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Name that fly; computers help make species identification child's play.


After struggling through fish biology, counting dorsal spines or fin rays to try to distinguish daces, darters, and minnows, I would never have believed that identifying species could be fun.

But the students at Lincoln Middle School Lincoln Middle School may refer to:
  • Lincoln Middle School (Santa Monica, California)
  • Lincoln Middle School (Gainesville, Florida)
  • Lincoln Middle School (Portland, Maine)
  • Lincoln Middle School (Washington, D.C.
 in Pullman, Wash., actually enjoy figuring out the names of their local flora and fauna. Last fall, botanist Richard Old visited that school. He first asked the stuthat student's name out of a pool of 180.

The students were dumbrounded. They couldn't wait for Old to do it again. For them, "it was like watching card tricks," Old recalls. "Then I told them they could identify plants with the same power. They were hooked ."

He proceeded to help the kids build an identification system -- called a "key"-- for all the plants in their school yard, letting them pick the "traits" and afterward letting them identify, or "key out," specimens based on these traits. Typically, keys make use of many technical terms. But for the students, "smells bad" or "feels squishy squish·y  
adj. squish·i·er, squish·i·est
1. Soft and wet; spongy.

2. Sloppily sentimental.

Adj. 1.
" worked as well as "pinnate pinnate

featherlike; said of a muscle in which the fibers lie at angles to its tendon. The fibers may be unipinnate, bipinnate, etc.
 foliage" or "clustered heads" as distinguishing characteristics -- thanks to a computer program created by Old. The program creates identification keys for all sorts of purposes and for use by all sorts of people. With this system, one can leave out the technical descriptions that stymie sty·mie also sty·my  
tr.v. sty·mied , sty·mie·ing also sty·my·ing , sty·mies
To thwart; stump: a problem in thermodynamics that stymied half the class.

n.
1.
 all but a few experts.

Like me and many other biology students, Old remembers all too well the frustration of keying out plants or animals he found. Once, he collected a 15foot-tall grass specimen. Although he knew that the plant's height made it unique, the identification guide forced him to examine the grass under the microscope before it led him to its name. "It just made me mad," recalls Old, now a botanist who does plant identification at Washington State University Washington State University, at Pullman; land-grant and state supported; chartered 1890, opened 1892 as an agriculture college. From 1905 to 1959 it was the State College of Washington.  in Pullman.

Later. while working as an agricultural extension Agricultural extension was once known as the application of scientific research and new knowledge to agricultural practices through farmer education. The field of extension now encompasses a wider range of communication and learning activities organised for rural people by  agent, he often found himself predicting a weed's identity based solely on a farmer's coarse description of the weed's height, habitat and flower color. anywhere in the . world, but I knew what [the farmer] was talking about. So I decided to put that ability into a system," Old explains. He designed an expert system, a computer program that works the way he thinks. Old later created a company, XID XID Exchange Identifier
XID Exchange of Identification (Cisco)
XID Maxville, Ontario, Canada - Maxville / via Rail Service (Airport Code)
XID X-Input Data
XID Exchange Identification
XID Transaction Id
 Services. Inc., in Pullman, to market this technology.

This winter, federal biologists joined Old in the push to computerize com·put·er·ize  
tr.v. com·put·er·ized, com·put·er·iz·ing, com·put·er·iz·es
1. To furnish with a computer or computer system.

2. To enter, process, or store (information) in a computer or system of computers.
 two jargon- and data-laden scientific disciplines, taxonomy and systematics systematics: see classification. , the studies of the classifications of organisms. In one case, the U.S. Department of Agriculture (USDA USDA,
n.pr See United States Department of Agriculture.
) has readied an expert system, complete with pictures, for identifying fruit flies. Elsewhere, both individuals and institutions are reworking species lists for on-line use (see sidebar).

This electronic revolution will make these disciplines and the knowledge they yield more accessible. Electronic communication can get data out faster than printed scientific journals, and expert systems can present those data in ways nonexperts can understand.

The emphasis on computerization com·put·er·ize  
tr.v. com·put·er·ized, com·put·er·iz·ing, com·put·er·iz·es
1. To furnish with a computer or computer system.

2. To enter, process, or store (information) in a computer or system of computers.
 also benefits those who spend long hours examining specimens in the hope of naming and determining the relationships among species, says E Christian Thompson, an entomologist at the USDA Systematic Entomology entomology, study of insects, an arthropod class that comprises about 900,000 known species, representing about three fourths of all the classified animal species.  Laboratory at the Smithsonian Institution Smithsonian Institution, research and education center, at Washington, D.C.; founded 1846 under terms of the will of James Smithson of London, who in 1829 bequeathed his fortune to the United States to create an establishment for the "increase and diffusion of  in Washington, D.C. Lacking the glamour and incomegenerating potential of research fields such as molecular biology molecular biology, scientific study of the molecular basis of life processes, including cellular respiration, excretion, and reproduction. The term molecular biology was coined in 1938 by Warren Weaver, then director of the natural sciences program at the Rockefeller , systematics has attracted less interest. Consequently, there are fewer opportunities for students to train for this work, Thompson says.

Yet the need for this expertise is expanding. Each year. Thompson and his colleagues identify more than 100,000 "unknowns" sent to them by state and federal agencies, universities, and companies both in the United States and abroad. In other laboratories throughout the world. thousands more "unknowns" are piling up on systematists' workbenches, creating a backlog of work that slows the assessment of biological diversity. Thompson is convinced that the development of easy-to-use computer programs can reduce some of this backlog by enabling people who are less well trained in taxonomic principles to identify more organisms on their own.

"I do believe it's going to be the way things are identified in the future." Old adds.

Old programmed his expert system to follow the logic people apply to narrow their choices of an organism's identity. With each trait, or character, considered, the computer rules out all but those plants (or animals) with that trait as well as all the preceding traits already registered.

"It's a much more efficient way of getting to the classification," Old says. It's also quite different from dichotomous di·chot·o·mous  
adj.
1. Divided or dividing into two parts or classifications.

2. Characterized by dichotomy.



di·chot
 keys, traditionally used to identify species. "Dichotomous keys are very rigid and very cumbersome, says Old. Rather than use a key correctly, "most people just flip through the pages," he adds.

Unlike written keys, which work only if traits are considered in a specified order, expert-system keys use whatever characteristics one knows -- in whatever order one presents them -- to home in on a plant's name. Because of the way his software is set up, Old says he can enter up to 500 traits about a new plant in less than 20 minutes. The setup lets him squeeze a data set with 500 characteristics for each of 1,000 plants into relatively little space in the computer's memory.

The program also provides helpful hints. If the person describing the plant runs out of ideas about what characters to consider, the computer evaluates the possible choices, then figures out and asks about a new trait that will easily distinguish one of those choices. Should someone not understand, for example, the difference between a spine and a prickle prickle /prick·le/ (prik´il)
1. a small, sharp spine or point.

2. a tingling or smarting sensation.prick´ly
, the computer's "help" file will describe them in words nonscientists can understand. A pointed stub A small software routine placed into a program that provides a common function. Stubs are used for a variety of purposes. For example, a stub might be installed in a client machine, and a counterpart installed in a server, where both are required to resolve some protocol, remote procedure , rigid enough to break the skin and draw blood, qualifies as a spine, while softer stubs stubs

The shares of equity in a firm that is financed almost completely with debt. Stubs are often created when firms go through a leveraged buyout or pay big cash dividends in order to fend off a takeover.
 are prickles, it says.

Already, several other researchers have seen the potential of this approach. Field scientists collecting tropical insects hope that having portable computers at their collection sites will speed classification. Another researcher wants to develop such a system for identifying poisonous plants, Old says.

Thompson and his colleagues have made expert-system keys even more user-friendly. Created for the USDA Animal and Plant Health Inspection Service, their program can thus far identify 67 fruit fly species. Eventually, the system will include data on the 200 most troublesome fruit flies USDA inspectors are likely to come across.

First, the group collected the necessary taxonomic information and reference data for these 200 insects. The researchers initially thought they could scan photographs or specimens with a video camera and load those images into the computer's memory. But when the project got off the ground four years ago, available technology did not provide enough resolution. So Thompson and his colleagues turned to artists' renderings. The finished program will include hundreds of drawings, of both whole insects and key features used in the identification process. Menus on the computer screen enable even a neophyte ne·o·phyte  
n.
1. A recent convert to a belief; a proselyte.

2. A beginner or novice: a neophyte at politics.

3.
a. Roman Catholic Church A newly ordained priest.
 to work through the program.

With dichotomous keys, one can arrive at the insect's name through only one route, says Thompson, Thus a single mistake can lead to an erroneous identification. But the computer works backward, forward, or circuitously, narrowing the choices based on traits considered in any order.

In addition, the computer program will allow the mismatch of one or two characters in the decision-making process and then help the user "correct" the mistake without having to start all over again. Finally, the fruit fly expert system gives detailed information about the insect once it is identified and provides ways to verify the identification, Thompson adds.

With this program, Thompson hopes to reduce greatly the number of "unknowns" he receives. And that pleases plant pathologist Rebecca A. Bech. As a coordinator of USDA inspectors who patrol the nation's borders, she can't wait until this system is up and running. "We're the first-line barrier to keeping these plant pests out," Bech says.

At each location, inspectors must be able to pick out exotic mollusks, insects, even seeds that cross U.S. borders. At ports, the inspectors board ships to take a close look at the cargo and packing material. When that cargo consists of produce, "quite often they will find flies flying around," says Thompson. In 1992, of 37,467 pests intercepted, 4,625 were fruit flies. Missing these pests can be devastating dev·as·tate  
tr.v. dev·as·tat·ed, dev·as·tat·ing, dev·as·tates
1. To lay waste; destroy.

2. To overwhelm; confound; stun: was devastated by the rude remark.
: For the 1993 to 1994 budget, California allocated $8.1 million to eradicate just one, the Mediterranean fruit fly Mediterranean fruit fly: see fruit fly.
Mediterranean fruit fly
 or Med fly

Fruit fly (Ceratitis capitata) proven to be particularly destructive to citrus crops, at great economic cost.
, Bech notes.

If the inspectors do not recognize the insects, they impound impound v. 1) to collect funds, in addition to installment payments, from a person who owes a debt secured by property, and place them in a special account to pay property taxes and insurance when due.  the cargo and send specimens to Bech's group -- or ultimately to Thompson's lab -- for identification. This causes costly delays in unloading, especially for highly perishable cargo. "If it's a Mediterranean fruit fly, they are going to destroy everything," says Thompson. Inspectors also must set up sampling traps near the ship's dock to monitor whether an infestation infestation /in·fes·ta·tion/ (-fes-ta´shun) parasitic attack or subsistence on the skin and/or its appendages, as by insects, mites, or ticks; sometimes used to denote parasitic invasion of the organs and tissues, as by helminths.  has begun.

Not too long ago, for example, a USDA inspector found fruit flies in ornamental pepper plants in a cargo of fresh-cut flowers. Because produce rarely passed through that port and because the ship came from a place that was not supposed to have these insects, the inspector impounded the cargo and sent specimens across the country for identification. It did, indeed, turn out to be a pest that required destroying the plants.

Says Bech: "If we had the fruit fly expert system, we would have been able to get on this immediately." there's the list o! the 4,629 currently recognized mammals. One can catch up on conservation efforts by pulling up onto the computer screen the BIoLOGICAL CONSERVATION NEWSLETTER AND BIBLIOGRAPHY. For more esoteric reading, try the newsletter of the American Society of Plant Taxonomists The American Society of Plant Taxonomists (ASPT) is a botanical organization formed in 1935 to "foster, encourage, and promote education and research in the field of plant taxonomy, to include those areas and fields of study that contribute to and bear upon taxonomy and herbaria",  

These resources, as well as a checklist of plants in the Guianas a guide to the National Herbarium's historical collections. and a computer program that helps researchers assess the relatedness of species, have become available through the Smithsonian Institution's Natural History Gopher Server.

Gopher servers are rest stops along that booming electronic highway called Internet. The gopher software enables users to gain access to databases at different institutions. By developing electronic databases, the National Museum of Natural History's Collections and Research Information System Program expects to keep the information more current and to make it more readily available to scientists and the public.

propriated money for the creation of a new Interior Department bureau, the Biological Survey, which will devote considerable resources to putting information about U.S. plants and animals Plants and Animals are a Canadian indie-rock band from Montreal, comprised of guitarist-vocalists Warren Spicer and Nic Basque, and drummer-vocalist Matthew Woodley.[1] They are signed to Secret City Records.  into electronic databases. Already., states are gathering and computerizing these kinds' of data (SN: 10/16/93, p. 248).

It's an awesome task. For example, USDA's E Christian Thompson is helping to compile a "telephone directory" of all the world's insects. His volume of the directory, which deals only with the 100,000 or so species of flies -- a small percentage of the world's millions of species -- will include the scientific name of the insect, the name of the person who first described it, and where and when the species was discovered. It will also give the name and phone number of an authority on that species and detail its classification. Within the next year, Thompson hopes to have complete information for North American North American

named after North America.


North American blastomycosis
see North American blastomycosis.

North American cattle tick
see boophilusannulatus.
 flies.

"Then," he says, smiling, "we'll go for the world."
COPYRIGHT 1994 Science Service, Inc.
No portion of this article can be reproduced without the express written permission from the copyright holder.
Copyright 1994, Gale Group. All rights reserved. Gale Group is a Thomson Corporation Company.

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Title Annotation:includes related article on electronically cataloging of biota
Author:Pennisi, Elizabeth
Publication:Science News
Date:Feb 12, 1994
Words:1861
Previous Article:Mendelson's web: a microbiologist spins a tale of mutant bacteria. (Neil Mendelson, Bacillus subtilis, macrofibers)
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