Tag Archives: ecology

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check out our partner blog, field notes on biology and culture, for short postings, links, quoted, and photographs surrounding the synapses between biology, literature, ethnography, and the “feeling of being there” with wildlife.

“Ecology” by Jack Collom

Surrounded by bone, surrounded by cells,
by rings, by rings of hell, by hair, surrounded by
air-is-a-thing, surrounded by silhouette, by honey-wet bees, yet
by skeletons of trees, surrounded by actual, yes, for practical
purposes, people, surrounded by surreal
popcorn, surrounded by the reborn: Surrender in the center
to surroundings. O surrender forever, never
end her, let her blend around, surrender to the surroundings that
surround the tender endo-surrender, that
tumble through the tumbling to that blue that
curls around the crumbling, to that, the blue that
rumbles under the sun bounding the pearl that
we walk on, talk on; we can chalk that
up to experience, sensing the brown here that’s
blue now, a drop of water surrounding a cow that’s
black & white, the warbling Blackburnian twitter that’s
machining midnight orange in the light that’s
glittering in the light green visible wind. That’s
the ticket to the tunnel through the thicket that’s
a cricket’s funnel of music to correct & pick it out
from under the wing that whirls up over & out.

Natural history books you should read before you die

I can’t say enough good things about The Natural Histories Project / Natural History Network, birthed out of a series of workshops to initiate dialogue between ecologists, geologists, educators, university presidents, and artists about the re-imaging of natural history. The audio and video clips of different perspectives on natural history are fantastic. But what really caught my eye was the Journal of Natural History and Experience, in particular the ongoing series of “101 Natural History Books That You Should Read Before You Die.”

So far, the (early) list includes the following.

The Log from the Sea of Cortez by John Steinbeck

A Naturalist on a Tropical Farm by Alexander Skutch

The Art of Falconry by Frederick von Hohenstaufen

Field Notes on Science and Nature by Michael Canfield

The Voyage of the Beagle by Charles Darwin

The Naturalist on the River Amazons by Henry Walter Bates

Personal Narrative of Travels to the Equinocital Regions of America by Alexander von Humboldt

It’s a great list so far (myself only having read, and only then in part, half of these). Having a community-agreed upon canon of works to read, or a reading list to guide you in general, is always welcome. Like having a steady professor-friend by your side to offer advice only an insider would harbor.

Observing for beauty

The Scientist does not study nature because it is useful to do so. He studies it because he takes pleasure in it; and he takes pleasure in it because it is beautiful.

– Jules Henri Poincare (fieldnotes from “Field Notes on Science and Nature”

Visualizing trophic interactions in an urban aquatic mesocosm

Variations in how to display the trophic interactions of an ecosystem—the food web, the regulating pressures between organisms of a particular space—have existed since the roots of the idea in community ecology. Nature—or, in particular, the relationships between organisms—has long been described as a web by many. Take, for example, the now-classic food web of Bear Island, the southernmost island of the Norwegian Svalbard archipelago, by Victor Summerhayes and Charles Elton in their seminal 1923 paper. In their illustration below, organisms are grouped into functional clusters, and arrows depict one organism being consumed by another, outlining a basis from which these systemic illustrations would build upon for decades.

Victor Summerhayes and Charles Elton's 1923 food web of Bear Island, Norway.

But this depiction of life wasn’t quite so scientifically until Charles Darwin published his On the Origin of Species in 1859, in which he wrote,

I am tempted to give one more instance showing how plants and animals remote in the scale of nature, are bound together by a web of complex relations. I shall hereafter have occasion to show that the exotic Lobelia fulgens is never visited in my garden by insects, and consequently, from its peculiar structure, never sets a seed. Nearly all our orchidaceous plants absolutely require the visits of insects to remove their pollen-masses and thus to fertilise them. I find from experiments that humblebees are almost indispensable to the fertilisation of the heartsease (Viola tricolor), for other bees do not visit this flower […] Hence we may infer as highly probable that, if the whole genus of humble-bees became extinct or very rare in England, the heartsease and red clover would become very rare, or wholly disappear. The number of humblebees in any district depends in a great measure upon the number of field mice, which destroy their combs and nests; and Col. Newman, who has long attended to the habits of humble-bees, believes that “more than two-thirds of them are thus destroyed all over England.” Now the number of mice is largely dependent, as every one knows, on the number of cats; and Col. Newman says, “Near villages and small towns I have found the nests of humblebees more numerous than elsewhere, which I attribute to the number of cats that destroy the mice.” Hence it is quite credible that the presence of a feline animal in large numbers in a district might determine, through the intervention first of mice and then of bees, the frequency of certain flowers in that district!

Darwin also described this web of complex relations as an entangled bank, “clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth,” and he reflected on how each of these forms, different they may be, are dependent on one another in direct and indirect pathways while at the same time producing the kinds of ecological pressures that lead to adaptation and the rise—or elimination—of species.

A species web of a slightly different kind: Charles Darwin's 1837 sketch of an evolutionary tree.

On the Origin of Species and Darwin’s subsequent writings were foremost about natural selection, the non-random process by which biological traits become more or less common in a population. But Darwin’s idea can be, and was, applied the same to how organisms themselves become more or less common in an ecosystem—the question became the following: what are those forces and relationships that allow some species to foster in a particular environment, while others only play a minor role? Community ecologists divide these species into two initial groups: autotrophs, which produce organic matter from inorganic substance to compose the primary level of an ecosystem (the first trophic level), and the heterotrophs (1+ trophic levels), which cannot fix carbon and thus must consume organisms from the initial or subsequent trophic bases. In terms of the relationships between the autotrophs and heterotrophs, food web ecology polarizes the dynamic between which group regulates the other. In bottom-up control, also known as donor control, the autotrophs (i.e., plants and algae) produce the primary resources, thereby maintaing the nutrient availability that organisms at higher trophic levels are dependent upon. Contrasting bottom-up control is the top-down dynamic, also known as a trophic cascade, in which predation and herbivory are the factors that dominate whether a species will thrive in an environment. More typically, however, analyses in community ecology strive for some middle ground between the two.

While the organization of a food web is inherently more complex—incorporating the movement of energy and mineral nutrients; dividing the heterotrophs into carnivores, herbivores, decomposers; delineating even further between competitor species, generalist consumers, specialist predators, etc—this basic model holds steady. Because this organization is predominantly a visual one—spatial and temporal patterns and variations are a large part of community dynamics in ecological research, as outlined in a recent review by Massol et al.—an interesting aspect of studying trophic interactions lies in the possibilities for visualizing data. The first graphical interpretation of a food web was published in 1880 by Lorenzo Camerano, in a manuscript entitled “On the equilibrium of living beings by means of reciprocal destruction.” Frustrated by his time’s scientific divide over which animals are useful or beneficial to agriculture, Camerano wrote the following.

To have an exact and clear idea, I repeat, of the relations between, for example, insectivorous birds and phytophagous insects, and between these and plants, these groups cannot be studied separately. Rather it is necessary to study each in relation to all other animals to see the general laws governing the equilibrium of animal and plant species.

While Camerano’s reasoning for the paper, published in the Accademia delle Scienze di Torino, was particular and applied towards the practical, his ultimate goal in the article and its resulting visualization was of general and theoretical concern.

Plate 1, Camerano 1880. Theoretical web of plant and animal interactions.

Compare that template of trophic relationships among organism groups—including primary producers, predators, ectoparasites, endoparasites, and carnivores—with a particular illustration of an ecological community of individual species with regard to enemies of a specific phylogenetic order, Coleoptera.

Plate 2, Camerano 1880. Web of interactions between Coleoptera, enemies of Coleoptera, and ecological enemies of those enemies.

In the former, more-theoretical visualization, Camerano sides with the theory of bottom-up control—vegetation is the base layer of the trophic sphere, with interactions between higher trophic levels expanding in outward rings. In the latter, allying with top-down ideas of control, complex relations are derived not from primary production, but rather from multiple pressures of predation, forming direct and indirect influences between heterotrophs. It is the latter depiction—with its emphasis on predator–prey relationships and linear–nonlinear associations between species—that has most influenced how many visualizations of trophic dynamics are drawn. In Summerhayes and Elton’s depiction of Bear Island, the first illustration in this article, the ecologists organized the biota with priority on that relationship between predator and prey—protozoa eat the bacteria, polar bears eat seals. Even where nutrients and zooplankton entered the situation, their connection to the rest of the system was given within the framework of consumption dynamics—bacteria consume nitrogen, worms eat dead plants, algae take in mineral salts.

And nor is this choice of visualization a poor or incorrect one. However, an interesting note lies in the shift between how to organize a food web in the 19th and early 20th centuries  and what kind of information should and can be included in more sophisticated images now. When one adds in the more quantitative turn in food web analysis—such as with ecological pyramids and trophic dynamics, both of which incorporate the second law of thermodynamics to consider how energy is conserved or lost as it passes between organisms—the complexity inherent in the early food webs above exponentially increases in magnitude.

The question in producing a food web is, then, how to produce a visualization of that complexity without overwhelming our perception of reality. Sacrifice quantitative rigor, and the illustration instead appears as illusion, an over-simplification. Introduce too much information, and the traceable dissolves into surplus. Such are the balancing acts Edward Tufte outlines in his 1983 The Visual Display of Quantitative Information. In the book, the statistician argues that good information design reveals the greatest number of ideas in the shortest time, with the least ink, in the smallest amount space, akin to what Italo Calvino described as lightness in literary prose—both must, in the end, tell not only a good story, but a proper one, without sacrificing either extreme of this information equilibrium.

As some of the first illustrations of food webs came from aquatic systems, bodies of water, as simultaneously self-contained microcosms and hubs in ecological networks, are good places to look for growing trends in data visualizations. An interesting and successful  update on the classic food web comes from a paper by Kevin Caillouët et al. in a 2008 paper on enclosed aquatic communities in New Orleans, Louisiana. After Hurricane Katrina flooded 80% of the city in August of 2005, floodwater from Lake Pontchartrain to the north inundated the urban terrain for over three weeks. By completely covering most regions of the city in brackish water, flooding resulted in the production of novel aquatic habitats in lowlands, depressions, and artificial containers, to name a few. Much as a forest fire produces a blank template from which previously occupied niches can be reclaimed and monocultures overthrown, Hurricane Katrina produced a blank template from which new food webs—new trophic interactions, in new magnitudes and organizations—could be drawn. In particular, on the back of research suggesting correlations between flooding and increased mosquito populations, Caillouët et al. sought to examine how these new aquatic communities would work for or against local mosquito populations, and how this in turn could influence the human risk of mosquito-borne diseases such as that caused by West Nile virus. In particular, the team examined the quasi-contained ecosystem of abandoned swimming pools, the largest of artificial containers and one of the most prone habitats to support mosquito larval development.

Caillouët et al. sample a flooded abandoned swimming pool in the Lakeview neighborhood of New Orleans.

By sampling pools in two flooded neighborhoods of New Orleans near the 17th Street Canal levee breach, the researchers were looking at this artificial environment as a mesocosm of sorts. Unlike the simplified microcosm, a controlled, laboratory-based ecosystem used to simulate and predict the behavior of its natural counterpart, a mesocosm instead brings the natural under controlled conditions, providing a link between observational field study and the artificiality of the laboratory. These mesocosms, which were being colonized by various invertebrates, fish, and mosquito species, allowed the team to ask the following questions about the composition of these new and temporary environments: if mosquito larvae were using the pools for development; if fish moved in from Lake Pontchartrain and were able to establish populations; if predatory invertebrates migrated to and colonized pools; and, lastly, if and to what extend these latter organism groups regulated mosquito populations.  To explore how these questions translate into science, Caillouët et al. relied on a conceptual model, the first step in transforming idea into design, the prerequisite for collecting and interpreting data.

Models and interpretations of aquatic community colonization post-Hurricane Katrina. Caillouët et al. 2008.

The conceptual model (A) of Caillouët et al. is not all too different, as a theoretical insight, from the initial plate by Camerano in 1880. Just as Camerano endeavored to clearly illustrate the relationships that draw together insectivorous birds and phytophagous insects, and between these and plants, the modern model food web illustrates the general relations between four main groups of organisms: the top predators, the specialist predators, the competitor species, and the prey. Much as Summerhayes and Elton used arrows in their 1923 depiction of an aquatic food web to illustrate the direction of the relationship between two or more organisms, the above model demonstrates a direct (and negative) effect of one group on another with solid lines, while dotted lines indicate an indirect (and therefore positive) effect. Continue reading

Jean-Henri Fabre on bees

The victuals are now collected: honey and flower-dust. If there is a pink carpet of sainfoin anywhere in the neighbourhood, tis there that the Mason goes plundering by preference, though it cost her a four hundred yards‘ journey every time. Her crop swells with honeyed exudations, her belly is floured with pollen. Back to the cell, which slowly fills; and back straightway to the harvest-field. And all day long, with not a sign of weariness, the same activity is maintained as long as the sun is high enough. When it is late, if the house is not yet closed, the Bee retires to her cell to spend the night there, head downwards, tip of her abdomen outside, a habit foreign to the Chalicodoma of the Sheds. Then and then alone the Mason rests; but it is a rest that is in a sense equivalent to work, for, thus placed, she blocks the entrance to the honey-store and defends her treasure against twilight or night marauders.

—Jean-Henri Fabre, “The Tribulations of the Mason Bee,” Mason Bees (1925)

"first contact," photograph by author.

Wet specimens 2

Rana pipiens. BCFS-32. My gaze snaps away from the floor and wanders to a shelf of amphibians, to another dust-covered lid on a jar in the corner. The body of the northern leopard frog is upside-down, its hind legs and pseudo-webbed toes curled, twisted and arched in opposite directions. Unlike its vibrant green pigmentation in life, the frog’s skin is now an almost translucent white, a byproduct of the preservative alcohol. What remains of its lived color are the brown spots that pattern the creature’s back and legs. But this skin seems delicate, like thin paper, like gift-wrap. It is transparent enough to show the outlines of ribs and the blue tinge of organs—the lungs, the heart, the gut. The inner workings of the frog’s head are nearly visible too, exhibiting the full form of two gelatinous black eyes, the iris no longer its characteristic golden hue. From within its open mouth, I see more blue.