Category: science

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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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#sciencespark? Or #sciencefuel?

Recently my twitter feed has had a number of #sciencespark tweets roll through it – tweets in which people describe the moment(s) in which their love for science first clicked.

Frankly, I have had trouble identifying my own #sciencespark because as far back as I can remember, I’ve always had a fascination for nature. Perhaps one tweet of the many among that hashtag that I can identify most with is this:

 

 

…because, with some variation, that’s a reasonable summary of story as well.

Many of my childhood summer days were spent outside literally and metaphorically turning over rocks to see what was underneath, or trying out the latest gadget that I had cobbled together from Dr. Zed’s instructions in Owl Magazine. At one point I even attempted (unsuccessful) mark-and-recapture experiments with grasshoppers that I caught. Besides the fact that the overall population of grasshoppers during a typical Alberta summer likely overwhelmed my meagre releases, I’m sure that the black permanent felt marker that I used to color their forewings didn’t do my research – or the grasshoppers – any favors either.

I also kept more animals in the house than you can likely imagine. These included mice, rats, hamsters, gerbils, budgies, a cockatiel, canaries, a dove, cats at various times, tropical fish, goldfish, and even a very short stint with Mexican jumping beans. Usually my family’s house was home to several of these species at once. Of course I bred many of these creatures – or, rather, they just did they will do left to their own devices – resulting in lines of cages in our hallway. Gerbils produce a lot of babies when left unchecked, as it turns out.

Mom, if you’re reading this – and really, who else reads this blog anyhow? – thanks for putting up with that!

Throughout my young life there were so many so-called #sciencesparks that I’d be hard-pressed to name only one that sent me along this trajectory. So I think I’d prefer to call this process #sciencefuel, because a spark implies the lighting of something that is not on fire. Fuel implies the maintenance of an existing flame.

My family was one that encouraged curiosity and investigation. Like I said, my mom put up with rodent cage wood shavings all over the floor. My dad would encourage my science fair work and would help me to find materials for my various other projects. They aided and abetted one of my major hobbies – fly fishing – that also required natural history knowledge in the forms of entomology and limnology. And our family spent a lot of time outside in general – on my uncle’s farm; helping (or getting in the way of) my dad with his beekeeping hobby; or camping in some pretty amazing places like the redwood forests of California, Death Valley, Jasper, or the west coast of Vancouver Island.

These activities, and many others, represented ongoing additions of fuel to the innate fire if inquiry that I believe most kids naturally have in them. In other words, I suspect that for most people it takes more than a single moment to drive a passion for anything, including science. In the case of science it takes engaged adults, encouragement and opportunity to read widely, permission to just explore and make a mess, and good resources (e.g. books, magazines, museums, national parks, community programs, etc.). Kids who are provided with this #sciencefuel on a steady and continual basis will develop into inquisitive and broad-minded adults.

Of course, even with regularly dropping another log into the innate fire, not every kid is going to specifically become a scientist. But every kid who grows up in this atmosphere will become someone who is capable of – and who enjoys – making an honest inquiry into the things that truly interest them and into phenomena that they are tuned to observe around them. Ultimately, these are the kind of people that our world needs more of, particularly as we face myriad growing challenges.

So if you have children of your own, or know children, or have opportunities to take your science or other passion to children, make the most of it. Add some #sciencefuel to the fire.

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Let’s go back to 1914

I am the editor of a small, regional journal called the Journal of the Entomological Society of British Columbia. Although it is a small journal – publishing a few papers and other items in a single issue each year – both the journal and the society that manages it have a deep history. The ESBC was founded in 1902, and the JESBC  has been around in one form or another since 1906 when it was called the Bulletin of the British Columbia Entomological Society.

That deep history combined with the fact that we currently publish excellent peer-reviewed reports that are of particular interest to entomologists working in the Pacific Northwest are what induce me to expend considerable time and effort on its yearly production. Our journal has been, and currently is, run mainly on volunteer efforts. It has always truly been a labor of love.

The JESBC has recently shifted to being completely open access. We are indexed on a number of major abstracting services. And our web editor has been spearheading an incredible effort to get all of our archives online and all of our citations over the years cross-referenced. In other words, our journal has always continued to evolve with the times, and we are working to ensure that trend continues.

As old issues have come online, I have enjoyed dipping into them to read some of the reports from the past. So, in what I intend to be a regular occurrence on this blog, I’d like to highlight a few of the items that I’ve read and that I hope may interest some of you as well.

Recently I was sampling volume 7 (1915), back when the journal was called the Proceedings of the Entomological Society of British Columbia (yes, we’ve had a number of name changes over the years). In it there are a number of articles that discuss a major “locust” infestation in the southern interior of British Columbia. From the reports, the insects involved were seemingly the migratory grasshopper, Melanoplus sanguinipes (called Melanoplus affinis in these reports) and the red-legged grasshopper, Melanoplus femurrubrum. Some very cursory research on my part found no other mentions of the infestation on the internet, so these reports may be the only easily accessible documentation of that event.

Here are some of my thoughts on several relevant articles from that issue:

Ruhman, M. 1915. Insect-notes from the Okanagan 1914. Proc. Entomol. Soc. British Columbia 7:7-11. LINK

This article is a survey of all of the recorded insect pest outbreaks in the Okanagan (southern interior) of BC. Besides being a comprehensive list with some very interesting and sometimes rather extensive notes on a variety of insects, the author mentions the grasshopper infestation briefly as follows:

…(the grasshoppers) are certainly plentiful enough to be taken notice of. Mr. Ben Hoy reports on the 14th that he visited a small orchard surrounded with range land practically defoliated by grasshoppers (species not identified) in Kelowna.

 

Wilson, T. 1915. The outbreak of locusts of 1914. Proc. Entomol. Soc. British Columbia 7:41-42. LINK

This paper outlines the geographical extent of the infestation and begins by particularly condemning the practice of “clean cultivation” – that is, removal of all weeds and alternate crop plants from near orchards and between the rows of trees – as a major driver of damage to orchards. In other words, maintenance of an orchard monoculture and the removal of alternate host plants for the grasshoppers meant that the grasshoppers turned to the fruit trees for food. This is, of course, an agricultural lesson that needs to be taken to heart even today.

Wilson also spent some time explaining the natural history of these insects and then lists what he feels are major reasons for the infestation:

The first reason I advance was the abnormally hot and dry season we have experienced, even for the Dry Belt. This condition was most conducive to the spread of these sun-loving dry-country insects. Second, the influx of settlers and the consequent diminution of the natural food of the locusts. Thirdly too heavy grazing on the range, or perhaps, more correctly stated, injudicious grazing on the range, has done away with the food-plants and forced the locusts to places where they would obtain the requisite amount of nutrition.

This is an interesting analysis, and one that provides a great picture of what was going on in the region at the time in terms of climate, culture, and biology.

 

Taylor, L.E. 1915. Notes on birds likely to be of service in the destruction of grasshoppers in the Nicola Valley. Proc. Entomol. Soc. British Columbia 7:43-45. LINK

Taylor provides an extensive list of birds that were likely to be present in the region at the time and gives estimates for how important they might have been as predators on grasshoppers. Besides being a potentially useful checklist of birds in the Nicola Valley in 1914, Taylor also vaguely mentions resources that he used to develop his estimates. It would be interesting to be able to dig up these reports and compare them to what, if anything, is known today about diets of various bird species.

 

Gibson, A. 1915. The Kansas remedy for the control of locusts. Proc. Entomol. Soc. British Columbia 7:45. LINK

This report is, frankly, frightening. But it is also a good glimpse into pest management back in the early-1900s. In this article, Gibson proposes experimenting with the “Kansas remedy” for control of grasshoppers. The Kansas remedy was comprised of:

Bran, 20 lb.; Paris green, 1 lb.; molasses, 2 quarts; lemons, 3 fruits; water, 3.5 gallons.

Most of the ingredients are identifiable. But what is that Paris green stuff? Well, it’s copper(II) acetoarsenite. As you might imagine, copper and arsenic make for a very toxic brew. And, being heavy metals, a persistent, toxic brew to be precise. I’m personally not a big fan of pesticides unless absolutely necessary, but I can say that I’m glad that what we do use today is safer than this.

I’m also curious to know if this concoction was ever tried in parts of British Columbia. According to the short article it was used in parts of eastern Canada. A bit of digging shows that it was also at least tested, if not used, elsewhere. If the areas that in which was used could be identified today, it would be interesting to survey longterm effects on biodiversity of heavy metals used in agricultural settings.

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Besides being an interesting glimpse into the past, these articles demonstrate the value of a longstanding, regional journal to the practice of science. I think that it is fair to say that without this journal (and others like it) reports like these would either never have been recorded in the first place or would have been buried in files somewhere and lost to contemporary analysis.

From these articles we learn that there was a substantial and damaging grasshopper infestation in the BC’s southern interior around 1914. We read some statements on the climatic conditions and the agricultural practices at the time that were thought to be partially responsible for driving this infestation. We are given a number of interesting natural history observations. We receive what amounts to a checklist of some birds in the region at that time (attention ornithologists!). And we are told about cultural and (sort of scary) chemical methods that were being proposed as pest management methods.

The JESBC, and other journals like it, are full of this type of information. Contemporary archiving, indexing, optical character recognition, cross referencing, and other means of resurrecting this literature are adding value to these fantastic resources. I imagine the value will continue to increase as imaginative people find new ways to sort through this kind of data.

In the meantime, we all now have the opportunity to use our own grey matter-based “technology” to learn from the past. I hope that as I pull out a few of these reports to highlight on this blog over the coming months you’ll also take some time to find some items that interest you.

If bump into anything interesting, feel free to share your finds here in the comments or on Twitter.

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Update (12 November 2013): Chris MacQuarrie pointed this out on Twitter:

Indeed, that is the case. Here is some more information on Norman Criddle and his mixture. Also of interest in that link is the mention of the Rocky Mountain locust, a once prominent species that ended up on the same tragic trajectory followed by the passenger pigeon and (very nearly) the plains bison.

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The “most admirable character in the history of science”

Today, 7 November 2013, is the 100th anniversary of the death of the great naturalist, explorer, entomologist (of course I had to mention that), and scholar-of-all-trades, Alfred Russel Wallace.

Wallace is remembered by many as one of the two co-discoverers of what we today consider the foundation of theory of evolution. The other discoverer being the much better known Charles Darwin.

Wallace and Darwin were both products of their age – a fact that is inescapable if you read their works. But, aside from that and the fact that they both came up with the same idea, in many ways they couldn’t have been more different. Darwin was born into privilege; Wallace was not. Darwin attended some of the best schools; Wallace did not. Darwin formulated his ideas while traveling and then mulled them over for years after returning home from his Beagle voyage; Wallace began to notice patterns in the field and worked toward sharing his ideas quickly. Darwin was financially secure for his entire life; Wallace often struggled to make ends meet and, in fact, did much of his collecting in order to sell specimens back home.

What did unite these two gentlemen was a love of nature and the discovery of an earth-shattering idea born of keen observation, intense study, and soaking in the scientific milieu of the time.

It’s usually very hard to say how an idea develops and who has absolute priority. New ideas, large or small, develop over time and are a direct result of trying other ideas on for size. Look at just about any scientific paper today, and you will usually see several co-authors. It was the same for the idea of natural selection. Others – contemporary and near-contemporary – such as Lamark and Darwin’s own grandfather, Erasmus, were giving the topic deep thought and consideration. Observations of life around them, and specimens brought back by intrepid adventurers like Bates and Wallace, told a tale of… something. It took Wallace and Darwin to put a finger on what exactly that something was.

While Wallace’s writings are sprinkled through with the idea, his thoughts are often summarized in what is called the Sarawak Law from a manuscript that he wrote while in Borneo entitled “On the Law Which Has Regulated the Introduction of New Species”:

Every species has come into existence coincident both in space and time with a pre-existing closely allied species.

These ideas, also discussed in an essay that Wallace sent to Darwin, prompted Darwin to get his well-developed thoughts down on paper. He and Wallace famously co-published the idea shortly thereafter, and then Darwin wrote and published his most famous book.

All this to say that while some continue to claim that “Darwin stole Wallace’s idea,” this could not be further from the truth. Both gentlemen were thinking along the same lines. Both, particularly Wallace, were open with their ideas and they engaged in discussion with each other on the topic. Both acted graciously toward the other during their entire lives. And both have an important place in history as the scholars who have helped to forge contemporary biology.

Over the past year or so, I have been reading Wallace’s “Malay Archipelago” a chapter or two at a time. What strikes me about his words, and what I believe is one of the biggest lessons that we should take from his life, is that sheer curiosity combined with a commitment to ongoing self-education and an ethic of hard work and focus will take you to intellectual places that no one has ever gone before. At some point, when I finally finish my slow read of his book, I plan to write a “review” (as if one is needed) of this literary masterpiece. Suffice it to say for now that besides his amazing observations of biological phenomenon, the reader can easily tell that Wallace was continually thinking about geography, geology, astronomy, social sciences, justice, culture, anthropology, economics, and on and on. He was continually observing, continually recording, and continually consolidating his thoughts. His scholarly example – and his gracious bearing and commitment to openness – is one that we need to foster more and more in our current era.

So, sometime over the next few days, why not spend some time dipping into a bit of what Wallace has written, and see how his scholarly and personal example might be important for our scholarly endeavors today and into the future.

Along with some of the links above, here are a few other resources to get you started:

As Attenborough says in his video:

For me, there is no more admirable character in the history of science.

It could not be said better.

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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