Friday, 21 February 2014

You what?

 I've mentioned in an earlier post that I find reading scientific writing tedious. Recently I've made life easier by giving up on reading the whole article and instead skimming it while looking for a particular morsel of information, but there are some papers that I have to read more thoroughly. These have been collecting in my "literature" folder like dregs of food trapped in the plughole after doing the washing up. I have to read them. They are reviews of methods that I'm using, or examples of studies very similar to mine. In the last few days, while taking time out from planning my field trip, I've been trying to slash my way through them.

Scientific jargon is a necessary evil, but even if you know what the words mean, there is so much jargon that it keeps tripping you up. For example, if I tell you the following (simplified) definitions:
  • Tree: a hypothesis of the evolutionary relationships of a group of animals
  • Clade: a group of organisms believed to comprise all the evolutionary descendants of a common ancestor
  • Paraphyletic: descended from a common evolutionary ancestor or ancestral group, but not including all the descendant groups
  • Haplotype: a particular short sequence of DNA that can differ between animals
Are you now able to read this sentence and immediately understand it, or do you have to work out its meaning carefully by going over it several times?
This tree is a strict consensus of 100 equally optimal trees (score = 11,152,168 rearrangements examined) recovered from the analysis and show that all five major clades are recovered but that clade 2 remains paraphyletic with respect to a single haplotype.
I am familiar with the meanings of the jargon words. But every scientific paper I read is full of sentences like the above, that stall the reader. Here's another little nugget, which does not use impenetrable jargon but is still thick and stodgy:
Haplotypes within some populations fail to unite at the 95% confidence level using TCS;  consequently, this methodology clearly over splits the group into an unreasonable number of species-level lineages (∼60). If a criterion of geographical concordance is employed,more than 20 species would be recognized within the A. atomarius complex.
What does TCS mean? Better go back through the paper and check. Over-use of non-commonplace acronyms is friggin tedious (By the way, it stands for Templeton, Crandall and Sing. (1992). Clarified?).

More experienced scientists might think there is no problem at all, that they can understand these sentences easily. But such thick language makes much of science impenetrable to less experienced readers (not to mention the fact that most scientific papers are hidden behind a paywall). They have to rely on interpretations in the media. Chinese whispers result in misunderstandings that can fuel pseudoscience, creationism, anti-vaccination and anti-medical societies. Scientists ask pseudoscientists for evidence to back up their claims. By evidence we mean papers. But how can we expect non-scientists to critically read and understand scientific papers when they are so tedious? I am interested in evolutionary biology and have a basic understanding of the jargon and methods used, and I find reading papers tedious.

What's the solution? I have a few ideas, but solving the problem will take much more consideration and evaluation of how we communicate science. Firstly, scientists should be trained how to write. Secondly, words such as "utilise" should be banned (if you mean use, say use. Why use a word that is longer and more complicated than necessary?). Thirdly, how about adding an easily interpreted abstract onto each scientific publication? Not the eye-watering stock cube of an abstract that usually adorns each paper, but one explaining in layman's terms what the scientists did, what they found, and the context of their research. That way their findings are less easily misinterpreted.

We can't blame the public for misunderstanding science. The blame falls on us for miscommunicating it. Science affects everyone, and scientists rely on the government (and therefore the public) for legislation and funding to enable research. There is every incentive for us to break down this communication barrier between scientists and everyone else.

Tuesday, 11 February 2014

Proposal complete

After three months of writing, a few hours arguing with Microsoft Word, and a few more hours remembering why I hate printers so much, I handed in my proposal today. Now it will be assessed. Like most things I write it is way too long, but my supervisors did not seem to have a problem with that (they seemed to think my proposal is good, which is encouraging), so I'll see what happens.

Now I have to plan my field trip, which begins on the 9th March (in theory - I have to give a seminar on my proposal first, which might delay things). I will start off around Banks Peninsula, collecting in the many locations where Cantuaria have been found (mostly C. dendyi). Then I'll head south through Otago and Central Otago, take a couple of days out to go to a conference, visit Southland and Stewart Island, then up through the West Coast to Nelson and Golden Bay. A brief stint in the North Island will be followed by a return trip via Marlborough. Some species I won't be able to find, so I will put out pitfall traps to check during my second, briefer field trip in June.

Should be good!

Monday, 10 February 2014

Visiting a previous life

Before I discovered spiders in a big way, I thought I would be a raptor biologist. I'd done various things with hawks for a few years when I started my masters. I had contacts, and I have always liked hawks. I liked all other animals too (except the apes...they are gross and weird in all the bad ways). But I had decided from the age of 10 that I would study hawks.

At university I learned that it is okay to change your mind and not stick rigidly to the original plan if a better option comes along. We mostly learnt about seabirds, big cats, red deer, fish and whales during my undergraduate degree. I wanted to do my masters on something different, something we hadn't learned about, and applied to work on katipo spider ecology (Latrodectus katipo). During that year, and the following year when I returned to the UK, I learned that while falcons are fun to fly and keep, spiders are infinitely more interesting and give better data. Also, arachnologists in general are much better people than ornithologists in general (ornithologists tend to see you as competition, while arachnologists by comparison seem to regard their colleagues as fellow explorers of the unknown). I decided I would carry on down the arachnology route to see how far I can get. I will most likely have to hop off this train to study other taxa at some point, but I'll ride it as far as it will go.

My falcon world has dwindled into a hobby (Falco subbuteo), and sometimes I think of giving it up altogether when I clash horns with a particularly nasty example of an ornithologist. But when I have fun with falcons it is really fun. Days spent tracking a falcon who can fly faster than you can drive; the flood of adrenalin when a rabbit you are hunting explodes out of its warren; the satisfaction of getting a hawk to eat from your glove for the first time. That was going to be my life. But I have found a better one - a deeper intrigue and sense of challenge, a whole world that is virtually unexplored. People used to tell me that nobody studies the New Zealand falcon (Falco novaseelandiae). That is a lie. Plenty of people study it, and there is little left to be discovered, when you consider the number of people who study even the most charismatic of spider species.

Down the spider-hole...
I went this weekend to visit some falcon breeders who I have known for a few years. Stepping back into the falcon world is like crossing a vortex into a different reality. I loved visiting, and there are some great falcon-related opportunities for me, so it can continue to be my hobby. But I am glad to return to my spidery world. If I could visit my 19-year-old self again, just as she is beginning university, I would say open your mind! There are weirder and more fascinating things out there that you don't even know about yet!

Monday, 3 February 2014

Essence of spider

I'm meeting with my supervisory team this Friday to discuss my methods, now that the proposal is almost done. While waiting for proposal corrections and stuff, I have been doing a few things that will hopefully mean I can hit the ground running when I get official permission from the university.

As I have slowly been facing the ugly truth that Cantuaria taxonomy is far from straightforward, I have been compiling pictures of the abdomens and genitalia so that I can quickly narrow any specimen down to a near match. This should speed up identifying each one that I collect. The definitive works on identifying New Zealand spiders are the "Spiders of New Zealand" books by Ray Forster and others. The second book in this series (Forster and Wilton, 1968) describes all known species of Cantuaria. I have been using it to identify the spiders I currently have in the freezer, focusing particularly on the genitalia but also claws and abdomen patterning, as the authors seem to consider those characters most useful to distinguishing species.

Claws on the end of a Cantuaria leg - note that there are 3 claws, and the bigger two ("superior" claws) have a big tooth near their base. Those are the kind of characters one looks for when trying to find what species a spider is.

However, my advisor and I have discovered that claws are pretty meaningless, varying in their notch patterns between individuals, and I emailed another spider guru who told me that he usually goes by male genitalia, and if he finds a female in the same place that looks similar then they are probably the same species. Most of the characters in the literature are next to useless. So....cock.

By the way, in case you are wondering what spider genitalia looks like, feast your eyes on these beauties...

The female's internal genitalia at the top, the male's palp at the bottom. Pretty cool structures, huh?

In addition to that, designing my proposal seminar, reading stuff, applying for permits (looooong laborious process) and "collecting" more Cantuaria (more like looking for them and not finding any - good job New Zealand is scenic), I started extracting some DNA from my specimens. DNA extraction sounds cool and is full of words like "Qiagen", "elution" and "lysis" but it really is just a case of making spider soup and then washing it through a sieve to get the muck out. You dissect the muscle out of a spider leg (easy in my spiders, I pity people working on the smaller species), add some protein-cracking enzyme to it and cook it overnight. What you have in the morning is free DNA floating about with a bunch of other stuff you don't want. You then wash the spider soup through a filter using a bunch of different buffers, but you get to use the centrifuge which is cool because it always sounds like it's going to take off. Then what you have is spider DNA suspended in a solution. Essence of spider. If you can follow a recipe, use a centrifuge and a pipette, you can extract DNA. My favourite bit is the dissection but my second favourite bit is all the labelling and categorising of the samples. Organisation is important in doing molecular work so I am in my element.

I just moved house and I'm helping my friend move house, and I am also house sitting, so I have many houses at the moment and am pretty knackered. I'm going to pick one of them to sleep in and say goodnight. Goodnight!