Using the ‘arsenic bacteria’ story as a teaching moment for undergraduates

The bacteria at the center of the debate
The bacteria at the center of the debate

Background: NASA funded scientists published an article in Science about bacteria using arsenic instead of phosphate in their DNA.  NASA held a press conference to promote their findings and comment on the importance of this discovery.  After reading the article, many scientists were not convinced that the discovery was as important as the authors were claiming, nor were they convinced that some of the methodology was sound.  And many of these scientists shared their doubts with the general public via blog posts, blog comments, twitter comments and other informal venues.  The NASA scientists fired back, saying that the scientific debate should happen through the formal process of peer review and publication.  Bloggers and science journalists responded by pointing out that they were the ones who held a press conference.  Carl Zimmer’s articles in Slate and in the Discover blog the Loom outline the issues nicely, and Ed Yong has a wonderful time line of how the story unfolded.

This story provides a unique teaching opportunity for faculty and librarians to discuss the issues of peer review and scientific communication with undergraduate students.

First, you have scientists on record saying that basically, the peer review system didn’t work as well as we’d like.  These scientists are saying that the scientific methods used were not as rigorous as they should have been.  In addition, many folks are arguing that what the scientists actually discovered isn’t nearly as important as the hype surrounding it makes it seem.

An in class discussion about this issue could center around several things:

  • Thinking critically about the methods – scientific criticisms of the article
  • Evaluating the importance of a new discovery – how good is peer review (or any other method of review) at evaluating this?
  • How are scientific discoveries represented in the media – do the stories about the science match up nicely with the science itself?  Students could analyze media stories from mainstream outlets as well as the original article.

Second, you have the controversy about where scientific debate should take place.  Some scientists see little value in the scientific blogosphere.  Many others (including myself) view it as a vital part of the communication between scientists and the general public.  In addition, blogger’s comments have led to the retraction of at least one article in a highly respected journal (that I know of).

An in class discussion about these issues could center around several themes:

  • What type of responsibility does a scientist have to communicate his/her discoveries with the general public?
  • How do less formal communication models (press conferences, blogs, etc.) interact with and relate to the formal communication process within science (peer reviewed articles)?
  • Who has a right to comment on a scientific article?  When should the authors respond to these comments directly?

The amount of information on this story available on the web is quite large, providing lots of opportunities for students to search for and find various opinions.  In addition, the science is multidisciplinary, allowing an opportunity for many courses to engage in these discussions.


The hidden landscape of scholarly publishing

Was the scholarly publishing landscape easier to understand when everything was in print? Image from Flickr user diylibrarian

Students tend to assume that all the information they need for a project (perhaps other than print books) is available freely online.  They may have rough ideas that some journals cost money (like magazine subscriptions) but I’m guessing that most students have a simplistic and rather naive concept of how they have access to information (I’d love to see some data on this).

Are we doing students a disservice by not making the details of the scholarly information landscape more prominent?

Libraries and information providers have worked hard to make much of this landscape transparent to the end user (including faculty).  If the student is on campus, many of the journal articles may appear “free” to the end user through a complex series of IP authentication, proxy servers and other behind-the-scenes technology.

When we teach students how to access information, we encourage them to use library databases, touting their scholarliness and focus.  But when users can access articles in JSTOR and ScienceDirect through a Google or Google Scholar search, the advantages of the paid databases are diminished.

We talk about journals, but we don’t talk about how we have access to them: free, direct from the publisher, in aggregators, etc.  We talk about ILL, but we rarely mention how they may find a copy of the paper archived on a website – students can discover this for themselves and then wonder if we really know what we are talking about.

We teach them about brainstorming keywords, narrowing or broadening their search as needed and identifying the types of information they may need.

But would it also be useful to them if they understood the nature of the scholarly information landscape?  Would it be easier for them to track down a copy of an article if they knew the possible ways that they might have access to it: (OA vs. subscription, direct publisher subscription vs. aggregators, final copy edited version vs. post-print)?

I’m starting to think that we need to start introducing some of these concepts to students as freshman, then build on them at advanced levels.  I’m just not exactly sure how to do this at the moment.

What is a DOI? Just the basics

Most of the students (and some of the faculty) I work with have no idea what a DOI is or why they should care.  This is what I tell them.

A DOI – Digital Object Identifier – is like a social security number for a journal article. They can be applied to other digital items as well, but you are most likely to encounter them in scholarly articles.

A DOI normally consists of numbers, letters and other punctuation.  It will look like this:



The DOI provides a way to permanently find a particular item.  Publishers and scholarly societies change their websites all the time.  Recently, a major publisher completely re-did their website, messing up all links into their site.  I was quite annoyed.  But the DOI could still link you to an article in a way that a URL couldn’t.

Incidentally, you can use the DOI to create a nice, neat compact URL for a journal article (instead of those really log URLs provided by some databases).  You just need to add a little bit to the front of the DOI:

DOI LogoYou can also use the DOI to quickly look up an article from your libraries homepage or this webpage.

To get a DOI, a publisher registers with a non-profit organization called CrossRef, and they work with the publisher to assign a unique number.

Increasingly, journals and citation styles are requiring authors to include DOIs in article citations where available.

For additional (and much more technical) information about DOIs, see the DOI website or the Wikipedia article about DOIs.

Strategic Searching of the Geoscience Literature – GSA Presentation

This afternoon I will be standing in front of my poster at the Geological Society of America Annual Meeting:  “Fueling Learning Outside the Classroom with Strategic Searching of the Geoscience Literature”.   Stop by if you are in the area.

The poster is a part of the Geoscience Education session “Learning Outside the Geoscience Classroom: Engaging Students Beyond the Lecture and Laboratory Setting

In this poster, we are presenting a plan for information literacy instruction in mid-level geology courses and including some concrete ideas for how geology professors can include some of these strategies in their classes whether or not they have a science librarian available to collaborate with.

Associated information:

Faculty, librarians and student research skills: are we on parallel paths?

ResearchBlogging.orgOne of the themes I’ve been writing a lot lately is that department faculty and librarians aren’t talking to each other as much as they should, especially in areas that they are both concerned about.  One of the biggest areas we need to be talking more about concerns student’s library research skills (or information literacy skills).  Librarians aren’t doing a lot of publishing in disciplinary college teaching journals, and we aren’t going to a lot of disciplinary conferences.

So when I saw two articles in the August/September issue of the Journal of College Science Teaching written by department faculty that included heavy doses of information about teaching library research skills, I began to be convinced that departmental faculty and librarians are on parallel paths with this issue.  It is wonderful that we are both exploring these issues, but the fact that our paths don’t intersect may lead to frustration on both sides.

Davies-Vollum, Katherine Sian, & Greengrove, Cheryl (2010). Developing a “Gateway” Course to Prepare Nontraditional Students for Success in Upper-Division Science Courses Journal of College Science Teaching, 40 (1), 28-33

Kitazono, Ana A (2010). A Journal-Club-Based Class that Promotes Active and Coorperative Learning of Biology Journal of College Science Teaching, 40 (1), 20-27

Both of these articles describe courses in the sciences in which information literacy skills make up an important part of the course content.  In both cases, the faculty consulted a librarian for assistance in teaching students about database searching, and the authors of both articles found this assistance to be helpful. But in both cases, the authors don’t cite a single article about information literacy from the library literature.  This is hardly surprising – these articles would be almost impossible to find in the typical databases used by scientists.

In a completely un-scientific perusal of articles from library journals concerning information literacy in the sciences (i.e. those that were on my computer or filed in my desk), I find that librarians aren’t citing this disciplinary literature either.

So we are both trying to figure out how to equip students with the skills they need to effectively search, locate and understand the scientific literature.  We are both writing articles about classes and exercises that can help students develop these skills, but we don’t seem to be talking to each other about these issues, at least in the formal literature about college-level science teaching.

I have had a lot of interesting conversations with faculty about how to develop these skills.  How can we move this discussion from informal hallway conversations into the formal literature?

I think this is up to the librarians.  I don’t think we can expect the faculty to start reading the library literature.  We need to keep our eyes on the disciplinary literature, take the opportunity to publish in them when appropriate, and present at disciplinary conferences.  And maybe get out of the library occasionally.

Getting students on the same page with their research skills

Most semesters I teach a few upper level biology seminars.  I’ve talked in the past about the kind of things I teach them, but one particular challenge has been on my mind lately:  getting all of the students on the same page.

Getting everyone to the same starting line can be tricky.  Image courtesy of Flickr user Andi Sidwell
Getting everyone to the same starting line can be tricky. Image courtesy of Flickr user Andi Sidwell

At the moment, information literacy instruction (through me) is not systematically incorporated into the biology curriculum.  The number of biology students has increased drastically in the past few years, so many of the assignments that used to require library research have been scaled back in an attempt to keep grading under control.

As a result, by the time they get to their senior seminar, some students have had experience in finding the primary literature, and some have not.  Some students can easily distinguish between a review article and a primary research article, and some cannot.  Some have experience using databases like Scopus, and some do not.

This creates challenges when designing an instruction session for these students.  Do I start at the very beginning, and never get to some more advanced topics, in order to get everyone up to speed?  Or do I just skim over the basics, hoping that the students will catch enough to enable them to do what they want to do?

My approach to this tends to depend on the desires of the course instructor.  Sometimes they are just looking for the basics.  Other times they are looking for something more.  I often have some of my own ideas, and we tend to meet in the middle.

One approach that I always use for this problem is to simply push the research consultation service that we have, and to encourage students to contact me with big or little questions.

Until we have a more systematic approach to information literacy instruction in this department, we will continue to miss students at the crucial sophomore and junior levels, and we will keep playing catch up in the senior seminars.  We’re working on it.

Managing Library Instruction Notes and Resources

Each semester, I teach a lot of library instruction sessions.  Sometimes I teach one-shot sessions, sometimes I do multiple sessions (2-5) in the same class.

In both cases, I create a lot of notes and “paperwork”.  For a typical one-shot session I normally end up with:

Lots of paperwork is created for each of my instruction sessions. Image courtesy of Flickr user Zach K
  • Notes from my initial meeting with the professor about the goals for the library session (normally in MS Word)
  • An outline for the lecture part of the class (normally in MS Word)
  • A pre-class assignment for the students (sometimes on paper, often via our LMS)
  • In-class worksheets for the session (normally on paper)
  • An in-class slide presentation (only about 10% of the time, usually in GoogleDocs for easy sharing)
  • A list of suggested resources for students to follow up on later (almost always via our LMS)
  • Online survey results from any assessment we do of the session (Google Docs, SurveyGizmo,

I have normally used Microsoft Word to produce the paper documents, and the HTML editor in or LMS for the electronic material.  I use the outlining tools in Microsoft Word since that is how I typically think about my notes and lectures.

But I’m not entirely happy with this arrangement.  For each class, the documents are separate.  I can file the Word documents together in a folder, and I try to keep to a standard naming convention, but this doesn’t include my online elements, and I would love to have the individual files linked together somehow.

So when I can’t focus on other work (like right now) I go in search of alternative tools that may help me out.

I’ve read some good things about Microsoft OneNote, but I’m on a Mac, and Parallels is running really slowly for me right now.  I’m looking at OmniOutliner, and I may download the 14 day trial.  I’ve tried using Google Docs (which I love for lots of other things), but the nested outlining is pretty poor, so it won’t meet one of my primary needs: the lecture outline.  I wonder about personal project management software, but I’m not sure that’s really what I need.

I have a feeling I will never have the perfect solution, but when I need to procrastinate, I will keep looking!

How do other librarians organize their teaching information?  How do instructors organize a semesters worth of teaching material?

Librarians need to publish in non-library journals

Now that I’ve convinced everyone to stop going to library conferences, I’d like to make the argument that we also need to start publishing in non-library journals.  Luckily, someone has already made the point for me, in a 2007 journal article that I just came across in the Journal of Academic Librarianship by Christy Stevens.

Library journals are full of articles about the importance of information literacy instruction.  Blogs, library magazines and twitter posts all discuss the best ways to collaborate with faculty to teach students these skills.  On rare occasions, disciplinary faculty publish articles about collaborations with librarians.

But faculty aren’t reading library journals.  And they aren’t reading library blogs either.  And some faculty seem unaware of the services that libraries are currently offering (the excellent ProfHacker blog often illustrates this.)  And according to Stevens, librarians could do a better job of publishing in disciplinary education journals.  She highlights calls from various librarian authors over the past 20 years to reach out to faculty through the disciplinary literature.

Stevens examined “discipline specific pedagogical journals” – the teaching journals for college professors to look for articles about information literacy, or even just libraries.  She looked at a few of my favorites, including the Journal of Geoscience Education, the Journal of College Science Teaching, and the Journal of Chemical Education.  For each of these journals, she identified articles that mention library research and articles that focused on information literacy.  Some of these articles mentioned libraries in passing, some mentioned particular library-related assignments, others discuss information literacy in more detail. (Incidentally, I would love to see the list of publications she ended up with).

Overall, a relatively small number of articles were found focusing on information literacy or library-related assignments.  She concludes that while there is not a lot of evidence of faculty/librarian collaboration on information literacy issues in these journals, things have improved since similar studies were done 10 or 20 years ago.

Faculty are much more likely to read pedagogical publications in their own disciplines, and librarians need to reach out to faculty in order to facilitate effective information literacy instruction.

So, instruction librarians need to stop publishing great articles about faculty-librarian collaborations in library journals and start publishing these articles in disciplinary journals.

Sounds simple, right?  Let’s do it.

Stevens, C. (2007). Beyond Preaching to the Choir: Information Literacy, Faculty Outreach, and Disciplinary Journals The Journal of Academic Librarianship, 33 (2), 254-267 DOI: 10.1016/j.acalib.2006.08.009

Designing the survey seems like the easy part

Right now I am neck deep in information literacy assessment survey results.

The instruction librarians and I spent a lot of time devising our instructional goals and objectives and then developing the assessment tool (for a one-shot info. lit. session in a first-year writing course).  There were a lot of meetings, and it was a lot of collaborative work.

Since the analysis of the results falls largely on me, however, right now the survey design seems like the easy part.

The assessment tool we designed has a lot of short answer questions, which require a lot of thought in order to effectively ‘grade’.  We strongly feel that these questions provide a more accurate picture of student understanding, but they can be tricky to analyze.

For example, we asked the students how they can tell the difference between a scholarly and a popular source.  I need to figure out how to mark this answer from one of our students:

it will say peer reviewed

Completely correct?  Somewhat correct? Not correct?

So I will spend the next few days (weeks?) trying to figure out how to condense all of this information into a nice neat package.

We’ll see how it goes.