January 2009 - tdwg - lists.tdwg.org

Re: [tdwg] [Taxacom] Semantic Web: What is a species?
by Richard Pyle 26 Jan '09

26 Jan '09

Richard Zander wrote: > Well, operationally, a species needs to be described and > published according to the rules, then survive the > marketplace of ideas. If by "rules" you mean codes of nomenclature, then they only apply to the name (label), not the species. It's the "marketplace of ideas" that serves as judge & jury for the definition of the species concept. > This is close to "what a community of > taxonomists say it is" and rather different from "what a > taxonomist says it is" (which I have also heard). An unfortunate reality is that in many cases the relevant "community" of taxonomists consists of only one individual taxonomist. And actually, it's very often the case that only one taxonomist "said" it (in the form of describing new species, ansd asserting synonymies); the rest of the community simply chooses to follow or not. Richard Jensen said: > If a species exists in the world, but no human is there to > observe it, is it real? That's the crux of the question. But I think a better way to think of it is: If "extra-terrestrial beings of a super-intelligence" arrived on our planet and classified all living things, would they come up with the same units as we have? Would they come up with a hierarchical classification scheme? If so, would they recognize one unit of classification in the hierarchy as being "special", moreseo than the others? Would those units correlate well with our "species"? Would they draw stick-figure cladograms as representations of evolutionary affinity? I suspect that in some cases there would be good congruency, and in other cases, not so much. A parallel test we can do without the extra-terrestrials is to compare traditional nomenclatures created by native peoples, independently of western science, and see what the correlation is. In my experience, the correlation is reasonably good in some cases, and in other cases ... not so much. > I am not vain enough to believe that all other species exist > solely because we humans are here to make observations about > our surroundings. > Trees falling in forests make noise whether anyone is there > or not - the physical disturbances created by the falling > tree, which our brain perceives as noise, still exist. > Unless, of course, you believe that nothing exists until or > unless it is perceived by a sentient being. If that's the > case, then the light coming from a star one million light > years away didn't exist until it was sensed. But if it didn't > exist until it was sensed, then how did it make the journey? > I find it terribly ego-centric to think that nothing else > exists except in the context of human perception. I don't think that's the issue. Nobody is claiming that organisms don't exist. The organisms would be here whether or not humans were here to observe them and (attempt to) classify them. I think we can all agree with that (at least for the purposes of this conversation). The question is whether there is a special circumscription of organisms (across time and space) whose boundaries are more clearly defined than other broader or more restrictive circumscriptions of organisms. Another way to visualize it is as some sort of "inflection point" on the evolutionary path, where the rate of divergence, or propensity to reproduce, or whatever fundamental metric of "species-ness" you want to use takes a sharp bend, relative to an otherwise smooth line before and after the bend. This would be the "speciation event", and would be objective evidence that species actually exist as units in nature with some basis in reality other than our human subjective interpetations. There would always be some fuzziness at the bend, but the point is that demarcations prior to the bend are in the realm of subspecies and other such arbitrary clusterings defined by humans, and demarcations after the bend are in the realm of genera, families, and other such arbitrary clusterings defined by humans, but the "species" demarcation has some basis in biological reality that is independent of human subjective interpretation. > Exactly what is a "natural" unit that exists in nature > independently of human interpretations? Does an atom of gold > qualify? How about a planet? > Unit implies something that can be individuated, most > typically as a consequence of connections, however defined, > between its constituent parts. You have suggested that > populations may be natural units, but the very concept of > population is linked to one or more of the many available > species definitions. If the point is that species are not > natural, then we have to know what "natural" means. Care to > give it a shot? "Natural" in this sense means "not invented by a human". The gold atom and the planet (probably) exist outside of human imagination. As mentioned above, individual organisms (probably) exist outside of human imagination. Populations, subspecies, species, genera, families ... these are all sets of individual organisms defined by humans. The question here is whether one of these kinds of sets (species) has more distinct boundaries based on properties of the organisms themselves, and is hence more "real" (independent of human imagination) than the other sets. My assertion is that "species" do not hold a special place on the scale of hierarchically nested sets. I would argue that, as a general rule (exceptions abound), the more restrictive the set, the more objective its boundaries. The set of organisms that includes two parents and all their offspring has fairly clear and objective boundaries. Expand that back several generations (great-great-great grandparents and all of their descendants), and the sets start to become a bit fuzzy and uneven (especially if individual organisms produce offspring through multiple mating events with different partners). Expand back further to what most of us would think of as a population, and the boundaries become even more fuzzy and arbitrary (i.e., rates of gene-flow among different populations may not be even or consistent over time, etc.) The further back you go (i.e., the more inclusive the sets become), in my perspective, the less clear the boundaries of the sets become. This is contrasted with the "species are real units of nature" perspective, which maintains that there is a particular zone -- a sweet-spot -- an inflection point -- a circumscription boundary -- that is "natural" (independent of human imagination), and therefore "real". From this perspective, the task of taxonomists is to discover these circumscription boundaries, and define species boundaries to be congruent with them. The fundamental premise is that the boundaries are defined by some metric of "propensity to reproduce" (or something similar). If we define a speciation event as the shift from high "propensity to reproduce" to low "propensity to reproduce", then cases where this shift is abrupt (proportional to the time between such shifts along the evolutionary path) are much easier to visualize as demarcations between species. And in such cases, it is very useful and practical to think of species as "real" units of nature, that exist in nature of human definitions, and are marked by these abrupt shifts. In cases where the shift is not so abrupt, and perhaps even continues long enough for another shift to begin (i.e., the tranisiton periods overlap), then species boundaries become much less clear, and it is much less useful to think of species as "real" entities in nature. My contention is, and has been, that almost none of these shifts are instantaneous (i.e., there are likely to be very few cases where an individual organism would be regarded as being a different species from its parents), and as such, there will always be some fuzziness in the boundaries. I'd love to ramble on (and on, and on, and on). But I suspect that only a very small percentage of readers have made it this far; and I've got other things to do today. Sorry for the bandwidth. Aloha, Rich

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Re: [tdwg] [Taxacom] Semantic Web: What is a species?
by Richard Pyle 26 Jan '09

26 Jan '09

I think of it in the same way that I think of the Ideal gas model. It works fine, provided the appropriate context. But more sophisticated equations are needed if & when the context warrants it. Physicists have no problem with this approach to rationalizing the natural world in a way that enables practical applications, without forgetting the underlying complexities that are really at play. So I think it's fine to make hypotheses and predictions based on the "Ideal Species Model", where species exist as natural entities with only minimally "fuzzy" boundaries, as a sort of first-order assumption. But when those hypotheses and predictions don't pan out, then one of the first things to examine is the assumption of "ISM" applicability (i.e., whether the "fuzzy" zones are proportionally more significant, or even dominant). In my world, as an "alpha-taxonomist", I often encounter cases where the ISM breaks down. But I suspect that, in the majority of cases where the notion of "species" is applied, the ISM serves the needs adequately. Aloha, Rich > -----Original Message----- > From: Richard Zander [mailto:Richard.Zander@mobot.org] > Sent: Monday, January 26, 2009 5:24 AM > To: Richard Pyle; tdwg(a)lists.tdwg.org; Taxacom(a)mailman.nhm.ku.edu > Subject: RE: [Taxacom] [tdwg] Semantic Web: What is a species? > > This is a good balance between scientific realism and total > subjectivity, but then what is the difference between > treating something as real for pragmatic purposes though > harboring reservations, and thinking it is real with no > reservations? Feedback from the great Out There when you are wrong? > > ***************************** > Richard H. Zander > Voice: 314-577-0276 > Missouri Botanical Garden > PO Box 299 > St. Louis, MO 63166-0299 USA > richard.zander(a)mobot.org > Web sites: http://www.mobot.org/plantscience/resbot/ > and http://www.mobot.org/plantscience/bfna/bfnamenu.htm > ***************************** > > -----Original Message----- > From: taxacom-bounces(a)mailman.nhm.ku.edu > [mailto:taxacom-bounces@mailman.nhm.ku.edu] On Behalf Of Richard Pyle > Sent: Saturday, January 24, 2009 6:55 PM > To: tdwg(a)lists.tdwg.org; Taxacom(a)mailman.nhm.ku.edu > Subject: Re: [Taxacom] [tdwg] Semantic Web: What is a species? > > > How do others think of species? > > I do not think that species are any more "real" than > subspecies, genera, and families. I believe all of these > things are abstract notions representing aggregate sets of > individual organisms, defined and labelled by humans in a way > that allows us to communicate with each other with some > degree of efficiency (though certainly not perfect efficiency). > > Having said that, I think it is highly practical in many > cases to treat units of "species" as though they were > cohesive, singular, "real" > entities > that exist in nature (within a given slice of geologic time) > independantly of human interpretations, because doing so also > facilitates communication. > This is particularly true in cases characterized by > realtively broad periods/populations of phenetic and/or > genetic stasis, homogeneity and consistency, punctuated by > relatively small periods/populations of phenetic and/or > genetic divergence, heterogeneity and spectral forms. I think > the dangers and problems (nomenclatural instability, poorly > supported hypotheses, confusing and conflicting lines of > evidence) are most evident when people attempt to apply > assumptions based on the "reality" of species to cases that > are not so characterized.

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Re: [tdwg] [Taxacom] Semantic Web: What is a species?
by Peter DeVries 25 Jan '09

25 Jan '09

Thanks to everyone for posting their comments. ;-) I think that this discussion is illustrative of two issues. Different people often have different ideas of what the same term means and in discussions these subtile differences are not always apparent. When matching or linking two terms or concepts via the Semantic Web, one needs to be aware that they may not actually have the same semantic meaning. If one of my collaborators chooses to tag their specimens with my species concept URI, they are saying that we share a common species concept. What I have been thinking about ,and what prompted the original post, was that I needed a more formal definition of what this species concept is. David Baum has a paper that will be coming out in Systematic Biology that discusses the issue of species concepts, and has some valuable insights. This issue is very complicated and I was not trying to oversimplify it. My goal was to foster thinking about the best way to implement these concepts on the Semantic Web. I had some additional thoughts that I would like to put out there. Animals seem to do a pretty good job of "recognizing" conspecifics through a number of different mechanisms. For them, species act as if they are real. What if species were mainly "real" things with fuzzy borders but our ability as humans to correctly recognize them and and their instances (specimens) is limited. We can only hypothesize that something is a species, but overtime, our hypotheses get closer to approximating the real species. This is a take on Plato's Allegory of the cave http://en.wikipedia.org/wiki/Allegory_of_the_cave And may be best illustrated by an example. We all know what a chair is, right? Now try to write a formal description of a chair that correctly accounts for all the known instances of chairs. Thanks to everyone for posting their thoughts, it has been very helpful. - Pete

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ESA 2008 Talk Using Semantic Web technologies to tie together disparate data about species .. Unique URI for each taxon
by Peter DeVries 25 Jan '09

25 Jan '09

I don't know how many of you are working with Semantic Web technologies, but I did a talk at the2008 Meeting of the Entomological Society of America Meeting in Reno. You can see it here : http://esa.confex.com/esa/2008/webprogram/Paper39190.html One of the issues that I have been struggling with is the need for a unique identifier for a species concept that stays the same despite changes in taxonomic hypotheses. When I brought this up earlier some mentioned that many considered the taxonomic hypothesis to be the species concept. I thought that this approach was wrong because it unnecessarily required me to convince one of my collaborators to adopt my taxonomic hypothesis when it was clear we were talking about the same species. To me a species is a real thing to which different taxonomic hypothesis are applied. With this in mind I implemented a system where each species has a unique URI which resolves according to the recommendations of the linked data community. You can see this service at: http://species.geospecies.org/ Here is the page for Culicidae http://species.geospecies.org/families/Culicidae Here is an example of the URI for Aedes vexans http://species.geospecies.org/spec_concept_uuid/0fcb5b7e-bcfc-4b56-b565-e1e… For a web browser this will resolve to the human readable page, for a semantic web crawler it will respond with RDF data. Here is journal reference marked up using the two major bibliography ontologies that includes what species concepts are included in the article. This allows publications to retain links to species concepts despite changes in nomenclature. http://rdf.geospecies.org/refs/sucaet2008wbr/index.rdf Here is an RDF file of species observation records (the web version is currently password protected) http://rdf.geospecies.org/observations/index.rdf I have chosen the UUID as the mechanism to make unique URI's not because of their inherent beauty, but because the allow anyone on almost any platform to create a unique id without worrying about to identical id's being created. For those interested, I can send you a PDF of my talk slides and text. I would also appreciate any feedback or suggestions :-) - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries(a)wisc.edu Insects of Wisconsin <http://insects.entomology.wisc.edu/> Spiders of Wisconsin <http://spiders.entomology.wisc.edu/> ------------------------------------------------------------

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Re: [tdwg] Semantic Web: What is a species?
by Richard Pyle 25 Jan '09

25 Jan '09

I've said it many times before on this list elsewhere: "A species is what community of taxonomists says it is." It also happens to be the de-facto operational definition ever since the notion of "species" first began, all the way through (and including) today. Until we have another definition that is broadly adopted by the taxonomic community, then it will remain the de-facto operational definition. What Darwin said in the 'Origin of Species' is still true today: "No one definition has as yet satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species." And, by the way, here's how Darwin, in his characteristically overly verbose way, had to say on the matter: "Hence, in determining whether a form should be ranked as a species or a variety, the opinion of naturalists having sound judgement and wide experience seems the only guide to follow. We must, however, in many cases, decide by a majority of naturalists, for few well-marked and well-known varieties can be named which have not been ranked as species by at least some competent judges." In other words, "A species is what community of taxonomists says it is." Aloha, Rich > -----Original Message----- > From: Bob Morris [mailto:morris.bob@gmail.com] > Sent: Sunday, January 25, 2009 7:28 AM > To: Richard Pyle > Cc: tdwg(a)lists.tdwg.org; Taxacom(a)mailman.nhm.ku.edu > Subject: Re: [tdwg] Semantic Web: What is a species? > > Ah, Rich, might I understand your position to be akin to that > of the U.S. Supreme Court Justice the Honorable Potter > Stewart whose concurring opinion in Jacobellis v. Ohio 378 > U.S. 184 (1964) contains the famous words, refering to "obscenity": > > "I shall not today attempt further to define the kinds of > material I understand to be embraced within that shorthand > description; and perhaps I could never succeed in > intelligibly doing so. But I know it when I see it, and the > motion picture involved in this case is not that." > > :-) > > Bob Morris > > > On Sun, Jan 25, 2009 at 6:44 AM, Richard Pyle > <deepreef(a)bishopmuseum.org> wrote: > > > > First, I think the comment that I *most* agree with is the > one made by > > Gurcharan Singh, that these conversations are endless (and will > > probably always be so). There are two reasons I can never seem to > > miss an opportunity to dive in and pontificate (Jim C., > that's your cue...): > > > > 1) I usually have a slightly different perspective at the end these > > conversations, than I had at the beginning (always a good > thing); and > > > > 2) I enjoy the intellectual challenge of trying to make the > same basic > > points each time using a different tact, and coming from a > different > > perspective. > > > > Now, Pete: > > > >> When a medical entomologist states that a species X, breeds in > >> shallow > > ephemeral pools and > >> has a preference for human blood meals do they mean > >> > >> The taxonomic hypothesis A. o. has these properties or > >> > >> the "natural" unit currently called A. o. has these properties ? > > > > Frankly, I don't think most medical entomologists think that deeply > > about it. In fact, I don't think most taxonomists even > think that deeply about. > > I suspect most biologists/scientists/laymen think of > species as "things" > > that exist in nature, and that these "things" have certain > properties > > that are consistent enough to allow predictions and such. > And I would > > wager that, in the vast majority of cases, they would do so > with good > > success. That doesn't make species "real" in my mind (or > even any more > > "real" than other taxonomic units -- in fact I think > populations are > > probably more demonstrably "real" than species). It just makes the > > notion of "species as real" a practical one (as if we > didn't already > > know that, after centuries of people thinking in those terms). > > > >> I think they mean the second and would benefit if the > statements made > > about that natural unit > >> could stay linked to the natural unit species concept over time. > >> > >> Unfortunately under the "species is the taxonomic > hypothesis" system > >> they > > don't. > >> > >> Does this help clarify the distinction I am trying to make? > > > > I'm not sure -- partly because I've never quite understood > what people > > mean by "species are hypotheses". By my reckoning, it's only an > > hypothesis if it's testable & falsifiable. As such, it only makes > > sense in the context of "species are real entities in > nature, and we > > can test whether our circumscriptions (aka taxon concepts) > match those > > real entities". So I've always thought of "species are hypotheses" > > and "species are real, natural entities" as being two sides > of the same coin. > > > > So I guess I don't understand the distinction you're > drawing between > > the two. > > > > Aloha, > > Rich > > > > > > _______________________________________________ > > tdwg mailing list > > tdwg(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg > > > > > > -- > Robert A. Morris > Professor of Computer Science > UMASS-Boston > ram(a)cs.umb.edu > http://bdei.cs.umb.edu/ > http://www.cs.umb.edu/~ram > http://www.cs.umb.edu/~ram/calendar.html > phone (+1)617 287 6466

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Semantic Web: What is a species?
by Peter DeVries 25 Jan '09

25 Jan '09

An interesting side discussion started up from my earlier post and I thought it might beworth discussion on the general list. I expect there will be a number of different opinions on this subject which might prove enlightening. What is a species? The way I have constructed my system I consider species to be real things too which different taxonomic hypothesis are applied. A collector or curator would then decide which species concept they believe is the best match for their specimen or group of specimens. Those individuals would then be tied to a particular species concept. (Not necessarily a specific genus species) Statements or properties could then be associated with particular species concepts. For instance: This Culicidoid species concept is a member of the Anophelinoid Group and thereby inherits the following properties: Maxillary palps about as long as proboscus, not strongly recurved Scutellum evenly rounded Scutellum seta more or less evenly distributed Most like diagram http://..... I am not sure that you could make useful statements like this if specimens are abstracted as an array of names, and if species are not real things that are separate from individual taxonomic hypothesis. Note I use Anophelinoid rather than Anophelinae to avoid tying this group of morphological characters to a specific taxonomic hypothesis. Under this model genera, families and subspecies (as they are now used) are thought of as human constructed clades and are not real in the same sense as species are real. A species exists whether or not a human has chosen to describe and name it. There also seems to be a difference in how ecologists, medical entomologists and taxonomists think of species. The former tend to view species as real things while the later see them as a human constructed grouping, where the taxonomic hypothesis is the species concept. >From the perspective of the semantic web, species concepts defined in these different ways have different meanings and may not be able to be merged directly. At least that is my current thinking .... How do others think of species? --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Semantic Web Linked Data Validator
by Peter DeVries 22 Jan '09

22 Jan '09

For those interested in making their data available on the Semantic Web, check out Vapour http://validator.linkeddata.org/vapour It provides a way to test if your URI's properly resolve. - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries(a)wisc.edu Insects of Wisconsin <http://insects.entomology.wisc.edu/> Spiders of Wisconsin <http://spiders.entomology.wisc.edu/> ------------------------------------------------------------

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FW: Database job
by Lee Belbin 07 Jan '09

07 Jan '09

Lee Belbin TDWG Secretariat From: Gary Rosenberg [mailto:rosenberg@ansp.org] Sent: Thursday, 8 January 2009 9:21 AM To: Lee Belbin Subject: Database job Hi Lee, I don't know if you've heard that the Academy of Natural Sciences is looking for a biodversity database manager. The ad was posted on taxacom, but some TDWG members might not have seen it. Could you circulating the link to the TDWG distribution list? http://www.ansp.org/about/employment.php#983 People can contact me if they have questions about the position. Best wishes, Gary Rosenberg """""""""""""""""""""""""""""""""""""""""""""""""""""""" Gary Rosenberg, Ph.D. Pilsbry Chair of Malacology Academy of Natural Sciences 1900 Benjamin Franklin Parkway Philadelphia, PA 19103-1195 USA Phone: 215-299-1033, Fax: 215-299-1170 Email: rosenberg(a)ansp.org http://clade.acnatsci.org/rosenberg http:///www.malacolog.org/ <http://www.malacolog.org/>

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Reminder: deadline for abstract submission to EGU Biodiversity Informatics Session
by Eamonn O Tuama (GBIF) 06 Jan '09

06 Jan '09

Dear Colleagues, We kindly remind you that the deadline for submitting an abstract to the European Geosciences Union (EGU) General Assembly 2009 is 13 January 2009! We cordially invite you to submit an abstract for the Biodiversity Informatics session, the main objective of which is to highlight the value of adopting informatics standards for both Biodiversity and Earth and Space Science disciplines thereby promoting interoperability across heterogeneous systems and, in particular, demonstrating how the kinds of observational data mobilised by the Global Biodiversity Information Facility network can be integrated with other geospatial data to address issues relating to climate change, protected area management, invasive species, etc. General information: http://meetings.copernicus.org/egu2009/index.html Biodiversity Informatics Session: http://meetingorganizer.copernicus.org/EGU2009/session/380 Guidance on abstract submission: http://meetings.copernicus.org/egu2009/abstract_management/index.html If you have any questions, please do not hesitate to contact one of the organisers: Convenor: Eamonn O Tuama; eotuama at gbif.org Co-convenor: Hannu Saarenmaa; hannu.saarenmaa at helsinki.fi Co-convenor: Jeremy Kerr; Jeremy.Kerr at uottawa.ca _______________________________________________ Éamonn Ó Tuama, Ph.D. (eotuama(a)gbif.org), Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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