Monthly Archives: October 2018

From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome (Fierer, et al. 2012)

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The two essays on microorganisms were concerned with very similar ideas with very different applications. While Martiny’s essay considered that the properties effecting macroorganisms may be helpful in understanding the dispersal of microorganisms globally, Fierer posits that perhaps those same properties may effect microorganisms on a much smaller scale, within each human being.

Fierer puts forth some interesting ideas such as succession among microbiome communities which could be initiated by disturbances such as treatment with antibiotics (Fig 3). I can’t quite figure out how to square that idea with any sort of climax, especially given the rapid and constant changes in the human microbiome. He also states that taxa of microorganisms may fit into biological niches within the body.

That having been said, I am hesitant to agree entirely with Fierer. As I mentioned in my discussion question last week, the conditions that determine behavior of one species or in one region don’t necessarily do the same to other populations. They may be useful as a guide as to what to study, though there can be no promise as to whether those studies would be fruitful. One particular hurdle facing this line of inquiry is the difficulty inherent in conducting studies given the diversity of microbiomes among individuals. How accurate is a control when abundances of taxa even within family members can vary by up to two orders of magnitude (Turnbaugh et al. 2009a)?

The Enchiridion. Epictetus (125 CE)

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The Enchiridion (literally, “The Handbook”), written by eminent stoic philosopher, Epictetus, challenged my uninformed assumptions about Stoicism as a school of thought, but not by much. The work is separated into 52 chapters that range in length from one to several paragraphs, but rarely more than a page, each containing a concise nugget of wisdom. The topics of these chapters are variations on a theme organized around the central theme that if it is part of you, you can and should control it, if it is not part of you, you cannot and should not try to control it.

Here, “part of you” includes your opinions, aims, emotions, desires, and aversions, all else is “beyond your power,” including your sickness or health, your property, and your reputation. One should endeavor to exercise complete control over everything within their power. Many of the examples are given as a duality of sorts, first presenting the external force that one would typically react to, then explaining why that reaction is damaging and one should instead look inward. If another insults you, it is not their insults that hurt you, but your reaction to those insults that hurts you; in other words, if you shrug off someone’s insults, they inflict nothing upon you.

Epictetus’s advice isn’t necessarily easy to follow, for example, I would completely avoid his advice to avoid endeavors to excite laughter, “for this may readily slide you into vulgarity.” More examples of controlling one’s emotions are to react when your favorite cup breaks as if a stranger had told you that their favorite cup had broken. The same piece of advice is blithely given regarding the death of a wife or child. This is all after Epictetus has said that if you see someone mourning, you may join them in order to comfort if you feel compelled, but do not take on any of their suffering as your own.

All of this is meant to lead to a life wherein a stoic, because of their rejection of seeking pleasure or accepting pain from the external world, is able to see what needs to be done and do it without growing emotional. As I’m writing this the example that comes to mind are the robots in Asimov’s “I, Robot”. (spoilers) The robots realized that in order to protect humanity from doing damage to themselves, they would have to take control from humanity. They declared war on humans and waged it without anger or fear in order to serve what they saw as the greater good. I wonder what Epictetus would have thought.

Experimental Zoogeography of Islands: The Colonization of Empty Islands. Daniel Simberloff and E.O. Wilson (1968)

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This study was of the events following a defaunation event on six islands of the coast of the Florida Keys, each island consisting of one or several mangroves. Simberloff and Wilson suggest that given time the population of species on each island will reach a predictable dynamic equilibrium consisting of a similar but constantly changing cast of species.

The issues I found with this research were several. The authors conducted only a single survey of each island plus two controls before the experiment began and used this is an assumed average species number on each island, a sample size far too small from which to draw any conclusions. Beginning from this survey, any information they glean about average species numbers may match up to an anomalous “average” and wrongfully confirm their theories. Throughout the experiment, the collection of data was too infrequent given the ephemeral nature of many of the species involved. The experiment also ended before any of the islands populations were found to have arrived at a dynamic equilibrium, so any similarity between the pre-defaunation survey and the final survey could be a case of a broken clock being “right” twice a day, in this case, right meaning supporting the theory put forward in the paper. Finally, there is no indication that the two control islands were surveyed more than once before and once after the experiment, which would have given a much clearer view of the properties and typical variance of a dynamic equilibrium.

Aside from the conduct of the experiment, I found the writing to be a bit lacking. I would have found technical details on how the surveys were conducted, and where each island was located relative to a source and each other to be helpful in filling out my understanding of the theory.

My feeling toward this essay isn’t that the authors’ theory is incorrect, it’s that the way the experiment was conducted left didn’t find conclusive enough evidence to confirm it.

Iphigenia in Aulis. Euripides(410BCE) Translated by George Theodoridis

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*Spoilers ahead*

I don’t think it would be at all interesting to write a plot synopsis of Iphigenia, so instead I’m going to do a quick analysis of each of the consequential characters and their major traits.

  • Agamemnon – King of Argos, Father of Iphigenia, Husband of Klytaimestra,
    • Loves Greece – Is the General of all fighting forces sailing to Troy. Sees conflict with Troy as the only way to protect Greece from raids carried out by barbarous Trojans.
    • Loves his Iphigenia – Doesn’t want to sacrifice his daughter but sees it as the only way to appease Artemis and carry on with the war.
    • Is strictly reactive – At each turn, from the first scene to the last, Agamemnon was reacting to the actions of others. He was told to sacrifice his daughter by Calchas, convinced to do so by Menelaos, forced to carry through with it by the actions of Odyssseus and so on.
  • Klytaimestra – Mother of Iphigenia, Wife of Agamemnon
    • Happiness/Grief – Exists in the play mostly to show pride that her daughter is going to marry a hero and then grief that she is going to be sacrificed. Her emotions are a sort of outsized reaction of what the audience is meant to feel for Iphigenia, particularly when she’s pleading with Achilles to save her. If she has a fault it is her womanliness, which is more of an issue with contemporary society making it impossible for her to act on her own to effect the outcome of the situation.
  • Old Man – Slave of Agamemnon and Klytaimestra
    • Loyalty – The only non-named character to make this list earned his place because of the multiple times he put himself in danger in order to carry out orders he had been given by his master, first by trying to retain his letter from Menelaos, then by exposing the sacrificial plot to Klytaimestra and Achilles. Both of these events were attempts to save Iphigenia’s life and save Klytaimestra from strife.
  • Achilles – Chief of contingent of the army, Greek Hero, son of goddess, Thetis
    • Honor/Duty – Achilles agrees to defend Iphigenia from her father and the hordes of Greek soldiers, not because she is innocent and deserves to be saved, but rather, he promises to save her because she was lured there using his name. Because Agamemnon used his name to lure Iphigenia there without his knowledge he feels responsible to protect her, however, Achilles explicitly states that had he been informed of the plot to lure Iphigenia before it was carried out he would have cosigned it. This demonstrates that it isn’t some “defense of the innocent” moral that he is guided by, but that his personal honor is most important to him.
  • Iphigenia – Daughter of Agamemnon and Klytiamestra, sacrifice to Artemis
    • Innocence – Iphigenia is the only character who is without a fault in my mind. She acts without pride or ulterior motive throughout the play, doing what she thinks is fair or what is best for all.
    • Selflessness – Being the only character that shows growth (honorable mention to Menelaos, who wasn’t important enough to make this list), Iphigenia goes from frantic at the thought of being sacrificed, to at peace with the idea. It is imparting this selflessness onto the audience that was the object of the play.

This is everyone I felt deserved a place on a “consequential characters” list. I was tempted to add Menelaos but I don’t see him as having a particular personality and his only action in the play was to foil the plot to get Iphigenia not to arrive, however that event didn’t necessarily have to be because of him, inclement weather stopping the messenger would have been just as effective.

Landscape Ecology: The Effect of Pattern on Process. Monica G Turner (1989)

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Landscape ecology differs from most other ecological theories we’ve read in class in the way it approaches seeing a region. Where Clements would see a climax, or succession toward a climax, or Gleason would see millions of individual organisms vying for space to spread their seeds and germinate, or where Paine, Connell, or MacArthur or others may be studying a single species or a narrow portion of an ecosystem, Turner is taking a wider view. When I imagine the map of a region a landscape ecologist would use, I imagine many overhead transparencies that were used in school when I was younger; one would have the type of vegetation growing in a region drawn on it, another would be a topographical map, another shows drainage, another soil nutrient content, and so on. Layering these transparencies atop one another, one would begin to see patterns emerge where certain types of vegetation always grew near a stream but only in regions where another type of vegetation grew upstream, or perhaps the probability of a hectacre of land succeeding from one phase to the next in a given number of years is increased in proximity to a certain type of soil nutrient.

One of the points I appreciated about the essay is that, while it didn’t address the topic directly, I saw it as something of an answer to Gleason’s issue with the definition of a plant association. I see landscape ecology, when employed on a mass scale, as able to show the overarching trends in vegetational growth that would satisfy Clements’ and other’s definition of an association, while also having the nuance to address smaller regions that were anomalous to the general trend.

A few of the issues I found with this theory were that the more data one collected, the more variables were involved. In order to account for those variables more data still would need to be collected and so on and so on. In addition, there is an issue of scale. Turner writes on page 175, “Landscape complexity has not been shown to be constant across a wide range of a spatial scales… Applying predictions made at one scale to other scales may be difficult if landscape structure varies with scale.” On page 180 she also says, “Elucidating the relationship between landscape pattern and ecological processes is a primary goal of ecological research on landscapes… achieving this goal may require the extrapolation of results obtained from small-scale experiments to broad scales.” The issue here is that at each scale the variables involved will fluctuate. The scales aren’t just small or broad scale either; every scale, while similar will have slightly different considerations. What this leaves one with are more unknown unknowns the more one extrapolates from data extracted from a different scale. However, this is unavoidable because a thorough survey of all variables at every scale in every region of the earth is impossible, a point the author also addresses.

Once I began to understand the process of landscape ecology the utility quickly became clear. Being able to predict the behavior of a plot of land based on how it can be expected to interact with surrounding plots of lands could be extremely useful and paint a more accurate image of the future. The author points out that this form of fortune telling could and should be used by conservationists in planning preserves among other uses. I largely agree with the theory and the author’s closing statement that through experimentation and testing of the theory it could develop to an even more powerful tool.

The Analects of Confucius. Confucius (551-479 BCE), Annotated by Robert Eno (2015)

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The Analects of Confucius are delivered to the reader in the form of truncated conversations, often only a sentence or two long. This format was initially difficult for me to read, but it grew easier and by the end of the reading I was glad not to have to read anything but the essential portions of speech. The Analects are separated into 20 books, each with its own theme, though sometimes what the theme was was lost on me.

There are several themes that show up repeatedly throughout the text. Dao, commonly translated as “The Way” or “The Path”, is something that can be shown to someone but that person must follow it themself. Li are the rituals one ought to follow in order to be honorable and respectable. Li applies both to behavior in court, making sacrifices to ancestors, and one’s reverence to their parents and older brothers. (I here say older brothers specifically rather than older siblings because women are only mentioned a few times throughout the reading and never in a position of respect or authority). Ren, difficult to translate satisfactorily, can be taken to mean humanity or goodness, though untranslated I found it easier to encompass the full idea of “those traits worth striving for in able to become a good, just person”. Junzi is literally a “true prince”, not one who gained their position by relation, but who possesses the traits that make one a good leader. A junzi doesn’t need to be in a position of power in the government, but they must be pursuant of ren.

My overall impression of Confucius is complicated. I appreciate his focus and desire on virtue coming from an individual trying to perfect themself and that only if one pursued personal perfection were they worthy to lead others. What I disagree about is that a good and just leader will make a good and just society. This attitude sees the lower classes as purely reactionary beings who have no reason of their own.

I have a lot more that I could say about the various themes of the reading and examples thereof, but I don’t think it would be either sufficient or interesting, so I’ll leave this writing as a brief one.

Metapopulation Dynamics. Illka Hanski (1998)

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Metapopulation Dynamics is different in both form and function from all the previous readings we’ve done in Ecological Thought and Practice. Rather than perform an experiment and explain the results, as Paine, Connell, Lubchenco and Menge, and MacArthur did, or speak to the ideas and terms used in ecological thought as Clements, Tansley, and Gleason did, Hanski instead provided arguments for a way of predicting the behavior and trends of species in a region.

While I was reading Metapopulation Dynamics I had to revise the way I thought about a metapopulation. Initially, I thought of fish in ponds; the same species may be in several ponds. While each pond has its own population, they could also be observed as a whole and studied as a metapopulation. This conceptualization fell apart when Hanski began speaking about colonization. A species of fish colonizing a pond that wasn’t already connected to their own pond wasn’t helpful to me. Hanski also mentions pathogens as an example. If I have the flu, I have a population of influenza virus cells in my body. Considered with others with the same virus, the virus could be studied as a metapopulation. Colonization would take place, for example, if I sneezed and the virus landed on a surface. The virus cells may get into a healthy person and infect them, thereby colonizing another suitable space, or it might die before it colonizes, a risk of migration. Ultimately, after working through both of these, it helped me understand the example Hanski used, the Glanville Fritillary butterfly.

Hanski spends a good deal of time explaining how metapopulation dynamics can be used to predict a species’ persistence. I can’t explain any of the equations used, but when factoring the area of separate “patches” of populations, distance of the patches from one another, time, population density of patches, total number of patches, and other factors, one ought to be able to predict the persistence or tendency toward extinction of a metapopulation.  In this essay, I take patch to be a region of what MacArthur would call “suitable space”

There are a few, perhaps pedantic, issues I had with this essay. I don’t understand why, as Hanski says on page 42, why “for long-term metapopulation persistence the expected number of new populations generated by one existing population during its lifetime in an otherwise empty patch network must be greater than one.” Would replacement not be persistence? I understand that stochasticity leads to unforeseen events which could lead to the destruction of a single population, but if that group has already replaced itself with another colony elsewhere, the species should persist.  This sort of made me think of Zeno’s arrow, but I’m not sure how useful of a tool that is, considering Zeno was a philosopher and Hanski was using math.

In the last few paragraphs of the article, Hanski advocates for conservation in what seemed to me to be an emotional appeal to others. I highlighted the sentences, “We do not know which fraction of currently endangered populations and species are already committed to metapopulation extinction in their present environments. A real worry is that such ‘living dead’ populations and species are numerous, especially because the delay in reaching the new equilibrium is particularly ling in just those cases that matter most, where the new equilibrium is metapopulation extinction.” This type of appeal is new to me in academic writing. I appreciate that he voiced it though. Studying and understanding the environment is interesting but ultimately useless if that information isn’t applied to the preservation of life on earth.

Impact of Food and Predation on the Snowshoe Hare Cycle. Charles Krebs, et al. (1995)

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This essay opens up with the declaration that there is a 10-year cycle in the population of snowshoe hares. The experiment conducted was to determine if that 10-year cycle could be effected by manipulation of predation and prevalence of food in the populated region.

To conduct this experiment, the authors manipulated the environment in several ways during the cycle that was taking place from 1987 to 1994. After partitioning the region into nine 1km-square blocks. In two blocks, fertilizer was spread to promote the growth of vegetation and provide a more ample source of food to the hares. In two blocks, food was made more abundant directly. One block was fenced off to prevent mammalian predation. One block both was fenced off to prevent mammalian predation, as well as had supplemental food introduced. The last three blocks were used as controls. It is important to note that in the two regions with fences, the fences were permeable to snowshoe hares, and that predation from avian predators was not restricted.

To avoid this summary becoming too long, I’m going to be brief in getting to the results. The fertilizer had a very slim effect on the overall trend of the growth, peak, and decline of the hare population. Supplemental food had a positive effect during the decline, increasing hare density anywhere from 1.5 to 6-fold during the decline. Predator exclosure had almost no effect until late decline when it increased hare density by up a similar 1.4 to 6-fold. Supplemental food and mammalian predator exclosure had the greatest effect; from the peak onward, it increased hare density by up to 11-fold.

Even with the two most successful manipulations in place, the decline in population was still incredibly pronounced. Several factors could contribute to this, for example, the predator exclosures were permeable by the hares, meaning they could leave the exclosures and be eaten by the predators. This does not explain why the hares in the block with additional food as well as predator exclusion would have left. Additionally, the exclosures were not protected from avian predators, which may have had a profound undocumented effect on hare population, particularly when not in competition for food with land-based predators.

The results of this show that there is at least one more factor other than food and mammalian predation causing the 10-year cycle in snowshoe hare population. A follow up study restricting both land-based and avian predators from entering a habitat with additional food would help to determine the effect of avian predation. Another experiment excluding mammalian predators with an electric fence permeable to the hares around a region with supplemental food where additionally the behaviors of the hares were tracked when they left the exclosure may help determine what led them to expose themselves to predation.

Ecology of Some Warblers of Northeastern Coniferous Forests. Robert H. MacArthur (1958)

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Ecology of Some Warblers of Northeastern Coniferous Forests asks one central question, how is it that five species of warblers with similar needs and similar capabilities are able to live in the same region without one species out-competing the others and all but the dominant one being eliminated. MacArthur hypothesized that the species were in balance with one another because the factor limiting each species growth was intraspecific competition rather than interspecific competition.

To determine which factors governed the competition among species and among individuals of a single species, MacArthur observed the behavior of the species to discover their feeding habits and zones, nesting, and territoriality.

Observations showed each of the five species had preferences in their feeding habits and nesting locations. The species-wide preference in feeding locations largely meant that when a particular species was hunting for food, it was more likely that another individual from its own species had been there than an individual of any other species. The preference in feeding zone directly correlated to preference in nesting zone and territoriality as well, given that each warbler tended to build their nest in their preferred feeding ground and defend just enough space as they needed to eat and provide for young.

Further evidence that most competition was intraspecific is that each species nested as slightly different times of the year, meaning that the need for food was greatest among a single species at a time rather than among all species at once. When considered along with the preference for a single feeding area, the likelihood of a particular zone being over-hunted, thereby leading to the mortality of fledglings, was due to the behavior of others of the same species. There were several times when new parents of fledglings would feed only one or two of their young.  This was shown to be the most common cause of mortality among fledglings.

To close the essay, MacArthur succinctly states that differences in feeding position, behavior, and nesting date reduce competition among species and instead focuses competition among individuals of each species.

Egypt: Ancient History of African Philosophy. Théophile Obenga (2005)

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The scales of Ma’at

In Egypt: Ancient History of African Philosophy, Théophile Obenga argues that African philosophy, or more specifically, Egyptian philosophy has been wrongfully excluded from philosophical canon, and more than simple inclusion, the study of Ma’at ought to be one of the most respected and well taught schools of philosophical thought.

One of the first issues Obenga approaches is that Egypt has been considered something other than African historically, either being considered the Near-East or Sub-Asian. The author doesn’t expressly address that the reason for this omission of Egypt as African was to justify the viewing of African people by Europeans as being lesser, while simultaneously being in awe of the Egypt’s progress as a civilization, though I’m sure in that debate he would have a more nuanced and vehement argument than I just gave.

Obenga goes on to express that in his view (though the essay is presented entirely as facts not up for debate) the first use of a word equivalent to philosopher was used in Egypt and written in hieroglyphics. He then spends several pages describing the form and meanings of many hieroglyphics while attempting to convince the reader that hieroglyphics are the only, best, and most effective way to convey meaning; for example, the symbols for “mouth”, “placenta”, and “papyrus, rolled up, tied and sealed” when combined mean “to know”. Get it?

I feel that if the essay were written by someone else or written as if it were a theory up for debate rather than a declaration of truth or a polemic against the prevailing academic thought of the time I would be far more likely to find it somewhat convincing. The central point that studies of philosophy have been euro-centric is absolutely true, the idea of philosophy very likely came about with the growth of city-states wherever they rose, including Egypt, but claims such as Egypt having no jails or social distinction between men and women for 35 centuries because of the power of Ma’at is too unbelievable and discredits the rest of Obenga’s work. (Not to say jails and social distinction among genders is innate to humans, but that’s another discussion for another time).