work and procrastination. As they work more, they procrastinate more - it's an even mixture.



I tried that during my masters and undergrad, and it works ok. Unfortunately though, it doesn't leave much time for anything else. If you are constantly doing a low level of work, you need to make sure you keep it up or you won't get much done. Long lunches, trips away, and movie nights with friends are inadvisable except on special occasions. It also frazzles your brain and makes work a bit mundane - going for coffee is a good break from work, because you have to walk around and get away from your desk, but checking facebook and email are terrible ways to take a breather. You're taking a break from staring at words on a screen to stare at different words on the same screen. However, nothing makes you feel like a dedicated student more than working late at night.

During my undergrad, I started making little changes in the way I studied and took breaks. Whenever I took a break, I wasn't allowed to think of anything sciencey. The same applied when I shut my computer down, or when I took a day off. I distracted myself by talking to people, having a change of scenery, or popping out for a walk. I found that having proper breaks concentrated my work a little more and stopped me from procrastinating so much during work time. It also meant I felt less fatigued, because my brain wasn't constantly doing the same thing and had a bit of variety.

This time last year, I went to a conference which had a workshop attached. At the workshop, one of the best tips that I heard was to guard your work time, and your spare time - i.e. don't let people distract you with meaningless conversation while you're trying to write, and don't do work-related things when you're on a break. At the same time, my advisor told me that he recommends treating your PhD like a full-time job: work 9-5 on weekdays, and have evenings and weekends off.

I have mostly stuck to the 9-5 schedule. It really works. If you work in 45 minute increments, with a 15 minute break after each one, and during work time don't check email or facebook or use your computer for anything other than work, you end up pretty exhausted at the end of the day. Nothing is more satisfying than knowing you worked hard and could not possibly have worked any harder. Also, treating your office as a work space and your home as a relaxing space helps me to sleep at night and work during the day. However, it's very difficult when others around you don't have the same routine. For a while I tried car pooling, but gave up when the other person couldn't get out of bed earlier than 10am and always wanted to leave work around 4 to work from home. I also find that social events usually last until late at night, which isn't great when you have to wake up at 7. Finally, there is always that twinge of guilt when I leave the office at 5, but my office mates will be slaving away until much later (although this is somewhat made up for by the smug feeling I get when I'm the first one in every morning). I also feel guilty when I see that in their free time, my friends read scientific literature for fun. Lately I have been doing more sciencey stuff in my free time, which makes me feel less guilty but also makes me less able to work to my full potential during work time.

Working 9-5 frees up time for hobbies, too, and gives me enough time to have a life. However, it's very difficult to break away from this routine if I want to do a bit of extra work - like pulling my all-nighter the other night. I had to go to Illustration Club at 5, then go home and feed the chickens and rabbits and do some falcon training, then hang out with friends for a bit because that's what we're all used to, and then finally when my flatmate was going to bed I headed back into uni to finish some DNA sequencing in time for the sequencing machine's last run before its holiday. The next day I got up early to do some more work, but ended up leaving work at 1 to sleep for a bit because I was so tired. Your body gets used to a particular routine, and breaking it is very hard!

If I had planned a bit better, I wouldn't have had to work late. I think in the future I will just be a bit more organised and stick to what seems to work for me.

Venom, vidi, Vikki

When people ask me if trapdoor spiders are poisonous, I usually say "yes" just to simplify things. But really, they are probably not poisonous, and very few spiders are. Poisonous animals are those which will make you sick if you eat them, whereas venomous animals deliver a bite or sting which causes anything from slight pain up to death.


 Trapdoor spiders are most definitely venomous; they rely on venom to subdue their larger prey items. I've always been quite interested in poisons and venoms, their evolution and effects on prey. However, most studies into venom seem fixated on its medical significance. This doesn't really interest me much, but it interests one of my colleagues, so we have a deal - I will do the spider squeezing and some of the analysis, and he will do the other magic that has to happen that I don't know about.

We've put together a few ideas towards a venom project which, if it doesn't work, won't take much time out of my study - but if it does work, it will be a good additional chapter in my thesis (and could perhaps take me further than that, but who knows?). Analysing venom seems pretty straightforward, as it is just a set of proteins (though it still presents a few healthy challenges), but getting the venom in the first place is the trickiest, and most important, part.

How you collect venom differs depending on the spider species. The Sydney funnelweb (Atrax robustus) is probably the easiest to collect from - if you annoy one (which isn't difficult, by all accounts), it rears up and exposes fangs that drip with venom. You can then just collect the venom from those droplets. Venom collection from other spiders involves knocking them out and then electrocuting them. Unfortunately they tend to vomit, so your samples can become contaminated very easily and you need to suck up the vomit as soon as it appears. A third method is similar to that used to milk snakes for their venom: getting the spider to bite through parafilm (thin plastic film) and deposit their venom in a tube. For that, you need an annoyed spider with big fangs. Luckily, all of the Cantuaria have fangs big enough to punch through parafilm.

It's annoying them that can be the problem. Large female spiders tend to be extremely volatile, and rear up into a threat stance as soon as you lift the lid of their container. However, smaller species, and males, tend to keep running away, and won't inject venom even if you hold them down and manually poke their fangs into the tube.

To start with, I annoyed the spiders by poking a parafilm-covered tube at them until they bit into it. However, they would often get a bit over-zealous and drive their fangs into the sides of the tube rather than through the top. It's amazing how far in front of their bodies they can bite. So instead, I now grab them with the tweezers and hold them above the tube, annoying them with it until they finally go postal. That method seems to work pretty well.

Another method I tried was to get the spider to bite a cotton bud and then wash the venom off into a container, but that diluted the venom too much.

A Bradford assay done on one of the venom samples from a particularly aggressive female has shown that the venom is concentrated, so we have enough to work on. I just have to get it from other spiders and see if there is much difference between the proteins. There are a few other things to work on too, but that will do for now.

In other news, it looks like I may have finished the first round of optimising PCR - yay! I have three working genes with which to construct a phylogeny. There are some stubborn samples which refuse to be sequenced, but I'll deal with those when I've exhausted the ones that work. I may not need them anyway.

Unwilling captives

Since I was tiny I have liked animals. My mam has recently highlighted this by emailing me (and posting on Facebook...) photos of smaller Vikki with an animal or two. These days my focus is studying them, but I've also kept them captive a lot. So far I have been able to overcome every challenge presented by species kept in captivity and, not to blow my own trumpet, but I have kept a few - rats, mice, snails, ladybirds, devil's coach horses, songbirds, raptors, stick insects, snakes, lizards, frogs, mantids, millipedes, scorpions, spiders and others. Most have been challenging at some time or other, but there's always something that can be done to make a captive specimen thrive.

And then there are Cantuaria.

They sit stubbornly on the surface of the beautiful clay soil that I have painstakingly dug up and pressed down, layer by layer, humidity monitored closely to mimic their natural habitat. They stay like statues, legs pulled in, thoroughly unhappy. I leave them for days and perhaps they build a shallow hole and a trapdoor and then they die in it. I did manage to keep one juvenile that had just left her mother's burrow for a month, and she built a fine tunnel and took prey. Then for whatever reason she decided her tunnel wasn't good enough any more, and she left it, built a shallower one, and died. It's sad, really sad, because these spiders haven't done anything to deserve this stressful existence that I have created for them. I am an incompetent god.

I have to keep them, though, for a couple of studies that will be awesome if they work. So I have been experimenting. Jars filled with soil didn't work. Buckets filled with soil didn't work. Then a few weeks ago, I was sent some spiders in the post from Invercargill. They were shipped in cotton wool. Each spider had built a deep tunnel in the cotton wool. So now, I am experimenting with the two captives I have left. One is in a tall jar with damp cotton wool, and one is in a tall jar with damp clay (I sieved it to make sure that only clay is present in the soil...). I have only just put them in there, but I hope they like it. Based on instructions on how to keep African red trapdoor spiders, which are in the same family (Idiopidae), my Cantuaria should make burrows in this. Fingers crossed!

One year into the PhD...what have I done, exactly?

This time last year, I enrolled as a PhD student. I have just enrolled for my second year. I have to do reports for my funders, so this is a good time to review what I have done.

What I said I would have done by now:
Completed my proposal and seminar
Collected female specimens from throughout NZ
Pitfall trapped males
2 conferences with presentations
Completed sequencing for phylogeny (yeah, right!)
Measured explanatory variables for genetic variability study

What I have actually done (completed objectives in bold):
Completed my proposal and seminar
Collected female specimens from throughout NZ
Been handed some males from the public, and pinpointed good places to set pitfall traps
2 conferences with presentations
Begun sequencing for phylogeny
Found someone to help me with genetic and ecology fieldwork early next year

So I have only really completed half of my objectives. But, looking back, my proposal was supposed to be unrealistic - it was trying to convince the university that I really could do everything in three years. I could probably have done all of that stuff, apart from completing sequencing, but not so thoroughly as to do it justice. I think I have done the most important stuff to a sufficient standard: I have specimens, and I've started doing stuff with them.

In addition to the stuff I said that I would do, I have started to collect venom for an exciting project that will probably fail but hopefully won't (more importantly, it will give me some experience which might help me to get a postdoc). I have a couple of collaborations that I am working on, and I have done a fair bit of public outreach (articles for magazines and newsletters, and advertising my project, and talking to people and showing them spiders). I've nearly finished a manuscript to send to a spider journal. I've also got a bit of teaching experience. This stuff is more career-building than PhD-building but it is really important; some of my friends who are completing their PhDs fear this black hole that they will fall into when it is all done and they have no postdoc.

I've learned a hell of a lot in the past year, and enjoyed the vast majority of it. My work ethic has fluctuated a bit - the best time was when I was living walking distance away from uni, and didn't have much in the way of friends, so I could come in at 9, be strict with myself and leave at 5. Now living in town and carpooling and having friends (most of which get up in the early afternoon and work till late evening, which doesn't suit me at all), I find it hard to work an 8 hour day. I'm still getting stuff done, but I need to be stricter with myself.

This last year has been a blast, and I'm looking forward to the coming year. Hopefully I'll do a bit better at meeting my objectives, but overall I don't think I have been unsuccessful this year.

D-N-yay!

It's taken a few headaches, but I have managed to get COI (cytochrome oxidase 1, a mitochondrial gene/section of DNA) to work so I can get sequences. There were a few hiccups at first - the negative (control sample that I run with water rather than spider DNA, to test for contamination) showed contamination, and the primers stuck to each other and themselves and basically anything that wasn't the DNA, and I used the wrong combination of primers for a bit.

So now I can show you the process from beginning to end, in infographic form.

My breakthrough with COI is not only encouraging and positive for my work (now I just have to get EF1g working and ITS working more reliably) - it's entrancing. I have collected spiders, and I now have sequences from them. I feel I have grown the wheat, milled the flour and baked a delicious loaf. I can't really get my head around how each wee spider is made up of heaps of little cells that contain sooooooooooo much information. Before now, I had collected samples, I had extracted DNA from samples, and I had sequenced DNA - but never all on the same sample. For some reason a huge part of me just assumed someone was doing some magic somewhere along the process that made it work, but this time I've made it work, and there was no magic involved - just lots of baking.

That really is all that one has to do to obtain DNA sequences.

Random musings and imposter syndrome

My supervisor asked how my work was going yesterday (I have a sneaking suspicion that he read my last post).

The truthful answer is that I have started getting good results from amplifying two genes (ITS and COI), and the third gene (EF1G) is proving tricky but I just have to keep trying different primers and may have to move onto a different nuclear gene (histone 3). I am also planning my 3 week field trip in September to try and fill in some of the gaps in my spider collection. And I am continuing to write my thesis, slowly but steadily.

But saying this all sounded pretty stupid. I have no results yet, and it sounded as though I was just making excuses for why I continue to take up desk and lab space. From a critical point of view, I really haven't done much. Why? I've been working at it, but my time has been spent optimising PCR which takes a long time (one of my friends spent his entire first year optimising PCR for earthworm samples, which contain a lot of inhibitors just like my samples do, only worse, because nothing worked for him).

My supervisor didn't seem to be disappointed or anything, but I can never read his body language anyway and I just have to hope that if he thought I was doing something wrong he would tell me. When he tells me I have done well at something, I think that I must have deceived him in some way, and now I have to struggle harder to live up to his new expectations. Getting praise is kind of stressful because I can't believe it, but not getting praise is more stressful because I think they have given up on me. The best kind of feedback is constructive criticism - at least then I know they are being honest, and believe that I can improve.

I am not sure if my fears of not being able to accomplish what I want, and of not living up to expectations, are justified or as the result of an imposter syndrome - a feeling that I am a fraud and do not deserve to be here. I'm surrounded by smart people who know loads of stuff that I don't, and talk in scientific ways, and being around them can be intimidating because I don't talk or think in sciencey ways compared to them. My mind is slow. I am not hyper-intelligent. Luckily, convincing myself that I know more about my particular area than they do helps. I have the hope that I am improving and learning, and soon I will grow to a similar or better standard than my colleagues. I have about 60 years of life left in me, hopefully, so that's plenty of time to improve.

Another thing that helps is thinking about how I critically evaluate other people, and thinking that other people probably look at others in a similar way. I normally assume someone is average unless they prove otherwise in a convincing way. So in order to be doing a PhD with smart people, I must have at some point appeared competent. I haven't knowingly put on a dishonest display of false competence, so hopefully it is the truth.

Who knows? The important thing is not to become disheartened by the future possibility of being "found out" to be stupider and less competent than people currently think I am. I just have to keep working at what I'm doing, and trying to make this project work, and I think I can do it. And then I would have earned my place here.

Also, yay! Bands! Not on all the samples, but I should just have to play a bit with annealing temperatures and concentrations of ingredients to make them work.