Monthly Archives: February 2007

Why are doctors afraid of “evolution”?

I’ve often wondered why it is that highly educated doctors and engineers so often appear in support of Intelligent Design Creationism in so-called “debates” in public fora in this country. You may have noticed this in the local example of such a public “debate” in last year’s “Ninth Great Fresno / Oxford Debate” over the proposition “Darwin was right”. Download the linked file with the program for that evening, and look at the panelists – two of the three on the “con” side were medical professionals.

And now, the online open access journal PLoS Biology, has published a very interesting, thought provoking article in the latest issue:

Antonovics J, Abbate JL, Baker CH, Daley D, Hood ME, et al. (2007) Evolution by Any Other Name: Antibiotic Resistance and Avoidance of the E-Word. PLoS Biol 5(2): e30 doi:10.1371/journal.pbio.0050030

As the above figure from the paper illustrates, it seems that there is resistance to use of the word evolution in medical journals even in papers specifically dealing with the evolution of antibiotic resistance!! More worrisome is the suggestion near the end of the article that federal funding agencies such as NSF & NIH may have (continue to?) actively discouraged use of the e-word in titles and abstracts of grant proposals, and (perhaps more darkly amusingly) that they may be shy also about encouraging sex:

Indeed, we were told by one researcher that in the title of one proposal, the authors were urged to change the phrase “the evolution of sex” to the more arcanely eloquent wording “the advantage of bi-parental genomic recombination.”

What does it mean for society if medical professionals and government funding agencies try to hide or run away from important facts of life like evolution (and sex) even in the context of professional peer-review?

Reminds me of this Doonesbury cartoon I saw last fall – what would you do if the roles shown here were reversed?

Conservation Challenges in Africa

Hi everyone,

This week we have three readings suggested by our guest speaker, Dr. Chantal Stoner:

  1. Newmark, W.D., Manyanza, D.M., Gamassa, D.M., and H.I. Sariko. 1994. The conflict between wildlife and local people living adjacent to protected areas in Tanzania: human density as a predictor. Conservation Biology 8:249-255.

  2. Thirgood, S.J., Mosser, A., Tham, S., Hopcraft, G., Mwangomo, E., Mlengeya, T., Kilewo, M., Fryxell, J.M., Sinclair, A. and Borner, M. 2004. Can parks protect migratory ungulates? The case of the Serengeti wildebeest. Animal Conservation, 7: 113-120.
  3. Struhsaker, T.T., Struhsaker, P.J., and Siex, K.S. 2005. Conserving Africa’s rain forests: problems in protected areas and possible solutions. Biological Conservation 123:45-54. [note: link takes you to an interview with Tom Struhsaker, the lead author of this paper; scroll down to the bottom of the interview for a link to the pdf reprint]

Continue reading below the fold for some discussion points from Chantal.

1) Newmark et al. 1994: This is an older paper but effectively illustrates the conflict between wildlife and human communities on the borders of protected areas in Tanzania. Some things to notice are the percentage of people reporting wildlife problems, differences in the control techniques used by people who felt they effectively controlled wildlife problems versus those who felt they could not, and the types of species that were easiest to control. How do you think people living next to the borders of protected areas view wildlife?

2) Thirgood et al. 2004: This is a case study of the movements of wildebeest relative to the borders of a set of protected areas. The main point of this paper is that a percentage of the wildebeests’ movements fall outside protected area boundaries. (Carnivores similarly tend to have ranges that tended to spill out of protected areas and encounter very high-human inducuded mortalities on the borders of protected areas.) Some things to think about are whether this small percentage is of concern, and whether or not protected areas are an effective conservation strategy for conserving wide-ranging species.

3) Struhsaker et al. 2004: This paper addresses the basic question of whether protected areas are an effective conservation strategy in Africa. In class, my talk will provide a background on a heated debate concerning whether the best strategy to conserve wildlife is to establish strictly protected areas where no human activities are allowed, or replace protected areas with other conservation schemes that include local communities (many strategies try to encompass both philosophies). The Struhsaker et al. 2004 paper is a review of the successes and failures of tropical protected areas in Africa. This paper does a nice job of summarizing the debate but I chose it because it illustrates a common method to assess the effectiveness of difference conservation strategies.

When you read this paper, you might consider the benefits and the weaknesses of Struhsaker’s approach. Do you think this is objective? Are there better ways to determine if a particular conservation strategy is effective? Or, is does this paper present the most realistic and logistically-feasible method of gauging whether a stategy (e.g., a protected area of community conservation project) is working? Do you think money should be allocated toward monitoring programs focusing on the status of wildlife species in protected areas? If you accept Struhsaker’s methodology, what do you think of his findings- do they show that protected areas are effective or not?

The papers will be on the blog or on blackboard. Dr. Katti is helping me put the papers up.

The Discussion of 2/12

In the paper by Tylianakis et. al., we mainly discussed about figure 1 and table 1. According to the figure, as you move from a forest to a rice field, the evenness in interactions drops. Also, it was mentioned in class that evenness, complexity, and stability are important to maintain species richness and resilience.
In the paper by Beckmann and Berger, we talked about how urban bears are becoming dependant on humans by scavenging on garbage rather than by foraging for themselves. This poses a threat to bears because when they are becoming adapted to getting “easy” food, they may lose their ability to forage in the wild. One example that we talked about in class was the house sparrow finch (I think it was the house finch [it’s actually the house sparrow – Madhu]). The house sparrow finch has become so dependent living in urban areas. Because of that, there are no house sparrows finches living in the wild. We also talked about how the European house sparrows finch were declining in Europe because of their dependence on urban areas. The reason for the decline in Europe is due to the changes in human activities.

In the paper by Battin, we talked about ecological traps. One example that was mentioned in the article that was talked about in class was the Cooper’s hawk example. As mentioned, urban areas are a major ecological trap for these birds. Feeding and building nests are not the problem for these birds. The problem is that these hawks, the nestlings, are capable of becoming infected by a pigeon disease. Urban areas are considered an ecological threat because at least 50% of nestlings die, when this is not the case for nestlings in the wild. This Cooper’s hawk example can be an example of the initial stage of adaptation – where the urban hawk population can evolve to become resistant to the disease. If not, the ecological trap may become a sink.

My opinions to these papers is that all of the papers we’ve read were quite interesting except the one by Tylianakis et. al. When reading it, I couldn’t readily understand the figure really well until it was further explained in class. As for the paper by Beckmann and Berger, it was really interesting because I thought about rock pigeon when we were talking about the house sparrow finch in class. From my current understanding, I have never seen a rock pigeon in the wild. I was thinking that if all people on earth were to disappear, I think this bird would eventually become extinct. In regards to the paper by Battin, it was quite interesting when it was mentioned in class that the urban environment as an ecological trap for hawks could also be an initial stage of settling in a new environment. This is interesting because an ecological trap could just be another term for colonization – since not all species colonizing a new habitat are readily adjusted to that environment.

Restoration ecology

We have discussed several areas in biology that largely revolve around issues of biodiversity and certainly, systems modified by humans. Restoration ecology is one such area that addresses how degraded habitats may be re-established either to its original or alternative state. This implies there must be specific goals that drive a restoration effort.

It seems the end goal of a restoration effort is to reinstate some semblance of the original biodiversity (at the primary/secondary producer level) of the ecosystem—i.e., a once pristine habitat. This objective assumes that other processes such as nutrient cycling and energy flow within trophic levels will follow. Moreover, the complexity of the system is being restored because ‘structure and specific processes’ will in some sense develop a “self-sustainable” system. A restoration effort may also serve the purpose of establishing an aesthetic attraction; must we warrant the need for such sites to facilitate carbon sequestration in trees and thus alleviate the problem of the United States as a net exporter of carbon?
Even if such goals are established, how certain are we of the desired outcome(s)? Further, may we apply such a strategy to all systems? It appears that such efforts are dependent on what systems are important to restore based on the goals mentioned above. For example, a degraded habitat where non-native plants interfere with an economically important crop resulting in yield loss versus a retired agriculture land with a selenium reservoir—a hotbed for some non-native plant species.
On the issue of alien/exotic/invasive/non-native/introduced species: we may remove (through mechanical, chemical control) “weeds” that interfere with native crops to increase net yield; this in part is based on the concept of preemption: something bigger (for e.g., greater seed mass of a non-native) may ‘out compete’ a native plant over a limiting resource. However, my limited but growing survey of the literature on this issue indicates that researchers often do not ascertain what the native and non native in question are competing for. In addition, perhaps it is easier to make a blanket statement that one species is out competed by another because the non-native and native have similar habitat templates, but in fact we have yet to investigate a range of physiological criteria in this area to support the concept of preemption. Thus, we may alter our restoration goals (may be less cost, effort?) if we better understand what processes drive non-native and native interactions.
But are such approaches practical? No doubt certain degraded systems require human intervention to reverse trends (e.g., regeneration failure of native plants in old-growth forests) but at what point do we determine our efforts are sufficient to allow ‘nature to take its course’? Indeed, is there a point in talking about an end goal (if there is no historic data on the structure of the system, how do we define an end goal?) or should such sciences shift toward a model based approach that can predict likely outcomes of a certain strategy? Not to generate further ecological angst, but the issue of climate change is likely to complicate our efforts because of a change in factors that limit the role of a species in its environment—ecological niche and result in species re-distribution.

Footprint the World

Answer To These Questions Below
1. Rough models are used in the calculation of footprints.
2. Specifics and details taken into account for footprint.
a) Water Use (whole) vs. Ag Consumption/Individual’s Consumption
3. What does the footprint actually mean?

Ecology Footprint:
The definition of ecological footprint is the land and water area a human population would hypothetically require in order to maintain provide the resources required to support the human population within a defined area and its ability to absorb its wastes production. In order to figure out the footprint the value of consumed goods is converted into physical area. The consumption of goods such as energy, food, water, building material and other consumables is transformed into acreage in global hectares (GHA) per capita. The acreage is assumed to be the area reflective the amount of land required to provides the earlier mentioned goods, or services. This means that the amount of water that is incorporated into the model the amount of water used in agriculture and the amount of water that is consumed by an individual.
Knowing the ecological footprint provides a reference point which stands as an indication for the amount of ecological burden being placed on a limited resource, regardless of whether or not the resources is renewable or not. If a resource is renewable the ecological footprint stands as a suggestion as to the amount of pressure being placed on “recharge” time of that particular resource, e.g. wood products. Ecological footprint can be also seen as chronicle marker. This aids in our understanding, “it’s not just what we are using, but also how much and how fast a resource is being diluted over a period of space and time.”

However, the reliability of calculating the ecological footprints does come into question because some of the assumptions it makes are inaccurate. This is largely due to the fact that the models that are used are largely based upon the simplifying estimates and assumptions. Furthermore, some of the models are largely based on the lifestyle index and economics of the Western Hemisphere, particular in the United States. So this may be a precaution to the fact that ecological footprinting models may not be applicable to all places. It is perhaps this reason that the number of planets calculated in the site may have differed so much when a different state was chosen.

Are people really afraid of Mr. Peanut?

A Western Scrub Jay – Mr. Peanut, our neighbor & my daughters’ friend

The Fresno Bee has been carrying several stories about birds in its pages lately, which is a good thing on the whole, but I can’t say I quite agree with the tone of the latest feature on the front of the Life section last saturday titled: Not wanted in your yard? What do you think? [and if you want to read the above article, you’ll have to click on the link very soon before it disappears behind the pay-per-view archive of the Bee – I’ll hang on to my paper copy in case you miss it online]

Depressingly (although perhaps not surprisingly), this prominent article, with the goal of helping readers deal with “problem” birds, set the wrong tone for me right off the bat by misidentifying one of our common urban denizens, the native Western Scrub Jay (pictured here) as a Blue Jay which does not even occur in this area! And then it goes on to portray these birds, which my daughters love to feed in our backyard in the Fresno High neighborhood, as fearsome creatures, to deal with whom one must

“Carry an umbrella for protection and to scare them off by flipping it open a couple of times.”

Huh??!! Are people really that scared of these jays? Mr. Peanut (thus named by my daughter Sanzari, although she won’t let me ascertain the Mr. part!) is tame enough to take peanuts from Sanzari’s hand, without frightening even her toddler sister. I suppose some people are paranoid about birds, but really now!!

And that isn’t the only thing wrong with this article. It identifies 8 taxa as unwanted birds: Pigeons, Cliff Swallows, Starlings, Acorn Woodpeckers, Northern Flickers, Blue Jays (sic), Geese and Ducks. How many of these would you not want to see in your neighborhood, especially given the rapid urbanization of the central valley? I think we can all agree that we wouldn’t miss the Pigeons and Starlings (although the Bee also had another article several weeks ago that was quite positive about the thousands of Starlings roosting up in the River Park shopping mall) so much, and perhaps the Goose-dung is a bit of a problem, and the occasional woodpecker may cache acorns in the walls of a house – but what about the rest on this blacklist? All native species that somehow manage to hang on even as we continue to expand our habitat, and bring a little cheer to otherwise dreary suburbs. Is it too much to expect people to figure out a way to live with some of these smaller creatures, particularly when they impose such a negligible “cost” on us? Biodiversity is becoming precious as it is, and plenty of us bemoan its loss in the distant Amazon rainforest and Antarctica – can’t we appreciate what remains in our own backyards? Are our homes and lawns so perfect that a little migratory cliff swallow nest will unmake our spring? Does the red flash of the Flicker’s wings as it flits from tree-trunk to tree-trunk not brighten up any yard? Even the author of this article acknowledges these positives, albeit not without a caveat, on the last line:

“And when they’re not leaving droppings or trying to build a colony under your eaves, they can be interesting to watch.”

So these birds may be seen, perhaps heard too, but they cannot be allowed to actually live their lives naturally in our midst. How rude of them to be answering nature’s call or raising babies in our view!!

Apart from this general tone of the article, it does mention several times that some of these birds and their nests are legally protected under the Migratory Bird Treaty Act. This is true, and with good reason – the law was enacted in 1918 (following several other legislative steps) in response to alarming declines in migratory birds due to active harvest by people during the late 1800s and early 1900s (and ironically enough, migrant birds underwent another significant decline in the closing decades of the 20th century, making this law that much more significant and relevant all over again) – so yes, removing that swallow nest at the wrong time may get you into trouble with the law, sure. But the article appears to regard this as another nuisance as you try to deal with these unwanted birds because

If they are [protected], you may be limited in what you can do and when.

So if that swallow nest bothers you, hose it off before there are eggs laid in it! Talk about missing the spirit and intent of the law! As an ornithologist, am I supposed to feel apologetic about inconveniencing a few folks by championing such laws (that might help prevent another Silent Spring)? Sorry, but no – instead, I would rather encourage you to appreciate the beauty of that swallow and the way it builds its nest for a fleeting summer of romance before making that long journey south for another uncertain winter.

What does this story imply for the theme of our class and this blog – reconciliation ecology? Well, that earlier story, about starlings roosting in the mall, had a better ring to it than this one does – ironic considering how much of a problem those European Starlings are to native birds!

Restoration from an Evolutionary Perspective

For this disscussion we have three papers to read. [Note by Madhu: Click on the paper titles below to read abstracts, and access the full reprint via Blackboard]

Palmer et al. 1997. Ecological Theory and Community Restoration Ecology.

Young et al. 2005. The ecology of restoration: historical links, emerging issues and unexplored realms.

Suding et al. 2004. Alternative states and positive feedbacks in restoration ecology. [this link is to the reprint PDF via the Suding lab web page]

Provided below is a brief background on Ecological Restoration and a few questions to think about.

Natural Habitats / Ecosystems are degraded, modified, and altered by human activities such as development. Ecological restoration offers a way to reverse the trend (habitat loss and degradation) and to create new opportunities for Biodiversity. Ecological restoration is the process of assisting the recovery of an ecosystem that has been degraded, damaged or destroyed. Restoration is done for many different reasons: for the recovery of endangered species, to reestablish communities, and to return ecosystem structures, functions and processes to natural conditions. The goal of restoration is to create habitats that possess the structural and functional attributes of the natural habitats that they are intended to replace and to create a self supporting ecosystem that is resilient to perturbation without the need for further assistance.

Types of restoration- Passive and Active restoration

Passive Restoration: requires little human input and allows ecosystems to recover on their own.

Active restoration: requires active human input such as modern farming techniques to jump start ecological processes such as plant dispersal and establishment. Most degraded habitats require active restoration.

Provided below are the Steps taken in Active Restoration to restore a degraded habitat.

1. Research the site’s land use history, and find out why this particular site needs to be restored.
2. Outline the objectives for the restoration project because there needs to be some practical means for measuring the success of a restoration project.
3. Identify a reference (remnant) site such as a natural landscape that has not been altered or affected by human activities that can be used to help guide restoration activities.
4. A detailed site description on both the degraded and reference site is conducted to determine vegetation structure (plant composition, density, cover, and height), faunal community structure (composition and relative abundance) not always done, soil type, topography, hydrology and microclimatic conditions.
5. Create a detailed restoration design and management schedule. Restoration designs are usually based upon project objectives, topography, hydrology, soil type, microclimate, native plant species composition at nearby reference sites, and sometimes habitat considerations for wildlife.
6. Implementation of restoration activities:
A. Ground preparation could include agricultural techniques such as spraying, disking, mowing, watering, burning and grazing to remove exotic plant species and prepare the ground for planting. In the event that the soil is contaminated or degraded other procedures will need to be taken to restore soil integrity. Soils on agricultural lands in the Central Valley of CA are generally very fertile and won’t require manipulations.
B. Jump start ecological processes by planting seedlings and cuttings.
C. Employ agriculture techniques such as watering, mowing, and spraying to increase plant establishment and survival.
7. Monitor the development of a restored landscape. Monitoring is an integral part of restoration and allows for rapid adaptation of management actions and can be used to evaluate and refine restoration practices.

You can follow the following link to the Society for Ecological Restoration (SER) website to learn more about SER Primer on Ecological Restoration and the Guidelines for Developing and Managing Ecological Restoration Projects.

Restoration Ecology is light on theory and assumes succession is applied. Restoration Ecology time scale is generally around 3-20 years and sometimes assumes that a site is restored once restoration activities cease. Restoration Ecologists also assume that a successful restoration project will provide favorable conditions for native biota and will be resilient to natural perturbations.

Most restoration projects, under logistical, economic, and knowledge constraints, focus on restoring habitat by reintroducing a subset of the native flora, hoping the remaining plant and animal species from the native community return on their own.

Research / monitoring efforts therefore emphasize the rapid recovery of
ecosystem processes, and have recently begun to address recovery of functional groups in communities.

Restored systems are an underexploited opportunity (“natural” experiments) for evolutionary ecologists to understand basic processes underlying the assembly and evolution of biological communities.

Greater efforts need to be taken to bridge the gap between understanding processes in the ecological (where current efforts areconcentrated) vs. the evolutionary timeframe (where the true implications for biodiversity will be played out). An evolutionary perspective will provide theoretical insights for community ecology and guide future restoration.

Provided below are a list of questions that we should all think about and dissucss in class on monday.

How will communities assemble in actively and passively restored systems.

What role and or effect will invasive species play and have in community assembly?

Most restoration activities (watering, mowing, invasive weed control) only last a few years years. How will community struture and function change in a restored system in 10, 30, or even 50 years once restoration activities cease?

Will communities be resilient to natural disturbances and pertubations?

What role will animals play in succession?

Will species interactions change such as predation, herbivory, and competition?

Minutes of from Class (29 January 2007)

Idea of Ecological Foot-printing:
1. Rough models are used in the calculation of footprints.
2. Specifics and details taken into account for footprint.
a) Water Use (whole) vs. Ag Consumption/Individual’s Consumption
3. What does the footprint actually mean?

Online Data From Article:
1. Does one Earth really account for all things, both produced and consumed?
a) Why is one Earth the max?
b) Is the one Earth static, or can it change?
2. The consumption of renewable and non-renewable resources.
3. Excel spreadsheet about global footprint from article.

Global Consumption:
1. Resources:
a) Food
b) Fuel
2. Ethics of change and impact on current trends.
a) Why change?
1. Calculating one’s own footprint online.
a) Why is there a difference when different countries are used?
b) Infrastructure and national averages as possible answers.
2. Extreme makeovers of individual’s lives vs. current trends of consumption.
a) Alternative are needed in order to create change.

Changes in Efficiency and Placement of Resource:
1. Litigation/lobbying vs. individual’s actions.
a) How can one person contribute and yet have a global impact?

1. Logistics
2. Ideas

1. Sign-ups

Field Trip Possibility:
1. San Francisco’s urban wildlife
2. Guinevere’s work