Tuesday, June 16, 2009

The End of the Line or over it?

This blog is about something I don’t know anything about, which believe it or not is a first for me. But I’ve been seeing a lot of news and reviews for a new documentary on overfishing, and although I can’t get to see it at the moment, I’m fascinated by the campaign to make this film into a happening, “An Inconvenient Truth of the Oceans.”

The film is called The End of the Line. Its makers describe it this way –
Imagine an ocean without fish. Imagine your meals without seafood. Imagine the global consequences. This is the future if we do not stop, think and act. In the film we see firsthand the effects of our global love affair with fish as food.

It examines the imminent extinction of bluefin tuna, brought on by increasing western demand for sushi; the impact on marine life resulting in huge overpopulation of jellyfish; and the profound implications of a future world with no fish that would bring certain mass starvation.
Filmed over two years, The End of the Line follows the investigative reporter Charles Clover as he confronts politicians and celebrity restaurateurs, who exhibit little regard for the damage they are doing to the oceans.

Overfishing – catching fish faster than their populations reproduce - is indeed a threat to the marine ecosystem, to the human food supply, and to the economic well-being of many regions. The UN Fisheries and Agriculture Organization’s 2008 report on the state of the world’s fisheries concluded that 75% of the fish stocks it monitors are fully exploited, overexploited, or depleted, and that sustainable management practices are lacking worldwide. The End of the Line explicitly aims to tackle this situation –

The film lays the responsibility squarely on consumers who innocently buy endangered fish, politicians who ignore the advice and pleas of scientists, fishermen who break quotas and fish illegally, and the global fishing industry that is slow to react to an impending disaster.

The End of the Line points to solutions that are simple and doable, but political will and activism are crucial to solve this international problem.

The End of the Line premiere at Sundance will also kick-off a global campaign for citizens to demand better marine policies. Leading international environmental organizations are lending their full support to the film.

The End of the Line will be released worldwide in 2009 using multiple formats and venues including theaters, broadcast and cable television networks, film festivals, online video campaigns, aquariums, museums and special screenings for environmental and educational organizations.

Now this is where it gets really interesting to me, this unabashed mingling of science and activism. I’ve found that I have to be very careful exposing introductory and non-majors students to subjective material. They often struggle to recognize the biases in advocacy science, or can be mislead into thinking that all scientific work comes with an agenda. I suspect though, that the blatancy of The End of the Line is exactly why it could work well as a teaching tool. From what I’ve seen, the film makes its points with a sledgehammer – that can open a lot of avenues for study. Students often react strongly to being hit over the head, and are motivated to dig deeper into a subject, to look for other ways of interpreting the data, and to debate the issues with their classmates.

The End of the Line will be released to theaters in selected cities on June 19th. In the meantime, you can poke into the story around the documentary at the sites below -

The End of the Line website

National Geographic has a page on the documentary, and links to their own articles and videos on overfishing

Babelgum is streaming segments of the film and additional videos online.

In addition, a number of science blogs have already reviewed the film. And the book of the same name by Charles Clover is widely available in bookstores and libraries.

Anyone seen The End of the Line? What did you think about it’s suitability for the classroom? I’ll blog again once I’ve watched.

Monday, June 1, 2009

You'll Never Walk Alone

The Human Genome Project was launched to map the DNA sequences carried inside every human cell. Now that the HGP is largely complete, biologists are working to map the DNA of our closest and most intimate companions, the bacteria carried in and upon every human body. The Human Microbiome Project seeks to identify and describe the complement of microbes that inhabit healthy humans, and to see how changes in that biota correlate with disease and other environmental disruptions. The project subdivides the body into biomes. In ecology, biomes are geographic regions characterized by distinct climate patterns and plant and animal communities. In the microbiome project, biomes are body regions distinguished by their physical and chemical conditions and their bacterial communities. The first steps in HMP research are sampling various biomes, such as the skin, digestive tract, nose and mouth and identifying and comparing their bacterial inhabitants.

Biologists have known for a long time that our skin teems with microbial life. But most of these bacteria don’t grow well in petri dishes, so it’s been very difficult to study them in any detail. DNA sequencing has provided a new way of exploring the microbiota. Ribosomal RNA is extracted from swab samples taken from a biome, sequenced, and analyzed to determine the diversity and composition of the bacterial community. The results of such a study of the skin have just been released. Samples collected from 20 places on the skin of each of 10 volunteers yielded over 1000 species from 200 different genera and 12 phyla. Samples from the same site on different people were far more similar than those from different spots on the same person, suggesting that the biota of human biomes do represent real communities. The forearm bacteria were the most diverse, averaging 44 species, with a paltry 19 found behind the ear.

Researchers now plan to gather samples from volunteers with skin disorders such as psoriasis, eczema, acne, and skin infections. They hope that differences in the bacterial communities between healthy and sick people will provide insights into the development and progression of disease and suggest new treatments.

As an active area of research and a novel way of approaching human health, the Human Microbiome Project has a lot of natural hooks for biology education. There’s something very charming and at the same time slightly unsettling about thinking of your body as a complex and crowded ecosystem, isn’t there? I find myself giving my forearms a lot of sidelong glances lately. Just what is going on over there?

Illustration: Skin sample sites for a study of bacterial diversity. Credit: Jane Ades, NHGRI

Sunday, May 17, 2009

Citizen science - distributed computing

Interested in searching out aliens? Want to help find a cure for cancer or muscular dystrophy? Discover more effective AIDS drugs? Breed more nutritious rice? Then try distributed computing. Distributed computing is the use of many separate but networked computers, each running the same program, to solve complex problems. When volunteers download the software for a particular project, their computers quietly set to work using idle processing power to sift through enormous data sets or crunch through intricate calculations. The combined efforts of many thousands of computers can make otherwise unworkable research possible.

Distributed computing is perhaps the most indifferent type of citizen science. You can participate without knowledge, effort, or observation. Nonetheless, these projects are valuable teaching tools. The home pages of most distributed computing projects include detailed information on the science involved, written specifically to capture the attention of non-scientists. Many include blogs, activities, and links designed to keep participants informed and engaged. Others have forums with often lively debate over the merits and problems of various projects. The range of projects is broad enough to include work that applies to any biology curriculum and that should appeal to most students. Besides the basic science of these projects, distributed computing also can be used to explore other topics, such as the ethical and practical implications of intellectual property rights and patents related to organisms, drugs, genes, and other biologic material, and the competition between diseases for funding and public attention.

Here are a few good places to get started. Googling distributed computing and volunteer computing will bring up many other resources.

SETI@home is the largest and best known distributed computing project. Users scan through radio signals from space searching for patterns that could indicate extra-terrestrial life.

Folding@home examines the links between the structure of proteins and diseases such as mad cow, Alzheimer’s, Parkinson’s, and Huntington’s.

BOINC is a software system that many distributed computing programs run on. The home site acts as a clearinghouse for projects, and includes tips on how to evaluate and choose programs. BOINC allows volunteers to divide up their computer time among multiple projects. Projects include work on malaria control, climate modeling, the evolution of DNA sequences, and the genetic links to disease.

The World Community Grid is dedicated to “projects that benefit humanity.” Current projects includes research on drugs targeting dengue fever, AIDS, muscular dystrophy, and cancer, on new strains of rice to combat famine, and on finding more efficient materials for use in solar cells.

Image - Lion, drawn by Morito Iokawa, age 5. Died of acute lymphocytic leukemia at age 6. The Help Fight Childhood Cancer Project is a distributed computing project run through the World Community Grid. Image credit - Children's Cancer Association of Japan.

Sunday, May 3, 2009

Swine flu (what else?)

The H1N1 virus
I’m confident there isn’t a biology class anywhere that hasn’t already talked about the swine flu. Or any biology blog either. But the flu and its fallout are going to be with us for a while, so I thought I’d post some links that might be helpful. Please comment with other good resources that you’ve found worthwhile.

Swine flu
  • The CDC’s H1N1 Flu page has the latest information on the current outbreak. Press releases, maps, prevention and treatment information, twitter updates, and photos.

  • Wired Science covers speculation on possible links between the virus and factory farms and the search for the ‘smoking pig.’

  • Reuters Swine Flu section is an archive of news articles, videos, and photographs of the current flu outbreak. It’s a good source for examining media coverage and public sentiment about the flu situation

  • The U.S. National Library of Medicine and National Institutes of Health have a very thorough review of influenza in general. It includes fact sheets, Q&A’s, tutorials, images, and links to almost everything you’d ever need to say about flu.

  • The pages on Flu Wiki aren’t consistent in quality but it does have a lot of information and is quite accessible to non-biologists.

  • PandemicFlu.gov describes how government agencies plan for influenza outbreaks and monitor national and international flu trends.

  • This World Health Organization chart describes the Pandemic Alert Levels being used internationally to characterize the stages of this and other pandemics.

  • The Great Pandemic is a Dept. of Health and Human Services site with terrific information on the social and medical context of the 1918-1919 influenza outbreak. Many of today’s swine flu worries draw on this event.

Every health scare is accompanied by a rash of unscientific, often flat-out crackpot, ideas as to its cause and cure. Bloggers are often the first line of defense against pseudoscience – independent scientists and health professionals, and even well-informed laymen can respond with a speed and vigor that government employees can rarely match.

  • Beyond the Short Coat takes on the notion that enemas can prevent swine flu.

  • Repectful Insolence addresses the enema claim too, and includes a particularly nice video on pseudoscience in general.

  • Scienceblogs.com is a good place to search for analyses of swine flu claims and coverage, but I’d be careful about directing students there because the commentary can get a bit rough.

Photo credit CDC/ C. S. Goldsmith and A. Balish

Sunday, April 19, 2009

Cry wolf

A slow, sad drama is unfolding on a remote island, in the process providing a tailor-made teaching window into population genetics and bioethics.

Isle Royale, a large, forested island on the northwest end of Lake Superior, is separated from the closest mainland by 15 miles of cold, deep water. This isolation has produced a unique and relatively simple wilderness ecosystem, which includes a pair of species – wolves and moose – tied together by a two-link food chain.

Moose arrived on Isle Royale sometime around 1900, after a long and dangerous swim from Canada or perhaps Minnesota. Wolves followed 40-50 years later, walking across on the ice of a particularly cold winter. Since then, the wolves have been the moose’s only predator, and the moose the wolves’ primary source of food. During the last 50 years, this relationship has been observed and recorded continuously by biologists with the National Park Service and Michigan Technological University. It is the longest running study of large mammal predator-prey relationships ever made, and it has provided many insights into how ecosystems develop and operate, and how they respond to environmental change. Recent work has revealed that this small but important community may be doomed.

Genetic testing has shown that the wolf packs on the island are all descended from a single female. After generations of inbreeding, the genetic diversity of the population has fallen by half, and most of the wolves are suffering from a congenital, inherited bone defect. This condition is marked by malformations and growths of the vertebrae, which interfere with spinal nerves and cause pain, muscle weakness, and paralysis. Many wolves also have extra vertebrae and early onset arthritis, which may be genetic as well. This discovery may explain recent declines in the island’s wolf population and suggests its future is likely to be both short and bleak.

Biologists and policy makers are now grappling with the difficult question of how to respond to the wolves’ predicament. Do they let nature take its course, and use the opportunity to learn more about the progress and consequences of local extinction events? Or do they attempt a “genetic intervention” and bring in one or more healthy, unrelated wolves to deepen the gene pool, which might both save the Isle Royale population and also provide valuable experience and knowledge on restoring the health of threatened species?

The story of wolves and moose on Isle Royale provides a wealth of opportunities for biology teachers. The ethical questions surrounding the wolves’ future are ripe for classroom discussions on conservation, wilderness, and the interplay between science and public policy. The data provided by 50 years of moose and wolf studies can easily be used to illustrate population dynamics, the founder effect, genetic drift, and interspecific competition. Students can be asked to use their knowledge of ecological processes to predict the environmental impact of wolf extinction on the island’s ecosystem as a whole, or to describe how even such a remote setting is influenced by regional and historical trends such as climate change and agricultural and wildlife management practices.

Photos courtesy of www.isleroyalewolf.org.