Living collections: biocuration in the broadest sense.
Article Type: Report
Subject: Natural history museums (Collections and collecting)
Natural history museums (Technology application)
Online databases (Design and construction)
Author: Flannery, Maura C.
Pub Date: 04/01/2009
Publication: Name: The American Biology Teacher Publisher: National Association of Biology Teachers Audience: Academic; Professional Format: Magazine/Journal Subject: Biological sciences; Education Copyright: COPYRIGHT 2009 National Association of Biology Teachers ISSN: 0002-7685
Issue: Date: April, 2009 Source Volume: 71 Source Issue: 4
Topic: Computer Subject: Online database; Technology application
Geographic: Geographic Scope: United States; United Kingdom Geographic Code: 1USA United States; 4EUUK United Kingdom
Accession Number: 246348875
Full Text: From where 1 live, it takes me about an hour and a half to get into Manhattan, so I like to get as much done as I can while I'm there. A couple of weeks ago, the New York Hall of Science was sponsoring a lecture on the new online Encyclopedia of Life (EOL) at the National Arts Club in Gramercy Park. I decided to start uptown with a visit to the American Museum of Natural History (AMNH). I hadn't been there in awhile and I wanted to spend some time in their temporary exhibitions, but most of all, I wanted to revisit the dioramas. Though I hadn't planned it for anything more than travel convenience, these two stops turned out to be closely linked because they both dealt with collections of living things.

It might seem that the AMNH represents the old style of collecting and the EOL the new, but I don't think things are that clear-cut. First of all, the AMNH is one of the partner institutions in the EOL, which I learned is a huge and very complex project involving several different endeavors and a host of sponsors. The presentation at the National Arts Club was given by Cathy Norton, Deputy Director of the BioDiversity Heritage Library, one of the key components of the EOL. In this column, I don't want to get bogged down in the intricate organization of this project, but I will mention a few facts that I found interesting, because they helped me make sense of a number of online collection projects I've learned about, and used, over the past few years. I hope this information will also prove useful to you, because these resources are only going to get better and more essential to biologists in the years ahead-but don't worry, I'll also get back to the dioramas.

Biodiversity Heritage Library

One way in which my two Manhattan destinations are related is that the AMNH is one of ten organizations involved in the BioDiversity Heritage Library. Two other similar institutions are also represented: the Field Museum in Chicago and the Natural History Museum, London. This consortium has agreed to digitize the key works in each collection, focusing on those published before 1923, the date after which copyright issues become more difficult. I am most familiar with Botanicus (http://www.botanicus.org), the part of this project, obviously enough, dealing with plants. It is being spearheaded by the Missouri Botanical Garden. Exploring this Web site is like getting physically lost in library stacks in which I could never really get lost, because I would never be let in. Many of the books here are too precious to be in open stacks.

But online, I can spend hours just leafing through Pierre-Joseph Redoute's massive masterpieces of botanical art, Les Liliacees. Last year I took a course at the New York Botanical Garden on the history of botanical illustration. Les Liliacees was one of the treasures we examined. Though there were only eight people in the class, we still felt crowded as each of us wanted to look closely at each image of a lily species-and we, of course, didn't turn the pages, but waited for a white-gloved book conservator to do so. On the Web, I can get a much better look at each and every page. And then I can turn to other treasures, dozens and dozens of them, and I can bookmark pages to share with my students. This is something I couldn't do very easily with the books I saw at the Botanical Garden, and it's definitely something that becomes less and less feasible to those who don't live in New York.

And what I am describing is just one small part of the BioDiversity Heritage Library (http://www.biodiversitylibrary. org/), which is just one part of the EOL. I hope this gives you some sense of the scale of this endeavor. The Library has just celebrated the scanning of its 10 millionth page. A good library is a great resource, and it used to be that one had to live near a good library to be able to use its resources on a regular basis. Interlibrary loan is a wonderful way to extend a library's reach, but they are not going to lend Les Liliacees. With the BioDiversity Heritage Library, readers also have access to books housed in Britain, and Cathy Norton spoke of plans to make agreements with institutions in other countries, to increase access to foreign-language publications. What she envisions is a network of resources available throughout the world, giving scholars everywhere equal access to intellectual wealth that has been localized to a great extent in the Western world.

The Encyclopedia of Life

The same access issue is at the heart of the EOUs efforts to eventually have information about all known species available electronically. It's not news to biologists that the preponderance of the world's species are found in areas that do not correspond to the sites of most of the information about these species. There are great herbaria in New York and London, though neither of these cities would be considered a biodiversity hotspot. Peoples around the world have become much more sensitive to what they see as a siphoning off of their economic and intellectual wealth in the form of organisms that are collected in their countries and then transported elsewhere to be studied, and in some cases to be exploited for profit. Making knowledge about all these organisms available electronically is a way to begin to right this wrong.

That is one of the major points that Cathy Norton emphasized in her presentation, but she also alluded to the challenges involved in making this a reality. While the EOL aspires to provide an informative page on each known species, the reality is that right now there is very limited information available on the site. They originally presented two dozen "exemplar" pages that gave the type of information they hope to eventually have available for all species. But 24 out of almost 2 million disappointed those who expected the Encyclopedia of Life (http://www.eol.org/) to be, well, encyclopedic. So the EOL quickly assembled pages on 200 species that people are familiar with, like humpback whales and potatoes, as well as more limited information on many others.

Randy Malamud (2008) mentions the sparse information available on the EOL but also questions it for more fundamental reasons. He cites cases where the availability of information on rare species has led to increased poaching and argues that resources might be better spent in trying to save species rather than post them on the Web. Malamud also brings up another question that seems to me even more crucial: Is looking at images of an organism on the Web-even videos--and learning about that species, really the same as being physically in its presence, or even being in the presence of its remains? In other words, are we missing something fundamental by experiencing life digitally? To me the answer is obviously "yes." The first time I heard Edward O. Wilson, who originated the idea of the EOL, describe it, I remember having two images in my head. He was speaking at the opening of new library and herbarium facilities at the New York Botanical Garden and so, not surprisingly, a herbarium sheet came to mind. The other image, of ants, was also not surprising, considering Wilson's research area.

I visualized examining a herbarium sheet or a tray of ants stored in a museum and then tried to visualize what it would be like to experience both of these electronically. Despite my best efforts, I couldn't convince myself that they were comparable experiences--because they aren't. The scanned images of herbarium sheets in the NYBG online collection are of extremely high quality (http://sciweb.nybg.org/science2/VirtualHerbariuin.asp), but still, looking at them is not the same as looking at sheets that are physically present. The scan does not pick up all the detail and dimensionality that binocular vision provides. The same is true of insect collections, and really of any specimens. The other side of the coin is that access to herbaria is limited. Even though online images are not the same as the real thing, much more is available to the average person electronically, and the future promises greater and greater access. The Linnaean Society of London has digitized many of the specimens Linnaeus himself used in his classification work (http://www.linnean.org/index.php?id=370). These are amazing to see both for their scientific as well as historical importance, and the digitization job is superb. You can focus in on particular portions of a specimen and the scanning of the herbarium sheets is so good that you can even see the texture of the paper on which the plants are mounted.

Physical Presence

But is it important to see the texture of the paper that backs a specimen? Is that really crucial? In terms of identifying a species, it obviously isn't. However, in terms of the experience of the specimen, I think it is, because it comes that much closer to actually having the specimen in front of you. I am as fascinated as the next person with images and the information and beauty they hold, but we have other senses as well that are probably more important to our acquisition of knowledge than we realize. Even if we can't touch a specimen, we can touch the paper it sits on or the jar that holds it. That is simply one more level of experience that contributes to our memory of the specimen.

I know that you are thinking I am overstating things here, but I just read a book that makes a similar point. Sherry Turkle (2008) has collected essays from her MIT students and from colleagues on their early experiences with objects-in other words, what they played with, what fascinated them when they were young. She asked them to describe these in terms of their later interest in science. While some of them do write about early interest in computers, many write about very simple childish things-for example, a geologist sees her play cooking set as getting her intrigued by the effects of heat, specifically, chocolate as a molten material. Jacks and marbles and dice were also early influences, which might make us reconsider some of those expensive toys we feel compelled to buy for children. These essays reminded me of my "experiments" with various soap powders in the laundry room, and my digging around in the garden as my mother did more serious planting and weeding. As of now, digitization can't recreate these experiences, except in highly sophisticated virtual reality labs-and it seems much easier just to send kids out in the backyard with a toy shovel or have them do a little cooking in the kitchen.

My point is that "real" collections still have a value. Many teachers have pressed plants or insect collections, and I think these are invaluable in teaching. But even when a specimen is behind glass in a museum, you get a better sense of its real size and its dimensionality. Cabinets of curiosity (MacGregor, 2007), of wonder, still have validity, as my trip to the AMNH reminded me. It is "wonder-ful" to wander among the dioramas. These halls are dimly lit which makes the viewer feel more a part of the scenes. They are designed to draw a person in and to create the illusion of being a part of each three-dimensional scene. A great deal of planning, art, and science went into creating these displays. While I was at the museum, I bought two books that made me appreciate natural history museum collections even more, and one of them was on the dioramas at the AMNH (Quinn, 2006). I have to admit that I bought it primarily for the pictures, as a way to have a "virtual" tour of the dioramas any time I wanted it. Yes, some of them are displayed on the Web, but not all of them-the Web still has its limitations. However, it turned out that the text is also fascinating. Stephen Quinn has worked on displays at the museum since 1974 so he knows them intimately and shares many behind-the-scenes stories. He explains the craftsmanship and artistry that goes into the taxidermy work on animal specimens and the recreation of plants, rocks, and other landscape features.

Natural History Museum, London

The other book I bought that day presents a very different view of another institution, the Natural History Museum, London (NHML). Again, it is a long-time employee giving the tour; this time, Richard Fortey (2008), a paleontologist who did research at the museum from 1970 until his retirement in 2006. While Quinn concentrates on exhibits and animals, Fortey focuses on behind-the-scenes activities, on the research and care of the museum's collections. He describes how the NHML houses not only public galleries, but research facilities and huge collections of plants and animals, as well as an extensive library. Fortey is a great writer whose other books are also a pleasure to read (1998, 2000). Here he really lets himself have fun With an institution he obviously loves, but he is also not afraid to literally expose some of its darker corners.

A few years ago I was lucky enough to have a brief tour behind the scenes at the NHML which made it easier for me to picture some of what Fortey describes: a rickety elevator, narrow halls, dense library stacks, crowded labs, and the beautiful wooden cabinets that house the herbarium specimens collected by Hans Sloane (whose extensive cabinet of curiosities became the 18th-century foundation of the British Museum from which the NHML was split off in the 19th century). Fortey also has great stories about the curators and researchers who have labored away within the museum's walls. They are really at the heart of the institution and at the heart of his book. Some of them he knew personally, some through the stories that were handed down from one generation of museum workers to the next.

As to public displays, the NHML has had a very different exhibition philosophy than the AMNH. Yes, just like the AMNH, it has a huge dinosaur at its main entrance: a replica of a Diplodocus that was originally at the Carnegie Museum in Pittsburgh, and its new Darwin Centre has state-of-the-art displays (Baker, 2008). But the museum resembles more a neo-gothic church than a neoclassical monument like the AMNH, and it houses few dioramas. The diorama, while popular in America and Sweden, never caught on in the rest of Europe. Karen Wonders (1990) argues that these countries were becoming aware of the value of their wilderness areas in the latter part of the 19th century when the diorama concept first came to the fore as a way to document these areas and share them. In London, Paris, and Rome, exhibit cases were filled with stuffed animals, without backgrounds, totally out of context, out of their natural environments-a frozen zoo (Snell & Tucker, 2003). One advantage of this approach is that it stresses species diversity. It is quite breathtaking to see an array of warblers or a phalanx of rodents, to he able to study variations on a theme. This unity in diversity is something that is not at all addressed in dioramas, and it gives a better sense of the vast collections that support museum exhibits.

The significance of the collections is something Fortey emphasizes throughout his book. He also stresses the close association among all the NHML's resources: its vast collection, its library, and its people-those involved in research and in public programs. He makes the museum itself seem like a living thing, with its various components interacting in wonderfully fruitful ways. Just as the museum itself is encyclopedic in its collections, including plants, animals, and geological specimens, his book tours each museum department and examines its wealth of resources, human and otherwise. He repeatedly stresses the important role the library serves as a source of information on the work of researchers all over the world, so that NHMLers don't duplicate efforts or name as a new species one that has already been described by someone else. While I have long appreciated the symbiotic relationship between researchers and specimens at great natural history museums, I hadn't considered how essential libraries are to this collaboration.

Libraries

I think we are all looking at libraries differently now as the very definition of "library" has changed so radically over the past ten years. A library is now at least as much a virtual as a physical entity. I visit our University library less than I did in the past, and yet use its resources much more. I am more likely to look up an article reference because in many cases I can do it from my computer. I don't have to walk to the library building, search the stacks for the volume I need, and then lug it to the Xerox machine where I copy page after page. At one time this was so much a fact of the teaching life that I didn't think much about it. Now it seems like a labor of Hercules. But from whom much is given, much is to be expected. If it's so easy to access references, then I should be expected to use more of them-and the same should hold true for my students. This brings me back to the EOL, and other Web resources.

If students don't have to haul themselves off to the library, if they can do research in their pajamas, then the time they save in transit and in book maneuvering can now be spent in careful selection of resources. This means that we all have to familiarize ourselves with what's available-and what isn't. As Malamud noted, the EOL is a long way from being the ultimate species catalogue, and even when it does develop more fully, there will still need to be some serious exploration by a user in order to get the most out of it. Online resources don't require the physical work that library research used to entail, but that doesn't mean that using them isn't time-consuming.

Remember when you had to pull volume after volume from shelves to find precisely what you wanted? Now you often have to explore Web page after Web page. Students don't necessarily understand the concept of finding precisely what they need. They often just go to Wikipedia and leave it at that. As Web resources get even richer, this strategy becomes less and less effective.

Biocuration

As far as I can see, this situation requires a great deal of work for teachers. We cannot expect our students to use online resources wisely if we don't know how to do it ourselves. And just as librarians, museum researchers, and collection curators worked with educators in the past, the same thing holds true today. There is even a name for the new field that deals with online biological collections: biocuration, which is defined as "the activity of organizing, representing and making biological information accessible to both humans and computers" (Howe et al., 2008). There are already a slew of biocuration projects underway and most of us have come across some of them. The Tree of Life is one of my favorites (http://tolweb.org/tree/). It seems to be a precursor to the EOL and, in fact, it is a participant in the EOL project. At the moment, the Tree of Life site has much more information directly available and is a great resource for students-definitely a step beyond Wikipedia, precisely because it is more carefully curated.

The term "curator" comes out of the museum world and refers to one who cares for and adds to a collection, whether it be biological specimens or works of art. It takes a great deal of knowledge and experience to be a good curator, the person who has the brains to figure out how to make a collection useful, what the public would like to see of the collection, and how to make choices about what to add to the collection. All this is true of biocurators as well. Last year I went to a workshop on visual databases and heard a lot about "metadata," a term that the librarians in attendance used with abandon, but I had to admit that I didn't know what it meant. It turns out to be the data used to describe and characterize an image so it can be found by those looking for it. In other words, if you are looking for a book about dogs, then "dog" is the search term you would use. But what if you want a picture of a dog? Unless that picture is tagged with search terms (like "dog"), unless there is "metadata" associated with it, that picture will be very difficult to find. This is one of the functions of biocurators, to make sure the metadata (the tags) associated with any artifact, whether it be an image of a molecule, a protein sequence, or a fossil, is thorough and specific.

As a user of databases, I don't really think about the intellectual work involved in setting them up and adding to them. But I need to, because it affects how I present problems in information literacy to students. There are some biological databases that are just not for the casual user; take dictyBase, for example. The homepage of its Web site (http://dictybase.org) describes it as "your central resource for the biology and genomics of the social amoeba Dictyostelium discoideum." Nowhere on the introductory pages is the term "slime mold" used and the opening information is written at a level that requires a certain biological sophistication. In other words, this is not someplace to send your average 9th-grade biology student. But for someone doing research on Dictyostelium, this site is a crucial tool. There are similar sites for other model biological species such a zebrafish (Danio rerio-http://zfin.org), fruit flies (Drosophila melanogaster-http://flyhase.org), and thale cress (Arabidopsis thaliana-http://arabidopsis.org). Even if they don't use them directly, it's good for students to know about these resources, to give them a sense of how integral the Web has become to biological research, just how massive the stores of information on many species are, and why biocuration is gaining in importance. Some of these resources, such as GenBank, which gives access to nucleotide, protein and structure databases, have education components where the resources have been tamed to make them more accessible to students and teachers (http://www. ncbi.nlm.nih.gov/Education/).

I seem to have wandered far from dioramas and fish in jars but that's just the point. These displays and gene sequences are both part of biology today. Now museum research is less about examining specimens and more about comparing genomes. And while Fortey very justifiably decries the changes wrought in his institution that make it less of a place for eccentrics pursuing their chosen species by themselves in dark corners of the museum, the riches of the NHML and of many others are now available to people all over the world. So we all can learn about the work of those eccentrics and of their descendents who still labor away at discovering the true size of the tree of life.

Note: I would like to thank Theresa Maylone for providing me with opportunities to hear Edward O. Wilson and to learn about metadata.

References

Baker, J. (2008). Q&A: Museum's metamorphosis is nearly complete. Nature, 455, 34.

Fortey, R. (1998). Life: A Natural History of the First Four Billion Years of Life on Earth. New York: Knopf.

Fortey, R. (2000). Trilobite: Eyewitness to Evolution. New York: Knopf.

Fortey, R. (2008). Dry Store Room No. 1: The Secret Life of the Natural History Museum. New York: Knopf.

Howe, D. et al. (2008). The future of biocuration. Nature, 455, 47-50.

MacGregor, A. (2007). Curiosity and Enlightenment: Collectors and Collections From the Sixteenth to the Nineteenth Century. New Haven, CT: Yale University Press.

Malamud, R. (2008). Life as we know it. Chronicle of Higher Education, 54(46), BT.

Quinn, S. C. (2006). Windows on Nature: The Great Habitat Dioramas of the American Museum of Natural History. New York: Abrams.

Snell, S. & Tucker, P. (2003). Life Through a Lens: Photographs From the Natural History Museum 1880 to 1950. London: Natural History Museum.

Turkle, S. (Ed.). (2008). Falling for Science: Objects in Mind. Cambridge, MA: MIT Press.

Wonders, K. (1990). The illusionary art of background painting in habitat dioramas. Curator, 33(2), 90-118.

MAURA C. FLANNERY is Professor of Biology and Director of the Center for Teaching and Learning at St. John's University, Jamaica, NY 11439; e-mail: flannerm@stjohns.edu. She earned a B.S. in biology from Marymount Manhattan College; an M.S., also in biology, from Boston College; and a Ph.D. in science education from New York University. Her major interests are in communicating science to the nonscientist and in the relationship between biology and art.
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