Monday, December 19, 2011

The story behind "Azana sinusa: remarks on range and records."

I previously promised to blog every one of my future publications. And finally, I am able to follow through on the first one. I'll be using Eisen's brilliant blog post about the "Stalking the 4th Domain" paper as a format guideline, but since this is very much a small scale natural history story rather than a large scale molecular biology story, I'm mostly making this up as I go. As a natural history story, it may not seem like science to all people. Taxonomist FPD Cotterill calls natural history an ideographic science, a science of details that provides the primary support for the wide scale theorems of law-like or nomothetic science. And as such, denigration of natural history does not fair well for biology in general. So I will pass by the naysayers and move forward.


Burington, ZL. 2011. Azana sinusa Coher, 1995 (Diptera: Mycetophilidae: Sciophilinae): remarks on range extension and collection records. Check List 7(6):815-816. PDF


The Backstory

In late 2010 I was attempting to organize the wet-stored specimens of Sciaroidea (fungus gnats) in the Clemson University Arthropod Collection. The CUAC does not have a very large collection of the group, only 100 to 200 specimens, most of them collected before 1990 by former students or in flight intercept traps. Fungus gnats are of great interest to me, since they are greatly understudied in North America, with perhaps less than 50% of all species described. In particular, I'm interested in the Family Keroplatidae, the predacious or web-spinning fungus gnats, the larvae of which spin a web of sticky silk to capture small arthropods or fungal spores. You may have heard of the cave glowworms of New Zealand, a popular ecotourist destination; these bioluminecent fungus gnat larvae are keroplatids.

I was using the genus key in the Manual of Nearctic Diptera (MND) (now available for free online) to identify the adults. Despite being thirty years old and somewhat out of date, the MND worked well enough for my purposes. When I identified specimens from two different vials as the genus Azana, Family Mycetophilidae, I was intrigued. The specimens were less than 10 cm in length, with a distinctive reduction or loss of the medial and cubital wing veins (see figure at end).

At the time of the Nearctic Manual's publication, no North American species of Azana had been described, although Vockeroth believed there was at least one species on the continent. Both Jean Laffoon and Elizabeth Fisher had previously noted collections of the genus which remain unconfirmed, from Minnesota and Cape Breton Island (Nova Scotia), respectively. It wasn't until 1995 that Edward Coher finally described this species from Maine, New Hampshire and Massachusetts as Azana sinusa, which tells you just how rarely collected this organism is. From an additional male specimen in the pinned collection, I was able to confirm from the genetalia that these were probably all A. sinusa Coher. Although Peter Kerr of California Department of Food and Agriculture recently described two new western species, A. malinamoena and A. frizzelli, A. sinusa remains the only Eastern species.

All these facts were not so intriguing as was the /location/ of the collections: the coastal plain and sandhills of South Carolina. The type specimens from Coher's paper were collected in the mountains and coastal areas of New England, approximately 1200 km to the North, with no specimens ever collected below 40 degrees latitude. Since this continues to be a poorly known, seldom collected species, and since the specimens I had found in the CUAC were so far outside the known range, I decided to publish this information.


The Journal


I wanted to put a note here about the journal I chose for publication, since most readers are probably not familiar with it. Check List is a peer reviewed, open access online journal specializing in regional species lists and notes on range and distribution. Traditionally, a short note such as this would have been published in Entomological News, but that particular journal has had a large backlog over the last year; as I already had one article waiting for publication in that journal, I thought it wise to try Check List. Though the website and editors are Brazilian, the journal is published in American English, and the editors were timely about corresponding with me. The best thing about this journal is that it's completely open access and free for authors. Since they do not publish anything that might be considered a nomenclatural act or new species descriptions, a print version is not necessary. It also means that there is no limit on publication size, and that what limits the publication speed is the peer review process, correspondence time, and copy editing. I will say that the journal guidelines are very picky about formatting, and I was asked to remake the distribution map I originally provided; this is perhaps for the best. I will definitely be coming back to this journal with future manuscripts. They fill a publication niche that used to be a large portion of the entomological literature, but fallen into disrespect because publishing short notes is nowadays seen as cheating, as padding one's CV.


The Denouement


Some readers may be wondering why I would take the time and effort to publish such a short note on the range of a rare and seemingly insignificant species. And I admit, the reviewers taxed me with this same question: is this really /worthy/ of publication? Well, certainly the editor would have rejected it outright if he didn't see something worthy in it. And of course, it would have never been published if the reviewers hadn't eventually felt it worthy. The photo I published with it is the first photo (to my knowledge) ever taken of this species, and the distributional data and map the most complete. It continues that we know essentially nothing of the biology of this species. Little information was contained on the specimen labels, and it's so rarely collected that trends are hard to draw. Coher, in his 1995 publication, said that the morphology of the mouthparts suggests the adults are nectar feeders, but we have no observations of this. Kerr collected his Azana species from flight intercept traps suspended from redwood in California. Might Azana sinusa as well dwell in the tree tops? There's no way of knowing from the scant information we have, though this behavior would suggest why it is rarely collected; combining the data from all publications, less than 50 specimens have ever been reported.

Overall, working on this manuscript has given me more puzzles than answers. But, I think it was overall good; it synthesizes the known information, and shows us a wider picture of the species than we realized. I never undertook the project as an attempt to pad my CV or make a name for myself. Goodness knows there are easier ways to accomplish this. The synthesizing and editing was far more work than I had anticipated, and the process far longer than I had hoped, but I think it turned out alright. Despite my past criticisms of Encyclopedia of Life, I plan to create a full entry using the information in this and previous publications.

The species Azana sinusa, and little forgotten or seldom noticed species everywhere, remind me of my favorite vignette from Aldo Leopold's A Sand County Almanac:

Within a few weeks now Draba, the smallest flower that blows, will sprinkle every sandy place with small blooms.

He who hopes for spring with upturned eye never sees so small a thing as Draba. He who despairs of spring with downcast eye steps on it, unknowing. He who searches for spring with his knees in the mud finds it, in abundance.

Draba asks, and gets, but scant allowance of warmth and comfort; it subsists on the leavings of unwanted time and space. Botany books give it two or three lines, but never a plate or portrait. Sand too poor and sun too weak for bigger, better blooms are good enough for Draba. After all it is no spring flower, but only a postscript to a hope.

Draba plucks no heartstrings. Its perfume, if there is any, is lost in the gusty winds. Its color is plain white. Its leaves wear a sensible woolly coat. Nothing eats it; it is too small. No poets sing of it. Some botanist once gave it a Latin name, and then forgot it. Altogether it is of no importance--just a small creature that does a small job quickly and well.

Leopold was king of qualitative natural history, he wrote in a way that even the smallest and seemingly insignificant of organisms glowed with individuality and purpose. While I don't claim to equal him by any means, I hope to shed some light on the matter of species like Azana sinusa, which now at least has a face to put on the name.

Azana sinusa male, left habitus

Tuesday, December 6, 2011

Misconceptions about taxonomy.

I know Gawker is supposed to be a snarky internet publication concerned more with the hipness of it's readers than relaying actual pieces of news, and vertebrate paleontology stories aren't exactly the general subject matter of this blog. But this article by Max Read on a new species of cerotopsid discovered in the basement of the British Museum which calls paleontologists "morons" is pure idiocy, and is a clear example of the public misunderstanding of how new species are discovered.

As I noted recently, natural history collections are repositories for specimens that grow in value over time from information added to these acquisitions by researchers. The true value of any individual specimen is often not revealed until years after it's acquisition. As curators and visiting scientists use the specimen for their research, include it in publications, and use that information to educate the public, the specimen increases in value. Even broken and fragmentary items like the fossil in question are not tossed out, and over time many of these items will end up in "cigar box limbo". What the former curator thought was a few rubbish pieces of a previously described cerotopsid dinosaur was nevertheless saved, and a century later found to represent a new, seemingly intermediate group between the well known Centrosaurus and Styracosaurus.

That this is a common occurrence would no doubt come as a surprise to Mr. Read. Many of the new species described every year are already sitting in the shelves of natural history collections around the world, sometimes for hundreds of years. These specimens are unidentified, or incorrectly identified, or identified as another closely related species. Figuring out which of these are new species is the job of an expert in that group who has the experience to tease out these minor differences and understand their taxonomic meaning. And it may not be until a hundred years after the acquisition till a taxonomist of that caliber comes along. The length of time between taxonomic revisions of a particular group is painfully long, and the number of available experts is spread thin across all the work that needs doing. This problem is called the Taxonomic Impediment, and as curatorial positions are retired and unfilled, the number of groups without experts only increases. What seems moronic to Mr. Read is actually an issue of funding for basic taxonomy, and not a lack of intelligence on the part of the British Museum's curators.

In addition, I don't think the general public understands just how much research goes into describing a new species. First, the researcher in question has to have some sort of expertise in the group so they can actually see that differences that would tip off an undescribed species. This requires years of careful observation; it's not something which can be taught in a classroom. Then the expert often has to examine the type specimens, which usually means travel to at least one distant museum. Finally, after all these tedious comparisons, the taxonomist has to publish the discovery, which requires illustrations, summaries of all the material examined, intense editing, and wrestling with reviewer comments.

The portrayal of the alpha taxonomist as a jungle explorer in pith helmet reaching down to pick up a flower or beetle, hoisting it high and dubbing it "Excaliber arthurius" on the spot is not only wrong, it misrepresents the true difficulty of our science. It makes people think that, well, paleontologists who find new species in their museum basement are morons. Or that throwing money at tropical expeditions is going to somehow, in itself, describe all species on the planet. Or that museums are defunct, musty, and mostly useless artifacts of the past. The truth is that taxonomists are underfunded, understaffed, and being shoved out of the picture by these misconceptions.

Saturday, December 3, 2011

Natural History Collections in a Nutshell.

Dr. Gamer, a beetle researcher at the British Museum of Natural History, has a nice blog post which illustrates what natural history collections do, using tiger beetles as an example.

Natural history collections in general are a repository for physical specimens, whether biological, geological, or anthropological. These objects are collected by researchers at the museum or donated by experts working in the field. A particular collection may have a local or worldwide scope, and may specialize in a particular group of organisms or topic, depending on the past interests of researchers connected with the collection. The objects or specimens are organized in a way that makes them easily retrievable for future research (such as a general reference system).

At some point a researcher will either come to the museum and look at these specimens, or request a loan. When the loan is returned, it's expected that the specimens will have some value added to them. Perhaps information about where they came from, or species identification. Either way, the objects are returned to the collection and add to its overall value.

This is the natural history collection (and natural history research) cycle in a nutshell: Collect specimens; Organize specimens; Loan specimens to experts; Specimens are returned with identification or other information to make the collection ever more complete and useful. Repeat indefinitely. A natural history collection grows in size and value over time from this small set of activities.

Museums are a step higher than this, and house multiple natural history collections. The growing value of the collections is used for research by the curators, and the curator's research is used to educate the public. But they are first and foremost for housing collections, which is where the value and primary work within a museum starts.

Monday, November 28, 2011

Picture of the Week: My Childhood 2.

My mother and father made several of these large jewelry cases into insect display boxes. This one was for a variety of things, specimens that didn't fit into the dragonfly and butterfly cases. We raised the four big saturniids at the top, the luna and Cercropia moths, from caterpilliars when I was 5. The Cercropia cocoon (top right center) was from one of those individuals. The Prometheus moth (center left) we hatched from the cocoon to its right. Most of the rest were collected by my father, but there are a few things there that I collected, maybe the first arthropods I ever collected. Down near the bottom right to the left of the sphinx moth is a tabanid and a millipede. I remember collecting those two somewhere between the age of 5 and 14. And I think the small mantid on the bottom left. I can tell because the mounting is far more haphazard and less perfect than the rest. My father is a perfectionist when it comes to these things, and it shows in how nice they look in this display case.

The uses and folly of DNA 'barcoding'.

According to Wired, DNA barcoding has gone mainstream. I fail to see how this is possible since sequencing technology, as cheap as it is becoming, continues to only be available to few and not the public. It's not like, for example, you can pick up a PCR kit and "Sony Deluxe Pirosequencer XL" on Amazon (though you can make your own gel eletrophoresis setup).

If you aren't familiar with the concept, a DNA 'barcode' is a short length of DNA sequence that can distinguish between closely related species. In most cases when people talk about it, they mean the mitochondrial gene Cytochrome C Oxidase subunit I (or COI for short). COI is found universally in all organisms that have mitochondria, so people talk about it being a "universal barcode", that could be potentially used to identify any (eukaryotic) organism on the planet.

The process for getting a sequence is relatively simple, assuming you have the technology. A small piece of the organism in question is broken down and run through a polymerase chain reaction cycle to amplify the COI gene fragments. Then it is sequenced, either through dye-terminator sequencing or the more fancy, faster, more expensive pirosequencing. The sequences are uploaded to a general reference database such as Bold Systems, which anyone can use to compare their sequences to a known set. The expectation is that the more species sequenced, the more likely you are to get a match.

And to the credit of the IBOL team, some of these applications are really cool, like using the sequence library to catch mislabeled fish in markets and restaurants. That's awesome, one more tool in the diagnostic toobox, albeit an expensive one. Since there are so many copies of mitochondrial DNA in most organisms, far more than nuclear DNA, you only need a very small fragment to obtain a sequence. If the specimen is just a slab of meat at market, no problem! Even holotype specimens can be sampled nondestructively.

But identification is really where the utility of DNA barcoding ends, and given the time and expense for obtaining each sequence, it is and will continue to be far easier to use traditional diagnostic methods in most cases. It is not a magic bullet, and it's certainly not a replacement for taxonomy or systematics. Thinking that an entire species can be reduced to a single, definitive sequence length of 500 base pairs from a few individuals is insane. It would be the same as claiming it's alright to dam up Yosemite Valley because we have some photographs. As I pointed out before, the goal of taxonomy is to track characters and their relationships, and assemble a general reference system which is descriptive, predictive and explanatory. The COI gene is one character, out of millions. Reducing species to this one character is pure folly.

The other problem is the definitive nature of these barcodes. They fail to address the temporal variation in a species as it changes over time, much less the spacial variation or level of variation within a single population. Not to mention, the individual base pairs, not the entire sequence pattern or some portion, are used as defining differences in an analysis. How can we use a few individuals to define an entire species, when we know that variation in the defining character, the sequence, exists even between those few individuals? At least taxonomists recognize this variability and only choose character consistent for all known individuals as definitive.

Species are hypotheses, and these hypotheses are going to change over time, but it seems the DNA barcoding proponents may still hold to immutable species concepts despite 150 years of evolutionary revolution in biology.

Sunday, November 27, 2011

Surprise, you have acquisitions!: Specimens in cigar box limbo.

While working and volunteering in the Clemson University Arthropod Collection (CUAC) during my master's program, I stumbled across many surprising (sometimes alarming) finds lost to decades in dark corners and cabinets. These included items such as:

  • Holotype specimens from a museum that no longer exists (found while cleaning my office out in the first week)
  • 30 year old loans
  • Boxes full of vials with code labeled specimens linked to notebooks, left by a former graduate student
  • Drawers of damaged (yet mostly salvageable) tropical insects for display
  • A folder containing 40 years of notes and other items of the great late entomologist Herbert H. Ross (more on that in a later post)

These things just happen in a collection too large for its space, with too little staff for it's size (and this is true at even the biggest museums now). Things are left there, loaned and shelved, acquired and forgotten. Some curators are proactive, but when the collection manager, who is responsible for the day to day care of the collection, leaves or changes some things will inevitably become purposeless and other things stacked on top. And the CUAC is not a large collection by any means, only about 1 million specimens housed in 2 rooms too small for the collection. If the above was found in such a small collection rebuilt after a fire in 1925, you can imagine the large amount of surprise "acquisitions" associated with larger or older institutions.

Cigar boxes full of papered specimens from SDNHM (© Nelvin C. Cepeda)


The San Diego Natural History Museum (SDNHM) has a collection comparable in size to the CUAC, but is about 75 years older. You would expect a collection of this size and age, including it's past space problems, to have specimens in limbo, and this is exactly the case. Twenty thousand insects papered in 75 cigar boxes is a huge project, which is probably why a portion has been put off for over 100 years. The insects not only have to be identified, but mounted, labeled, repaired, and placed in the greater collection; in other words, they need to be fully curated. The project received a 275 thousand dollar grant to do this and more, which is reasonable. It means that, factoring out other costs, the museum can afford to pay several people for several years to make things happen, depending on whether they use sla-, I mean, grad student workers or full professionals (the former will work for less).

Some of the commenters on the article question the use of grant money to complete this project, but I don't think they understand the scale and scope of "specimen limbo" projects. Assuming the people working on these are doing this full time, I'm not even sure the project can get done in a couple years. Every specimen will require individual care, and while the mounting, identification, and labeling may take only an hour per specimen, the relaxing time is hours to days, and only so many specimens can be relaxed at once. We're talking maybe several hours work for 20,000 specimens, which is at least 500 weeks or over nine and a half years of work for a single person. Assuming, of course, that they are working full time on this project, 40 hours a week, year round. This is a massive task, and like I said, every collection has at least one of these specimen limbo projects. There is no quick fix, only long tedious work.


ETA: It really burns me when people question funding to already underfunded, understaffed natural history collections. So I left a longer, more ranty, uh, rant over at the article. Since it is more ranty and less coherent I'll let it stay there.

Monday, November 14, 2011

Picture of the Week: My Childhood.


This insect case of dragonflies was filled by my father. I remember him collecting some of these; most were collected before I was born. The specimens are faded by years of light, but they are still valuable to me, and remind me of my childhood. I still associate mothballs with the smell of home due to these old converted jewelry boxes.

The Six Principles of the ICZN: First Reviser.

The Principle of the First Reviser is stated thus:

When the precedence between names or nomenclatural acts cannot be objectively determined, the precedence is fixed by the action of the first author citing in a pulished work those names or acts and selecting from them; this author is termed the "First Reviser". (24.2.1)


This is an extension of the Principle of Priority as I discussed earlier, and it's meant to clear up controversy over the precedence of names when either the publication date, original spelling or publication of synonyms in the same manuscript makes it unclear which name has priority and is therefore valid. The First Reviser is the first person to cite the work(s) in question in a published manuscript and state which name is valid or available.

Linnaeus's Systema Naturae (1758) has many examples of this principle, since so many of the names were later found to be subjective synonyms (i.e. they referred to the same species as determined by later authors). One would be the snowy owl, which was given two names (Strix scandiaca and S. nyctea), later determined to be synonyms. The First Reviser, Lonnberg, gave precedence to S. scandiaca, which became the fixed name upon his publication in 1931 (Note: it is not the /valid/ name, which is now Bubo scandiaca due to a genus change (Ed.: twice! as pointed out by Christopher Taylor). In general, the name printed earlier in the manuscript is given precedence in the case of subjective synonymy, but this is a rule of thumb required by the ICZN.

Another case where this principle applies is when the publication of two names, later determined to be synonyms, are on so close a date that it cannot be determined which was published earlier, the First Reviser decides precedence. With pre-20th century publications or personally published manuscripts it can sometimes be difficult to determine the exact day of publication, so synonyms published within the same month which cannot be determined to the day would fall under this ruling.

The third case where the First Reviser is necessary is when multiple spellings are used by the original author and it is unclear which spelling is considered valid. If even one of the original authors have used one of the spellings in a subsequent work, that spelling is then fixed and doesn't require a First Reviser. The rule of thumb is to fix the spelling used most often, or first in the manuscript, but this is not required. Unlike the earlier cases, the misspelling is considered to be unavailable and treated as unpublished.

Monday, November 7, 2011

Relaxing insects.

No, this isn't about the calming powers of butterflies. The Nature Plus Beetle Blog has an excellent post of relaxing beetles using a kitchen steamer. Usually, entomologists use these glass hydration chambers, but this is an excellent idea for hard bodied insects. I especially like the use of thyme oil as an anti-fungal. 10 minutes apparently is all it takes to hydrate a batch of beetles to the point where they won't be damaged in mounting. It's also a good explanation of point mounting.

I would really like to see a post by someone on removing insects from alcohol to be pinned. I've experimented with xylene and 100% ethanol, but neither of these is satisfactory for Diptera or Trichoptera. I've heard good things about HMDS (hexamethyldisilazane), but I've never been able to get my hands on any to try it out.

Tuesday, November 1, 2011

A General Reference System: the goal of biological nomenclature.

Recently, I read this post by artist James Prosek on the failure of scientific names to capture the beauty and diversity he saw in his subjects, fish and birds. And while I generally agree with assessment that past authorities should not be taken at face value, I'm struck by the same sort of discontent at changing taxonomy as I read in Naming Nature. In both there is a tendency to dismiss biological nomenclature as unnecessary or not based in reality, an appeal to emotional response similar to the story Richard Feynman told about his artist friend. The name only adds to the beauty of the organism, because the name, really, all names in biology, act as a general reference system for information about organisms and their relationships.

A general reference system is the ultimate purpose of taxonomy as a science, as proposed by Willi Hennig in Biological Systematics (1966). And it has unfortunately been limited in advancement recently by many molecular studies that do not even attempt to put names on their hypothetical taxa. Often these are done for some particular purpose, to assist some particular investigation, but as Quentin D Wheeler points out, taxonomy is at its best when done for it's own sake, in investigation of the diversity of life as the distribution of that diversity (characters), and ultimating in a general reference system for all biology.

So what is a 'general reference system', and what makes a good one? David Allen of the famous (or infamous, depending on your inclination) Getting Things Done productivity method suggests building a reference filing system that is both simple and dynamic, so that any one piece of information could be filed in only a few places. Limiting the complexity means that files can be quickly and easily removed and rearranged as needed. Though more complicated than Allen's system, the International Codes of Nomenclature attempt a stable yet dynamic system for holding information about biodiversity by assigning unique identifiers (scientific names) and rules on how to apply them. But the complete, best reference system goes deeper than just assigning unique names; we don't, for example, organize our names alphabetically. For a higher reason, we put the names in a branching hierarchy of groups. The reason for this, of course, is evolution.

As Hennig explained, the general reference system should map the known lineages of life, and therefore hold information not only in the nodes (the names of species or higher taxa) but also in the pattern of the hierarchy. This fulfills Darwin's hope that 'descent with modification' would be integrated into all fields of study in natural history sciences, and that "[o]ur classifications will come to be, as far as they can be so made, genealogies" (Chapter 14, On the Origin of Species).

In the light of Evolution, the best general reference system will have three qualities: it will be descriptive, it will predict, and it will explain. It describes, through the pattern of the hierarchy, what we know so far of the phylogeny: which species are most closely related, which groups all share close common ancestors, which lineages have which characters, both molecular and morphological. It predicts the distribution of characters in organisms that are yet not fully know to us; since all mammals feed their young with milk secreting glands post-natally, we would hypothesize any newly discovered mammal would do the same. Likewise, we would hypothesize that any newly discovered insect would have 6 legs and three major body segments. Or that a new grasshopper would be plant feeding. We can predict that a new species of Wolffia is a flowering plant, despite the flowers being rare and nearly impossible to find. And finally, it explains the distribution of characters and diversity of life, and provides hypotheses towards explaining the routes of evolution of those characters. This is why monophyletic groupings are so important; whenever a paraphyletic or polyphyletic group is coined, the system looses predictive and explanatory power.

The general reference system is a tool, THE tool, the ULTIMATE tool of the biologist. It's the filing system that makes everything work. And the names that disturb the umwelt and bother molecular systematists are what keep track of all this information, all the information ever written about every group and relationship. Through the biological species concept we know the reality of species and through systematics we know the reality of their relationships. The general reference system of biological nomenclature ties these together and only adds to the beauty of every organism.

Monday, October 31, 2011

Inkscape tutorial for taxonomists.

If my readers are anything like me, we are all often disappointed with the way our line drawings turn out. I spend hours with a microscope, freehand drawing with a gridded eye piece, trace and ink on vellum, scan to computer, clean up in GIMP, and hope that the finished product is passable. My illustrations tend to be pixellated and messy after rescaling. What was that again, a harpago or a seta?

The expensive alternative is making a basic line drawing (no inking, no clean up), scanning and importing the image into Adobe Illustrator, and tracing a vector image from the hand drawing. I say expensive because Illustrator will run you about $450 USD; roughly the same amount as a new Asus Eee PC netbook. At the moment I don't have that kind of money, which I expect is true for most taxahackers and pro-am entomologists. For those of you who can afford the CS software suite, Dr. Ralph Holzenthal has an excellent guide to the program for entomologists.

I recently found Inkscape to be an excellent, inexpensive alternative to Illustrator. The software is a free, open source vector image program which can operate on Windows, Mac OS, and Linux platforms, and it can do almost everything that Illustrator can do with a few exceptions. In addition, continuous updates mean the tools are constantly improving.

In the rest of this post I'll be presenting my basic methods for line drawing illustration in Inkscape. Before you use this, I'd suggest doing some of the tutorials on this page, or at least completing the kokeshi doll tutorial. Once you know these basics, the rest of this post will make sense.

Line Drawing Tutorial in Inkscape

1. Before you even open inkscape, you need your drawing or other image scanned and saved as some sort of image file. Jpeg, tiff, or bmp works best.

2. Open inkscape, go to File > Import, and select your image from file. The drawing will be imported directly into the open Inkscape window.

3. First, you probably want to resize the image to the area of the 8x11 provided. This will make it easier for when you make plates with other images for publication.

4. Open up the Layers and Fill and Stroke tooboxes (ctrl+shift+L and ctrl+shift+F, respectively). It's good to have these two open at all times, because you will be shifting back and forth between them repeatedly.

5. In Layers, right click Layer 1 and add a new layer, above the original layer. Make Layer one about 50% opacity with the slide bar below, so you can tell the difference between your original and the vectors you are laying on top. If you are not actively working on a particular layer, it's best to click the lock icon next to the layer name to keep any changes from being made. The eye icon makes the highlighted layer invisible, which is useful for checking how your vector image compares to the original as you progress.

6. If your image isn't bilaterally symetrical, you're ready to start with the outlines. If however it is symmetrical, there is a simple way you can preserve symmetry. In the original layer, draw a line through the center of the illustration using the bezier tool, and make sure it's vertical or horizontal by holding control. Now rotate the image using the general selection tool so that it runs through the center of the drawing symmetrically. Now your work is cut in half, because you only have to trace half the drawing! When one half is done (details and all), just duplicate (ctrl+d) and flip the duplicate, and line them up opposite, then group them using ctrl+g.

7. The first step in any image is tracing the outline and major inner lines with the bezier tool. This works best if you try to straddle curves portions with nodes, as this will make the curves smoother. Once you've finished a portion, select the nodes and click the "make selected nodes auto-smooth" button on the top toolbar. Now adjust the curves so they match the lines underneath using the edit paths tool. You can adjust the width of the lines in the fill and stroke toolbar, under the stroke style tab. I tend to use several sizes throughout the drawing, wider for outlines and heavily sclerotized regions, thinner for structures within the outline and membrane.

8. Once the lines are done, it's time to fill in the details. Since fill shadings can get expensive in publications, I tend to use stippling. The easiest way to do this is to make a small circle with the circle tool the size you want the stiples, trace object to path (ctrl+shift+c), drag it across the drawing and press spacebar where you want the dots. If you drag and press spacebar, you can 'stamp' any path on your illustration, which can be useful for repetative details. I recommend making different layers for outline, shading, inner structures, setae, and annuli, as well as any other major details, so you can't alter or interfere with what you've already done while working on the next part.

9. Inner structures (those that would be on the interior of the specimen but are shown as if the surface is transparent) can be traced using the stippling as above, or traced as a path with the bezier tool and in stroke style, change the line in the dashes drop down menu to a dotted or dashed line, according to your preference. In my experience, the line width should be comparable to the outline line width, or the dots won't show very well.

10. Setae, and their corresponding basal annuli, are by far the most difficult detail to work in Inkscape. Unlike Illustrator, Inkscape does not yet have a custom brushes ability, so all setae have to be crafted, resized and placed by hand. Despite this issue, I've developed a work around.
  • First, open a new Inkscape document.
  • Create a series of vertical triangles of several lengths using the bezier tool with the shape drop down menu (in the top toolbar on the left) set to 'triangle in'. These will probably look way too wide at this point; don't worry about that.
  • Select all the triangles and object to path (shift+ctrl+c)
  • Use the side arrows on the general selection tool to make the triangles thinner.
  • Make annuli by using different sizes and shapes of unfilled ovals using the circle tool, and make them paths
  • Save the document and keep it open. Now you have a general reference file of setae and annuli for any project. ctrl+c to copy and ctrl+v to paste them in your illustration
  • If you paste a few models near the side of the illustration, you can drag and stamp them using spacebar, just as the stippling. I suggest doing the setae first and annuli second.
  • Once the seta is in the illustration, you can alter the length and width and rotate it using the general selection tool. Don't worry about curves, the next step will take care of that.
  • Since we traced all our "brushes" to path, their shape can be altered with the edit paths tool. To curve a seta, pull one edge to the side so it bows out, then pull the other towards it to narrow it. You can add more nodes by double clicking so the seta has more than one major curve.
  • With the annuli, I try to position them so that the setal base is barely visible, the size varying with the width of the seta.
11. Arrows to various structures can be added using the regular bezier shape with the stroke and fill option 'start marker' set to the arrow shape of your choosing. You can also make arrows by combining a regular bezier line with an arrow in shape and grouping them; this can be stamped just as the rest of the paths.

12. Labels can be added with the text tool on the sidebar, and resized and rotated just as any other path. I suggest waiting to add these till all your illustrations are in plates so the labels and figure numbers are all the same size.

13. Once all the details are done, resize as necessary, set the original layer (the one with the hand drawing) to invisible, and save the illustration as an svg file.

14. Vector files are great as working illustrations, but to put them in a word processing document as a picture, they have to be converted into something more normal. Export the image as a bitmap using shift+ctrl+e. You can choose the width and height, as well as the density of pixels per inch (dpi). For now, I suggest something between 800 and 1000 dpi. Exporting will save the picture as a bitmap file with your specified settings. You can easily convert the bitmap to a jpeg or tiff by saving it as such in GIMP.


I guarantee your illustrations will look better than ever using this program. There are all kinds of ways you can tweek the image and details beyond the basic methods above, including ways I haven't discovered yet.

Monday, October 24, 2011

Book Review: Atlas of Ohio Aquatic Insects Volume I. Trichoptera.

Brian Armitage et al. recently published an atlas of the Trichoptera of Ohio (teaser here), and to be honest it was not what I was expecting. Armitage and his colleague Steve Hamilton have published a number of caddisfly atlases in the past covering the entire fauna of several North American families. Generally, these are guidebooks with genus keys and species pages with summaries, maps, and illustrations of male genitalia. And although trichopterologists have been waiting 15 years for the next volume to come out (if it ever will come out), these are great resources. I was expecting the Ohio book to be similar, with lots of illustrations of genitalia, a definitive diagnostic guidebook to the Trichoptera of Ohio. A 'new Ross 1944' if you will.

Although the book has many nice distributional maps, several checklists and many years of collection data, it is not what I would consider to be an atlas by the earlier works. The only genitalic illustrations are associated with the determination of a few new hydroptilid species, and no keys to genera or species of any kind. The publication is a very nice contribution to our knowledge of the distribution of species, and compiles a great deal of information, but what would be far more useful is an atlas of the diagnostic kind. For $25 dollars and with my small budget, the content doesn't match the price.

And I really am disappointed that it's unclear if the atlas series will ever be completed. I have distant plans to complete a very basic pictorial atlas of male genitalia with an accompanying genus key (similar to Hans Malicky's Atlas of European Trichoptera), but this is in very early development and I have far less resources than these authors. A good guidebook for the North American Trichoptera adults would be a major boon for professional entomologists and pro-ams/taxahackers alike.

Available through Ohio Biological Survey

Phryganeidae: The Giant Casemakers.

The Phryganeidae are a small family of caddisflies distributed throughout North America, Europe, and Asia. Wiggins (1996) lists the total as 15 genera and ~75 species; by my count from the World Trichoptera Checklist (Morse 2011) there are 80 extant and 37 fossil species. This family includes the largest known caddisflies. The larvae are case makers (as the common name suggests), and fashion tube cases of spiral or circular wrapped vegetation.
Oligostomis pardalis larva (© D.S. Chandler / Discover Life)

The genus name Phryganea has a long history of use, starting in the 10th edition of the Systema Naturae (Linnaeus 1758). Carl von Linne included 17 species of caddisflies in this work, all under the genus Phryganea (from the French word for caddisflies). Needless to say, most of these species have been removed to other families and genera. At the time, caddisflies, stoneflies, dragonflies and mayflies were all included under the order Neuroptera; it wasn't until 1813 that the Order Trichoptera was erected. Due to the original status of the genus, there are many nomenes dubius and synonyms that by far outnumber the species now in the entire family.

Banksiola dossuaria (© Trichoptera Barcode of Life)

In addition to large size (often greater than 25 mm), the adults are characterized by colorization ranging from the black and white checkers of Banksiola to the fall leaf orange of Ptilostomis to the yellow and dark purple of Eubasillissa. The largest species, Eubasillissa regina, is over 4 cm with an 7 to 8 cm wingspan. Dr. John Morse, who has spent much time collecting and studying aquatic insects in Southeast Asia, told me they look like a small bird with a strange flight pattern from afar.

Eubasilissa regina, the worlds largest caddisfly.

The larvae often have contrasting patterns of orange and black stripes on head and thorax, and are just as impressive as the adults in size. One of the most curious larval tendencies is the ease at which they leave their cases behind when disturbed. If one larva looses it's case and other of a similar size is occupied nearby, the two larvae will fight over the case (as illustrated in this video). Though they inhabit a wide variety of aquatic habitats, they are found most often around the roots and stems of aquatic vegetation, and in root balls of woody plants, with a diet of mostly aquatic invertebrates.

The definitive guide for the family is an eponymously named book by Glen Wiggins (1998), and despite being over ten years old is still in print and in demand. The book includes genus keys and diagnoses for all the species know at its publication, including all 28 North American species. Wiggins splits the family into the Yphriinae (which includes a single species of Yphria from Western North America), and the Phryganeinae, though the separation is drawn due to 'primitive characters' possessed by Yphria is to me not particularly convincing, and may be paraphyletic.


References

Morse, J.C. (ed.) 2011. Trichoptera World Checklist. http://entweb.clemson.edu/database/trichopt/index.htm [Accessed 24 October 2011.]

Wiggins GB. 1977. Larvae of the North American Caddisfly Genera. University of Toronto Press, Toronto, ON.

Wiggins, G.B. 1998. The Caddisfly Family Phryganeidae (Trichoptera). University of Toronto Press, Toronto, ON.

Thursday, September 29, 2011

Possible new endangered listing for southeastern aquatic insects.

The Center for Biological Diversity and other environmental groups petitioned the US Fish and Wildlife Service last year to give 404 southeastern aquatic species federal endangered listing, and it looks like FWS will finally be addressing 374 of these:

Species announced today include 13 amphibians, six amphipods, 17 beetles, three birds, four butterflies, six caddisflies, 81 crayfish, 14 dragonflies, 43 fish, one springfly, two isopods, four mammals, one moth, 35 mussels, six non-vascular plants, 12 reptiles, 43 snails, eight stoneflies and 75 vascular plants, FWS said.

Of the 9 species of caddisflies from the original 404 petition on the Center for Biological Diversity website, the below six are being considered (full list is here).

  • Hydroptila sykorai
  • Agarodes logani
  • Lepidostoma morsei
  • Triaenodes tridontus
  • Oecetis parva
  • Oxyethira setosa
I collected one of those during my masters research in good numbers, outside it's supposed range (not saying which right now). The article detailing the range extension is in review at the moment, and I do hope it will be published before a decision is reached because it may challenge the need for an endangered status for that species.

The list includes 44 other insects in addition to the caddisflies (though the silk moth and the butterflies are not /really/ aquatic, they have larvae feeding on plants which are often semi-aquatic). I do appreciate insect conservation minded people in an environmental movement which often focuses exclusively on megafauna.

Tuesday, July 5, 2011

When honomyny goes wrong.

Christopher Taylor (Catalogue of Organisms) just published this excellent post in reference to Dr. O'Hara's recent paper in Zootaxa on the CESA itch. The CESA itch (not to be confused with the mihi itch) is a particular recent condition of certain taxonomists who are inclined to scour online databases for potential homonyms and publish them en masse, regardless of what groups these researchers are actually competent in, and often without the basic research to do it properly. This malady is named after the Centre for Entomological Studies Ankara, where Drs. Kocak and Kemal enjoy combing the web for new homonyms and naming their replacements after CESA. Which wouldn't be that bad if the results weren't amateurish taxonomic hack jobs.

Since Mr. Taylor has covered CESA-itch in detail, I would just like to outline one particularly grievous example from Dr. O'Hara's paper. An example that is close to my heart since it involves Trichoptera AND Sciaroidea.

Allomyia is a perfectly valid genus of Trichoptera (Fam. Apataniidae) published by Nathan Banks in 1916. Two objective homonyms were published soon after, Allomyia Felt 1918 (a genus of cecidomyiid gnats) and Allomyia Malloch 1919 (a genus of scathophagid muscoid flies). It was later revealed that Allomyia Felt was a junior subjective synonym of Oligotrophus Latreille 1805, and Allomyia Malloch was replaced with Allomyella (by Malloch himself, in 1923), so neither of these are in conflict.

More recently, two more homonyms have been described separately, by Fedotova in 1991 and Ren in 1998. Both of these were still in conflict at the time of Kocak and Kemal's 2010 paper. They had coined Sauricesa as a replacement for Allomyia Fedotova 1991, unaware of the homonyms by Ren, Felt, and Malloch, and that Fedotova's name had already been replaced by Gagne in 2004. They were apparently even unaware that Fedotova was describing a genus of Cecidomyiidae, not Tabanidae.

Given their complete unawareness and ineptitude at primary research, Kocak and Kemal moved 20 species from Apataniidae, Cecidomyiidae, and Scathophagidae to Tabanidae, a collection of not just Diptera but also Trichoptera! Let me clarify: these authors moved species across orders of insects. They put caddisflies in with the horseflies. And they did so because they cared more about publishing papers than getting things right, about blindly surfing computer databases than researching primary literature. This could have been done right, easily.

As it stands, Allomyia Ren 1998 has not yet been replaced, but given the gross incompetence of people who blindly replace homonyms, I think that task is best left to an expert in tabanid flies.

Thursday, April 7, 2011

Molecular techniques and species discovery.

I received a link to this poll in my e-mail through the Entomological Collections Network listserv. While I appreciate being able to give my imput, most of the important questions, (e.g. "do you think molecular techniques help in species discovery" were yes/no questions with no space for comments. The most interesting of these was "Do you think molecular techniques can accelerate species description?" To which I answered no, emphatically.

Despite complaints to the contrary, species description is not a particularly difficult process. While Botanical and Zoological Nomenclature differ in that the botanical code requires the primary description to be written in Latin, they otherwise have all the same features. There is a brief introduction and materials and methods, followed by the diagnosis (short description meant to separate the new species from other known members of that group) and description (longer statement of all aspects of the morphology). Typically there are illustrations, which can be achieved with a microscope that has a grid eyepiece (or a camera, if you're lucky enough to work with larger organisms). Then the material examined, remarks on biology, systematics and distribution, and works cited. I have already discussed techniques to accelerate the activities that go into species description before the actual writing part. Notice that none of those include any molecular techniques.

The simple truth is, while molecular techniques may speed up the process of resolving cryptic species complexes, they seldom (if ever?) increase the speed at which species are described. Current estimates are that there are millions of undescribed species on Earth, most of those being arthropods. And I propose that many of these are sitting in museums and unsorted trap samples. The ICZN still requires a formal description for a name to be recognized, and without a name it's very difficult to talk about something. If you look at what characters people are using in their descriptions and diagnoses, 99% of the time these are gross morphology. And, for the vast majority of all the species yet to be described, this is all that is necessary. To make things easier, there are journals such as Zootaxa which specialize in publishing descriptions of new species, and have accelerated peer review and publication time within a month.

Accelerated species description will not occur when everyone has a lab equipped with a pyrosequencer. Accelerated species description will occur when biologists as morphologists spend more time contemplating Evenhuis' Steps to Enlightenment and Taxonomic Nirvanna. The only way species get described is by writing a paper, and the only way diagnoses and descriptions get written is by looking at the organisms. Collecting from poorly sampled regions, sorting old trap samples, building taxonomic libraries, photographing and illustrating type specimens, and many many hours at the microscope examining morphology, these are how species description will accelerate. Not by molecular techniques.

Friday, April 1, 2011

We just lost a giant.

Thomas Eisner died last friday.

If you have not read For Love of Insects, I highly suggest it. E.O Wilson called him a modern Jean Henri Fabre for good reason.

One note about the NY Times article: check out the black and white photo of Eisner at his scope. My advisor pointed out that it's a Wild M5, what many still consider is the ultimate stereo microscope for it's simplicity, durability and clarity of optics. I have one (not my own) at my lab bench, and I plan on purchasing one eventually. Production of these scopes ceased in the 1980s and Leica scopes (the company Wild Herrburg merged with) are just not the same quality. It's telling that great biologists such as Eisner used this very scope.

Book Review: Foundations of Systematics and Biogeography.

Ebach and Williams "new" book has been out for several years now, and while Platnick, Brower, and Amorim previously weighed in, none of these are as critical and scathing as Ferris's recent review in Cladistics.

The book does, though, contain things we did not know—indeed, there are things here that no one has ever known. Among these revelations are that cephalaspids are placoderms; that Haeckel was responsible for grouping by overall similarity whereas Cuvier and Huxley had nothing to do with it; that Sokal and Sneath (1963) were primarily interested in phylogeny; that Nelson never accepted transformation; that Hennig used only congruent characters, because Sokal and Sneath said so; that paraphyly has no connection with symplesiomorphy; that DNA sequences have no hierarchic structure—unless used by Patterson; that parsimony is limited to binary characters, is closely linked to grouping by overall similarity, and does not draw conclusions of homoplasy; that reversals do not really happen and would be plesiomorphies if they did; that all un3ts data are phenetic—unless used by Patterson; that 3ta and ppa are not methods, being inspection of the data instead; that transformation is a myth; and that transformation is nonetheless distortion. A reader would have to be rather poorly informed to fall for this nonsense, which is to say that the book has obviously been designed to victimize just such readers. Ignorance is strength. This brings us back to Platnick's (2009, p. 281) central comment:

It should be especially useful for students.

Like Williams and Ebach, he has realized that tricking the least experienced students is the only chance that 3ta has left. No doubt publishers relish such recommendations. If Platnick’s endorsement were believed, Springer would get their $90 a head regardless of the damage done to students.

Ouch.

I haven't yet had time to purchase a copy and read it, so I can't really weigh in from my perspective. Generally, I trust the evidence Ferris presents in his review. The main conflict centers around the use of three taxa analysis (3ta), and whether or not it is a useful method for phylogenetic inference. This old method takes three taxa from a set to be analyzed, decides which two are more closely related to each other than to the third, and puts them back into the mix, rinse, repeat, until all relationships are resolved. This seems to me to be a wholly inefficient way of parsimoniously finding a summary of relationships, and according to Ferris's review, may be more likely to create paraphyletic groupings than path finding the shortest trees by heuristics (approximation) and collapsing to a consensus. Consider if you had 30 species to search, which is millions of combinations. This is not the same as simply trying to resolve the relationship between three taxa alone. The simplicity of such an arangement means there are only three hypotheses (topologies), of which one is correct. An example would be simply trying to find the relationship of Ephemeroptera, Odonata and Neoptera. Relationships within each of those groups or outside are irrelevant to the question: are Ephemeroptera and Odonata more closely related to each other than either is to the Neoptera? Another issue I find is the emphasis that a so called "reversal" of a character could never be considered a synapomorphy. To which I ask, at what level?

Farris's comments makes the whole of Foundations seem to be a strange reactionary piece against traditional pattern cladistics, whereas traditional pattern cladistics is seen as reactionary by many molecular biologists today. I am not saying I'm going to remove Urhomology from my blogroll; I still value many of the statements Ebach and Williams have made there. It was while reading through the backposts I was inspired to write the statement "Homology is the key to the heart of biology", which continues to be a motto for me in regards to the importance of homology (synapomorphy) in figuring out the history of life and the pattern of evolution. I appreciate their rejection of paraphyly and their use of the term phylophenetics when discussing molecular phylogenetics as it is done currently. Even if the authors dwell on false or bad premises it does not carry that those ideas could not be instrumentally true in regards to the right premises.

When I finally purchase and read Foundations of Systematics and Biogeography, I'll let you know if my opinions change.

Wednesday, March 23, 2011

Characters, characters everywhere...

With the sort of technology available today for sequencing and the speed at which it proceeds, it's no wonder that researchers want assembly processes for double-barrel shotgun sequencing fragments to be faster as well. Thus this contest. Nature doesn't provide the species names or further details about the assembly procedures, but these don't concern me much.

When it comes to full genome sequencing projects, as a systematist I'm more concerned with the characters (the actual sequence of base pairs) and how they are used in phylogenetic inference. With pyrosequencing and other next generation sequencers, very soon it will become inexpensive and fast to sequence the entire genome of any organism. Ignoring the amount of information involved and the amount of digital space it will take to store all this information, what is one to do with all these characters?

Some people, or I should say, many modern systematists would like nothing better than to shove the entire genomes of species within a taxon (never mind that genomes are character sets of individuals, not species) and let an algorithm sift through the mess and work it out. I'd like to point out that this has been done before, and is generally regarded as a unfortunate but necessary stepping stone on the way to more scientifically acceptable methods. Still, the temptation for easy answers is alluring.

Consider this, however. We have a number of assembled genomes (by whatever method) and we have aligned them (hopefully not manually) so we can examine the shared areas. Could we possibly design a program which will automatically find shared sequences lengths and highlight them from longest to shortest, and discard those sequence lengths below a cutoff? Then we could actually look at the sequence lengths that may matter (there still will be homoplasy) and consider these entire shared sections to be our hypothetical homologs. We could then code the sequence lengths as individual characters and run a more traditional style phylogenetic inference. This may actually be faster than the "mass shoving" scenario, as there are less potential relationships for a computer to compare. It also removes a great deal of homoplasy which interferes with our hypothesis testing. More characters (if the characters are not specially shared) is not always better. Millions of characters will not give greater resolution to a phylogeny if 80% of them are either different or shared single base pairs scattered among non-shared lengths. Part of scientific efficiency is designing a crucial experiment which will quickly eliminate alternative hypotheses (PDF). Using an entire genome in a phylogenetic inference is like setting sail on Lake Superior in a kayak without a map or compass and hoping you'll hit Isle Royale after several days travel.


Edit: The process of a priori selecting characters for a phylogenetic inference is not new nor is it unusual. All morphological cladistics works within this method. Ignoring and not including non-pattern (homoplasy) in sequences is no different than disregarding highly variable morphology (e.g. color) or bland uniformity. Like all good science, not including unnecessary data is a matter of efficiency.

Tuesday, March 22, 2011

The Extinction of Taxonomists?

This topic has been covered twice already this year. As one older systematist told me, this is a long term decline, not a sharp decrease. Whether caused by change of careers to molecular biology, a decline in museum and systematics funding, or a combination of the two in addition to correlating factors of alienation from nature, the number of systematists who focus on traditional taxonomy is and has been declining for a quarter of a century or more.

My first response to such doom and gloom is "I'm not dead yet!". The numbers are declining but there are still young people interested in morphology based revisions and alpha taxonomy. My second comment is to suggest greater emphasis on decentralization of research. There's a reason I put "taxahacker" in my title box; individually driven research is the future of our field just as it was the origin. If it means a secret guild with unassuming 9-to-5 office jobs coming home to pour over specimens under the microscope in their basements, so be it. We are the oldest profession, and unless all life on this planet ceases to be there is no getting rid of us.

Monday, March 21, 2011

Book Review: Naming Nature.

My graduate adviser recently loaned me a copy of Carol Yoon's Naming Nature: the clash between science and instinct. Booklist's review stated it's "impossible to put down", which I found to be the case. I finished Naming Nature in one evening, finding it simultaneously inspiring and infuriating, and therefore deeply engaging. The next day I suggested it to all of my colleagues, calling it the best popular science book on systematics ever written.

Yoon's main premise is there exists an innate human tendency to order and classify the natural world in distinct and evolutionarily conserved categories. She calls this the umwelt (prouounced oom-velt), from the german word meaning "the environment" or "the surrounding world". Psychologists use this term to refer to the collective phenomenon in the environment capable of effecting an organism or individual. In ecology it has been used to refer to phenomenon that individuals within a particular species are able to recognize. Yoon suggests there is an umwelt for every species, and that the human umwelt consists of a set of conserved categories and a instinctual need to classify the natural world in consistent ways. The evidence she uses to support the concept is varied but intuitive. I finally now have a word to put on this concept which has been floating around my head for several years, which was as I said, inspiring.

However, as I continued to read, I became increasingly frustrated with her conclusions. The human umwelt is very local in time and space, applying to what an individual sees on a daily basis and qualified by what matters most in terms of survival or aesthetics. This is in contrast to the deeply non-local scientific understanding of life, which extends across the entire planet and backwards in time billions of years. Humans are not generally prepared to drop their biologically and culturally grounded categories for something much more immense, so there is a conflict. Yoon's conclusion is that scientific discoveries (including progress in systematics from Linnaeus to evolutionary taxonomy all the way to Cladistics) have alienated humans from their own umwelten, and her solution is to return to the classic categories, going as so far as to call a whale a fish in the final chapter of the book. All the while she complains about how those nasty cladists (myself included) have "killed the fish", "Fish" not being a monophyletic taxon including a common ancestor and all descendents, therefore invalid as a taxonomic grouping under the rules of Cladistics. Yoon claims that our new categories have made people alienated and apathetic, and therefore caused the extinction of many species.

After providing this exquisite description of the human umwelt as revealed by science, this was all so backwards. Modern systematics through cladistics has added so much to our understanding of Life and our own evolutionary heritage. The many species we know of today were only revealed by the very methods that Yoon claims to be the cause of their demise. And it's very clear that we haven't lost our abilities or we would be as lost as the brain damaged people she describes who cannot tell a lion from a raven. Even those systematists which work with molecules still retain this capacity, although their skills are not as strong as the classic morphological systematist. It seems her ire is misplaced.

The conclusion I have come to is very different. The human umwelt seems indeed to exist, and is conflict with science in it's classic form and categories. However, this conflict is not irreconcilable, nor is it ultimately the cause of species extinctions or human apathy. There are many other causes for these things, which are the subject of an entirely different discussion. The route to reconciliation is retraining of the umwelt to include evolutionarily real categories, which takes great time and effort but is entirely doable. The umwelt consists of a series of gestalten (singular: gestalt; German for "shape or form") which are the snapshots that allow immediate sensory identification of a living thing. Changing of the umwelt consists of training ones gestaltenspeicher ("gestalt-memory") until the categories fall in line with science.

And from personal experience, I can say that I understand and accept these modern categories and do not feel any alienation from the natural world. In fact, my understanding has brought me closer to life. As Eliezer Yudowsky the AI researcher and rationalist has stated on several occasions, "If we cannot take joy in the merely real, our lives will be empty indeed". I strongly suggest reading Yoon's book for the bits about umwalt and some insight into the history of systematics, but not to take her conclusions to heart. Instead, embrace the evolutionary understanding of life and train your own gestaltenspeicher; such things bring so much more joy than any foolish return to ignorance might grant over the short term.

Naming Nature at Amazon.com

More on umwelt from a biosemiotics perspective

The Six Principles of the ICZN: Coordination.

Now that we've established Binomial Nomenclature and Priority as founding principles of zoological nomenclature, we at least have a stable system of classification. However, there are still some loose ends to tie up.

Article 36. Principle of Coordination.

36.1. Statement of the Principle of Coordination applied to family-group names. A name established for a taxon at any rank in the family group is deemed to have been simultaneously established for nominal taxa at all other ranks in the family group; all these taxa have the same type genus, and their names are formed from the stem of the name of the type genus [Art. 29.3] with appropriate change of suffix [Art. 34.1]. The name has the same authorship and date at every rank.

Articles 43 and 46 provide the same statements in relation to genus-group and species group names.

Essentially, when a new name is created in the family group (superfamily, family, subfamily, tribe, subtribe), genus group (genus and subgenus) or species group (species and subspecies), by this principle all other names are "created" on the same date, even if they are not discussed at that time. They exist in a sort of potential state until they are first talked about, at which point the author and date associated with the "new" taxon is referred to publication by which it was created coordinately.

For example, if I published a new family, Ecksidae Burington 2011, by Principle of Coordination Superfamily Ecksoidea, Subfamily Ecksinae, Tribe Ecksini, and Subtribe Ecksina would all be considered considered created at that point, even though I don't talk about them. If another author comes along later and decides to discuss the subfamily Ecksinae, even though it had never been formally discussed before that point, it would still be considered to be Ecksinae Burington 2011 by this principle.

This seems to be a completely unnecessary Principle until you consider the habits of taxonomists. We often enjoy raising or lowering the ranks of various groups to suit ease of classification and/or personal taste. If these groupings weren't already created in potential, you can imagine the cacophony of names and dates that could arise from this process. Again, like all other aspects of The Code, the Principle of Coordination is meant to preserve the stability of zoological nomenclature, in this case by stopping problems before they even arise. This principle also prevents the orphaning of taxa by the "type" clause; I'll be discussing typification more later.

Saturday, March 19, 2011

Changes in Science Publishing.

Recently, Johnathan Eisen and his colleages at UC-Davis published this paper in PLoSOne. The paper deals with shotgun sequencing (breaking up DNA into many small segments and sequencing the pieces, fitting them together where they overlap) of environmental samples from the ocean, and while interesting on it's own merit is not why I bring it up. The very interesting thing about this paper is that the authors have chosen to forgo a press release through the university press office, and have instead used Eisen's professional blog to provide commentary on the article.

I note - we are not doing a press release for the paper, for a few reasons. But one of them is that, well, I am starting to hate press releases. So I guess this is kind of my press release. But this will be a bit longer than most press... releases. I note - my key fear here is that somehow in my communications with the press or in our text in the paper or in this post I will overstate our findings. Here is the punchline - we found some very phylogenetically novel forms of phylogenetic marker genes in metagenomic data. We do not have a conclusive explanation for the origin of these sequences. They may be from novel viruses. The may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses. But we just don't know.
PZ Myers pointed out just how revolutionary this is, and how it should scare people who are not currently up to snuff on communicating. This is the new model of science, public, accessible, and direct. The obvious advantage is no misinterpretation or distortion occurs as the information moves from authors and journal article through science journalists and reporters to the public. Eisen has made it very clear that he has no explanation for where the strange sequences have come, only hypotheses, and because of this it's impossible for this research to be interpreted any other way (though journalists may still try with hype words). It is very much like giving a seminar on your research for the whole world.

The disadvantage (to those unexperienced with blogging) is every scientist may soon be expected to blog their discoveries simultaneously with publication. In addition, journals will continue to become more open access, so science will be more accessible to the public in raw form, necessitating explanation that the layperson can understand.

In this brave new world, I've decided to become an early adopter. I've changed my profile so this blog has my name and face, and I pledge to blog every single publication from this point on. As I am not yet published (one article nearly in press, two more on the way), this means that I pledge to blog every publication I ever write in my entire life.

In addition, I'm going to be updating this blog more often. I still need to finish the Principles of the ICZN series, which I had forgotten about.

Watch this space; the changes will continue.