Monday, December 20, 2010

Chickadee 65290 and This Blog -- A Matter of Endurance

This blog turned two years old today, a venerable age in the blogosphere and a vulnerable one as well.  Prompted by this birthday, a symbol of endurance came to mind – a chickadee banded in 1937 by conservationist and writer Aldo Leopold (1887–1948) with band numbered 65290.  I was surprised that this unbidden symbol wasn’t from the world of paleontology, but, so it goes.

In A Sand County Almanac and Sketches Here and There (1949), Leopold described how each year he and his family, over the course of the winter, banded birds they trapped on their farm.  The records of banded birds that ventured back into the traps over the years provided life histories of the winged inhabitants of this land.  As he wrote,
. . . to the old-timer the banding of new birds becomes merely pleasant routine; the real thrill lies in the recapture of some bird banded long ago, some bird whose age, adventures, and previous condition of appetite are perhaps better known to you than to the bird himself.

Chickadee 65290 and six other chickadees tagged in 1937 comprised the band of brothers and sisters of the “class of 1937.”

Here is a black-capped chickadee, captured in a photo taken by Danielle Langlois.  I assume that this is the species of chickadee banded by Leopold.  The Cornell Lab of Ornithology notes that this bird is “almost universally considered ‘cute’.”  Too true.

Over the next several years 65290 proved himself to be a survivor.  Leopold characterized 65290’s ability to endure as his “extraordinary capacity for living,” somehow greater in this bird than that of his brothers and sisters who fell to the wayside.  The attrition rate of the seven members of the class of 1937 was high.  Over half disappeared by the next winter, leaving but three.  Another was lost by the third winter.  65290 appeared the fifth winter, the sole representative of the chickadees born in 1937, and never reappeared again.

The hold on life of 65290 became even more startling when Leopold considered that, of the total number of chickadees banded during the entire decade (97), apparently only this single bird experienced a fifth winter.  The stark reality of the life of a chickadee is embodied in these statistics – 69% vanished sometime before their second winter and another 20% were lost before their third.

He pondered why life is so nasty, brutish, and short for the chickadee, a bird whose size means it has few enemies.

That whimsical fellow called Evolution, . . . , tried shrinking the chickadee until he was just too big to be snapped up by flycatchers as an insect, and just too little to be pursued by hawks and owls as meat.
The villain in the piece?  The weather, at times delivering lethal punches of shifting winds, rain, and sudden drops in temperature, is “the only killer so devoid of both humor and dimension as to kill a chickadee.”  Leopold acknowledged that, over time, wise choices may have graced the life of this particular bird, particularly that of finding dry shelter from the storm, shelter that shielded a tiny body from all sides, keeping any abrupt shift in wind direction from spelling death during the night.

In closing, Leopold offered a kind of prayer:

65290 has long since gone to his reward.  I hope that in his new woods, great oaks full of ants’ eggs keep falling all day long, with never a wind to ruffle his composure or take the edge off his appetite.  And I hope that he still wears my band.

Credit for Photograph
The photograph above of a chickadee is reproduced under the terms of the GNU Free Documentation License.  It is available on the web at this link.

Tuesday, December 14, 2010

Observing the Details of Nature ~ Naturalist Jean Henri Fabre

That inimitable observer, M. Fabre, . . . .
~ Charles Darwin, The Descent of Man

The ability to observe, to pay attention to detail – yes, a desirable attribute, particularly for someone interested in natural history.

A recent incident just served to confirm that it’s not really one of mine.  Guided by my skillful proofreading hand, an article in my fossil club’s newsletter offered up three different ways of spelling the name of a river in Mississippi.  Cold comfort that one variant was actually correct.  To cap it off, one of the misspellings was in the article’s title.  Human trumped technology since I ran a spell checker and evidently accepted each of those spellings.

Then there’s the great naturalist Jean Henri Fabre (1823 – 1915), whose close, careful observations of insect life in nature came to define him.  My recent, very belated discovery of Fabre prompts this post, and, nicely, it’s within striking range of his birthday on the 22nd of December.

Employed as a teacher until late middle age, Fabre was a keen cataloger of the minute details of the natural world around him.  For nearly the last four decades of his life, he supported himself with many articles and books, and the natural world he examined was largely defined by the limits of a small walled-in plot of land in Serignan in Provence, France.  Primarily, he studied insects – their anatomy and their behavior – and did it with such skill that, even as a young man, he impressed that consummate observer Charles Darwin.

Darwin cited him in On The Origin of Species when Fabre was only in his late 30s.  In Darwin’s discussion of how natural selection might modify animals’ instincts by taking advantage of an occasional, opportunistic action, he notes that:

. . . M. Fabre has lately shown good reason for believing that although the Tachytes nigra [a predatory solitary wasp] generally makes its own burrow and stores it with paralysed prey for its own larvae to feed on, yet that when this insect finds a burrow already made and stored by another sphex [a digger wasp], it takes advantage of the prize, and becomes for the occasion parasitic.  In this case, as with the supposed case of the cuckoo, I can see no difficulty in natural selection making an occasional habit permanent, if of advantage to the species, and if the insect whose next and stored food are those feloniously appropriated, be not thus exterminated.  (1859 edition)
Though the two communicated warmly on occasion late in Darwin’s life, Fabre remained a critic of the theory of evolution by natural selection.  In a letter to Fabre dated January 31, 1880, Darwin is quintessentially Darwin, friendly, deferential, and assertive.  He begins by praising a recent volume of Fabre’s Souvenirs entomologiques (which ultimately grew to a 10-volume series of books published over some 30 years).  Darwin writes, “Never have the wonderful habits of insects been more vividly described, and it is almost as good to read about them as to see them.”  He then goes on the offensive, first, gently asking Fabre to correct an incident involving Darwin’s grandfather Erasmus Darwin that was recounted in the book; he generously presumes it was due to a faulty translation Fabre read about the incident.  More pointedly, he takes Fabre to task for his dismissal of the theory.  Darwin delivers a somewhat stinging rebuke within the cloak of a compliment – pure Darwin:
I am sorry that you are so strongly opposed to the Descent theory; I have found the searching for the history of each structure or instinct an excellent aid to observation; and wonderful observer as you are, it would suggest new points to you.  (The Life and Letters of Charles Darwin, 1887)
Fabre had ended his book with a lament about the death of his young son.  Darwin, who knew first hand the pain of the loss of a child, responds with heartfelt emotion:   “Permit me to add, that when I read the last sentence in your book, I sympathised deeply with you.”  But, science will out, and he immediately adds a postscript in which he comments approvingly on Fabre’s account of insects finding their way home, and suggests an experiment for Fabre to try.

Fabre wedded his powers of observation to a writing style of passion, poetry, and immediacy.  It is interesting to contrast his prose with Darwin’s.  The latter’s is eminently serviceable and readable, but the syntax can be complex and the prose seldom rises to the heights Fabre seemed to achieve effortlessly.  Their differing motives for writing had much to do with it.  Darwin built scientific arguments, proposed profound theories and defended same.  Fabre wrote to chronicle his observations and, perhaps even more relevant, to put bread on the table; by necessity, he was seeking a broader, popular audience.

The power of Fabre’s writing was not lost on the naturalist and writer Gerald Durrell who, at age 10 in the mid 1930s, was introduced to Fabre’s books by his older brother Lawrence, the novelist.  Gerald Durrell wrote that Fabre “opened up a magical world” in which, not only was strange insect behavior described and explained, but all of nature was at play, “from mushrooms to fossils and his writing meant that you were suddenly transported out into the open air instead of, as with so many Victorian naturalists, into a museum.”  (The Amateur Naturalist:  A Practical Guide, 1984)

Of Fabre’s written work that I’ve sampled, some essays absolutely enthrall me, and other pieces, despite the lyricism of the writing, leave me a bit cold, particularly when the naturalist delights in describing some of the more egregious behaviors of insects.  In the latter category, here’s Fabre on the Ammophila, a wasp, whose larvae are parasitic on caterpillars and sawflies:
Let us recall the table-manners of a larva living on prey, the Ammophila’s for instance, when devouring its Caterpillar.  A hole is made in the victim’s side; and the head and neck of the nursling dive deep into the wound, to root luxuriously among the entrails.  (The Life of the Fly, 1913)
Writing is lovely, topic not so much.  Easy to understand the attraction of a passage like this to a 10-year old.

Then there’s the Fabre who delights me, and it is telling, I suppose, that much of what I really like is often not the careful, detailed observations of insects and their behavior, but the personal asides and his expansive prose sojourns through natural history.  For example, in The Life of the Weevil (a 1922 compilation of the essays on weevils that appeared in the 10 volumes of the Souvenirs entomologiques), Fabre describes how, in the wintertime in Provence when “the insect takes an enforced rest,” he gains some amusement from numismatics, studying the Roman, Greek, and other ancient coins that local farmers find when they till the soil.  A coin strikes his fancy and, in flowing prose, he describes the details of the portrait on it:
On the obverse, a head of Diana of Ephesus, chub-faced, full-cheeked, thick-lipped.  A receding forehead, surmounted by a diadem; an abundant head of hair, streaming down the neck in a cascade of curls; heavy eardrops, a pearl necklace, a bow slung over the shoulder.
Still he finds this study of coins pales in comparison to “another science of numismatics, far superior and less costly, which, with its medals, the fossils, tells us the history of life.  I refer to the numismatics of stones.”  The very stone house in which he lives is the repository of this history of life, inspiring Fabre to language that approaches poetry:
My very window-sill, the confidant of bygone ages, talks to me of a vanished world.  It is, literally speaking, an ossuary, whose every particle retains the imprint of past lives.  That block of stone has lived.  Prickly spines of Sea-urchins, teeth and vertebrae of fish, broken pieces of shells and fragments of madrepores [a kind of coral] form a conglomeration of dead existences.  Examined stone by stone, my house would resolve itself into a reliquary, a rag-fair of ancient things that were once alive.
That block of stone has lived.  A perfect line.

Fabre describes the quarries from which the stone used in the building was dug and expounds on the myriad fossils that come forth from the rock.  He captures perfectly how teeth, particularly shark teeth, stand out from other fossils because they are “still wonderfully polished in the midst of their rough matrix and as bright with enamel as in the fresh state.”  These teeth and the other fossils tell him of a very different ancient landscape, or, more properly, shallow seascape.  How they appear in the matrix suggests to him the nature of waters that were once here, the proximity of land, and how these many creatures died.  Though he may not have embraced Darwin’s theory, Fabre recognized that entire species had been “mown down” by “that patient renewer of the harmony of things.”

Within the sheets that flake from a local stone, he finds perfectly preserved fossil fish.  These stone pages contain marine and terrestrial fossils, including his favorite organisms, insects.  And when he finds tiny gnats, he memorializes them in the contradiction between their life and their death:
What shall we say of these frail Midges enshrined intact in their marly reliquary?  The feeble creature, which our fingers could not pick up without crushing it, remains undisturbed beneath the weight of the mountains!

Source of Pictures
Each picture of Fabre comes from Commons.wikimedia.  Reportedly the copyrights on these images have expired.  The first picture can be found here and the second here.

Thursday, December 2, 2010

A Romantic's View of Expert Systems

Who will identify all the fossils that are just now starting to weather from the rocks?
~ Roger L. Kaesler

I am a romantic about many aspects of paleontology, including the sages that grace the science.  I suspect it helps that I am also an amateur at all of this and have never been behind the scenes.  My fleeting encounters with professional paleontologists have left me with the impression that each has a profound grasp of his or her domain, an ability to see the micro and the macro at once.  They define the term expert.  Yes, it’s a romantic view.

I rarely have the opportunity to turn to one of those paleontological sages when I’m faced with the challenge of identifying precisely what genus or species of shark gave up the fossil tooth that lies before me.  My next best approach involves identification guides, articles, a few key websites, and the like.

One resource that I’ve always thought held promise was sort of an “expert in a box” or, more accurately, an expert in a “knowledge base” (to use a term from computer-based expert systems, something else for which I also have amateur status or less).  A knowledge base for fossil identification could take one of several forms and need not be delivered through technology.  It might be a series of “rules” (e.g., IF/THEN statements) with an initial rule that draws some basic distinction within the ranks of the type of fossil specimen being studied.

An example of such a set of rules was prepared several years ago by Robert Purdy of the Smithsonian Institution.  A Key to the Common Genera of Neogene Shark Teeth (revised March 2006) is a set of 50 rules, each of which has 2 possible responses.  The response to a rule dictates which rule the user moves to next or whether a possible identification of the shark genus is ready to be offered.  Purdy’s Rule 1 requires the user to decide whether the fossil tooth has (a) one cusp or (b) several cusps.  That clearly is a fundamental difference that separates fossil shark teeth.  In Purdy’s key, if the tooth has a single cusp, then the user moves on to Rule 2; if multiple cusps, Rule 25 is the destination.  Though there are 50 such rules, some identifications come quickly, after invoking only a few rules.  The genus of the cow shark tooth, pictured below (image on left is of the lingual side, image of right is of the labial) can be identified as Notorynchus in three steps – Rules 1, 25, and 26.

I have to admit that when I applied the key to the pictured tooth I made a judgment call on the last rule choosing between the (a) and (b) options of Rule 26.  Rule 26(a) applies to a tooth with 3 to 4 cusplets while Rule 26(b) cites 7 to 10 cusplets.  This tooth appears not to fall into either category, having instead about five cusplets.  I decided to go with the option that came closest to the specimen, Rule 26(a), which immediately generated the Notorynchus identification.  Of course, with this particular tooth, I’d already consulted my other resources, though not a living expert, and “knew” where the process should be heading – Notorynchus.

I have spent some time working on a knowledge base (in Excel) to help in the identification at the species level of fossil teeth from Carcharhinus sharks, the so-called gray or requiem sharks.  Bretton Kent in his seminal Fossil Sharks of the Chesapeake Bay Region (1994) captures the essence of why, absent a human expert at my beck and call, I’ve invested time in trying to build this knowledge base.  “The identification of individual Carcharhinus species based solely on teeth can be difficult given the degree of convergence in tooth form among different lineages.”  (p. 80)

It also shouldn’t be surprising that distinguishing among species through a set of rules may be even more problematic than using rules to distinguish among genera as in Purdy’s key.  Differences among fossil specimens from diverse species are frequently very subtle.  For instance, serrations can either present or absent.  Pretty obvious, except sometimes serrations are tiny, requiring a hand lens to see.  When do serrations shift from being no longer tiny and difficult to see, but regular?  When are they no longer regular but coarse?  At the extremes the differences are obvious, but, there is, to use Kent’s word, convergence that requires distinguishing among shades of gray.

So, in my limited experience, the application of a knowledge base isn’t always, or even usually, akin to following a single, obvious thread directly from specimen to a conclusion about identity.  Rather, there are knots to contend with and these stem largely from the fact that we’re dealing with what were once living organisms which are inherently variable, with a fossilizing process that introduces variability, and with rules that are more or less useful depending upon how carefully they’ve been worded.  Ultimately, one needs to use some informed judgment.  A knowledge base can be useful in the identification of a specimen, but, from my perspective, not sufficient.

Several decades ago, expert systems emerged from work in computer-based artificial intelligence.  An expert system was defined as “a computer program designed to model the problem-solving ability of a human expert.”  (John Durkin, Application of Expert Systems in the Sciences, Ohio Journal of Science, vol. 90, no. 5, 1990, p.171.)  Among the components of such a system that Durkin identified were (1) a knowledge base and (2) something called an “inference engine” which integrated the data input by the user with the information residing in the knowledge base to craft a solution to the problem under analysis.  Apparently, the inference engine would be programmed to deal with the uncertainty introduced by incomplete information, yielding probabilities for different solutions.  Fossil identification was one problem that some programmed expert systems to address.

I recently stumbled across the presidential address to The Paleontological Society delivered by paleontologist and geologist Roger L. Kaesler in 1992, nearly 20 years ago.  In it, Kaesler stated that paleontology faced a future with far too few paleontologists who were immersed and expert in the taxonomy, evolutionary history, and geography of major groups of fossils.  He warned that “an acute shortage of systematic paleontologists” threatened the science.  (A Window of Opportunity:  Peering into a New Century of Paleontology, Journal of Paleontology, vol. 67, no. 3, 1993.)  He saw a 15-year window of opportunity in which to prepare for this future, and suggested that one promising way to preserve the systematists’ knowledge and bring it to bear on future fossil finds was the building and application of expert systems.

The window of opportunity Kaesler identified closed in 2007 (sadly, that was also the year he died).  I wonder, has the dearth of systematic paleontologists has come to pass, an event that he apparently thought inevitable?  Is the science increasingly relying on an array of expert systems to identify and classify fossils, and to define their relationships among each other?

As for the first question, in a recent (2008) piece, Norman MacLeod, the Keeper of Paleontology at the Natural History Museum in London, writes, "This expertise deficiency, which has come to be called the 'taxonomic impediment', is with us now and will only become more serious as time goes by unless some means is found to address its effects."  (Introduction, Automated Taxon Identification in Systematics:  Theory, Approaches and Applications, edited by MacLeod, 2008, p. 3).  He is writing not just about a shortage of individuals with systematic knowledge affecting paleontology but more broadly, including biology and zoology.

As for the second, MacLeod posits that the dream of automated taxon identification in general, not just of paleontological remains but also of extant organisms, is still alive but clearly has yet to be realized.  He concedes that "most practicing taxonomists still believe such systems are the stuff of science fiction."

I’m too much of a romantic and a bit soured by my brief encounters with efforts to capture knowledge in a box to think we can ever replace that human expert, that systematic paleontologist who seemingly knows it all in his or her domain.

In Trilobite:  Eyewitness to Evolution (2000), Richard Fortey describes his early years at the University of Cambridge’s Sedgwick Museum of Earth Sciences, where he labored to extract trilobites from material he had collected at Spitsbergen, north of the Arctic Circle.  The renowned paleontologist Harry Whittington was mentoring him, his “guru.”  For Fortey, Whittington does what an irreplaceable human expert system does.  Fortey writes,

From time to time Harry Whittington would appear and make encouraging remarks, or put me right when I placed the wrong head and tail together. (p. 38)

Whittington died earlier this year (2010) at the age of 94.
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