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Daring botany.

I have just turned 60 and have decided to begin an exploration of the plant world. This is really an embarrassing thing to admit: that I've been a biologist for 40 years and I've finally turned my attention to the organisms responsible for life on earth as we know it. I have definitely suffered from "plant blindness" (Allen, 2003), though it hasn't been quite absolute. I loved to garden with my mother, I keep coming back to investigations of the life and work of the plant morphologist Agnes Arber (Flannery, 2005), and for the past two years I've been taking courses in botanical illustration at the New York Botanical Garden (NYBG). But this spring, two things happened that really took the scales off my eyes. First, I was invited by Ethel Stanley of Beloit College (a "real" botanist) to do a joint presentation on Seeing Plants: Visualization in Plant Biology at a BioQUEST educational symposium (http://bioquest.org/BSA2007). This was to be held in July before the Botany and Plant Biology Joint Congress in Chicago. It was definitely hubris on my part to accept this invitation, but Ethel assured me that I could concentrate on the visualization part and she would do the "real" plant biology.

Plant Morphology

Also this spring, I took a course called Plant Morphology for Botanical Illustrators at the NYBG. It was taught by Dr. Dick Rauh, who has a Ph.D. in botany and is a noted botanical artist. Dick is also my role model. He started work on his doctorate when he retired from the field of film special effects. Since I am a typical student, I had listened to the student gossip on Dick and knew that he was good, but tough, and he proved to live up to his reputation. However, I also found him one of the most subtly passionate teachers I've ever had. He is definitely a traditionalist in how he presents material: lecture followed by lab is his style. But his lectures are punctuated with questions--going both ways--and with asides on some of the more fascinating characteristics of flowering plants. In 8 weeks, we managed to cover the basics of plant morphology, from the different types of pericarpal tissue to the intricacies of leaf shape, and we examined specimens from 24 angiosperm families. The purpose of the course was to give botanical illustrators some sense of how plants are put together and how they vary. This was definitely a watered-down version of a "real" plant morphology course, but because it was taught by Dr. Rauh, all the students developed a hunger for more of the same. If these 24 families have such variety and such fascinating adaptations, imagine what is in store for us if we explore further, and with the resources of the NYBG available to us, there's enough to keep a botanical artist--even one a lot younger than 60--busy for a lifetime.

In all the courses I've taken at the Garden, I've felt overwhelmed by my level of ignorance. Since I have no art background, getting into botanical illustration meant not only learning to draw plants, but learning to draw, and more than that, even learning to hold a pencil correctly. It has been a humbling experience and one that has made me much more attuned to my students' problems. I now have a better appreciation for the multiple layers involved in learning a discipline. At the same time I had to learn how to hold a pencil, think about shading a two-dimensional space to make it appear three-dimensional, and accurately reproduce a plant form. These were just too many things to think about at once. While we did learn them one at a time, we eventually had to attempt to put these skills together, and that was a stretch for me, much as it is for my students to learn vocabulary, concepts, and scientific ways of thinking all at once.

It is this idea of layers that I've become much more aware of since venturing into the plant world. In plant morphology, there is vocabulary galore, but this is only a minor aspect of the challenge. There is also thinking in three dimensions, learning about developmental processes, and dealing with a range of variations that is staggering. What fun! Dick's attitude is that every challenge brings rewards in terms of interesting ideas and beautiful structures. Yes, schizocarp is an awkward word, but think about how much information it carries; it describes a dry fruit with carpels that split at maturity. Sure, there's a lot to fertilization and seed formation, but consider that this whole process includes the remnants of the alternation of generations and you have to be impressed by what plants pull off. As I sit here writing this, I have an urge to pull out one of my textbooks and get back to work. There are all kinds of assessment instruments, but to me, this is the sure sign of a great teacher.

As a student, I'm afraid that I fail to match the level of excellence found in Dick Rauh and the other faculty at the NYBG. But I am enthusiastic, and this is what led me to decide to use plants as the focus for my course this fall. It's a core course in scientific inquiry built around the concept of evolution, but each year I like to draw examples from a particular area of biology. I've used plants before, but I feel that this time I bring more to the topic, I bring Dick's passion, and also eyes trained to look more carefully at the green world. It seems like a perfect time to do this because plants appear to be "hot" right now and plant blindness seems on the wane. Plants are in the news as harbinger's of global warming (Davey, 2007) and as a possible means to ease this phenomenon (Reay, 2007), as well as being a solution to our dependence on foreign oil (Brainard, 2007).

All these issues were prominent at the Joint Congress. There was so much going on there, especially for someone who was also trying to adjust to a new scientific culture, that it made the overload I felt in plant morphology class seem trivial. While I have attended many education and science education meetings over the years, I haven't been to a blatantly scientific conference in decades, so I definitely experienced culture shock. Posters were just becoming common when I was in graduate school, now they are everywhere, and so are the tubes used to tote them around. And the visual sophistication of the posters is fascinating: backgrounds range from jet black to pale photos of the presenter's campus or plant of choice. Just walking around can give you an education in how to present masses of data in understandable formats--and also how not to do it.

Databases

I hate to admit it, but when I was in graduate school, the calculator was the technological equivalent of the iPhone. Now, computers are everywhere, as are the scientific data they manage. Also impressive is the sophistication of the databases available to plant scientists, and to the general public, on the Web. There was an entire symposium on this topic. Called "The World of Plants at Your Fingertips," it was a great introduction for someone like me who barely know about the existence of these resources, let alone their depth and potential.

Information literacy is a popular education buzzword at the moment. In its most limited sense, it means being able to use a library's resources to find information, but in a broader sense, it involves understanding how knowledge is used, evaluated, and created in a particular discipline. There are definitely discipline-specific aspects to being information literate. I can navigate general databases to find a reference, know a bit about general biology resources, and have a good grasp of the Web resources dealing with evolution. I have some sense of what PubMed with its reference database and the NCBI Web site with its protein and nucleic acid sequence data can do, but as with other aspects of plant biology, the plant databases are virgin territory for me. I had bookmarked the link for the PLANTS Database, managed by the US Department of Agriculture, but I can't say that I know my way around the site (http://www.plants.usda.gov). After the guided tour we had at the workshop and a few minutes just now wandering around the site, I realize three things. First, this is a massive and powerful resource; second, it will take time and thought to appreciate its potential; three, doing this work is absolutely necessary for taming this site for my students.

By "taming" I mean developing guided activities so students come to understand the power of this resource without getting lost in its size and intricacies. I am more and more convinced that this will become a large part of my role as teacher in the future. I have heard endless presentations on how teachers have to assume the role of guides for their students, but until I began to wrestle with Web resources I didn't appreciate what a challenge this is. I may be reacting to Dick Rauh's enthusiasm, but I don't see this as a laborious task ; it is more a source of excitement. It really is like exploring a new world, a visually exciting one, that is available right at my desk.

NBII, the National Biological Information Infrastructure, is another huge, government-sponsored database; it's administered by the Biological Informatics Office of the US Geological Survey (http://www.nbii.gov), so navigating through all this information means, in part, navigating through a web of government bureaucracy. But I can't complain because these resources are endlessly rich. The NBII includes not just plants, but all types of organisms, and because of its sponsor, it is a map-rich site with all kinds of environmental information.

At the workshop, we were also introduced to the new Encyclopedia of Life that is in development now but which promises to be just what its name implies--a database with information on all known species (http://www.eol.org/home. html). The project makes others seem small, but there are several important databases that are worth mentioning. Also recently launched, Botanicus is sponsored by a consortium of institutions and spearheaded by the St. Louis Botanical Garden (http://www. botanicus.org). They are digitizing thousands of their books and journals, most published before 1925, when the copyright laws made copying printed materials more problematic. Much of the material is text based, but there are enough images to satisfy a picture addict like myself. If funding continues, then more and more treasures of the botanical literature will be digitized.

Also dependent on funding is the digitizing of herbarium specimens. At the workshop, there was a presentation on a consortium of California herbaria created to make their collections available online (http://ucjeps.berkeley.edu/consortium/about. html). Jepson Herbarium at the University of California, Berkeley is spearheading this effort, and Bruce Baldwin of the Jepson showed how interactive its database is (http://ucjeps.berkeley. edu/interchange/). Since specimens are being contributed from many sources, there are cases where the same species may be identified differently in different collections. There is a comment box with each entry giving experts the opportunity to annotate the information and make the entries more accurate and informative. Also, mapping software is incorporated so that the geographical distribution for each species can be displayed, or at the very least, the location where a specimen was collected. For someone like myself who is more familiar with mapping genes, this use of geographical information systems is amazing. I consider myself very fortunate to have attended a session like this just as I am trying to orient myself in the plant world. It really does involve a different type of thinking, one in which three-dimensional space is important in a way that's more obvious than in the more two-dimensional world of gene and protein sequences.

Of course, all organisms live in an environment, but because plants are stationary, their space is better defined and can be seen more as an extension of themselves. The Jepson database includes mapping software that allows you to see photos of the areas where plants were collected, giving the specimens an exciting, you-are-there, quality. This is just one of a large number of projects aimed at digitizing herbaria collections. The New York Botanical Gardens has already made 850,000 of its specimens available electronically with the ultimate goal of digitizing its seven million-piece collection (http://sciweb.nybg.org/science2/ VirtualHerbarium.asp). The Field Museum in Chicago also has a large project focusing on its huge collection of neotropical plant specimens (http://fm2.fieldmuseum.org/plantguides/).

Theory

Plants in three-dimensional space was also one of the topics touched upon by James Collins, Assistant Director of the Biological Sciences at the National Science Foundation (NSF), who spoke on "Plant Biology into the 21st Century: Where to from Here." He referred to three biological themes that NSF is focusing on. They are systems biology which looks at the complexity of the living world, issues in biology and society, and encouraging the development of a solid theoretical base for biology. As a botanical example of the latter, he cited a recent article on inflorescence form and development (Prusinkiewicz et al., 2007). The authors looked at three inflorescence structures that occur in nature: the panicle, the raceme, and the cyme. They compared these to theoretical structures that don't exist, and from this information attempted to come up with a model with an evolutionary perspective about how the existing types could be related to each other through genetic change.

Since I had just learned about racemes, etc. in my morphology class, this topic interested me. Here was a way of joining the genetic world I am more familiar with to my new-found interests, though I must admit that things got quite technical when the authors introduced a theoretical 3-D morphospace. But basically, they focused on two architectural genes from Arabidopsis, TFL1 and LFY. A mutation in either gene produces a plant with inflorescence changes, so form alteration is related to genetic change. The authors argued that these changes are, in turn, related to fitness in particular environments; for example: "With unlimited pollination and a growing season of fixed length, the optimal inflorescence architecture is a panicle ... because the plant can delay flowering by keeping its meristems in a vegetative state until the latest time needed for fruit production, thus maximizing branching and the number of fruits" (p. 1455). But in areas where the climate is less stable, this strategy may not work, and it may be more adaptive to produce racemes or cymes where only a fraction of the meristems produce flowers at any one time. A study like this suggests that James Collins is right: it is important to attempt to create a theoretical structure which will not only link different kinds of biological information--in this case evolutionary concepts, genetics, and modeling--but also create a foundation for further investigation.

Barcoding

The last presentation I went to at the Congress was one of the best. W. John Kress of the National Museum of Natural History spoke on DNA barcoding. While I had read about this idea and its implementation, I feel that after this talk, I finally have a grasp of what it involves. Kress began by describing the basic idea: find a DNA sequence that is common to all species and yet is quite variable across species. In essence, this sequence becomes a unique barcode--or fingerprint--that can be used to easily identify species. Like the human genome program, this project has gone from the wild idea phase to implementation in a relatively short period of time. The concept of DNA barcoding only surfaced in 2002, and today there are several projects already working to make the barcoding of all species a reality. The acronym for this plan is BOL: the Barcode of Life. There is now CBOL, the Consortium for the Barcode of Life (http://www. barcoding.si.edu/AboutCBOL.htm), and iBol, the International Barcode of Life project that is based at the University of Guelph in Canada. iBol aims to barcode five million specimens for a half million species in five years (and I have to mention that this includes FISHBOL for the piscine world). However, little of this work has dealt with the plant world.

One of the fundamental problems in barcoding is to find a sequence that is both variable and ubiquitous. CBOL uses the cytochrome c oxidase subunit 1 gene (CO1) from the mitochondrial genome because it provides 95% accuracy of identification for animals, and there are just a few groups without enough variability. Kress then explained why it has proven difficult to find a comparable sequence for land plants. CO1 doesn't work because it doesn't have enough variability in plants, so several groups of plant researchers have been looking for a workable sequence for the botanical world. Kress mentioned several teams, including one at the Royal Botanic Garden at Kew in Britain, and then went into the work being done by his group at the NMNH, that is part of the Smithsonian Institution. They decided to look for a sequence in the chloroplast genome because it is peculiar to plants, is small, and has been well-studied in a number of species. Their criteria were that the sequence had to be relatively short, between 300 and 800 base pairs (bps) in length (CO1 is about 600 bp), the sequence needed to be variable enough to differentiate among species, and it had to be found in all land plants.

When the NMNH group screened chloroplast genomes, they came up with several candidate regions. Further study led them to decide that a sequence called trnH-psbA was the best bet; it was about 450 bp in length, was a noncoding region so it was variable, and it was found in most plants whose genomes they studied. Using this sequence they were able to accurately identify 80% of the species they tested. Meanwhile, workers at Kew had taken a different tack and used coding regions from the chloroplast genome. As with the iBOL project, it is essential that there be consensus on the sequence to be used and a final decision will be made soon. Kress had just come from a meeting of the groups involved in this work, so he probably has a good sense of what the final answer will be. Though he didn't make any firm statement, he did suggest that a likely outcome would be to use two sequences, Kew's coding region as well as NMNH's trnH-psbA.

Even used together, the identification rate with these sequences is 88% as opposed to the animal identification at 95%. But Kress noted that even when the process doesn't yield the right species, it usually does give the right genus and family. He ended his presentation by illustrating how barcoding might eventually be done in the field, because that is the ultimate aim of this project: to document the diversity of life around the globe. One of the aims of barcoding experts is to create a handheld device into which a small piece of tissue could be inserted and analyzed. This gadget would be linked via satellite to databases for sequence comparison. Before you run to RadioShack to look for it, I should note that now the devices used for barcoding are table-top size, but there are already prototypes for smaller versions, so Kress thinks it's possible that small devices will be available for testing within a few years.

Some taxonomists and other biologists consider the very idea of barcoding as going in the opposite direction to the route biology should be taking. The very term has connotations of commodification and simplification, while biologists should be using their resources to study the complexity and richness of life. Barcoding seems to strip biology of its exquisite intricacy even more than gene sequencing, the other large-scale project that many biologists see as overly reductionistic. I can definitely see their argument. Describing an orchid species in terms of a few hundred DNA base pairs does seem the ultimate in sterility, but if this is the quickest way to identify a plant as a new species, a new source of wonder in nature, then it may be worth it. Kress emphasized that barcoding is not a replacement for the work of taxonomists, it does not provide phylogenetic data, but rather it is identification tool and another data set to describe a specimen or species. As someone who is outside the fray, I see barcoding as a fascinating development that can illuminate the living world in a new way, and is also interesting study in the sociology of science, in how an idea is introduced, gains currency, and ultimately becomes actualized and institutionalized.

Conclusion

I learned a great deal at the Joint Congress, including how little I really know about the plant world. My trip to Chicago provided a wealth of information and also gave me a sense of what botany and plant science are about today. I went to a symposium on leaf shape because that was a topic of interest to Agnes Arber (1879-1960), a plant morphologist who is dear to my heart. There I discovered that the basic questions she explored, such as how much of leaf shape is adaptive, are still being studied; no clear answers are available. There I also heard an interesting presentation by Nancy Dengler on how compound leaves form in monocots, the plants that Arber herself studied. Dengler has found evidence that compound leaves form more by schizogeny or splitting of the whole leaf rather accomplished through programmed cell death rather than by mechanical rupture the tissue (Arunika, 2004). This presentation was very specific and circumscribed, very different from the one on the barcoding of all life on earth. These examples show the breadth of the Congress and explain why I came away from it even more excited about plants than I had been before. I just read an essay on teaching in which Gail Griffin (1995) writes that we teach what we need to learn. That comment is ringing in my ears. For a variety of reasons, at this point in my life I need to learn about plants, and having to teach about them this fall is daring me to do it now.

References

Allen, W. (2003). Plant blindness. BioScience, 53(10), 926.

Arunika, H., Gunawardenaa, N., Greenwood, J. & Dengler, N. (2004). Programmed cell death remodels lace plant leaf shape during development. The Plant Cell, 16, 60-73.

Brainard, J. (2007, April 20). The big deals in biofuels. The Chronicle of Higher Education, A19-A22.

Davey, M. (2007, July 11). A beetle and balmy weather may bench a baseball staple. The New York Times, A1, A14.

Flannery, M. C. (2005). Agnes arber in the 21st century. The Systematist, 24, 13-17.

Griffin, G. (1995). Season of the Witch: Border Lines, Marginal Notes. Pasadena, CA: Trilogy Books.

Prusinkiewicz, P., Erasmus, Y., Lane, B., Harder, L. & Coen, E. (2007). Evolution and development of inflorescence architectures. Science, 316, 1452-1456.

Reay, D. (2007). Spring-time for sinks. Nature, 446, 727-728.

MAURA C. FLANNERY, DEPARTMENT EDITOR

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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Title Annotation:BIOLOGY TODAY
Author:Flannery, Maura C.
Publication:The American Biology Teacher
Geographic Code:1USA
Date:Oct 1, 2007
Words:3962
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