The Plant Press

Observing the 100th Anniversary of Armistice Day: the Common Poppy

From Plant Press, Vol. 21, No. 4, October 2018.

November 11, 2018, is Veteran’s Day and the 100^th anniversary of Armistice Day. Armistice Day is commemorated to mark the armistice signed between the Allies of World War I and Germany for the end of fighting on the Western Front of World War I. The armistice took effect in 1918 at eleven o'clock in the morning—the “eleventh hour of the eleventh day of the eleventh month.” Veteran’s Day, the official United States public holiday to honor military veterans, coincides with Armistice Day and Remembrance Day (also known as Poppy Day), a memorial day observed by the British Commonwealth of Nations member states to remember the members of the armed forces who have died in the line of duty.

Papaver rhoeas (photo by Gary Houston [CC0], from Wikimedia Commons)

The common poppy, Papaver rhoeas, is worn in many countries on Armistice Day in order to commemorate those who lost their lives during warfare. The poppy became the symbol of remembrance soon after the publication of “In Flanders Fields,” a war poem written by Canadian Lieutenant Colonel John McCrae. The poem gives reference to the red poppies that grew over the graves of fallen soldiers:

Take up our quarrel with the foe:
To you from failing hands we throw
The torch; be yours to hold it high.
If ye break faith with us who die
We shall not sleep, though poppies grow
In Flanders fields.

Papaver rhoeas, an annual herbaceous species in the Papaveraceae, has a long-lived soil seed bank that readily germinates in disturbed soils. The plant was readily observed blooming on the battlefields during the war. The species is believed to be native to southern Europe, North Africa, and temperate Asia, but has become naturalized outside of this range.

A specimen of Papaver rhoeas collected in 1910 by Herman Knoche in Montpellier, France.

The U.S. National Herbarium has databased nine specimens of Papaver rhoeas from its collections. These specimens range from Lebanon and Iraq to Spain and the Canary Islands, and they date from the 1890s to the 1970s. The specimen shown here was collected on 19 May 1910 by American botanist Herman Knoche in Montpellier, France.

Staff Research & Activities

From Plant Press, Vol. 21, No. 4, October 2018.

Stuart Davies, David Kenfack, Lauren Krizel, Mauro Lepore, and Gabriel Arellano traveled to Nové Hrady, Czechia for the 8^th Annual ForestGEO Analytical Workshop from 19 July to 3 August. The workshop provided an opportunity to bring global participants together to foster research and scientific collaborations. Participants also embarked on two field-site visits to the ForestGEO Zofin plot located in the Novohradské Mountains.

On 28 September, Gary Krupnick participated in a panel discussion after the showing of the film, Seed: The Untold Story, during a “film-talkback” series of the Rappahannock Association for Arts and Community (RAAC). In partnership with the Smithsonian Conservation Biology Institute and the American Conservation Film Festival, RAAC hosted a special Farm Tour Edition of the talkback series featuring farming-related films over two nights. Seed: The Untold Story follows passionate seed keepers protecting a 12,000 year-old food legacy. In the last century, 94 percent of our seed varieties have disappeared. As biotech chemical companies control the majority of our seeds, farmers, scientists, lawyers, and indigenous seed keepers fight a David and Goliath battle to defend the future of our food. The film showing and discussion took place at the Little Washington Theater in Washington, Virginia.

Alice Tangerini served as one of the committee organizers and as a participant in the Guild of Natural Science Illustrators 2018 conference held in Washington, DC from 14-21 July. The conference marked the 50^th anniversary of the formation of the Guild, which began at NMNH with a core group of local and NMNH staff illustrators. This year’s conference was held mainly at American University with a day at the NMNH featuring behind-the-scene tours of the research departments, workshops led by Guild members in the Q?rius education center, and talks in Baird Auditorium. Tangerini and volunteer Mary Monsma chaired the Committees on signage and way-finding and catering. Tours of the Botany Department were led by Leslie Brothers and Meghann Toner, with Tangerini providing a final stop at her office. An exhibit of Guild work was displayed at the AAAS Building, for which Tangerni provided a selection of historic artworks from the Botanical Art Collection.

Machine Learning in a Natural World

From Plant Press, Vol. 21, No. 4, October 2018.

By Alex White

For many biologists, a core joy of our work is observing the natural world, formulating questions about our observations, and testing our ideas using clever experiments. Days are spent exploring museum cabinets or mountain valleys – few of us dream up romantic visions of deskwork at the computer. Computational research, however, is no doubt on the rise in biology, fueled by shrinking infrastructure costs, rapid computational advances, and a growing literacy among biologists in the relevant programming tools.

With more and more specimens being digitized, deep learning models can one day ask questions about quantitative traits such as leaf shape. (photo courtesy of NMNH)

Two rapidly growing fields of ecology and evolution – (phylo)genomics and niche modeling – have already revealed the utility of computational tools when applied to biological questions, with far reaching implications for both basic research and conservation planning, particularly for plants. Yet the well of computational resources has just barely been tapped. For one, genomics and niche modeling take advantage of stereotypical data sources for studying ecology and evolution – sequence data and presence-absence data – but there are many non-traditional sources of data that computers are now poised to ingest and analyze with astonishing speed. These include complex data that machines are well suited to organize for analysis, such as continuous signals (light, audio, chemical, etc.), meshes from 3D scans, and images, whether microscopic, satellite, or traditional. And speed? Consider the latest collaboration between Berkeley National Laboratory, Oak Ridge National Laboratory, and NVIDIA (Kurth et al. 2018, arXiv:1810.01993), in which Kurth et al. showcased a machine learning model operating at 1.13 exaflops (10¹⁸ calculations per second). Their model was trained in under 3 hours to detect the pixel-level presence of tropical storms in exceptionally large (3.5 TB) atmospheric datasets. Such “deep learning” models hold promise for studying biological questions, but their development in the context of ecology and evolution is still in its early days.

Deep learning defines a class of computational models that are characterized by linking together a hierarchical chain of data transformations and calculations (i.e., fairly simple matrix algebra) to probabilistically “learn” features of a given dataset. Often, these models are used to supply predictions for a related dataset based on common features (this is called supervised learning and is the most common deep learning approach). One can easily visualize the steps involved in a simple deep learning model using Excel – indeed the most complex component is the learning process, where “known” datasets are passed through the model and thousands of randomly initialized parameters are updated iteratively to improve the model predictions. Primary layers of the models learn rough scale representations of the data where deeper layers learn fine scale differences between the features of interest.

One of the most common applications of deep learning is for object detection in images, where a labeled dataset of images is used to train a model that subsequently is used to predict the labels of unknown images. In 2012, the state-of-the-art image model was able to detect the differences between images containing dogs and those containing cats with an accuracy of approximately 80%. With the proper know-how, one can now build and train a dogs vs. cats model with near perfect accuracy in a matter of minutes.

With these rapid advances in mind, the goal of my postdoctoral research is to develop these methods for use in ecology and evolution and apply them to better understand patterns of biodiversity hidden within complex and noisy datasets. For example, colleagues and I at the University of Chicago recently developed a machine-learning model to evaluate ecological assemblages and their (phylogenetic, functional, and taxonomic) structure. Using this model, we can integrate local community surveys, phylogenetic trees, and biogeographic scale data to quantitatively characterize the regional distribution of biotas and their contributions to individual local assemblages. Unlike the examples I provided above, this model is unsupervised (meaning there are no known labels) and makes use of biogeographic data as images to learn the spatial relationships between species in order to generate characteristic biotas. We are currently using this approach to examine the relationship between bird and plant communities across the forest patches in the Himalayas, and we are finding strong concomitance between the structural patterns in both groups. While we are now working to examine the biological basis of this association with more fieldwork, it was the model itself that was the primary heuristic we used to detect this pattern (the methods are available as an R package called ecostructure).

30 Years of the Biological Diversity of the Guiana Shield Program

From Plant Press, Vol. 21, No. 2, April 2018.

Kaieteur Falls, Guyana. (photo by Carol L. Kelloff)

The Biological Diversity of the Guiana Shield Program (BDG) recently celebrated its 30th anniversary. This dynamic program seeks to document, study, and preserve the biological diversity of the Guiana Shield. The Shield is a natural area occupying the northeast corner of South America and has a rich and poorly explored biodiversity. Understanding diversity in the area is complicated by the fact that it encompasses six political units (Guyana, Suriname, French Guiana, and parts of Colombia, Venezuela, and Brazil) and five languages. The Shield includes a wide variety of habitats including the unique "Lost World" tepuis and towering greenheart forests as well as savannas, lowland and montane forests, and coastal mangrove areas each of which has a complex interaction of plants and animals.

BDG has worked to explore this rich diversity and to make the information available and useful to the public and a variety of agencies. Although based in the Department of Botany at the National Museum of Natural History, the program has interacted with scientists in almost all of the Natural History biodiversity departments as well as the National Zoo, Smithsonian Tropical Research Institute, and the Smithsonian Conservation Biology Institute.

To accomplish its goals, BDG has a worldwide network of collaborators. In fact, the program has worked with over 850 people in research, education, training, and outreach. These efforts have resulted in tens of thousands of new collections that have been used to address a variety of questions from the basic “What is it?” and “Where does it live/grow?” to synthetic ones, such as “What is it related to?”, “What are the levels of endemism?”, “Are there adaptive radiations?”, "Where are the highest areas of species richness and endemism?", "Where should future expeditions go?”, and others.

Chair With A View: What’s Going On

From Plant Press, Vol. 21, No. 2, April 2018.

By Laurence J. Dorr

As much as I enjoy writing, I know I would never make it as a newspaper columnist. I have trouble meeting deadlines. I wait for inspiration or for a clever hook. Then the words flow relatively easily through a dozen or more drafts. If neither inspiration nor metaphorical fishing tackle save me, then I struggle. I have written a fair number of these columns, some confessional and others sermon-like. A few I knowingly structured as telegraphed messages: I laid out what I planned to do as chair to make a select few employees understand what I wanted to accomplish. I have discarded almost as many drafts of this column as I have completed. I have an extensive folder of scrunched up and discarded word processing documents, the electronic equivalent of paper balls tossed toward the trash can.

The activities of the department are something that I have not devoted much time to describing in these columns. For this, I am perhaps remiss. We have been busy the last few years and we have devoted enormous resources (planning, staff time, and money) to improving the U.S. National Herbarium. I hope the results are beginning to be visible. To begin with, there has been a physical overhaul of the herbarium. We converted our four compactor-bays from electrical to mechanical assist controls. We have gone from endless malfunctions to almost none, and some of us are getting more exercise in the bargain. We have added over 200 new herbarium cabinets, many of them replacements for older substandard wooden cabinets and yet others constructed to address the needs of special collections such as our bulky bamboos. These new cases permit some expansion but more importantly allow decompression of sections of the herbarium where specimens now are too tightly packed. Our goal is to remove and replace all of the substandard cabinetry in the herbarium. We also have mostly decluttered our common space although we still have far too much Botany material stored in the attic. (Yes, there is an attic in the Natural History building).

[Image] The physical overhaul of the U.S. National Herbarium includes the addition of mechanical-assist controlled compactor bays and the replacement of wooden cabinets with new herbarium cabinets. (photo by Gary Krupnick)

With generous financial support from the Smithsonian’s Digitization Program Office (DPO), Office of the Chief Information Officer (OCIO), and from the Sant Director of the National Museum of Natural History (NMNH) we have digitized more than 1.5 million herbarium specimens, including not only capturing images but also transcribing label data. We have accomplished this while continuing to operate the herbarium as normal. In other words, we have been able to do this without closing sections of the collection. It is difficult to convey to those who only visit us electronically the enormous behind-the-scenes preparation involved in our digitization project, but it exists and one of the less obvious benefits of digitization is that we are improving the physical curation of the entire collection.

Donation of Walter Lewis’ Pollen Slide Collection

From Plant Press, Vol. 21, No. 1, January 2018.

By Erika M. Gardner

In November 2017, Erika Gardner traveled to Washington University to pack and ship 225 slide boxes of Walter Lewis’ systematic pollen slide collection, recently donated by Lewis and his wife, Memory Elvin-Lewis, to the Smithsonian’s Department of Botany.

Memory Elvin-Lewis and Dr. Walter Lewis present three herbarium cases of Walter’s lifelong work of systematic pollen slides. (photo by Erika Gardner)

Lewis is a retired professor from Washington University in Saint Louis, Missouri. During his career at Washington University, he was a prominent ethnobotanist, a pioneer in polyploidy research, and a palynologist. Lewis produced 37 palynology scientific journal publications and wrote Airborne and Allergenic Pollen of North America (1983). He also authored the books Medicinal Botany: Plants Affecting Human Health (2003) and Polyploidy: Biological Relevance (1980). These publications advanced our knowledge about the important relationships between plants and people.

The slide collection was stored at Washington University in three standard size herbarium cases. Each box was carefully prepared by Gardner with bubble wrap in order to prevent the glass slides from breaking during transit. It took three large rolls of bubble wrap to pack the entire shipment. In total, 15 cardboard boxes of slide boxes were safely shipped to Washington, DC. The next phase will be to assess the quantity and quality of the slides, inventory, and then properly store and house the slides with the slide collection at the U.S. National Herbarium.

 

Left: Slide boxes prepared and ready to be bubble wrapped for shipped.
Right: Fully loaded trunk. Bubble wrap--the best resource for packing slide boxes. (photos by Erika Gardner)

Updates from Botany Information Management Team

From Plant Press, Vol. 21, No. 1, January 2018.

The U.S. National Herbarium is starting off 2018 having reached a new milestone. Half of the approximately 5 million specimens housed in the herbarium now have a digital record, with more than 2.5 million specimens databased (1.3 million are also imaged). These digital records are all available for searching and exploring on the Department of Botany’s online specimen catalog.

Solanum aviculare, collected in 1910 in Te Aroha, New Zealand, represents one of the recently digitized families, Solanaceae. Over 2.5 million specimens are now available for viewing in the Botany Specimen Catalog.

With more and more families joining the ranks of “completely digitized”, the herbarium is regularly updating its Inventoried Plant Groups list on the Department of Botany website. If you have a question about whether a group has been inventoried, please visit the site, or contact Laura Tancredi.

In October 2017, the Information Management Team resumed use of the conveyor belt to digitize specimens from select plant families. In the last quarter of 2017, the team completed the imaging of the following families: Lamiaceae, Solanaceae, and all eight families between Campanulaceae and Asteraceae. In the coming months, the conveyor belt team will be imaging Acanthaceae, the Boraginaceae group, Melastomataceae, and Ericaceae. If any researchers plan to work in these families between now and March 2017, please contact Sylvia Orli.

Digitization work also continues through the Smithsonian Transcription Center. After 3.5 years and over 70 crowdsourcing projects, the Euphorbiaceae are now fully inventoried and transcribed. Interested volunteers are needed to continue the transcribing of specimens. Please visit the Smithsonian Transcription Center to view the herbarium’s current projects, Hippocastanoideae and Santalaceae.

The Grass Reorganization Project is in full swing. The Poaceae will be reorganized phylogenetically and each genus has now been assigned a genus number. The contractors are finishing up the re-foldering and annotating of subfamily Bambusoideae, and these pressed specimens will soon join the families mentioned above to be imaged by the conveyor belt team.

The grass reorganization team will continue processing the rest of the Poaceae in the coming year with completion of the project expected sometime in mid-2019. In the meantime, please expect some inconvenience while working in this family.

Botany Department Takes Part in the Shenzhen Nomenclature Section at IBC

From Plant Press, Vol. 20, No. 4, October 2017.

Vicki Funk, Eric Schuettpelz, Paul Peterson, Laurence Dorr, and Konstantin Romaschenko attending the Nomenclature Section of the XIX IBC in Shenzhen, China. (photo by unknown passerby)

The Nomenclature Section of the XIX International Botanical Congress (IBC) was held at University Town, Shenzhen, China, from 17–21 July 2017, during the week prior to the main International Botanical Congress. The Section was attended by 155 participants from 30 countries. The average attendance (based on counts made by Vicki Funk) at any one point was 120-130 people. The event celebrated the 150^th anniversary of the first rules for naming, i.e., Alphonse de Candolle’s Lois de la Nomenclature Botanique.

Vicki Funk at the Nomenclature Section of the XIX IBC in Shenzhen, China, with the “yes” and “no” voting boxes. (photo by Sandra Knapp)

Before the deliberations began on the morning of 17 July, De-Yuan Hong, one of the two Honorary Presidents of the Organizing Committee of the XIX IBC, welcomed the participants on behalf of the IBC. He emphasized that nomenclature is a cornerstone of taxonomy, as well as all of the botanical sciences. The deliberations during the rest of the week were chaired by Sandra Knapp, President of the Nomenclature Section, while expertise on the Code itself was provided by Nicholas Turland, Rapporteur-général, and John Wiersema, Vice Rapporteur and Research Associate in NMNH Department of Botany.

The Botany Department had good representation at the Section meeting with active participation by staff members Laurence Dorr (Chairman), Vicki Funk, Eric Schuettpelz, and Paul Peterson, and by Research Associates Konstantin Romaschenko and Robert Soreng.

In total 397 proposals to amend the Code were submitted for consideration, plus 16 from the floor. This is the largest number presented to any Botanical Congress since the Stockholm Congress of 1950. Most of the decisions were decided by a show of hands, but some required a card vote where attendees voted by placing their card in a either a yes or a no box.

Botanists Endorse Shenzhen Declaration on Plant Sciences

From Plant Press, Vol. 20, No. 4, October 2017.

Over 7,000 botanists from 77 countries gathered in Shenzhen, China during the last week of July to participate in the XIX International Botanical Congress. A pivotal outcome of the conference was the release of the Shenzhen Declaration on Plant Sciences. Written by a committee of 14 botanists, including W. John Kress and Jun Wen from the Smithsonian’s Department of Botany, the Declaration calls for botanists to focus their work in ways to help society mitigate the detrimental impacts of human activities on plants and habitats with a goal of sustainability for future generations. It was recently published in the Journal of Systematics and Evolution and PhytoKeys.

The XIX IBC Opening Ceremony. (photo by the International Botanical Congress)

The Declaration is structured around seven priorities that are far-reaching and broad in their scope: urging botanists to frame their studies in the context of a changing world; increasing the amount of funding to achieve global sustainability; boosting international collaboration across disciplines; developing new technologies; identifying all plant species before they go extinct; safeguarding traditional botanical knowledge; and heightening greater public engagement.

With the accelerating rate of change our planet and our societies are experiencing, the intent of the Declaration is a clear commitment to strategic action. Plants are not optional, and are vital to a functioning ecosystem. By framing all botanical disciplines (taxonomy, development, evolution, ecology, physiology, and genetics) in the context of our rapidly changing globe, botanists can contribute to the formation of a sustainable and healthy world.

ForestGEO Hosts Summer Data Analysis Workshop

From Plant Press, Vol. 20, No. 4, October 2017.

The Center for Tropical Forest Science - Forest Global Earth Observations (CTFS-ForestGEO) hosted 64 participants from 19 countries on 16-31 July 2017 in Rio Grande, Puerto Rico near the ForestGEO plot in Luquillo for their 7^th annual data analysis workshop. It was 2 weeks of hands-on mentoring by senior scientists from ForestGEO and the Smithsonian Tropical Research Institute (STRI) to graduate students and postdocs to collaborate on their research. The goal is to have these up and coming researchers publish their papers post-workshop.

The participants of the 7th annual ForestGEO data analysis workshop

The annual workshops are an ongoing collaboration between ForestGEO and the Chinese Forest Biodiversity Monitoring Network (CforBio) with the Chinese Academy of Sciences. The U.S. National Science Foundation has provided financial support for the workshops since 2011 with the grant entitled, “Integrating functional, phylogenetic and genetic components of diversity for an improved understanding of forest structure, dynamics, and change.” At the workshop participants worked meticulously on forest site analyses focused on biomass and carbon storage, spatial dynamics, demography, and seed-seedling and phenology dynamics.

The workshop ended with a full day of scientific presentations where each participant gave a 5-minute lightning talk. All participants shared research findings from the workshop and received feedback and ideas about how to keep their research projects moving forward.