Reading 365 (or, rather, 230) papers a year

Tags

#230papers, papers, reading, time management

A couple of years ago, a number of scientists on Twitter decided to try and read 365 scientific papers in a calendar year. Joshua Drew summarized his efforts and results quite well, and Jacquelyn Gill provides a great introduction to the motivation for “365 papers” (among other efforts) on the Contemplative Mammoth. And over the holiday break, as I was sorting out my “To Read” folder, I realized that it was getting rather full, and I needed a strategy to get that number down from about 972 to something more… manageable.

I think this is a neat idea, and by joining together with others completing the same goal can act as encouragement (something we use with Shut Up and Write sessions), but it can also make those not participating feel guilty about not keeping on top of their own “To Read” lists. The Twitter hashtag #365papers also explicitly implies that all 365 days of the year are available for work, which is far from the truth. At my organization, we budget for 230 working days in a year, which accounts for weekends, statutory/bank holidays, annual leave, and other non-work days (e.g., professional development). So I’m going to try for #230papers.

The astute among you will have noticed that 230 < 972, and there’s a very high probability that papers published in 2017 will be of interest to me, so it’s certain that my “To Read” folder won’t shrink by much.

It turns out that 972 is not less than 230.

So in addition, I’m adopting a ruthless culling approach: if I can’t remember why I downloaded the paper after reading the abstract, I’ll delete it (unless it appears to have taken some effort to obtain, or is from an obscure source).

I’m also hoping this will also kick-start my blog posts this year, which have lagged of late. I certainly won’t write about every paper, but I’ll post a list of papers and monthly tallies below for those playing along at home, and I’ll try to tweet links periodically with the #230papers hashtag.

Here’s to a brain-expanding knowledge-assimilating 2017!

See the full list here.

Best Practices

Tags

science studies, software, taxonomy, writing

When I started my career in science more than a decade ago, I had no idea that I would find aspects of how and why we science so interesting. When I first came across scientific papers on these subjects (rather than on birds or mercury or migration, which I was studying at the time), I put them in a folder called “Thought Papers”, and even blogged about one of them here.

I think it was this folder of papers (which now stands at >100) has generated more “deep thought” about science than an equivalent number of ecological / marine / conservation papers. I’ve even written what I would call a “thought paper” on the problems with unpaid work, which is prevalent in science. But lately I’ve wondered about the efficacy and impact of these contributions.

Back in 2012, Fields Medalist Tim Gowers initiated a campaign dubbed “The Cost of Knowledge” aimed at publishing giant Elsevier, wherein signatories pledged to not serve on editorial boards, review for journals, or submit their work to titles published by Elsevier in protest of its practices. This week, an analysis published in the journal Frontiers in Research Metrics and Analytics examined the publishing record of approximately 1000 signatories from psychology and chemistry (out of the roughly 16,000 signatories in total) who had pledged to not publish in an Elsevier title, and found that more than a third had actually done just that in the intervening four years. They outline a number explanations and interpretations of the data, and I encourage your to check it out.

My point here isn’t to dive into the potentially questionable business practices of Elsevier, but to contemplate the laundry list of things that significant portions of the scientific community view as “bad”, and that have been pointed out in a variety of fora, yet continue. One could add to this list the proper citation of computer packages/software or taxonomic authorities, reporting effect sizes rather than just p-values, acknowledging reviewers, putting figures & legends together, making meaningful statements about author contributions, using reproducible methods (or describing methods in sufficient detail that they could be recreated), managing and archiving data, the relative importance of the Impact Factor, and more. In fact, PLOS Computational Biology has a very successful series called “10 simple rules“, which invited authors to propose, well, 10 simple rules for their topic of choice.

The social scientists among you are probably all to familiar for the reasons why these practices, which as a scientific community we generally see as Good Things, aren’t adopted more widely, or are adopted in only a “flash in the pan” way, and quickly die off. I certainly don’t expect the ideas espoused <5 years ago to propagate across all of Science in such a short time, but I find myself exasperated when, for the nth time, I mention these ideas and am met with a blank stare.

One reason for this is that very often these ideas are broadcast to those who are already likely to espouse them (the whole “preaching to the choir” syndrome). Most recently, as Morgan Jackson pointed out on Twitter, a paper that highlights the importance of citing taxonomic papers was published in a taxonomic journal.

The other is that science is a very distributed community – there’s no Head of World Science, and even influential organizations like the Royal Society, or the National Academy of Science of the USA, or Росси́йская Aкаде́мия Hау́к (Russian Academy of Sciences) have little, if any, influence on their members to follow what might be called “best practices”. Ultimately, it comes down to journal editors and reviewers (and even if I make some of these points as a reviewer, they can easily be ignored by authors or over-ruled by editors). And given that there are ever more suggestions for How To Science each year, it can be tough to keep up with them all.

As a MSc student, my supervisor mandated that we attach a checklist to the front of our manuscripts for his review (yes, we printed them off!). Were all tables necessary? All figures? Were any duplicative? Were all references cited listed, and vice versa? Had it been reviewed by another lab member? Were pages numbered? He would only read it if these were all checked off. Is it time to think about a broader checklist? True, many journals have something equivalent in their Author’s Guidelines, but they’re often ignored or inconsistent.

While I could come up with some things with which to populate such a list, it’s likely to be very field specific. And even then, dear reader, I’m likely already preaching to the choir, and adoption, anyway, will be far less than 100% and likely decrease with time.

Does technology make field work less immersive?

Tags

field, field camps, glow in the dark kitchen spatula ping pong, technology

Since 2001, I’ve spent the better part of my summers in wonderful, amazing locations for weeks at a time.  From the Bay of Fundy (home to 10-12m tides that come in and out twice a day), to a 4000-foot active volcano with about 2 million seabirds in the far western Aleutian Islands, to the largest Atlantic puffin colony in North America, I’ve soaked up the natural world.

But I fear the experienced I had (and helped others have) is in peril.  The threat, you see, is nearly everywhere and spreading fast.  It’s teh internetz.

Now before you accuse me of being a Luddite, and throwing my sabots into the cogs of progress, hear me out.  I’m a frequent (habitual?) user of online tools (like this blog), and I have an unhealthy relationship with email checking (which I really need to work on, I know).  But despite these, when I find myself on a seabird island, or on a boat at sea, or waking up at 3am to catch swallows underneath highway overpasses, anything connected to the internet is far from my mind.

The Before-time

Aeons ago, when phones were something that were attached to a wall with a giant wheel of numbers (and often a little but after this), the evenings in field camps were often spent in conversation, playing cards, engaging in “extra-curricular” natural science, reading, writing, thinking, exploring (or playing glow-in-the-dark kitchen-spatula ping pong).  I loved this “free” time in the field, because it meant I could often catch up on books I didn’t have (find) time to read during the academic year. (In a distinctively non-Luddite approach, I find carrying an e-Reader much easier than my former cadré of 15-20 books, especially when landing/loading field camps.)

In 2005, I recall one particular discussion about whether we should haul out the old 1970s vintage TV from the closet, and try to find the VCR to hook it up and watch Pirates of the Caribbean one rainy evening (we were at an active light station with ample power, and living in an old Coast Guard house).  “Really? Watch a movie in the field?” I recall one team member saying as if the concept was totally foreign.  Because it was.  In the end, we did manage to drag the TV and VCR out, find the video cassette, and spent the night laughing and eating popcorn.

Double-click, then swipe and tap

Fast forward a few years.  Now, nearly everyone has their own laptop, and their own TV shows and/or movies downloaded or on DVD.  Many field camps (especially those run by large organizations) are now equipped with internet connections, if not wifi and full-on cell coverage, and many evenings are spent sitting around the common room checking email, and basically being “in the office”.

Why?

For me, being in the field is an immersive experience.  Whether my tent is flapping at 3am in 40-knot winds (forcing me to get up, go to the temporary building, and read Barney’s Version by headlamp), or the auklets flying in at sunset are putting on what we affectionately called “The Show”, it’s all part of being in the field.

It ain’t all bad

Things like smart phones can be used extensively by those in the field, epitomized by this recent paper by Amber Teacher.  But as has often been said, with great power comes great responsibility.  Sure the phones can be used to figure out a bird call, or connect with experts through Twitter, but they can also be used for email, and text messages – the very things I enjoy not having in the field.

I’ve heard from more and more colleagues that this year, they’ve resolved to spend less time online.  I achieve the same goal through immersive field work.  And I’ve been fairly lucky so far in that my camp-mates have all generally shared a similar philosophy when it comes to personal technology in the field.  But now, movie nights are more common, and on our research island in Newfoundland, there’s cell coverage, which is fantastic for field safety and coordinating with folks in the mainland and keeping in touch with family.  I wonder how long, though, before evenings spent around the table playing Dutch Blitz are behind us.

And I, like many I’m sure, enjoy the respite from being instantly contactable through myriad channels (email, phone, office, Twitter, Facebook, telegraph station).  I love writing and outlining new projects in the field (particularly in the mornings with a pot of tea and CBC Radio before everyone else is up).

 

So how do you approach the non-science parts of field camp life, and the increasing presence of technology?

 

Sex, gender, and when “modern” sensibilities go wrong

Tags

birds, gender, sex, writing

Ladies and gentlemen, the following may come as a shock, but sex and gender are NOT the same thing.  Now, before you get your knickers in a knot, let us visit the most hallowed of resources on the Queen’s English – the Oxford English Dictionary.

So sayeth the OED: the word sex is derived from middle French (c. 1200), and was first used to describe male and female humans around about 1475.  Now, this esteemed tome also mentions the recent trend of conflating sex with gender (which we’ll define shortly).  Some time in the 1960s, gender began to replace sex when describing males and females.

Gender is so aptly defined by the OED that I’ll reproduce the entire thing:

3b. – The state of being male or female as expressed by social or cultural distinctions and differences, rather than biological ones; the collective attributes or traits associated with a particular sex, or determined as a result of one’s sex. Also: a (male or female) group characterized in this way.

Put simplistically, gender is one’s conception of self, while sex refers to the biological reproductive bits betwixt our legs (for the moment, I’ll acknowledge, but not discuss the much more complex cases of intersexual, and others).

Putting these definitions to use, humans have both a biological sex, and also a gender identity.  In the majority of cases, these are cis (or the same), where biological males self-identify as males, and biological females self-identify their gender as females.  When these two do not align, an individual may identify as transgendered or transsexual.

But I digress.  The important point is that gender is a self-bestowed identity, while sex is a biological phenomenon related to reproduction.

Science is full of attempts to over-complicate, and loves jargon.  Why say “methods” when you can say “methodology”?  I think that a part of this desire to appear more sophisticated or erudite, and less vulgar in scientific writing has resulted in the wholesale replacement of sex with gender by some authors, editors, and copyeditors.

Lest there be any misconception about the point of this post: sex ≠ gender.

It is impossible to identify the gender of a butterfly (the butterfly’s internalized concept of self), while it’s sex can be readily apparent.  The same goes for fish, birds, mammals, amphibians, tardigrades, ctenophores, or sea urchins.  Until we have a way to convey the human concept of gender to these animals, and understand their response, we will never know their gender (or if indeed they have a gender at all, or multiple genders for that matter).  So when writing about differences between male and female animals, stick to sex, and avoid gender.

And if you’re curious, just flip through the latest issue of your organismal journal of choice and see how the authors describe males and females.  I mostly study birds, so I had a quick flip through the 2009 issues of a number of bird journals to see what prevailed:

Journal	Sex	Gender	% Gender
Auk	41	0	0%
Bird Conservation International	7	1	13%
Bird Study	14	1	7%
Condor	38	0	0%
Ibis	21	4	16%
Journal of Avian Biology	25	3	11%
Journal of Field Ornithology	18	1	5%
Journal of Ornithology	30	4	12%
Journal of Raptor Research	17	1	6%
Ornis Fennica	5	0	0%
Ringing & Migration	8	0	0%
Waterbirds	18	5	22%
Wilson Journal of Ornithology	0	36	100%

At the time, the Wilson Journal of Ornithology had a policy to replace sex with gender (a policy that, I can gladly report, has now been reversed).  What’s evident from this table is that just about every journal has a mish-mash that largely depends on the author (only The Auk and The Condor had a copyediting policy of replacing gender with sex).  Yet there’s an increasing use of gender (rather than sex) in journal titles in the sciences.

Drop the pretence, and the desire to overly-technify the most simple concept: sex.

 

* And before anyone asks, I would argue that the bellbird in this article is more properly “intersex”, not transgender.

** And before any botanists or mycologists start filling my inbox with complaints, yes, I know plants have male and female sexes. Fungi apparently have 36,000 sexes!

Too many endangered tigers in Nepal?

Tags

great auks, Nepal, polar bears, Sea of Slaughter, tigers, wildlife conflict, wolves

Sorry for the lack of posts this week – I’ve been inundated with lab work and preparing samples for stable-isotope analysis.

Last week, the BBC reported that Nepal would start culling wildlife, including endangered species, because of an increase in human-wildlife conflict.  As long as there have been humans and wildlife, there’s been conflict – with responsibility on both sides.  Though lately, I think the balance has shifted, and humans have become the aggressors, and it’s hard not to see why.

Last summer, hunters in New Brunswick and Newfoundland each shot and killed the first wolf in those provinces in over a century, the hunters apparently mistaking them for the smaller bobcat or coyote.  And we wonder why some species never seem to recover? (note the smile on the hunter’s face in the photos that accompany these articles)

In his must-read book Sea of Slaughter, Farley Mowat* paints a picture of what North America looked like before European colonization, and the brutal accounts of extinction, exploitation, and destruction that was left in the wake of fishermen, colonists, and explorers as late as the early 20^th century.

“These [Great Auks] are as big as geese … and they multiple so infinitely upon a certain flat island that men drive them from hence upon a board, into their boats by the hundreds at a time, as if God had made the innocency of so poor a creature to become such an admirable instrument for the sustenation of man” – Richard Whitbourne, c. 1600

“Never in my life did I regret the want of ammunition so much as on this day … Thus ended in disappointment, the boblest day’s sport I ever saw: for we only got one skin, although we had killed six [polar] bears” – George Cartwright, 1778

“The behaviour of Robert Peary, one of the two North American claimants to the discovery of the North Pole is typical … The treatment meted out to [polar] bears by Peary’s expeditions [alone resulted in the destruction of at least 2000 of them” – Farley Moway, “Sea of Slaughter”, 1983

A couple of years ago, Josh Donlan and Chris Wilcox, in a very controversial paper in Nature, arguing that we should reintroduce large megafauna to North America to “restore” the ecosystem.  While I think their argument was not intended to be serious (sabre-toothed Smilodon cats roaming outside Toronto or Vancouver might irk some), it raises an important point for restoration ecology: restoration to what?  As Mowat points out in his book, eastern North American ecosystems were pillaged starting 500 years ago (those on the Pacific coast a bit later, and in the centre of the continent later still).  But is restoration to a state similar to 100 years ago actually “restoration”?  And, as Donlan and Wilcox point out, why stop with Vancouver Island marmots and wood bison?

I did my PhD at Memorial University of Newfoundland, and spent 4 years on the island.  It’s one of the most degraded ecosystems in Canada.  Numerous endemic subspecies (e.g., wolf, pine marten) have been extirpated or endangered, and countless introduced species (from rats to moose) wreak havoc on the native ecosystem and prevent the reestablishment of native fauna.  Newfoundland and Labrador has the lowest population density of any province in Canada (though this is, in large part, due to the mainland part of the province), and is home to just over 500,000 people.  If ever there was a case where human-wildlife “conflict” should be reduced, it’s here.

But if we want wolves back in Newfoundland, and tigers in Nepal (and why not?), we can’t keep shooting them.

*Full disclose: he and I are actually distant cousins.

Small museum collections with big impacts

Tags

AMNH, museums, ROM, UAM

I have been busy in the lab this week, but I’m working on a post that should appear on Friday.  As a teaser: I’ll discuss Nepal and Great Auks.

I wanted to point out a letter in this week’s Nature from Kevin Winker and Jack Withrow at the University of Alaska Museum of the North in Fairbanks, AK (it’s publicly available).  They highlight the large contribution that their relatively small collection has made to avian research.  The UAM has less than 10,000 bird specimens, which is tiny (by comparison, the American Museum of Natural History has ~875,000 bird specimens, and the Royal Ontario Museum about 214,000).  Yet, as an institution, the UAM has an h-index of 42 (meaning that 42 of its papers has been cited at least 42 times).  As someone who works with museums fairly regularly (although I haven’t had the chance to work with UAM), this is a nice bit of publicity that will hopefully influence those who fund such important institutions.

A tray of the Critically Endangered Kittlitz’s Murrelet (Brachyramphus brevirostris) at the American Museum of Natural History. © 2010 ALB.

Should the method (or site) drive the questions?

Tags

freeman dyson, ideas, peter galison, thomas kuhn, thought paper, tools

When I started my PhD, I also started a folder of what I called “thought papers”.  These weren’t related to my research, but were papers that made me stop for a minute and think about an issue.  Mostly, they were editorials or commentaries (many in BioScience, Nature, or Science, but also in the Journal of Wildlife Management, or Avian Conservation and Ecology*).  Should scientists be advocates? Is there a double standard among conservation biologists (the old “do as I say, not as I do” argument)?  How can we improve the process of peer-review?

These “thought papers” will form the basis of many of my posts, so let’s get started.

Last month, physicist Freeman Dyson wrote a commentary in Science comparing the current state of research in the physical sciences to the 1950s where two camps sought to lead the way: those driven by ideas, and those driven by post-war technology and tools.  Dyson concluded that, at the end of 2012, the two camps were neck and neck in terms of the exciting discoveries they produce.

The same can be said of the biological sciences in general, and ecology in particular.  In the Kuhnian camp of ideas, we have the great luminaries: Hutchinson, Lotka, Volterra, Hubbell, and Reznick, to name a few.  Their ideas (and experiments) on competition, biogeography, and evolution are foundational to population and community ecology.  In the Galisonian camp of technologies, we have everything from Mullis, and Hebert (PCR and DNA “barcoding”) to the continued miniaturization of biologgers that can now be used on small songbirds.

There’s no doubt that these tools have been great advances in ecological research, and the same could be said for the ideas.  But which should drive research?

In the early days of a new technique or tool (e.g., small biologgers, stable-isotope analysis, to name a couple), the number of studies that are basically “Technique/tool X on species Y in location Z” can be high.  These early days (perhaps we could call them “academic puberty”?) can last a long time – up to 15-20 years in my experience.

The first few times these tools are used, it’s new and exciting.  But as costs decrease and the tools become more available, late adopters begin where the field began, not where the field is now.  As a concrete example, the decrease in price and increased availability of inductively-coupled plasma mass spectrometry (ICP-MS), an instrument that can simultaneously measure concentrations of dozens of elements from vanadium to toxic elements like lead, mercury, arsenic, and cadmium has resulted in a proliferation of studies that simply document the concentrations of these elements in a given tissue of a given species at a given site.  Are these studies without merit?  Of course not.  But can we, as a community, make better use of research dollars and equipment time?  Absolutely.  How?  By shifting from these descriptive (and mostly local interest) studies to hypothesis testing, meta-analyses, and comparative work.

Since this blog is titled “The Lab and Field” (which sort of sounds like an old English pub), do we see the same phenomenon in field studies?  I think so.  But instead of the ideas/tools dichotomy (which is, itself, perhaps a false one), we have the ideas/field site or ideas/focal species conflict.  Though this is not entirely separable from the application of tools, since in many cases, researchers working at a particular site or with a particular species or group of species will often use these systems to apply the new and exciting tools, irrespective of whether their system is necessarily a good one in which to use these tools.

By now, you’ve probably realised that I’m more of a Kuhnian than a Galisonian, preferring ideas to tools.  But like most things, I think there’s a Kuhn-Galison spectrum, not two absolute “camps”.  I do use lab tools to advance my understanding of natural systems, but I’m predisposed to use the tools I know (stable-isotope analysis, for example).  So I probably look for questions or ideas that can be developed using these tools.

And like Freeman Dyson, I recognize the need for the development of both tools and ideas – one without the other leads to an incomplete understanding of natural systems. The trick is finding the right balance.

 

*Full disclosure: I’m on the ACE editorial board.  Check us out! www.ace-eco.org