Showing posts with label Scholarly Journals. Show all posts
Showing posts with label Scholarly Journals. Show all posts

Thursday, October 7, 2021

Finding the Mother Tree

 Suzanne Simard, "Finding the Mother Tree: Discovering the Wisdom of the Forest," Alfred A. Knopf, 2001. 

I spent the day writing up my planting reports before mailing my envelope of yellow needles to the government lab to have the nutrition levels analyzed and checking the office for reference volumes about mushrooms.  There were plenty of resources about logging, but books on biology were scarce as hen's teeth.  I called the town library, glad to learn that there was a mushroom reference guide on their shelves.  [p. 24]

...

I collected the mushroom book and filed my report on the plantation but vowed to keep my observations quiet and do my homework.  I often feared I'd been hired into the men's club as a token of changing times, and my goose would be cooked if I came up with a half-baked idea about how mushrooms or pink or yellow quilts of fungus on roots affected seedling growth. [p.24]

...

Then I discovered what I was looking for.  After days of searching journals in the university library, I happened upon a new article by a young Swedish researcher, Kristina Arnebrant, who'd just found that shared mycorrhizal fungal species could link alder with pine, delivering nitrogen directly.  I sped through the pages, stunned. [p.121]

...

I dashed out of the stacks and called Robyn from a phone in the foyer.  [p.121]

COMMENT

Simard describes instances where library materials offered answers to her forest observations.  The book is an excellent account of the progress of scientific research, describing a process of observation, literature research  and review and experimental design.  However, by the last chapter Simard says that the scientific method is too limited to fully understand the complexity of the world.  She writes

 I'd been taught in the university to take apart the ecosystem, to reduce it into its parts, to study the trees and plants and soils in isolation, so that I could look at the forest objectively.  This dissection, this control and categorization and cauterization were supposed to bring clarity, credibility, and validation to any findings.  When I followed these steps of taking the system apart to look at the pieces, I was able to publish my results, and I soon learned that it was almost impossible for a study of the diversity and connectivity of a whole ecosystem to get into print. [p. 283]

Simard finds that her "discoveries" were already part of indigenous knowledge, but of course there was no published record of this knowledge and even if there had been, forresters wouldn't have read it.   

 

 

 


Thursday, July 23, 2020

Follow the Science. Back to the Classroom

Dale R. Wagner.  "Follow the Science. Back to the Classroom." Salt Lake Tribune, July 22, 2020.  https://www.sltrib.com/opinion/commentary/2020/07/22/dale-r-wagner-follow/

     There is no shortage of legitimate peer-reviewed research on the topic. Combining the search terms “COVID-19” with “children” and “school closure” resulted in 143 articles in PubMed, a database of the National Library of Medicine. The journal citations that accompany my statements are “open access,” meaning that anyone can view the article online in its entirety without a fee or journal subscription.

     

 COMMENT

     In this editorial the author is using open-access articles in scholarly journals to consider COVID-19 studies.  Many journals have made COVID-19 research publicly available, at least temporarily.  The National Library of Medicine maintains the database that makes these articles easy to find. 

Thursday, June 4, 2020

How to Read Coronavirus Studies Like a Scientist

Carl Zimmer, "How to Read Coronavirus Studies Like a Scientist." New York Times, Jun 2, 2020, p. D7.

     The National Library of Medicine's Database at the start of June contains over 17,000 published papers about he new coronavirus.  A website called bioRxiv, which hosts studies that have yet to go through peer review, contains over 4,000 papers.
     In earlier times, few people aside from scientists would have laid eyes on these papers.  Months or years after they were written, they'd wind up in printed journals tucked away on a library shelf.  But now the world can surf the rising tide of research on the new coronavirus. The vast majority of papers about it can be read free online.
     But just because scientific papers are easier to get hold of doesn't mean that they are easier to make sense of.  Reading them can be a challenge for the layperson, even one with some science education.  It's not just the jargon that scientists use to compress a lot of results into a small space. Just like sonnets, sagas and short stories, scientific papers are a genre with its own unwritten rules, rules that have developed over generations. 
COMMENT

   This article offers a variation of the library "dusty shelves" with unread articles tucked away until they were rescued by online distribution. Many publishers have made COVID-19 studies open-access, but in fact there are usually paywalls between laypeople and scientific journal  literature.   The article offers helpful advice for how to approach scientific literature.  The article mentions NLM databases and a medical pre-print archive.  Medical information has its own unique information system because it can be so urgent for doctors and public health agencies to have up-to-date research. 

Thursday, February 14, 2019

It's a Dog's World in the Lab

James Gorman. “It’s a Dog’s World in the Lab: When it Comes to Research, Scientists Favor Canines Over Cats by a Large Margin.” New York Times, December 30, 2018 p.F14 [Originally Published Feb. 26]

And now the numbers: A search of Pub Med, a database that include most biomedical journals, yielded 139,858 results for cats and 2,850,000 for dogs.  These are sample searches, of course, and don't say much about the kind of research that was undertaken. As for journalism, my searches on the news database Nexis for dogs and cats kept returning more than 3,000 hits, which my screen warned my would take a long time to retrieve.  So I settled for searches of “dog genome” and “cat genome.” The result, 20 for dogs, 6 for cats.  The dog genome was sequenced before the cat genome.      I would caution against concluding anything based on this haphazard browsing other than the results do back up the researchers’ sense that there’s more research on dogs. 
COMMENT

      Journal databases provide a quick and dirty estimate of the relative number of scientific studies.  The researcher used Pub Med for scholarly journals and Nexis for news, two databases that most librarians would be familiar with. One assumes that the author was a savvy enough searcher to realize that the letters "CAT" and "DOG" don't always mean felines and canines.

   The author does not actually say whether these databases were from a library or not.  Pub Med is a service of the National Library of Medicine, though, so it's technically a library regardless. Nexis is an expensive subscription so a library is the most likely point of access.

     When people search online databases they often miss the fact that they are a library service.  Scholars at universities sometimes claim that they never use the library because they can find all the articles they need online.  These researchers don't realize that the library has paid for their access or that convenient links to articles from Google Scholar are thanks to library software that integrates database subscriptions into the search.

A more formal version of this kind of citation analysis is frequently used in bibliometric studies to trace the development of scholarship-- say the use of the word "Sustainability" after the publication of the Brundtland Report, [1] or the rise of the word "Anthopocene" as a metaphor for human influence on the Earth. [2]
   
   [1] Schubert, András, and István Láng. "The literature aftermath of the Brundtland report ‘Our Common Future’. A scientometric study based on citations in science and social science journals." Environment, Development and Sustainability 7, no. 1 (2005): 1-8.


[2] Belli, Simone. "Mapping a Controversy of our Time: The Anthropocene." inquiry 30, no. 2 (2004): 225-248.


Brondizio, Eduardo S., Karen O’brien, Xuemei Bai, Frank Biermann, Will Steffen, Frans Berkhout, Christophe Cudennec et al. "Re-conceptualizing the Anthropocene: A call for collaboration." Global Environmental Change 39 (2016): 318-327.

Sunday, February 10, 2019

The Overstory



Richard Powers, The Overstory, WW Norton & Company, 2018.

NEELAY MEHTA

     He works for months on a role-playing space opera slated to be his greatest giveaway yet. The graphics are sixteen-bit high-res sprites, come to life in sixty-four glorious colors.  He heads out on a hunt for surreal bestiaries to populate his planets.  Late one spring evening he winds up in the Stanford main library, poring over the covers of golden age pulp sci-fi magazines and flipping through the pages of Dr. Seuss. The pictures resemble the mad vegetation in those cheap Vishnu and Krishna comics from his childhood. [108]

DOUGLAS PAVLICEK

     He's missed the complimentary continental breakfast by four hours.  But the clerk sells him an orange, a chocolate bar, and a cup of coffee, three priceless tree treasures that get him to the public library.  There he finds a librarian to help him research. The man pulls several volumes of policy and code off the shelf, and together they search. The answer isn't good.  Thing Two, that loud bastard, was right. Planting seedlings has done nothing but green-light more colossal clear-cuts. It's dinnertime when Douggie accepts this fact beyond all doubt.  He has eaten nothing all day since his three tree gifts. But the idea of eating again-- ever-- nauseates him. [187]
    He doesn't leave Portland right away.  He heads back to the public library, to read up on guerrilla forestry.  His old librarian friend there continues to be more than helpful.  The man seems to have a little thing for Douggie, despite his aroma. Or maybe because. Some people get off on the loam.  A news story of an action near the Salmon-Huckleberry Wilderness gets his attention-- an outfit training people how to blockade logging roads.  [206]

PATRICIA WESTERFORD

     Journal articles have always been hard enough.  Her years as an outcast come back to her each time she writes one, even when she's only one of a dozen coauthors. She feels even more anxiety when others are on board.  She'd sooner retire again than inflict on those beloved colleagues anything like what she once suffered. Yet even journal articles are a walk in the woods compared to writing for the public.  Scientific papers sit in archives, matters of indifference to almost everyone.  But this millstone book; She's sure to be mocked and misunderstood in the press.  And she'll never earn out what her publisher has already paid. [219]

ADAM APPICH

     He squeezed through a channel in the milling crowd, alongside the People's Library.  He can't help grazing the shelves and bins. There's Milgram's Obedience to Authority, marked up with a  million tiny marginal words. There's a collection of Tagore. Lots of Thoreau, and even more copies of You vs. Wall Street.  Free circulation, on the honor system.  Smells like democracy to him.
      Six thousand books, and out of all of them all, one small volume floats up to the surface of its heap like a fossil coughed out of a peat bog. The Golden Guide to Insects.  Bright yellow-- the only real edition that classic ever had.  In shock, Adam picks it up and opens to the title page, ready to see his own name gouged there in smudgy no.2 all-caps balloons.  But the name is someone else's, inked in Palmer Method cursive: Raymond B. [427]

DOROTHY CAZALY

     The knock gets faster and louder.  She crosses through the living room, reviewing in her head the defense of their property rights that Ray has helped her prepare.  She has spent days at the public library and the municipal building learning how to read local ordinances, legal precedent, and municipal code.  She has brought back copies to her husband for explanation, one stunted syllable at a time.  She has pored through books, compiling stats on just how criminal mowing, watering, and fertilizing are, just how much good a reforested area and a half can do. All the arguments of sanity and sense are on her side. [468]

COMMENT

      The nine main characters in this novel use libraries in various ways that turn out to be pivotal to their life stories. The Dr. Suess book used by Neelay, the computer game designer, is pretty clearly The Lorax; Two of the characters use the library for civic engagement to investigate laws and policies, leading to acts of civil disobedience in defense of trees; The small-town librarian is portrayed as helpful, and maybe even a bit  conspiratorial in support of environmental activism; At the Occupy Wall Street library, an explicit metaphor for Democracy, one character reconnects with his childhood innocence, which leads him to an act of noble self-sacrifice.

     In her evaluation of the academic library Patricia, a field biologist, describes the contrast between unreadable scientific information and the stories that people tell to actually make sense of the world understand (another character, a psychologist named Adam Appich,  makes the same point from a different perspective), and a third storyteller is not a library user but a mystic who hears the voice of the trees directly without the filter of  science or human interpretation.

     These libraries are not just incidental plot devices.   In the narrative they offer enlightenment. The the library is almost like an oracle, offering up a book or new article that shows the next step.  This book is not anti-science, but one of the themes is about information--  laws and policies can be wrongheaded and scientific prejudices can prevent people from connecting with the mysteries of the world around them.  Nonetheless, the truth is there for people who take time to do their library research.
      

Monday, January 21, 2019

The Fifth Risk


Michael Lewis, The Fifth Risk, W.W. Norton & Company, 2018.

     Kathy hadn't taken her brother seriously.  You really think they're going to hire an oceanographer? A girl????      
     A few weeks later she ran across the call for astronauts again, this time in a science journal. They really did seem to want women scientists. And she sensed that she might be the sort of woman they were looking for.  "I never brought normal girl books home from the library," she recalled.  "I was fascinated by maps and the stories they told." She was handy, too, and quick to figure out how things worked. [p. 137]

COMMENT

     Kathy Sullivan did become an astronaut.  Then she joined the National Oceanic and Atmospheric Administration (NOAA) and figured out how to re-frame tornado warnings in order to get people to actually pay attention to tornado warnings and take cover.  That is to say, her scientific work has saved the lives of many people.

     She describes her own identity as a scientist in terms of library borrowing -- a  scientist is someone who doesn't read "normal girl books."  This comment relates to a previous post, What are We Teaching Boys when We Discourage Them from Reading Books about Girls?  in which a librarian (who should know better) shames boys for reading a "girl's" book.  Likewise, Sullivan must have felt some degree of adult disapproval for reading "boy's" books.  Why else would she think that an interest in maps was not "normal" for girls?   (I also happen to love maps)

    The library offers a valuable kind of  anonymity.  A child with a library card can take a book off the shelf and take it home to read without ever asking for anyone else's permission.  This freedom for kids to chose what to read, even if adults or other kids don't like it, is mentioned over and over in library stories as a formative experience in the search for identity.

Friday, November 9, 2018

The Best American Poetry, 2018


David Lehman series ed., Dana Gioia, guest ed., The Best American Poetry, 2018, (Best American Poetry Series) Scribner Poetry, 2018.

     My editorial method was simple and unoriginal.  For twelve months (starting October 2016) I spent two or three hours each day reading new poetry. I read through every journal I could find as well as dozens of online journals. I bought piles of unfamiliar small magazines and subscribed to new journals. I read every issue of every literary magazine in my university's large periodical room.  When I traveled, I brought along a separate bag of journals to read on the plane or in the hotel room.  Meanwhile the series editor sent me weekly packets of poems that had caught his attention.  I initially wondered if David Lehman might want to press his suggestions. He is a persuasive advocate for the poetry he loves.  Lehman, however, gave me complete editorial autonomy.  I told no one outside my family that I had taken on the assignment. I didn't want to be lobbied by poet friends and acquaintances.
    I'm not sure how many thousands of poems I read. I surely broke the five-digit mark. Every time a poem grabbed my attention, I earmarked it or printed it out for rereading. My studio became a mountain range of periodicals, printouts, and photocopies. The most interesting part of the process was rereading and comparing the hundreds of poems that had made the first cut. Week after week I read and sorted the poems into three scientific categories -- Yes, No, Maybe.  After much agonizing, I made the final selections. 

COMMENT 

     This tale of extreme research raises a question: Why didn't the university library's large periodical room have more poetry journals? Actually, I can answer that one myself.  Many years ago during a budget shortfall the library where I worked slashed periodical subscriptions. The poetry journals were the first to go.  They weren't expensive -- we could have bought all of them for less than the cost of one science journal subscription.  But library use statistics indicated that almost nobody ever read them. 
     One problem was, most literary journals weren't listed in any of our indexes. Nowadays, Project Muse indexes a few of the well-known poetry journals (most of them represented in this book according to an appended "List of Magazines where the Poems were First Published"). But there are also zillions of small-press poetry journals. In order to submit to them, the poet sends in a few poems with a small fee that presumably keeps the journal going. After a while, this process of fee-based submission becomes deeply discouraging. It feels like everyone submits poems but nobody reads. 
     Yet libraries are nonetheless doing a disservice by ignoring poetry.  The mistake, I think, is trying to focus on  "important" poetry. There are a few poets who are famous enough so that their books are likely to circulate (I'd say Mary Oliver, Wendell Berry, Billy Collins, Maya Angelou, etc...  I doubt that Gioia particularly likes any of them).  However, I'd argue that the  most important poetry for librarians to collect is localized, written by the local community of writers (including at local institutions of higher education) but also (don't laugh) nature poetry. Gioia identifies an emerging trend of politically charged place-based poetics.  He writes, "The nature poem had become the major vehicle for political meditation and protest.  The bright innocence of Walt Whitman's American Eden has been overtaken by Robinson Jeffers's dark prophesy of spacious modern civilization."
    While librarians were busy cutting poetry from our collections, the poetic form has re-emerged as an particularly  important voice responding to the slow emergency of the Anthropocene. The Dark Mountain Project explicitly makes the Robinson Jeffers connection, and in Uncivilised Poetics (Dark Mounain10) the editors write "What's the point of poetry when the streets of Syria have been bombed beyond recognition? What's the point of poetry when the permafrost is melting?  But poetry matters because it offers an alternative reality --it refuses the logical, reductionist, materialist aspects of industrial cult; aslant, it invites us to feel our way in the dark." If libraries want to capture this important voice, they are going to have to rediscover poetry. 
    
   
    
    
     




Thursday, November 1, 2018

Discovery Interrupted

Jeffrey Friedman, “Discovery, Interrupted: How World War I Delayed a Treatment for Diabetes and Derailed one Man’s Chance for Immortality," Harper’s, vol 337, no.2022, Nov. 2018, pp. 45-54.
My research began as a browsing of letters and laboratory notes on the Rockefeller University archives, and later expanded to include study of the materials housed at Yale, Johns Hopikns, and the American Philosophical Society in Philadelphia, as well as conversations with members of Kleiner’s family. I published an earlier consideration of the scientific aspects of Kleiner’s story in Nature Medicine, a medical journal, in 2010. 

COMMENT

     This description of the research process is given in a footnote.  Perhaps Friedman is used to writing for journals and couldn’t bear to leave out the citations for a popular magazine. Or maybe he just found digging around in the archives to be such an interesting and delightful passtime that he wanted to tell us about it.            
     The article is about an obscure researcher named Israel Kleiner who almost discovered a cure for diabetes (the people who eventually did won a Nobel Prize for medicine in 1923). Friedman writes, “I immediately wanted to know more about Kleiner and his story especially given my own interest in hormone research.”  
     The research problem— Kleiner was not at all famous. He worked alone in his lab. His few published journal articles, including one “masterpiece,” were written without co-authors. He later became a college administrator. What documentation of his life existed was in records from the places he had worked and in the memory of people who knew him. What Friedman discovered in the archives is a kind of bureaucratic tragedy. Even though Kleiner was on the verge of a major breakthrough, the director of the Rockefeller Institute fired him because he thought infectious disease research was more important than diabetes research. After all, in the era before antibiotics soldiers died from infections, not from diabetes.  (There may also have been anti-Semitism going on). Friedmam thinks the director lost sight of the value of pursuing knowledge for its own sake. He writes, “scientific inquiry is an arc of knowledge, a series of steps on a path toward a deeper understanding of the unknown, and the breakthroughs only come because of the body of knowledge that previous observations have built.”  Libraries store this body of knowledge in the form of scholarly journals. 
     All these years later, Friedman feels a sense of outrage on behalf of Kleiner. He writes, “I can say with certainty that under similar circumstances neither I nor most other ambitious scientist I know would have maintained Kleiner’s apparent sense of equanimity about his missed opportunity.” And yet it is still true that researchers can only do their work if they have funding and lab space.  No matter how objective science is, money is always political, and that means so is missing information in the scientific record. 

Friday, September 7, 2018

Branching Out



Nalini Nadkarni. "Branching Out," in Nature Love Medicine: Essays on Wildness and Wellness. ed. by Thomas Lowe Fleischner, 2017, pp. 27-40.

                Although immense amounts of knowledge are contained in the science libraries around the world, rates of deforestation, climate change, species invasion, and over-consumption if tree-derived products are increasing.  Humans— especially those living in urban environments and working in windowless cubicles— are more and more separated from their connections to trees, soils and wind.  Midway into my academic career, I realized that communication of all my scientific findings to scientists — through my academic papers and talks at ecology conferences —did very little to fulfill my childhood dream of being a grownup who protected trees. [p. 31]

COMMENT

 The fact that so much academic writing has no market has misled some academic librarians into misunderstanding the motivation and interests of academic authors. Often, academic writing is an indirect path to the rewards of scholarly reputation, job promotion and successful grant applications, valued according to citation statistics. Some librarians therefore assume that scholars only care about reputation. However, in this case Nadkarni has a much larger goal. She wants her writing to create change in the world. This ambition places her squarely into an academic no-man’s-land between science and activism.

      There has long been an ongoing debate among scientists regarding the role of activism in the sciences and where to place appropriate limits. In his classic textbook, Fundamentals of Ecology (1953), Eugene Odum hoped that ecology would emerge as an  interdisciplinary bridge between science and society.  Instead what happened is the vocabulary shifted.  "Ecology" became more scientifically focused and integrated in Biology departments. The term “environmentalism” gained favor to imply ecological activism. In the academic environment, biological scientists criticized environmental studies as  being a “church of the environment” for idealistic students.  Eventually, the word “environmentalism” was deemed too narrow and after the Brundtland Report (1987) it was replaced by the word “sustainability." Sustainability was defined by a triple bottom line of ecology, economics and society, an attempt to deliberately pull science and society back together.  However, once again scientists balked at the fuzziness of social science and policy. The ideas of sustainable development, criticized as insufficiently evidence-based, spun off  “sustainability science” on the one hand and “resilience” on the other.  And so it goes.  As each new term becomes “tainted” by association with activism, scientists imagine that the next effort to save the planet will succeed due to rigorous standards of objectivity.

     In the end, Nadkarni was not able to create change within the context of pure science. Instead she engaged with humanities by inviting “forest novices” to help interpret what she was seeing —  artists, dancers, musicians, and indigenous people from the Arctic who have never seen a tree.  
 
     Academic librarians like to structure collections and organizations to mirror the structure of  academic departments at a university, but that means libraries are bound by the same limitations. Interdisciplinary ideas can end up marginalized, or caught in a tug-of-war of words and definitions. I wonder how many of the science libraries that have Nadkarni’s academic papers also have a video of the dance performance inspired by her work?

Wednesday, July 25, 2018

Six Degrees

Mark Lynas. Six Degrees: Our Future on a Hotter Planet. National Geographic. 2004. 
I had already begun to sift through the latest scientific literature on global warming. I knew from earlier research on High Tide that scientists have now made hundreds of projections— mostly based on complex computer models— of how future global warming will affect everything from corn crops in Tanzania to snowfall in the Alps. Occasionally a particularly striking study makes headlines in the newspapers, but the vast majority of these forecasts are burred in obscure specialist journals, destined to be read only by other climatologists. Most of these journals are taken by Oxford University’s Radcliffe Science Library where they sit—undisturbed for weeks or even years on their dimly lit shelves— just a mile or so down the road from my own house. I realized that it was almost as if I had a Delphic Oracle in my back garden or Nostradamus living next door— except that these scientific prophesies were already coming true. 
Earlier that year I had begun to make a daily pilgrimage down to the Radcliffe Science Library basement with my laptop, where as the weeks passed by I trawled through tens of thousands of scientific papers. Season came and went and I barely noticed. Each relevant article, I slotted into a spreadsheet—papers about two degrees of global warming went into the two-degree slot , papers about five degrees of global warming went into the five-degree slot, and so on. Not all were computer model projections— some of the most interesting material came from plaeoclimate studies, investigations of how variations in temperatures have affected the planet during previous global-warming events in prehistory. These records of past greenhouse episodes, I realized, could be analogs for the future; they, too, slotted into my six-degrees table according to the temperatures of the climatic period they represented. 
At the end I found I had something truly unique: a degree-by-degree guide to our planet’s future. 

COMMENT 

     This anecdote describes extreme research — a kind that few librarians imagine in any of our information literacy models. Lynas' goal is to construct an idiosyncratic index of scholarly journal articles based on their relation to global climate change. In order to do this he has become a library super-user, sorting through tens of thousands of scholarly articles (the final book lists 300 citations).  Because of the huge number and the reference to his laptop, I assume that at least some of the “shelves” he refers to are metaphorical. He certainly must have used electronic search engines to locate articles and save the most interesting ones for a closer read. 

     Lynas supposes that few other people read these journals. If that’s true his oracle is highly vulnerable to library budget cuts. The project scope depends upon having access to the enormous set of  shared resources in a large science library. Paying even fairly small access fees for so many articles could make the project cost prohibitive and the time lag to wait for thousands of articles “on-demand” would vastly extend the time needed to write the book.  It would probably also trigger some kind of backlash from librarians.

      More than once I've seen librarian colleagues act disdainful towards super-users like Lynas whom they accuse of taking up more than their “fair share” of library resources. Obviously, that could only be true when library resources are privatized through policies like inter-library loan or purchase-on- demand which provide a single copy for a single user. Ironically, these policies are enacted on the theory that it is cheaper to buy obscure articles than it is to store "undisturbed" journals. 

 If the Radcliffe Science Library was keeping track of journal use, the librarians might have noticed a sudden upswing of interest in climate science even though the heavy use of journal articles on the topic actually represents a single researcher writing a single ambitious book. The book sold well, though, so the project had a cascading effect distributing information far more widely than the direct audience of scholars.  It might even be said that the library collection subsidized a much broader sharing of public knowledge about the effects of  climate change. In that sense, use statistics would actually vastly underestimate the impact of the articles.