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27 Sep 2012

How the Web Can Help Identify Countless Undiscovered Species

Taxonomist Quentin Wheeler is calling for a concerted effort to classify the millions of unidentified species in the world. In an interview with Yale Environment 360, he talks about the new field of “cybertaxonomy” and how it is harnessing the Web to speed up the effort to catalog life on earth.
By diane toomey

Each year, about 18,000 new species of plants and animals are discovered and described by science. That may sound like a lot, but entomologist and taxonomist Quentin Wheeler thinks it is woefully inadequate. Wheeler is the founding director of the International Institute for Species Exploration at Arizona State University, and along with such renowned colleagues as E.O. Wilson and Peter Raven, he is calling for an intensive international effort in the next 50 years to discover the estimated 8 to 10 million species that remain unknown.

Quentin Wheeler
Arizona State University
Quentin Wheeler
In an interview with Yale Environment 360 contributor Diane Toomey, Wheeler said the time has never been more critical to carry out such a project, considering the rapid rate of biodiversity loss. But the tools now available to identify all the world’s species and share that knowledge globally are impressive, he noted. Most important is the advent of what he calls “cybertaxonomy,” which harnesses the power of the Internet to take three-dimensional pictures of specimens or place millions of pages of taxonomic information online — all in the service of identifying countless unknown species.

Wheeler foresees a future, not far off, when scientists and amateurs use the Web to build an enormous species database. “We’re leveling the playing field,” said Wheeler, “not only for students and scientists in developing nations, but also for students and faculty at smaller institutions, and amateurs in particular.”

Yale Environment 360: Each year about 18,000 new plants and animals are discovered and described, but it seems that you’re not all that impressed with it.

Quentin Wheeler: Well, it does sound like a large number and it’s a pretty good start. But it’s only a start. After about 250 years of discovering and describing species, we will soon reach 2 million named species. Our best estimate is that there are at least 8 to 10 million additional species awaiting discovery, and that’s not counting the microbial world.

e360: Make the case, if you will, from an environmental perspective, why an all-out taxonomic survey is needed.

Wheeler: Well, the environmental argument is the most obvious and easy one, which is we need to create a baseline understanding of the biosphere. Unless we know what species exist and where they are distributed on earth, we are at a huge disadvantage to detect or monitor changes in biodiversity. It is difficult to know whether a species is invasive in an ecosystem where it doesn’t belong, or whether species are going extinct silently, unless you establish that baseline of knowing what’s there to begin with.

e360: What groups of organisms, taxonomically speaking, are in the worst shape?

Wheeler: Most groups are under pressure and our knowledge about how much pressure they’re under is really quite indirect. We know that most species are fairly limited in their distributions, either ecologically or

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Quentin Wheeler discusses how “cybertaxonomy” can help scientists — and amateur taxonomists — better catalog life on earth.

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geographically. And as we see habitats disappear and become degraded, we can infer that those species that are unique to those places are disappearing as those places are modified and disappearing. But that’s a pretty unsatisfactory, crude estimate of what’s happening, and another argument for establishing a baseline of what species exist and where is so that we can have pretty precise measures of the rates of extinction, which habitats are being impacted most, and which taxa are suffering most.

e360: People might be surprised to learn that a lot of what remains unknown is sitting under our noses in the back rooms and basements of museums and other institutions. So what are the impediments to having those specimens identified?

Wheeler: The primary impediment is the paucity of experts available. A second bottleneck is just the accessibility of collections. In the past it’s been pretty labor-intensive, requiring travel and expenditure of time and resources to get the expert and the collections in the same place. And that’s something where an investment in cyber infrastructure to create what we call “cyber taxonomy” will relieve a good deal of that. There was a paper
Natural history collections are an unmined treasure trove of new species.”
published in the Proceedings of the National Academy of Sciences last year by an international group of botanists. They looked at what we might call the “dwell time,” the amount of time between the actual collection of a specimen representing a new species and putting it into an herbarium, and the date at which an expert actually gets around to describing and naming that species. Twenty-five percent of the species sit in an herbarium for at least 50 years or more before they are described. So natural history collections are an un-mined treasure trove of new species. Based on the amount of backlogs in herbaria, that group of authors suggested that a very significant percentage of the new species of flowering plants yet to be described are probably already sitting there waiting to be described and named.

e360: The digitization of these collections would help enormously, I take it.

Wheeler: Absolutely. Digitizing them suddenly makes them available online. In the right hands, an even imperfect image can often allow an expert to exclude the possibility that it’s a particular species or to definitively conclude that it is a new one.

e360: So what percentage of these collections are digitized and what are the impediments to getting the rest of them digitized?

Wheeler: It’s a small percentage so far that’s digitized. The New York Botanical Garden, for example, has completed the digitization of all of their primary type specimens. About 125,000 of them are openly available online now and allow botanists to answer a multitude of questions about species identity and the correct application of a scientific name, all from the comfort of their office or laboratory, which is astounding. The biggest challenge is that we estimate there are perhaps 3 billion specimens in the natural history museums and herbaria of the world, so digitizing them all is no small matter.

e360: You were talking about the impediments to getting specimens digitized. Is it a matter of funding, or will, or technology?

Wheeler: The technology is coming along so rapidly so that the unit cost of digitizing is getting much lower. The National Science Foundation has an initiative underway to digitize collections and that’s helping to advance
We will have potential access from a computer anywhere in the world to two-thirds of all insect species on earth.”
the process considerably. [These] libraries of archived images are invaluable. You can go online 24/7, see the images you need to see. But occasionally they don’t capture the information you need, so what do we do next? We have just finished a collaborative project with the Smithsonian Institution and the natural history museums in London and Paris and a small business in Virginia called Visionary Digital. We’ve engineered and designed and constructed several remotely operable microscopes. And the first generation of these is targeted specifically for insect collections.

Insects account for about half of all the named species so if we can master that, we’ve mastered at least half the backlog. So these instruments will allow an expert to examine, to manipulate the specimen on multiple axes, and actually take photographs remotely so that you can accomplish what you typically would accomplish by visiting a museum.

e360: You’re going to be launching these telemicroscopy systems in December?

Wheeler: That is correct. We have installed the instruments in London and Paris. The Smithsonian one actually just shipped today. Right now, if I want to see a specimen in London or Paris at the Smithsonian, I don’t need to travel to those cities. With just those three museums alone, we estimate that they hold more than 650,000 type specimens for insects. So approximately two-thirds of all the insects on earth, we suddenly have potential access to from a computer anywhere in the world.

e360: So when a new specimen is collected at some point in the future are you saying that it then would immediately be digitized? It would be placed in the hands of a robot and photographed in the appropriate way?

Wheeler: Well this was one of the lessons that I learned when I moved to Arizona, to the Southwest, was the cowboy logic that the first thing you do when you find yourself in a hole is stop digging. It’s absolutely inexcusable that we’re continuing to add to the backlog of un-databased, un-digitized specimens. But to make that efficient and not absorb the limited resources that most collections have to take care of their existing specimens, we do need to look at ways of automating the process of digitizing specimens on a routine basis as they come in. We have plans for an automated digitization machine that would create 3D images of specimens.

e360: You’ve even talked about automating identification itself.

Wheeler: People have been working with image recognition software and some of the results have been surprisingly effective. If you think about facial recognition software, that same technology can be used to allow computers to scan and match shapes up to known libraries. In at least one project I’m aware of that dealt with really complex anatomical structures, they were able to achieve well over 90-percent accuracy in identifying species in an automated fashion. So there’s great potential there for imaging. And then of course using molecular markers, using bits of DNA to uniquely identify specimens is another area that’s developing very rapidly.

e360: And are taxonomists waiting with baited breath for these innovations, or are they being dragged kicking and screaming into the 21st century?

Wheeler: Well, all of the above. Some people are more excited about this than others. The legitimate hesitancy that I’ve seen in some essays
Some are concerned that embracing cyber infrastructure will divert us from on-the-ground work.”
published in scientific journals are some of my colleagues, particularly in South America, who are concerned that embracing cyber infrastructure will simply be the latest diversion of resources away from the serious work that we need to do, which is boots-on-the-ground collections, making sure that we’re actually getting the taxonomy done and not just diverting all of our resources into another wave of new technology.

e360: How do researchers in the developing world, where much of the planet’s biodiversity resides, figure into your vision of a global taxonomic survey? And what are the barriers to their participation?

Wheeler: The barriers to scientists working in developing countries are primarily that most of the type specimens described over the last couple of centuries reside in museums or herbaria in Europe or North America. And literature has been another constraint. In the past, it was a privileged few professionals who had access to a world-class library. And in taxonomy, unlike most branches of science, you routinely have to go back and study and understand papers published beginning in 1758 and some of that early literature is very difficult to access. But digitization is subtly changing all of this.

View gallery
Snub Nosed Monkey Northern Myanmar

Thomas Geissmann/Fauna & Flora International
The snub-nosed monkey, discovered in Northern Myanmar in 2010.
The Biodiversity Heritage Library Project has digitized well over 30 million pages of the literature and we’ll eventually have the last two-and-a-half centuries of taxonomic knowledge openly available to anyone. Along with cyber taxonomy, one of the most important things is what I would call democratization of taxonomy. And this means that we’re leveling the playing field, not only for students and scientists in developing nations but also for students and faculty at smaller institutions, and amateurs in particular. In the past there was a glass ceiling if you were an amateur, and if you became very passionate about a group, you couldn’t get access to the rare specimens, the types, or the old literature. And suddenly all those are going to be available. I think it’s exciting and inevitable and it’s going to be a really important part of the workforce in the 21st century.

e360: So some Harvard professor may be upstaged by a 12-year-old in Iowa?

Wheeler: Well, I wouldn’t rule it out. You know, those beady-eyed specialists seem to crop up in the most unexpected places. But, again, it levels the playing field by opening the resources to everyone so you’ll be able to go as far as your passion and your interest and your talents will take you.

e360: You readily admit that taxonomists are underfunded, overworked and get no respect. The way you’ve described, it’s like you guys are the scientific equivalent of a redheaded stepchild. So how does the field fight back?

Wheeler: I think the greatest advantage we have is that the specimens themselves are so visually stunning. And the evolutionary adaptations are so unbelievably unpredictable. You look at things and wonder how it was ever possible that something so incredible came about. And as we digitize
As we digitize this information, I think the real renaissance will come from grassroots support.”
all of this information and make it available to the public, I think that the real renaissance will come from grassroots support and as we make it easier for amateur taxonomists and citizen scientists to actually roll up their sleeves and help us with this incredible project to explore and map all the species on the surface of an entire planet. I think the excitement of the enterprise, the intellectual rewards of participating, and the stunning diversity that has resulted from evolution on this planet, will [prevail]. Because it really is a now-or-never situation...

Earth a hundred years from now is going to look incredibly different. Biodiversity is going to be decimated and we have a huge ethical or moral responsibility here, because we’re the first generation fully aware of the biodiversity crisis and that millions of species may not survive the 21st century. And we’re the last generation with the opportunity to fully inventory them, at least leave behind some specimens and natural history observations that honor the fact that they existed, so that future generations that are curious about biodiversity will be able to visit a museum or an herbarium and explore a level of biodiversity that won’t be part of the world they live in.

e360: The cause to identify all of the species that remain unknown began a couple of decades ago, and the National Science Foundation has funded planetary biodiversity inventories for a few groups of organisms. But that’s hardly a global effort. Do you think this latest call to action will get more traction?

Wheeler: [We held] a meeting we called “Sustain What: Mission to Explore and Conserve Biodiversity” in New York. It was a remarkably diverse group of scientists and engineers and scholars, everyone from sociologists of science to computer engineers. Probably the largest single block were a group of really exciting, forward-looking ecologists, and a number of taxonomists, of course. And we were unanimous that this mission can be done. It’s quite feasible, given existing technology, to set out on a mission to discover and describe 10 million species in 50 years. And we found several paths to that end.

e360: But it will take money.

Wheeler: But there are enormous hidden costs to failing to do this. We will make poor decisions about conservation and end up with less biodiversity in the long run than we might have done if we had enough data to begin with. We will be unable to intercept invasive species at our ports of
There are enormous hidden costs to failing to do this.”
entry because we don’t recognize them as being foreign. Maybe the greatest opportunity cost of all is the knowledge associated with the unique features of all these species. And there are intellectual, scientific and practical dimensions of that. By failing to explore these species, on a practical level, we fail to realize the potential of what’s being called bio-mimicry, where you look at the evolutionary adaptations of species. After all, they have faced the same survival issues that humanity has and they’ve solved them in amazingly diverse and often far more sustainable ways than we have so far.

So by studying 3.6 or 3.8 billion years of natural selection, which has worked tirelessly, that for all those billions of years doing random trial and error experiments, we have this vast library of the results of those experiments. But each species that goes extinct leaves no fossil evidence behind so unless we have collected and described and stuffed them into a museum somewhere, those promising opportunities we have to solve problems simply disappear. But I would argue that the greatest cost of all though is to our humanity. There is nothing more uniquely human than our incredible curiosity about our origins. Where did the universe come from? And the biological cosmos is no less amazing than the physical cosmos and we’ve barely begun the exploration of that.

e360: You’ve written that the confluence of the technological advances with the urgency of the biodiversity crisis suggest a window of opportunity for taxonomy, but you say this window is closing as “surrogates for taxonomic knowledge vie for support in lieu of serious science.” What did you mean by that?

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Wheeler: That was maybe a little harsh reaction on my part to advocates for alternative ways of assessing species. What I had in mind was DNA barcoding. There are suggestions that we simply use a short fragment of an arbitrarily chosen gene, create a unique identifier so we can identify species, and this is actually an incredibly important step forward in progress if it’s used deliberately, in a way that reinforces taxonomy, rather than replaces it. Unfortunately, and I just reviewed yesterday a grant proposal for a funding agency in Europe where precisely this is being proposed: Let’s just bypass that hard work of taxonomy and let’s just go out and collect lots of stuff and sequence it. And if there are a few percentage differences in the genome, then we’ll just proclaim them to be species. And the only world in which replacing taxonomy with something like DNA barcoding makes sense is a world in which taxonomy is seen as a service.

If your goal is only to identify things, then this is an incredibly useful tool because you can identify a fragment of a specimen. If someone tried to smuggle a CITES [Convention on International Trade in Endangered Species of Wild Fauna and Flora]-protected species of a plant, from rootstock, we could identify it and catch them red-handed and so forth. So there are lots and lots of really positive aspects of this. But when it works well, it’s because we already know what species are in terms of deep, well-considered, evolutionary theories. And then once we know what a species is, once we understand its genetic variation, then it’s quite possible to develop these DNA markers to help us do identifications, and all that’s for the good.

ABOUT THE AUTHOR


Diane Toomey, who conducted this interview for Yale Environment 360, is an award-winning public radio journalist who has worked at Marketplace, the World Vision Report and Living on Earth, where she was the science editor. She also has reported on science, medicine and the environment for WUNC, the public radio station in Chapel Hill, N.C.
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COMMENTS


Fascinating topic and line of questioning. This is a glimpse of the future. More like this one please.

Posted by Lucia de l'Esplanade on 27 Sep 2012


Wonderful interview! I am especially excited for prospects of taxonomic pictural keys for indexing spp as an app on smart phones for field researchers and recreationers. Mr. Wheeler, I invite you to become a member of iAMscientist at http://www.iamscientist.com and join the peer process of on line collaboration.

Thank you Quentin and Diane.

Posted by Jennifer Leonard on 05 Dec 2012



 

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