This Sunday (i.e. the day after tomorrow) I'm heading to Adelaide to participate in the week-long National Postgraduate Training Workshop in Systematics that has been organised by the ABRS (Australian Biological Resources Study). This represents a quite welcome initiative and I personally hope that it becomes a regular occurrence - formal training in taxonomic methods is actually something of a rarity, and many of us (including yours truly) have had to essentially make a lot of it up as we go along.
As a result, I probably won't be posting anything for the next week - far too busy, darlings. See you all a week from Monday!
Field of Science
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Change of address1 year ago in Variety of Life
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Change of address1 year ago in Catalogue of Organisms
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Earth Day: Pogo and our responsibility1 year ago in Doc Madhattan
Showing posts with label Great Taxonomy Crisis. Show all posts
Showing posts with label Great Taxonomy Crisis. Show all posts
Poor Taxonomic Practice takes some F****ing Liberties!
Bortolus, A. 2008. Error cascades in the biological sciences: the unwanted consequences of using bad taxonomy in ecology. Ambio 37 (2): 114-118.
As you may have guessed from the title of this post, I'm kind of pissed. I got forwarded a copy of this paper earlier today, and was horrified by the results presented in it. Bortolus presents the results of a paper survey of 80 ecological papers published from 2005 to 2007 in ten top-ranked peer-reviewed ecology journals. The subjects of this survey were community ecology studies dealing with more than one species of organism, and for each study Bortolus took note of the sources for the identifications of the taxa surveyed. I hardly need point out how significant such identifications would be for the papers in question - after all, if the subjects of an ecological study are not reliably identified then the usefulness and significance of the entire study comes into question. So you would think that it would be pretty important for the authors to demonstrate the firmness of their identifications, no? Well, let me show you the graph of the results:
Note that the numbers do not necessarily add up to 100%. A single paper might haved used more than one form of identification. I also disagree slightly with Bortolus' treatment of "grey" (not or not significantly peer-reviewed) literature - lumping the citation of field guides in with unpublished theses does somewhat overlook that excellent field guides do exist for some taxa (most notably birds), and even amateurs without formal taxonomic experience may through these field guides hold a significant amount of expertise in identifying the taxa covered (also, of course, field guides are widely available and consultable while theses are not). Nevertheless, let me point out the part of the results that has incensed me the most. It's the second bar from the left. Fully a third of the papers surveyed gave no authority whatsoever for the identity of the species surveyed! It's not as if the bar was set particularly high for citing an authority, either. Acknowledging the input of a taxonomist who identified specimens (or having a taxonomist as one of the authors) counted. Noting that one of the authors of the paper had personally identified the taxa counted, or the use of a cited identification key, counted. All it would have taken in most cases would have been a couple of sentences. And yet, it seems that this is a couple of sentences too many in a lot of cases.
Of course, the availability of voucher specimens would do a lot to alleviate these concerns. I've written before about the importance of voucher specimens that allow other researchers to check specimen identifications. so how many of the papers surveyed noted the availability of voucher specimens?
2.5%.
Yes, you read right. Two point fricking five percent. What is more, those papers that did record voucher specimens were invariably among those that acknowledged the input of a professional taxonomist in some way, and so were probably not among the more suspect class in the first place.
As is de rigeur in this kind of discussion, Bortolus gives us examples of the kind of errors that can result from poor taxonomic practice. Some errors are fairly innocuous, but others can have fairly serious consequences. There's the case of a restoration programme in San Francisco that included the propagation and replanting of the native littoral grass Spartina foliosa. Unfortunately, the actual specimens propagated were not S. foliosa, but the non-native S. densiflora, and as a result of the programme S. densiflora was transformed from a minor adventive to a significant invasive. There's the case of three morphologically similar but ecologically distinct Mytilus mussel species, the decline of one of which due to the invasive spread of another went unnoticed for many years. There's the case of a failure to distinguish Anopheles mosquito species in Burma resulting in the long-term targeting of a non-malaria-carrying species by control programmes instead of the actual malaria vector. Bad taxonomy does matter.
Some of my readers may protest that it seems a little harsh to expect identification sources from authors who may be very familiar with the species involved and hence might be trusted to identify them reliably. To which I reply, bullshit. One of the main principles of science is that it is not enough to simply assert that one "just knows". And besides, is it really asking that much? Biomolecular studies, for instance, are expected to include full details of methods used, and it would not be considered unusual for an author to cite Saiki et al. (1988), no matter how many thousands of PCR reactions that author might have conducted during their career. Also, there are significant ethical considerations involved. In failing to cite or acknowledge their identification sources, authors are doing a significant disservice to the taxonomists on whose work their own relies. It is exactly this assumption that the reliability of taxon identifications can be taken for granted that has resulted in the undervaluing and loss of taxonomic expertise in many parts of the world. Is a passing mention in the acknowledgements really that much to ask?
As you may have guessed from the title of this post, I'm kind of pissed. I got forwarded a copy of this paper earlier today, and was horrified by the results presented in it. Bortolus presents the results of a paper survey of 80 ecological papers published from 2005 to 2007 in ten top-ranked peer-reviewed ecology journals. The subjects of this survey were community ecology studies dealing with more than one species of organism, and for each study Bortolus took note of the sources for the identifications of the taxa surveyed. I hardly need point out how significant such identifications would be for the papers in question - after all, if the subjects of an ecological study are not reliably identified then the usefulness and significance of the entire study comes into question. So you would think that it would be pretty important for the authors to demonstrate the firmness of their identifications, no? Well, let me show you the graph of the results:
Note that the numbers do not necessarily add up to 100%. A single paper might haved used more than one form of identification. I also disagree slightly with Bortolus' treatment of "grey" (not or not significantly peer-reviewed) literature - lumping the citation of field guides in with unpublished theses does somewhat overlook that excellent field guides do exist for some taxa (most notably birds), and even amateurs without formal taxonomic experience may through these field guides hold a significant amount of expertise in identifying the taxa covered (also, of course, field guides are widely available and consultable while theses are not). Nevertheless, let me point out the part of the results that has incensed me the most. It's the second bar from the left. Fully a third of the papers surveyed gave no authority whatsoever for the identity of the species surveyed! It's not as if the bar was set particularly high for citing an authority, either. Acknowledging the input of a taxonomist who identified specimens (or having a taxonomist as one of the authors) counted. Noting that one of the authors of the paper had personally identified the taxa counted, or the use of a cited identification key, counted. All it would have taken in most cases would have been a couple of sentences. And yet, it seems that this is a couple of sentences too many in a lot of cases.
Of course, the availability of voucher specimens would do a lot to alleviate these concerns. I've written before about the importance of voucher specimens that allow other researchers to check specimen identifications. so how many of the papers surveyed noted the availability of voucher specimens?
2.5%.
Yes, you read right. Two point fricking five percent. What is more, those papers that did record voucher specimens were invariably among those that acknowledged the input of a professional taxonomist in some way, and so were probably not among the more suspect class in the first place.
As is de rigeur in this kind of discussion, Bortolus gives us examples of the kind of errors that can result from poor taxonomic practice. Some errors are fairly innocuous, but others can have fairly serious consequences. There's the case of a restoration programme in San Francisco that included the propagation and replanting of the native littoral grass Spartina foliosa. Unfortunately, the actual specimens propagated were not S. foliosa, but the non-native S. densiflora, and as a result of the programme S. densiflora was transformed from a minor adventive to a significant invasive. There's the case of three morphologically similar but ecologically distinct Mytilus mussel species, the decline of one of which due to the invasive spread of another went unnoticed for many years. There's the case of a failure to distinguish Anopheles mosquito species in Burma resulting in the long-term targeting of a non-malaria-carrying species by control programmes instead of the actual malaria vector. Bad taxonomy does matter.
Some of my readers may protest that it seems a little harsh to expect identification sources from authors who may be very familiar with the species involved and hence might be trusted to identify them reliably. To which I reply, bullshit. One of the main principles of science is that it is not enough to simply assert that one "just knows". And besides, is it really asking that much? Biomolecular studies, for instance, are expected to include full details of methods used, and it would not be considered unusual for an author to cite Saiki et al. (1988), no matter how many thousands of PCR reactions that author might have conducted during their career. Also, there are significant ethical considerations involved. In failing to cite or acknowledge their identification sources, authors are doing a significant disservice to the taxonomists on whose work their own relies. It is exactly this assumption that the reliability of taxon identifications can be taken for granted that has resulted in the undervaluing and loss of taxonomic expertise in many parts of the world. Is a passing mention in the acknowledgements really that much to ask?
The Importance of Vouchers: Even Molecular Workers Need Herbaria
Those of you who have seen the Monty Python movie The Meaning of Life may recall a scene near the beginning where a woman is brought into a hospital to have a baby, only to have attention to her condition overshadowed by the attention lavished by the hospital staff on their expensive equipment and machines going "ping". Part of the joke, of course, is that a lot of their flashy machinery is completely unnecessary under normal circumstances, considering that women have been successfully having babies without it for as long as there have been women to have babies. The other part is that while we all see the ridiculousness of the situation in the movie, we still all fall for the flashy expensive option in real life. If we go to hospital ourselves, we still damn want the machine that goes "ping".
The proposed closure of the Utrecht Herbarium is actually just another example of a general trend of recent years towards the downsizing and reduction in prestige of natural history collections everywhere. In these days of biochemical assays and gene sequencers, many people, unfortunately including many university and museum directors, seem to find specimen collections just a little antiquarian and hokey. Surely modern genomic and proteomic techniques have rendered such things obsolete? No, they haven't. Molecular investigations don't remove the need for physical specimen storage. Indeed, they make it even more important than before.
Yesterday, I wrote on the importance of conserving type specimens. Type specimens are a special type of voucher specimen, and I thought I'd enlarge today on the significance of voucher specimens in general. A voucher is a representative specimen of the organisms used in a study, such as the specimen used as the source of DNA for a molecular study or a specimen collected as part of an ecological survey. Like type specimens, voucher specimens allow for the confirmation of the identity of the species referred to in the study. They therefore provide a backup against misleading results due to such things as misidentification, changing species concepts, etc.
Apparently one of the projects that has been going on at the Utrecht Herbarium involves the identification of native medicinal plants used in Suriname, so I'll take that as a hypothetical example. Imagine that a researcher working on one of these medicinal plants, call it the "big-leaved bungleflower", manages to extract an active compound from it that he dubs "ifeelfantasticin", and which shows a great deal of promise in medical tests. The problem is that no-one else is able to extract that compound from the big-leaved bungleflower, despite much effort. Despair seems inevitable, until someone decides to check the voucher specimens that the original researcher deposited from his original study. At that point, it becomes clear that the original researcher was not using specimens of big-leaved bungleflower as he had thought, but actually the similar purple-leaved bungleflower. Focus switches to the latter species, ifeelfantasticin is recovered once more, and medical history is made.
Without the voucher specimens, the error would have never been corrected so easily. Griffiths and Bates (2002) report on a real life example of voucher specimens allowing the explanation of unusual results, when a molecular study on New World vultures was seemingly unable to distinguish between greater (Cathartes melambrotus) and lesser (C. burrovianus) yellow-headed vultures. Re-examination of the original specimens indicated that some had been misidentified, including one specimen that had been deposited in a collection before the two species were recognised as distinct.
Unfortunately, all too many researchers still fail to deposit vouchers for studies (Agerer et al., 2000; Wheeler, 2003). Dennis (1960, as quoted in Agerer et al., 2000) commented that "records that cannot be verified are mere waste paper". The need for proper natural history collections remains as strong now as ever.
REFERENCES
Agerer, R., J. Ammirati, P. Blanz, R. Courtecuisse, D. E. Desjardin, W. Gams, N. Hallenberg, R. Halling, D. L. Hawksworth, E. Horak, R. P. Korf, G. M. Mueller, F. Oberwinkler, G. Rambold, R. C. Summerbell, D. Triebel & R. Watling. 2000. Open letter to the scientific community of mycologists: “Always deposit vouchers”. Mycorrhiza 10 (2): 95-97.
Griffiths, C. S., & J. M. Bates. 2002. Morphology, genetics and the value of voucher specimens: an example with Cathartes vultures. Journal of Raptor Research 36 (3): 183-187.
Wheeler, T. A. 2003. The role of voucher specimens in validating faunistic and ecological research. Biological Survey of Canada (Terrestrial Arthropods) Document series no. 9. Ottawa.
The Significance of Type Specimens, and More on Utrecht
Last week I brought up the topic of the Utrecht Herbarium, which faces imminent closure as of June 1. Since then I have been in touch with Renske Ek, who started the petition against the closure. The closure of the herbarium is primarily a cost-cutting measure, and has been under consideration for some time, though it was not announced officially until the 26th of March. The most significant question you might be asking, though, is what is to become of the collection after the closure?
Let me remind you that, as well as over 800,000 specimens, the Utrecht Herbarium holds over 10,000 type specimens. What, some of you may ask, is a type specimen? When a new species is described, the author will select one of his/her specimens (or sometimes, a collection of specimens) of that species to act as the 'type'. That specimen then becomes the definitive example of that species. From that point, if the question ever arises, "What species does "species name X" refer to?", the answer essentially is, "The species that "type specimen X" belongs to". The type specimen also allows the identification of the species if the original published description turns out to be inadequate somehow. Imagine that a taxonomist working on ants describes a new species. He describes the new species' colour, ornamentation of the body, shape of its head, and calls it "species 1". Many years later, another ant taxonomist discovers that the area where the earlier taxo got his specimens from is actually home to two very similar species. One is the earlier author's "species 1", the other is a new "species 2". The problem is, the two species are identical in colour, body ornamentation and shape of the head. They can be distinguished by the shape of the antennae, but the earlier taxonomist, not realising that the shape of the antennae was going to turn out to be significant, never included it in his original description. How is the later taxonomist to work out which of the two species he has on hand is "species 1"? That is where the type specimen comes into play - even if the original description didn't include the appearance of the antenna, the later taxonomist can always look at the type specimen and fill in the missing details.
The type specimen means that a species name is not just a vague philosophical concept, but is tied to a real tangible object. As a result, it is critical that any type specimen is preserved and remains accessible to future researchers. If a collection is locked away from visitors, the specimens are unable to serve their purpose. Also, a locked collection does not simply sit intact until such a time as it is ever opened. Biological collections require constant maintenance and monitoring. After all, these are pieces of dead plant and animal matter we're talking about - their natural tendency is to decay. Alcohol and other preservatives can evaporate, dried insects or plants may be eaten by beetles, and when the collection finally gets opened up again, all that is left is unrecognisable dust and mush. The collected specimens, and type specimens in particular, have failed in their purpose.
Unfortunately, at present there seems to be no clear plan for what is to happen to the Utrecht herbarium collection after closure. Plans to transfer it to the Universiteit Leiden appear to have been shelved due to lack of funding. It seems to have been hoped that the Nederlands Centrum voor Biodiversiteit (Dutch Centre for Biodiversity) currently being put together would offer a permanent home for the collection, but it is unlikely that the Centre will be up and running before the herbarium closes.
Whatever is to become of the Utrecht Herbarium itself, it is imperative that the collection, particularly the type specimens, remains curated and accessible somewhere. Failure to ensure this would be an unforgivable tragedy.
Postscript: David Shorthouse of iSpiders has also commented on the situation.
Let me remind you that, as well as over 800,000 specimens, the Utrecht Herbarium holds over 10,000 type specimens. What, some of you may ask, is a type specimen? When a new species is described, the author will select one of his/her specimens (or sometimes, a collection of specimens) of that species to act as the 'type'. That specimen then becomes the definitive example of that species. From that point, if the question ever arises, "What species does "species name X" refer to?", the answer essentially is, "The species that "type specimen X" belongs to". The type specimen also allows the identification of the species if the original published description turns out to be inadequate somehow. Imagine that a taxonomist working on ants describes a new species. He describes the new species' colour, ornamentation of the body, shape of its head, and calls it "species 1". Many years later, another ant taxonomist discovers that the area where the earlier taxo got his specimens from is actually home to two very similar species. One is the earlier author's "species 1", the other is a new "species 2". The problem is, the two species are identical in colour, body ornamentation and shape of the head. They can be distinguished by the shape of the antennae, but the earlier taxonomist, not realising that the shape of the antennae was going to turn out to be significant, never included it in his original description. How is the later taxonomist to work out which of the two species he has on hand is "species 1"? That is where the type specimen comes into play - even if the original description didn't include the appearance of the antenna, the later taxonomist can always look at the type specimen and fill in the missing details.
The type specimen means that a species name is not just a vague philosophical concept, but is tied to a real tangible object. As a result, it is critical that any type specimen is preserved and remains accessible to future researchers. If a collection is locked away from visitors, the specimens are unable to serve their purpose. Also, a locked collection does not simply sit intact until such a time as it is ever opened. Biological collections require constant maintenance and monitoring. After all, these are pieces of dead plant and animal matter we're talking about - their natural tendency is to decay. Alcohol and other preservatives can evaporate, dried insects or plants may be eaten by beetles, and when the collection finally gets opened up again, all that is left is unrecognisable dust and mush. The collected specimens, and type specimens in particular, have failed in their purpose.
Unfortunately, at present there seems to be no clear plan for what is to happen to the Utrecht herbarium collection after closure. Plans to transfer it to the Universiteit Leiden appear to have been shelved due to lack of funding. It seems to have been hoped that the Nederlands Centrum voor Biodiversiteit (Dutch Centre for Biodiversity) currently being put together would offer a permanent home for the collection, but it is unlikely that the Centre will be up and running before the herbarium closes.
Whatever is to become of the Utrecht Herbarium itself, it is imperative that the collection, particularly the type specimens, remains curated and accessible somewhere. Failure to ensure this would be an unforgivable tragedy.
Postscript: David Shorthouse of iSpiders has also commented on the situation.
An Endangered Herbarium
A message that came through yesterday on the TAXACOM mailling list informs us that the University Board of Utrecht University in the Netherlands has announced plans to close the university herbarium as of the 1st of June, with access to the collections by researchers to cease immediately as of that date.
The Utrecht Herbarium holds a collection of over 800,000 specimens, including more than 10,000 type specimens. The central focus of research at the university is on plant biodiversity in tropical South America, particularly Suriname. Among the current research projects is investigation of the taxonomic identity of medicinal plants used in Suriname, information that will be vital in developing wider applications of the species involved.
The Utrecht Herbarium is part of the Nationaal Herbarium Nederland, which also includes branches at the Universiteit Leiden and the Wageningen University, and would have also been an significant part of the integrated Netherlands Centre for Biodiversity currently being developed. There are currently four PhD students among the staff at the herbarium.
For more information on the significance of the Utrecht Herbarium, and a petition against its closure and, go here. The website of the Utrecht Herbarium is here, and that of the Nationaal Herbarium Nederland is here. Other blog reactions to the closure can be found at Myrmecos and The Other 95%. I will endeavour to keep you all abreast of further developments.
The Utrecht Herbarium holds a collection of over 800,000 specimens, including more than 10,000 type specimens. The central focus of research at the university is on plant biodiversity in tropical South America, particularly Suriname. Among the current research projects is investigation of the taxonomic identity of medicinal plants used in Suriname, information that will be vital in developing wider applications of the species involved.
The Utrecht Herbarium is part of the Nationaal Herbarium Nederland, which also includes branches at the Universiteit Leiden and the Wageningen University, and would have also been an significant part of the integrated Netherlands Centre for Biodiversity currently being developed. There are currently four PhD students among the staff at the herbarium.
For more information on the significance of the Utrecht Herbarium, and a petition against its closure and, go here. The website of the Utrecht Herbarium is here, and that of the Nationaal Herbarium Nederland is here. Other blog reactions to the closure can be found at Myrmecos and The Other 95%. I will endeavour to keep you all abreast of further developments.
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