Friday, January 28, 2011

Mark W. Moffett

Mark W. Moffett, who has been called "The Indiana Jones of Entomology," delivered the Museum of Biological Diversity's Annual Pubic Lecture, at 7 p.m. Friday (1/28). Moffett has penned more than 20 articles for National Geographic, which has featured nearly 500 of his images. The lecture was titled "Adventures Among Ants: One Man's Remote Explorations to Chart an Alien Social World," and dealt with how ant civilization parallels human civilization. He also has a new book out.

Explanations of Diversity in Amazonia

Dr. William Balée, Professor of Anthropology at Tulane University combined ecological and anthropological research to show that biological diversity in Amazonia is tied to prehistoric and continuing native agricultural and cultural practices. Great species lists! Intriguing idea: that humans can live in harmony with nature and anthropogenic landscapes can add to ecological diversity.

Wednesday, January 26, 2011


Evolving Positive and Negative Affect?

In Don Norman's book, Emotional Design: Why We Love or Hate Everyday Objects, he lists some of the factors that Decision Science implicates as innately predisposing humans to either positive or negative affect:

"What are people genetically programmed for? Those situations and
objects that, throughout evolutionary history, offer food, warmth, or protection
give rise to positive affect. These conditions include:

warm, comfortably lit places,
temperate climate,
sweet tastes and smells,
bright, highly saturated hues,
“soothing” sounds and simple melodies and rhythms,
harmonious music and sounds,
smiling faces,
rhythmic beats,
“attractive” people,
symmetrical objects,
rounded, smooth objects
“sensuous” feelings, sounds, and shapes.

Similarly, here are some of the conditions that appear to produce automatic
negative affect:

sudden, unexpected loud sounds or bright lights,
“looming” objects (objects that appear to be about to hit the observer),
extreme hot or cold,
extremely bright lights or loud sounds,
empty, flat terrain (deserts),
crowded dense terrain (jungles or forests),
crowds of people,
rotting smells, decaying foods
bitter tastes,
sharp objects,
harsh, abrupt sounds,
grating and discordant sounds,
misshapen human bodies,
snakes and spiders,
human feces (and its smell),
other people’s body fluids,
vomit. "

Maps of the Upper Atmosphere

Google Ngrams


Saturday, January 22, 2011

Climatology Indicators: PDO, ENSO, etc

Warm Phase Cool Phase

Pacific Decadal Oscillation. We are likely moving into the cool phase of this oscillation, when sea surface temperatures along the West Coast are, on average, a bit cooler than normal.

For watching changes in ENSO, MJO, blocking, and teleconnections like the AO and NAO:

Patterns in 500mb height

Microbiome and Disease: Experimentation, Gulf War Syndrome, and Mycoplasma

Humans are host to a large number of bacteria which may influence health and disease. Whether or not any given microorganism, such as E coli, becomes pathogenic is not understood. What is becoming increasingly clear is that, in addition to exogenous influences such as diet and exercise, endogenous factors such as bacteria (and genetics!) are crucial determinants of human health. Carl Zimmer, science writer, has proclaimed: "I, for one, welcome our microbial overlords!" after reviewing recent research establishing that certain bacteria can lead to obesity. His famous New York Times fecal transplant article is here.

In the absence of scientific certainty, groups of concerned citizens have begun moving forward, experimenting with antibiotics and probiotics to try to nudge the population dynamics of their microbiome toward healthier states. This emerging field, combined with the failure of the medical community to communicate and collaborate with patients who are sick and aren't being helped by currently available diagnosis or treatment has created fertile ground for web-based DIY experimentation. The community of Chronic Fatigue Syndrome sufferers in particular have latched onto research examining possible links between a tiny gram-negative bacterium called Mycoplasma fermentans and Gulf War Syndrome. The bacteria, which can apparently be a member of normal human microbial flora, is implicated in the vague symptoms of GWS, and by extension, CFS. A definitive book on GWS found little evidence to suggest such a link, but the initiator the research, Dr. Nicholson, has forged ahead nonetheless, starting a nonprofit research lab to investigate and link between Mycoplasma fermentans and health problems.

It is unfortunate that so much of the information available online is anecdotal. If these types of alternative medical practices could keep better data it may be possible to scientifically evaluate them. However, in the absence of peer-reviewed double blind trials, it appears many people are simply grasping for any treatment that offers hope, no matter how unsupported. Indeed, the scientific jury is still out, and this developing field may see fringe transformed into mainstream.

Research into M. fermentans is certainly controversial, but continuing: see, for example:

Kawahito et al. Mycoplasma fermentans glycolipid-antigen as a pathogen of rheumatoid arthritis. Biochemical and Biophysical Research Communications. 2008;369(2):561-566.

Thursday, January 20, 2011

Economic Incentives and Water Quality in Ohio

Brent Sohngen, a professor in Ohio State University’s Department of Agricultural, Environmental and Development Economics, presented “Economic Incentives and Water Quality in Ohio”, an interesting talk about paying farmers for the reductions in runoff pollution they deliver. This economics-inspired approach differs from that typical of Soil and Water Conservation grants that pays for specific installations like riparian buffer strips, containment ponds for sewage, and conservation research program fallow fields.

Dr. Sohngen experimentally signed a contract that would pay farmers for pollution reductions in a small watershed in West Ohio. Unfortunately pollution increased when one of the farmers in the watershed decided to double his hog production. Still, Dr. Sohngen thinks the technique has promise, given that the farmers were responsible for more pollution than a nearby town's wastewater treatment plant. Given what we are willing to pay to upgrade the plant, shouldn't we be willing to pay a similar amount to the farmers?

I like the idea, but the economic logic seems to falter because it is based only on what society is willing to pay, not the cost to the farmer. I would have liked to ask about how much money, given the farmer's decision to invest in additional hogs, it would actually take for the farmer to pollute less. What is the opportunity cost of reduced pollution?

Tuesday, January 18, 2011

20th Century Weather Data

It is possible to graphically plot weather data from any point on the Earth from any date over the last 100-or so years using GrADS software and data from NOAA's NOMADS data access platform. Or see a summary of other data sources.

Monday, January 17, 2011

Pourbaix diagram

A Pourbaix diagram is used to show mineral solubility or metal valence, graphed on a Redox (Eh)/pH graph:

Emergy is not the new Money

Emergy analysis aims to document and compare the amount of energy required to produce different products. In comparison to Embodied Energy analysis, which measures just human inputs of energy, Emergy analysis measures both natural and human energy inputs. The laudable goal is to put all calculations in the same currency so that everything can be compared. However, emergy is an impossible concept and, in the end, really just weird.

First, it is weird economics. In fact, it is Marxist economics because Emergy, like Marxism, seeks to go beyond the capitalist system that assigns value based on demand to an alternative system based on supply. But then Emergy turns around and assigns emergy to dollars, a blatant contradiction. Also, emergy is not able to account for opportunity costs. For example, there is still no way to value the salmon that would have lived had it not been for the dam that destroyed their spawning grounds.

Second, it is a weird way of valuing raw resources (inputs). Putting everything in terms of solar energy makes some sense, but not when a dubious logic is used to convert rain and wind into solar equivalents, let alone when metal ores are assigned an arbitrary emergy. The urge to put everything into a hegemonic coinage is as old as the simplifying instinct, and as faulty. Everything can't be reduced to solar energy. Sustainability needs a more adaptive system and a more adaptive framework to ask questions.

Third, it has weird system diagrams (see above). While they look cool at first, one quickly realizes their myriad failings by comparing emergy diagrams to contemporaneous dynamic stock-and-flow modeling software like Stella. Also, emergy puts the controlling forces in the same format as the flows of energy, confusing both.

Fourth, it is weird ecology. The idea of "resources required" for a certain product seems to assume that the resources are "used up" in making that product, but ecosystems don't work that way. The grass that the cow eats might otherwise have died and decomposed, or if a cow eats all the grass in the lot it may create better habitat for some bird species. Presence and absence, especially of niches, are not physical qualities of a habitat. An emergy-type analysis applied to fishing suggests that eating one tuna is equivalent to eating 1,000 sardines, but that is only true if you have to farm the sardines to feed a farmed tuna. In the wild, that tuna has already eaten 1,000 sardines, whether you now eat the tuna or not. In fact, your eating the tuna may spare the next 1,000 sardines from being eaten! While it may be desirable to spare the tuna for other reasons, emergy fails any.

Fifth, it is a weird idea of sustainability. Emergy explicitly doesn't want to "double count" sun and wind, yet a smart farmer could do just that by harvesting wind energy and solar energy. Emergy doesn't do a good job of figuring out what is sustainable versus what isn't: it provides a plethora of weird ratios for calculating "Environmental Yield Ratio" and other indices of sustainability, but these ratios are all based on predetermined categorization of whether a given input is sustainable or not, thus assuming the very thing they seek to prove.

To put everything in the same system to compare everything comes from a good motivation but the conclusions end up being trivial. In my humble opinion, it may be impossible to accurately compare fish and electricity and sedimentation in terms of the energy that went in to them. Weirdly, dollars are still best.

3D Protein Structures!

Friday, January 14, 2011

UMBS Tree Girdling Study

Granger Causality

Need for closure OR Indecisive

I had thought that disagreement over Evolutionary Theory or Global Warming could be reinterpreted as an opportunity to engage other curious minds. As science becomes more egalitarian and open, more and more interested, educated citizens will join the debate. If science can learn with them (collaborative, constructivist model of knowledge), rather than teach toward them (defiency model of education in which learners need to be filled up with knowledge) we could realize a great opportunity.

However, not all arguers are open to persuasion. In complex, competing-message environments today some people pick their opinions first. Kruglanski has described a personality scale of closure/openess in decision-making. (Kruglanski, 1993)

He asked:

Which phrases do you agree with?

I find that a well ordered life with regular hours suits my temperament.
I feel uncomfortable when I don't understand the reason why an event occurred in my life.
I don't like to go into a situation without knowing what I can expect from it.
When I am confused about an important issue, I feel very upset.
I usually make important decisions quickly and confidently
I don't like to be with people who are capable of unexpected actions.
I dislike it when a person's statement could mean many different things
I'd rather know bad news than stay in a state of uncertainty.


When I go shopping, I have difficulty deciding exactly what it is that I want.
I tend to put off making important decisions until the last possible moment
I would describe myself as indecisive.
My personal space is usually messy and disorganized
I tend to struggle with most decisions

Kruglanski, A. W., Webster, D. M., & Klem, A. (1993). Motivated resistance and openness to persuasion in the presence or absence of prior information. Journal of Personality and Social Psychology, 65 (5), 861-876

Wednesday, January 12, 2011

Tuesday, January 11, 2011

Managing Great Lakes Forests for Climate Change Mitigation

Dr. Peter Curtis presents information from the FASET project at UMBS in this video presentation produced as part of The Ohio State University's Changing Climate webinar series.