Category: open access

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Harrington’s 1881 field notes and thoughts for today

The earth covered by its first mantle of snow reminds one that the collecting season is virtually ended, and the lengthening evenings allure one to the study fireside to go carefully over note books and collections and to read the recorded labors of fellow Entomologists.

So begins William Hague Harrington as he recapped his personal entomological observations from the summer of 1881 near to Ottawa, Ontario.

It was this sentence that first caught my eye while I was browsing around the deep back issues of The Canadian Entomologist. Perhaps it was the reference to snow just as the warmest days of the year are beginning. Perhaps is was simply the language that Harrington used. But either way it prompted me to find out more about the entomologist behind these words.

According to his obituary in the June 1918 issue of The Canadian Entomologist, Harrington was born in 1852 in Nova Scotia. After his formal education he worked in the Canadian civil service in various roles until he retired in 1916. He passed away shortly after that, in 1918.

Prior to that, in 1879, he was one of the founders and charter members of the Ottawa Field-Naturalists’ Club, an organization that is still active today and which publishes The Canadian Field-Naturalist. He was secretary-treasurer, secretary, and president of that club at various times. He was also an active member of the Entomological Society of Ontario, and was president of that organization for a couple of years. His obituary lists close to 50 articles published in The Canadian Entomologist and more than 50 published elsewhere. The article topics range widely with, as his obituary notes, a substantial focus on Coleoptera and Hymenoptera.

Besides – and I’d argue more important than – his scientific accomplishments, he was described as:

(q)uiet in nature and unassuming, even retiring at times, Harrington was held in high regard by all who knew him.

Reading his summary of his 1881 field notes I think that we can see hints of both his “quiet nature” and his expertise as a natural historian. The notes are both contemplative and full of useful information.

His discussion begins with collections of “mud-wasps” – I am guessing that he was referring to the black and yellow mud-dauber Sceliphron caementarium, although he calls them Polestes annulatus – on 15 March 1881. These he describes as collecting nest material from the “pulverized macadam” of the streets of Ottawa and building nests on the side of the Parliament buildings.

He goes on to discuss various butterflies, the full onslaught of mosquitoes around 24 April, and an early emergence of some buptrestid beetles. Other spring-emerging, conifer-feeding species that year included Pissodes spp. weevils and sawflies.

Harrington’s attention to detail is present throughout this short essay. Take, for instance, his discussion of fireflies:

During May the curious larvae of certain Lampyridae were often seen in damp woods, crawling on the trunks of trees, such as cedar, or affixed by the tail to the bark, undergoing their metamorphoses in a similar manner to the larvae of the Coccinellidae. Some reared at home emerged as Photinus angulatus [Note: although this species name appears commonly in the literature of the time, I am not sure of the current taxonomy]. The larvae, and to a less degree, the pupae, emitted a strong greenish glow from two of the posterior segments; the imago being, of course, one of our common “fire flies.” Some of the larvae were thickly covered beneath with small ticks, of a bright vermilion color, which had their pointed heads plunged between the armored segments of the larvae. They were not dislodged, but walked rapidly when free. By these little parasites the larva were so weakened as to perish before completing their transformation.

During the spring he also took two trips – one to Wakefield Cave (here, I assume) with some friends, and one with the Ottawa Field-Naturalist’s Club to Montebello. On both trips he successfully collected a large number of insects, including a number of tiger beetles.

After that he states that “my opportunities for collecting were few, and my notes correspondingly scanty.” As for all of us, life’s necessities and other urgent (and less-urgent) issues often take precedence. Harrington finishes off his compilation mentioning early-October collections a few specimens of a cotton moth that seemed to be a seasonal and accidental invader of Canada.

A couple of things struck me about this compilation of notes. First, the fact that Harrington obviously took the time to take good field notes and then to publish them in this summarized form is wonderful. Not only is it a record of what he did and saw in 1881, but it provides some interesting information that others may be able to follow up on over 125 years later. His attention to detail and drive to get the information out to the public in curated and archived form is a great example to follow. These days a scientific paper is the usual, highly distilled, production of field and lab notes. Should we be thinking more about how to regularly compile our field and lab notes in this way as well? Would such information be useful to future generations of biologists? Are there curated and archived venues that would take such compilations today? I can’t think of any, but I’d love to be informed if there are.

And second, for all of the current discussion of “citizen science,” it is obvious that citizen science has been alive and well for decades, if not centuries. Harrington was not what most would consider to be a “scientist” today. But he most definitely was just exactly that. The current push towards large- and small-scale, often online, citizen science initiatives simply picks up a baton that has been passed along through multiple generations. Much of the science done in previous generations was done by people exactly like Harrington – lay citizens with a deep interest in the natural world around them. In other words, new times require new methods, but not a new spirit of fascination. Fascination is always present.

So, a big thanks to William Hague Harrington for his contributions and his foresight and care to ensure that his observations are still here for us to read about and learn from.

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Reprints back then… but what now?

“Back in my day…”

I sort of feel like I’m saying that more and more these days. It must be a symptom of advancing age. Today that geezer sentiment was stimulated by this tweet:

For those of you who haven’t been “in the business” long enough to remember the ritual, it went something like this. I would read a paper of interest and write out various references from it that I needed to get my hands on for deeper understanding of the topic. Then I’d head to the library and do the cart-photocopier shuffle. I’d generally find all of the articles that I was after, but often one or two key papers would be missing. So I’d head back to the department mailroom and would pick up a card that looked something like this. After filling out the card and mailing it, I’d wait a few weeks and would (usually) happily find a copy of the paper in my mailbox sent to me personally from the corresponding author. Sometimes the author would have even taken the time to write a short greeting on the reprint.

Most labs maintained a stock of reprints. When you published a paper, you’d have the option of buying paper reprints in various quantities from the publisher. There was often much discussion to decide about how many you thought you’d need to purchase. If you ran out, you’d photocopy the last one to replenish your pile. Some piles would dwindle quickly. Others would just collect sad no-citation dust.

However I haven’t even thought about reprints for years now, other than occasionally stumbling across my remaining stocks of reprints occupying space in my file cabinet (which I also hardly ever venture into anymore). I haven’t been asked for a reprint in ages. I haven’t asked for a reprint in ages. In fact, I can’t even remember the last time either of those events occurred.

To some extent, this is a good thing. It means:

  • many people these days have good access to most journals, and open access is having a good effect.
  • most journals now maintain good archives of even their oldest material.
  • information is often available immediately and at our fingertips.
  • I no longer need to rely on hoping that my request gets to a corresponding author (who could have left that institution years ago), or that the author takes the time to send me the paper.
  • less paper use and happier forests.

On the other hand, there are still many places in the world, and many institutions, without adequate access to scientific literature. Even today not all journals maintain deep archives. And no library, even those that are otherwise well-stocked, subscribe to all archives of all journals. This latter point is becoming more and more the case as subscription costs rise and budgets dwindle. But we have email, and #IcanhazPDF, and open access venues – all of which should help with these issues.

I was reminded of these “on the other hand” points this week when I set out to get my hands on this paper. Surprisingly to me at least, our library only listed the paper version of this article in their stacks. So…

Once at the library, I located the journal and found that the volume was missing from the shelf. Egads! Back down the circulation desk, where I filled out a form that would send a student assistant scurrying around the library looking for the missing volume. At that point, I’d had about enough fun reliving the 90s, and even though there is a valid debate about the effects of #icanhazPDF, I made my Twitter request. Thanks to Chris MacQuarrie and the magic of the internet, the article was on its way to me in a jiffy. Later on in the day the library notified me that they’d found the truant volume…

So obviously the demise of the old paper reprint/mail system is a good thing, right? Perhaps. For the most part I agree.

However, despite what may be thought of as its shortcomings (shortcomings now due merely to technological advances), a reprint request was much more than a request for a single article. More than simply that, a request used to serve as one more thread in a network between real people. A request represented one more potential conduit to collaborative discussion. It wasn’t the paper in the mail that was important so much as it was the tangible connection to someone else with similar research interests. Thankfully things like Twitter, Google Scholar, and various other up-and-coming services help to reveal linkages and keep the conversation going for those who participate. Participation in the emerging system and getting others to do the same is what is vital. And participation is what we need to be encouraging.

The biggest tragedy of non-participation for all of us is a lack of key influences on the ongoing discussion of our craft. It’s easy to relegate nay-sayers to the dinosaur bin. But their diverse and experienced voices are vital to understand where we’ve been and where we’re going. The sunset of network building via rituals like reprint requests does not represent the end of an era as much as it reveals new and exciting possibilities for even more meaningful connections. The more ideas, data, opinions, and interpretations that we have on board, the better for all of us and the better for the progress of science.

I am fully aware that blog posts like this are the proverbial preaching to the choir. So, how do we convince our colleagues who are still not part of the emerging conversation to join with us? Reprint requests, and many of our previous network building methods, are fading away. We don’t want voices with important knowledge, wisdom, and experience to fade with them.

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It’s cold out there!

Most of us would find it pretty hard to live outside all winter anywhere in Canada, let alone in places where temperatures routinely dip below -30ºC. But this is exactly what the mountain pine beetle (and many other insects) does. The question is, of course, how does it pull this off? What is it about mountain pine beetle larval physiology that allows the insects to make it through long months of deep cold?

A paper by Tiffany Bonnett and others, that recently came out of our lab, probes this process in pine beetles in a way that has not been done before. The publication is entitled “Global and comparative proteomic profiling of overwintering and developing mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae), larvae” and is available as an open access publication. We have also published the raw genomics data online at figshare. You can find those data here, here, and here.

 

What did we do?

Larval mountain pine beetles were collected from trees near to Valemount, BC during the early autumn and late autumn, and then again during the early spring and late spring. The larval beetles were prepared in the lab so that we could use a process called iTRAQ to assess all of the proteins present in the larvae at each of the different collection time points. Essentially we took four snapshots – two in the autumn and two in the spring – an then compared them to each other see what was changing. This gave us a huge amount of data to work with and we used statistics to tell us which proteins increased or decreased in prevalence across either the autumn or the spring.

 

What did we find?

Among other things:

  • Larvae expend a fair amount of energy on detoxification of host resin compounds, both in preparation for the winter, and then during feeding after winter is over.
  • Stress physiology plays a large role in this entire process, particularly in the autumn as the larvae are dealing with host tree resin toxins and readying themselves for the upcoming onset of winter.
  • We saw evidence for the involvement of several compounds that may play an antifreeze role.
  • There is an evident shift between emphasizing overwintering preparations (in the autumn) and emphasizing completing development (in the spring), consistent with expected shifting priorities at different points in the life cycle.

 

Why is this novel?

The overwintering larvae of the mountain pine beetle remain nestled under the protective bark of their host tree. This makes them quite difficult to work with, and until now not very much information had been generated on this life stage, particularly in the context of winter survival. This work, which has harnessed the power of some very useful genomics databases, has cracked the door (or the bark?) open to allow us to see in broad sweeping terms what is going on in this insect during this vital time in its life cycle. We have seen aspects of larval mountain pine beetle physiology that have never been seen before, and that provides the power to ask new questions and to investigate key genes and pathways in a much more directed manner.

 

Why is this important?

Up until now, the main known winter survival mechanism for larval mountain pine beetles was the accumulation of glycerol in the autumn. Glycerol acts as a natural antifreeze and is part of the overwintering survival tool kit of many insects. But in most known cases, glycerol is not the only part of the equation, and we didn’t think that it was the sole story in mountain pine beetle either. And it turns out that we were correct with that guess – there are a lot of other things going on as well.

In a larger sense, this means that we now have targets to focus on as we work to understand how deep winter cold can impact populations. Overwintering mortality is one of the major factors contributing to control of bark beetle populations. Now that the mountain pine beetle is moving from the cold interior of British Columbia into even-colder central Alberta, a major research question relates to the climate in its expanding geographical range and how that is going to affect the insect’s potential spread to other regions. Overlay that question with the impacts of climate change, and it should be apparent that understanding mountain pine beetle overwintering physiology is becoming more and more vital.

 

Where do we go from here?

We now have numerous potential gene targets to look at, any of which is a project unto itself. Because we have shown in other work that larval mountain pine beetles in the late summer are feeding on potentially very toxic food, we are interested in finding out how larval ability to detoxify and digest their food in the autumn can make or break their chances for winter survival. We suspect that certain larvae are better adapted than others at dealing with the nutritional challenges that they face, and thus better able to produce antifreeze compounds and the other components that allow overwintering success.

In other words, we suspect that there is variation in the mountain pine beetle population that results in some larvae surviving the winter while others don’t. We, along with collaborators, hope to determine which genes are important in this process and how selection pressure in their historical and expanding ranges are changing mountain pine beetle populations.

Some of our key questions are:

  • How do specific proteins function in protecting larvae from the cold?
  • What happens if we “knock out” some of those proteins?
  • What characteristics of tree defense and nutrition make some host trees more or less likely to allow the resident larvae to survive a winter?
  • Do adult beetle parents choose trees based in any way on how their young may fare?
  • Where in the genome should we expect to see natural selection as the insects move into colder and more inhospitable regions? How will these evolutionary shifts be observed in changes in behavior and physiology?
  • What are the larger implications of climate change on these processes?

As you can see – and as is the case with science in general – this paper not only provides some answers, but also provides fertile ground for more questions. This work, and other related work in our larger mountain pine beetle system genomics project, has given us the means to chase down some of the answers. We are looking forward to the interesting work ahead. Since this publication and its associated data are all open access, we also look forward to seeing what other people might find to do with our data.

ResearchBlogging.org
Tiffany R. Bonnett, Jeanne A. Robert, Caitlin Pitt, Jordie D. Fraser, Christopher I. Keeling, Jörg Bohlmann, Dezene P.W. Huber (2012). Global and comparative proteomic profiling of overwintering and developing mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae), larvae Insect Biochemistry and Molecular Biology DOI: 10.1016/j.ibmb.2012.08.003

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My Voyage(er)

What were you doing on 25 August 2012? Now think back (those of you who were even born then), and tell me what you were doing on 5 September 1977.

In my case, last year on 25 August my family and some friends were hiking in the Valley of the Five Lakes in Jasper National Park. My two boys, five- and three-years old at the time (bookending the crew below, in red and blue shirts, respectively), were enjoying time exploring nature in one of the most beautiful spots on earth.

Eli (on the left) and Marcus (on the right) take a break with some friends during a hike in Jasper National Park.

On 5 September 1977 (here I go, revealing my advanced age) I was five-years old – like my oldest son in the photograph – and it was Labor Day. Just as he was in that photograph above, I was getting ready for my first day of first grade and the beginning of my formal educational journey.

Why are these two dates important beyond my personal reminiscing? Back on 5 September 1977, Voyager 1 was launched on its scientific journey. And on 25 August 2012 it is estimated that Voyager 1 became the first human-made interstellar spacecraft in history.

This has hit me pretty squarely over the past few days since this announcement. As it turns out, Voyager 1 and her sister, Voyager 2, were among the major influences of my scientific pursuits. Both probes launched just as I began first grade, and Voyager 2 sent home some of its final photographs (of Neptune) in the summer of 1989, just a couple of months after I had graduated from high school.

All through grade school my cohort and I were amazed by the spectacular photographs sent back from these probes, photographs that remain iconic to this day. During those years my fascination with nature grew in many different directions, shaped in no small part by this awesome example of basic scientific exploration. My growing realization that the universe around us was such an incredible place made me want to explore my own corner of the earth. And the living things in my yard and neighborhood were right there and available for me to study. Being given the opportunity to imagine then (as I’ve been doing again over the past few days) where the Voyager probes may go and what (or who) they may encounter over the upcoming eons pushed me towards finding out all that I could about at least one small part of the puzzle.

NASA’s Voyager program is a prime example of why we need basic science not to only survive on the scraps thrown to it by applied science, but to thrive, well-fed, on its own. Voyager has not only shown us more about our universe than we ever knew (and the probes are still sending back data!), but it has doubtless been instrumental in inspiring many among an entire generation of kids to become the scientists of today. I’m sure that I’m not the only scientist about my age who felt a wave of nostalgia – and even re-inspiration – over the past few days as we remembered some old friends who went on a long journey.

Now that the Voyager spacecraft are exiting our solar system to explore the universe expanding before them, I wonder what will inspire my two boys as they explore their own expanding world.

In the current climate that prioritizes applied science far over basic research, who and what are the “Voyagers” of 2013 that will fascinate and inspire a new generation?

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Happy birthday, PeerJ

A quick post to note PeerJ‘s first birthday.

PeerJ is a biological open access journal – backed by an excellent publishing team, an advisory board replete with luminaries, and a diverse editorial board – that also happens to come with some interesting twists that are bound to change the scientific publishing paradigm.

First, instead of paying an open access publishing fee for each paper that is accepted, authors each pay a lifetime membership fee (paid memberships start at US$99). If you and your co-authors have a membership, you can publish in PeerJ. In order to keep up your membership, you need to regularly participate in journal activities such as editing, reviewing, or commenting on articles. In other words, with one membership you can publish open access articles in PeerJ for life.

That, in itself, is a twist that makes PeerJ unique.

The second twist – and the one that I’d like to briefly focus on here – is PeerJ PrePrints.

A preprint is a not-yet-peer-reviewed version of a manuscript that is placed on a public server for early dissemination to the rest of the scientific community. Preprints serve to provide early access by other researchers to data, results, and interpretations. They allow for pre-review discussion and criticism of the ideas that, if taken to heart by the authors, serve to strengthen the manuscript for eventual peer review and publication. And, when uploaded to a recognized preprint service, preprints set a date-stamped precedent for the ideas that they contain. To great extent, a preprint is simply a conference presentation or poster in formal manuscript form with broader access and better DOI-based citation/recognition.

Physicists, astronomers, computer scientists, and mathematicians (to name a few) have dealt in preprints for many years now. For some reason, the biological sciences have languished behind in this regard. But things are changing. Rapidly.

And PeerJ has played a major role in that change over the past year.

As of this post, there are 29 PeerJ PrePrints at the journal site, some of which are in their V.2 or V.3 forms (yes, you can update your preprint as you receive comments, etc.). That list is bound to grow in the coming years.

Keep an eye on PeerJ. It’s going places. I’m hoping that my lab will soon submit a few preprints and journal articles, and I hope that you are considering it as well.

NOTE #1: While the world of biological academic publishing is changing in regard to preprints, there are still some hold-out journals which either have ambiguous policies or which flat-out reject papers that have been published as preprints. You can use these tools – here and here – to make decisions regarding preprinting of your upcoming manuscript.

NOTE #2: At the membership link, you’ll have noticed that there is a free membership that allows you to submit one public PeerJ Preprint per year. So it’s a great way to try out the system without spending a single dime.