Teaching Biology Blog

The End of the Line or over it?

2009-06-16T18:54:00.001-07:00

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.

You'll Never Walk Alone

2009-06-01T06:51:00.000-07:00

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

Citizen science - distributed computing

2009-05-17T20:19:00.000-07:00

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.

Swine flu (what else?)

2009-05-03T09:32:00.000-07:00

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

Influenza

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.

Pandemics

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.

Pseudoscience
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

It's DNA Day - do you know where your genome is?

2009-04-24T19:06:00.001-07:00

Today, April 25th, is the 7th annual National DNA Day, a day designated by Congress to celebrate 2 genetic milestones – the discovery of the DNA double helix in February 1953, and the announcement 50 years and a month later of the complete human genome sequence. This year’s commemoration includes all the usual suspects – special talks and programs online and at museums and universities as well as multiple news stories, blogs, and articles in scientific magazines.

There’s also a new twist this year – you can bid in an ebay auction to have your very own personal genome sequenced:

"The X PRIZE Foundation, an educational nonprofit prize institute dedicated to fostering radical breakthroughs for the benefit of humanity, and Knome, Inc., a leading personal genomics company, are working together to provide a unique opportunity. Through this special charity auction you will have the opportunity to accelerate the field of personalized medicine and join an elite group of genomic pioneers by receiving a comprehensive private analysis and interpretation of your very own whole genome sequence. Retail value alone is $99,500."

Among other things, the winning bidder will receive a flash drive containing a digital copy of his genome sequence (how cool would that be?) and an “interpretation” of the risk potential in his genome. Wow. Although genome sequencing is still ridiculously pricey, and new research on genetic variation suggests that individual genomes may not be as useful in predicting disease as once hoped, I am amazed anyway. Who would have thought genetics would come so far so fast? How long will it be until everyone has their genome sequence tucked away on a drive along with U2’s latest album and their vacation pictures?

If having your genome sequenced is out of the picture, DNA Day still provides a lot of useful genetic resources.

The National Human Genome Research Institute has a DNA Day page with transcripts of chats between students and geneticists, as well as webcasts and presentations.

The American Society of Human Genetics has a video series on DNA and links to finding local scientists who will give classroom presentations on genetics.

Stanford and the University of Utah both have instructions for simple, do-it-yourself DNA extraction experiments.

The Dolan DNA Learning Center has animations, videos, lectures, and interactive activities on DNA, genetics, genomes, and cancer. Their DNA Interactive program is especially good and includes a thorough Teacher’s Guide.

Cry wolf

2009-04-19T18:23:00.000-07:00

A slow, sad drama is unfolding on a remote island, in the process providing a tailor-made for 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’ 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.

Non-Majors Biology Course added to Hippocampus

2009-04-12T14:31:00.000-07:00

Looking for a complete online biology course or just extra information on a topic or two to supplement material you already have? A few ideas for assignments and activities that students can do on their own? Hippocampus’ newest offering, Non-Majors Biology, may be just what you’re looking for. This one-semester course is an introduction to the grand sweep of life on Earth and provides a basic understanding of the processes that shape and sustain it. It describes the ecological ties that bind organisms to one another and to their environment and explores the promising, perilous dance of humans and nature.

Topics include the science of biology, the structure and function of cells, tissues and organs, cellular processes, cell division and the life cycle, principles of inheritance, evolution, the diversity of life, and ecology.

After completing this course, students should understand:
• The scope and methods of biology
• The internal organization of living organisms
• The life cycle of cells
• The flow of energy and matter through organisms and ecosystems
• The evolution and diversity of life on Earth
• The principles of ecology

All that, and like all the content on Hippocampus, it’s free too. Non-Majors Biology is the result of social authoring. Three biologists (I was one of them) wrote the chapters independently, so there are some gaps and some overlaps as well as variations in style and tone, but all the basics are covered.

By the way, if you’ve never tried social authoring, it’s worth a shot. As in all writing or teaching projects, I learned and relearned a lot of biology in the process. And it was eye-opening to see what other teachers thought belonged in a basic biology course and how they organized and explained important scientific principles. There’s definitely more than one way to skin a cat.

Check it out, and please feel free to offer comments and critiques either here or over on Hippocampus. There’s an exclamation point icon on the tool bar in every chapter that brings up a feedback box.

HIV caught in the act

2009-04-04T18:16:00.000-07:00

This week I’ve been watching invading microbes once again, but this time the bad guys win. The video above shows the spread of HIV between two cells. Made possible by a combination of technological and genetic engineering, it represents an important advance in understanding the behavior of these deadly infectious particles. A team of researchers altered the genetic code of a strain of HIV, inserting a protein that glows green under blue light, and then introduced cells infected with the altered virus into a culture of human T cells. Over the course of several days, they watched and photographed the results.

Viruses are parasites. They move into a cell and hijack its metabolic machinery to turn out multiple copies of the viral genome. Eventually the cell overloads and bursts, releasing the new viruses into the blood and lymph where they search for new host cells. This interval is a time of vulnerability – outside the protective membrane of a cell, the viruses can be attacked by the immune system and anti-viral drugs. (Witness the hapless bacteria in my previous blog.)

As this video shows, HIV spreads in a different manner, one that avoids the dangers faced by free-range viruses. An infected cell, colored green by its high HIV count, brushes alongside a healthy T cell, and a number of viruses gather just inside the cell membrane, along the contact point. The infected cell pokes the side of the T cell with a finger-like extension called a viral synapse, triggering the T cell to engulf the synapse and its deadly cargo.

This could be a very helpful discovery in the fight to combat AIDS. Attempts to develop an effective AIDS vaccine have been unsuccessful, probably because most were aimed at teaching the immune system to recognize and attack HIV circulating in the blood stream. Now that it is clear that the primary internal spread of the virus is directly from cell to cell, researchers can work on drugs that inhibit the formation of synapses by infected cells and their endocytosis by healthy ones. It also seems likely that HIV’s mechanism for infection will provide insight on the behaviors of viruses that cause other intractable diseases.

There’s still so much to learn about how life works, so much biology left to do – it’s exciting.

Bacteria can run but they can't hide

2009-03-29T11:14:00.000-07:00

I just stumbled across this video of a neutrophil chasing down and engulfing a bacterium. Although it’s one of those old, slightly grainy science films from the 1950's, there is something really compelling about the frantic vibrations of the bacterium, the remorseless pursuit by the neutrophil, and their eerily silent battle among the red blood cells. It’s a little Hitchcockian, don't you think? I leaned forward while I watched it, and now I can’t help anthropomorphizing the heck out of it while I discuss it. Although that isn’t completely out of line, since this very scene is being repeated a million times over right now inside me and you and every human. At any rate, it was interesting enough to get me to google around a bit to refresh my memory on just what the heck a neutrophil is and does. So you go, 1950's filmstrip.

As is so often the case in biology, what looks like a simple process – see bacteria, catch bacteria, kill bacteria – is actually quite complex. Neutrophils are one variety of a kind of white blood cells called granular leucocytes, which form a major part of the immune system. The cell membrane of each neutrophil is studded with chemical receptors. These receptors are specialized to detect the proteins that immune cells release when they encounter an infection or inflammation. When neutrophils receive such calls for help, they follow their chemical gradient back to the source with great speed. Upon arrival, foreign bacteria are destroyed through phagocytosis – the neutrophils engulf and then digest the invaders. The bacteria do get revenge of a sort. Eventually the neutrophils die, and are themselves phagocytosed and subsequently turned into pus, which isn’t a particularly glorious end for such staunch defenders.

Neutrophil (yellow) engulfing anthrax bacteria (orange). Scale bar is 5um. From PLoS Pathogens Vol. 1(3) November 2005.

Spring has sprung

2009-03-22T11:46:00.000-07:00

It’s just now become spring officially, but in my backyard it was here a week or two ago, when I could see the first show of yellow on the tips of the daffodils. Because of course that’s how spring arrives, rolling out in a slow, predictable sweep across latitudes and landscapes. Only, spring flowers aren’t as reliable as they used to be. All the seasons have begun to creep, as climate change has its way with temperature and precipitation patterns.

As biologists work to understand how organisms and ecosystems are responding to shifting seasons, they’re taking a new look at an old science. Phenology is the study of the timing of natural events, such as when a lake freezes over, a plant’s buds break open, or the first migratory bird touches down. Farmers used to use these observations for clues of when to plant and when to harvest. Now biologists are turning to them for clues to how global warming is affecting the natural rhythms of species and communities. They compare the dates of various phenophases (events in the life cycles of plants and animals) across a wide area over multiple seasons, looking for patterns and trends.

This work relies on many thousands of non-scientists to do the heavy lifting - local observers who watch and report when leaves and flowers appear and wither and when birds and butterflies come and go. That’s where teachers and students can get involved. In the last few years, several phenological projects have gone online, making it remarkably easy to join in. Two of the best are BudBurst and The National Phenology Network.

BudBurst is breezier, more colorful, and easier to navigate. It also includes date and species maps that show the location and content of recent reports, which allow you to compare the timing of events in your area with those around the country, and to get a general sense of the ebb and flow of the seasons.

The USA National Phenology Network is on the austere side, but contains more detailed information on each plant species and how to recognize each phenophase. It also has a more extensive set of links and resources, and plans to expand to include animal observations in 2010.

Both these sites provide ideas and guides for incorporating phenology into the classroom. In the process, students will learn how to observe and describe nature, and collect and share scientific data. Phenology is especially appropriate for distance education. It’s a simple and straightforward exercise that can be done easily, without supervision. Depending on how widely scattered students are, distinct regional difference should show up and provide the opportunity for exploring climatic and ecological variations.

Phenology is only one area in which interested amateurs can make significant contributions to scientific knowledge. There are many others, from bird counts and nest watches to weather monitoring and sifting through radio transmissions from space. Participating in “citizen science” can give students a feel for how science is done and maybe even a continuing interest in biology that lasts long after a course is over. Have you incorporated citizen science into your classroom? Was it effective and valuable, or did it seem more like busy work to your students than real science? I’ll be discussing other citizen science options in later blogs.

Photo by Martin Hirteiter

Those who can, doodle

2009-03-15T14:34:00.000-07:00

JFK's White House Doodles
I’ve been seeing lots of news stories lately about a research study that suggests that doodling improves memory. A group of test subjects who were directed to doodle while listening to a series of long, dull conversations remembered the details much better than the group who simply sat and listened. It seems that the brain is adapted to be active, and if the world doesn’t supply enough stimulation to keep it going, it’ll make it’s own through daydreaming. Doodling keeps the brain just busy enough that it continues to pay attention to the outside world. Daydreaming takes more mental effort, and distracts the mind from its surroundings.

There are obvious implications for teaching in this. As a biology student, I doodled a lot – the citric acid cycle, that would do it. The electron transport chain, every time. But I mainly did it when I thought I could do it on the down low, sitting in the back of the room or in a large lecture hall. In a smaller class, I became the master of the glassy stare and the falsely inquisitive head tilt instead.

As a teacher, I’m sure I’ve given more than one doodler the skunk eye. Now I wonder if I should encourage it. Every lecture has its boring bits – anything that keeps a student learning through the dull spots is worth using. Maybe I need to add doodles to the hands-on demo, the small-group discussion pause, the 5 minute stretch and soda break, and all the other straighten up and pay attention tricks. At the least, I'll try and see doodling as a genuine attempt to learn rather than as a surefire sign of slacking.

The TEACH Act: Copyright in the Classroom, part 3

2009-02-28T12:16:00.000-08:00

You thought copyright was confusing before, but no, this is where it gets tricky – copyright law in online education. When you post something copyrighted on a web page or send it across the internet, you are in a sense publishing that material, and that’s quite different than showing a slide for a few minutes in a classroom or handing around a photocopied article to a few students. That’s giving everyone, everywhere the ability to take or use someone else’s work without compensation.

In order to address the unique aspects of online education and copyright law, Congress passed the TEACH Act in 2002. The Technology, Education and Copyright Harmonization Act made it legal for teachers employed by accredited schools to use copyrighted materials in online education in pretty much the same ways they could be used in face-to-face classroom settings. Sounds great, eh? Oh, but there’s a catch – there are a set of conditions that must be met for the TEACH Act to apply:

Those conditions are tough to meet, especially the ones about controlling downloads and access. Luckily, all is not lost if you cannot do it.

Links - Instead of giving your students copies of copyrighted material, give them the links to go the original sources online. It’s more efficient anyway. All you have to do is check frequently to make sure the links are still good.

Permissions - Copyright holders will often grant permission to use their work for a fee or for educational purposes. Sometimes an email is all it takes, but more often it’s a lengthy process.

Fair use - The fair use exemption to copyright law can still be used in online education, but you need to be very careful. As a practical matter, your treatment of someone else’s intellectual property in the classroom is just between you and your conscience. It might make it hard to insist that your students do not plagiarize when you make someone else work free, and all but impossible to show them that science is all about honest and ethical inquiry. But the chances of being caught or prosecuted for copyright infringement are vanishingly small.

With distance education, though, it’s a different story. Once you put something online it’s there for anyone with a search engine and a professional or financial stake in protecting their rights to find. So I suggest you post as little copyrighted material as possible (use links instead), and show good faith by always crediting the author when you do. Once a class is over, take the material down.

For more detailed information on the TEACH Act and distance education, visit these sites -

TEACH Act Toolkit
Stanford Library's Fair Use website

Well, it seems fair to me: Copyright in the Classroom, part 2

2009-02-20T18:18:00.000-08:00

Anyone who teaches biology needs to use copyrighted material. You can’t convey the scope of life on Earth or the complexity of biological processes or the secret inner life of cells without using pictures, videos, and diagrams. Only a small amount of the good stuff is in the public domain, so there’s really no way to avoid copyright issues. Here are some options --

Creative Commons – Look for material with a Creative Commons license. Many authors are willing to share their work with some strings attached. Various CC licenses give the public permission to copy, distribute, and display material as long as the copyright holder is credited or the work is not altered or used for profit. Frequently the graphics and photos on Wikipedia and flickr and articles in online science journals have attribution/non-commercial licenses – just follow the simple rules and they are free for the using.

Fair Use – U.S. copyright law allows educators to use copyrighted materials legally under the principle of fair use. A set of 4 kind of squishy conditions are weighed to determine if a use is fair. Here they are, as described by the Association of Research Libraries (I can copy their discussion here, because it’s published under a Creative Commons Attribution-
NonCommercial 2.5 License):

This “fair use” provision of copyright law doesn’t provide hard and fast rules to tell you whether a use qualifies as fair. Instead, the unique facts regarding a use lead you to a reasoned conclusion. Your evaluation should weigh four factors:

1. Purpose and character: If your use is for teaching at a nonprofit educational institution, this is a factor favoring fair use. The scale tips further in favor of fair use if access is restricted to your students.

2. Nature of copyrighted work: Is the work fact-based, published, or out-of-print? These factors weigh in favor of fair use.

3. Amount used: Using a small portion of a whole work would weigh toward fairness. But sometimes it may be fair to use an entire work (such as an image) if it is needed for your instructional purpose.

4. Market effect: A use is more likely to be fair if it does not harm the potential market for or value of the copyrighted work. But if it does, this could weigh more heavily against fair use than the other factors.

Consider each of these factors, but all of them do not have to be favorable to make your use a fair one. When the factors in the aggregate weigh toward fairness, your use is better justified. When the factors tip the scales in the other direction, your need to obtain permission from the copyright holder increases. Don’t worry that the answer isn’t crystal clear. Just decide whether the factors weigh enough toward fairness so that you are comfortable not seeking permission. Some suggest reliance on the “golden rule” — if you were the copyright holder, would you see the use as fair and not expect to be asked for permission?

Fair use allows teachers to use, reproduce, and distribute copyrighted material in the classroom. But in return, teachers are required to exercise restraint. You cannot copy all or most of a textbook or workbook so that students do not have to buy them. You can’t copy a nature program off the tv and show it every semester if it is available for sale or rent. You are not allowed to put together a thick packet of articles for your students to buy from you or the local copy shop. Be reasonable - the people who write textbooks and make films need to make a living.

Copyright Clearance – If you really need to use copyrighted material in a way that doesn’t fall under fair use, you can and must get permission. Most textbook publishers will sell clearances that allow making lots of copies for educational uses. You can seek permission yourself, or use a clearance services. Many scientists and other copyright holders will also grant permission for you to use a photo or illustration or other material if you ask nicely and want to use it in a way they find reasonable.

For more information on copyright and classroom teaching, check out Stanford University’s website on Copyright and Fair Use. It’s fabulous.

Next time, the TEACH Act and copyright law in distance education.

Copywhat? Copyright in the Classroom, part 1

2009-02-15T17:44:00.000-08:00

Science and teaching are both collaborative ventures. Every scientific discovery is built on the work that came before it, and scientists freely, eagerly share their ideas with one another. Teaching is all about sharing knowledge as much as possible. I wonder if that’s why so many science teachers have so little regard for copyright law? And we don't, we really don’t. I know I’ve happily used copyrighted photos and diagrams in almost every lecture, shown bootleg nature videos a lot more than once, and photocopied plenty of articles for lab handouts. None of that ever gave me a second thought. Until now.

I’ve spent the past several months editing an online biology course put together by social authoring – different professors write each chapter and supply illustrations, homework and lab assignments. I was taken aback, no, I was stunned, well actually I was sent into sputtering fits and rants by how often people sent in copyrighted material. They weren’t trying to pull a fast one, they genuinely thought it was okay. Okay to copy definitions because they were just a sentence or two. Okay to use someone else’s chart if they wrote their own description of it. Okay to cut and paste data or directions since they’d been using them for years in their classes.

Once I calmed down a little, I realized that although I did know all of that was illegal, I was not all that up on the details of copyright law. Was what I did in the classroom legal? Or when I posted material on my class web page or emailed information to a student, how about then? I’ve been exploring the convoluted rules of copyright law and fair use and distance education, and am going to share it all with you. Whee! This is the first of a series of blogs on copyright in the classroom. If I confuse you or myself along the way, I hope you’ll speak up.

Let’s start with the basics:

Copyright – U.S. copyright law gives the author of a work the exclusive rights to reproduce, distribute, and display all or part of that work for varying periods of time. Material published before 1923 is now in the public domain. Work created in 1978 or later is copyrighted for lifetime of the author plus 70 years. The stuff produced between 1923 and 1978 is in a bit of a gray area. The best bet is to assume anything younger than 1923 is copyrighted unless it specifically says otherwise.

It’s important to note that copyright law protects the expression of ideas, like articles, drawings, and videos, but it doesn’t apply to the ideas themselves. It’s a violation of law to copy a genome map produced by a biotech firm, but it is perfectly legal to describe the genome in your own words.

Public domain – Material in the public domain is a form of public property and it can be copied and reproduced at will, though it is still considered unethical not to attribute the work to the original author. Public domain works include material whose copyright has expired or whose authors have waived some or all of their rights. It’s important to realize putting material out for public view is not the same as putting it in the public domain. Writings and graphics on the internet fall under copyright laws as much as if they were written on paper. Again, it’s best to assume that anything you find online is copyrighted unless it clearly says otherwise.

One thing that often trips up science teachers is U.S. government works. Material produced by the federal government and its employees is in the public domain, and a good thing too because they put out some of the best science. But government scientists often collaborate with people who work in the private sector, and they frequently retain the rights to their work even if they grant the government permission to use it in a publication. Make sure you read the fine print.

So those are the basics of copyright and public domain. In later blogs, I’ll cover how you can and can’t use copyrighted material in face-to-face and distance education, the doctrine of fair use, and the TEACH Act.

What's new in science?

2009-01-31T17:25:00.000-08:00

How will I know without the Weekly World News?

In my last blog I described a couple of ideas for helping students notice how often biology pops up in the news. I think it’s useful because it helps them to see science not as a collection of random facts they have to memorize but as a natural part of their lives. It's just as important for me to keep aware of what is new in science, if I’m going to communicate to my students that the field is full of excitement and promise and is worth pursuing. If I’m not interested in what I’m teaching, they sure as heck won’t be either.

I admit it’s not easy. I spend a lot of time in paperwork these days and hardly any in the field or at conferences. I try to keep up with my specialty, but I don’t have a bunch of colleagues to argue with all night over pizza anymore. I don’t have easy access to a great library with the latest journals and books anymore. It can be really tempting to keep using the same course notes, the same examples and illustrations, the same labs as I did last
semester or the one before that. But I know I’d be bored, and it would show, if I did. Besides – I love science. I love finding things out. I love reading about discoveries and unexpected connections and even finding out that something I thought I knew is completely wrong. Why else would I be here?

So I keep up with science, as much as I can. Luckily the internet does all the heavy lifting. It’s full of sites that gather and summarize the latest research. My list of bookmarks gets longer all the time, but these are some of my favorites:

Science Daily – the most complete source. It updates several times a day, has separate sections for videos and pictures, and includes reference articles along with the news.

Science News – doesn’t update as often as some of the others, but includes articles aimed specifically at kids

LiveScience – navigation is a little clunky and finding the news takes a little digging, but the columnists are quirky and interesting

These sites are also good places to send students who are looking for research or paper topics, and also those who have shown more than a passing interest in biology. It’ll be hard for many of them to stop at just one click.

Do any of you have other good websites to recommend? If you don’t do it online, how do you keep up with the new ideas and research results in biology?

Breaking Biology: Butter Not

2009-01-18T19:03:00.000-08:00

Farewell, sweet peanut.

The widening outbreak of salmonella in peanut butter products is an inconvenience for many and a tragedy for some, but it’s also a fantastic opportunity for teachers to bring biology home. From the details of the investigation to more general explorations, there’s something for everyone in food and food safety. A few obvious starting places for discussion and research include:

Bacterial infections

Immune response

Food safety

Food borne illness

The National Peanut Research Lab (who knew?)

Mostly I teach non-majors, students who need some science credits and take biology or geology simply because they sound less awful than chemistry and physics. They learn it, and they even like it, but it’s a challenge to get them to see that they live it. Events like this outbreak can make the difference.

Even less dramatic news is worth working into the classroom. One of my first college professors brought a newspaper into class every few days and handed out random sections to everyone. The first person who found a story or ad and could make an argument for how it related to material covered in the last lecture got extra credit points. Another gave over a lecture or lab entirely once a month to research and discuss the latest natural disaster (it was California, so there was also something). I often assign students to put together a Breaking Subject Matter News journal over the course of a semester.

Anyone else have ideas on incorporating current events into teaching biology? Do you plan for surprise events in your syllabus or lesson plan, or work them in somehow if they happen?

Year in Science 2009

2009-01-11T14:55:00.000-08:00

I’ve just stumbled across a group called the Coalition on the Public Understanding of Science (COPUS) that bills itself as “a grassroots effort whose goal is to engage sectors of the public in science to increase their understanding of the nature of science and its value to society.” Well, we sure could use some of that. COPUS has declared 2009 the Year of Science, and has laid out an ambitious plan to encourage scientists, educators, and institutions to do something locally to excite their communities about science, like giving lectures, going into classrooms, and starting Science Cafes.

Each month has an assigned theme:

January - Process and Nature of Science; Communicating Science
February - Evolution
March - Physics and Technology
April - Energy Resources
May - Sustainability and the Environment
June - Ocean and Water
July - Astronomy
August - Weather and Climate
September - Biodiversity and Conservation
October - Geosciences and Planet Earth
November - Chemistry
December - Science and Health

COPUS has set up a website to coordinate and track events, provide links to educational resources, and support blogs and discussion boards. At the moment it looks a bit thin – so far there aren’t many events or many participants. The monthly themes won’t be addressed before their time, so there isn’t much content yet. January does include a link to UC Berkeley’s new Understanding Science website, which also looks like it could be good but isn’t quite complete.

It will be interesting to check back in during the next few months and see if the Year of Science picks up steam, or remains a well-meaning endeavor that never quite takes off.

The Year in Biology - A Look Ahead at 2009

2009-01-04T12:39:00.000-08:00

I'm melting, melting. Ohhhhh,
what a world, what a world.
2009 is shaping up to be a big but bumpy year in science. President-elect Obama has pledged to give science a more prominent and respected place in his administration, but the economic crisis is sure to lead to lots of cuts and painful decisions in government and foundation funding of scientific research.

Regardless of funding, no one puts science in a corner altogether, especially when the world is faced with issues that simply won’t go away, like climate change, epidemics and pandemics, shrinking food and water resources, and the promises and perils of genetic engineering. Last month, Science magazine published a special issue highlighting the breakthroughs of 2008 that also included predictions for 2009. Here are a few of Science’s picks for biologic stories to watch out for this year:

Plant genomics. Genomes of major grain and fruit crops and biofuel plants should be completed and/or published this year. As always, these advances will be touted as having the potential to feed the hungry and solve the energy crisis. Neither of those is likely to actually happen in 2009, but we might well take a few small steps towards healthier, cheaper, more widely available foodstuffs.

Ocean acidification. Everyone knows that carbon dioxide levels in the air are rising, and have been for some time. Fewer people know or care that the oceans absorb a great deal of that CO2. On the one hand, that’s been a swell chemical reaction, because it has helped moderate atmospheric levels of the gas. On the other hand, it’s unfortunate for sea creatures, because it lowers the pH of seawater. Expect more research results and publicity this year on the consequences of acidification, which include interference with the ability of corals and plankton to secrete hard parts, die-offs of fish and shellfish larvae, and disruption of marine food chains. Science is skeptical that the public will care about the plight of microscopic plants who don’t have big sad eyes. Yeah, me too.

Global Climate Treaty, The Sequel. An international summit on climate in Copenhagen will try to establish a binding agreement to reduce greenhouse gas emissions. The cooperation of the world’s biggest emitter, the United States, will be crucial, as will that of the developing world. This agreement will replace the Kyoto Protocol, which expires in 2012. Considering how well that worked, what could go wrong? Right?

The Year in Biology - A Look Back at 2008

2008-12-28T18:57:00.000-08:00

Scientists are just like everyone else – we can’t stop ourselves from making “best of” year-end lists. It’s an amazingly subjective and unscientific exercise, but what the hey? I always enjoy looking at them to see what I’ve missed while I’ve been focused on teaching the basics.

Science magazine wraps up each year with a special issue devoted to its choice of Breakthroughs of the Year, and biology did well in 2008. The winner – cell reprogramming, based on two lines of work. In the first, researchers removed mature skin cells from a woman with neural degeneration, coaxed them into becoming stem cells, and then directed them to develop into nerve cells. This technique will allow scientists to watch cells as they progress through puzzling, hard to study diseases like ALS and MS. Another, equally promising reprogramming breakthrough turned one kind of adult cell directly into another type of adult cells, without the intermediate stem cell stage and within the body and not in a petri dish. Biologists converted ordinary pancreatic cells in diabetic mice into pancreatic beta cells, which produce insulin. If the technique translates well into humans, it may someday allow the sick to be healed by reprogramming their own cells to grow new tissues and organs.

Runners-up included a couple of other biologic topics, including success in decoding the DNA of genes for pancreatic, brain and lung cancers, which should be very helpful in diagnosis and treatment. Molecular biologists invented a laser microscopic that allowed them to make lab movies of the growth of zebrafish from fertilized egg to embryo, which they can play back and forth to trace tissue development. And paleogenomics made great strides with the refinement of cheap, fast sequencing techniques that led to identifying the genomes of a cave bear, a Neanderthal, and most of a woolly mammoth. Of course, the media immediately began asking scientists if they will now try cloning a mammoth – a few dozen more viewings of Jurassic Park may help them decide.

Science News has a much longer and much more accessible list of science stories of 2008. It includes not just cellular and genetic breakthroughs, but also organismal and ecologic research, from the Red List census of threatened and endangered species to a troubling decline in US life expectancy to links between human disease and a chemical found in plastic food and water containers.

And finally, just to prove there’ll always be an England, the Guardian has an illustrated list of its favorite scientific studies of 2008, which includes giant rats, UFOs, GI Joe’s sex appeal, and the smell of fear in skydivers' sweat.

Next week - what to look for in 2009.

Science and the presidency

2008-12-21T15:02:00.000-08:00

Most biology courses spend a lot of time on the basic science of how life works, and on the inescapable consequences of biology on the human condition. Few go into much detail on the gatekeeper that stands between science and the public good - politics. And that’s a shame, because very few students will go on to become biologists, but almost all of them will be voters. I think it’s very important for students to understand how scientific knowledge is translated into scientific policies, regulations, and laws. How research is directed by the dispersal of government grants, how economic and health impacts are weighted by regulatory agencies, how public perceptions of scientific issues are shaped by political perspectives. What better time to examine those issues than during the transition between presidential administrations?

During his latest weekly address, President-Elect Obama described his view of science.

Because the truth is that promoting science isn’t just about providing resources—it’s about protecting free and open inquiry. It’s about ensuring that facts and evidence are never twisted or obscured by politics or ideology. It’s about listening to what our scientists have to say, even when it’s inconvenient—especially when it’s inconvenient. Because the highest purpose of science is the search for knowledge, truth and a greater understanding of the world around us. That will be my goal as President of the United States—and I could not have a better team to guide me in this work.

If emotions weren’t alien to me (I’m a scientist), that would probably choke me up a little.

Obama then went on to announce several members of his science team:

John Holdren, director of the White House Office of Science and Technology Policy
Jane Lubchenco, director of the National Oceanographic at Atmospheric Administration
Harold Varmus, co-chair President’s Council of Advisors on Science and Technology
Eric Lander, co-chair President’s Council of Advisors on Science and Technology

Here’s a video of the entire address -

It would be a useful exercise in science and public policy for students to investigate what these government agencies do. They could also look into the scientific backgrounds of these advisors for some ideas of the topics that might be a priority in an Obama administration. Holdren has a history of advocating for action on global warming. Lubchenco’s work has focused on climate change and overfishing. Varmus won a Nobel Prize for research into the causes of cancer. Lander has been extensively involved in the Human Genome Project.

Other clues to the scientific plans of the new president can be found at Your Seat at the Table, which lists the organizations the presidential transition team has met with, posts copies of the documents they’ve given the team, and provides a place to discuss and question the issues. Sifting through the long list of meetings and proposals is pretty eye-opening. Reading the comments people have posted is too.

Picture this - photography and biology

2008-12-14T18:10:00.000-08:00

Biology is everywhere - you just have to look

An effective biology course can give students a new way to look at the world around them. Photography is a very useful tool in pushing them to literally see their surroundings through a different perspective. Digital cameras, disposable point and shoots, and camera phones make it easy for students to take and transmit images. Sending them out to ponder and photograph animals and plants adds a do-it-yourself but still directed field trip experience to an online course.

There are several different approaches that work well. One is to give the students a topic and send them out to find images that illuminate it. You might give them broad themes like photosynthesis or competition or plant succession. Or have them choose an environmental challenge like attracting mates or coping with drought and then document the strategies used by a few different species to solve the problem. Each photo or set of photos should be accompanied by a write up that explains the biology involved. Chose the assignments carefully, so that students have to really look at their surroundings and think through what they’ve learned in the course. Otherwise it just becomes a digital version of the dreaded 6th grade leaf collection.

On the other hand, a photographic show and tell can be a good way to get students talking to one another, and about biologic topics. Have a class upload photos of their pets to start a group discussion on artificial versus natural selection or the adaptive value of cuteness. Get them to post pictures of their lunch as a starting point to describe energy flow through ecosystems or debate the production and labeling of genetically modified organisms. Ask them to photograph their favorite outdoor spaces as a springboard to evaluating the value of wilderness and open space, or their sense of place in the natural world.

First Bear in Space? Not So Fast, Teddy.

2008-12-07T14:18:00.001-08:00

It’s been all over the news that bears broke the space barrier for very first time this week. Four small teddy bears were wrapped into space suits designed by school kids, strapped to a weather balloon, and lofted 18 miles up. They came back down a few hours later, frosty but otherwise none the worse for wear. Members of the Cambridge University Science Club organized the venture in order to study weather conditions in the stratosphere and means of insulating against them.

I salute the plush adventurers on their accomplishments, but I have to point out that another group of bears more or less beat the stuffing out of them a few months earlier. A box full of water bears orbited the earth on a satellite back in September, and they didn’t use no stinkin’ space suits either. Water bears, or tardigrades, are tiny eight-legged invertebrates much admired by scientists for their ability to survive almost anything. Once in space, the desiccated animals were exposed to open vacuum and to cosmic and/or solar radiation. Amazingly, when they got back to Earth many of the creatures revived and went on to lay viable eggs. These are the first animals ever to survive unprotected in space, and biologists hope to learn how tardigrades are able to repair DNA damage more efficiently than humans can.

I'm charmed by bears in space, and more than a little jealous. It is a truth universally acknowledged that a scientist in possession of an object is in need of an excuse to shoot it into space. It is equally true that everyone who can shoehorn in on the action will think it’s the coolest thing ever.

The Daily Mail interviewed participants in the stuffed bear ascent –

Thia Unsworth, 12, from Parkside College, helped to design the spacesuit for M.A.T. She said: 'It was unbelievable to see the balloon take off and it's incredible to see the pictures of the teddy bears in space. I've always loved science before, but I now understand how it helps in the real world.'

Wired Science quoted Petra Rettberg, a microbiologist who helped design the tardigrade experiment –

"It'll just be interesting to see what the mechanisms are in tardigrades, compared to the very simple ones in bacteria and more complex systems in higher organisms," she said. "But in addition, it's just fun."

Man - don't you wish you and your students could fling something into space? It'd be so much fun, but you could tell everyone it was for science, and they'd only snort just a little bit because they'd secretly think it was a hoot, too. So for those of us stuck on the ground, what can we do to make students love science? To "understand how it helps in the real world?" If you've got a good technique, let me know. I'll be passing along some ideas in future blogs.

On 'On the Origin of Species'

2008-11-23T17:50:00.000-08:00

Tomorrow, November 24, is the 149th anniversary of the publication of On the Origin of Species, a book that launched a scientific revolution and forever altered our understanding of who we are. In the last century and a half, both the book and its author have become icons, household names that most people recognize but many only know in a superficial and caricatured way. Charles Darwin, morose old man with a big white beard, who took a boat ride one day and got hit in the head with a finch, thus discovering evolution. The theory of evolution, aka survival of the fittest, except it must not be true because it’s still only a theory after all this time.

This next year is going to be a great time for getting to know both the man and the theory better. Events are planned all over the globe throughout 2009 to celebrate Darwin’s 200th birthday and his seminal book’s 150th. There will be something for everyone from the most accomplished evolutionary biologist to the most reluctant student. Some will offer a nostalgic remembrance of times past, while others look ahead to future scientific breakthroughs that stand on Darwin’s shoulders. For example:

Retrace the voyage of the Beagle by private jet

View the evolutionary tree doodles in Darwin’s own notebooks at the Natural History Museum in London

Catch the Galapagos Mountain Boys performing evolutionary tracks from their album Darwin, Darn It! in San Diego

Attend a colloquium on ‘The Impact of Darwinism on Human Sciences’ in Boston.

None of those in your budget or neighborhood? Then check with your local library, museum, and university for special readings, lectures, tours, and courses. Search online for outlines of Darwin’s life and all of his writings, and for analyses of his work. Browse through the coming avalanche of books and articles to learn how advancements in biology and chemistry and genetics since 1859 have enriched and altered the theory of evolution.

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.
---Charles Darwin

What the heck is a hippocampus?

2008-11-16T16:59:00.000-08:00

You may have noticed the little Hippocampus logo up there on the header and the Hippocampus links in the column just to the right, or you may have clicked on a link in an earlier blog and found yourself transported to Hippocampus itself. But do you actually know what it is? Have you tied grabbing ahold of it and giving it a spin around the room yet?

Hippocampus is a free online educational resource for high school and college students and teachers. Its goal is to provide quality multi-media information to anyone who wants it. You can use the courses as is, pick out bits here and there, teach it in reverse – go ahead, whatever works for you, we won’t mind.

There are three biology courses up at Hippocampus, AP Bio 1 and 2 and Environmental Science. The course material is the heart of the site and it is very good, with plenty of lessons, assignments, assessments, and text and video presentations. But just lately the content around the courses has been upgraded too. There are tools to customize each subject, a new mini-site that makes it easier to browse through the topics, a better search engine, and links to cool sites like NOAA Learning Objects and the National Science Foundation. If you haven’t been over to Hippocampus recently, go check it out. They have made it better than it was. Better…stronger…faster. They have the technology, and now so can you.

Census of Marine Life

2008-11-09T15:02:00.001-08:00

The Census of Marine Life is one of the most ambitious projects ever undertaken – to discover and count every species of marine creature on Earth. Starting today and continuing for the rest of the week, Census scientists are releasing updates on their progress as part of the World Conference on Marine Biodiversity, which begins in Valencia, Spain, on Tuesday. As always with these periodic reports, the results include some of the coolest things I’ve ever seen.

I’m not alone in being delighted – news reports about underwater singles bars for great white sharks, sea star cities, and octopus expressways are popping up all over the internet.

The Census provides almost as many teaching opportunities as it does species. There are gorgeous photos and videos on the various websites of the institutions involved in the project, and detailed explanations of the findings and implications of the work. Any curriculum that includes basic biologic topics like the importance of diversity, the impacts of overfishing and ocean pollution, and the ongoing effects of climate change will benefit from the data gathered by the Census.

Along with all of that, there is a sense of wonder and excitement that runs through every expedition log and scientific report – there is still so much to see and to discover and to understand. That is as much a gift as the results of the research. I doubt I’d be a biologist if it wasn’t for the Undersea World of Jacques Cousteau. Sitting in my Wisconsin living room, I felt connected to the distant sea and sensed the tug of kinship with its inhabitants. I wonder if the Census of Marine Life could provide the same spark of interest and recognition and that same fierce urge to protect the oceans to a new generation?

The Tyranny of the Test Bank

2008-11-02T18:33:00.000-08:00

I’ve spent the last few days working on test bank questions for an online non-majors biology course. Every time I do this, and I do it every time I work on a course, I can’t help but wonder why. Why are test banks so popular? What do instructors do with them? Because even though I write them for a living, I never use them when I teach.

Part of the problem is that test bank questions are multiple choice. Not that there’s anything wrong with that. These questions can cover a lot of material easily, and they are a simple, straightforward way of checking for a grasp of basic facts. Multiple choice questions can also require critical, even intuitive thinking from students. For most students they are comfortable and familiar and they don’t require anything as intimidating as legible handwriting or logical argument. I always include some on every exam I write for my own students. But it makes me very uneasy to think that an entire exam might be made of these. They are too limited, and too rigid – they don’t let students get creative and they don’t give me a chance to understand not just what my students know, but also what they almost know and how they think.

My main problem with test banks though, is that I believe instructors should write their own exams just as much as I believe students should take their tests on their own. I don’t stand in the front of the room and simply read from the text, so I don’t give an exam that only covers the text. I teach from my own perspective and I color my time with students with my own experiences and ideas. Why then would I use questions that are utterly impersonal? How can I demand that students go beyond memorization to original thinking if I’m not willing to go to the effort of writing an original exam?

So while I work, it nags at me. Are test banks as sketchy as I fear? Tell me if you use them, if you think I'm full of hot air. Do I just need to give overworked and underpaid instructors a break, get off my high horse, and hand over the questions? Can anyone give me a reason to stop worrying and love the test bank?

Some of my best friends are fruit flies

2008-10-26T21:49:00.000-07:00

Fruit flies went mainstream this week, when a vice-presidential candidate scorned their study as taking research dollars away from work that helps people. That was a foolish claim, almost instantly debunked – fruit flies have improved the human condition enormously in the last century.

So fruit flies are imdisputably cool. But this wasn’t the first time politicians have called out supposedly goofy research conducted by obviously egg-headed scientists as a grievous waste of taxpayer’s money, and it assuredly won’t be the last. I think we need to do a better job teaching students to look beyond the obvious. Most biology classes describe how science is done (observation, hypothesis, testing) and they trumpet a handful of scientific breakthroughs (say the discovery of penicillin, or the description of the DNA double helix). But do we talk enough about the long and winding road from the one to the other?

I think it would be useful to have students research research. Get them to poke at work that seems frivolous and see if they can imagine what bigger things it might lead to, or if it’s really as dumb as it sounds. And have them track award-winning research back to its humble beginnings, and wonder if it would have seemed as worthwhile then as it does now. I can suggest two good places to start, far apart in prestige but perhaps not so distant in teaching value.

The Nobel Prizes are awarded for outstanding achievement, to people who “have conferred the greatest benefit on mankind.” The scientific awards are generally given only after the passage of time has shown the importance and rigor of the original research. The 2008 Nobel Prize in Medicine was awarded to scientists who discovered the viruses that cause cervical cancer and AIDS. The Nobel website has all there is to know about the awards – descriptions of winning research and interviews with the laureates, videos, educational games, news articles, and links.

At the other end of the spectrum are the Ig Noble Prizes, which “honor achievements that first make people laugh, and then make them think. The prizes are intended to celebrate the unusual, honor the imaginative -- and spur people's interest in science, medicine, and technology.” This year’s winners include researchers who determined that the fleas on dogs jump higher than the fleas on cats, and an award split between scientists who proved that Coca-Cola is an effective spermicide and others who showed that it is not. The Ig Nobel Awards fall under the umbrella of the Annals of Improbable Research. Their website too contains descriptions of the winning research, videos, games, and other commentary.

Soup's on -- Miller-Urey experiment

2008-10-19T21:01:00.000-07:00

I caught up with an old friend today, my good buddy primordial soup. Primordial soup is a nickname for Earth’s ancient, abiotic oceans, meant to suggest the watery mix of chemicals and sediments in which life somehow began. The phrase became famous back in the 1950s, when biologists Stanley Miller and Harold Urey threw some chemicals in a beaker, zapped them with electric charges, and – it’s alive! Well, actually, it's amino acids – not quite life, but life’s building blocks. The simple but startling Miller-Urey experiments became famous, and soon found a place in every geology and biology textbook as a compelling hypothesis for the origin of life.

I encountered primordial soup decades later in college, and it was love at first hearing. The words put a vivid picture in my mind that still lingers all these years later. The aching loneliness of the empty sky and the silent sea, then a sharp crack of lightning, and in the darkness and the deep, something stirs.

The ingredients and the power of primordial soup have changed over time. Miller used a mixture heavy in methane and ammonia, but some later researchers suggested that the early atmosphere was much richer in carbon dioxide and nitrogen, gases too inert to be jump-started by a little lightning. For a time primordial soup was pushed to the back burner.

But now comes word of a new, improved recipe. Chemist Jeffery Bada recently found some old vials tucked away in a cardboard box, sealed results from one of Miller and Urey’s experimental variations. The scientists had added a jet of steam to the experiment to simulate volcanic activity. When Bada analyzed the 55-year old residue in the vials, he found all of the amino acids produced in earlier experiments, plus 10 more. This work suggests that the composition of the atmosphere as a whole may have been less important than the conditions around volcanoes. Geysers and hot springs on the flanks of active volcanoes receive frequent injections of steam and reactive gases. A lucky lightning strike into a primeval Old Faithful may have been the first link in the chain of life.

The story of primordial soup isn’t just about the origin of life, it’s a story about science. A story about how science never stops, but keeps looking and asking questions, and rummaging around in the dusty cupboards of the world. I’m thrilled to have my primordial soup back, and I wonder if some student out there right now will read those words and feel a stir on the back of her neck just like I did.

The Red List

2008-10-12T19:00:00.001-07:00

Last week the International Union for the Conservation of Nature (IUCN) released its annual Red List, a scientific census of the conservation status of plant and animal species. The list is not comprehensive – it covers only 45,000 species, out of the roughly 2 million known and 5 or 10 or 15 million estimated to exist. But it’s a useful snapshot of how the diversity and abundance of life as we know it is changing over time. And it provides yet another terrible, teachable lesson on the harsh realities of biology.

The status of the Fishing Cat of southeast Asia has been changed from Vulnerable to Endangered, because of widespread losses of its preferred wetlands habitat.

The Red List is a natural for online research into conservation issues. Students can use the IUCN website to look into the methodology, evaluate the threat categories, and contemplate the implications of situations such as ‘extinct in the wild’ and ‘data deficient.’ They can compare the yearly reports, browse the photo galleries and case studies of mainly the very cutest endangered animals, and compare trends and patterns in terrestrial and marine life. The list is also an obvious jumping off point for further study of conservation, habitat degradation, and the fate of particular species or ecosystems.

Education these days also demands something beyond facts and figures and objective assessments. No lesson is complete without open-ended, free-range discussion questions. They practically write themselves when it comes to the conservation of endangered species and extinction – there are so many ethical, political, and social aspects involved, so much blame to lay, so many hard decisions to debate. These are subjects that students have opinions on, opinions they’ll share without having to be poked at with a sharp stick.

I don’t know about you, but for the most part I’ve found that students think extinction is bad. But cynicism and indifference do pop up too, and I’ve been surprised that they’re a lot more prevalent in students right out of high school than they are in older returning adults. Does early, repeated exposure to Barney make extinction seem less troubling?

Photo by Bob Bennett, osfimages.com

If it bleeds, it leads?

2008-09-27T20:46:00.000-07:00

I was browsing around the science magazine websites this weekend, admiring this year’s winners of the International Science and Engineering Visualization Challenge. The contest has a lofty purpose, laid out on its homepage at the National Science Foundation –

Some of science’s most powerful statements are not made in words. From the diagrams of DaVinci to Rosalind Franklin’s x-rays, visualization of research has a long and literally illustrious history. To illustrate is to enlighten.

How many people would have heard of fractal geometry or the double helix or solar flares if they had been described solely in words? In a world where science literacy is dismayingly rare, illustrations provide the most immediate and influential connection between scientists and other citizens, and the best hope for nurturing popular interest. Indeed, they are now a necessity for public understanding of research developments.

The National Science Foundation (NSF) and Science created the International Science and Engineering Visualization Challenge to celebrate that grand tradition—and to encourage its continued growth. The spirit of the competition is for communicating science, engineering and technology for education and journalistic purposes.

Well now, that’s pretty cool. And so are the images. You can see thumbnails at NSF, and nice big slideshows at National Geographic and msnbc.

I couldn’t help noticing how many of the stories announcing the winners led not with this 1st place photo of diatoms, called ‘The Glass Forest’…
Photo by Mario De Stefano, The Second University of Naples

...but with this honorable mention image of the a squid's fanged suckers, ‘Squid Suckers: The Little Monsters That Feed the Beast.’

Photo by Jessica D. Schiffman and Caroline L. Schauer, Drexel University

What is it about the scary side of science that is so much more appealing? Now that I think about it, I realize I’ve always loaded my earth and biological science courses with earthquakes and volcanoes, plagues and pestilence and things that go bump in the night. It’s an easy hook, but I wonder if it’s the best one. Is repeated reference to the violent and the flashy parts of biological processes simply a way to engage students so they pay some attention to the duller stuff? Or does making biology seem more like the latest video game than part of ordinary life distance them from understanding their real place in the natural world? By emphasizing nature red in tooth and claw are we teaching science or presenting edutainment?

Classroom Discussion Topic: FDA Guidelines for Genetically Engineered Animals

2008-09-20T18:27:00.000-07:00

Tastes just like chicken?

If you eat, take drugs, or have a pet, the FDA has a little something special just for you.

This week the agency released a draft of the guidelines it intends to follow when genetically engineered animals are up for approval for commercial use. Although these procedures have already been in use for quite a while, this release spells out the process for the first time, and also includes a one month period for public comment.

As spelled out by the FDA, GE animals fall into 6 categories:

· Biopharm animals are those that have undergone genetic engineering to produce particular substances, such as human insulin, for pharmaceutical use.

· Research animals may be engineered to make them more susceptible to particular diseases, such as cancer, in order to gain a better basic understanding of the disease for the development of new therapies or in order to evaluate new medical therapies.

· Xenotransplant animals are being engineered so they can be used as sources for cells, tissues or organs that can be used for transplantation into humans.

· Companion animals that are modified to enrich or enhance their interaction with humans (i.e., hypoallergenic pets).

· Disease resistant animals may be used either for food use or biopharm applications. These animals have received modifications that make them resistant to common diseases, such as mastitis (a very painful infection of the udder) in dairy cows, or particularly deadly diseases, such as bovine spongiform encephalopathy (BSE).

· Food use animals have been engineered to provide healthier meat, such as pigs that contain healthy omega-3 fatty acids at levels comparable to those in fish.

The toughness of the approval process varies by category. For pets, not so much. For food, the rules are fairly stringent.

The information provided along with the draft regulation is surprisingly readable and informative for government work. It defines genetic engineering, discusses the areas of concern surrounding the safety and effectiveness of GE animals, and provides a clear step by step overview of the approval process. It’s also up front about several features of the guidelines that are obvious topics for classroom debate and passionate letters to the editor: many of the steps are suggestions, not regulations; the agency can waive the rules whenever it sees fit; and the big one – GE foods will not have to be labeled. The FDA is also glad to admit that its guidelines do not take into account the wider ethical questions of genetic engineering.

It's very easy to use genetic engineering in the classroom for the shock and awe of it all - when you play on people's fears, at least they stay awake. It's a little harder to have a balanced, thoughtful discussion of this complicated topic, but the FDA guidelines, which weave together the science, economics, and legalities of GE in one nice, topical package, are a good jumping off point.

Science Debate 2008

2008-09-08T20:16:00.000-07:00

It’s 3 a.m. The polar ice caps are melting. Drug-resistant staph infections are spreading out of hospitals and into communities. A pollution-driven dead zone is swallowing up thousands of square miles in the Gulf of Mexico. Who do you want answering the phone in the White House?

Do you know where the presidential and congressional candidates stand on science issues? I don’t, not in any detail, and I’d sure like to. One place to start learning is sciencedebate2008.com. Science Debate 2008 is an initiative calling for a presidential debate on the scientific issues that challenge our country. The initiative reads in part:

We have noticed that science and technology lie at the center of a very large number of the policy issues facing our nation and the world - issues that profoundly affect our national and economic security as science and technology continue to transform our lives. No matter one's political stripe, these issues pose important pragmatic policy challenges.

We believe these scientific and technological policy challenges can bring out the best in the entrepreneurial American spirit. America can be a leader in finding cures for our worst diseases, inventing the best alternative energy sources, and graduating the most scientifically literate children in the world - or we can concede these economic and humanitarian benefits to other countries.

Organized by many of this country’s leading scientists and scientific organizations, signers of the initiative identified the following areas of most immediate concern:

Climate Change
Conservation and Species Loss
The Future of The Oceans
Fresh Water: Drought, Pollution, Ownership
Population Growth and the Environment
Renewable Energy Research
Global Diseases and Pandemics
Stem Cell Research
Antibiotic Resistant Bacteria
Drug Patents, Generic Drugs
The Genome
Bioethics
Scientific Innovation and Economic Growth
Improving Science Education
Space Exploration
Preserving Scientific Integrity in Government
Energy Policy

With just 2 months left until election day, it’s sadly clear that there will be no presidential debate devoted to these topics. But the site still has a lot to offer. For teachers, the initiative is a great way to introduce the complicated, controversial relationships between science, politics, and public policy. For students, the discussions of why science should be the focus of presidential attention help illustrate that biology and geology and physics mean more to their lives than just something they have to learn for a test. For all of us, the list of the 14 most important science questions facing America, and the candidates' responses (or not) are a primer on the science and policy issues that we neglect at our own peril.

Everything I know about the Central Dogma I learned on youtube

2008-08-16T19:47:00.000-07:00

A few people have the gift of seeing the world in a grain of sand, but most of us have a hard time staying interested in things we can’t actually observe. Protein synthesis may be an intricate dance whose delicate steps trace out the patterns of life itself, but it pretty much defines boring when diagrammed in a book or on a blackboard. Sure meiosis is all about the sex, but trying to keep all those phases straight isn’t going to start a single heart beating any faster.

So how do you convey the beauty of the submicroscopic processes ticking away beneath our skin? How do you make what you can barely pronounce and can’t possibly see not just real, but remarkable? Try youtube. Tucked in amongst the outtakes from American Idol and the videos of laughing babies and lolcats is a surprising amount of biology, from the sublime…

to the cheerfully ridiculous.

The first one made me lean forward and the second made me laugh – I’m going to remember both of them for quite a while. I bet students will too.

There’s a couple of things to keep in mind if you are going to use youtube to teach or to learn.

Quality varies. Some of these videos are professional works produced by universities and biomedical researchers, others are class projects that likely didn’t pass.

Videos are easy come, easy go. Check your links frequently, and keep exploring, because you never know what might show up.

Be creative with your search terms, because uploaders don't always use the most obvious labels. Start with broad topics, and make sure to look through the related video list that pops up with every search.

My biology blog! You found it!

2008-08-08T18:21:00.000-07:00

Welcome to the Hippocampus Biology Blog! I’m writing this biology blog under slightly false pretenses - I’m actually a paleontologist. I like dead creatures, not only merely dead but really most sincerely dead creatures, just a little bit better than the living ones. All the same, there is an undeniable wonder to seeing the power and beauty and diversity of life in action, right before my eyes. And so I’ve studied and taught biology as well as earth sciences in the field and in museums and the classroom. These days I’m most often the ghost in the machine – I write and edit content for online science courses.

That’s what this blog is going to be about – biology and the web. (Maybe a little paleontology now and then too, when I can slip in it while no one is looking.) The internet has become an exhilarating, bewildering place for biology teachers and students alike. There’s page after page about just about every topic imaginable, but sifting through them can be daunting. What information is reliable? What can be used at will and what is copyrighted? Which websites will still be there tomorrow or next week? How do you take advantage of the constant flow of new information and avoid turning online courses into an easy way of not having to think too much about a lesson plan? Is the internet a boon to learning or plagiarism’s handmaiden? Should Wikipedia be applauded or taken out behind the barn and slapped silly?

I dunno, not altogether. But I’m learning. I hope this blog will help me, and help you too. Each week I’ll be talking about some of the questions and discoveries and worries that go in to designing online courses. I’ll be exploring websites that I’ve used or found that remind me why biology is just so damn cool. I’ll be asking for your comments about what you love, hate, or just don’t get about biology on the internet.

If you’ve ever taught an online course or taken one, if you’ve used information on the net to teach or learn biology, I hope you’ll chime in.

Photo by Dennis Mosner