Friday, June 25, 2010

Cows and Coral

I thought it made perfect sense to go fossiling before I traveled to Philadelphia to celebrate Bloomsday on June 16th, the day when James Joyce’s Ulysses takes place. Part of the celebration involves listening to a marathon reading of the novel. Engaging the mind and body in understanding the landscape, its place and time, and in searching for the hidden, obscure, beautiful, and sometimes profound – that’s often the essence of reading Ulysses and also of fossil hunting.

So, we drove far north into Pennsylvania, ending up some 100 miles from the New York state line. There, in a farmer’s field, we spent a few hot hours peeling layers of shale from an outcropping of the Mahantango Formation, Middle Devonian (~ 390 million years ago). Tools of choice – hammers and chisels, and putty knives.

Those many millions of years ago, this was sea bottom, and the marine denizens here were a rich array of invertebrates, including trilobites, crinoids, corals, bryozoans, pelecypods, and brachiopods. Rock was shedding off mountains to the east, a source of sediment that ultimately buried these creatures. The Holy Grail of our quest was the trilobite, but only one of us was successful and it wasn’t me.

Rather, I found myself collecting coral, a solitary kind, often called horn coral. Perhaps my finds were Streptelasma, but I don’t know. These coral are in the order Rugosa and are described as rugose coral.

Please excuse the digression but the word rugose calls out for exploration. My spellchecker doesn’t like rugose which isn’t surprising since that’s often the case when trying to sift through the language involved in identifying species. This is certainly not a word that ever came close to my own personal vocabulary. But, rugose is a wonderful adjective, nestled quite happily in the English language (as attested to by The American Heritage Dictionary of The English Language, 3rd edition, 1996). It means “wrinkled” or “ridged” as in “his rugose cheek.” Botany likes it, using it to describe surfaces that are very wrinkled, such as leaves with prominent networks of veins. The word comes from the Latin rugosus which, in turn, is from the Latin ruga meaning “wrinkle.” Earlier this week, New York Times columnist Verlyn Klinkenborg wrote an interesting column about the song of the Swainson’s thrush. He briefly described the naming of this thrush, and commented:
It’s always this way with species. You go searching for their identity and end up entangled in thickets of human knowledge and language.

His particular thicket was composed of the myriad descriptions of the bird’s song, mine in this case was the limit of my vocabulary.

To the coral.

Each of these photos is of a different specimen. The outer wall (epitheca) of these fossils is often white as in the first image above. On some specimens, two interesting markings on this outer layer are clearly evident (second image). The horizontal ridges are growth lines and the vertical ridges mark the internal rib-like structures (septa) that extend down the interior of the coral. These are the wrinkles that make these coral rugose. The corals grew up and out from the small end. Identification of genus and species depends on distinguishing among such elements as the patterns that the septa make which aren’t very clear in the specimens I found. The best view above (third photo) looks into the horn of a coral, offering some detail. But many of my finds were somewhat flattened, greatly obscuring the patterns of the septa, and suggesting that the corals’ burial may not have been gentle and gradual.

The day was memorable in a couple of ways. First, the abundance of the coral was staggering, but I, for a long while, had no clue what surrounded me. Only after the day had worn on and I had tired of splitting shale, did I wander a level expanse in the middle of the outcrop, hoping to catch some mosaic-eyed trilobite staring up at me.

Curious, I thought, a flock of birds must settle in these trees in the evening, or else why is the rocky ground so covered with their dried white droppings.

But, when I crouched to scan the ground from my knees, I saw that those small blotches of white were not avian poop at all. They were solitary corals that had weathered free from the shale. With a concerted effort, I repressed that small voice that initially warned me, “No, don’t touch it, that’s bird s**t,” and I filled my bag.

The second hallmark of this day of fossil farming was bovine. As we toiled in the sun, unseen cows mooed musically at us from the other side of a cluster of trees. “Woodwinds mooing cows,” as Joyce’s Leopold Bloom aptly characterized the instruments and their sound. These unseen cows were our Greek chorus, offering a running, and often mildly negative, commentary on our efforts to unpack this shale. Usually lowing gently during the afternoon, they could protest loudly when a hammer clanged against a particularly recalcitrant piece of shale. “No, no trilobite there,” the chorus sang.

Just a moment in time involving unseen cows and fossil coral.

Friday, June 18, 2010

An Adult Completes Yet Another Science Fair Project

Grass is to have on the ground with dirt under it and clover in it.

~ Ruth Krauss, A Hole Is To Dig: A First Book of First Definitions

For three years now, I have been watching a small 64 square (well, roughly square) foot portion of my front yard. This little plot slopes from one section of a retaining wall to the street in front of the house. Three years ago, after the rupture of a large water pipe and the ensuing repairs, that little plot was nothing more than a pile of dirt and rock. Anticipating the initiation of a much delayed county project to build a sidewalk that would consume that plot, I left it alone, save for an occasional pass of a weed-wacker and the pulling up of a dandelion or two.

(Uprooting dandelions would have not sat well with Emily Dickinson who was fond of the weed, describing it in one poem as a signal of the end of winter and, even more, a symbol of immortality. The poem begins: “The Dandelion’s pallid tube/Astonishes the Grass, . . . .”. When it recreated her garden for its exhibit entitled Emily Dickinson’s Garden: The Poetry of Flowers, the New York Botanical Garden carefully nurtured dandelions, apparently a first for its gardeners.)

Clearly, nature abhors (loves) a vacuum. My plot is now populated with a rich array of wildflowers, though, I agree, many of them are what others would call “weeds.”

How to capture the transformation of this piece of land located in the mid-Atlantic area? I will try pictures, a list, and graphs.


During the first week of this June, the slope offered up a flowery show. A few pictures might tell part of the tale.

A List

A list of those wildflower species in bloom at that point can tell another part of the story, giving some sense of the diversity. After trying my hand at identifying fossils for several years, it seemed a remarkably similar process to work with extant plants. Though there’s something to be said about having the entire organism at hand in its “natural” environment, the identification can still depend upon subtle distinctions that require expertise (as the “unknown” entry below attests). In this list, the identifications, scientific names, and categorizations as “Native” or “Alien” are all based on A Field Guide to Wildflowers by Roger Tory Peterson and Margaret McKenny (copyright 1968). In general, I’m confident in the identifications, well, as confident as one who only dabbles in botany can be.

Common NameScientific NameNativeAlien
BugleAjuga reptans*
Common NightshadeSolanum nigrum*
Field Sow-ThistleSonchus arvensis*
Grass-Leaved Golden-AsterChrysopsis graminifolia*
Hop CloverTrifolium agrarium*
Indian StrawberryDuchesnea indica*
Lance-Leaved Coreopsis (Tickweed)Coreopsis lanceolata*
Long-Bristled SmartweedPolygonum cespitosum*
White CloverTrifolium repens*
Whorled Wood AsterAster acuminatus*
Yellow Wood-SorrelOxalis stricta*
Unknown 1???

Species-Area Curves

I very much like to wear the “citizen scientist” mantle, but pictures and a list don’t quite entitle me to wear it. Rather, a yellowing 17-year-old article, uncovered during a recent spring cleaning of my files, offered the necessary inspiration and tools. The piece, entitled Biodiversity in the Backyard ran in the January 1993 issue of the Scientific American as that issue’s The Amateur Scientist column, and was written by Henry S. Horn, Princeton University professor of ecology and evolutionary biology. In it, he described a wonderful ecology activity exploring the calculation and meaning of a species-area curve, an activity he developed originally as part of a summer program for grade school teachers. Pretty heady stuff for grade school teachers and, by extension, their students. Over the years, the project has reached many higher level students as well. It’s an inspiring blend of field work, mathematical analysis, and hypothesizing. And, when I tore it out of the magazine those many years ago, I thought that this would make a grand science fair project for me and one of my children. When the time came, my children, rightly suspicious of my enthusiasm, declined the invitation.

So, a week ago, I (alone) finally followed the steps of the project described by Horn. My effort differed in key, possibly “fatal” ways. First, the sheer size of the terrain under analysis was dramatically different. His participants worked on a stretch of lawn on the Princeton campus that was 256 square meters, not something paltry like my 64 square foot plot. Horn’s folks inventoried all vegetation found, while I restricted myself to those plants that were in flower. [Later edit: I should clarify that Horn's folks did not worry about identifying the correct common or scientific names for their individual species. Rather, they distinguished separate species solely on the basis of leaf shape and gave species new informal names for the project. Frankly, part of the fun for me was the process of trying to affix the correct scientific label to each species. Limiting myself to plants presently in flower made this much easier.]

Regardless of the possible misguided nature of my venture, I plowed ahead. A comment at the outset on the species-area curve. Though, as I will describe below, there isn’t just one such curve, they all are graphic representations of the relationship between changes in the area under analysis and the number of unique species found. These curves are not restricted to plants. Insects and animals are fair game, though a more difficult prey given their mobility. The basic message of species-area curves is that as area increases the likelihood of encountering more species also increases. More on that message later.

I inventoried the plant species that were flowering during the first week of June in my plot, after I subdivided the plot into a nested sequence of smaller square blocks as shown below. The initial four blocks (numbered 1 through 4) were each one foot by one foot squares, the next three (5-7) were each two by two squares, and the next three (8-10) were four by four squares. Horn subdivided his plot similarly, though his initial blocks were one meter by one meter, and he created three additional blocks, each eight meters by eight meters.

The key piece of calculated data was a running cumulative total of unique species found, beginning with the smallest block (1) and ending with the largest (10). The table below shows the distribution of the species by block. The number in the block in which a species first appears is colored red – these are the species identifications that were added to the running total. (The use of the number "1" in the species' blocks was a matter of convenience for calculating the running totals. More than one specimen of a particular species might well have been found in a particular block.)

From these data, I graphed the relationship between the increasing cumulative total number of species (Y axis) against the increasing cumulative area (X axis). Plotting these data points and connecting them with straight lines produced a species-area curve (its “Type I – Horn Variation” label will come clear in a bit) that has a definite stair step aspect to it at the outset (where the number of species remained static while the area was increasing) and approaches a smooth curve as the area increases.

What does this graph convey? (Besides that I am devoting a lot of time to this little exercise.) Not unexpectedly, its message is that, as the cumulative area rises, the cumulative number of species found is likely to rise. Seemingly a truism, this relationship between area and number of species has a prominent place in ecology. Samuel M. Scheiner, biologist in the National Science Foundation’s Division of Environmental Biology, has written:

This increase of species number with area has been called one of the few laws of ecology, making species-area curves a prime measure of ecological patterns. (Six types of species-area curves, Global Ecology and Biogeography, 2003, p. 441.)

According to Scheiner, at its most basic level, this growth in the number of species is a function of two developments related to expanding the area analyzed. First, a larger area is likely to have more individual specimens, raising the probability that new species will be found. Further, as the reach of the sampled area is increased, the likelihood that environmentally different locations will be included rises, and such locations are more likely to be occupied by species different from those already encountered.

In the article cited above, Scheiner analyzed six different species-area curves, asserting that the appropriate use of each may vary. They differ in terms of the arrangement of individual blocks within the area being analyzed – a uniform grid of contiguous blocks of the same size is at one end of the spectrum while noncontiguous blocks of differing sizes (think islands) is at the other. The Type I curves (of which Horn’s is a variation) involve single counts and may result in the stair step pattern; most of the others are based on averages of the number of species found in various blocks of the same size and generate smooth curves. These curves differ in other dimensions, including whether they are sensitive to spatial arrangements of species within the area.

For the sport of it, I tackled the calculation of a Type IIA species-area curve for my plot. This curve is generated by calculating the average number of species in contiguous blocks of different sizes across the entire area under analysis. I began with one foot square blocks of which there were 64 in the 8 foot by 8 foot plot. I then calculated the average number of species in all possible two foot by two foot squares within the plot – 49 such squares exist. Similar calculations were made for squares of increasing sizes up to eight by eight foot squares (obviously, just one in this plot). Here are my calculations:

Block Dimensions (Ft.)Avg. # Species Per Block
1 x 11.23
2 x 22.71
3 x 34.50
4 x 46.28
5 x 57.88
6 x 69.11
7 x 710.75
8 x 812.00

And then I graphed the average number of species by block size. A very nice species-area curve emerges, one that is actually a smooth (well, almost smooth) curve.

So what’s been gained by all of this? Well, I had some fun. I made some sense of a baffling riot of colorful plants that colonized a patch of dirt and rock. And even this small plot appears to support the basic message of the species-area curve. And, yes, it would have been a winning science fair project for child . . . and father.

Later Postscript
I've been thinking about the consequences of limiting my sample to those plants in bloom at a particular point in June. To the extent that a species-area curve is a measure of the distributional patterns of all of the species occupying a specified area, the inventory I made of the plant species in bloom on my plot raises some concerns. Is there any reason to suspect that, by limiting my sample as I did, that the core relationship of number of species to cumulative area should be different? Certainly, none of the methods I used would allow for the number of species to decrease as the area grew. Further, it shouldn't affect the logic that using average counts of species would smooth out the stair steps of the Type I curve and yield a smooth curve that was likely to show fewer new species added after an initial steep climb. Limiting my inventory to plants in bloom certainly made identification of species easier (my guide is keyed to flower colors), but the attribute of being in bloom was in addition to the fundamental one of having established a foothold in my plot of land, and it certainly had consequences for the species counts in each block. I don't know its consequences for overall results. Still, there are myriad variables to consider. When a plant is in bloom is a function of many factors, presumably including when other plants are in bloom, when and where pollinators are active, rainfall, sunlight, temperature, . . . . Does this change the meaning of what I've calculated? Ah, part of the beauty of the effort is revealing the questions after questions.

Friday, June 4, 2010

Of Mice and Megafauna

The travails associated with opening my summer cottage each spring help explain why I enjoy some of the recent research on the extinction of the North and South American megafauna. This fauna of very large mammals which went extinct at the end of the Pleistocene Epoch (about 11,500 years ago), included such creatures as 15 foot tall woolly mammoths (image on left below), “smaller” mastodons at roughly 8 feet high (image on right), giant ground sloths the size of elephants, bear-sized giant beavers, and saber-toothed cats on the order of today’s Siberian tiger.

The link between the megafauna extinction research and my summer cottage is the lowly house mouse (Mus musculus) which checks in with a body of between 3 to 4 inches in length, complemented by a tail of perhaps equal length.

In the slender volume entitled The Ecology of a Summer House (1984), the late biologist Vincent Dethier painted a loving portrait of nature within the confines of a summer bungalow in Maine over the course of summer and into winter, ending with the deep snows of December. A renowned expert on flies and on insect behavior, he brought a scientist’s precise perspective to the subject, and coupled it with an artist’s sensitivity to life and death. As was only natural, mice and summer homes were joined in the book.

For as long as I can remember there had been wood mice in the bungalow. They were year-round residents, true natives. Each summer when we opened the house there would be numerous signs of their winter occupancy despite all efforts to discourage it. (p. 22)

Wood mice (Apodemus sylvaticus), despite their destructiveness and, perhaps because of their “air of delicate charm,” were treated by Dethier with a gentle hand. Still, he was enough of scientist to experiment with one mouse mother and her pups to see if she really knew how many she had (she didn’t).

Every spring, when I first approach the front door of my summer cottage, it is with a sense of anticipation tinged with definite dread, the latter a feeling I suspect Dethier never experienced with his bungalow. Though the cottage has been without its human occupants for nearly all of the fall and winter seasons, it has not been unoccupied. The wintering-over residents are most likely to have included, among others, house mice, not Dethier’s cuter wood mice.

A first order of business in opening the cottage for the season is searching for evidence of mice amid the dust and cobwebs. Sure, this involves some scanning for destruction, but that’s usually well hidden, waiting to be discovered late one night when, in desperate need of sleep, I unfold the sofa bed or reach into the bottom of the chest with the blankets.

The best evidence, the telltale sign, that few, some, or hordes of mice partied here in my absence is mouse scat. Though it’s hard to be precise in using this evidence to measure the extent to which the mice wintered over within these walls, with experience I have developed an instinctive internal gauge about these things.

Upon reflection, I have had to conclude that my annual spring “analysis” of mouse scat and its implications for the state of the cottage predisposes me to appreciate recent research on the extinction of the American megafauna.

This research grapples with what appear to me to be among the core questions of paleobiology: When did some set of events occur? What were the causes? What were the consequences? In this case, the key event is the extinction of the megafauna. Scientists know these large animals were still around at roughly 15,000 years ago and by the end of the Pleistocene were gone. Timing is everything. It is particularly critical for weighing the various alternative explanations offered up for this extinction. These extinction theories include (1) climate change dooming the megafauna, (2) newly arrived Paleo-Indians hunting the animals to extinction, (3) those same Paleo-Indians bringing some virulent disease that decimated the megafauna, or (4) the impact of a comet setting off a catastrophic chain of events that led to the extinction. (For an overview of these theories, see End of the Big Beasts by Peter Tyson, on NOVA Beta Evolution page, March 1, 2009.)

I think that one avenue of research on the megafaunal extinction is particularly brilliant and therein lies the summer cottage link. This thinking begins with the understanding that the herbivores among the megafauna consumed a huge amount of plant biomass and, as a result, must have generated copious amounts of dung, as in, say, mastodon scat. It also stands to reason that this waste would have become home to dung-living fungi, particularly Sporormiella, which produce spores on dung. Further, as a result of ingesting so much cellulose, it makes sense that the herbivore megafauna emitted vast amounts of methane.

A couple of recent analyses are very clever in using this scenario to fashion answers to questions surrounding the megafaunal extinction. Jacquelyn Gill of the University of Wisconsin and her colleagues analyze cores of sediment taken from the bottom of a lake in Indiana (supplemented with data from New York lakes), and measure changes in the presence in the cores of Sporormiella spores. (Pleistocene Megafaunal Collapse, Novel Plant Communities, and Enhanced Fire Regimes in North America, Science, November 20, 2009). The spores are washed from the dung into the lakes by “slopewash” and their relative abundance at different levels in the cores are taken to reflect the waxing and waning of the megafauna. I love this example of that “indirect” scientific approach – if something cannot be measured or witnessed directly, find some associated effect that can be.

What do Gill et al. find? They conclude that the inception of a significant decline in the Sporormiella spores pegs the beginning of the megafaunal decline at 14,800 years ago, with full collapse at about 13,700 years, and apparently extinction at about 11,500 years. So, the ultimate extirpation of this fauna took awhile. With these dates in hand, they offer various conclusions, among them, that the “rapid-extinction hypotheses” are wrong, so no comet impact (even the most likely candidate occurred at 12,900 years ago which is well after the onset of the decline) and no “Paleo-Indian blitzkrieg” bringing the megafauna down. They acknowledge that humans may well have contributed to the decline. Of interest, among other findings, they posit that significant changes in vegetation followed the megafaunal decline, and that the megafauna decline began during a warm period and well before the sudden cooling associated with the Younger Dryas period.

The second piece of research is one I just came across. It is a tightly reasoned, mathematical analysis that explores the potential impact of the megafauna extinction on the amount of methane in the atmosphere and the consequences for the climate. The authors, led by biologist Felisa A. Smith of the University of New Mexico, marshal data on 114 megafauna herbivores that died out at the end of the Pleistocene. (Felisa A. Smith, et al. Methane emissions from extinct megafauna, Nature Geoscience, published online May 23, 2010.) Using estimated data on the body masses of these herbivores, their per square kilometer density, and their ranges, the authors calculate that these animals’ combined annual methane production was 9.6 teragrams (9,600,000 metric tons). When those animals went extinct, that methane contribution to the atmosphere ended. Since methane is a greenhouse gas and its loss could have had substantial consequences for the climate, Smith et al. relate their findings to data on atmospheric methane concentrations derived from ice-core records. Their ultimate conclusion?

We find that the loss of megafauna could explain 12.5 to 100% of the atmospheric decrease in methane observed at the onset of the Younger Dryas. . . . [O]ur calculations suggest that decreased methane emissions caused by the extinction of the New World megafauna could have played a role in the Younger Dryas cooling event.

Though each of these studies addresses a different, though related, set of questions, there is one critical area in which they don’t agree – the time period over which the extinction occurred. As noted, the megafaunal march to extinction revealed in Gill’s data begins about 14,800 years ago, reaches collapse about 13,700 years, and extinction by 11,500 years. Smith, in contrast, places the timing of the extinction across a time period from 13,400 years ago to perhaps 12,500 years, supported in this by the decline in methane concentrations shown in the ice-core data. As a consequence of these differences, Gill would have the decline and collapse of the megafauna take place well before the beginning of the Younger Dryas cooling, a climatic change Smith suggests could itself be attributed in part to the extinction. Significantly (I think), the ice-core data in Smith’s piece seem to show rising methane concentrations for several hundred years after Gill would have the megafauna decline begin in earnest. More research and thinking may be in order.

Regardless, both of these analyses show intellectual virtuosity in their efforts to extract meaning from their data. I enjoyed them both. Smith’s analysis was especially hard to resist because in her acknowledgements she thanks the NPR news quiz show Wait Wait . . . Don’t Tell Me for “providing critical stimulus and motivation to pursue the project.”

As for the role of humans in the demise of the megafauna, we don’t have an answer, but many of us certainly are inclined to believe it wasn’t inconsequential. I turn back to Dethier and the wood mice in his summer bungalow.

The mice, like all other creatures in the house, lived in the territory of nature’s greatest predator, ignorant of the power of life and death that he held over them. Nothing is too large to be slain or too small to be obliterated. In the world at large we can kill them all, from the sperm whale to the virus. What was I to do with the mice? (p. 24)

Source of Images

Both images are from the Smithsonian Institution and were taken by Dane A. Penland in 1977. The mammoth picture can be found here and that of the mastodon here.
Nature Blog Network