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Dear Buggy: a discussion on data

A belated Happy New Year to all!

Buggy is back for his first post of the year. This is also my first post in a while; put that down to a combination of conference season, project planning season and too much holiday cheer.

I recently had an exchange on Twitter exchange with a colleague (and yes, before you ask we are allowed to use social media at work) about where scientists could deposit their data on the web at the end of a study. I had a few suggestions (and, as usual, a few opinions) about how, where and why we should be depositing our data.

As science moves towards a more ‘open source’, philosophy making data available as part of the publication process is becoming more common. Of course the taxonomists, systematists and gene-jockies amongst us have been doing that for a while, using systems like NCBI’s GenBank. Where the revolution (if I could be so bold as to use that word) is coming is in the ecological sciences. Expectations amongst publishers and in the broader scientific community are changing twoards expecting that data will be made available online and in an accessible format. To accommodate this, a number of projects have been launched that are meant to be a place for us to publish data sets.

But why publish your data? In theory raw data was always available: you just needed to ask for it. In practice, people can refuse, move on or pass away; data can be lost, formats can change and software can go obsolete which makes the reuse of data difficult. Publishing your data solves this problem.

Publishing your data also makes your work reproducible. With access to your data and your analysis code, anyone can repeat your work – or better yet, extend your work and gain new insight. In fact, in a great many fields your paper will not be published until you deposit the data (see here, for instance). I’d also argue that if your research is publically funded you have an obligation to make your data available. Of course, that is, after you’re done with it!

So why don’t more of us share our data? Well the biggest fear, of course, is that you might get ‘scooped’. That’s reasonable, but I think it’s unfounded, and here’s why: we expect that if someone wants to use our ideas, they will cite us. Otherwise it’s plagiarism (or at least bad manners), and there are ways to deal with that. So, extending that logic,  It’s reasonable to expect that if someone wishes to use our data, they will cite us as well (and now you can even track those citations!)

I’d go further and state that the benefits to publishing data outweighs the pitfalls. From an ‘economic’ perspective we can gain professional currency in the form of citations (see here and here), which have value in application, tenure and promotion packages.

Professionally, publishing data can help you attract new collaborators and new research opportunities. Publishing your data is just one more way people can become aware of you and your work and that awareness is important.  There is the old saying that data without context is just noise. If your data can be applied elsewhere, only you as the collector can provide that additional insight into the specifics of your system. That insight can help to explain new results, but it can also lead to new hypotheses and collaborations with people you may never have otherwise interacted with (or who would have never read your paper).

Personally, I think that the potential for greater insight resulting from others ‘playing around’ with your data can only result in a deeper understanding of your own system. And really, isn’t that something we’re all after?

Below is a list of some places where you can publish your data. Do you have any other suggestions, or want to share your experiences with publishing data? Let me know in the comments.

Buggy.

(With thanks to Simon Bridge of Natural Resources Canada Canadian Forest Service for suggesting I write this up.)

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Dryad 

From their about page: “Dryad is both an international repository of data underlying peer-reviewed articles in the basic and applied biosciences, and a membership organization, governed by journals, publishers, scientific societies, and other stakeholders. Dryad welcomes data submissions related to published, or accepted, scholarly publications.”

The Ecological Society of America’s Data Registry  

A data repository for articles published in the ESA’s journals)

treebase

A repository for phylogentic trees and data

Or find a journal where you can publish the data as a digital appendix like I did here.

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Tropical fieldwork in France: the Nouragues station in French Guiana

By Sean McCann, PhD Canidate in Biological Sciences at Simon Fraser University

9/10 ant-mimicking mantids recommend tropical fieldwork for prevention of insect withdrawal.  (Photo: S. McCann)

9/10 ant-mimicking mantids recommend tropical fieldwork for prevention of insect withdrawal. (Photo: S. McCann)

At this stage of the long dark Canadian winter, thoughts of tropical fieldwork should be going through the heads of all sensible entomologists…If you find yourself longing for the moist and insect-filled paradise of the Neotropics, or even if that is what your research plans call for, let me introduce you to the wonders of French Guiana.

Topography near the Inselberg Camp.  (Photo: S. McCann)

Topography near the Inselberg Camp. (Photo: S. McCann)

French Guiana is situated just north of Brazil on the Atlantic coast of South America, and remains to this day an overseas Department of France.  Both French and Creole are spoken, so Canadians should feel right at home.

French Guiana truly shines as a biodiversity and natural areas hotspot because unlike many countries in the Amazonian forest region, it has not experienced extensive deforestation. The immense expanses of unlogged rainforest are truly impressive.

The Inselberg des Nourages on a clear day.  View not guaranteed, depends on the season. (Photo: S. McCann)

The Inselberg des Nourages on a clear day. View not guaranteed, depends on the season. (Photo: S. McCann)

There is quite active citizen science in Guyane as well, of particular interest is the SEAG, or Société Entomologique Antilles Guyane: http://insectafgseag.myspecies.info/. This society has conducted numerous expeditions focused on collection and identification of many insect taxa, and represents a great resource of local knowledge of the insect fauna.

Finding a cryptic owlfly nymph is always a nice surprise (unless you are a cricket) (Photo: S. McCann)

Finding a cryptic owlfly nymph is always a nice surprise (unless you are a cricket) (Photo: S. McCann)

I have done all my tropical fieldwork at the Nouragues station, supported by an annual grant program that seeks to assist visiting scientists with the travel and logistical expenses involved with a tropical field season. My work has centred on a bird which is a specialist predator of social wasps, the Red-throated Caracara.

Red-throated Caracaras are specialist predators of social wasps, and a common resident of the Nouragues Reserve. (Photo: S. McCann)

Red-throated Caracaras are specialist predators of social wasps, and a common resident of the Nouragues Reserve. (Photo: S. McCann)

The 1000 km 2 Nouragues reserve is located approximately 100 km SSW of Cayenne, and was established in 1995 to be both a refuge free of development and to facilitate research on Neotropical forest dynamics.

Army ants (Eciton spp.) are one of the wonders of the Neotropical raindforests. Go. See. Them. (Photo: S. McCann)

Army ants (Eciton spp.) are one of the wonders of the Neotropical raindforests. Go. See. Them. (Photo: S. McCann)

There are two research camps, the Inselberg Camp, situated just beneath a 420 m granite mountain, the Inselberg des Nouragues, and the camp at Saut Pararé, situated just below a series of high rapids on the Arataye River. The camps are accessible by helicopter, or you can take a motorized canoe (pirogue) to the Saut Pararé camp.  Both camps are administered by the CNRS (Centre Nationale de Recherche Scientifique) which has an office in Cayenne. Field costs are €20/day for students and postdocs and €35 per day for established researchers. Travel to the station can be expensive, but sharing the cost of helicopters/pirogues with other researchers can bring the costs down considerably.

Access to various parts of the forest is facilitated by an extensive trail system . Data on tree species and flowering/fruiting phenology in two large research plots at the Inselberg Camp are available. At the Pararé camp, there are also many trails, although not as extensive as at the Inselberg camp, as well as access to riverine and palm swamp habitats. Lists of species of birds, bats, fish and trees are available, and there is an impressive list of scientific data already published:  http://www.nouragues.cnrs.fr/F-publications.html.

SM7

UV lamps attract a nice variety of insects. These are particularly fabulous. Start your collection today! (Photo: S. McCann)

The camps are comfortable, with covered shelters (carbets) for sleeping and eating, and there is electricity and running water at each station (it is the rainforest!). There is also a satellite internet connection which is adequate for email and keeping in touch with labs and colleagues. Food is provided, and is quite good (as one might expect at a French field station!), cooking/cleaning duties are shared.

The kitchen carbet by moonlight. (Photo: S. McCann)

The kitchen carbet by moonlight. (Photo: S. McCann)

If you are a student or a researcher at the planning or pre-planning stages of a Neotropical research program, there is no better time than now to submit a research proposal to the scientific committee of the station. The recently announced call for proposals will fund projects to a maximum of €9000, which would nicely cover the transportation and field costs for a several-month expedition. The deadline is Feb. 14, 2013. For more information, the details are available here: http://www.nouragues.cnrs.fr/indexenglish.html

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One of the fringe benefits of running the ESC/ESAB JAM 2012 photo competition was getting a glimpse into what other people where interested in. One of the most unusual images we received was submitted by Marilyn Light, entitled “Trialeurodes sp.”.

Trialeurodes sp. with impostor…

The photomicrograph (a focus-stacked image, produced with Zerene Stacker) shows a fourth stage whitefly pupa case. Whitefly are hemipteran herbivores that are often found feeding on the underside of leaves.The species we know most about is the greenhouse whitefly (Trialeurodes vaporariorum), a pest that damages food crops by feeding on them and by spreading viruses. To control whitefly, growers resort to using the wasp Encarsia formosa. In this photograph we see a species of whitefly that was found on a wild orchid, the showy lady’s slipper (Cypripedium reginae Walter). The glassy spines are typical of some whitefly pupa, but what is amazing about this picture is that the creature inside is not a whitefly. Looking closer at the lower left of the image you can see the brownish-orange eyes of the head of a parasitoid wasp, with the thorax and abdomen almost filling the case. Marilyn has included the following information with the image:

"Lady Slippers, Cypripedium reginae found along the Jordan Valley Trail, East Jordan Michigan" from Wikipedia

The showy lady’s slipper orchid, Cypripedium reginae Walter, forms large colonies in fen wetlands. The insect herbivore assemblage of this orchid includes Trialeurodes sp. Cockerell (Hemiptera: Sternorrhyncha: Aleyrodidae) which was first observed by us in 2009 on orchids growing in stressed habitat. Eric Maw, CNC, determined this whitefly to be an undescribed Trialeurodes. Subsequently, we have found isolated infestations in a second orchid population which is less subject to drought stress. The whitefly is parasitized by Encarsia sp. Förster (Hymenoptera: Chalcidoidea: Aphelinidae). During microscopic examination of one 4 th stage nymph (pupa) case that had been removed from a freshly collected orchid leaf on September 22, 2012, I photographed a parasitoid that was soon to emerge. About half of the other cases examined had been parasitized.

Of course, being who I am, I was curious not only about the image, but also about the person who took it. I asked Marilyn to tell me a bit about herself and how the image came to be…

“I am a member of the ESC but do not earn my living through entomology. I am retired from the University of Ottawa Professional Training Service.

My interest in insect population dynamics begins with my experience in 1948-49 during an eastern tent caterpillar outbreak in Montreal: I was 7 years old. My dad showed me the the stages and how to distinguish male and female moths. My first teaching opportunity was with my Grade 2 classmates on the insect and its life history. Ever since I have been learning so I can teach others. In 1951, after the outbreak was subsiding, I observed a large caterpillar walking alone on a twig. It burst when touched, exuding pink fluid. I was to later learn that it had been infected with a virus. I remain fascinated by the delicate balance in nature, between plants and herbivores, and between herbivores, their pests and diseases.

My husband and I have been tracking wild orchid populations since 1985, examining how they are impacted by climatic variables, disturbance, pollinator behaviour, and insect herbivores. The dynamic of insect herbivore populations with their respective biological controls and the orchids is a natural extension of the work.

There is a paucity of information about insect biology except with species of economic importance or conservation value. Our investigations will hopefully serve to fill this gap. We publish regularly in both peer-reviewed and popular media.”

Professional work by dedicated ‘amateurs’! More of Marilyn’s work can be seen in the study, Potential impact of insect herbivores on orchid conservation. (Light, M. H. S. and MacConaill, M., 2011. European Journal of Environmental Sciences: Vol. 1, No. 2, pp. 115–124) and Possible Consequences of Walking off the Trail (Light, M. H. S., and M. MacConaill, 2008. Orchids: 77: pp 128-133). She is well known in the orchid community in Canada and abroad, and is author of the book, Growing Orchids in the Caribbean (Macmillan Caribbean, 1995).

Female of Polistes parametricus Buck Vespidae Wasp
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Taxonomic adventures in the world of paper wasps (Polistes, Vespidae)

By Matthias Buck, Royal Alberta Museum, Edmonton

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For many of us who are working as taxonomists, describing new species has become somewhat of a routine. Sometimes it can even become a burdensome chore: I am thinking about those of us who work on hyperdiverse groups of insects in the tropics where almost every species is undescribed (case in point: one of my former lab mates recently described 170 new species of a single genus of Diptera in one paper!). However, the feeling is very different when new species unexpectedly show up in iconic groups that were thought to be well-known. Suddenly, common and familiar creatures turn into an exciting new research frontier, providing a fresh rush of adrenaline!

Mug shot of a female of Polistes hirsuticornis Buck. Vespidae Wasp

Mug shot of a female of Polistes hirsuticornis Buck. The hairs on the basal articles of the flagellum are longer than in related species (Photo credit D.K.B. Cheung & M. Buck).

This is what happened a few years ago when I started working on the vespids of the northeast. The family Vespidae (which includes mason wasps, paper wasps, yellowjackets and hornets) is most diverse in warmer parts of the World, as is the majority of stinging wasps. Doing a review of the northeastern Nearctic fauna therefore didn’t seem to be a very promising project for taxonomic novelty. Especially considering that the fauna of the eastern half of the continent is significantly less diverse and far better known than that of the west.

To my utmost surprise the study (published 2008 in the Canadian Journal of Arthropod Identification) not only turned up four new species of mason wasps but also two new paper wasps (Polistes). As you know, paper wasps are some of the most iconic species in the world of wasps, almost as much as their odious relatives, the yellowjackets. Further to that, they have received great attention as model organisms for the study of social behaviour and its evolution in insects. Finding not only one, but two new species in a group like this was beyond what I expected in my wildest dreams.

So how did it come to pass? As a novice to paper wasps I expected that reviewing the taxonomy of such a high-profile group would be like a walk in the park. Weren’t there scores of scientists before me who seemingly had no difficulties in identifying these sizeable and handsome insects for their behavioral studies, filling up cabinets of specimens in collections across the continent? Or so I thought! After months of fruitless staring through the microscope my nonchalant attitude gradually turned into frustration. One of the species, the common and widespread Northern Paper Wasp (Polistes fuscatus), was so variable that it blended virtually into almost every other species in the same subgenus. Previously published keys gave me a pretty clear sense of what typical specimens of each species look like, but where were the objective criteria that would allow me to identify the numerous intermediate forms? Truly, I found myself in a taxonomic quagmire!

Aedeagus of Polistes parametricus Buck. Vespidae Wasp

Aedeagus (penis) of Polistes parametricus Buck. The size, shape and position of teeth is diagnostic with regard to P. fuscatus and P. metricus, with which this species was previously confused (Photo credit D.K.B. Cheung & M. Buck).

Grasping for straws I turned to three taxonomic methods that had not been applied to Polistes before: DNA barcoding, detailed study of male genitalic features and morphometric analysis. During the previous months, I had rounded up a number of puzzling specimens which represented the spearhead of my taxonomic headaches, and submitted them for sequencing. The results came back like a thunderclap, turning my anguish into cautious excitement: the DNA barcodes of these troublemakerswere clearly different from any of the described species. With renewed energy I launched into a detailed morphological study which led to the discovery of several new diagnostic characters, confirming the distinctness of these wasps beyond a doubt. A lot of hard work had finally paid off, and I was looking at the first newly discovered species of paper wasps in eastern North America since 1836 when Amédée Louis Michel Lepeletier de Saint-Fargeau described Polistes rubiginosus!

Female of Polistes parametricus Buck Vespidae Wasp

Female of Polistes parametricus Buck nectaring on goldenrod in West Virginia (Photo credit: Donna Race).

Since molecular methods, and in particular DNA barcoding, have received a lot of attention in recent years, it seems opportune to share some of my experiences working on Polistes. Unlike a few other taxa (such as spider wasps, Pompilidae), vespids sequence nicely and easily from pinned specimens, which makes them an ideal group for this kind of study. I found the sequence data extremely helpful but they certainly did not provide the cure of all taxonomic confusion. Barcoding uncovered an unexpected genetic diversity below the species level, which proved to be hard to interpret in the absence of other data. In Polistes there is no hint of a “barcoding gap”, which postulates that genetic distances between individuals of the same species are (nearly) always greater than those between conspecific individuals. In fact, some of the species were genetically so similar that they differed by a mere 2 base pairs (out of 658). Nonetheless, the combination of molecular data with fine-scale morphology resulted in a quantum leap forward for Polistes taxonomy. Just days ago, I found out that a group of researchers in Germany and Switzerland are making similar progress on European paper wasps using a nearly identical approach.

My research paper on eastern Nearctic Polistes, including formal descriptions of Polistes hirsuticornis Buck and P. parametricus Buck, was published in the journal Zootaxa on October 1st.
Matthias Buck, Tyler P. Cobb, Julie K. Stahlhut, & Robert H. Hanner (2012). Unravelling cryptic species diversity in eastern Nearctic paper wasps, Polistes (Fuscopolistes), using male genitalia, morphometrics and DNA barcoding, with descriptions of two new species (Hymenoptera: Vespidae) Zootaxa, 3502, 1-48 Other: urn:lsid:zoobank.org:pub:6126D769-A131-49DD-B07F-0386E62FF5B9

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Popular galls on Poplar

Hi, my name is Holly Caravan and I am a PhD student in Dr. Tom Chapman’s social insect lab at Memorial University of Newfoundland. Currently my work is focused on galling aphids and their potential for antimicrobial activity within the gall. This past summer I visited Dr. Patrick Abbot’s lab at Vanderbilt University (Nashville, TN) where I was able to access three species of galling aphids. But, to address the ultimate goal of my research, I want to include the species Pemphigus spyrothecae which produces spiral galls on Lombardy poplar, Populus nigra. This species has a soldier caste which is morphologically specialized, different from the other three species I have already researched. I am looking for any information on locations of this aphid species in Canada; Newfoundland would be ideal, but my hopes are not high! Attached are links with pictures of the host tree and the spiral galls produced by the aphids. Any information would be greatly appreciated! I can be contacted at holly.caravan@gmail.com or hcaravan@mun.ca!

http://www.naturespot.org.uk/species/pemphigus-spyrothecae

http://www.parkwoodpines.com.au/html/lombardy_Poplar.html

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Australia’s call for international researchers: A Canadian entomologist in the Outback

Jacob Coates is an MSc student in the Chapman Entomology Lab at Memorial University of Newfoundland and Labrador.

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Cockroach – Photo by Jacob Coates

If you’ve never thought of visiting Australia, you’re making a terrible mistake. I just recently returned from a 6 month stint in Sydney based out of a Lab in Macquarie University. I carried out lab and field work on several species of gall-inducing thrips. I owe this great trip to the Australian Endeavour’s Awards, An Australian government run program which takes applications from students all over the world and to those lucky enough to be accepted, ships you to an Australian University with a wage, living allowance and travel cash. On top of getting some serious work done I enjoyed snorkeling around the many beaches, hiking in the Blue Mountains, and took part in the City 2 Surf road race where over 80,000 individuals take to the streets of Sydney to run the largest road race in the world.

Southern Queensland Red Road – Photo by Jacob Coates

In early June I completed a field trip into Southern Queensland to collect insect samples. Tenting through the outback presented some difficulties like torrential downpours, cold nights, and very sloppy road conditions (Nearly sinking a 4×4 in a flooded dirt road). Despite the problems, after nearly 2500 kms and 10 days of driving I returned to Sydney with thrips samples in hand and a very dirty truck to clean. Amazing wildlife, epic landscapes and great people await everyone in the outback, without a doubt the best trip of my life.

Jacob Coates

For those interested about the Endeavour’s award go to http://www.deewr.gov.au/International/EndeavourAwards/Pages/Home.aspx It’s well worth your time.

Culex pipiens photo by Kate Bassett
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New Mosquito Record on Newfoundland

Today’s post is by Kate Bassett of Memorial University. If you’d like more information about her work, she encourages you to contact her.

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Hi,

I’m a graduate student at Memorial University (MUN, St. John’s, Newfoundland and Labrador), nearing the end of my masters…hopefully :). My research project is focused on a wildlife issue. Snowshoe hare, Newfoundland’s only Lagomorph, suffer from infection by California serogroup viruses (snowshoe hare virus and Jamestown Canyon virus). Helped by the province’s Chief Veterinarian Officer Dr. Hugh Whitney, I sampled the blood and tested for infection in wild hares and laboratory rabbits used as sentinels.  This work was based in part in the laboratory led by microbiologist Dr. Andrew Lang at MUN, as well as working with the team at the National Microbiology Lab headed by Dr. Michael Drebot in Winnipeg. But, my project also included studying mosquitoes that are thought to transmit these viruses. That part of my project was based in the social insect lab at MUN headed by Dr. Tom Chapman.

I spent two summers catching mosquitoes. Consequently, I can’t miss them. I seem to have permanently altered my hearing and vision such that a mosquito in flight always grabs my attention. Last May while putting in a load of laundry, a specimen alighted on the washer. I dropped everything and ran upstairs for my aspirator, and made it back to collect this girl to identify at work. I froze her and didn’t get around to id’ing until later in the summer, and I was shocked to see that it may be Culex pipiens. This mosquito gains attention on the East Coast of North America because it can transmit West Nile Virus, and when I made this determination the worst West Nile viral outbreak in N.A. was underway and centered in Texas. I was uncertain of my morphological identification, so I added a leg or two of this specimen to my DNA barcoding work, and I waited for the outcome. When the sequence confirmed by identification, I put out a press release, which had me immediately doing live interviews on TV and Radio. I didn’t have a lot of time to think about it, I just went from interview to interview. It was a good experience; I do recommend it. I should add that we don’t have confirmation of West Nile Virus in Newfoundland, but we don’t know what lies ahead. Drs. Lang (aslang@mun.ca), Chapman (tomc@mun.ca) and Whitney (hughwhitney@gov.nl.ca) are looking for students to pick up where I am leaving off.

Culex pipiens photo by Kate Bassett

Here’s a picture of Cx. pipiens I took using a digital camera mounted on a dissecting scope. I used the program Helicon for producing a wide focal plane. It’s not the one that I got in May and fingerprinted, but another one that I got last weekend (September, 2012), also in my house!

Mosquito field trials at the Guelph Turfgrass Institute
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How was your summer?

Mosquito field trials at the Guelph Turfgrass Institute

Sometimes field work can look a little unconventional, like using large screened tents for a mosquito repellent trial. This original (yet ultimately unsuccessful) idea came from some work I did at the Guelph Turfgrass Institute in 2011.

Another field season has come and gone (mostly, I bet there are some field crop entomologists still out collecting data), and the entomology conference season will soon be upon us. But before you wrap yourself up in a nice warm cocoon of fresh data in preparation for the coming winter, we’d love to hear how your summer went!

The only thing better than obtaining exciting new data is the great story about how you got it! Maybe you traveled to a new location (or had an adventure on the way to your normally-mundane field site), met some interesting new people, took some photos you’re proud of, or did your best MacGyver impression by rigging your equipment together using only duct tape, dental floss and that perfectly shaped twig you found. Being the start of a new semester, maybe you’ve started a new project or joined a new lab and want to introduce yourself, your work, and put out a call for specimens.

Whatever your situation, the ESC Blog is a great place to share your story and earn the adoration of your peers for heroics and valor in the face of p > 0.05! Simply send us an email (entsoccanada@gmail.com) with your story (and a few pictures if you can) and we’ll help bring your story to the masses.

We know you’ll be swapping stories with newfound friends over beer at the ESC meeting in a few weeks, so hopefully you’ll consider sharing them with everyone a little sooner. We promise, we’ll ooh & ahh at all the appropriate moments (and not tell your advisor how the dent in the rental truck really got there)!

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Determining authorship for a peer-reviewed scientific publication

By Chris Buddle
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Authorship on written work should never be taken lightly.  Authorship implies ownership and responsibility for the ideas and content portrayed as the written word.  In science, our currency is the written word, in the form of peer-reviewed articles submitted and published in scientific journals, and multi-authored works are the norm (sometimes to ridiculous degrees!).   Being an author on a paper is critically important for success in academia: the number of publications on your CV can get you job interviews, scholarships, and often leads to increased research funding.  Scientists are often judged by publication metrics, and although we may not like this system, it remains prevalent.  With this context I pose the following question: What is the process by which an individual is granted the privilege of being an author on a peer-reviewed journal article?  This blog post will provide an objective method to determine authorship for a publication, and by sharing it, I hope it helps bring some clarity to the issue.

(Note: as a biologist, I am drawing from my experiences publishing in the fields of ecology and entomology, and in my role as the Editor-in-Chief for a scientific journal, The Canadian Entomologist – the ideas presented below may not be transferable to other fields of study).

A paper that resulted from a graduate class; should all these individuals be authors on this paper? (yes, of course!)

The method outlined below starts by thinking about five main stages in the publication process, and there are individuals associated with each stage:

1. Research concept, framework, and question:  The research process leading to a publication has a conceptual backbone – it is the overarching research framework.  The background ideas and concepts that initiate the research that leads to a publication come from somewhere (…and someone).  Although the end product of research may be the publication, a good research question is at the start, and drives the entire process.  Without a solid framework for research, and a clear question, the research will simply never be in a form suitable for publication.   The person (or people) who developed the big-picture ideas, research framework, and research question are to be considered as authors on the final publication.  In the University framework, this is often an academic who has developed a laboratory and research program around a thematic area of study.

2.  Funding.  Someone has to pay for research – whether it be a large, collaborative research grant that supports many graduate students, or whether it be a small grant from a local conservation agency.  An individual scientist applied for money, and was able to support the research that leads to the publication.  These monies could directly support the research (e.g., provide travel funds, purchase of equipment), the individual doing the research (e.g., pays the graduate student stipend, or technician), or the monies could offset the costs associated with the publication process itself (e.g., many journals charge authors to submit their work, also known as page charges).    The individual(s) who pay for the research need to be considered as authors on the final publication resulting from the research.  More often than not, this individual is the main “supervisor” of a research laboratory, but could also be important collaborators on grant applications, often from other Universities or Institutions.

3. Research design and data collection:  Once the overall research question is in place, and funding secured, the actual research must be designed and executed.  These are placed together under one heading because it is difficult to separate the two, nor should they be separated.  You cannot design a project without attention to how data are collected, nor can you collect data without a clear design.  In a typical University environment, Master’s and PhD students are intimately associated with this part of the research equation, and spend a very significant portion of their time in design and data collection mode.  Without a doubt, the individual(s) who “design and do” the research must be considered as authors.

4.  Data analyses, and manuscript preparation:  The next step in the process is taking the data, crunching the numbers, preparing figures and tables, and writing a first draft of the manuscript.  This is a very important step in the process, as this is the stage where the research gets transformed into a cohesive form.  In a typical University laboratory, this is often done by Master’s students, PhD students, or post-docs, and the product of this stage is often (part of) a graduate student’s thesis.   However, it is also quite likely that a research associate, technician, or Honour’s student be involved at this stage, or that this stage is done by multiple individuals.  For example, data management and analyses may be done by a research technician whereas the head researcher does the bulk of the synthetic writing.  Regardless, one or many individuals may be involved in this stage of the publication process, and all of these people must be considered as authors on the final product.

5. Editing, manuscript submission, and the post-submission process: The aforementioned stage is certainly not the final stage.  A great deal of time and effort goes into the editing process, and quite often the editing and re-writing of manuscripts is done by different individuals than those who wrote the first draft.  Important collaborators and colleagues may be asked to read and edit the first draft and/or other students within a laboratory may work to fine-tune a manuscript.  Most likely, the supervisor of a graduate students invests a lot of time and energy at this stage, and works to get the manuscript in a form that is ready to be submitted to a scientific journal.   The submission process itself can also be difficult and daunting – papers must be formatted to fit the style requirements for specific journals, and the on-line submission process can take a long time.  After the manuscript has been submitted and reviewed by peers, it will most likely return to authors with requests for revisions.  These revisions can be lengthy, difficult, and require significant input (perhaps from many individuals).   For all these reasons, this fifth stage of the publication process cannot be undervalued, and the individual(s) associated with editing, submitting and dealing with revisions must be considered as authors.

Those five categories help define the main stages that lead to a scientific publication, and there are individuals associated with each stage.  Here’s the formula to consider adopting when considering which individuals should be authors on the final product:  if an individual contributed significantly to three or more of the above stages, they should be an author on the final paper.  Here’s an example: in a ‘typical’ research laboratory, the supervisor likely has a big-picture research question that s/he is working on (Stage 1) and has secured funding to complete that project (Stage 2).  A Master’s student, working with this supervisor, will work on the design and collect the data (Stage 3), and as they prepare their thesis, will do the bulk of the data analysis and write the first draft of the paper (Stage 4).  In most cases, the editing and manuscript submission process is shared by the supervisor and the student, and both individuals are likely involved with the revisions of the manuscript after it has been peer-reviewed (Stage 5).  In this case, both individuals clearly contributed to at least three of five categories, and the paper should be authored by both individuals.

A classic example of a paper with a graduate student and supervisor as co-authors.

What about the research assistant that helped collect data? – since they only contributed to Stage 3, they are not considered as an author.  The same is true of a collaborator at a different University who may have helped secure the funding (Stage 2), but did not help with the process in any other way – they do not qualify as authors on this work.   It is quite possible that a post-doc in a laboratory contributes to multiple stages, even on a single Master’s project. For example, the post-doc may have helped secure the funding, assisted significantly with data analysis, and helped to edit the final paper – this entitles them to authorship.

This entire method may be considered too rigid, and cannot really be implemented given the complexities of the research process, and given personalities and politics associated with the research process. Furthermore, many researchers may include their friends on publications, in hopes that the favour will be returned so both individuals increase their publication numbers.    I do not think this is ethical, and overall, if an individual did not contribute to the research process in a significant way, they should not be authors.  The method outlined above provides one way to help determine how this ‘significant way’ can be determined objectively.  The process is certainly not without fault, nor will it work in all circumstances, but perhaps it will help to define roles and help to consider seriously who should be considered as authors on papers.

I can also admit that I have not always contributed to “3 of 5 stages” on all the paper for which I am an author, so you can call me a hypocrite.  That’s OK, (I’ve been called worse), and I reiterate that the process outlined above is context-dependent, and simply provides a framework, or guide, for thinking about this important issue in science.

I am certainly not alone in this discussion, nor with this concept – Paul Friedman wrote about this (in A New Standard for Authorship) and the method in analogous to the one outlined above (although with more categories).  Some journals also specify their expectations for authorship.  As an example, in its instructions to authors, PNAS states that ‘Authorship should be limited to those who have contributed substantially to the work’, and request that contributions be spelled out clearly.  This is a good idea, and forces people to think about the issue.

I’ll finish with two more important points:  First, determining authorship, and thinking about authorship, must be a transparent and clear process.  Graduate students must not be surprised when their supervisor states that some other researcher will be an author on their work – this should have been clear from the start.  A discussion about authorship must occur early in the research process.  Full stop.

Second, another key question is the order of authors.  For example, when is the student’s name first on a publication, and the supervisor second?  What’s the convention for your field of study? Who should be second author when there are four or five co-authors?  This is a complicated question and, you guessed it, one that will be addressed in a future blog post!

Please share your thoughts… how does your laboratory deal with the question of authorship on scientific papers?

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Here be giants. How do they breathe?

By Brent Sinclair, University of Western Ontario
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I’m currently on sabbatical in the Department of Zoology, University of Otago in Dunedin New Zealand.  This is the department where I did my PhD, so it is an opportunity to come back to familiar territory and re-connect with all sorts of people and places from the past.  It’s not a very insect department, but there is a lot of interesting work on ecology, parasites and freshwater biology.  A sabbatical is all about recharging scientific and creative batteries, so my main goal here is to write and read and think (and drink coffee and run and hike – but that’s for a different blog), but I felt that I also needed to justify coming all this way by actually gathering some data while I’m here.  Respirometry is the perfect answer – once set up, it’s possible to gather data on metabolic rates, breathing patterns and water loss at the expense of only a few minutes at each end of a run, leaving plenty of space for writing and drinking New Zealand’s excellent coffee in between.

What is respirometry?

Respirometry is the science (art?) of measuring the products and substrates of respiration – depending on your strategy, you can measure oxygen consumption and/or carbon dioxide production (to get a handle on metabolic rate) and water loss – among other things.  Because I work on generally small insects at generally low temperatures, we mainly measure carbon dioxide production and water loss (the instruments are much more sensitive), and can do some clever calculations to turn this into estimates of metabolic rate.

The equipment itself can look quite intimidating – and certainly like Science – with plenty of tubes and wires (when I calibrate the water channel, there’s even a bubbling flask!), but it’s not that difficult once you figure out what everything is doing, and it looks scary enough that other people generally don’t mess with it.  We pass CO2-free, dry air over an insect, and measure the CO2 and water vapour in the excurrent air – all the CO2 and water vapour must have come from the insect, so we can calculate how much it is breathing out.  The equipment we use is from a company in Las Vegas called Sable Systems International.  Sable Systems’ head honcho, John Lighton, is an insect physiologist who has published in places like Nature and PNAS, which means that when he designs the equipment, he often has insects in mind.

The respirometry system set up in a controlled-temperature room at the University of Otago. CO2-free dry air is supplied by the gas cylinder, and passes through a chamber containing the insect housed in a temperature-controlled chamber (the big grey cooler box), before going on to an infra-red gas analyser (the green box), which uses IR absorbance to measure CO2 and H2O.

What else can we learn from respirometry?

As well as a simple measure of metabolism, it is possible to use respirometry to determine the thermal sensitivity of metabolism (this is important in understanding the effects of climate change), as well as the metabolic costs of various environmental stresses, like freezing or chilling.  We can also use respirometry to study how insects breathe (there is much debate surrounding the adaptive significance of the Discontinuous Gas Exchange Cycles observed in some insects), and we can also use respirometry to figure out how much water is being lost across the cuticle of insects – even small ones like individual flies!

What am I …er… respirometing?

After 65 million years of evolution without mammals, New Zealand has an amazing array of endemism and some pretty weird insects.  My favourites are the alpine insects, which include impressive radiations of cockroaches, stick insects and weta – large Orthoptera related to the Jerusalem crickets of North America.  The mountains are fairly young (<3 million years old), so it’s possible to do all sorts of work comparing alpine species with their lowland relatives .

A group of alpine weta, Hemideina maori found under a stone at 1400 m a.s.l. on the Rock and Pillar Range, Central Otago, New Zealand. The males defend harems of 2-7 females. Female weta can weigh over 5 g, and males over 7 g, making them the heaviest insect known to survive internal ice formation. Photo by B. Sinclair.

Of course, it is the most fun to work on the big, weird insects.  So far I’ve been putting alpine weta (Hemideina maori, Orthoptera: Anostostomatidae) and New Zealand’s longest insect, the gloriously-named phasmid  Argosarchus horridus through their paces.  Male alpine weta can weigh up to 7 g, and are the largest insect species known to withstand internal ice formation.  The stick insects can easily reach 4 g, and posed some unique challenges in respirometry – with a body form so long and stick-like, it makes perfect sense to use a converted spaghetti-storage container!

A large female Argosarchus horridus (this one weighs a shade over 3 g) ready to go in her respirometry chamber. Photo by B. Sinclair.

The main questions I will be addressing will be about the evolution of thermal sensitivity and water loss in alpine insects, but the great thing about respirometry is that I never know what I’ll find along the way!

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Brent Sinclair is an Associate Professor at the University of Western Ontario.  He is the 2012 recipient of the Entomological Society of Canada’s C. Gordon Hewitt Award.