Digitization: A Boost to Circulation

In the last two (1,2) posts, I’ve discussed how herbarium specimens have circulated since they were first created, and also how sometimes specimens get stuck in a limbo of uncurated collections.  Now I want to discuss how circulation has changed thanks to the massive digitization projects of the 21st century.  This is a familiar story to those in the herbarium world, but I’ll quickly review it for those who aren’t lucky enough hang around herbaria.  The upshot of digitization is that now everyone can hang around them, at least virtually. 

Digitization is very much tied to the development of computer technologies, but also to globalization that has brought an awareness that the planet we live on is a shared asset and a shared responsibility.  Over the years there have been a number of international conferences and agreements that articulated this vision and made it actionable.  The 1993 international  Convention on Biological Diversity gave each nation sovereignty over its biological wealth, which implies knowledge of that wealth.  This led to the 2002 Global Strategy for Plant Conservation with later updates and goals including a global flora of all known plants with online access, the best way to make the information widely available.  While this goal has yet to be met in full, there have been significant advances toward it.  

In the early 21st century, the Andrew W. Mellon Foundation spearheaded the digitization of type specimens so that researchers around the world could access the plants that were used in describing species.  Because of the way many specimens circulated—collected in the species-rich tropics and transported to botanist-rich Europe and North America—researchers in developing nations did not have ready access to these materials.  Botanical literature was also relatively unavailable so the project digitized many publications of the past as well.  This project morphed into the portal JSTOR Global Plants and also set the stage for other large-scale digitization projects such as ADBC (Advancing Digitization of Biodiversity Collections) in the United States with its massive iDigBio portal and what ultimately became DiSSCo (Distributed System of Biodiversity Collections) in Europe.  Meanwhile GBIF (Global Biodiversity Information Facility) has aggregated data from these projects and others worldwide to create the largest portal for natural history collections along with observational data. 

While an amazing achievement, digitization has not totally solved access problems for those in developing nations.  They often do not have the hardware, software, and internet connections to make good use of these resources.  Still, digitization has broadened availability in other ways.  It was difficult for those not involved in botanical research to visit herbaria, if for no other reason than specimens’ fragility; each use opens the possibility of damage.  This is not a problem with a digital collection, so students can study specimens on the web as can curious gardeners and artists looking for new forms of inspiration, leading to greater plant awareness, a positive counter to what has been called plant blindness. 

Digital collections have already had a major impact on the ways specimens are used in research (Heberling et al., 2021).  For phenological work, botanists can now search GBIF for a particular species and by checking a specimen’s flowering or fruiting status against the date it was collected, they can see if there is a pattern of change in the dates over a period of 100 years or more.  They may check hundreds or even thousands of specimens, something that wouldn’t be possible for physical examination.  Niche or species distribution modeling, determining areas that might provide suitable habitat for a species based on what is known about its range, is another area where digital specimens are pivotal:  geographic coordinate data on where plants were collected are used to create a model of the environmental conditions that meet a species’ habitat requirements.  This research is helpful in identifying possible collection areas and also where a species might be able to grow as the climate changes. 

There’s also an increase in the use of artificial intelligence (AI) tools to recognize traits like leaf shape and even to identify species.  This work requires a great deal of computer power and sophisticated neural networking techniques, so it’s costly in both technology and human input.  However the field is advancing rapidly in exciting ways.  Botanists foresee being able to rapidly analyzing large numbers of specimens and at least sorting them into families or genera if not species.  However, at the moment even the identification of leaf shapes is still in its infancy.  When deep learning AI techniques are tested in identifying specimens, this is done on carefully selected specimen sets.  It requires a great deal of computer capacity, but the increasing frequency with which AI projects presented at conferences on digital specimens suggests that these tools will soon become widely used in biodiversity research.             

I should add that there are obviously many research areas where digital specimens cannot possibly replace the real thing.  There is no DNA in a data file.  Specimens have proved to be goldmines for those working on plant genetics.  As sequencing techniques become more sophisticated, even the rather short degraded DNA fragments found in specimens, hundreds if not thousands of years old, can provide substantial information on a plant’s relationship to other species.  But this isn’t the only reason why physical specimens need to be retained.  They can give clues on chemical changes in plants under siege from herbivores (Zangerl & Berenbaum, 2005), and more than one entomologist has found new insect species hidden away on plant specimens (Whitehead, 2016).  Each specimen is unique:  a particular plant collected at a particular place and time, and therefore irreplaceable.

References

Heberling, J. M., Miller, J. T., Noesgaard, D., Weingart, S. B., & Schigel, D. (2021). Data integration enables global biodiversity synthesis. Proceedings of the National Academy of Sciences, 118(6). https://doi.org/10.1073/pnas.2018093118

Whitehead, D. R. (1976). Collecting Beetles in Exotic Places: The Herbarium. The Coleopterists Bulletin, 30(3), 249–250.

Zangerl, A., & Berenbaum, M. (2005). Increase in toxicity of an invasive weed after reassociation with its coevolved herbivore. Proceedings of the National Academy of Sciences, 102(43), 15529–15532. https://doi.org/10.1073/pnas.0507805102

Getting the Most Out of Herbaria: In So Many Ways

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Images from Tweet sent by the Georgia Southern University Herbarium

So far in this series of posts on the uses of herbarium specimens in research (1,2,3), I’ve stuck to those that are most commonly discussed:  taxonomic and floristic work, environmental change studies, and phylogenetics.  But there are many other uses, with the variety increasing because digitization makes specimen information more easily available to a broader audience.  There have been studies on the presence of plant pathogens in specimens, including fungal infections (Kido and Hood, 2019).  Anther smut was found detected on specimens through visual inspection under a microscope (Antonovics et al., 2003).  Recently, sensitive DNA sequencing techniques have made it possible to detect bacterial infections by differentiating between pathogen and host DNA.  There is even Defense Department interest in such research.  The Center for the Study of Weapons of Mass Destruction in Washington DC issued a report where they outline why natural history collections can be sources of information in the work of protecting against biological warfare.

Different groups of researchers look at herbarium specimens very differently.  Those investigating fungi might focus on the roots, such as in a study about the successful extraction of arbuscular mycorrhizal fungal DNA from vascular plant roots.  Other botanists have developed techniques for systematically evaluating the amount of herbivore damage to leaves by using a grid system (Meineke & Davies, 2019).  While it’s common to find dead insects on a specimen, snails hiding out are more of a surprise.  Researchers examining lichens and bryophytes from the Galapagos Islands found that 10% of 400 specimens had at least one of eight different micro-mollusk species adhering to them.  There was even a new species discovered.  It is not unusual for new plant species to be found among herbarium specimens (Bebber, 2010), but snails are another thing.

Specimens can also be useful before trips to collect more specimens; Kew Botanic Gardens has a handbook with specimen images as a guide for collectors.  Searching databases for where a particularly narrowly endemic species was found in the past increases a botanist’s chances of finding it again.  One approach is searching for associated species in locality information.  Botanists are being encouraged to list such data to make specimens more valuable in ecological studies.  Another way to enhance specimens is to link them to other types of data such as iNaturalist observations from the same locale.  Heberling and Isaac (2019) describe how they are doing this at the Carnegie Museum of Natural History’s herbarium in Pittsburgh.  The iNaturalist data can include photos taken on the site by citizen scientists.  These visual records may document traits such as flower color and form that are difficult to preserve in dried specimens.   There may also be information about the surrounding habitat.  Having these items linked to specimens is a step toward the development of what is termed the Extended Specimen Network, with the specimen is at the center of linked resources providing information on the genetics, ecology, and morphology of the species (see earlier post).

Besides scientific uses, herbaria can also have what could be termed sociological uses.  There are several ways in which digitization of natural history collections could lead to more diversity among researchers.  Online access means that those interested in taxonomy who are living in developing nations can more easily access not only specimen data but related research through such portals as GBIF.  This also makes it easier for them to find research partners in developed nations.  A very different approach to expanding diversity has been employed by several institutions in the United States:  enlisting those in juvenile detention centers and those recently released from such facilities in digitizing specimens.  These projects not only provide employment, but also broaden the participants’ experience of science and of working with databases.  It is a nice example of thinking more creatively about expanding the population of those interested in nature and opening up herbaria in novel ways.  The iDigBio project held a webinar on this topic to make the natural history collection community aware of this approach, document the progress that has already been made, and encourage other ways to think outside the box in drawing people to natural history.

I haven’t mentioned using herbarium collections in outreach programs because I covered this in a recent post.  However, I have recently come across a few examples that seem too good to ignore.  The first is a “Hookathon: Hacking the Herbarium” at the Royal Botanic Gardens, Kew.  This was an all-day citizen science event to digitize items in Kew’s massive collection of material related to Joseph Dalton Hooker, who led the garden for many years during the second half of the 19th century.  This was also a means to advertise the collection’s existence and its variety, including specimens, manuscripts, letters, and drawings.  At the University of Manchester in Britain, the herbarium opened its doors to students during the exam period for “well-being” events so they could unwind by drawing specimens and incidentally find out what a herbarium is about.   I would like to end with a political, yes a political, example of outreach.  A Tweet from the Georgia Southern University Herbarium reminded residents about voting and put in a plug for the state symbol, the peach, with a beautiful fertile specimen.  This is outreach at its most creative.

References

Antonovics, J., Hood, M. E., Thrall, P. H., Abrams, J. Y., & Duthie, G. M. (2003). Herbarium studies on the distribution of anther-smut fungus (Microbotryum violaceum) and Silene species (Caryophyllaceae) in the Eastern United States. American Journal of Botany, 90(10), 1522–1531.

Bebber, D. P., Carine, M. A., Wood, J. R. I., Wortley, A. H., Harris, D. J., Prance, G. T., Davidse, G., Page, J., Pennington, T. D., Robson, N. K. B., & Scotland, R. W. (2010). Herbaria are a major frontier for species discovery. Proceedings of the National Academy of Sciences, 107(51), 22169–22171.

Heberling, J. M., & Isaac, B. L. (2018). iNaturalist as a tool to expand the research value of museum specimens. Applications in Plant Sciences, 6(11).

Kido, A., & Hood, M. E. (2020). Mining new sources of natural history observations for disease interactions. American Journal of Botany, 107(1), 3–11.

Meineke, E. K., & Davies, T. J. (2019). Museum specimens provide novel insights into changing plant–herbivore interactions. Phil. Trans. R. Soc. B, 374(1763), 1-14.

Getting the Most Out of Herbaria: Systematics and Chemistry

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Murder Most Florid by Mark Spencer, London: Quadrille, 2019

As mentioned in the last post, herbaria, both real and virtual, are most frequently visited by taxonomists, who are usually studying particular plant taxa or preparing flora of areas ranging in size from city parks to entire countries.  These are the traditional uses of plant collections and are still crucial.  However, several things have changed.  Now the “visit” is often to digital portals rather than onsite, making it much easier for researchers to look at specimens from far-flung institutions, IF the material has been digitized, and particularly if it is available through aggregators such as iDigBio, GBIF or JSTOR Global Plants with their links to massive numbers of specimens.  Still, coverage is uneven, with some collections more fully digitized than others.  Also changed is the way taxonomic information, once generated, is distributed.  Many flora are now published virtually, with or without an accompanying paper format.  The 2012 International Code of Nomenclature for Algae, Fungi, and Plants made it acceptable to publish descriptions of new species digitally as long as they were responsibly published and properly archived.

Plant taxonomy is also changing because of its increasing links with genetics.  Most treatments of species and genera now include DNA sequencing data.  While this has been going on for decades, the last ten years or so have seen greater use of DNA data derived from samples taken from herbarium specimens, with NGS, next-generation sequencing (NSG) making this possible. NGS techniques utilize small pieces of degraded DNA found in dried plant material easier to sequence and to determine how such sequences fit together to provide meaningful results.  That this work has revolutionized taxonomy is hardly news.  Still, it is interesting to look at how the information has solved various puzzles, such as the origin of European potatoes or the origin of the pathogenic Phytophthora strain responsible for the Irish potato famine of the 1840s.  In a study of the genetics of grapes, researchers used over 200-year-old specimens from the herbarium at the Royal Botanical Garden in Madrid.  These plants were collected by Simón de Rojas Clemente y Rubio, considered one of the founders of the botanical study of grape vines, especially varieties used in wine-making.

DNA is not the only chemical being extracted from specimens to glean useful information about plants and also about their ecological relationships.  For example, researchers in Copenhagen tested specimens of four species of Salvia used for medicinal purposes for levels of terpenoids, known to have medicinal applications.  These plants were collected over the past 150 years.  While the terpenoid levels did decrease with the specimen’s age, the “chemical composition of four Salvia species are predominantly defined by species, and there was a substantially smaller effect of year of sampling.  Given these results, herbarium collections may well represent a considerably underused resource for chemical analyses.”  Also being investigated are secondary metabolites that plants produce to control herbivore damage.  In one study researchers were able to extract pyrrolizidine alkaloids from plants in the Apocynaceae family that includes milkweed.  The specimens were as much as 150 years old, and even in those treated with alcohol or mercuric chloride, alkaloids were detectable.

There has also been work on the presence of heavy metal pollutants in collections as a way of tracking contamination.  A study at Brown University in Providence, Rhode Island analyzed samples from specimens collected around the city from 1846 to 1916, compared with newly collected ones.  Levels of copper and zinc remained relatively consistent, but lead levels were much lower in plants growing in Providence today.  It was impossible to test accurately for another toxic heavy metal, mercury, because mercuric chloride was so often used to prevent insect damage to specimens.  While toxic metals in plants might make them seem less palatable as food sources, there is an emerging field of agromining:  growing plants that are hyper-accumulators of metals like lead and mercury to eventually reduce soil contamination.  Herbarium specimens can be used to discover how long areas have been contaminated and also to identify species that are particularly good at extracting metals.  There are even some who think that growing plants in nickel-rich soil could be a way to extract this metal for sale.

Such studies suggest that the possible uses of specimens are only limited by the ingenuity of researchers in coming up with them.  It is fun to see what they can ferret out.   The British botanist Mark Spencer recently published a book on his work as a forensic botanist.  It has a great title:  Murder Most Florid (2019).  He was at the herbarium at the Natural History Museum, London curating the British and European collections when he was first asked by the police to aid in a murder investigation.  Human remains have been found in a forested area and had apparently been there for several years.  Would he be able to determine the time more precisely by studying plants at the site?  I don’t want to spoil this story or the other great ones in the book, but I will say that Spencer explains why a herbarium is essential for the work he does, now that he has become much more involved in forensics.

Reference

Spencer, M. (2019). Murder Most Florid: Inside the Mind of a Forensic Botanist. London, UK: Quadrille.

Getting the Most Out of Herbaria

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Representation of Digitization 2.0 from “Digitization and the Future of Natural History Collections,” Hedrick, et al., BioScience, February 2020.

In our culture there is a direct connection between usefulness and value, so it’s not surprising that the arguments for preserving natural history collections entail how useful they are in many scientific endeavors.  The late Smithsonian taxonomist, Vicki Funk, is well-known for her 2003 commentary, “100 Uses for an Herbarium (Well at Least 72).”  More recently there have been articles on how collections have been utilized in the past and on how they could be employed in the future.  These studies take into account how specimen digitization is opening new ways of employing specimens in biological inquiry.  This series of posts will deal with some of these avenues, beginning with the general overview presented here.

Last fall, Heberling, Prather, and Tonsor published an article (2019) that reported on a computational text analysis of over 13,000 journal articles published between 1923 to 2017 and dealing with plant collections.  Investigation of the abstracts categorized the research into 22 topics ranging from taxonomic monographs and revisions as the most common, to morphology and anatomy ranking twenty-second.  Taxonomic work rated as most frequent throughout the study period and for most subtopics in this area the output was relatively steady over time.  However, the authors found that more recently, there have been a wider variety of topics employing herbarium specimens.  These include DNA sequencing of specimen samples and investigations of shifts in phenology over time, along with other measures of environmental change.

While there is nothing particularly shocking about the findings, this is still an important study.  First, it is broad in terms of both the time span and the number of articles covered.  Also, the authors used a rigorous methodology to come up with categories and to apply these to the texts.  Finally, this publication gives those in the natural history collection community a good citation in bolstering their case for the increasing importance of their work:  its increasing breadth promises to grow in the future if properly supported.  Another interesting, though narrower, survey in the same vein was conducted by researchers at the herbarium of the Natural History Museum, London (Carine et al., 2018).  They used 12 categories condensed from Funk’s longer list, analyzed articles published between 2013-2016 by means of the Web of Science, and then compared these results with a survey of researchers who visited NHM to use the herbarium.  In both approaches, taxonomic work ranked highest, but coming in second among the herbarium visitors was historical research.  This is in light of the herbarium’s large and rich historic collection including the herbaria of Hans Sloane and Joseph Banks.  The authors note that this number also reflects their recent work to encourage historical research.

While the studies just cited looked at past work, several publications highlight the bright promise of natural history collections in the digital age.  The author of one of these articles, “Collections-based science in the 21st Century,” is Vicki Funk (2018).  She notes that it is not only the great increase in specimen data now available on line that renders specimens so useful, but also the fact that what is called “next generation” DNA sequencing makes it more feasible and easier to sequence partially degraded DNA, the type found in most specimens.  This opens all kinds of possibilities for phylogenies based in part on specimen data as well as work in evolutionary medicine and ecology.  Georeferencing specimens also opens the way for several kinds of studies including niche modeling and climate change forecasts.

Shelley James and her coworkers give a long list of research projects using herbarium data:  “The addition of non‐traditional digitized data fields, user annotation capability, and born‐digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision‐making, and other scholarly and creative activities” (p. 1).  However, this bright future will only come about through investment of resources that go beyond just getting data online.  The information has to be properly coded so it can be easily retrieved in many different ways and integrated with a variety of other systems so that specimen data is tied to DNA sequences, as well as to ecological evidence and the taxonomic literature.  These are examples of what is coming to be called Digitization 2.0, that is, building on the initial digitization of label data and imaging by integrating this input with genetic and ecological data and by augmenting it with more sophisticated forms of visualization.

European researchers are coming to similar conclusions.  Besnard et al. list many of the same uses mentioned above, noting that this data can be helpful in managing genetic crop resources and monitoring crop pathogens.  Lang and her coauthors provide a good review of employing specimen data to study global environmental change with an emphasis on tracking climate change, the spread of invasive species, and on the effects of pollution and habitat change.  And while I don’t want to put a damper on these bold plans, Bingham et al. have written a comprehensive article on the large number of portals and other digital projects at various levels from the local to the international.  Many of these are not closely tied to or integrated with other projects, and some closely duplicate the efforts of others, so there seem to be too many cooks in the kitchen.  This doesn’t make sense in light of the limited financial and human resources available and the vast job to be done.  Despite this, there are some very interesting projects successfully using herbarium data, and I will touch on them in the next several posts.

References

Carine, M. A., Cesar, E. A., Ellis, L., Hunnex, J., Paul, A. M., Prakash, R., Rumsey, F. J., Wajer, J., Wilbraham, J., & Yesilyurt, J. C. (2018). Examining the spectra of herbarium uses and users. Botany Letters, 0(0), 1–9.

Funk, V. A. (2018). Collections-based science in the 21st Century. Journal of Systematics and Evolution, 56(3), 175–193.

Heberling, M., Prather, L. A., & Tonsor, S. (2019). The changing uses of herbarium data in an era of global change. BioScience, 69(10), 812–822.

Opening Up Herbaria: Higher Education

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Website for BLUE: Biodiversity Literacy in Undergraduate Education

When I majored in biology in the late 1960s, the focus was on cellular biology.  Our year-long intro biology course concentrated on molecules, cells, genetics, and human physiology.  Taxonomy was almost completely skipped over.  This was probably worse than eliminating it completely because a quick tour was head-spinning, and we were left with little more than the idea that the living world is full of exotic creatures with tongue-tying names, definitely an aspect of biology to avoid.  During the fall semester, I fell in love with electron microscope images of cells and that set my educational course.  If I could see a living thing, I wasn’t interested in it.  Out of fifteen biology majors in my cohort, only one went into organismal biology, becoming an oceanographer studying copepods.

While many of my generation continued on to careers in ecology, few ended up in systematics, and the movement away from this discipline remains a trend to this day.  The result is that there are not many botanists and zoologists who have expertise in accurate species identification.  This is particularly ironic because species are still being discovered.  However among plants, a quarter are left undescribed for 50 years or more after they were first found (Bebber et al., 2010).  With the dawn of the 21st century, targeted efforts have been underway to bring back what can broadly be called natural history:  studying biology at the organismal level.  In part this trend is the result of the massive NSF project over the past 10 years to work toward digitizing information on the nation’s natural history collections.

As collections are scrutinized, many discoveries are made, and just the scope of the collections has reawakened interest in them, in what they say about the natural world.  The Society of Herbarium Curators is playing a larger and larger role in this work, as it encourages interest in herbaria among many constituencies, including young people considering careers in systematics and botanical biodiversity.  One of the more disturbing discoveries is the number of species known from old collections that haven’t been found again in the 20th and 21st centuries.  Another is that scientific species names are a foreign language for most of us.  I definitely include myself here.  Until I got on my botany kick, I knew more bacterial than plant genera.  Catching up isn’t easy but it feels good when I can identify a species and name it correctly.  And it’s that good feeling, among other things, that botanists are attempting to pass on to more of today’s students.

In the last post, I wrote about bringing natural history into K-12 classrooms.  Here I want to mention programs to do the same in higher education.  This is a huge topic because it has several different strata.  Among undergraduates, there are some who will major in biology and go on to work in ecology, systematics, and related fields.  But the vast majority will not.  These are the students I taught and that I still worry about.  If they are interested in anything biological, besides issues of health, it is organisms they can see.  Yet much of biology education is devoted to cells and molecules.  The first semester I taught I was shocked to find that my nonmajors did not find protein synthesis fascinating, and they still don’t.  I tried to find ways to make it tantalizing, and finally turned to dealing with another problem:  plant blindness.  I found this an easier sell.  Students were much more likely to find trees on campus to observe than to stumble on a ribosome.  There are now many natural history activities geared to such students including a project developed at the Université catholique de Louvain that could be adapted in many ways.  In addition, Brad Balukjian has written persuasively on why he has just begun a natural history and sustainability program at a California community college.

For those majoring in biology, there is definitely an upswing of interest in fields focused on biodiversity.  The NSF-sponsored program, BLUE: Biodiversity Literacy in Undergraduate Education, aims at developing a set of biodiversity competencies for undergraduates.  These would include not only a focus on organismal biology and ecology, but also on digital literacy and bioinformatics, which will be essential for future professionals.  It is exciting to see a field form around these ideas, some of which are centuries old, and some only beginning to gel.   Natural history collections are essential to these efforts because they hold a great deal of the history of the natural world.  They are also where the living world of today will be recorded.  As I have mentioned a number of times, I volunteer at the A.C. Moore Herbarium at the University of South Carolina, Columbia.  It is alive with undergraduate students who as student workers and interns have learned a great deal about botany by digitizing label information and imaging specimens.  Among the specimens are those collected in the mid-19th century by the planter and botanist Henry Ravenel.  These are on permanent loan from Converse College, and provide a picture of the flora of South Carolina of the past.  There are also graduate students in environmental studies who are contributing specimen vouchers from their work in the field.  Herrick Brown, the A.C. Moore Curator, whose doctoral work dealt with seed dispersal and climate modeling (Brown & Wethey, 2019), has plans to foster participation by more students in the herbarium’s activities.  It is an exciting place to be!

References

Bebber, D. P., Carine, M. A., Wood, J. R. I., Wortley, A. H., Harris, D. J., Prance, G. T., … Scotland, R. W. (2010). Herbaria are a major frontier for species discovery. Proceedings of the National Academy of Sciences, 107(51), 22169–22171.

Brown, H. H. K., & Wethey, D. S. (2019). Observations on anthesis, fruit development, and seed dispersal in Gordonia lasianthus (theaceae). Journal of the Botanical Research Institute of Texas, 13(1), 185–196.

Opening Up Herbaria: K-12 Education

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iDigBio resource page for K-12 education

As I mentioned in the last post, many of those responding to herbarium outreach programs are senior citizens with time and expertise to share.  As a member of this population I obviously consider their contributions significant.  But let’s face it, we are short-term participants in the herbarium renaissance.  To build a firm foundation for the herbaria of the future, young people’s interest must be captured and nurtured.  In my post on outreach, I mentioned a number of clever ways herbaria, botanic gardens, and natural history museums are luring youngsters into the world of plant preservation and conservation.  In this post, I want to look at programs to integrate natural history into the K-12 curriculum.

For obvious reasons, animals are often the focus of natural history education.  I am hardly going to dis an entire kingdom, especially because many botanists tell of being fascinated by bugs, snakes, or small rodents when they were young.  Hunting for these eventually led them to see the plants that many animals call home.  At this point, plant blindness has almost become a cliché in biology, though I think it is still real, at least among adults.  Children are physically closer to the ground and therefore to the world of plants, and this is one reason that early education about plants makes sense (Sanders et al., 2014).

I also think that simple is better.  The artist Georgia O’Keeffe became fascinated by flowers when she was seven years old, when a teacher distributed tulips to examine.  It opened a new world for O’Keeffe and led to her amazing floral works.  When I was a freshman in high school, where I had my first exposure to real science education, our teacher sent us home for spring break with the assignment to simply notice the changes of spring.  This was memorable for me in part because it wasn’t “real” homework:  no reading or writing required.  But what really struck me was how much there was to see:  tulips opening with so much inside each bloom that I had never noticed before, buds on trees, weeds springing up in sidewalk cracks.  I didn’t become an artist because of this experience, but I did realize that close observation was fun; this might have been the start of my becoming a biologist.

To bring herbaria into this, I think pressing plants is a great way to observe them.  The first step is selecting a specimen.  This means looking for a good candidate:  are there flowers or berries, is this a representative sample?  Just looking might lead to discovery of more traits like tendrils, or hairs on the leaves, or small features of the flower.  Then wrestling the specimen into place on a sheet of newspaper so it presses well can lead to other discoveries, such as the thickness of the fruit or how easy or difficult the stem is to bend.  In other words, collecting leads to knowing a plant, having a tactile relationship with it as well as a visual one.  There might even be scent involved.  Yes, the specimen does need to be identified and labeled, but this should be done with gentle encouragement rather than as a hurdle to be overcome or a quiz to be passed.

I am not arguing that children’s exposure to nature should be just about observation and nothing more, but I think direct experience should definitely be at the core of any exercise.  The University of Reading recently staged a day-long symposium called “The Big Botany Challenge.”  There were 80 participants from 50 different schools, botanic gardens, research institutions, conservation organizations, etc.  By the end of the day, the room was abuzz with ideas that had been shared among the presenters and other participants.  One speaker, Nigel Chaffey, advocated for “botany by stealth.”  Since many students aren’t interested in plants, he asks:  “Why not smuggle bits of plant information into lessons on geography, history, art and computing?”  Coincidently, I recently heard Rudy Mancke, the naturalist in residence at the University of South Carolina, Columbia, make a similar suggestion, but for a different reason.  He argued that since humans are part of nature, every subject is related to it:  the natural world is the thread the runs through all disciplines, and they should be taught with this in mind.

Because interest in natural history education is rising, there is a wealth of information on the web to guide teachers.  It is ideal if projects deal with plants from nearby areas.  It’s difficult for students to relate to a tropical plant if they are living in Maine, in the sense that their learning won’t be reinforced by coming upon such plants in the outdoors.  There are several sites that offer diverse activities, such as iDigBio in the United States and the Big Botany Challenge in Britain.  Canada has the Children and Nature Network and Australia has activities through its Atlas of Living Australia.  While the plants may be different in far-off lands, the activities may provide novel ideas that could be adapted to any ecosystem.

I want to end this post with a niggling thought from the very back of my mind.  A number of historians of natural history, including Lynn Barber (1980), argue that the 19th-century rage for natural history started to dim when the subject began to be taught in schools.  Then it became work.  While I don’t think this means that natural history should not be a part of a student’s education, it should cause teachers to think twice before making forays into nature too focused on standards and not on joy.

References

Barber, L. (1980). The Heyday of Natural History. Garden City, NY: Doubleday.

Davies, P., Sanders, D. L., & Amos, R. (2014). Learning in cultivated gardens and other outdoor landscapes. In C. J. Boulter, M. J. Reiss, & D. L. Sanders (Eds.), Darwin-Inspired Learning (pp. 47–58).

Opening Up Herbaria: Citizen Science

2 Notes from Nature

Notes from Nature website with herbarium transcription projects

It’s almost 10 years since I first read about citizen science in an article by Amy Mayer (2010) on amateur naturalists recording phenology information.  I tucked the idea away as interesting, since I taught nonscientists and saw this as a possible way to engage them in observation.  Today, with citizen science being a buzzword in the natural history collection community, it’s difficult to image that it could have been a novel idea in the recent past (Flannery, 2016).  Mayer writes that the term was probably first used by Cornell University’s Laboratory of Ornithology for projects tracking bird populations.  Ornithology has a strong tradition of respecting and using amateur expertise, but now this approach has spread much more broadly.

At the last iDigBio research conference, there were many references to the use of iNaturalist data in studies on phenology and species distribution.  iNaturalist is a robust platform that allows participants—and anyone can become a participant by registering—to record their observations.  Many use their cell phones or other mobile devices to provide images as well as identification and location information.  There are now so many individuals entering data that researchers can have confidence in this information.  In order to build community, participants can create local groups and share findings in a new form of the natural history societies that were common at the end of the 19th century (Barber, 1980).  In fact, there is an aspiration that iNaturalist and other such sites can lead to a new flowering of natural history, with appreciation for biodiversity and its conservation as central to this trend.  The National Ecological Observatory Network (NEON) has organized a number of these projects.

Another major digital tool that also deals with natural history data and relates directly to herbaria is Notes from Nature, a segment of Zooinverse, which describes itself as “People Powered Research” and hosts projects in many scientific areas.  Notes from Nature is a platform where users can participate in projects to, for example, digitize the information on specimen labels.  On the website there are links to assignments from a variety of different institutions; these can involve anything from insects to salamanders to plants.  In fact, the preponderance of these tasks deal with plants and with transcribing specimen labels.  Right now there are projects listed about plants from the Southeast, California, and Florida.  New York Botanical Garden and Missouri Botanical Garden both have global projects, with NYBG’s focus on historical records.  Just think, anyone anywhere can look at beautiful specimens and transcribe them, thus aiding science and satisfying an urge to know more.  Many herbarium curators have noted that their projects are often completed quickly.  Notes from Nature and comparable sites like the Australian DigiVol have mechanisms for checking the data so the information that’s actually uploaded to portals such the Australasian Virtual Herbarium for Australian and New Zealand herbaria, CCH for California herbaria, and SERNEC for southeastern US herbaria are accurate.

There are also many other ways to get involved in digital endeavors.  The Smithsonian Institution has a transcription center that provides access to tasks dealing with several of their collections, including the field notes of scientists affiliated with the National Museum of Natural History.  The Field Notes Project, a collaboration between the Smithsonian and Biodiversity Heritage Library (BHL), has been going on for a number of years.  Its results are now available through BHL, which also has other citizen science projects including ones dealing with annotating the thousands of images available through BHL and its Flickr site.  The latter is a wonderful place to visually wander when in need of inspiration or of an aesthetic lift.

I have emphasized sites in the United States, but Citizen Science is a global phenomenon.  The British have herbaria@home and the French, Les Herbonautes.  Besides transcription efforts, there are many environmental monitoring projects, including ones in Japan to measure the continuing radiation effects of the reactor damage at Fukushima after the Tohoku earthquake in 2011 (Irwin, 2018).  In Belgium there has been a collaboration to monitor air quality; about 20,000 people signed on, each paying ten Euros to do so.  The logic for this is that participants would be more committed to sending data if they have an economic stake.  The ubiquity of cell phones makes it possible for even those in less developed nations to become involved, and researchers are encouraging participation in a number of agricultural as well as biodiversity initiatives.  Some worry about the validity of the data and what if anything can be extrapolated from it.  However, the citizen science model, as it is refined, could provide a wealth of important information for science in the future, while also building a more science-engaged public.

Many types of citizen science are sources of free labor for natural history collections.  The large number of senior citizens around at the moment contributes one important pool, and young people doing service projects and internships represent another.  I should also note that such projects compose a small portion of the Citizen Science landscape that also encompasses special interest groups involved in environmental issues and conservation.  Others deal with medical issues.  Broadly, Citizen Science is about members of the public wanting to be involved in scientific issues in order to understand them better and to have their voices heard.  As a citizen scientist transcribing specimens at the A.C. Moore Herbarium at the University of South Carolina, Columbia, I can attest to it being a great way to become part of the natural history enterprise.

References

Barber, L. (1980). The Heyday of Natural History. Garden City, NY: Doubleday.

Flannery, M. (2016). Citizen science helps botany flourish. Plant Science Bulletin, 62(1), 10–15.

Irwin, A. (2018). Citizen science comes of Age. Nature, 562, 480–482.

Mayer, A. (2010). Phenology and citizen science. BioScience, 60(3), 172–175.

On the Road, Learning about Herbaria: Digitization

iDigBio Portal

I recently went north, to Yale University, for the third annual Digital Data Biodiversity Research Conference, sponsored by iDigBio, the NSF-sponsored project to digitize natural history specimens.  I attended the first of these conferences two years ago at the University of Michigan (see earlier post).  Both were fascinating and informative, but also different from each other, in that the focus of attention in this field has moved beyond digitizing collections to using digitized collections.  This seems a healthy trend, but as Katherine LeVan of National Ecological Observatory Network (NEON) mentioned, only 6% of insect collections have been even partially digitized, and Anna Monfils of Central Michigan University noted that iDigBio has information from 624 of 1600 natural history collections in the United States.  Admittedly, it’s mostly small collections that aren’t represented, but Monfils went on to show that smaller collections hold larger than expected numbers of local specimens, providing finer grained information on biodiversity.

Despite the caveat about coverage, the results of the NSF funding is impressive and is leading to an explosion in the use of this data.  It is difficult to keep up with the number of publications employing herbarium specimens as sources of information for studies on phenological changes, tracking invasive species, and monitoring herbivore damage.  While the earlier conference included sessions on using data for niche modeling, the meeting at Yale also had presentations on how to integrate such data with other kinds of information.  Integration was definitely a major theme, and two large-scale projects are front and center in this work.  Nico Franz of Arizona State University is principle investigator in NEON, a massive NSF-funded project that includes 22 observatories collecting ecological data, including specimens, and then using that data in studies on environmental change.  Franz noted that while other projects might collect data over short periods of time, NEON plans for the long-term and for building strong communities sharing and using that data.

Another large sale project, one headed by Yale professor Walter Jetz, is called Map of Life (MOL).  Here again, integration is central to this endeavor that invites researchers to upload their biodiversity data and also to take advantage of the wealth of data and tools available through its portal.  As the name implies, biogeography is an important focus, and users can search for distribution maps for species and create species lists for particular areas .  As with many digital projects, this one still has a long way to go in terms of living up to its name, which implies a much broader species representation than is now available.  In a session led by MOL developers, it became clear that the issue of how different kinds of data can be integrated is still extremely fraught.  Even databases for different groups of organisms, vertebrates versus invertebrates for example, are difficult to integrate because important data fields are not consistent:  what is essential in one field, might not be noteworthy at all in another or might be handled in a different way.  Progress is being made, but as Roderick Page of the University of Glasgow notes, even linking to scientific literature is hardly a trivial task, to say nothing of more sophisticated linking.

While this may seem discouraging, there were also many bright points in the presentations.  The massive Global Biodiversity Information Facility (GBIF) has, as I write, 1,330,535,865 occurrence records, that is, data on specimens and observations.  Last year, GBIF launched an impressive new website and often adds new features.  While the tools available through GBIF are not as sophisticated as with some other portals, it is still an incredible resource since iDigBio data is fed into GBIF as well as data from projects around the world.  For example, data from the University of South Carolina, Columbia A.C. Moore Herbarium where I volunteer, which was fed into SERNEC and iDigBio, is now also available in GBIF, so researchers worldwide can access data on this collection that is particularly rich in South Carolina plants.  This was not an easy undertaking—nothing in the digital world is—and it’s important to always keep that in mind as developers have flights of fancy about could be possible in the future.

Another conference highlight for me involved the use of sophisticated neural network software, such as that coming out of the Center for Brain Science at Harvard University.  James Hanken, Professor of Zoology and Director of the Museum of Comparative Zoology at Harvard, reported on a project to scan slides of embryological sections and then use the neural network software to create 3-D reconstructions of the embryos.  Caroline Strömberg of the University of Washington discussed a project to build a 3-D index of shapes for phytoliths, microfossils from grass leaves that can be more accurate for identifying species than pollen grains.  Her lab has studied 200 species and has quantified 3-D shapes, even printing them in 3-D to literally get a feel for them.  They used this information in a study of phytoliths from a dinosaur digestive track suggesting that grasses are older than previously thought.  Others have questioned these results, so Strömberg’s group is now refining the identification process, measuring more points on the phytolith surface.  Reporting on another paleontological study, Rose Aubery of the University of Illinois described image analysis done with Surangi W. Punyasena on plant fossil cuticle specimens to obtain taxonomic information about ancient ecosystems.  What all these presentations had in common was the use of massive computational power to analyze 3-D images.  At the first conference, reports of 3-D imaging were impressive, but now it is the analysis that has taken center stage.  This is a good sign:  all that data is proving valuable.

Vicki Funk: Thinking Big about Collections

4 ala

This is a last in a series of posts [1,2,3] on the plant systematist Vicky Funk and her recent review article on collections-based research.  Since Funk is a research scientist and curator in the National Museum of Natural History’s (NMNH) Botany Department, it isn’t surprising that she begins a section on the future use of collections with stats on herbaria.  The NMNH, part of the Smithsonian Institution, is home to the U.S. National Herbarium, with a collection of over five million specimens.  The goal there and at many herbaria is to digitize the data for all specimens and in some cases to also image them.  If this could be done at every herbarium, the data would serve as a potent research tool not only for taxonomists but for ecologists, conservationists, and researchers in other fields who never before considered using the information about plants available in herbaria.

One burgeoning field based on the availability of digital specimen images is computer vision and machine learning techniques that make automated plant identification possible.  It is sort of face recognition for plants and is developing to the point that herbarium specimens can be sorted rather well, though the processes are hardly at the point where identification is as good as that done by taxonomists.  However, machine sorting could be employed as a way to narrow down the number of specimens a researcher would have to look at in hunting for new species.  One recent report the computer was able to distinguish between moss groups better than the human eye could.

Funk cites several successful digitization projects, noting that the Atlas of Living Australia is a particularly comprehensive one that has resulted in online access to all records of Australian plant specimens held in the country’s national herbaria.  Australia is also at the forefront in developing software tools to assist researchers in extracting as much information as possible and in the most effective ways.  However, Funk sees the future as going beyond national or even regional databases:  “A Central Portal so all resources are available to everyone is critical.  It is particularly important that these efforts are making the data and images available to researchers in the countries where the specimens were collected, thereby supporting research in those countries” (p. 185).  She is referring to the fact that the bulk of specimens collected in developing countries, particularly during their colonial pasts, are held in European and North American herbaria.  A first attempt to make these specimens broadly available was the Andrew W. Mellon Foundation funding of type specimen digitization, the results now accessible through JSTOR Global Plants along with a great deal of supporting botanical literature.

But what Funk visualizes is something more comprehensive, and as an example, she describes a project funded by the Powell Center of the US Geological Service.  It focuses on the approximately 2500 species of North American Compositae (Asteraceae) and the location data on hundreds of thousands of specimens aggregated from GBIF (includes information from institutions outside the US), BISON (from US government institutions) and iDigBio (US private institutions).  Funk notes that this data is not only aggregated but “cleaned” to make sure it is of high quality, an issue that critics of aggregation emphasize.  The data is then integrated with environmental and geophysical data on geochemistry, climate, topography, etc., as well as phylogenetics—including gene sequences from GenBank.  Think of the power of this:  linking specimens with sequence and environmental data.   This is truly a harbinger of a new age in collections-based research.  It is amazing that ten years ago, just digitizing data and imaging specimens was considered a feat, with the Paris Herbarium’s plan to digitize most of its specimens considered daring.  Now the assembly line method they used has become relatively common, and other large herbaria have substantial percentages of their collections digitized and imaged.

Linking natural history collections to genetic data banks means uniting the two great arms of bioinformatics.  It is a biologist’s dream come true, and this connection will become even more powerful when environmental data is brought into the mix—a much more complex process.  But Funk has seen the digital world burgeon and has been one of the forces behind making it applicable to systematics.  She has also helped make systematics valuable to other fields such as phylogenetics and the growing discipline of phylogenomic—being able to sequence and compare entire genomes.  This is the result of new sequencing techniques that utilize fragmented DNA, just the type available in herbarium specimens.  Drawing on an example from the Asteraceae, Funk cites a study in which the entire genomes of 93 of 95 Solidago, goldenrod, herbarium specimens were sequenced with the plants ranging in age from 5-45 years (Beck & Simple, 2015).

In closing Funk notes:  “One exciting trend is the developing field of Integrative Systematics where collections-based systematics is combined with extensive field studies, phylogenetics, phylogenomics, detailed morphological studies, biogeographic inferences and diversification analysis to present a more comprehensive global” (p. 187).  She also argues for the maintenance of collections in educational institutions to insure the instruction of future generations of systematists; the digitization of cleared leaf slides, anatomy slides, pollen images, chromosome count images, and illustrations to fill out the information available to researches; and finally a series of symposia on the Tree of Life where systematists can map out a research agenda for the rest of the 21st century.

References

Beck, J. B., & Semple, J. C. (2015). Next-Generation Sampling: Pairing Genomics with Herbarium Specimens Provides Species-Level Signal in Solidago (Asteraceae). Applications in Plant Sciences, 3(6), 1500014.

Libraries and Botany: Digital Resources

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Second edition of Basil Soulsby’s catalog of the works of Linnaeus, Biodiversity Heritage Library

One of the attractive features of the meeting of botanical and horticultural librarians that I attended in New York recently (see the last two posts 1,2) is that it included both Europeans and Americans.  Since Europe is home to so many historical collections of specimens, manuscripts, and botanical art, it was great to learn more about these treasures.  It was even better to discover how many of these resources are now available digitally.  One of the high points of the meeting for me was the presentation by Félix Alonso, head librarian at the Royal Botanic Garden in Madrid.  I already knew that this library has a magnificent collection because many of its treasures are available through the Biodiversity Heritage Library (BHL), and I was glad to hear that the institution is developing a new interface to make it more user-friendly.  Accessibility was Alonso’s major theme, as he outlined plans to move the library from a collection-centered to a service-centered focus, including opening it to children for the first time in its 250-year history.

Yet another group meeting at NYBG along with the European and American librarians, was the Linnaeus Link Project, an international collaboration among libraries with significant holdings dealing with Carl Linnaeus.  It is funded, maintained, and coordinated by the Linnean Society of London, which holds the bulk of Linnaeus’s specimens, manuscripts, and books, bought from his widow by the British botanist James Edward Smith in 1784.  However, a number of institutions also have substantial holdings, and the project aims to make all the Linnaeus material available through a union catalog.  Lynda Brooks and Isabelle Charmantier of the Linnean Society Library presented on Linnaeus Link and that’s how I was introduced to “Soulsby numbers” used to identify each record.  Basil Soulsby produced the second edition of his Catalogue of the Works of Linnaeus in 1933, recording all Linnaean writings and works about Linnaeus published up to 1931; the last entry was number 3874.  Linnaeus Link uses these numbers to identify items in the Union Catalogue and is also assigning post-Soulsby numbers to items not mentioned by Soulsby; there are over 400 of these.  This project gives a glimpse into the world of librarianship and the meticulous processes involved in coordinating materials spread out over several countries.

Isabelle Charmantier also presented on the work being done to digitize the Linnean Society collections, which go well beyond those of Linnaeus and include the herbarium of the society’s founder James Edward Smith, as well as his seed collection that is now being conserved.  The seeds are still enclosed in their original wrappers that include letters, sermons, newspapers—obviously of value in themselves.  There are also the archives of Linnean Society Fellows such as Charles Darwin and Alfred Russel Wallace, and art including the watercolors of Nepalese plants that were done by an Indian artist under the direction of Francis Buchanan Hamilton.  He traveled to Nepal in 1802-1803 and recorded over a thousand species there.  Charmantier noted that at the moment, the Society has data on three platforms with variable metadata and would like to undertake the major task of uniting them, thus making the information available to users through a single search engine.

Another great botanical library is at the Royal Botanic Garden, Kew and the head of the library, Fiona Ainsworth, described its massive holdings: 300,000 books and pamphlets, 200,000 works of art, and 7,000,000 archive sheets.  At the moment, there is no digital catalog for the art collection, and it would be ideal to have it along with the herbarium and economic botany collections cataloged in one system with the library.  That is part of Kew’s plans for the future.  For the present, it is working on a five-year project to digitize and transcribe over 2000 Joseph Dalton Hooker letters, that are available on the Kew Library website.  This is a tremendous resource, especially when seen in relation to the letters of two great American botanists Asa Gray, whose correspondence has been digitized at Harvard University, and John Torrey, whose letters are now being digitized and transcribed at New York Botanical Garden (NYBG).

Stephen Sinon, NYBG’s archivist and curator of Special Collections, described the ongoing Torrey Transcription Project.  The noted 19th-century botanist John Torrey spent his life in New York and taught at both Columbia and Princeton.  He gave his letters and herbarium to Columbia College (now Columbia University), but these were transferred to NYBG when it was founded in 1898.  Most of the Torrey letters are incoming correspondence.  Almost ten thousand pages have been digitized and over 2,500 transcribed by volunteers through a crowdsourcing website.  This massive undertaking is being funded by NEH and the Carnegie Foundation of New York.  The resulting digital images are available not only through the NYBG’s Mertz Library website, but on BHL, Archive.org, and the Digital Public Library of America (DPLA).  Mentioning this project moves me away from my focus on Europe in this post, but it’s a reminder that botany knows no borders and has always been a global enterprise.  Torrey, Gray, and Hooker knew each other, wrote extensively among themselves, and visited each other’s countries.  The Americans and the British were also rivals in describing American plants, with Hooker and his colleague George Bentham avidly courting collectors, particularly in Canada, but they did not spurn US collections as well.  Torrey and Gray were well aware of this; the letters between them have many mentions of needing to name American plants quickly to prevent the British from doing it first.