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.