Monday, November 29, 2010

The Six Principles of the ICZN: Binomial nomenclature.

Before Linnaeus, the scientific naming of species was very messy. There was no standard way of going about it. Names were often long descriptive phrases in Latin (which was the standard scholarly language of the time). For example, a species of Geranium was written like the following:

GERANIUM pedunculis bifloris, calycibus pyramidatis angulatis rugosis, foliis quinquelobis rotundatis.

Needless to say, if names are to act as a reference system the above is extremely cumbersome. At the time of Linnaeus, an unimaginable amount of species were being discovered over a relatively short period of time. A simpler system was badly needed, and binomial nomenclature filled this need. Linnaeus consistently used binomial nomenclature for his Systema Naturae and it was popularized further by like minded workers of the day in Zoology and Botany. When the first code of zoological nomenclature came into use, the Strickland Code (1845), the use of binomial nomenclature was made a rule, and has been retained through the subsequent codes, up to today's 4th edition of the ICZN.

It is stated thus -

The scientific name of a species, and not of a taxon of any other rank, is a combination of two names (a binomen), the first being the generic name and the second being the specific name. The generic name must begin with an upper-case letter and the specific name must begin with a lower-case letter.
(From ICZN, Article 5)

The Principle of Binomial Nomenclature provides for a stable and easily recognizable scientific species name. Only a species name is made of two names, the first capitalized and the second lowercase. The Code gives further corollary statements on subspecies trinomens, higher ranks than species being of only one word, but this follows the general statement of the principle above. Its our starting point in zoology. With a two word name where no other names are two words, there's no room for ambiguity.

With the possible ease of a 1 word system, a person may wonder why Linnaeus didn't just use that? The answer is, in a monomial system one would quickly run out of names for all the animals. With a binomial system, the number of combinations is nearly infinite (when I try to calculate it, my graphing calculator gives me an overflow error for n=1 million; it gives me overflow for 10,000 for that matter).

Sunday, November 28, 2010

Book Review: Darwin and the Barnacle.

Several years ago I attended a discussion class reading On the Origin of Species, first edition. Like most biologists, I had never read the book (though thankfully more biologists have read it than the ICZN), and it was very enlightening to study the entire document as a group, chapter by chapter, and discuss the contents both in relation to science in the mid 1800s and today.

One of the little tidbits I learned about Charles during that class was his years of work on barnacles. He spent ten years of his life, prior to the publication of On the Origin of Species, studying barnacles just so he could place a single strange species into context. And at the time this seemed quite incredible, much like being told that George Washington cut down the cherry tree or Kerry Mullis discovered PCR during an acid trip. It was a historical myth, maybe true, a little factoid, a morsel, etc.

Rebecca Stott takes this morsel and explodes it into a full blown thanksgiving feast with a 20 lb. turkey and loads of mashed potatoes. She begins with Darwn's childhood experiences with marine invertebrates and works her way up to the discovery of what he called "Mr. Arthrobalanus" on a beach in Chile. What started as a 6 month project became a 10 year task, during which he published 4 large volumes on all known extinct and extant barnacles. Stott serves this through the gravy of interpretive biography, and while she is not a biologist she handles the biology quite nicely. Most people who try to tackle writing about Darwin screw it up by completely misunderstanding On the Origin, littering the text with references to "survival of the fittest", and other spoonfuls much like finding your piece of turkey is nothing but boney bits, or your cranberry sauce is full of seeds. Thankfully she had a full team of Darwin specialists aiding her research. There was only once I felt she mishandled the theory, and it was quickly forgotten with the tastiness of the rest.

Darwin and the Barnacle had me sitting up in bed late at night to finish it. This is the tale of what Darwin did BEFORE he published his main course. It is not dry in the least. It's the moist bird you had the pleasure of sharing with family last Thursday (I hope).

Also, I'm all out of Thanksgiving puns.

Saturday, November 27, 2010

The Six Principles of the ICZN: Intro

Recently, I read the International Code of Zoological Nomenclature (ICZN) in it's entirety. The Code is sometimes considered to be the constitution or rulebook of zoology. It defines how new species names and other taxa can be created and then later revised. The Code provides the ground for all other work in zoology, because if we couldn't somehow classify and summarize the units of life in some meaningful and standard way, the whole of biology would be a disordered mess.

Unfortunately, very few biologists have actually read The Code (or for non zoologists, the comparable documents, the International Code of Botanical Nomenclature, and the International Code for the Nomenclature of Bacteria), and because of this there is very little understanding of WHY we have the Code and why it is ultimately responsible for stability in biology as a whole.

Over the next several weeks I will be reviewing The Code through the six principles that are the main guideposts in zoological nomenclature, why they are important, and how to interpret and use them.

Species concepts.

After reviewing the arguments of species as real entities vs. species as made up configurations for the past several hours, I remain a pluralist on the topic of species concepts.

The Biological Species concept by Ernst Mayr (members of metapopulations that actually or potentially interbreed) works quite well for large animals that undergo only sexual reproduction. Such organisms can be easily observed for discrete interbreeding over time. But what about those populations that show discrete yet sympatric behaviors and habits in the field yet interbreed easily in the laboratory. Would these be considered species? Do these actually offer discrete units? Under the Ecological Species concept (isolated phenetic clusters of individuals sharing a particular niche) they would.

This is all well and good for laboratory animals. But how about those organisms that don't easily take well to experimentation? How about asexual animals, where breeding doesn't occur, or those organisms (like plants) that easily hybridize? Do we once again scrap "species"?

And yet, there are other concepts we can use (a good list is in the book Speciation - Coyn and Orr) that do not rely on a strict and exacting understanding of the direct mechanisms or processes to obtain understanding. In systematics, we aim to describe and understand biodiversity. The title "species" is used in multiple ways to best describe different organisms. Of course we would love to test the biology and ecology of every candidate species on this planet; almost always this is currently impossible or unfeasible. Unless we are to simply give up on describing and understanding biodiversity, there needs to be some way to separate and describe units we believe are candidates species. With the biodiversity crisis, we cannot wait for every or even most units to be verified. Operational concepts provide a framework for describing species that the Biological Species concept could not. Homeostatic Property Cluster theory provides basis for species in asexual organisms like Eubacteria and Archaea.

So I remain a pluralist. A scientific method should make the world LESS confusing and not more so. Rejecting the reality of species or retaining only one species concept means that only very little of the diversity on this planet will make sense. And even if species are just arbitrary human conceptualizations making discrete compartmentalizations of continuous diversity, well, how else would you suggest making any sense of it? A good scientist knows that the best way to tackle a problem is to break it down into workable pieces.

Friday, November 19, 2010

A question pertaining to selection vs. inheritance.

Hypothetical situation:

If there was a community of organisms which for all purposes had infinite longevity (ie they would not die of old age), and zero reproduction (ie no new cohorts), would selection still occur?

Wednesday, November 17, 2010

Clearing insects: Lactic Acid vs. KOH

Using Google searches, I have found little information on clearing of insects to observe their structure. What information that is available does not relate the benefits and detriments of various clearing agents. Here I will summarize these issues, especially to show the benefit of using lactic acid contrasted with hydroxides.

Potassium hydroxide (KOH: also known as caustic potash or lye) is a strongly basic chemical that has historically been most often used for insect clearing. It is stored as a solid and dissolved in distilled water for use, usually as a 10% solution. When heated, soft tissue is quickly destroyed as well as lightly sclerotized cuticle. Continued exposure to KOH will cause the chitonous matrix of cuticle to become sticky and soft, and a specimen left in KOH for extended periods will become clear and dissolve into invisibility. The destructive process can be slowed down by clearing in room temperature solution rather than heated, but a specimen exposed to KOH cannot ever be neutralized completely. Many old slides of specimens, including holotypes, today seem to contain nothing due to the long term caustic action of this chemical. In addition, once a specimen is placed in glycerin for viewing, it cannot be returned to KOH for more clearing.

Sodium hydroxide (NaOH) has similarly been used in clearing. It has the same properties of KOH, except it is reported that it is less caustic on weakly sclerotized tissue and membrane (Gurney et al. 1964).

Lactic acid (2-hydroxypropanoic acid) is a weakly acidic chemical now coming into favor as a clearing agent. It is stored as a fluid, usually at 80% concentration, and can be used directly. Unlike the previous hydroxides, lactic acid will not indefinitely clear material, even when heated. Membraneous and weakly sclerotized structures are retained while muscle and fat are dissolved. Lactic acid also will cause membraneous structures to expand under heat, which can make the treatment useful for eversing an aedeagus stuck within a phallocrypt. In addition, the specimen can be passed through glycerin and returned to the clearing solution if needed.

I have begun using lactic acid for all my clearing. The benefits are obvious, with some precautions. First, since heating causes expansion of tissue, sometimes specimens will explode. Therefore, only low circulating heat rather than boiling should be used. Second, while weakly sclerotized structures will be retained, intersegmental membrane is more likely to be broken over time. Gentle care when using probes and forceps will insure the parts stay connected.


Gurney, A. B.; Kramer, J. P.; Steyskal, G. C. 1964. Some techniques for the
preparation, study, and storage in microvials of insect genitalia. Annals of the
Entomological Society of America 57:240-242.

Tuesday, November 16, 2010

Criticisms of Encyclopedia of Life.

When I first heard E.O. Wilson's TED prize wish (see: I too applauded the endevour to create an online "encyclopedia" with a webpage for every species, where research could be uploaded and shared openly with the world. Such a resource would be to the benefit of every person. As a comparative biologist I appreciate synthetic resources of information on life, whereas most species descriptions now are spread far and wide in the literature.

However, after two years the Encyclopedia of Life database is no closer to it's ten year goal. If there are 1.8 described species, then contributors must write 500 species pages a day! This is hardly occurring. Even the so called exemplar pages have little information, mostly taken from other web pages such as Wikipedia. It seems the database is mostly a vehicular framework for flicker photos of wildlife, from what little is available. And even that, the mere task of uploading photographs, is difficult and requires a Flicker account.

It is not only that there are few people uploading information, it's also that each piece requires curation from an "expert", meaning it takes even longer for a page to be complete.

I cannot help but be cynical, even with Wilson giving his full support. People just don't have the time to provide to such a project to make it useful. I hope I am wrong.