Jumat, 28 November 2008


I love Thanksgiving. As a foreigner I'm hardly expected to return home for the occasion, and as a holiday it has few expectations (especially if you observe Buy Nothing Day). So basically I get a really nice long weekend to catch up on stuff. I'm on my third book of the weekend, the third chapter of a textbook I'm reviewing and in between those endeavors I am catching up on a few websites I'd bookmarked to explore in more detail when I had time. One of these, that admittedly I bookmarked a long time ago, was Erik Ringmar's blog. Ringmar was a lecturer at the prestigious London School of Economics (or LSE), who got into trouble for his blog when he fairly openly criticized the school. The article in question, a report of an open day address, is actually rather refreshing for its honesty and hardly seems that critical to me. In a similar vein I found this post, of advice to prospective PhD students, to be worthy of mention. Do read right to the end though....

Kamis, 27 November 2008

Bren events next week

I hope you all had a good Thanksgiving. Don't forget tomorrow is Buy Nothing Day:

Now in its 17th year, Buy Nothing Day is celebrated every November by environmentalists, social activists and concerned citizens in over 65 countries around the world. Over the years, Buy Nothing Day (followed by Buy Nothing Christmas) has exploded into a global movement, inspiring the world’s citizens to live more simply and buy a whole lot less.

On a slightly related note, the Bren school of Environmental Science and Management has two environmentally themed seminars next week:

Tuesday, Dec. 2, 200812:30 - 1:30 p.m. in Bren Hall 1414
Professor Ramprasad Sengupta
Centre for Economic Studies and Planning, Jawaharlal Nehru University , New Delhi , India
High Economic Growth, Equity, and Sustainable Energy Development of India.

Wednesday, Dec. 3, 2008 4:00 - 5:00 p.m. in Bren Hall 1424
Miriam Haran, PhD
Former Director General, Israeli Ministry of the Environment Head, MBA Environmental Management Program Ono Academic College Kiryat Ono, Israel
Financial Meltdown Does not Slow Global Warming: The Environment in Israel

Senin, 24 November 2008


The website 'On this day in peace history' is noting today (Nov 24th) as the 149th anniversary of the publication of Charles Darwin's 'On the Origin of Species by Means of Natural Selection, or The Preservation of Favoured Races in the Struggle for Life.' Wikipedia, citing a Darwin biography by Adrian Desmond, has it going on sale on the 22nd of November (and selling out almost instantly). A random sampling of a couple of other websites suggests Wikipedia may be correct. Of greater certainty is the fact that in just a few short months, on February 12th, it will be the bicentennial of the birth of Charles Darwin. What better way to pre-celebrate Valentine's day? (Except by listening to the promising and bizarre combination of Patti Smith and Phillip Glass celebrating the work of Allen Ginsburg in Campbell Hall).

In honor of this possible anniversary (or not), enjoy these YouTube clips. You've probably seen the first one. The second one won a lot of advertising awards. Both of them misrepresent evolution in several important ways but that's part of the fun.....

Coral reef seminar today

EEMB Seminar speaker today is EEMB's own Nichole Price. 
Nichole is giving her PhD exit seminar:
"Processes structuring benthic communities on a coral reef".
4pm, Monday, in the MSRB Auditorium.

Re-creating Extinct Animals

According to a recent article in the New York Times, advances in DNA sequencing and genetic engineering techniques are leading to cautious optimism among scientists that someday it may be possible to bring extinct animals back to life. But it will not be easy. DNA undergoes decay after death, falling apart into little pieces within about 60,000 years. Determining the correct sequence of an extinct species’ DNA requires special DNA sequencers that can analyze the tiny pieces and then calculate how they were aligned in the original intact molecule.

The second step would be to actually reconstruct the deciphered DNA code back into intact DNA once again. One way would be to “reverse engineer” the DNA of a close living relative species until it is similar to the known sequence of the extinct species. So far this has not been possible because of the sheer numbers of base pairs (perhaps half a million) that would need to be modified. But researchers are hopeful that techniques will be available soon to modify up to 50,000 sites at a time. The extinct species’ DNA would then be inserted into an egg of the living relative and incubated in that relative until birth.

How would your students react if it were to be announced one day that an extinct human such as a Neanderthal had been reverse engineered and then born to a modern human or a primate mother?!

Sabtu, 22 November 2008

Dumb eco-questions you were afraid to ask

Not directly CCS Biology related but since sustainability is the theme du jour I thought I'd post this here in the hope that somebody might learn something. At UC Berkeley I worked with a lot of students on recycling projects as they investigated an interesting variety of topics from the economics of single stream versus mutliple stream recycling to the contribution of the homeless to the recycling industry. The message I came away with is that recycling is a complicated, constantly changing and sometimes counter intuitive industry.

For example single stream recycling (where all recycling is collected in one bin) is becoming increasingly popular because collection costs are lowest and new technology allows some quite efficient sorting of materials at the depot. However recycling agencies discovered that the less restrictive you make the instructions - the more you collect. ie if you say 'All plastics' you collect a lot more (of ALL kinds of plastics) than if you say only 'Plastics #1 and #2' and if you say something like 'Only #1PETE and #2HDPE blow molded plastic jugs and bottles' you collect least of all because people get confused and end up chucking a lot more in the garbage. But the truth is that in many areas there is ONLY a market for the aforementioned #1 and blow molded#2. So they collect everything but then end up chucking away everything else so that they can get more of #1 and #2. Confused? Try persuading your friends that in most cases they are better off throwing away plastics (at least of #3 and greater), even if their recycling company collects them, because putting them in the recycling devalues the value of the recycling.

This does differ a bit from place to place and depends on your local collection agency and what the local market is for recycling products. I was reminded of this because New Scientist had an article this week on 'Dumb eco-questions you were afraid to ask' that covers a few of these recycling issues. Including the popular, and much debated pizza box question. I'm not sure why they call them dumb though, most of these are pretty good questions.

Coincidentally Popular Mechanics had an article on 'Recycling Myths: Popular Mechanics Debunks 5 Half Truths about Recycling' this month which contains some useful ecomomic information about the recycling industry.

Rabu, 19 November 2008

Ginkgo Doesn't Prevent Dementia

According to a study in the Journal of the American Medical Association, daily doses of the popular herbal antioxidant Ginkgo biloba neither prevent nor delay the onset of dementia (cognitive impairment). The most common type of dementia is Alzheimer’s disease.

Herbal extracts of Ginkgo remain popular as a memory enhancer, even though previous scientific evidence showed that Ginkgo just doesn’t enhance memory. So don't expect this latest finding regarding dementia to put much of a dent in Ginkgo’s annual sales of over $200 million. Good marketing apparently trumps good science.

Selasa, 18 November 2008

CCS Biology Colloquium Resources available outside the Biology Departments

The following is an incomplete list of resources available for research purposes outside of MCDB and EEMB, both on campus and otherwise in Santa Barbara.

Anthro has a teaching/reference collection of skeletal material of vertebrates that is largely focused to the interpretation of human habitation sites, but the collection and associated courses can be invaluable to students interested in questions of hard-part anatomy of vertebrates.

Biomolecular Science and Engineering
The Interdepartmental Graduate Program in Biomolecular Science and Engineering epitomizes the highly interdisciplinary approach to research and education that is the hallmark of UC Santa Barbara. In this context BMSE offers a unique mix for graduate training and research at the frontiers of Biochemistry, Molecular Biology, Bioengineering and Biomolecular Materials. The BMSE Program may be for graduates, but an examination of Faculty research pages will lead you to some laboratories working on the forefront of materials and nano-technology where you might find a research option. See particularly:

The Bren School of Environmental Sciences and Policy
The Bren School is technically a graduate program. However, there are some good biological folk there, and if you can talk your way in, so much the better:

Environmental Studies

Geological Sciences
The department has several mass spectrometric facilities focused upon paleoclimatology recorded by isotopes of Carbon, Oxygen, strontium and others. These isotopes can be used to track other things too. The Paleontological Collections. Ostensibly part of the Museum of Systematics and Ecology, but housed in PSB South. Largely focused upon invertebrate fossils, particularly of the last 60 million years of southern California.

Extraordinary strengths in remote sensing; both in the use of existing technology and the development of new technologies. Very important for any research involving widespread geographic coverage.
The Department of Geography hosts a wonderful resource, Spatial@UCSB, dedicated to visualizing and analyzing data in a 3D manner. They offer consultation on your data sets at specific hours.

The Evolutionary Psychology program has strong ties to the Neurobiology Research Institute. People include:
Psychology also contains many people who overlap in interests with MCDB:
Chemistry and Biochemistry

The sixteen faculty in the area of Biochemistry center around the common themes of bio-organic and bio-inorganic reaction mechanisms, protein-nucleic acid recognition, nucleic acid structure and dynamics, and membrane transport. They can offer expertise in a number of experimental tools such as Xray diffraction, computer graphics and computational analysis.

    The UCSB Library
    Beyond standard library resources, UCSB hosts the "Map and Imagery Library" (MIL) in the first floor of the SEL wing. This is a national repository, and has both digital and paper images of just about any kind of geographic reference you could want. This includes:
    • Topographic maps
    • Geologic Maps
    • Maps & volumes summarizing vegetation, climate, hydrology, cultural and other features;
    • Aerial photographs from landsat down to old plane-flown photographs.
    • And much more!
    The Marine Science Institute
    The Marine Science Institute (MSI), established at the University of California, Santa Barbara in 1969, is the focus for marine, coastal zone, and freshwater research; marine policy studies; and educational outreach in marine science. MSI administers and supports research projects involving faculty, professional researchers, technical staff, graduate students, and undergraduate students from 14 disciplines. There are a LARGE number of researchers associated with the MSI who are not faculty in one of the biology departments – and many are very student friendly. Some specific faculty to check out include :
    Carrie Culver, Tom Dudley, Jenny Dugan, Mark Page, Dan Reed, Kevin Lafferty and Milton Love (See especially Milton Love’s web page – it’s cool!). A complete list of MSI associated faculty can be found here.
    PISCO (Partnership for Interdisciplinary Studies of Coastal Oceans) is a large, long-term, ecosystem research and monitoring program that involves Santa Barbara and three other West Coast campuses (Oregon State, Stanford and UCSC).

    Cheadle Center for the Study of Biodiversity and Ecosystem Restoration (CCBER)
    Located under the south end of the stadium. Used to be the Museum of Systematics and Ecology in EEMB, now independent. Houses the plant and animal collections of the University. Hosts a range of research projects, particularly concerning biodiversity and the reclamation of local ecosystems. Very strong programs in outreach to local school children. Check out their internships.

    National Center for Ecological Analysis and Synthesis (NCEAS)
    An outstanding international think tank on anything ecological and a lot evolutionary. It is a cross road of visiting scientists, in house researchers and periodic work groups who have access to a series of immense computerized databases that allow researchers to seek out explanations for gross patterns in Nature. Many UCSB faculty and graduate students participate, and there are frequent opportunities to work as paid data-collectors or enterers. NCEAS is located on State Street, in the center of the Paseo Nuevo. Note that they have a Thursday lunch seminar that hosts internationally known scholars.

    The UC Natural Reserve System.
    The UC System is unusual (not quite unique) in owning its own set of natural reserves dedicated to instruction and research. Each reserve is selected as representative of an important ecosystem in California. Most are managed by resident scientists. All are available for visitation or research with proper initial approval (signing of waiver forms indicating respect of the property, etc. ). Each Reserve has its own web site, and most list past research conducted on the Reserve. A good way to see who is doing what.

    UCSB has one on campus (Coal Oil Point Note particularly here that Cristina Sandoval (director of Coal Oil Point) is an active researcher who interacts with undergrads) and two nearby (Sedgwick Ranch & Carpinteria Salt Marsh). We also manage the Santa Cruz Island Reserve, the Kenneth S. Norris Rancho Marino Reserve near Cambria, the Sierra Nevada Aquatic Research Lab in Bishop, and the Valentine Camp on the eastern face of the High Sierra.


    Channel Islands National Park (And the Channel Islands National Marine Sanctuary)
    The National Park Service manages several of the Channel Islands, and is interested in supporting research on them. Most of their voucher specimens come to Museum of Natural History

    Lotusland Botanic Garden
    Located in Montecito, Lotusland occupies 38 acres, much planted with exotic plant species in striking array. Lotusland has the world's third largest collection of cycads, and outstanding collections of Agave, Aloe and cool-tolerant palms. The garden is looking to become increasingly involved in research.

    Santa Barbara Botanic Garden
    Nearly a century old, the garden focuses upon native Californian plants. It has an outstanding living collection arranged by habitats, and a good library and herbarium focused in native flora. The Garden has a long-standing reputation for research into native Californian plants, and the biogeography of the Channel Islands. Research students interested in botany would do well to explore this.

    Santa Barbara Museum of Natural History and Sea Center.

    The Museum of Natural History is likewise nearly a century old, and has an established research reputation. It has internationally-recognized collections of living Mollusca and bird egg shells, and a very strong collection of marine invertebrates of the Santa Barbara Channel. Other collections include an excellent collection of mammals, particularly marine mammals, of southern California, a wide range of fossil whale material, a decent insect collection, and collections of particularly Pleistocene fossil marine and terrestrial organisms. It hosts active researchers working on - Marine Mammals Krista A. Fahy, Michelle L. Berman, - Marine octopods, F. G. Hochberg - Marine gastropods, Henry Chaney - Marine Mollusca, Paul Valentich Scott - Entomology - Michael Caterino - see his spectacular site on the California Beetle project, Ethnobotany, Jan Timbrook and Vertebrate Biology, Paul Collins.

    Santa Barbara Zoological Gardens

    The Zoo is mostly dedicated to the culture and reproduction of living, endangered, taxa. However, while they might not take kindly to dissecting a living animal, they certainly offer opportunities to examine behavior, and who knows what else might be worked out.

    USC Wrigley Marine Science Center, Catalina Island

    For those of you with marine interests, a local (SoCal) resource is the Wrigley Marine Science Center on Catalina island, run by USC. It offers research opportunities and summer courses.

    Senin, 17 November 2008


    Foldit is a computer game that was released in May of this year that allows amateurs to compete against, and collaborate with, specialists to design protein structures. Introductory levels teach the general governing concepts that users must understand before moving on to design complicated, potentially useful molecules. This is an interesting example of the potential power of distributed computing. Human brains currently manipulate three dimensional structures much better than computers. It is hoped that by studying how humans solve puzzles better computer algorithms will be devised. The YouTube video below gives a nice overview of the game.

    Kamis, 13 November 2008

    How flies find stuff.

    Next week's EEMB seminar speaker will be Dr. Michael Dickinson, professor of bioengineering at the California Institute of Technology.  Michael's research merges behavioural ecology and bioengineering to study how flies perceive and navigate their environment. His work (and talks) are very exciting and has resulted in his being awarded a prestigious MacArthur Foundation prize (a very big deal). For more information on Michael's research, check out his page at Caltech.

    This talk will be on Monday at 4pm in Psych 1924 (note venue change).

    I have heard Michael talk many times and can assure you that this will be a great talk. Strongly recommended for all, regardless of your interest in flies, flight or stuff.

    Surrogate Grandmother

    According to an Associated Press article that appeared in many major newspapers and news services yesterday, a 56-year-old woman gave birth last month to triplets. The event was noteworthy because the three baby girls were actually her biological granddaughters.

    Apparently a young couple could not conceive because the woman had had a hysterectomy. So they used in vitro fertilization (IVF) to produce their embryos, which were then implanted into the young woman’s 56-year-old mother.

    My class took quite an interest in the many and varied reproductive possibilities raised by modern IVF techniques. They understood the obvious benefit, which is to enable some infertile couples to have children of their own. They also quickly grasped that it could also be used (in combination with preimplantation genetic diagnosis) to choose a child’s sex, to avoid having a child with certain genetic disorders, or even to cure an older sibling of a genetic disorder (See the Current Issue in Human Biology 5th ed., pp. 396-397). But they didn’t come up with this scenario!

    Rabu, 12 November 2008

    Reef fish seminar

    I would like to announce the following invited research seminar by Dr Michel Kulbicki of the University of Perpignan. The seminar will be presented in the main Auditorium of the Marine Science Institute Research Building on Tuesday, November 25th from 4-5PM and is sponsored by the Moorea Coral Reef LTER site.

    Michel Kulbicki is based at the Insitut de Recherche pour le Développement in Perpignan, France. He was originally trained in biology and fish ecology at the Institut National d'Agronomie de Paris and Oregon State University. After four years of work on tuna fisheries and echointegration, he came to reef fish ecology in 1985. He was then based in New Caledonia where he worked until 2004. During his stay there, he had the opportunity to conduct fieldwork in New Caledonia, French Polynesia, Tonga and Fiji. His major interests lie in linking the characteristics of reef fish assemblages (e.g. species composition, functional groups, trophic or size structure) to factors at various spatial scales, from local (reef type, fishing pressure, coral cover) to regional (island size, island type, degree of isolation). He is also interested in developing better methods to survey reef fish and in associating information on fish obtained via underwater visual censuses with information on the environment obtained via remote sensing.

    Seminar Title: Macro-ecology and understanding the large scale functioning of reef fish assemblages in the Pacific

    Abstract: The regional species and functional diversity of reef fishes determines to a significant extent the local species and functional diversity of these fishes in the Pacific. As regional diversity is related to large scale factors such as island size and connectivity, distance to the biodiversity center, latitude, these factors also play a role on the distribution and composition of local reef fish diversity. Amongst the life history traits, (adult) size follows gradients linked to island size and connectivity. Species range is also found to be correlated to species (adult) size and larval duration and is also correlated to island size and connectivity. Colonizing ability can be as well related to (adult) size (finding mates, reproductive capacity, resource limitation). These findings explain why on small isolated islands the proportion of large species is higher than on large connected islands in the Pacific. One of the major consequence is the shape of the diversity-biomass relationship which presents a steeper slope on small isolated islands but reaches lower values of biomass because of lower diversity. The implications for management are important, in particular this shows how small islands will be far more fragile to fishing than larger or well connected islands. These findings may find applications in other systems where "ecological islands" exist.

    Selasa, 11 November 2008

    Whatever Happened to Golden Rice?

    Golden rice was once heralded as a cure for vitamin A deficiency, which kills or blinds children in poorer countries worldwide. But twelve years after its development golden rice is still not being produced and distributed. The primary reason is categorical opposition to all genetically engineered (GE) foods by organizations such as Greenpeace. Greenpeace argues that although golden rice might indeed benefit vitamin-deficient children, acceptance of golden rice would open the door to other GE crops that Greenpeace vehemently opposes.

    In the face of intense, well-organized opposition, government regulatory agencies have been reluctant to approve GE crops, including golden rice. The company holding the patent on golden rice eventually gave up, saying there was no money in it. It's still being studied in a few labs by humanitarian organizations such as World Food Day, but don’t expect to see it on grocery shelves any time soon. That's too bad, for golden rice really is a product that could help people in need, as opposed to just helping food producers and manufacturers.

    Senin, 10 November 2008

    Seminar this evening

    If your days are just packed then how about an early evening seminar?

    Monday evening seminar (tonight) will be presented by Dr. Deborah Gordon from Stanford University. Her talk is entitled:

    Ecology and behavior of Argentine Ants in California.

    LOCATION: CCBER Classroom at Harder Stadium,
    TIME: 6-7 PM

    Minggu, 09 November 2008

    Wonders of ocean life counted in massive census

    I'm not sure exactly why this is the lead story on the CNN website right now, slow news day?, but it's good to see some biology there.

    A city of brittle stars off the coast of New Zealand, an Antarctic expressway where octopuses ride along in a flow of extra salty water and a carpet of tiny crustaceans on the Gulf of Mexico sea floor are among the wonders discovered by researchers compiling a massive census of marine life.

    Sabtu, 08 November 2008

    Society of Undergraduate Biologists

    I already posted this once but I'll give it another shout. Get involved now whilst the club is getting going and you can get in on the ground floor. One moment you'll be a community organizer and the next moment......


    The Society of Undergraduate Biologists (SUB) was formed by students at UCSB with the desire to promote widespread scientific communication both within the undergraduate biology community and between the students and the faculty members of the CCS, MCDB and EEMB departments. The organization will strive, alongside the respective biology departments, to foster a community of well-rounded and active scientists through its platforms of communication, mentorship, and the promotion of undergraduate research.


    Research: SUB will strive to promote undergraduate research as both an essential part of an undergraduate’s education and as an asset to the scientific community. SUB will support those undergraduates already involved and will encourage those still yet to participate. Future goals: Obtaining special funding for undergraduate research; Undergraduate research seminars; Encouraging involvement in undergraduate research; Featuring UCSB research through the org. website and events.
    Mentorship: The biology degrees offered by the CCS, EEMB and MCDB departments allow students to explore exciting educational challenges and opportunities. SUB will facilitate a system of mentorship in which undergraduates, throughout all four years of their degree, can look to others for advice in maximizing their experience at UCSB. Future goals: Graduate student-undergraduate student mentorship program; Promotion of departmental peer advisors; Events for incoming freshmen; Study group organization; Grad school admissions seminars. Communication: Science is a group effort. Communication is key. SUB will promote a well-informed undergraduate community by facilitating communication amongst undergraduates, between students and faculty, and between biology departments. Future goals: Promotion of departmental events (seminars, symposia, etc.); Undergraduate science-focused social events; Faculty-student events.

    Kamis, 06 November 2008

    REU site

    A couple of the students on Wednesday mentioned the National Science Foundation's Research Experience for Undergraduates program. NSF maintains an extensive website where you can find details of what the REU program is all about and allows you to list the sites by subject or state. The list of sites in the Biological Sciences is impressive. Many (most?) of the REU programs run over the summer so this is early notice of something you may want to consider for next summer.

    Rabu, 05 November 2008

    Ecosystem services seminar

    Ashok Khosla
    Chairman, Development Alternatives Group India President
    International Union for Conservation of Nature
    Tuesday, Nov. 18, 2008
    12:30 - 1:30 p.m.
    Bren Hall 1414

    "The Importance of Including the Value of Ecosystem Services in Economic Calculations "

    Scientists in Japan clone mice that had been frozen for 16 years


    They suggest this leads to the possibility of cloning extinct species from the cells of frozen animals like mammoths. I've also heard the idea that being able to clone animals could lead to an ethical meat option for vegans and vegetarians (no animal would be harmed as the meat would be grown by itself in a lab).

    Sabtu, 01 November 2008

    New Nutrient Standards for Packaged Foods

    Finally, someone has decided to make it easy for consumers to pick the healthiest packaged foods! A coalition of some of the biggest food companies has teamed up with scientists and the federal government to develop and promote a simple front-of-package logo called “Smart Choices” to indicate that a food meets certain nutritional standards. The standards include limited quantities of total and saturated fats, cholesterol, added sugars and salt, as well as minimum quantities of nutrients for good health, such as calcium, potassium, fiber, and certain vitamins. And like the “Heart Healthy” program originally developed by the American Heart Association, the new program is based on good scientific evidence.

    Once consumers understand what the logo means and accept its underlying health assumptions, they can simply look for the logo on the front of the package. “Pattern recognizers” such as myself (who can’t find their favorite products in the grocery store if the manufacturer changes the packaging!) will appreciate the help in picking healthful foods. The logo is a green check mark in a square along with the words, “Smart Choices Program”. For a complete listing of the nutritional requirements to earn the Smart Choices label, visit the Smart Choices website. The logo should begin appearing on products in stores by the middle of next year.
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