Africa, mother of humanity, as seen by the Apollo 17 astronauts

Progress Report

1 May 2008

Today we write our final post, at least as a part of this class. To date we've contributed 2,268.42 credits towards the climate prediction project. Hearkening back to the purpose of grid computing, this is significant, even when compared with the impressive 48,672,572.62 credits contributed by CCS Lancaster, the primary contributor. To put things into perspective, our contribution thus far represents only 4 credits for every one hundred thousand that they have. However, for most Americans living in a metropolitan area, 25,000 people live within ten miles of home. Thus, just that many contributors in one city could match what was done by a major research effort spanning five countries.

Work done
climateprediction.net member since1 Apr 2008
Total credit2,268.42
Recent average credit15.32
climateprediction.net Specific Equivalencies
HadSM3 Model-Years15.00
HadSM3 Complete (45-year) Runs0.33

We have contributed 15 model years worth of data through HadSM3.

HadSM3 stands for Hadley Centre coupled model, Slab Model 3. The Hadley Centre, in the United Kingdom, developed a small group of climate modeling programs, each suitable to a specific task. Slab Model 3 is a purposefully less developed model; it treats Earth's oceans as a 'slab', thus its' name. Subtracting oceanic currents and relying on previous oceanic temperature measurements simplifies the model greatly. SM3 is appropriate in certain circumstances.
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Climate Change and Human Health

27 April 2008

We were recently asked to "describe a disease or disorder thought to be caused in part by human induced climate change" and to "discuss what portion of its variation is environmental". We chose infectious diseases as our focus. Dr. Robert Shope classified infectious diseases by the number of factors that characterize their spread. A two-factor disease, such as Measles, requires only the Morbillivirus and a human host. As such, two-factor diseases tend to persist wherever human to human transmission is possible, which is truly anywhere two or more people exist and interact and have contact with anyone else. Thus, two-factor diseases tend not to vary greatly with changing environment (Shope, 1991). Though, one dangerous exception can be found in Cholera, a dangerous water-borne illness caused by Vibrio cholerae infection. Incidence of Cholera epidemics increase when harsh storms strike low lying regions. It acts as a 'faux' three-factor disease through fecal/oral transmission amongst members of a community.

However, a true three-factor disease, such as Dengue, uses an intermediate. Flavivirus requires a mosquito (such as Aedes aegypti) to infect a human host. As the intermediate is sensitive to such conditions as mean temperature, humidity and length of breeding season, Dengue and many other similar three and four-factor diseases can and likely will become more widespread with GCC (Shope, 1991). Indeed, as growth zones shift farther North, disease-transmitting insects persist longer and across more inhabited ranges.

Dr. Shope added, "In the special case of segmented genome viruses, ecological overlap of populations creates an abundant opportunity for reassortment of genes that could increase the virulence of the progeny virus. There is no way to anticipate these events, but their potential argues for maintaining a strong biomedical infrastructure and watching closely for new diseases." (Shope, 1991). Thus, human-induced GCC can also yield new viruses by allowing existing ones to overlap and exchange genes in a newly found environment common to both.

The spread of two-factor diseases, such as Cholera, can be effected by climate change. Our immune response to them is generally qualitative. Malaria and other 'three plus' factor diseases, while also responsive to climate change, have a quantitative effect with respect to the genes of their hosts and the environmental factors that promote or inhibit their progress (Mackinnon et al. 2005). Our best defense is to combine strategies that decrease climate change with efforts to monitor the growing ranges and changes available to such diseases.

Mackinnon MJ, Mwangi TW, Snow RW, Marsh K, Williams TN. 2005. Heritability of malaria in Africa. Public Library of Science: Medicine 2(12):e340.

Shope, R. E. 1991. Global climate change and infectious diseases. Environmental Health Perspectives 96: 171-74.
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Response to Dr. Walker's questions

10 April 2008

Our teacher, Dr. Walker, assigned us to briefly discuss what we have learned based on specific interviews (given and read) and chapter 18 (The Cambrian Explosion and Beyond)...

As Nathan said in his response, discussing evolution without thinking of the environment...is really just a waste of time. The only way evolution exists, functions, is because of the environment. That is one thing I hadn't considered before this project, the huge changes our earth has gone through and how it has affected varying species. I actually really enjoyed reading chapter 18 on the Cambrian Explosion. As a kid, like most, this type of stuff was really the most interesting part of science. Imagining old animals, extinctions, and drifting of land masses was amazing! The section on mechanisms for extinction was particularly interesting, and really explained the material fairly and well. As we all know most people do not accept evolution. I have read differing views, and I can see some validity in all areas, empirical or not...but when looking at the facts of the environments history (which we can physical examine!) and how that affects an ever changing present number of species, it seems almost incomprehensible to deny this compelling evidence.

Response to Dr. Walker's questions

10 April 2008

This post is my personal response to our professor’s questions – “what have I learned?” and “why it is important for an environmental scientist to know about evolution?”.

Briefly, I learned from our interview with Dr. Scholes and my readings of Dr. Barnosky’s findings the importance of establishing realistic parameters in evolutionary research. Whether these parameters are temporal, spatial or functional, too broad a range can disguise (“average out”) important results while too narrow a range can yield too small a sample to demonstrate any result at all. Dr. Barnosky tested ever larger ranges of time until one proper to his team’s research interests was found; they broadened the spatial range until it was greater than a single population being studied, yet smaller than an entire biome. Only then did relevant trends become apparent. When I consider the public discourse regarding our impact upon the environment and biodiversity, these methods highlighted instances of flawed reasoning, many of which I was guilty of prior to these experiences.

Additionally, I learned that human activities generally impact the biosphere through greater rates of extinction and the results of such extinction events. Speciation as a result of our impact upon the climate is very unlikely, perhaps impossible, due to the brief range of time we are likely to affect the environment. That very fact is startling as it reminded me of the average lifespan of mammalian species Dr. Barnosky mentioned and our place within it.

Finally, I think it is essential that an environmental scientist be well educated in the mechanisms, trends and effects of evolution, as the environment is in part comprised of all of the living forms within it. Knowledge of evolution is required to understand why the environment was as it was, why it is what it is today, why it is changing, and what it may be in the future. I think that any approach to environmental science in the absence of evolution is like trying to understand a machine comprised of a vast number of unpredictable parts, with no knowledge of what force causes the whole to operate as it does. In this way evolution is a force applied to a ‘medium number system’ (Weinberg 2001) thus, understanding evolutionary forces exempts an environmental scientist from having to know every single part and action amongst this vast number – the trends applied to an appropriately chosen sample are sufficient as the theory of evolution is one of the most successful scientific generalizations ever developed.

-nrw

Weinberg, GM. An Introduction to General Systems Thinking. New York: Dorset House Publishing; 2001. 20 p.

A Discussion of GCC and Evolution

26 March 2008

The next step in our service learning project was to synthesize the aims of the grid computing project we’ve been contributing to with some of the major aspects of evolution covered in class. To this end, our professor, Dr. Walker, gave us five questions to address. Our responses to these questions are based upon our previous interview with Dr. Scholes and some recommended writings of Dr. Anthony Barnosky, a paleontologist serving as curator of the Museum of Paleontology at UCLA.

Two pronounced possibilities of climate change are extinction and speciation. We were first asked whether or not we think human-induced GCC could lead to speciation. Before our interview with Dr. Scholes or our review of Dr. Barnosky’s research, we would have thought that possible, as were a population adapted to a particular climate to see that climate disrupted, it might migrate to two or more different regions similar to the climate they’ve adapted to and, in time, become reproductively isolated. However, in an interview with the American Institute of Biological Science, Dr. Barnosky stressed that the key to addressing such a question is in the scale of time considered (Barnosky 2005). His specific approach was to define the scale of time into four categories. The first is ‘historical time’, which contains the previous thousand years of human record. ‘Deglacial/millenial time’, which corresponds with the cycles of glacial advance and retreat, are approximately 50000 years in duration. ‘Orbital time’, which corresponds with cycles of cooling and warming caused by Milankovitch oscillations, change climate across one to two hundred thousand years. Finally, ‘tectonic time’, the largest cycle, describes geologically induced climate change associated with the movements of the tectonic plates. Tectonic time spans millions to tens of millions of years (Barnosky 2001).

Barnosky and his team then set about testing what scale of climate change mammalian speciation requires, beginning with samples related to the smallest scale, historical time. They correlated the fossil record of a large, specimen-rich range of Montana, Wyoming and Idaho with relevant paleoclimactic data. Their results suggest that sustained climate change greater than the Milankovitch scale (~100000 years), extending into the average mammalian species lifespan (~1 to 2 million years) is required for speciation where climate change is the cause (Barnosky 2001). Based upon this, we think that human-induced GCC is an improbable mechanism of speciation, due to the scale Barnosky found necessary.

Secondly, in what other ways can GCC affect evolution? Some observed responses to climate change in terms of range, density and reproductive rates of various species have been noticed (Barnosky 2001). Regarding the range of a given species, populations will migrate to regions more suited to their adaptations when climate changes. As Dr. Scholes pointed out, when a given region loses a species due to extinction or changing range, the interactions it had with other species is left unfulfilled. While the exact results are difficult to predict, the colonization of an area by another species is almost certain.

Also, when a population changes its range, it may be prone to novel selection pressures it isn’t adapted to, such as parasites and predators (Barnosky 2005). Another factor related to range is whether or not a species is widely dispersed or tightly grouped. Widely dispersed species generally have better odds of survival than tightly grouped ones due to the gene flow allowed through greater dispersal. Human-induced GCC may not be sufficiently extreme or prolonged to cause speciation, but it will cause populations to change range, adapt in terms of phenotypic frequency within a population or, become extinct.

We were also asked to think deeply about how the project we’re contributing to through climateprediction.net relates to paleontology, and vice versa. Often times one approach to understanding a question is insufficient to answer it, unless augmented by another. One example of this was in the first descriptions of the fossil record itself. Initially, there was no known way to independently determine the age of a rock containing a fossil. A fossil-bearing rock could only be dated with respect to others – by superposition – younger than a lower layer yet older than a higher layer. Ultimately, radio isotope dating allowed a fossil-bearing rock to be dated concretely and without relation to other rocks. In this example, geologists and paleontologists put cutting edge developments in physics to great use.

Both the fossil record and grid-computing are, in isolation, flawed guides in predicting actual consequences of GCC. While paleontology can tell us what existed and for approximately how long, it can’t tell us what existed, yet hasn’t been found or, wasn’t a good candidate for fossilization to begin with. Thus, in the fossil record, we have a limited range of data. Similarly, yet in reverse, grid-computing projects can offer us approximations of a vast range of climatic data. While one offers us certainty without totality, the other offers totality, without certainty. We think that the efforts of Dr. Barnosky and others to combine paleontology with paleoclimatic, current and predicted climatic data is the most likely to predict actual consequences.

And as human activities are the cause of these consequences, we should address the question Dr. Barnosky answered in the affirmative; have humans changed evolution? While humans haven’t changed the mechanisms of evolution itself, we think our species offers at least three unique challenges to the balance that evolution has established. The first such challenge is that, unlike all other species, which are adapted to what their environment has been, we are capable of adapting to what it is and may be in the future … perhaps even what we wish it to be. One example of this can be seen in weaponry. Many adaptive weapons can be seen in other species – the poisonous weapons of snakes, the piercing and sawing weapons of many insects, the crushing weapons of crabs, the slicing weapons of reptiles and mammals and many more besides. Humans can not only mimic the adaptations we see in other species, adaptations that took many generations to develop, we can also develop novel weapons which have no natural precedent, such as chemical defoliants, lasers, even psychological weapons.

The second way we think humans offer a unique challenge to evolutionary balance lays in the fact that we can transplant genes between species which would never exchange them naturally. There are many examples of this, although one of the strangest was in the design of a plant which glows at night when growing in soil rich in explosive agents. This plant, designed to warn Vietnamese farmers of hidden landmines, combined genes from a plant and an insect in a way that certainly would never have occurred through any known mechanisms of evolution. Virology presents a third challenge. While all other species are constantly in a state of coevolution with the viruses that infect them, humans are capable of seeking out future antigens, yielding them inactive and distributing them for the production of predictive antibodies in the immune systems of others. In a sense, humans are unique in having a ‘collective’ immune system. Such advantages allow our species to grow far beyond its natural capacity, which brings us back to the causes of human-induced GCC.

Finally, we were asked to determine why the “Red Queen” and “Court Jester” hypotheses, coined by Dr. Barnosky, are named so. “Red Queen” posits that the primary force of evolution is the competition between members of a species and its predators, prey and parasites. This ongoing state of coevolution was named for a character from Lewis Carroll’s Through the Looking Glass. Therein, the Red Queen described her hopeless game with the words “It takes all the running you can do, to keep in the same place” (Carroll, 1871). Otherwise said, a species must continually adapt to maintain survivability with respect to the species it interacts with. Alternatively, “Court Jester” posits that interactions between members of a species and environmental conditions are primary. This name is probably a reference to a medieval court jester, whose task it was to do whatever he could to appease any member of the royal court, where jester is species and the whims of the court members are the ever-changing environment.

Barnosky, A. 2001. Distinguishing the effects of the red queen and court jester on Miocene mammal evolution in the Northern Rocky Mountains. Journal of Vertebrate Paleontology 21(1): 172 – 185.

Barnosky, A. 2005. Climate change and speciation of mammals. Interview with American Institute of Biological Sciences. March 2006.

Kansas, coal and GCC

25 February 2008

Since our interview with Dr. Scholes of 14 February, we've received some very interesting comments. We felt one of these would be best served by a new post. On 25 February, John Martellaro
added...

"Kansas residents can address this issue right now by supporting efforts to block the construction of two huge coal-fired electric generating stations. Contact your state legislators and urge them to uphold the expected veto by Gov. Kathleen Sebelius of the recent legislation designed to override the denial of permits for these plants."

While we're new to this issue, what we've read suggests this legislation has at least two troubling points. First, it would encourage a greater use of CO2 emitting coal as an energy source, due mainly to its low cost and availability. Second, the legislation would make Kansas a very convenient alternate location for future plants which would be either legally prohibited or more closely regulated in a neighboring state.

Two articles which we found informative are:

Colorado Renewable Energy Society:

http://www.cres-energy.org/clips/clips_07nov12_ks.html

The Wichita Eagle:

http://www.kansas.com/news/legislature/story/298494.html

Once you've decided what you think about this issue -- contact your member of Congress -- let them know what you think:

http://www.da.ks.gov/phonebook/congressman.htm

Interview with Dr. Chad Scholes

21 February 2008

On the 14th of February our team interviewed Dr. Chad Scholes, PhD. Dr. Scholes is the academic advisor of one our team members. He has taught at Rockhurst University for the past six years. He currently teaches General Biology II, Plant Biology and Biology Field Trip, as well as Environmental Science, which he team-teaches with Dr. Chapman, Associate Professor of Chemistry.

Dr. Scholes research focus is plant ecology. He received his undergraduate and doctorate degrees at South Dakota State University and his masters degree at the University of South Dakota.

Our interview began with a few points we had termed "questions of dismissal". As the name suggests, these were questions regarding whether global climate change is real and how much of it can be attributed to human activity. He began by offering us an article from Newsweek which demonstrated the ongoing conflict between the efforts of mainstream climate researchers and "skeptics", many of whom are privately-funded by interested industries (Sharon Begley, "The Truth about Denial," Newsweek, 13 August 2007, 20-29.). Dr. Scholes added, "…there is a scientific consensus…" that GCC (global climate change) is occurring and that human activities are the major cause of it. Further, the main question now facing the public is how much change will be allowed to occur, and how rapidly.

The remainder of our time together was spent discussing what the evolutionary impacts of GCC might be. Dr. Scholes continued, framing the problem inherent in tying these two questions together. While evolution generally occurs across vast periods of time, GCC can only be roughly predicted across the next 20 to 200 years -- the greater the range of the model, the less certainty it offers.

Thus, his touchstone was one of the only examples of understood "short-term evolution", extinctions and their effects.

This evolutionary trend is likely when organisms fail to adapt to a new set of environmental conditions. GCC provides these changes. By natural selection, organisms are adapted to what their environment has been, not what it will be. We can speak of these adaptations as responses to temperature, length of seasons, availability of groundwater, et cetera. GCC presents populations with variations far greater than the historical norm.

And as GCC challenges these populations, the niches left vacant will most likely be filled by what Dr. Scholes termed "opportunistic species". These opportunists could be native species with great fecundity and strong colonizing instincts or invasive species, those accidentally introduced from another biome.

Dr. Scholes offered us the example of mountain-top biomes. He likened these to islands where cooler conditions have allowed the continued viability of Pleistocene epoch populations. As the accumulation of ice in these regions decreases due to GCC, the "mountain as an island" is no longer protected, encouraging extinction.

Another evolutionary trend, he added, are the effects of changing growth zones. He offered us an example in the Vermont state quarter, which features a Maple tree offering sap for syrup. “Trees generally do not respond well to changes in the length of seasons”, he said. He also emphasized that as air currents bring warm air farther North, trees like these might only survive in Canada – effects like this may also cause a loss of agricultural land in the American lower middle-west, where Rockhurst University is located.

Finally, another evolutionary trend is how GCC is altering migratory habits. Flying animals, such as insects and birds, perform ecosystem services for many of the populations they encounter, such as plant pollination. From our human perspective, the pollination of fruit plants is a fine example, as we consume their offerings. As GCC alters existing migratory patterns, the members of many ecological communities will be affected, either by the introduction of a new species or the absence of one depended upon.

Ultimately, GCC is and will continue to cause both extinctions and movement. Whether a population migrates, exists across a different range or ceases to exist entirely, all organisms they once interacted with are affected. In most cases, the ecosystem services a species provides is not thoroughly understood… the evolutionary impacts of GCC are thus more difficult to predict than climate change itself.

Quaeitur

11 February 2008

The question has been raised, what is distributed computing? Why is it used? We hope today's entry will help to flesh out the process that occurs between our home computers and the larger project.

Computer processors work on data. When we use our computers independently, it is similar to a person on a cart pulling a load with one horse. Here, the power is limited yet the control is (potentially) complete.

When a load is larger than the power of the strongest available horse, a team of them is needed. This presents a challenge: how are those horses coordinated? The problem is worsened if we replace some of the horses with mules, donkeys or elephants -- this is a challenge to distributed computing projects -- the computers are independent and aren't identical.

Whether a team is pulling a load of 'stuff' or data, there must be control. Distributed computing projects employ a load manager, much as a team of horses has one driver with reigns. This divides workload among the 'clients' (or animals), making sure each one isn't overburdened, while maintaining control. To accomplish this, software called middleware acts as a translator between different types of 'client' computers and the resources they work upon. Just as a successful team's force is coordinated in one direction, our computers can work together meaningfully.

What is the larger effort that climateprediction.net works towards? Initially, climate models could only be solved by supercomputers. Yet even then the most powerful supercomputer could only solve a "simple " model -- one with a narrow range for a given variable (atmospheric carbon dioxide, sulphur, et cetera). Often these models were limited to only one value, the one judged most likely. This project uses distributed computing to solve far more challenging models, where human impacts on the environment are evaluated more broadly and finely. When our computers work together, they can, collectively, solve larger problems than many super-computers.

Quod me nutrit me destruit

07 February 2008

..."That which nourishes me also destroys me" seems an apt phrase in light of global climate change. It could refer either to the world or our way with it.

Megan, Nick and I created this blog with that in mind, to share our work in helping to predict and understand the evolutionary impacts of climate change.

We first became involved, through our professor Dr. Mindy Walker, as contributors to a distributed computing effort. The effort we're contributing to, www.climateprediction.net, takes an immense problem -- in this case, finding the set of most probable outcomes of a climate model, and divides that task among a number of volunteering "client" computers sufficient to solve it.

This is just one way in which all of us can help the scientific community understand our impact upon the Earth. We've provided links to valuable resources which can help you get informed and involved!