MORPHOLOGY STILL KICKING

Much of the literature over the past couple of decades could give the reader the impression that whenever conflict exists in cladistic patterns indicated by DNA and morphology, DNA is to be assumed correct.  After all, morphology is so complicated, variable, subjective, and old-fashioned.  And it requires learning so many polysyllabic Classic-rooted terms, comparing hundreds or thousands of specimens, often making pain-staking dissections or preparations, and thinking... oh, so much thinking.  Afterall, as Platnick's classic 1979 "transformation" paper detailed morphological data, unlike DNA, cannot simply be described (as A, C, T, or G) but requires formulation of explicit and falsifiable hypotheses about homology and polarity.  Complexity, as it turns out, is the stuff of historical signal:  the more complex the structure the more stringently Occam's razor and Dollo's principle apply.  Simple = little or no historical information content.  The greater the complexity of the charcter, the greater the potential for cladistic signal.  Carefully developed concepts of characters have the curious property of lacking variation (they are classic examples of Popper's all-or-nothing claims about the world) and the notorious variation in morphology actually results from a confusion between informative systematic characters and infra-specific (or intra-clade) traits.  Failure to think deeply and carefully assess informative vs uninformative or to loose sight of the distinction between info relevant to population genetics rather than taxonomy results in bewildering variation.  No kidding.  Morphological characters are no more subjective than assumptions about various models and rates of molecular change.  And as for old, don't get me started.  Morphology and the DNA coding it are — ready?  drum roll, please — the same age.  And if old just means morphology has been studied longer, then it is all for the good.  Thinking about complicated and interesting questions for a long time is and will always remain advisable.

Enough rant.  If you have not yet seen Gauthier et al's paper (title page above) or the discussion of it by Losos et al. in 12 December 2012 issue of Science (p. 1428) run, don't walk, to your library (or online subscription).  I was excited by Gary Nelson's chapter in Milestones in Systematics in 2004 (edited by David Williams and Peter Forey) on the arrested development of cladistics in part because it called for returned focus on individual characters rather than an unhealthy, disproportionate focus on "tree" construction.  If Dr. Nelson's paper was the shot heard 'round the world to reawaken a revolution begun by Hennig, then Gauthier et al.'s paper may be the first full-scale engagement in a long-overdue battle to recall why we studied phylogeny to begin with.  It was and is to understand the origin and evolution of all the complex and wonderfully improbable evolutionary novelties that make biodiversity, well, diverse.  Unless we study the complex characters of morphology (and behavior and developmental genetics and...) themselves, then we lose sight of what is most interesting about pursuing cladograms, and we deprive ourselves of many of the most intellectually challenging and gratifying aspects of comparative biology.  And considering that 10,000,000 of an estimated 12,000,000 living species of plants and animals with complex morphologies (apologies to microbes with fascinating complex characters, of which there are many) remain unknown to science, a return to exploring the Cosmos of anatomical diversity is essential if we are to progress beyond arguing over cladograms for the fraction of already known homologies and species.  Given recent advances in digitization and a potential on the horizon for comparing any specimen from any museum side-by-side at any time, the number of morphological apomorphies about to be discovered will be mind-boggling.  Morphologists are on the threshold of waging shock-and-awe warfare as details of the evolution of life on earth is revealed.  Lock and load.

Public/Science Dual Purposed Exhibit

During a recent visit to the Museum fur Naturkunde in Berlin I was really impressed by a beautiful example of science/public dual usage of an exhibit.  You hear lots of rhetoric about sharing "behind the scenes" research collections with the public but few go beyond creation of a fishbowl with a window on staff preparing fossils or pressing plants.  Such peeks at science as it happens is a great idea, but the reason people should get off the sofa and visit a natural history museum is the see the real thing, to be in the presence of actual specimens that are old, rare, unique, historically or otherwise significant.

The Berlin specimen of Archaeopteryx is fantastically housed and displayed.  It is in a small room that adds to the inescapable sense that you are seeing something truly special.  Crowds wait their turn to step into the small, dimly lit room where the specimen is on display.  The obvious comparison is the chaos in the Louvre as people nudge their way close enough to the Mona Lisa to see her.

The Archaeopteryx is behind bullet proof glass like the U. S. Constitution in Washington, DC, providing exceptional security yet allowing the public to be close enough to examine the impression in detail.  When a scientist visits Berlin to study the specimen the room is secured by a closing door with the scientist inside and then the case opens to allow access to the fossil.  This is a brilliantly designed and constructed exhibit that through its architectural gravitas conveys to the public that this is an exceptionally valuable specimen.  This use of technology to allow the public to be so close to this paleontological treasure while it is not being studied by visiting scientists, yet enable direct access by scientists as needed, is a model that should be carefully studied and adapted to share other rare research specimens with an appreciative and curious public.

ROBOT(e) telemicroscopy unit during final testing in our laboratory before shipment to Europe. PHOTO: Erik Holsinger, Arizona State University).

One Small Step for Engineering, One Giant Leap for Cybertaxonomy


Tim Gostony, the wizard behind the software that operates ROBOT(e), will be in London and Paris next week making final adjustments to the instruments that I sat up there a couple of months ago, and the third unit was set up at the Smithsonian just a couple of weeks ago.  Following Tim's hardware and software upgrades we will do final testing of the units and then make plans for an official launch of the network.

ROBOT(e) is an acronym for Remotely Operable Benchmarking Of Types (Entomology), our first generation of functional remotely operable digital microscopes.  The idea is simple.  At a pre-arranged date and hour a curator places a type or rare specimen in the pin holder.  That's it until the specimen needs to be returned to the collection.  The remote user logs in and remotely turns on the electrical supply for the camera, lift, five microstep motors, and lamps.  The user has total control and can manipulate the specimen on multiple axes:  spinning 360 degrees, tilting (to see ventral surface) 180 degrees, moving on X or Y axis, and raising or lowering camera on Z axis.  The user chooses between auto and manual focus and with the click of a button can take a high resolution image of the specimen that can be saved both to a local hard disk and backup up to the host museum's hard disk.

Access to type specimens continues to be a major bottleneck to progress in species exploration and nomenclature.  More and more databases rely on Linnaean binominals as unique identifiers for species, yet types are not consulted as often as they should be to keep pace with advancing concepts of species.  The idea, of course, is that over time a growing archive of images will obviate the need to handle types either in person or with such a remote instrument... but that is a long way off at this date.

Three instruments may sound like a modest start, but by placing them in the world's three largest insect collections students and researchers around the world have potential access to more than 600,000 insect type specimens representing a very serious percentage of insect species.  They also open the possibility for online teaching using the most rare material and virtual repatriation of types, allowing scientists and students in developing nations of origin to access, study, and photograph type and rare specimens collected within their borders.

ROBOT(e) could easily be modified to handle a wide variety of biological, anthropological, and geological museum objects with just a small amount of development money.  We received a generous grant from the Virginia M. Ullman Foundation that fully funded the software development and construction of the prototype.  The final three instruments were funded by the IISE and with generous in-kind donation of engineering expertise, time, and parts by Visionary Digital, Inc.  Without this amazingly generous donation the final instruments could not have been built.

The network and first generation instruments are a proof of concept and we are already working on ideas for enhancements such as enhanced light control to create shadows, automated image montages, a measuring function, and 3D imaging, just to name a few.  We are hoping to next find an investor or investors that make these add on features possible and that allow us to take the next step into cybertaxonomy.

We have been working on a concept for a truly robotic imaging system for types.  Without special knowledge of the taxon, a curator or technician places a type in the instrument and presses a button.  Fifty images are automatically taken and stitched together to form a 3D, zoom-able, rotatable "e-type."  This high throughput instrument is necessary to deal with the back log of insect type specimens estimated at 2.5 to 3 million in number.  We calculate that fewer than two dozen such instruments could generate 1 million e-types in five years... and faster, of course, with more units.  Several such units would be needed in the large museums and others would be nomads going museum to museum.  When the backlog is caught up, the instruments would be permanently housed in regional e-typification centers where individual taxonomists and smaller institutions could send types to be digitized.

A discussion of how ROBOT(e) fits into a wider strategy to deal with insect type specimens (that are, incidentally, half of all types) can be found in our recent paper: 

Wheeler, Q.D. et al. 2012: Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity. Systematics and biodiversity, 10(1): 1-20.
doi: 10.1080/14772000.2012.665095

A free PDF can be downloaded from:
http://www.tandfonline.com/doi/abs/10.1080/14772000.2012.665095

Botanists have been leading the charge and have a great deal of the digitization of herbarium type specimens completed.  Once the insects are done, the herbaria plus hundreds of other efforts around the world would bring us closer to the vision of having all types digitized than could have been imagined prior to cybertaxonomic instrumentation.

The Same Old New Species

From time to time I receive irate feedback from a reader of my column, New to Nature, in London's The Observer newspaper concerning my use of the phrase "new species."  The reader notes that the species is not new but rather new to science.  The gentle reader is, of course, absolutely correct.  For the record I accept the results of Francesco Redi's experiments and I reject spontaneous generation as well as rancid meat.  While I have seen examples of small, isolated populations of insects that seem to have attained full species status since the retreat of the Wisconsin glaciation cycle ca. 12.000 years ago, it is the case that most species require hundreds of thousands to millions of years to reach species status.  Thus, once and for all, I use the phrase "new species" merely as a shorthand for the less alphabetically parsimonious "species new to science."

The wrath of readers would be far better directed to those who persist in wasting perfectly good binominals on species-in-the-making (that is, the dreaded and always to be avoided subspecies) rather than demonstrably full species and those who would use the word species for mere arbitrary, average genetic distances such as DNA barcodes.  These are worse than neo-Creation, out-of-the-blue, species claims for they are not species at all.  It is more productive to argue over the origins of species than to dilute the concept to meaninglessness.

A great deal of the plight of taxonomy arises from a confusion between the study of species and the study of species-in-the-making (commonly known as population biology) with the implicit supposition that species are not objective entities in nature.  They are only subjective to the extent that one fails to distinguish between the objects of study of pop bio and taxonomy.

Much to the chagrin of the more critical readers I shall continue to refer to new species under the possibly overly charitable view that even a minimal understanding of evolution will lead to the conclusion that I mean species new to science.  

Ernst Mayr's Alpha, Beta, and Gamma levels of taxonomy did nothing to preserve the dignity of so-called descriptive taxonomy.  Based on comments in the early pages of his 1942 Systematics and the Origin of Species, I suspect this was not an accident.  Relegating revisionary work to the lowest rung on a progressively more scientific conceptual ladder with evolutionary considerations at the top was indeed his design.  This made for a positive future for right-headed population-thinkers but left the observer thinking descriptive taxonomy was an anachronistic field for hermits in collections peering from under green eye shades and adjusting their armbands to reach that top pigeonhole.

It is time that we tease apart the diverse sub-fields of taxonomy and treat each with the dignity and importance befitting them.  They each play coequally important scientific roles and are quite interdependent making it undesirable to treat them otherwise.  What might a classification in place of Mayr's Greek letters be?  Here is one stab at it.

1. Analytical Taxonomy:  the sub-discipline of taxonomy concerned with formal descriptions of characters and species.  Such descriptions are themselves based on rigorous, explicit, testable hypotheses about characters and a sophisticated set of theories and methods generally associated with character analysis and distinguishing informative characters from uninformative, polymorphic "traits".  The corroborated hypotheses of analytical taxonomy are the factual foundations for phylogeny and phylogenetic classifications.

2. Phylogenetic Taxonomy/Systematics:  the sub-discipline of taxonomy that is focused on cladistic analysis and phylogenetic classification.

3. Phyloinformatics and Nomenclature:  the sub-discipline of taxonomy concerned with the efficient application of Linnaean nomenclature to provide unique identifiers for species in the form of binomials, a set of informative names for monophyletic higher taxa, and the management of taxonomic data, information, and knowledge in digital databases.

4. Translational Taxonomy:  the sub-discipline of taxonomy that focuses on translating knowledge of characters, species, and clades into useful applied information for the benefit of science and society.  The most familiar and simple example are accurate species identifications for field biologists.  A rapidly emerging example is biomimicry where evolutionary adapations are co-opted by engineers, chemists, designers, and others to solve real-world problems.

You will immediately see, also, that these four branches of taxonomy are overlapping with permeable boundaries.  This may benefit from a little tweaking but is, I submit, a step forward from Mayr's alpha/beta/gamma scheme.

Camoflaged Classification

“Camoflaging of courses to make them appear vocational is becoming an art of its own, and it is amusing to see colleges listing the only vocational benefit derivable from their courses of art as that of teaching art.

“If a course is limited to training teachers and those teachers are to teach others, just when will the vocational practice of the individual begin? How some schools do hate to roll up their sleeves and begin on the dishes!

“They will teach the lofty principles, only the theory, and George can flounder around and find the application later. And that is just why all the American Georges are about fifty years late in industrial art today.”

— Pedro J. Lemos, Leland Stanford Junior University, “The Industrial-Arts Magazine,” 1919.

The roll-up-your-sleeves, boots on the ground work of taxonomy is in a position not entirely dissimilar to that of the industrial arts at the turn of the last century. You can only talk about prosaic matters such as writing functional diagnostic keys or informative species descriptions, publishing floras or revisions or monographs, or translating cladograms (or, more often, neo-phenetic branching diagrams) into formal classifications and names, in hushed tones. Rather than openly celebrating the reciprocal illumination among fossils, anatomy, ontogeny, and molecular sequences, we as a community accede to the politically correct view that "phylogenies" are reconstructed from molecular data and that other characters are simply hung on this received knowledge of branching patterns like ornaments on a Christmas tree, after the fact and uncritically analyzed. We teach theory of phylogenetics and train students in the latest moelcular techiques, with no expectation that degree recipients will do much to address the messy, real world challenge of exploring, discovering, describing, classifying, and naming the ten million species of plants and animals that remain unknown to science. Refined, intelligent, right-minded people simply don't do taxonomy. They only teach the popular bits of it.

All Species Are Not Created Equally

The time has come for the tree-hugging, feel good conservation philosophy of the 1970s to take off its rose-colored glasses, step out of the hot tub, and towel off. As increasing numbers of species are threatened by extinction in the biodiversity crisis, it is increasingly critical that we adopt policies and goals that are informed by objective science and make tough choices based on explicitly accepted criteria.

There are of course competing goals in conservation. Are you concerned about ecological services? Evidence of phylogenetic history? Access to Nature's storehouse of answers to environmental challenges? George Will recently quipped that a great project like Hoover Dam could not be completed today as a public works program because an endangered minnow would be identified and bring the whole idea to a halt. There are times and places where a single species is so interesting or important that its preserveration should trump competing issues. There are other times and places where the Sophie's Choice should be made in order to save that trump card for an even more important moment.

As much as I wish we could save every species it is an unrealistic aim in the new world disorder. Our generation is going to oversee the extinction of hundreds of thousands if not millions of species and we can do so in one of two ways. We can pretend that our hands are clean and that we are just powerless witnesses to this biodiversity decimation and take our chances on some random outcome of the greatest species diversity bottleneck since the K-T boundary, or we can gather the fundamental taxonomic information necessary to make tough, but informed, choices and try to minimize the losses during this genetic dark age.

The only rational end game for conservation should be to maximize biodiversity as measured in phylogenetic and ecological diversity, not in simple numbers of species. Sustainable ecosystems are most probable given high levels of species diversity and if we knew enough about species and their distributions and relationships, we could prioritize the species, clades, ecosystems, and places most essential to a diverse and dynamic biosphere. This is, of course, a very imperfect approach but it is better than flying blind and accepting a random outcome.

Underneath our collective aversion to turning to objective science is an otherwise noble attempt to act as if all species had equal value. Such equality would be an admirable view were there no biodiversity crisis and were there even a remote chance of saving every species. Sadly, there are no such chances and clinging to policies that rest on such a false assumption is a dangerous path. Species are not equal. Losing Gingko biloba, the last living species of a branch of the tree of life, is a different proposition than losing one species of Atheta (a staphylinid beetle) in a genus with more than 2,000 living species that bear a remarkable resemblance one to another.

It is also disingenuous to pretend that current enforcement of species protection is anything like equal. Most endangered species are rare arthropods that no one has taken the time to get red listed, so we lavish protection on a handful of charismatic megafaunal species while ignoring invertebrates that may well be as or more important functional components of ecosytems.

Species are not equal in their contribution to phylogenetic knowledge, to ecological function, or to some other facet of biological diversity and we should not pretend in the middle of a biodiversity crisis that they deserve equal protection. This is PC heresy, of course, but it is good science, good public policy, and our last best hope for a sustainable biodiversity level that meets our future ecological service and intellectual curiosity needs.