What does it mean to “do science”?

May 27, 2016 / Chris Buddle / 3 Comments

This is a guest post by PhD student Shaun Turney. I fully endorse it. It’s awesome.

As a scientist, when I’m brushing my teeth, I’m doing science.

This thought occurred to me yesterday as I was trying to reason myself out of a bout of imposter syndrome.

I was thinking: I don’t work hard enough to be a good scientist. I haven’t even done any science all day. I helped a francophone colleague with grammar, I read some stories on Eureka Alert, and I wrote up a field work budget. And that’s just some of the more useful sounding stuff: I also spent a fair amount of time playing basketball with a boy I mentor, cooking dinner, staring into space, telling my partner about my imposter syndrome issue, and reading a science fiction book. I looked through zero microscopes, wrote zero papers, and made zero hypotheses.

I convinced my brain to stop bullying me by distracting it with a question: What does it mean to “do science”?

Shaun Turney, vacuuming the Tundra. It’s part of doing science.

It would help to know first what exactly “science” is, but philosophers are nowhere near resolving that debate. Science is often defined as a set of processes or tools, the most notable of which being the scientific method. Science is also the body of knowledge produced by that set of processes. These definitions seem pretty solid until you prod them a little: which tools and processes count as scientific? Which knowledge counts as being part of Science? What is “knowledge”, for that matter!

So “Doing science” could be roughly and problematically defined as carrying out scientific processes, like the scientific method, to add to science’s body of knowledge.

But tell me: Is wiping down the counters after your experiment part of running an experiment? Does arguing over beers about whose study organism can jump the highest count as a scientific debate? Can writing a blog post about your research count as writing a paper?

I think times are a-changing enough that many scientists, especially early-career scientists, would feel comfortable with including some instances of lab “house-keeping”, socializing (ie, networking), and social media-ing as part of doing science. Here’s a more radical proposition: taking care of yourself is also part of doing science.

Here’s a strange-but-true thought: If you’re a scientist, your body is a piece of scientific equipment. Your mind is an even more important piece of scientific equipment. If maintaining scientific equipment is a part of doing science, then equally so is maintaining your mind and body. This fuzzy line between doing science and not-doing science is especially evident in field work. In the field, ensuring that your traps don’t get holes and the soles of your feet don’t get holes are equally important parts of the scientific process.

We wear gloves when working with hazardous chemicals, and we consider this part of our scientific protocol. I brush my teeth before engaging in scientific debate so I don’t repel anyone with my breath, and this is part of my scientific protocol. We read papers and sketch down ideas to encourage our minds to come up with interesting hypotheses, and we consider this part of the scientific process. I play with children and read science fiction to encourage my mind to come up with interesting hypotheses, and this is part of my scientific process.

Pyramids of species richness

March 30, 2016March 30, 2016 / Chris Buddle / 1 Comment

This post is written by PhD student Shaun Turney, and highlights a recent publication from the lab.

Two years ago, I was finishing my MSc and considering whether I’d like to do a PhD, and if so, with whom. I met with Chris and we threw around a few ideas for PhD projects. It was when he brought up a certain mystery that my decision to do a PhD in his lab was cemented. The mystery? Chris and his former PhD student Crystal Ernst were puzzled why there seem to be so many carnivores on the Arctic tundra, and relatively few herbivores to feed them.

How could it be possible? Is there a high level of cannibalism? (But then it would be like pulling oneself up by ones bootstraps — how does the energy and biomass enter the carnivore population in the first place?) Are the carnivores really omnivores? Is our methodology for sampling the tundra biota biased towards carnivores? Is the transfer of energy from herbivores to carnivores somehow more efficient (less energy loss) than in other ecosystems? These sorts of questions touch on some fundamental questions in ecology and I was hooked.

Shaun Turney, vacuuming the Tundra.

It seemed to me the logical first step would be to find out what is a typical predator-prey ratio. In what proportions are the organisms in an ecosystem divided up from plant (lowest trophic level) to top predator (highest trophic level)? The answer to that questions has already been very much explored when it comes to biomass and abundance. Charles Elton explained about 80 years ago that typically the mass and number of organisms form “pyramids”: They decrease with trophic level because energy is lost with each transfer from resource to consumer. But what about diversity? How does the number of species change with trophic level?

I decided to look at the food webs in the data base GlobalWeb to answer this question, and we just published a paper in Oikos on this topic. I found that typically ecosystems form “pyramids of species richness”, just like the pyramid of numbers and pyramid of biomass described by Elton. But some types of ecosystems, notably in terrestrial ecosystems, we can consistently observe a uniform distribution or even an “upside-down pyramid” rather than a pyramid like Elton described. That is, there are consistently cases where there more carnivore species than herbivore species in an ecosystem.

An example of aquatic compared to terrestrial food-web structure (from Turney and Buddle)

So evidently, at least when it comes to diversity, the pattern that Chris has observed in the tundra is not so unusual! The next step for me is to try to figure out why. Stay tuned!

Reference:

Turney S and CM Buddle. Pyramids of species richness: the determinants and distribution of species diversity across trophic levels. Oikos. DOI: 10.1111/oik.03404

Bog spiders: family composition and sex ratios

March 21, 2016 / Chris Buddle / 2 Comments

This is the second post by Honour’s undergraduate student Kamil Chatila-Amos – he has been busy working on identifying LOTS of spiders from bogs of northern Quebec. His first blog post introduced his project: this one gives a glimpse into the data…

My project is focused on studying spiders from bogs in the James Bay region of Quebec. Five bogs along the James Bay highway were sampled with pan traps every week for four sampling periods. In the full project I’m looking at how abiotic factors (i.e. pH, water table, latitude, etc.) and the plant community affect the arachnid community composition. For now, let’s look at how the spider families are distributed in these sites:

The first thing that might strike you if you are familiar with the area and its spider fauna is that in 4 out of 5 sites, neither Lycosidae (wolf spiders) nor Linyphiidae (subfamily Erigoninae) are the most abundant family. Previous studies in similar habitats tend to find a much greater proportion of those two taxa (Aitchison-Benell 1994; Koponen 1994). All sites except the first have more Gnaphosids than Lycosids. However, the breakdown within families is very different. Whereas the Lycosids are represented by 19 species, there were only five species within the Gnaphosidae. Even more impressive is that one Gnaphosidae species represents 99% of the family. Indeed, Gnaphosa microps alone represents a fifth of all arachnids I collected.

I’ve come to like Gnaphosa microps a lot! The family Gnaphosidae is pretty easy to identify thanks to their long and separate spinnerets, colour and eye placement. Even the palps, which are unique to species, are fairly easy to recognize. It ranges in size from 5.4 – 7.1 millimeters which is a large enough size so it isn’t a hassle to manipulate.

Gnaphosa microps, seen from above. Photo from the Biodiversity Institute of Ontario through Barcode of Life Data Systems

Gnaphosa microps is by no means a star of the spider world but we still know a fair bit about it. It is a holarctic species meaning it can be found in almost all of the northern hemisphere, even as far as Turkey (Seyyar et al. 2008). It is usually found in in open boreal forests, alluvial meadows and bogs. A nocturnal species, it spends its days in a silk retreat under moss or debris and hunts at night by catching prey on the ground (Ovcharenko et al. 1992). Even though sampling has been done very near my sites and in similar habitats (Koponen 1994) I still haven’t found another study where it was the most abundant species.

Another interesting tidbit about this species is just how skewed their sex ratio is. According to my data, males outnumber females almost 10 to 1! Now this does not mean it is always like this in nature, this ratio can be explained by sexually dimorphic behavior. This means that the males would behave differently than females in a way that would increase their odds of falling into traps. Indeed, according to Vollrath and Parker (1992) spider species with sedentary females have smaller, roving males. And like their model predicts the G. microps males are a bit smaller than the females.

Sex ratio of Gnaphosa microps, collected in bogs

So what’s next? I still need to retrieve the COI barcode of all my species and that will be possible thanks to the University of Guelph’s Biodiversity Institute of Ontario. This is to make sure my identifications are indeed correct. As a first time spider taxonomist it’s great to be able to confirm my work in a way that still is not widely available. Today I received the plate in which I’ll load the spider tissue and I am amazed at how tiny it is. I guess they just need 2mm per spider but I still expected it to be much more impressive. Hopefully I don’t get any nasty surprises once the DNA data comes back, although some of those tiny Linyphiids did give me a pretty bad headache…

References:

Aitchison-Benell CW. 1994. Bog Arachnids (Araneae, Opiliones) From Manitoba Taiga. Mem. Entomol. Soc. Canada 126:21–31.

Koponen S. 1994. Ground-living spiders, opilionids, and pseudoscorpions of peatlands in Quebec. Mem. Entomol. Soc. Canada 126:41–60.

Ovcharenko VI, Platnick NI, Sung T. 1992. A review of the North Asian ground spiders of the genus Gnaphosa (Araneae, Gnaphosidae). Bull. Am. Museum Nat. Hist. 212:1-92

Seyyar O, Ayyıldız N, Topçu A. 2008. Updated Checklist of Ground Spiders (Araneae: Gnaphosidae) of Turkey, with Zoogeographical and Faunistic Remarks. Entomol. News 119:509–520.

Vollrath F, Parker GA. 1992. Sexual dimorphism and distorted sex ratios in spiders. Nature 360:156–159.

Natural history of canopy-dwelling beetles: More than just ‘Fun Facts’

March 11, 2016March 11, 2016 / Chris Buddle / Leave a comment

This is the second post by undergraduate student Jessica Turgeon – she’s doing an Honour’s project in the lab; here’s her first post that introduces the project. Since that first post, Jessica has spent a LOT of time at the microscope, and has identified over 120 species of spiders and beetles from forest canopies and understory habitats.

Every species has a different story to tell and each one of these is equally interesting. I sometimes think about natural history as ‘fun facts’: something interesting about an organism (or species) to tell children so that they can appreciate nature. As my time at McGill progressed and my knowledge of the natural world deepened, I realized that the ‘fun facts’ are actually built upon a very strong scientific foundation, and can help us understand results of research projects. Natural history can sometimes be reduced to ‘fun facts’ but it’s a whole lot more than that!

The European Snout Beetle on a pin.

I decided that perhaps I should look at the natural history of some of my species and maybe this would shed light on some patterns that I’m seeing within the data. The most abundant beetle species was Phyllobius oblongus (Curculionidae) with 69 individuals. Interestingly, we only collected this species in the first half of our sampling season and they were mainly collected on black maple and sugar maple trees. To try and understand why this is so, I turned to the species’ natural history, and to the literature.

These weevils tend to eat fresh leaf shoots and prefer the soft leaves found on maple trees. Once the maple’s leaves are fully-grown, P. oblongus moves on to plants with indeterminate growth, like raspberry bushes (Coyle et al. 2010). This corresponds exactly to our data: the beetles were found on our black and sugar maples during the beginning of summer and then they taper off as the season progressed!

Beetle data: the European Snout Beetle was only collected during the beginning of the season.

To make this even more interesting, P. oblongus is an invasive species. Its common name is the European Snout Beetle and was accidentally introduced into North Eastern North America in the early 1900s. While most invasive species are a cause for concern, both the Canadian and American governments largely ignore this species. It may inflict some damage to trees but not enough to be worried about. They’re more annoying to researchers than anything since they congregate in the trees in large numbers!

The second most abundant beetle species in the collections was Glischrochilus sanguinolentus (Nitulidae). This species is native to Canada and rather abundant. Species in this genus are called sap beetles but this species in particular is more commonly called a picnic beetle. Large groups of G. sanguinolentus swarm to picnics since they are attracted to sweet food, which ruins the picnics. In nature, they feed on the sap produced by injured trees – hopefully not an indication that the trees we were climbing were damaged!

The natural histories of species open new doors to understanding how organisms live and interact with one another. I thought that it was strange that P. oblongus completely disappeared from my samples midway through the sampling season and its natural history explained why this was so. Picnic beetles eat the exuding sap of an injured tree so in the future I’ll be on the lookout so that I don’t accidentally climb a broken tree! So really, natural history is more than just ‘fun facts’; it helps us understand patterns and to better understand how our natural world works.

References

Coyle, D.R., Jordan, M.S. and Raffa, K.F., 2010. Host plant phenology affects performance of an invasive weevil, Phyllobius oblongus (Coleoptera: Curculionidae), in a northern hardwood forest. Environmental entomology,39(5), pp.1539-1544

Evans, A.V., 2014. Beetles of eastern North America. Princeton University Press.

Bog spiders: a serendipitous research project

January 22, 2016January 22, 2016 / Chris Buddle / 2 Comments

This is a guest post, written by an Honour’s undergrad student in the lab, Kamil Chatila-Amos. It’s the first of two posts about his work, and the goal of this post is to introduce Kamil and his research project.

Research can be serendipitous and spontaneous, and that’s certainly the story of how my honour’s project started! I spent last winter working on howler monkeys in Panama (which is a story in itself) and although I adored every second of it, it certainly made me out of touch with the McGill world. When I came back, most of my friends had found themselves a summer research job and even an honours supervisor for the upcoming semester.

So there I was, barely a week after my return, erratically filling out online job applications in the lobby of one of our buildings. I was looking at all kinds of opportunities: herbarium employee in Edmonton, ichthyology assistant in Wisconsin, plant surveying in Vaudreuil, bird surveys in Ontario, insectarium employee in Montreal. I was applying to anything and everything that was still available. Little did I know that the arthropod ecology lab is right next to the lobby… Chris walked by, saw me and stopped to chat. (Well it’s more accurate to say he talked to me while quickly walking to his next meeting)*. Turns out, a student of Terry Wheeler (another entomology Prof. at Macdonald campus), Amélie Grégoire Taillefer, was going to post a job online that very afternoon! She was looking for a field assistant to help her catch flies in bogs in the James Bay area.

A couple days later I was northern-bound! A 15 hour drive north of Montreal is the town of Matagami and about 30 km north of there is Lake Matagami, along which we were staying. In a yurt. A yurt!!! Basically, a large round tent of Mongolian origins. They’re big and this one had a minimal kitchen and shower. But the fact remains that it’s a tent with the isolative properties of canvas. It got pretty cold those first couple weeks and dropped below freezing a few nights. At least it had a fireplace. (It’s actually a great place for people wanting to explore that area of Québec and the owners are wonderful. Go check them out at ecogiteslacmatagami.ca)

Kamil_Yurt

The work itself was great. The first week, we explored the area for suitable bogs to install her pantraps. That’s when I realized how awesome bogs are. There are so many things to eat in bogs! Cattails, cranberries, Labrador tea, cloud berries, chanterelles, boletes, black flies…

For the remainder of the trip two days a week were spent visiting our five sites and harvesting the pantraps filled with flies, dragonflies, crickets, spiders and the occasional putrid mouse. The following two or three days we would sort through the samples, separating the lower flies (Nematocera) from the rest.

Ready for some serious bog-sweeping.

After the first week I couldn’t help but notice just how many spiders we were catching. Mostly out of pity I think, I decided to sort out the spiders as well. I felt bad throwing them out… Fast forward to five weeks later and I’m heading back to Montreal with a bagful of vials filled with dead spiders. (My roommates were not very fond of having them in our freezer).

A few weeks later I set up a meeting with Chris and essentially barged into his office with the spiders to ask to work in his lab. It took a while (and quite a bit of convincing) but here I am, sorting through spiders and writing blog posts!

The research project we structured has two components. The first part will look at how the community composition of spiders varies between the five sampled bogs. Second, I’m lucky enough to have the opportunity to try DNA barcoding using COI markers. This part remains very blurry right now**, but I’m very excited to see where it leads.

Kamil hard at work in the lab!

If it weren’t for serendipity I would not have gone to James Bay this summer. And if it weren’t for being spontaneous, I would not have sorted out the spiders and would not be working in Chris’ lab right now. But spontaneity does have its down sides. I didn’t plan far enough ahead** and in hindsight, I should have collected some insect orders to be able to do a more in depth ecological analysis.

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* um, yes, I spend a LOT of time in meetings, and often have discussions and chats with student on my way to and from those meetings!

** for what it’s worth, research is often blurry, and planning ahead isn’t always possible!

Summer in the trees: Undergrad research on canopy spiders and beetles

December 10, 2015December 10, 2015 / Chris Buddle / 1 Comment

Note: this post is written by undergraduate Honour’s student Jessica Turgeon, who is a member of the arthropod ecology laboratory. This post is part of the requirements for her project, and is an introduction to her research.

I’ve always been interested in nature and the environment but was never a big fan of insects. As time went on and I learned to appreciate all organisms big and small I realized that I didn’t really have a preferred “pet taxon” but rather was interested in ecology and community structure. I found others that my interests were shared with other members of the arthropod ecology lab, and I was able to start an Honour’s project in the lab earlier this fall.

Using a beat-sheet in the tree canopy, to collect arthropods

I was given an opportunity to do an internship at Kenauk Nature, a 65,000-acre plot of land near Montebello, Quebec. This property is primarily used for the hunting and fishing industries, but they are branching into scientific research. Kenauk was keen to support three McGill interns to complete the Black Maple project, the pilot project for Kenauk Institute.

The Black Maple project revolves around black maples, since Kenauk is the only area in Quebec to have a black maple stand. The project consisted of three sub-projects, one for each intern and each project dealing with a different taxon. While the two other students worked on plants and birds, my project was about arthropods and their diversity in Kenauk. We wanted to characterise the community structures of beetles and spiders based on vertical stratification and tree species: this involved tree-climbing!

Jessica – getting ready to climb up!

During the summer, I looked at abundance data and concluded that beetles were more abundant in the upper canopy and that spiders were more abundant in the understorey. This internship transitioned into my Honour’s project, where I plan to look at species richness and functional diversity to answer my questions on community assemblages. To my knowledge, this has never been done at Kenauk Nature and would provide great baseline data for the owners of the property.

We sampled in three sites, each containing three trees. Each site had one sugar maple (Acer saccharum), one black maple (Acer nigrum) and one American basswood (Tilia americana). Within each tree we sampled five times: twice in the understorey, once in the middle canopy and twice in the upper canopy. We also used two different types of traps: beat sheets, an active technique, and Lindgren funnels, a passive technique. Both trap types are specialized, with beating more tailored towards spiders and Lindgren funnels invented to collect beetles. When beating a branch, the arthropods fall on a 1m² sheet and are then collected whereas Lindgren funnels are hung in a tree and passively collect arthropods that fly into it.

As part of our job, we learned how to use a single ropes climbing system, a one-person method of using ropes to climb a tree. All three interns caught on quickly and it easily became our favourite part of the job. However, we did have to sort through the samples, a job requirement that wasn’t nearly as fun as climbing trees. But this is what happens in ecology: you romp around in the woods to collect your data then spend time in the lab analysing them. It was nice to experience this first-hand and I must say, I liked it and am looking forward to future projects like this.

Now that the summer is over and collection is completed, I spend all of my free time in the lab identifying beetles and spiders. All of the beetles are identified and about half of the spiders are identified. From this work, Kenauk Nature can proudly say that the property supports 24 families representing 117 species of beetles! Once the Kenauk Institute officially launches, more rigorous research can be done to try and increase these numbers.

Learning Taxonomy… spider drawings (of male palps) help.

All in all, from the sampling in the summer to the identification in the lab, this has been a great experience. Here’s to hoping the second half of my honours project will be as equally fun and challenging as the first half was! Stay tuned for a blog post to be published in the spring of 2016: it will summarize the main results from this Honour’s project.

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