Month: February 2012

How to review a scientific paper

/ Chris Buddle / 2 Comments

Last week’s post focused on WHY it’s good to review papers. This week, the focus is on HOW to review a paper. By “paper” I mean a manuscript resulting from primary research, submitted to peer-reviewed scientific journal. The ideas and opinions here are drawn from my own experience in the fields of ecology / entomology - not all the comments will apply to all fields.

Reviews of a research paper will vary tremendously depending on the experience and expertise of the individual, the research discipline, and depending on what people think a ‘review’ ought to be. For example, reviewers sometimes approach a manuscript as if they were copy-editors, and spend a lot of time and energy fixing grammar, sentence structure, and other stylistic / editorial issues within a paper. This is not a productive use of your time - these things can be done by (paid) copy-editors further along in the publication process. Instead, a good review should (i) focus on the scientific quality, (ii) ensure that the overall paper delivers the research message appropriately, (iii) assess that the manuscript fits within the aims and scope of the journal, and (iv) confirm that the manuscript is aligned with the field of study. Of course, a readable and clean paper makes this much easier (another reason authors should make sure their manuscripts are error-free, and readable, prior to submission!).

For most reviews, two reads of a paper are required. My advice is to read a manuscript from start to finish, and then walk away for a day or so. This lets the material settle and work away in mysterious ways, out of your conscious thought. Upon return, do another read, only this time write down positive and negative comments about the paper, using the following list for guidance:

Big Picture: What is the conceptual framework, and is it a good one? Do the author’s make a convincing argument about the broader rationale behind their research? Do they use (recent and old) literature effectively?

Research Question: One of most important parts of a paper is the section dealing with the overall research question / hypothesis / prediction. Think carefully about this section: it must be clear, concise, logical, and ‘testable’. Everything in the rest of the paper must relate directly to the objectives of the study.

Methods: fundamentally, do they make sense? Remember, the scientific method is about repeatability of an experiment: could you do the project using the described methods? Are the methods up-to-date? Where might they lead to errors or biases?

Data management/analyses: How were data managed after they were collected? What was the overall data management and analysis strategy? What are the response variables measured and what is the unit of statistical replication? What test(s) did the authors complete? What assumptions do these tests require and did they do tests to ensure they did not violate the assumptions? Are ‘controls’ required, and if so, what are they and how are they dealt with in a statistical framework?

Results: are the figures/tables presented in an effective manner? Are they clear and relate directly to the research questions? Do they make sense in light of the data analysis strategy? What’s missing? Is their supplementary information (is it accessible, elsewhere)?

Discussion: a discussion section of a paper is meant to be somewhat speculative, but it should not wander uncontrollably from the data and results. Does the discussion section suggest alternative explanations for patterns, or do the author’s merely use this part of their paper in an act of self-congratulation? Do the author’s point to some of the flaws in the study and offer ways to improve the experiment? Do the author’s return to the overall (broad) conceptual framework and revisit this in a meaningful way?

Literature Cited: did they miss important papers? Are there any unusual trends? (e.g., too many citations of unpublished works or personal communications, too may citations of the author’s friends, ignored old literature, depended too heavily on old literature?)

Working through this list will help come up with the key issues with a manuscript. In addition, it may be useful to think about some of the following broader points:

• Does the paper move the discipline forward in a new and exciting way or is the work largely confirmatory?

• Is the research driven by a ‘cool’ system, or a specific taxa, ecosystem or place, or is the research driven by a strong research question and the system/taxa/place are secondary?

• Does the research make linkages to larger social/economic/environmental issues? Should it? Do the author’s use larger environmental issues or politics just to ‘look important’, or are the linkages necessary and meaningful?

• Is the work original or a re-hashing of someone else’s approach (perhaps in a different system or with a different model organism)?

• Is the work appropriate for the journal?

This last point is quite important - your review must be within the ‘context’ of the journal, and of your discipline. You don’t want to review a natural history paper in a focused entomological journal in the same way that you would review a paper about theoretical mathematical models for a general ecological journal. Always keep the journal’s audience in mind.

In theory, you should now be ready to write your review and submitting it to the journal. Submitting your actual review typically involves three tasks. For most journals, reviewers are asked to provide comments for the authors, confidential comments to the editor, and reviewers are typically asked to rate the manuscript.

The first task, and the one that takes the most time and energy, is to write all your comments that will be forwarded to the authors. Try to keep your comments and writing concise, and clear. In general, a review of 1-2 pages (single-spaced) is a good goal - most reviews are much shorter than that, but if you follow the points discussed above, you will be providing a very helpful and high quality review, and it will take you more than a page to do so.

Always start your review with a quick one-paragraph summary of the work (this shows that you read it!). You should then try to provide authors some positive feedback before delving into (constructive) criticisms. Always keep the tone of your writing even-handed, and constructive. Don’t be mean (this sure won’t help your scientific karma!). I recommend first providing general ‘big picture’ criticisms, and then follow with a section of ‘specific comments’ - this can be where you can highlight those stylistic/editorial issues that have been uncovered. In general, it is useful to provide a numbered list of your criticisms (you may even wish to use subheadings, e.g., taken from the list above) - this helps authors respond to your comments in a clear manner, and also assists the editorial board for the journal.

Without experience doing reviews, it is likely that a good review will take a long time to complete (i.e. > half a day). However, it does get easier, and I believe that after practice, a good review can be completed within a couple of hours, provided you know the discipline well.

The review, as I have discussed it above, is really for the authors, and is to help the Editor(s) make a final decision about a manuscript. In your comments to the authors, you must avoid making any statements about whether the paper should be published (or not) - this is not the job of a reviewer! In fact, these kind of statements can place an editorial board in an awkward position if reviewers make claims about whether a paper is publishable - a journal may have to refuse (good) paper simply due to page constraints, or the fact that a paper may be a poor fit within a particular issue. The Editors (and publishers) make all these final decisions, not you!

The second task is when you provide confidential comments to the editors, and this is a place where you can be more candid, and can certainly make your opinions known about whether the work is publishable.

The third and final task is where you get to score or rate the paper. This should align with your actual review. For example, it’s pretty bad form to be highly critical in written review and than rate the paper as ‘acceptable in its present form’. Or, providing and short and positive review should not typically equate with a rejection!

The style of these scales vary tremendously, but most having wording something like this:

-Accept in its present form with no revisions

-Accept after minor revisions (re-review unnecessary)

-Accept after major revisions (after re-review)

-Reject but encourage re-submission in another form (e.g. short paper)

-Reject

If your review uncovers more than a couple of significant criticisms, it’s likely you will select Major revisions. Minor revisions are typically more related to specific concerns with specific sections of the manuscript and minor revisions generally do not require authors to rework sections of their paper (e.g., new analyses, different presentations of results, rewriting a discussion).

Now you’re done. Phew. Take a break until the next request comes in…

Review a paper, it’s worth it.

/ Chris Buddle / 2 Comments

Although it takes precious time, it is important to review papers - it keeps the wheels of academia churning away, and without reviewers, the peer-review process is dead and peer-review is the cornerstone of scientific publishing. However, the review process is typically anonymous so why would anyone review papers? What’s the benefit to an individual? Why not just cheat the system and publish papers without ever reviewing papers? Here are six arguments about why all researchers should review papers.

[ an aside …. academic publishing is undergoing significant changes these days, and there are other models that may eventually replace the current peer-review system. But all that is discussion for some future blog post! ]

1. Responsibility. If you publish papers, it is your responsibility to review papers. A constructive and high quality review improves your own work and you owe it to other authors to provide the same (or better!) service.

2. Learning. You can learn a lot from reviewing papers, including new techniques and methods (e.g., analytical, field and laboratory methods). Reviewing papers keeps you up-to-date on the literature within your discipline. I find it exceedingly difficult to keep on top of current literature, in part because of the proliferation of journals in recent years, and because life is busy. Reviewing papers in your discipline helps you understand what other scientists are reading and citing, and can often point you to literature you would have otherwise missed. Reviewing papers can also show you what NOT to do with your own research! I am often amazing and sometimes stunned at mistakes uncovered when reviewing papers, and this in turn allows for a more critical approach with the research coming from my own laboratory.

3. Benchmarking. Reviewing papers allows you to stay on top of current theories, hypotheses, and controversies within your discipline, which allows you to embrace a stronger conceptual framework for your own research. This allows for a very current and often insightful benchmark for your own research.

4. Personalities. Reviewing provides you with a nice window into the ‘personality’ of science and the ‘personalities’ in science. It allows you to interact with editorial boards, and allows you to read what people in your discipline say to editors (i.e., in their cover letters), and can provide you important insights about the personalities of leading researchers in your field. In the competitive and often political world of scientific publishing, such insights can be useful as you maneuver through the peer-review process and work on your own manuscripts.

5. Validation. Being asked to review a paper means that someone out there values you and your work. ‘They’ have decided that you are one of a select few researchers who has the skill set needed to evaluate a piece of primary research. Feeling valued comes far too infrequently yet is important for morale and overall well-being (read: take it when you can get it).

6. Scientific karma. What goes around comes around. Cliché, perhaps, but I believe firmly that you can do yourself a lot of good by reviewing papers. It can be a small world, and important personalities in science will remember you if you do a high quality review. Continually refusing to do reviews will also put you in a negative spotlight, and people will also remember this. Being collegial, and being willing to share your expertise, is a responsibility, and in many ways, a gift. Good things will happen if you help out your scientific community. As an anecdote, when I was gearing up for tenure at McGill, I provided a review for the journal Ecography. My review was selected as being high quality, and valuable, and the editorial board of that journal sent me a mug, and a nice letter of thanks (yes, a REAL letter!). I put a copy of that letter into my tenure dossier to illustrate that the broader scientific community recognizes the value of this kind of contribution. I do not know if that letter made any real difference in the tenure process at my institution, but I’m quite sure that it didn’t hurt.

The journal Ecography

To finish with a couple of practical questions:

How much reviewing should you do? This is a tricky question. When starting out your career, I think reviewing at least as much as you publish is a good idea. Later, and as your skills at reviewing become more efficient, I think it possible to review perhaps one paper per month. That being said, when a review request comes along that is precisely in your area of expertise, do not refuse!

Is it OK to say no? If you are under tight time constraints, if the area of research is beyond your expertise, or if you have a clear conflict of interest that will interfere with your ability to provide an unbiased review, you can and certainly should refuse a invitation to review. However, please do the editor(s) a favour and suggest other potential reviewers that you think would be qualified.

How do you go about reviewing a paper in a timely and efficient manner? That is discussion for a future blog post!

Now, go check that e-mail… you may have a review request waiting.

Spiders do not bite.

/ Chris Buddle / 172 Comments

Last week, the arthropod lab was lucky enough to be highlighted on the website “Montreal Openfile”. When discussing our work with spiders as related to McGill’s spider collection, I was asked about the most common misconception about spiders, and I responded quickly with the following:

There are a lot of misconceptions about spiders. The most common is the idea that spiders frequently bite people – they do not. Most so-called spider bites are caused by something else. Spiders generally have no interest in biting us, and would rather feed upon invertebrates. I have been working with spiders for over 15 years, and I have handled many, many kinds of live spiders and I have never been attacked by a spider.

It is really quite astounding - almost anyone you talk to seem to know someone who has been bitten by a spider and/or they themselves have a personal story about a spider that bit them. These stories often include anecdotes like “it really, really hurt“, “the wound swelled up and festered“, “I was bitten over and over again in the middle of the night“, “the spider ran right at me and bit me” etc. Related directly to this are the numerous questions I get about the brown recluse spider, and its occurrence in Quebec. If I believed everything that people told me, I would NOT be an Arachnologist, and I would fear for my life - Venomous spiders everywhere!!!

Female wolf spider (Lycosidae) on my hand. She is carrying an egg sac.

Time for a reality check - Spider bites are very, very rare and other more likely causal factors should be given priority. Let me go into detail:

1) Misdiagnosis: other animals are more likely to be the cause of so-called “spider bites”. The usual and more likely suspects include things like wasps, ants, bedbugs, black flies, etc. Message: these kinds arthropods are known to sting, bite, or “feed” upon mammals! (…and reactions to some of these can certainly be severe, and serious). How do I know that spiders rarely cause reactions in humans? Two reasons: experience and the scientific literature (i.e., evidence or lack thereof). For example, a few years ago colleagues of mine (Robb Bennett & Rick Vetter) wrote about this in a paper for Canadian physicians:

The title of the paper on spider bites

There are two key pieces of information in this article: first, the medical community must recognize the possibilities of other likely causal factors for symptoms sometimes attributed to spider bites. Second, to properly verify a spider bite, the spider needs to be collected and properly identified. This takes me to the next point - the importance of taxonomy.

2) Incorrect identification: Several years ago a woman approached me after a pest-control company sprayed her home - she brought me specimens of the ‘deadly’ spider that they had sprayed for. It was NOT a dangerous spiders - it was a completely harmless wolf spider (Family Lycosidae) from the genus Trochosa. She saw a spider, called in the professionals, and these professionals did not accurately identify the spider (they told her it was a brown recluse). TAXONOMY IS IMPORANT and TAXONOMIC EXPERTISE is essential. It is critical that a careful identification is done (by an expert!) on any spider that supposedly bites someone. In my experience, a casual image search on the Internet will not suffice, and will likely confuse the situation, and perhaps cause undue alarm. [as an aside, this blog post about ‘the taxonomy fail index’ is worth a look]

3) Spider behaviour: Spiders are “scared” of humans. Ok, I recognize this is anthropomorphizing things, but the reality is that if you approach a spider, it usually runs away, or completely ignores us. With the exception of jumping spiders, most spiders have very poor eyesight and respond to other stimuli (e.g., vibrations, light/dark). Humans make a lot of noise, and cause a spider’s entire habitat to shake, rumble and roll. Furthermore, spiders prefer to live in damp, dark places, and when we lift up an old shoe box, or sweep under the fridge, we sometimes disrupt a spider but if you wait a minute, they invariably run back to darkness. Spiders would rather run and hide than hang out with us.

4) Home range: Venomous spiders (i.e., to humans!) just don’t live in Canada. Of the almost 40,000 spider species, globally, there are less than a dozen or so that can cause serious health problems to the average, healthy human, and these do not occur naturally in Canada (Australia, however, is a different story!). One of the authors of the paper mentioned above (Rick Vetter) has a terrific website devoted to the “myth” of the brown recluse. Also, his list of publications will take you to some key literature on the broader topic of medically important spiders. Rick has put together a terrific map showing the distribution range of the brown recluse, and I’ve copied it below. As you can see, Canada is not part of the native range of the brown recluse (or its close relatives):

Range of the brown recluse & its relatives

5) Spider food: Spiders prey upon invertebrates and for the vast majority of spider species their venom is suited for invertebrates. Their venom can certainly pack a punch, but it is generally not suited for vertebrates (at least certainly not in northern climes, there are spiders elsewhere who do prey upon birds, for example).

6) Biological constraints: For many species, the “fangs” of spiders (which are located at the end of the Chelicerae) are just too weak and small to be able to break the skin. I have held many spiders and watched as they work away at trying to bite me, but they just can’t pull it off. Our skin is generally too tough for their little, wimpy fangs. Here’s a photo to show this (it’s another wolf spider, trying unsuccessfully to bite me):

A male wolf spider (Family Lycosidae) "attacking" me.

To summarize this rather lengthy post: in general, and in this part of the world, venomous spiders are rare, and bites from venomous spider bites are exceedingly rare, and I would argue that most suspected spider bites are not actually caused by spiders. The risk of a spider bite is very, very low. If you want to reduce risk, it’s far more dangerous to get in a car than be bitten by a spider.

Writing this post has inspired me to think about other misconceptions about spiders. Stay tuned…there’s a lot more to come!

From McGill to Antarctica

/ Chris Buddle

This is the second part in the series of “where are they now”, devoted to students from our laboratory who have moved on to other adventures (click here for Part 1). I just could not resist writing about Zach Sylvain - Zach was a Master’s student in the lab a few years ago. He did a fascinating project at the Morgan Arboretum, all about the effects of habitat variation on oribatid mite diversity. His main research paper, titled “Effects of forest stand type on oribatid mite (Acari: Oribatida) assemblages in a southwestern Quebec forest” was published in Pedobiologia in 2010.

Zach on a field trip (somewhere south)

Zach was a terrific graduate student - he worked extremely hard, became an expert on identification of Oribatid mites (not an easy task) and wrote a high quality Master’s thesis. After McGill, Zach headed west, and landed in Diana Wall’s “Soil Biodiversity and Ecosystem Functioning Lab” at Colorado State University:

Diana Wall is truly one of the lead scientists, globally, on the functional ecology of soil organisms. It was a perfect fit for Zach. In this laboratory, Zach’s Ph.D. is about the following:

His research into the community ecology of nematodes and oribatid mites focuses on drivers of their biodiversity such as soil moisture and the implications this diversity has for ecosystem functioning. Zach works at the Konza Prairie, Shortgrass Steppe, Jornada Basin and McMurdo Dry Valleys Long Term Ecological Research (LTER) sites. At these sites his research investigates how communities of soil animals are structured at varying levels of soil moisture, and how these communities respond to experimental manipulations of precipitation. This research investigates these trends at several scales and will provide insight into what consequences global climate change may have for belowground ecosystems.

taken from: http://rydberg.biology.colostate.edu/sites/walllab/people/zachary-sylvain/

Did you read that carefully?

Yes, it said the “McMurdo Dry Valley”. Here’s a link to the broader project: http://www.mcmlter.org/

Sampling, in Antarctica

And, yes, that is in Antarctica. Zach was able to travel to that incredible continent just over the past couple of month. I am insanely jealous. Although not known as being a biodiversity hotspot, Antarctica is nevertheless truly fascinating and home to a wonderful suite of invertebrates.

Zach was kind enough to let me use a couple of his photographs for this post. This all looks very exciting and we eagerly await the results of his research!

Zach's tent, Antarctica

McGill’s Spider Collection

/ Chris Buddle / 2 Comments

Over 600 species of spiders are known from Quebec… we know this because people (including many in my laboratory!) collect them, identify them, publish papers on them, and store the specimens in an entomological collection. McGill’s spider collection is located in the basement of the Centennial Centre, at Macdonald Campus, and it is part of the Lyman Entomological Museum.

Over the past couple of weeks, our laboratory has been lucky to host an intern, Niki. She is visiting us as part of her program at Vanier College, and is in our laboratory because she is passionate about entomology and arachnology. Part of Niki’s work was to help me re-organize this spider voucher collection:

McGill's Spider Collection

Each drawer of the collection contains a number of vials, with different species represented in each vial. Vouchers are specimens that have been identified as part of some project in the past, and before we publish our work, the species that were identified go into individual vials, with a proper label (i.e., containing data about locality, habitat and identity). This allows experts to verify our identifications (and correct them if necessary!), and vouchers are therefore the ‘hard evidence’ that we did our work, and exemplify the principles of repeatability in our kind of science.

The Biological Survey of Canada published an excellent brief all about voucher specimens, written by Terry Wheeler. Here’s a nice quote from that document:

“Designation of voucher specimens is a long-established practice in systematic research, through the designation of type specimens of newly described species. The requirement for a one-to-one correspondence between a scientific name and a real organism is undoubtedly responsible for the convention in systematics of depositing authoritatively identified specimens from a study in a research collection, whether the specimens are types or not.”

A spider collection is a little peculiar. In contrast to most insect collections (in which the insects are stored dry, individually, on pins), spiders are stored long-term in vials, and preserved in ethanol. This means they require some curation - i.e., now and then someone has to make sure the ethanol hasn’t evaporated, the labels are still in good shape, and the vials are undamaged. Spider vouchers are also a little different because a single vial may contain several individuals of the same species, and often representatives of both sex.

Individual vials, each containing a different species

The Lyman Entomological Museum’s spider vouchers are reasonably well organized, but over the past few years, specimens from some past projects still had to be incorporated into the collection - this is what Niki helped with. Niki also helped to electronically database the collection. This is a very important step, also, since we want to eventually make the data from this collection freely available on-line. This will mean that others can find out what species are in our collection, and discover what habitats/locations they are from.

If the collection interests you, send me an e-mail and book a visit!