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.

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.

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

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?

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.

Open data

by Dezene Huber and Paul Fields, reblogged from the ESC-SEC Blog.

Have you ever read a paper and, after digesting it for a bit, thought: “I wish I could play with the data”?

Perhaps you thought that another statistical test was more appropriate for the data and would provide a different interpretation than the one given by the authors. Maybe you had completed a similar experiment and you wanted to conduct a deeper comparison of the results than would be possible by simply assessing a set of bar graphs or a table of statistical values. Maybe you were working on a meta-analysis and the entire data set would have been extremely useful in your work. Perhaps you thought that you had detected a flaw in the study, and you would have liked to test the data to see if your hunch was correct.

Whatever your reason for wishing to access to the data, and this list probably just skims the surface of the sea of possibilities, you often only have one option for getting your hands on the spread sheets or other data outputs from the study – contacting the corresponding author.

Sometimes that works. Often times it does not.

  • The corresponding author may no longer be affiliated with the listed contact information. Tracking her down might not be easy, particularly if she has moved on from academic or government research.
  • The corresponding author may no longer be alive, the fate of us all.
  • You may be able to track down the author, but the data may no longer be available. Perhaps the student or postdoc that produced it is now out of contact with the PI. But even if efforts have been made to retain lab notebooks and similar items, is the data easily sharable?
  • And, even if it is potentially sharable (for instance, in an Excel file), are the PI’s records organized enough to find it?*
  • The author may be unwilling to share the data for one reason or another.

Molly (2011) covers many of the above points and also goes into much greater depth on the topic of open data than we are able to do here.

In many fields of study, the issues that we mention above are the rule rather than the exception. Some readers may note that a few fields have had policies to avoid issues like this for some time. For instance, genomics researchers have long used repositories such as NCBI to deposit data at the time of a study being published. And taxonomists have deposited labeled voucher specimens in curated collections for longer than any of us have been alive. Even in those cases, however, there are usually data outputs from studies associated with the deposited material that never again see the light of day. So even those exceptions that prove the rule are part of the rule of a lack of access to data.

But, what if things were different? What might a coherent open data policy look like? The Amsterdam Manifesto, which is still a work in progress, may be a good start. Its points are simple, but potentially paradigm-shifting. It states that:

  1. Data should be considered citable products of research.
  2. Such data should be held in persistent public repositories.
  3. If a publication is based on data not included in the text, those data should be cited in the publication.
  4. A data citation in a publication should resemble a bibliographic citation.
  5. A data citation should include a unique persistent identifier (a DataCite DOI recommended, unless other persistent identifiers are in use within the community).
  6. The identifier should resolve to provide either direct access to the data or information on accessibility.
  7. If data citation supports versioning of the data set, it should provide a method to access all the versions.
  8. Data citation should support attribution of credit to all contributors.

This line of reasoning is no longer just left to back-of-napkin scrawls. Open access to long term, citable data is slowly becoming the norm rather than the exception. Several journals have begun require, or at least strongly suggest, deposition of all data associated with a study at the time of submission. These include PeerJ and various PLoS journals. It is more than likely that other journals will do the same, now that this ball is rolling.

The benefits of open data are numerous (Molloy, 2011). They include the fact that full disclosure of data allows for verification of your results by others. Openness also allows others to use your data in ways that you may not have anticipated. It ensures that the data reside alongside the papers that stemmed from them. It reduces the likelihood that your data may be lost due to various common circumstances. Above all it takes the most common of scientific outputs – the peer reviewed paper – and adds lasting value for ongoing use by others. We believe that these benefits outweigh the two main costs:  the time taken to organize the data and the effort involved in posting in an online data repository.

If this interests you, and we hope that it does, the next question on your mind is probably “where can I deposit the data for my next paper?” There are a number of options available that allow citable

(DOI) archiving of all sorts of data types (text, spreadsheets, photographs, videos, even that poster or presentation file from your last conference presentation). These include figshare, Dryad, various institutional repositories, and others. You can search for specific repositories at OpenDOAR using a number of criteria. When choosing a data repository, it is important that you ensure that it is backed up by a system such as CLOCKSS.

Along with the ongoing expansion of open access publishing options, open data archiving is beginning to come into its own. Perhaps you can think of novel ways to prepare and share the data from your next manuscript, talk, or poster presentation for use by a wide and diverse audience.

—–

* To illustrate this point, one of us (DH) still has access to the data for the papers that stemmed from his Ph.D. thesis research. Or at least he thinks that he does. They currently reside on the hard drive of the Bondi blue iMac that he used to write his thesis, and that is now stored in a crawlspace under the stairs at his house. Maybe it still works and maybe the data could be retrieved. But it would entail a fair bit of work to do that (not to mention trying to remember the file structure more than a decade later). And digital media have a shelf life, so data retrieval may be out of the question at this point anyhow.

Open access… Canada?

Today marked a major milestone for open science. Specifically, the Obama administration announced a directive that all US federal agencies which receive over $100 million in funds for research and development work on creating a plan to ensure open access to all research outputs within a reasonable time frame.

To quote from the Obama administration memorandum:

“To achieve the Administration’s commitment to increase access to federally funded published research and digital scientific data, Federal agencies investing in research and development must have clear and coordinated policies for increasing such access.”

You can read more about it here, and here.

A number of other countries, including Canada, have mandatory open access policies for some of their taxpayer-funded research, but for the most part the policies apply to health-related research. And in many cases you can also find research stemming directly from federal scientists freely available on the web.

In some cases (e.g. the UK and Australia and a few others) open access is mandated for all federally funded research. And now that the US has taken this step to full openness, I think that it’s fair to say that there is a lot of pressure on countries that haven’t done the same to get moving down that track.

I’m looking at you, Canada!

Like many other countries on that list, Canada has some mandatory open access policies, but they mainly pertain to health sciences. There have been rumblings of more openness from the Canadian government, as noted by one of my Twitter contacts:

…but the steps taken by the UK, Australia, and now the US are good indicators that Canada’s steps so far have been baby steps at best. It’s time for that to change.

Why should we, as Canadians, call for a mandatory open access policy for all federally funded research? Here, in brief, are a few reasons that come to mind, and I know that there are more:

  • Fairness. Taxpayers paid for the research. Why should they also have to pay to access the results of the research?
  • Open access accelerates the pace of discovery. Although I’m at a small university, the UNBC library is well-stocked with many journals that the folks in my research program and I use. But we occasionally come across articles that we need that are unavailable. The choice then is to keep looking for the information elsewhere, pay up at the paywall, or go through the interlibrary loan process. Our librarians are superb at getting access to individual journal articles that we need, but not everyone is so lucky to be affiliated with a good library at a good institution. There are many scientists who do not have access to these kind of services, and they either have to pay or hope to find the information elsewhere. And most members of the general public have absolutely no access to such services at all. Open access removes those barriers and allows research to move ahead more efficiently.
  • Open access makes research more relevant and reduces the temptation to “hoard” data. Open access allows other researchers and the general public to look at research outputs in all sorts of unpredictable ways. Full accessibility lets the full diversity of interests see and think about the work and, hopefully, take it to new and unpredictable places. In addition, while my little corner of the scientific endeavor (forest entomology, for the most part) is generally not beset by researchers afraid of being “scooped,” this tendency is present to some extent in all fields, and to a large extent in certain fields. Hoarding of data in order to hopefully glean the research glory results in competitive, rather than collaborative, use of research dollars. Replicated efforts in several competing labs may drive research to move faster, but it also sucks up declining research dollars in identical endeavors. Open access, and particularly the tendency toward open data that comes along with it, erodes these tendencies and promotes collaboration instead. The rise of biological preprint servers such as PeerJ PrerPrints and the biological portion of Arxiv also facilitate the erosion of meaningless competition.
  • Open access makes research institutions more relevant. In an era when universities are struggling with funding and, in some cases, public perception, the ability to freely disseminate the useful products of research to the public provides incentive for taxpayers to pressure governments for better funding of postsecondary education. If research results are behind paywalls, they remain mainly unknown to the public and, thus, irrelevant. If the results are irrelevant, so are the institutions in which they were produced.
  • Open access allows the public to see firsthand the evidence-based results that should be driving public policy. Ideally, all governments should consult honestly with scientists about medical, environmental, social, and other issues as they create policy. Realistically, most governments do this only as much as is optimal for their own political agenda. By removing all restrictions to access to research outputs – combined with a growing tendency for scientists to explain their research results to the public – governments will also have to be more transparent in their consultations with researchers. Perhaps we can move to a time when research drives policy rather than seeing policy attempt drive research.

It is, indeed, fantastic to see the US take this big step. And, as noted above, the US is not the first country to do this. It’s now time for the Canadian public to ask our government to start to take this issue more seriously as well, too.

PeerJ, today!

Along with being Darwin’s birthday, 12 February 2013 marks the official launch of the first articles on PeerJ.

In case you haven’t heard about it already, PeerJ is a brand new open access journal, with a twist. Or, actually, a few twists.

For instance, instead of a pay-per-article fee, PeerJ has all authors buy a lifetime membership in the journal. There are several levels of membership, depending on how much publishing you think that you might do on a yearly basis. And there are no yearly renewal fees. Instead, you maintain your membership by taking part in journal activities. For instance, if you review one article a year, your membership will stay active. This fee/membership model allows for an ongoing revenue stream (when members publish with new co-authors who are not yet members), and also stimulates ongoing and growing involvement in the journal by a diverse group of scientists.

Another welcome innovation that some other open access journals are also embracing is the insistence that authors co-publish their data with their paper in a repository such as figshare. This concept is not new to many disciplines. Genomics researchers have been publishing data along with their papers for years using repositories such as those provided by NCBI. But with the growth of the internet, there is no reason that all data associated with a paper can’t be publicly and permanently available in a citable format. By making data public in this way it is easy to anticipate that others will be able to use and build on the data in new and exciting ways.

PeerJ also commits to publishing any work that is rigorous, no matter how “cool” or “sexy” it is… or is not. To quote: “PeerJ evaluates articles based only on an objective determination of scientific and methodological soundness, not on subjective determinations of ‘impact,’ ‘novelty’ or ‘interest’.”

And one last twist that I’ll mention (please see this launch-day blog post from PeerJ for more information), authors can choose to publish the full peer review documentation alongside their accepted article. Besides giving some great insight into the review process, it also allows readers to study other expert opinion on the work and come to their own decisions.

PeerJ has an impressive advisory board that includes five Nobel laureates. It also has a huge and diverse board of academic editors, of which I’m a member (no Nobel Prize for me yet, however). I also have the honor of having been the handling academic editor on one of the first thirty articles in PeerJ.

And, one last note. PeerJ PrePrints is also going to come online in a few weeks as well. If you are familiar with physics and mathematics, you doubtless have heard of preprint servers such as Arxiv. Researchers in those fields have been publishing their preprints (nearly final draft) papers online for years. This is a constructive practice as it allows the larger community to see and comment on results as they come out. This both strengthens the eventual manuscript for final publication and it allows the research community to use the results immediately instead of waiting for the final publication. Of course, it also helps the researcher to establish priority for the work.

Historically, many journals in biological fields have had issues with the use of preprint servers as they have considered such early deposition of a manuscript as “prior publication.” This, too, is changing and I expect that the growing use of PeerJ PrePrints, and others like it, will make the change final.

I am under no illusions that the shift to a more open publishing and data sharing paradigm will be completely smooth sailing. As with anything new, there are going to be challenges and opposition from some corners to doing things in a new way. But the internet has changed the way that we do everything else in our society, often for the better. There is no reason that academic publishing and dispersal of research outputs should remain in the era of the printing press. PeerJ, and other publishers, are working diligently to guide our larger research community through this process of continual innovation.

Exciting times!

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Update: Some great coverage here, here, and here.

Bark beetles on ice

Over the next while I plan to blog about various papers that have come out of our research program. I won’t get to all of them, obviously. But I do plan to pick and choose a few recent ones, and/or ones that have been highlights to this point in my career.

I’m going to begin with a very recent paper from my lab on bark beetle larval overwintering physiology. The paper is entitled “Global and comparative proteomic profiling of overwintering and developing mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae), larvae” and is available in open access here.

Context: Mountain pine beetles usually spend their winters as small, young larvae under the bark of their host tree. In this location, they are exposed to extremely cold temperatures, sometimes ranging below –30°C and even pushing down towards -40°C. Mountain pine beetle larvae survive those temperatures by resisting freezing. Sometime in the autumn they begin to accumulate at least one antifreeze compound (glycerol) in their bodies, and then in the spring they presumably return that antifreeze compound (and perhaps others) to general metabolism for energy to complete their development

Cold temperatures have historically limited the range of the mountain pine beetle both in terms of longitude and latitude, and in terms of elevation. However, climate change has reduced the probability of cold winter temperatures – particularly the probability of extreme cold events fairly early in the autumn or fairly late in the spring. At those ‘shoulder seasons’ the larval insects have either not accumulated enough antifreeze compounds in their tissues (autumn, around Hallowe’en) or have metabolized most of it (spring, around Easter). Those are the vulnerable periods, and deep cold at those can cause populations to crash rapidly.

The lack of unseasonal cold events or of generally very deep cold in the heart of the winter over the past years has been one factor that has driven the dramatic outbreak that we’ve seen in British Columbia. In addition, historically colder areas such as the eastern slopes of the Rockies and central Alberta or high elevation areas in the Rockies have not been as cold either. This has allowed mountain pine beetles to survive winters and to move into hosts, such as jack pine and whitebark pine, that they have not historically used in the recorded past. In the case of jack pine outbreaks, the fear is that the beetle, freed from its main confine on west slope of the Rockies, is poised to move across Canada’s boreal forest. In the case of whitebark pine, the insect may further endanger already-threatened trees that are important to higher alpine ecosystems.

What we did: Up until now, the main known antifreeze compound in mountain pine beetle larva has been glycerol. We suspected that there was more to the insect’s overwintering physiology than just that, as most insects use several strategies to avoid freezing. So we conducted a proteomics experiment. That means that we surveyed the levels of all of the proteins in early-autumn larvae and compared them to levels of proteins in late-autumn larvae to look for changes. Similarly, we compared the levels of all detectable proteins between early-spring and late-spring larvae. Because we now have copious amounts of genomic data for the mountain pine beetle, we could identify which proteins did what in the insect and we could draw some conclusions as to which metabolic pathways and physiological processes were activated or deactivated in overwintering larvae at different times of the year.

What we found: In total we found 1507 proteins in all of our larval samples. Of these, 33 either increased or decreased in their levels between early- and late-autumn and 473 either increased or decreased in their levels between early- and late spring. Of the proteins that were present in either increased or decreased levels in one of the two seasons, 18 of them showed such changes in both seasons. This Venn diagram from the paper shows this general result:

 

 

These proteins can be classified into a number of general functional groups, as seen in this pie chart from the paper:

 

Of course, large groupings are not as informative as looking at individual proteins. So that is what we did, as I will write about in the next section.

What this means: In proteomics work like this, when we are dealing with hundreds of proteins, it is obvious that there is so much complexity that it would take untold pixels to explain everything. In fact, like may ‘-omics’ studies, the original authors (us, in this case) have to pick and choose things that seem interesting to them and then leave it to others wearing different research glasses to find other interesting trends. What follows are a few highlights that we noticed in the context of our research program. Our hope is that others will take our data and find other interesting things that we may have missed.

Glycerol: Our results confirm past work implicating glycerol as an important antifreeze compound in the mountain pine beetle. The data also confirm previous work in our lab (Fraser 2011, referenced in the paper) that shows certain glycerol biosynthetic genes being upregulated in the autumn and downregulated in the spring. Of particular note were the extreme variations in an enzyme called PEPCK (phosphoenolpyruvate carboxykinase) which likely indicates some level of nutritional stress in larvae heading into the cold of winter.

Trehalose: Trehalose is a major hemolymph (insect “blood”) sugar, and it has been found to be important in insect cold tolerance in other species. The levels of an enzyme involved in trehalose biosynthesis increased significantly in the autumn and decreased significantly in the spring, indicating that trehalose might function alongside glycerol as an antifreeze compound.

2-deoxyglucose: The largest autumn increases and spring decreases for any protein that we observed was for one enzyme that is involved in the biosynthesis of 2-deoxyglucose. By looking at what 2-deoxyglucose does in other organisms, we can make some guesses as to what it is doing in the mountain pine beetle. It is possible that 2-deoxyglucose regulates larval metabolism to direct energy flow appropriately toward overwintering in the autumn; that it acts in stress physiology as the insect enters a difficult period of its life; or that it is functional as an antifreeze compound. It’s also possible that it functions in more than of these roles. What is clear is that this metabolite, not previously detected in this species, is likely very important in mountain pine beetle overwintering physiology. So we have some work on our hands to figure out exactly what it’s doing.

Stress, in general: The levels of a number of proteins associated with stress physiology – for instance ferritin, superoxide dismutase and phospholipid hydroperoxide glutathione peroxidase – increased in the autumn and, in some cases, decreased again in the spring. The fact that winter is a stressful period in a mountain pine beetle’s life cycle is obvious from the basic ecology of the organism. We now have a number of stress physiology protein targets to investigate in further research.

Energy use during development: The increases and decreases of particular enzymes involved in basic metabolism indicate that mountain pine beetle larvae put most of their resources into overwintering preparation in the autumn, and only when they have survived to the spring do they begin to divert resources to ongoing developmental processes.

Detoxification of host defenses: A number of proteins commonly involved in detoxification of host chemical defenses were present in autumn larvae but, for the most part, showed reductions in the larvae as the spring progressed. Previous work in our lab has shown that larvae in the late-summer experience extremely high levels of host defense compounds. So autumn larvae are working hard to get prepared for overwintering while also dealing with a toxic environment. Once the winter is over, and the host tree is long dead, it is likely that residual host toxins have either been removed by the beetle’s symbiotic fungi or that they have naturally degraded or dissipated. In any case, the detoxification enzymes are seeming not needed to nearly the degree in the late spring that they were during the autumn. The larvae that survive living in a toxic wasteland in the autumn and that do not freeze to death in the winter are then free to use remaining stores of energy plus whatever they can glean from their host tree to complete their developmental cycle through the spring and early-summer.

Why this is important: This is the first comprehensive look at what is going on in an overwintering bark beetle. While there has been a bit of previous physiological work on mountain pine beetles and a few other bark beetle species, our work in the Tria Project has moved us into the post-genomic era for the mountain pine beetle. That means that we have an extensive genomic database and that we can conduct experiments like this that reveal the workings of a number of physiological systems all at once. We are doing other ‘-omics’ work as well on overwintering mountain pine beetle larvae, including transcriptomics (monitoring messenger RNA levels during different seasons) and directed metabolomics (monitoring specific metabolites related to overwintering) work. And we are doing experiments where we track the expression of specific genes and the activity of specific enzymes revealed to be important during this phase of the insect’s life cycle. Of course our lab, alone, can’t do all of the experimentation suggested by these results. In fact, the data are so extensive that we can’t even conceive of all of the potential experiments. That is what is cool about ‘-omics’ research – there’s no telling who will look at it and think “ah ha! I have a great idea!”

Ultimately we hope that this paper has blown the door open on bark beetle overwintering physiology. Further research is bound to uncover new and interesting results, and since winter cold and climate change play such a large role in the growth of mountain pine beetle populations, such results will help us to understand better where and how the beetles are spreading into new regions and new, susceptible hosts.

Where we are going with this: As I mentioned above, the amount of data from this one study is staggering. This is our lab’s first publication from the larger Tria Project and there are others in the works. Some of them will also produce similar copious data. Others have been designed to look at specific small portions of this study and of some of our other data. We are currently focusing in on some of the metabolic pathways and physiological processes that I mentioned above. And we hope that others are able to take our data and use it for different analyses. For instance, we have surveyed protein levels across much of the larval developmental period. Perhaps others interested in insect development will find and be able to use new information on development in the Coleoptera (beetles) generally, and in bark beetles and other weevils specifically.

This was a really fun study. We certainly hope that the data will be as useful to others as it has been for us already. This work has also moved our research program firmly into the realm of insect overwintering research, and it has been a great introduction for us into proteomics and the era of “big data” in the biological sciences.

ResearchBlogging.org

Bonnett TR, Robert JA, Pitt C, Fraser JD, Keeling CI, Bohlmann J, & Huber DP (2012). Global and comparative proteomic profiling of overwintering and developing mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae), larvae. Insect biochemistry and molecular biology, 42 (12), 890-901 PMID: 22982448

The rise of biological preprints

Although I’m not particularly long-in-the-tooth, for my entire scientific life I have known that publishers (at least in my field) do not accept papers that have been published elsewhere. And while workers in fields like mathematics and physics have long been able to post preprints of their work prior to peer review and subsequent publication in a journal, researchers in the biological sciences have generally not been allowed to do that. This is because most, if not all, journals that accept biological research manuscripts have historically considered posting a preprint as prior publication. And papers that have been previously published are, rightly, persona non grata in reputable journals.

This “prior publication” attitude toward preprints is a pity because such posting has many upsides (outlined in detail here and here and here) and very few downsides. As an editor of a small journal, and a regular reviewer for a large number of other journals in my field, I can attest to the fact that posting to such a service, in which members of the community can comment and critique an article prior to review, would have helped to strengthen just about every manuscript that has ever come across my desktop.

Some of the biggest advantages of preprint posting that I can see are:

Increased community involvement in the scientific process: Scientists at all levels would be able to take part in reading, processing, and commenting on others’ work. Amateurs would also have access to the process and could provide their often-valuable input as well. That would build community, connections, and collaborations. And that would, in turn, help to strengthen and improve the scientific endeavor in general.

Providing authors with valuable feedback and allowing them to improve their work prior to a formal review: As an editor and reviewer I understand quite intimately the (generally thankless) time and effort that it takes to process an article from first submission to final publication. As an author, I know what it feels like to have the “reject” button pressed on a study that I have invested blood and sweat into. In both cases, prior thoughtful advice and critique from the larger community would help to make the formal process smoother.

Results become visible and public more rapidly: Again, as an editor, I know how long it can take for a paper to move from submission to publication. While some traditional journals have done their best to speed things along in recent years, we all have stories of papers that have languished for eons on some editor’s or reviewer’s desk, holding up the publication of the work for even years. Preprint posting does an end-around, allowing the work to be seen immediately and reducing the irritation that slow processing by a journal might cause. The rest of the scientific community would have access to results that may improve research in other labs or even other fields prior to official acceptance and formal publication.

Less fear about being scooped: I’m thankful that my area of biology generally moves at merely a moderate clip. I’m also thankful that, in general, colleagues in my field are much more willing and eager to collaborate than to compete. However, I’m fully aware that not all fields are like this. In those fields, researchers rightly worry about another lab beating them to the punch. Preprint posting, as it is fully public, would give a researcher a claim to precedence that could be fully validated as necessary. Personally, I see this is the least important of the reasons for posting to a preprint server. But I understand that it is a consideration for many.

In the last little while many major publishers have changed their tune on this. Most recently that included the stable of journals held by the Ecological Society of America. In addition, a new kid on the block, PeerJ, is going to run a preprint service as a part of its overall open access journal offering. This is a trend that is being welcomed by many in the field. And it’s one more example of how scientific publishing is necessarily changing – I think for the better – as it is stretched by new technologies and concomitant new ways of doing things.