Friday, December 18, 2009

Underserved medicine seminar series

I've heard great things about this seminar series in the past.

One of the 6 programs of Doctors Without Walls is the underserved medicine seminar series at UCSB. We have a great line up of speakers this year! The class has 35 enrolled students but is held in a large lecture hall so we can accommodate attendance by others and invite faculty and staff to attend when they can.
Dr Mimi Doohan MD PhD
PS There is always a lively Q and A session at the end of every presentation.

Scheduled Speakers:

Underserved Medicine Course (MCDB 194MD):
UCSB Molecular, Cellular and Developmental Biology (MCDB) Department
Thursdays 6-7:50pm, Winter quarter 2010
Location: Broida 1640
Course Instructor: Dr Mimi Doohan, MCDB adjunct faculty

Jan 7
Course Introduction
Dr Mimi Doohan MD PhD
Family physician
Doctors Without Walls-Santa Babara Street Medicine-founder/medical director

Jan 14
Modern Day Slavery and Human Trafficking in the 21st century
Thomas F. Burke MD
Chief, Division of Global Health and Human Rights, MGH
Faculty, Departments of Emergency Medicine and Pediatrics
Massachusetts General Hospital
Harvard Medical School

Jan 21
Medicine in Crisis Zones
Jason Prystowsky MD
Doctors Without Borders
Faculty, Department of Emergency Medicine Loma Linda University
Faculty, Department of Emergency Medicine UCLA

Jan 28
Health Care Reform
Congresswoman Lois Capps
23rd district of California

Feb 4
Womens Health:
Alice Levine CNM
Womens Free Homeless Clinic at Transition House
Scotti Warren, Americorp Member
Annette Perez, Transition House, Director of Operations
Jennifer Ferraez, LCSW
Morgane Naveau, UCSB student volunteer

Feb 11
Surgical Care of the Underserved
David Thoman MD
Director of Trauma and Associate Director of Surgical Education

Santa Barbara Cottage Hospital Charity Thoman MD, MPH
Resident Physician, Internal Medicine

Santa Barbara Cottage Hospital

Feb 18
LGBT Health (Lesbian, Gay, Bisexual, Transgendered)
David Selberg
Executive Director
Pacific Pride Foundation, Santa Barbara CA

Feb 25
Medical Tourism
Eric McFarland MD PhD
Robert Gayou MD

March 4
Care of Veterans
Robert Gaines MD
Medical director, Santa Barbara County Veterans Administration Clinic

March 11
Care of the Unshetlered Homeless
Jim Withers MD
Founder and director, International Street Medicine Institute
Founder and director, Operation Safety Net, Pittsburgh P


Wednesday, December 9, 2009

Summer research opportunity #2

Caitlin passed on this reminder:

I thought it might be important to note that REU deadlines are usually between the second week of January and early March.

REU stands for Research Experience for Undergraduates and is an NSF funded program that is one of the largest sources of funding for undergraduate summer research. You apply to the individual REU sites for the funding so you need to do your homework.

Access the full list of REU sites here for Biological Sciences and here for a wider list of subjects.
Click on the individual sites to find full details and application details.

Winter internship opportunity

Bruce Tiffney passed this one on:

CCBER has several Coastal Fund-supported restoration intern positions (~ 6 hr/week) available this winter as well as several paid student worker positions (~10hr/week) available for students interested in developing their hands-on restoration skills. Lots of planting, plant identification, site maintenance, nursery work and camaraderie in the field!
Please send e-mail of interest including mention of relevant experience, winter schedule and an indication of the amount of time you want workduring the work week to Lisa Stratton:

Thank you very much,


Lisa Stratton, Ph.D.
Cheadle Center for Biodiversity & Ecological Restoration (CCBER)
Harder South, Rm 1005
UCSB, MC 9615
Santa Barbara, CA 93106

Office: (805) 893-4158
Fax: (805) 893-4222

Summer Research opportunity #1

Kathy Foltz passed this one on:

Dear Colleague:

We would appreciate you sharing the following opportunity with your students.

Caltech is excited to announce two summer research opportunities available to continuing undergraduate students. Questions about these programs can be directed to Carol Casey at or (626) 395-2887.


The MURF program aims to increase the participation of underrepresented students (such as African American, Hispanic, and Native American, females who are underrepresented in their discipline, and first-generation college students) in science and engineering Ph.D. or M.D./Ph.D. programs and to make Caltech's programs more visible to students not traditionally exposed to

Eligibility: Students must be current sophomores through non-graduating seniors and must be U.S. citizens or U.S. permanent residents. A minimum GPA of 3.0 is required.

Support: MURF students will receive a $6000 award for the ten-week program.
Additional housing and travel support may be provided.

Application: Online applications are due January 13, 2010.

For more information, please visit


Caltech's Amgen Scholars Program is geared towards students in biology, chemistry, and biotechnology fields. Some of these fields include biology, biochemistry, bioengineering, chemical and biomolecular engineering, and chemistry.

Eligibility: Students must be current sophomores through non-graduating seniors, must be attending a four-year university, and must be U.S. citizens or U.S. permanent residents. A minimum GPA of 3.2 is required.

Support: Amgen Scholars will receive a $5500 award, round-trip air transportation, a generous housing allowance, and a food allowance.

Application: Online applications are due February 16, 2010.

For more information, please visit

Carol Casey
Associate Director
Student-Faculty Programs
California Institute of Technology
Mail Code 330-87
Pasadena, CA 91125
(626) 395-2887

Thursday, December 3, 2009

Show Your Working

From the BBC: 'Show Your Working': What 'ClimateGate' means.'

The "ClimateGate" affair - the publication of e-mails and documents hacked or leaked from one of the world's leading climate research institutions - is being intensely debated on the web. But what does it imply for climate science? Here, Mike Hulme and Jerome Ravetz say it shows that we need a more concerted effort to explain and engage the public in understanding the processes and practices of science and scientists.

Tuesday, December 1, 2009

Ecological Consequences of Natural Oil Contamination

Heather Coleman
PhD Candidate Wednesday, Dec. 2, 2009
2:00 p.m.
Bren Hall Dean's Conference Room (2436)
"Ecological Consequences of Natural Oil Contamination"
Faculty Advisor: Hunter Lenihan

Wednesday, November 25, 2009

Faculty Research Interests

Faculty in EEMB and MCDB sorted by Research Interests

Molecular genetics
Plant molecular biol
Microbial Pathogenesis
Neurobiology (molecular/cellular neuroscience)
Quantitative Biology/Omics
Developmental Biology
Virology and Immunology
Cell Cycle/Cell Biology
Stem Cell Biology see also UCSB center for Stem Cell Biology and Engineering
    Biological oceanography
    Freshwater ecology
    Physiological ecology
      Plant ecology
      Marine ecology
      Plant genetics/evolution
      Parasitology and Infectious Diseases
      Community Ecology
      Mathematical ecology
      Microbial ecology

      Origin of disease seminar

      BMSE and Biochemistry Seminars

      MRL 2053 at 11 am on Wednesday December 2nd

      Dr. Jamey Marth, Dept of MCDB and BMSE, UC Santa Barbara

      Seminar Title: "A Unified Approach to Discovering the Origins of Disease"

      Monday, November 23, 2009


      Gerick Bergsma will be presenting his PhD work on how direct and indirect effects of a coral mutualist propagate through a reef community.
      4pm today in the MSI auditorium.

      Dan Reed will be speaking at the Monday night CCBER Conservation and Restoration Seminar Series tonight, Nov. 23rd, 6-7pm, Rm 1013 Harder on
      The use of artificial reefs to mitigate the loss of kelp forest habitat caused by the operation of a coastal power plant.

      Thursday, November 19, 2009

      No such thing as a free lunch (or book)

      Copies of the Origin of Species, complete with a brand new and scientifically dodgy introduction by evangelist Ray Comfort, are being handed out by the Arbor right now(across from main library entrance). If you want a free copy of the Origin make sure you pick up, or print out, this bookmark courtesy of the National Center for Science Educations 'Don't Diss Darwin webpage.'

      Thursday, November 12, 2009

      The Green Initiative Fund

      The Green Initiative Fund (TGIF), a student-governed committee awarding grants for sustainability projects on the UCSB campus, is currently soliciting project proposals for the 2009-10 grant cycle. Any UCSB student, staff, or faculty member is eligible for funding for projects that reduce the university's impact on the environment. Ideal projects will show a quantifiable change (energy, waste, water reduction, etc.) while also educating the campus community.

      Do you work in a campus department that could use a little money to create a program that leads to behavioral change - turning off lights, purchasing Environmentally Preferable Products, purchasing reusable coffee cups, etc.? Are you a faculty member that would like to perform a small research project on a sustainability issue affecting UCSB? Are you a student member of a campus group that could use a little seed money to start that environmental initiative? All of these are perfect projects for TGIF funding!

      If you have an idea for a project, but need some help fleshing it out, please contact the TGIF Grants Manager, Jill Richardson at

      Applications are available now and due on Monday, January 25, 2010.

      For more information on previously funded projects or to download the application, please visit the TGIF web site:

      We look forward to reading your proposals!

      The TGIF Grants Committee

      Tuesday, November 10, 2009

      How bacteria talk

      Not a substitute for attending a talk on campus but as an additional treat check out this TED talk by Bonnie Bassler on how bacteria talk.

      If you haven't discovered the TED talks yet then you should check out the website - the world's most fascinating thinkers and doers, are challenged to give the talk of their lives - in just 18 minutes.

      Once you start watching it's hard to stop and it beats watching another cat playing piano on YouTube.....

      Thursday, November 5, 2009

      Bren Research seminar

      Jeffrey McDonnell
      Richardson Chair, Watershed Science
      Distinguished Professor of Hydrology
      Oregon State University

      Thursday, Nov. 19, 2009
      12:30 - 1:30 p.m.
      Bren Hall 1414

      "The two water worlds paradox: Isotope evidence that trees and streams
      return different water pools to the hydrosphere"

      Anatomy of Viral Persistence

      Don't forget the seminar assignment for the Biology Colloquium. There's lots of good seminars going on right now but the pickings may get slimmer as we head into Thanksgiving week and the end of the quarter.

      Today's MCDB Seminar:

      “The Anatomy of Viral Persistence”

      Michael B.A. Oldstone, M.D.
      Department of Immunology and Microbial Science
      The Scripps Research Institute, La Jolla

      Thursday, November 5, 2009
      3:30 p.m. - 4:30 p.m.
      Rathmann Auditorium, LSB 1001

      Friday, October 30, 2009

      Monday's eemb seminar

      Hanna Kokko will be giving the EEMB departmental seminar next week. Dr Kokko is a behavioral ecologist and theorist and will likely discuss her work on the evolution of sex roles, population dynamics, and sperm parasites (Amazon mollies).

      Title:From individuals to populations ... and back
      Date: Nov 2
      Time: 4:00 pm
      Location: MSR Auditorium

      Thursday, October 29, 2009

      Fantastic opportunity

      Part Time Research and Curatorial Assistant

      Opportunity for Biology student with excellent computer and statistical skills to assist with curating of entomology collection, statistical analysis of collection data and creation of collection data-base. Hours are extremely flexible and can be adapted to your schedule, ideally averaging about 10 hours per week. Some work can be performed at your home, some where the collection is located about 15 minutes from campus. Potential exists for junior author status on future scientific papers.

      Initial projects will include analysis of 20 years of flight period data for evidence of local impact of global warming, and comparison of post-wildfire collecting data with 10 years of base line records to evaluate habitat recovery.

      This large (60,000 specimen) collection is in need of a good computerized data-base using File Maker Pro or other data base application on Mac OSX that will be compatible with data systems at two Natural History Museums. Other curatorial and collection organization tasks are also needed. This is could be a two year or even longer opportunity for the right student. There is additional potential for studies of the student's own design utilizing the collection.

      Compensation: $10 per hour.

      For further information or to apply contact Paul Russell, 805 682-6960,

      Saturday, October 17, 2009

      Voyage of the Beagle finger puppets

      Brilliant. Check out the three finches with three different beaks.....

      You know you want to make them....

      There's a template available here along with patterns for various other crocheted items (octopus, squid, jellyfish, prawn and mustaches (?))

      Friday, October 16, 2009

      Charles Darwin - The True story



      Dr. John van Wyhe
      Christ's College, Cambridge
      Director, The Complete Work of Charles Darwin Online

      2:00 PM, Webb Hall 1100

      This year is the 200th anniversary of the birth of Charles Darwin and the 150th of the publication of Origin of Species. Yet much of what is commonly known about Darwin is wrong. He did not discover evolution on the Galapagos, Darwin's finches were not the turning point, he did not keep his theory secret for 20 years, he was not trying undermine religion and he was not an atheist. This talk reveals the real Darwin and outlines what he really did and said in a clear and entertaining way.

      Tuesday, October 13, 2009

      RISE - Research Internships in Science and Engineering

      This looks like a great opportunity to pursue summer research activities in Germany in the fields of biology, chemistry, physics, earth sciences & Engineering.
      Undergraduate students work with research groups at universities and top research institutions across Germany for a period of 1.5 to 3 months during the summer. RISE interns are matched with doctoral students whom they assist and who serve as their mentors. The working language will be English. All scholarship holders receive stipends from the DAAD to help cover living expenses, while partner universities and research institutes provide housing assistance. In 2010 we hope to have 300 interns.

      The application period for undergraduate students from the US, Canada, and the UK, who wish to take part in an internship during summer 2010, is:
      December 7, 2009 to January 31, 2010.

      Friday, October 9, 2009

      Writing, Reading, and Reviewing Scientific Articles

      This coming week in the bio colloquium we're reading an article from the primary literature. To provide general background on the elements of a scientific paper we also handed out "guidelines for writing a scientific paper". To help you think about it from the other end (reviewer vs. writer) you may want to see what guidelines the scientific journals provide their reviewers, that is, what helps us decide whether a paper is "publishable" by a given journal. This is useful in writing (and reading) a paper to see what the "critics" are looking for.

      Here is the link for reviewers for the journal, Ecology:

      Also informative is the "Reviewers Information Pack" ( for everything you might want to know about the review process for journal articles. This is provided by Elsevier, which publishes Developmental Biology, and hundreds of other journals (

      Here's their reviewers' home page:

      Thursday, October 8, 2009


      I wish to bring the following scholarship competitions to the attention of students and faculty in your program.

      Scholarships with Campus Application Deadline of January 7, 2010
      • Barry M. Goldwater Scholarship
      • Harry S. Truman Scholarship
      • David Boren Scholarships for Study Abroad
      Scholarships with Campus Application Deadline of February 3, 2010
      • Beinecke Scholarship
      • Donald A. Strauss Scholarship
      • Morris K. Udall Scholarship
      These prestigious scholarships require campus endorsement. This necessitates campus application deadlines well in advance of the agency deadline. Scholarship information and application instructions may be found on the URCA web site.

      Students interested in applying should begin the application process NOW.
      Please contact the Campus Scholarship Director, as soon as possible to confirm your interest and to have your questions answered regarding the campus application and nomination processes.

      Thursday, October 1, 2009

      Regional Evolution Meeting and Lab opportunity

      The Oakley lab is looking for some volunteers... it wouldn't be very high level stuff, but it would be a nice introduction to lab work - possibly ideal for freshmen who just want to wet their toes a little without fear of a commitment! It would be a couple hours a week helping with a behavioral experiment to determine mate choice in ostracods. If you are interested in this then contact me (John) and I will pass on the contact information. Also, courtesy of Todd Oakley, comes the following announcement:

      This year the WEB (Western Evolutionary Biologists) meeting will be held at UC-Berkeley. The UC organization NERE funds travel expenses to the meeting. Each campus has funds for this, for which Todd Oakley has responsibility at UCSB. UCSB-NERE will fund the travel expenses on a first come-first serve basis. First people to register get priority for free travel. In the past, there has been enough funds to fund everyone interested, but this year is the first year in more distant Berkeley.

      If you'd like to give a talk or poster, note the deadline for abstract submission is not too long from now (Oct 16).

      The WEB web site and registration is here:

      Movie about life in a molecular biology lab

      MCDB Movie
      Thursday, October 1, 2009
      LSB Auditorium (1001)
      Movie screening: "Naturally Obsessed: the making of a scientist" (links to movie website)

      Mixing humor with heartbreak, the film takes a profoundly real yet intensely dramatic story about life in a molecular biology lab.

      Film review from the Washington Post

      Wednesday, September 30, 2009

      21st Century Environmental Challenges in a Global Context

      Each year, the College of Letters and Science sponsors two distinguished endowed programs, the Critical Issues in America program and the Arthur N. Rupe Great Debates Series. This year the topic for the Critical Issues in America program is "Forty Years after the Big Spill - Looking Back, Looking Ahead: 21st Century Environmental Challenges in a Global Context." Led by Dehlsen Professor of Environmental Studies William Freudenberg and supported by Water Policy Program Director Robert Wilkinson, the program references an historical benchmark - for the campus as well as the nation - and addresses a breadth of environmental challenges for the 21st century with a strong, interdisciplinary group of core faculty and key collaborators.

      All talks are free and open to the public.

      TOMORROW, Thursday, October 1: Wm. Freudenburg: "The Tragedy of the Un-Commons?" 12:30 - 1:45 p.m. in Lotte Lehmann Hall

      Wednesday, October 21: Bill Gibson, CSU Long Beach: "Re-Enchanting the World," 2:00 - 2:50 p.m., in Bren 4016

      Wednesday, October 28: Kai Lee, Packard Foundation: "Humans in the Landscape," 2:00 - 2:50 p.m., in Bren 4016

      Wednesday, November 4: Doug Bevington, "Environment Now: The Rebirth of Environmentalism," 2:00 - 2:50 p.m., in Bren 4016

      Tuesday, November 10: Riki Ott: "Learning the Lessons of the Exxon Valdez Oil Spill," 12:30 - 1:45 p.m. in Lotte Lehmann Hall.

      As the academic year unfolds, please continue to look for events related to this exciting and timely Critical Issues in America program.

      Thursday, September 24, 2009

      Seminar: CREB and the Search for Memory Enhancers

      "CREB and the Search for Memory Enhancers"

      Tim Tully, Dart Neuroscience
      Mosher Alumni House
      Alumni Hall, 2nd floor
      Thursday September 24th, 4:00 PM

      Tim Tully utilizes the study of fruit flies to elucidate genes related to memory formation. His experiments on "photographic memory" in fruit flies were the first demonstration of genetically enhanced memory. His work opens the possibility of developments in effective treatments for both behavioral and pharmacological memory loss in humans. Dr. Tully’s research was featured in the 2004 PBS special entitled /A Gene You Won’t Forget/.

      Wednesday, September 23, 2009

      Visit Sedgewick Reserve and do good deeds...

      WANTED: students who would like to come up and help our Outdoor Classroom students (4th graders) identify mostly insects, some lizards (no snakes to date) and an occasional mouse or vole in the pitfall traps? The dates are October 28, 29; Dec. 9, 17; and April 14, 15. It would only be for about two hours each day (9:30 - 11:30ish). Please reply to Sue Eisaguirre at 686-1941, ext 4. or

      Thursday, June 25, 2009

      Research Opportunity

      The goal of the study is to compare the methane ground/atmosphere exchange between two sites, one using effluent organic fertilization and the other using solid manure fertilization. The site secured is a 500 acre dairy/orchard in the heart of the central valley. I have already secured instruments and lab space in cooperation with Prof. Schimel and will be in constant communication wtih him as well as Prof. Melack and Prof. King. I'm looking for someone that is interested in coming aboard to help me run samples within the lab.

      Contact Matthew Christian if you are interested

      Tuesday, June 9, 2009

      Habitat Restoration Assistant

      UCSB’s Coal Oil Point Reserve currently has an opening for a Habitat Restoration Assistant beginning July1st , and continuing through the end of the year. The Assistant will help with implementing restoration projects and gain valuable experience with hands-on restoration techniques and principles. The assistant will work with the Reserve Steward, a Restoration Ecologist and student interns and participate in all aspects of restoration: removal of non-native plants, seed collection, plant propagation, preparation for intern and volunteer workdays, and
      enhancement and preservation of existing restoration sites.

      This is a great opportunity to gain field experience in restoration techniques, native plant propagation, and volunteer supervision. The assistant will be employed for approximately 6-10hours/ week at a pay rate of $10/hour. Applicant must be a UCSB student, and available for the entire summer. Preferred availability is Friday mornings (~8:30-12:30) plus one other weekday morning (9-12noon), and able to commit to occasional weekend time (~one Saturday/per month). Students eligible for work study in the Fall are strongly encouraged to apply!

      To apply, send resume and class schedule/time availability for summer and fall quarter to: Tara Longwell at and Darlene Chirman

      Thursday, June 4, 2009

      Neurobiology research opportunity

      CCS Bio major Veronica Pessino tells me that a that a grad- student friend of hers in the Feinstein lab is looking for an undergrad to help him out. He would love a CCS student and asked Veronica to see if anyone is interested. His name is Jack Reifert.

      If any of you are interested in neurobiology writ large, this could be a real opportunity to get a great start at lab research in a very nice lab!

      Tuesday, June 2, 2009

      This is the end

      Okay I'm all blogged out. If anyone is still reading this then here are a couple of end of quarter wrap up announcements.
      • The last lectures are now up as pdf files on the right hand side. I think the only one missing is the first part of today.
      • The answers to the ecology quiz I handed out are here with a few comments.
      • For Thursday remember YOU are presenting. Don't make it a lecture, make it INTERESTING (oops, that didn't sound right). Remember you are supposed to be passionate about this so tell us something cool you investigated.

      Monday, June 1, 2009



      On Friday I thought I'd post something about the bioswales at Manzanita village that I briefly mentioned in class. However I couldn't actually find any particularly good links online.

      Today I open 93106, the weekly faculty and staff newspaper to find an article about the restoration project and the bioswales - Restoration Project Provides Model for Future Environmental Efforts.

      The principal challenge of the restoration was creating an ecologically functional habitat in such close proximity to an urban environment. If untreated, fertilizers from the courtyard lawns and seagull guano from the residence hall roofs are washed into the ocean and nearby lagoon during rainstorms. This can cause algal blooms that are unsightly and can smother the fish.
      CCBER used the excess nutrients in the water to its advantage by creating bioswales — vegetated channels that use plants to purify water runoff before it flows into the nearby lagoon. More than 1,300 feet of bioswales treat some 75 percent of Manzanita’s storm water runoff.

      Friday, May 29, 2009

      The best stats you've ever seen

      I used this video in a different class but I think everyone should see it, and it is relevant to our discussion about human population growth.

      You've never seen data presented like this. With the drama and urgency of a sportscaster, statistics guru Hans Rosling debunks myths about the so-called "developing world."

      And the best part about it is that the software is now available at the Gapminder website so you can play with it yourself and look at changes through time of all sorts of environmental, social and geographical parameters.

      Thursday, May 28, 2009

      This semesters most intriguing title

      The Bren School of Environmental Science & Management at the University of California, Santa Barbara presents:
      Forest Rohwer, Professor, San Diego State University
      Monday, June 1, 2009, 12:30 - 1:30 p.m. Bren Hall 1414
      Playing with Snot: What can corals teach us about cystic fibrosis?

      Wednesday, May 27, 2009


      Kathy pointed me to an interesting editorial in Nature today about the recent fossil primate discovery I mentioned here last week.

      The article, entitled Media Frenzy, has the subhead:

      A hyped-up fossil find highlights the potential dangers of publicity machines.

      Take a look at the original paper in PLoS ONE, Nature's original report and today's editorial.

      Do you agree with Nature's assertion that:
      In principle, there is no reason why science should not be accompanied by highly proactive publicity machines. But in practice, such arrangements introduce conflicting incentives that can all too easily undermine the process of the assessment and communication of science.

      Do you think the authors of the original paper did anything wrong?
      Do you think the journalists who covered the story have been accurate in their reporting?

      (The image above, which is from Nature's original report, is called 'monkey-man.jpg'. This is exactly the sort of misleading hype that Nature is railing against!)

      Tuesday, May 26, 2009

      Vicars and badgers

      In the Church of England (which I'm not going to begin to explain), vicar is the title given to parish priests. Vicars wear a variety of different vestments but are typically seen in black and white robes like that in the picture. When you see a picture of a vicar, or any other priest type person for that matter, you have an image not only of that person's physical appearance but also of their role in the community.

      In Charles Elton's 1927 book on 'Animal Ecology' he says:
      "[W]hen an ecologist says 'there goes a badger,' he should include in his thoughts some definite idea of the animal's place in the community to which it belongs, just as if he had said, 'there goes the vicar.'"

      This is a very evocative illustration of the 'niche' concept.

      I'm sometimes a little reluctant to mention this to American students because I feel obliged to explain a little about vicars and badgers. European badgers are more distinctly black and white striped than their American equivalents so what Elton was saying was that we don't just think of a vicar as a person in black and white clothing, and we shouldn't think of a badger like that. We should try to think of the animals' place in the community.

      (Contrary to the opinion of some, there is no such thing as a 'giant man-eating badger'. I almost wished I had spent my life in the British military just so I could have been the person to make the following statement:

      UK military spokesman Major Mike Shearer said: "We can categorically state that we have not released man-eating badgers into the area." You can read the full story here.)

      Friday, May 22, 2009


      Who among us has not contemplated nature and been inspired to learn about the connectedness within diversity? In this sense, natural history has attracted not only the scientist, but the artist and poet; natural history has become the romantic science. The romance of natural history stems from our desire to relate to the natural world, to regain a connectedness to it, and to preserve its diversity.

      Saturdaze has partnered with the Santa Barbara Museum of Natural History and has funded a scholarship to encourage research that helps to explain one or another "entangled bank". The Saturdaze Scholarship for Natural History Research rewards exceptional students attempting to discover interactions in nature. Saturdaze and the Museum share the goal of . . .Inspiring a Passion for the Natural World

      Maximum award amount: $2,000
      Application Deadline: 15 June for 15 July scholarship award
      Award Date: 15 July

      Eligibility: (1) attended a college or university as an undergraduate in a biological sciences major in either San Luis Obispo or Santa Barbara County during the year prior to application, and (2) actively involved in research in the spirit of natural history.

      To apply online visit the Saturdaze website.

      Thursday, May 21, 2009

      More Cohen

      Joel Cohen, who wrote 'How many people can the earth support', and is different to the Joel Cohen who is half of the Cohen brothers movie directing team (Fargo, The Big Lebowski, No Country for Old Men etc) had a recent Commentary published in Nature suggesting one important step we could make in controlling world population growth: Make Secondary Education Universal. It's a short article, only a couple of pages, and well worth a quick read.

      Universal, high-quality primary and secondary education is achievable within 25 years. Educating all children well is a worthwhile, affordable and achievable strategy to develop people who can cope with problems foreseen and unforeseen.

      And just to follow up on class, if everyone on earth lived an American lifestyle then, under current technology at least, it seems unlikely the earth could support more than 2 billion people. As I mentioned, and you are hopefully aware, we are currently heading towards 7 billion....

      Tuesday, May 19, 2009

      For Thursday

      For this Thursday please bring your laptop (if you have one, no need to buy one specially.....) and download the Populus program onto it if you didn't already do this last quarter.

      Also, please complete the list of topics that Claudia handed out and bring that to class. If you'd rather complete this electronically the form is here.

      If you look at CNN online you may have seen this report on the homepage today:
      Scientists piece together human ancestry
      Scientists hailed Tuesday a 47-million-year-old fossil of an ancient "small cat"-sized primate as a possible common ancestor of monkeys, primates and humans. Scientists say the fossil, dubbed "Ida," is a transitional species, living around the time the primate lineage split into two groups: A line that would eventually produce humans, primates and monkeys, and another that would give rise to lemurs and other primates.

      What I noticed particularly about this report was that CNN linked directly to the original research paper in PLoS ONE: Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. Another victory for Open Access publishing.

      Monday, May 18, 2009


      Not exactly the most surprising prediction but in a blog posting last year, Most obvious nickname ever..., I wrote:
      'If there was a regular 140m or 150m event I imagine the world land speed record would be set over that distance.'

      Unless I'm reading the wrong news sources the news that a human has just exceeded 25mph in an athletic event for essentially the first time ever has received remarkably little attention.

      On a cold and rainy Sunday in Manchester, England, on a specially laid out 150m track on the streets Usain Bolt made it look easy. His time, 14.35 works out at 10.453 m/s or 23.38mph. even more impressively the final 100m of the 150m (ie a 100m with a flying start) was timed at 8.72. This works out to be 11.468m/s or 25.65mph.

      Friday, May 15, 2009

      EEMB job candidate talk

      Professor Edward McCauley (University of Calgary) is a candidate for Director of the National Center for Ecological Analysis and Synthesis (NCEAS) and for appointment as a Professor in EEMB. He will give a talk in EEMB on Monday 18th May.

      Theory and Experiment in Ecology: A balance of forces
      Monday 18 May, 12 noon, MSRB Auditorium

      Ed's interests cover many areas of ecology, so this should be of broad interest.

      Thursday, May 14, 2009

      Talking Prairie Dogs

      In this week's New Scientist magazine is a report of a paper just out in the journal 'Animal Cognition': Prairie dog alarm calls encode labels about predator colors.

      Prairie dogs talk some pretty colourful talk. Not only do their alarm calls tell others about the type and size of approaching predators, but it seems they can also warn of the hue of an imminent threat.

      Gunnison's prairie dogs are burrowing rodents that live in the grasslands of North America. Con Slobodchikoff of Northern Arizona University in Flagstaff and his colleagues had previously shown that they produce different alarm calls in response to humans, coyotes, domestic dogs and red-tailed hawks. For humans, the calls even vary according to the person's size. They react differently towards each call, all hiding if approached by humans, whereas only nearby animals hide if it is a hawk.

      In the latest study, the team recorded the alarm calls as three similar-sized women wearing blue, yellow or green T-shirts walked past the prairie dogs 99 times. They found that the calls were similar for green and yellow T-shirts, but significantly different for blue.

      Prairie dogs have dichromatic vision, a form of colour blindness where only two of the three primary colours can be discerned. As they are sensitive to blue and yellow, this explains why they cannot distinguish green. Still, the fact that they can "talk" colour "probably makes this the most sophisticated animal communication system that has been decoded so far," says Slobodchikoff.

      Wednesday, May 13, 2009

      How the Immune System Works

      The immune system IS amazing. My ONLY goal in the brief time we have to talk about it is to make you want to learn more about it. Whilst there are several courses here that you can take there is also a book that I can highly recommend.

      If you want something that falls between the single chapter in an introductory biology textbook and the hefty tome of an immunology text then I can recommend 'How the Immune System Works' by Lauren Sompayrac. If you want to learn more about the immune system, including some cutting edge stuff, but don't want to take a whole course then this impressively slim book (144 pages for $30) is the way to go.

      I'm linking to Amazon so you can see the impressive reviews this book has collected: 32 of the 39 reviews are 5 star. There are several other books in the series. 'How Cancer Works' by the same author is also pretty good. These are slim books, it isn't hard to read a chapter a day and in about a week you can have a pretty good understanding of the immune system or cancer.

      Tuesday, May 12, 2009


      I briefly mentioned Regulatory T cells today as a relatively newly discovered (or rediscovered depending on your viewpoint) part of our immune system. These are also known as suppressive T cells, but the cool kids just call them Tregs. (Like T. rex.....)

      Here are a couple of recent papers that will give you an entry into the literature in this field.

      The Journal Immunology had a series of review articles in 2007 to mark their 50th anniversary. One of these was entitled:
      Special regulatory T cell review: The suppression problem!
      The concept of T-cell mediated suppression evolved more than 30 years ago. At that time it spawned many claims that have not stood the test of time. The rediscovery of suppression phenomena and regulatory T cells over the past 15 years created schizophrenic responses amongst immunologists. Some claimed that the new proponents of suppression were, once again, bringing immunology into disrepute, whilst others have embraced the field with great enthusiasm and novel approaches to clarification. Without faithful repetition of the "old" experiments, it is difficult to establish what was right and what was wrong. Nevertheless, immunologists must now accept that a good number of the old claims were overstated, and reflected poor scientific discipline.

      Tregs and allergic disease
      Allergic diseases such as asthma, rhinitis, and eczema are increasing in prevalence and affect up to 15% of populations in Westernized countries.
      In summary, current evidence suggests that human CD4+CD25+ T cells and IL-10–producing Tregs have the capacity to suppress Th2 responses to allergen and that this process may be defective in those who develop allergic sensitization.

      Monday, May 11, 2009

      Undergraduate Research Colloquium

      Each year the College of Letters and Science celebrates undergraduate research at UCSB by hosting a colloquium where students from all over campus showcase their research activities. This year's Undergraduate Research Colloquium is being held, Thursday, May 14, 11:30 to 2:00 p.m. in the Corwin Pavilion.

      This year's event is showcasing 175 poster presentations. Projects from all colleges, and disciplines - the arts, humanities, social sciences, sciences and engineering - will be presented.

      This is a great opportunity to see some of the research undergraduates are involved in at UCSB. It's also a good chance to see how they present that research and to give you some ideas for when you come to present your own work.

      Thursday, May 7, 2009

      Monday Seminars

      UCSB Distinguished Lecturer Series in Neuroscience:
      The Brain's Mechanisms for Mapping and Remembering the Spatial Environment
      Drs. Edvard & May-Britt Moser Kavli Institute for Systems Neuroscience, NTNU, Trondheim, Norway
      Monday, May 11, 2009 @ 1:00pm Marine Science Institute Auditorium, Marine Science Building 1302


      And the Monday CCBER Conservation & Restoration Seminar for May 11th will be Sarah Chaney from Channel Islands National Park who will speak on:
      Islands in the Fog: The Missing Cloud Forests of Santa Rosa Island

      6-7pm, Monday May 11th, Cheadle Classroom, 1013 Harder South

      Science Roundup

      A jawfish at Riviera Beach, Florida displaying the eggs he'll hold in his mouth till they hatch. photograph by Steven Kovacs of Clewiston, Florida, first place winner Marine Animal Portraiture in National Geographic's Annual Underwater Photos competition.

      As we get towards the end of our fabulous tour of biology it's time to catch up with some advances and events that have taken place during the last few months. A brief snippet from each and a link. Enjoy.

      Rise Of Oxygen Caused Earth's Earliest Ice Age
      Geologists may have uncovered the answer to an age-old question - an ice-age-old question, that is. It appears that Earth's earliest ice ages may have been due to the rise of oxygen in Earth's atmosphere, which consumed atmospheric greenhouse gases and chilled the earth.

      Scaling of Soaring Seabirds and Implications for Flight Abilities of Giant Pterosaurs
      Giant pterosaurs, colossal winged reptiles that lived alongside the dinosaurs, have long been considered the heaviest animals ever to take to the skies. But new research suggests that the notion of giant pterosaurs soaring over Earth simply doesn't fly.

      Congruence of morphologically-defined genera with molecular phylogenies
      Scientists using molecular techniques assert that genetics more accurately determines evolutionary relationships than does a comparison of physical characteristics preserved in fossils. But how inaccurate, really, were the fossils? Jablonski and Finarelli compared the molecular data to data based on the kinds of features used to distinguish fossil lineages for 228 mammal and 197 mollusk lineages at the genus level.

      No matter how they looked at it, the lineages defined by their fossil forms "showed an imperfect but very good fit to the molecular data," Jablonski said. The fits were generally far better than random. The few exceptions included freshwater clams, "a complete disaster," he said.

      Jablonski interprets the results as good news for evolutionary studies. The work backs up a huge range of analyses among living and fossil animals, from trends in increasing body size in mammal lineages, to the dramatic ups and downs of diversity reported in the fossil record of evolutionary bursts and mass extinctions.

      Bigfoot hobbit could be ancient island human
      Two studies add a new twist to the plot. One claims that the skeleton's ape-like feet push back its ancestry near the dawn of Homo. Another argues that the hobbit is a later offshoot of Homo erectus, dwarfed by aeons of island isolation.

      Swine Flu: the Predictable Pandemic
      New Scientist has a collection of articles on Swine Flu that are really good at answering the various questions you might have

      Wednesday, May 6, 2009

      Multivitamins and pill wranglers

      The post below reminded me about the big multivitamin study that was carried out earlier this year that I posted a blog article about last quarter: Magic pill.

      (T)he study was so large and looked at so many aspects of health that it had a lot of statistical power to detect even a small effect. The study involved more than 160,000 women roughly split between those that took regular multivitamins and those that didn't. Eight years later they looked at a variety of disease incidences, including cancer (almost 10,000 cases) and cruder measures such as total mortality (again almost 10,000 deaths). Not even a hint of a difference.

      This confirmed earlier studies by the NIH in 2006:"Most of the studies we examined do not provide strong evidence for beneficial health-related effects of supplements taken singly, in pairs, or in combinations of three or more." And by the United Kingdom's Food Standards Agency in 2007: "Vitamin and mineral supplements are not a replacement for good eating habits and supplements are unnecessary for healthy adults who eat a balanced diet."

      For an interesting counterpoint consider this posting, Where's my pill wrangler?, from last year.

      'Kurzweil does not believe in half measures. He takes 180 to 210 vitamin and mineral supplements a day, so many that he doesn't have time to organize them all himself. So he's hired a pill wrangler, who takes them out of their bottles and sorts them into daily doses, which he carries everywhere in plastic bags.'

      Kurzweil believes that radical technological advances will be made throughout the 21st century, and that many of those advances will benefit the field of medicine. Kurzweil has thus focused himself towards following a maximally healthy lifestyle to heighten his odds of living to see the day when science can make him immortal. His opinion on vitamin and health supplements is to take virtually anything that MIGHT have a positive effect even if the evidence is weak PROVIDED that the evidence is strong that it does no harm.

      Tuesday, May 5, 2009

      Carrot power

      Many people believe that carrots are good for their eyesight. There is a germ of truth in this in that carrots are indeed a good source of vitamin A, and vitamin A is required for, among other things, correct functioning of the visual system. However just because they are required for correct functioning does not necessarily mean that eating more of them will improve your vision. The origin of the myth that carrots are good for your eyesight dates back to World War II and the Battle of Britain that occurred in 1940 and marked a turning point in the war. The Battle of Britain refers to the air battle between the German and British air forces for air superiority. A German victory would have permitted a cross channel invasion of England.

      Although the principles of Radar had been known for a long time it was British scientists who produced the first working system, enabling ground controllers to direct British planes to intercept German planes in poor visibility and at night. In order to maintain their advantage the British spread the rumor that their pilots were being successful because of their extraordinarily good eyesight. A feat that was achieved by the mass consumption of carrots. This rumor affected both the Germans and the British. Due to the blackout at night and the frequent requirement to move to air-raid shelters people were keen to improve their night vision and carrots were readily available from allotments and gardens.

      I do not know whether the Germans fell for this story. There are a few suspicious parts to it that may not have been fully understood at the time. Or maybe this was a sneaky part of the plan, to encourage German pilots to poison themselves with large amounts of Vitamin A. As Claudia pointed out today, if you want to propose ingesting large amounts of a vitamin you might be better off picking one that is water, rather than fat, soluble. As vitamin A is fat-soluble, disposing of any excesses taken in through diet is much harder than with water-soluble vitamins B and C. As such, vitamin A toxicity can result. This can lead to nausea, jaundice, irritability, vomiting, blurry vision, headaches, muscle and abdominal pain and weakness, drowsiness and altered mental status. Too many carrots will also cause you to turn orange from the accumulating beta-carotene. Another good source, in fact a much better source, of vitamin A is liver. Too much liver is even worse and can kill you quite quickly as Arctic explorers who were reduced to eating polar bear and sled dog liver discovered. Polar bears have very high concentrations of vitamin A in their liver and the native Inuit were well aware of this fact:

      After killing a bear, the Inuit ate the meat and used the fur to make warm trousers for men and kamiks for women. An average polar bear would yield three pairs of trousers and one kamik. The only part of the bear that was not used was the liver. This was immediately thrown out, as it could make even the sled dogs violently ill.
      From Polar Bear International.

      Monday, May 4, 2009

      Seminars this week

      Dr. Bill Fagan
      Riverine Landscapes: Exploring Connectivity, Extinction Risk, and Biogeography in an Alternative Geometry.
      Monday, 4-5pm in MSRB Auditorium

      Or go crazy and go downtown,

      Impacts of rising carbon dioxide and tropospheric ozone on the growth and productivity of trees
      Victoria Wittig, University of Illinois at Urbana-Champaign
      NCEAS Ecolunch seminar.
      Thursday, May 7, 12:15 PM
      GENERAL INFORMATION: Ecolunches are Thursdays, at 12:15 pm (brown bag
      lunch) National Center for Ecological Analysis and Synthesis, 735 State
      St., Suite 300, Santa Barbara, CA 93101 Phone: (805) 892-2500

      and a big one coming up in two weeks:
      Dr. Edward McCauley, candidate for the NCEAS Director position.
      Seminar - Theory and Experiment in Ecology: A balance of forces
      Edward McCauley, Ph.D., Department of Biological Sciences, University of Calgary
      Date: Monday, May 18
      Time: 12:00pm - 1:00pm
      Location: MSRB Auditorium, Marine Science Institute

      Friday, May 1, 2009

      Fetal hemoglobin and sickle cell anemia

      Speaking of hemoglobin, I find it amazing that newborn babies have a different type of hemoglobin, fetal hemoglobin, that will be completely replaced by the adult form within a few weeks of birth. The fetal hemoglobin binds oxygen more readily than the adult form, thereby allowing the developing fetus to obtain access to oxygen from the mother's bloodstream via the placenta. The reactivation of fetal hemoglobin synthesis in adults has been used to treat sickle-cell disease since 1995.

      When fetal hemoglobin production is switched off after birth, normal children begin producing hemoglobin A. But children with sickle-cell disease instead begin producing a long, slender form of hemoglobin called hemoglobin S. This variety of hemoglobin causes red blood cells to change their shape from round to sickle-shaped, which have a greater tendency to stack on top of one another and crowd blood vessels causing a variety of problems. If fetal hemoglobin remains the predominant form of hemoglobin after birth, however, these problems can be reduced.

      Nature Medicine covered the breakthrough discovery of fetal hemoglobin promoting drugs such as hydroxyurea in 1995: Sickle cell paths converge on hydroxyurea.

      Wednesday, April 29, 2009

      Anticipatory Thermogenesis

      Yesterday Claudia mentioned that although control of the autonomic nervous system is generally considered to be involuntary we can, in addition, actually consciously influence many of these systems.

      Posting a reference to Tim Noakes yesterday reminded me of his recent work with Lewis Gordon Pugh, a British 'Environmentalist, Explorer and Swimmer.'

      Pugh is most famous for his cold water swims which he usually does to publicize global warming and the melting ice-caps. These swims are done without a wetsuit, in water as cold as zero degrees centigrade (because of the salt seawater freezes a couple of degrees below zero).

      An article in New Scientist magazine a few months ago reveals some of the science behind Pugh's remarkable ability. Most interesting was the discovery by his trainer, the aforementioned Tim Noakes, that Pugh is able to consciously raise his body temperature.

      As the swim gets closer, he psychs himself up by listening to music by the likes of Eminem and P. Diddy. In the minutes before entering the water, Pugh recalls these emotions and is able to raise his core temperature, without doing any physical exercise, to 38.4 °C. That's an extraordinary 1.4 °C above his normal body temperature. Such "anticipatory thermogenesis" has been observed before, but not to such a high degree.

      You can read the actual paper in the appropriately named 'Journal of Thermal Biology': Body temperatures during three long-distance polar swims in water of 0–3 °C.

      Pugh appears to have reached some of the limits of the human body:

      In 2007 he swam 1 kilometre in the coldest water yet - a glacial -1.7 °C - at the geographic North Pole.

      "When I went below 0 °C the cells in my fingers started to freeze. It took another four months before I could feel my hands again," he says. After reaching his goal of swimming both in the Arctic and in Antarctica, Pugh has for now hung up his towel.

      Tuesday, April 28, 2009

      Muscle pain - four recent(ish) papers and one new class

      A good question today about why your heart never aches after exercise - after all, a good bout of exercise works your heart just as much, if not more, than any other muscle.

      There's a simple answer, the heart doesn't have the same type of pain receptors as the muscles, but a fuller answer is much more interesting and shows some surprising gaps in our knowledge.

      There are two types of muscle 'pain' associated with exercise. There is fatigue during exercise, and we don't really know what causes that, and there is pain after exercise (DOMS or Delayed Onset muscle Soreness), and we don't really know what causes that! The cause of fatigue is a pretty hot topic. One theory is that it is caused by a problem with the calcium flow inside muscle cells. One of the functions of calcium is to help control muscle contractions. Recent research published in PNAS found that after extended high-intensity exercise, small channels in the muscle cells begin to leak calcium, which leads to weakened muscle contractions. This leaked calcium also stimulates an enzyme that attacks muscle fibers and also leads to fatigue. It is really surprising to me that such a basic phenomenon is still fairly unknown.

      DOMS is thought to be caused by a breakdown of muscle fibers and microscopic tears in muscle tissue that occurs as a result of exercise. This typically occurs 1 to 2 days after exercise, particularly if the exercise is new or extreme. There is also evidence that DOMS is more extreme if the muscle movement is eccentric - that is the muscle elongates whilst under tension (eg lowering a weight, starting out with your hand by your shoulder and gradually lowering the weight will produce an eccentric contraction of the biceps muscle).

      It used to be thought that lactic acid was involved in both these phenomena but recent evidence suggests that lactic acid may have been unfairly blamed for years and that it may play a more useful role.

      In both these cases actual pain is probably caused primarily by swelling which puts pressure on nerves and produces the sensation of muscle pain.

      Although the heart does not have the same type of stretch receptor that registers this type of pain it does have some pain receptors. Strangely enough it has the same type of nerve receptors that register the burning sensation from the capsaicin in hot peppers. These are the receptors that are thought to cause the sensation of chest pain from a heart attack. The heart may be less vulnerable to DOMS since it does not undergo eccentric contraction.

      All of this is somewhat complicated by the role of the brain. Obviously it is in your interest to stop exercising before damage occurs to your muscles, and, in particular, to your heart. Tim Noakes, a South African sports scientist, has renewed interest in a rather old theory, that Noakes calls the 'Central Governor Model', that the brain is the primary organ that dictates how fast, how long, and how hard humans can exercise.

      As you can tell I find this whole intersection of physiology and exercise very interesting. So I have bitten the bullet and next quarter (ie Fall 2009) I will be teaching a CCS class on Endurance Physiology. This will be a seminar format class where we read and discuss papers very much like those listed above and look critically at the evidence for and against various theories and the implications these have for the way people train for what I have generally termed endurance events (swimming, cycling, and running or, for those crazy enough, all three). Loosely inspired by the fact that for the first time in over 25 years Santa Barbara will have a large Marathon event in the fall of 2009.

      Monday, April 27, 2009

      End the University as We Know It

      Check out this Op-Ed, entitled 'End the University as We Know It' from the New York Times yesterday.

      For many years, I have told students, “Do not do what I do; rather, take whatever I have to offer and do with it what I could never imagine doing and then come back and tell me about it.” My hope is that colleges and universities will be shaken out of their complacency and will open academia to a future we cannot conceive.

      How many?

      Dr Meg Lowman is the EEMB Seminar Speaker today (Monday 27th), 4:00 pm in the MSRB Auditorium in the MSI Building.

      "Plant-insect interactions in tropical rain forest canopies - 10 million or 100 million species?"

      Dr Lowman is Professor of Biology and Environmental Studies and Director of Environmental Initiatives, New College of Florida. Meg pioneered the science of forest canopy ecology, helping to develop the current techniques for canopy access and using them to study processes that maintain biodiversity in tropical forest canopies. Her most recent work focuses on environmental education and outreach, the role of science in environmental policy, and the development of research coordination networks (especially NEON).

      Friday, April 24, 2009

      More Llama

      Hopefully some of you braved the hippies to see the Dalai Lama today. In other Llama related news BoingBoing had a great article today on how Llamas are involved in the war on terror - Llamas: Nature's Cute & Fluffy Crusaders Against Bioterrorism.

      Llama blood may one day be able to help soldiers, scientists and city officials set up an early-warning system against the tiniest weapons of terror--biological agents like anthrax and smallpox. Authorities have long worried that, were these diseases to get loose, it would be difficult to know anything was wrong until innocent people started dying. Llama blood might provide a better detection method.

      How? Antibodies, the tiny molecules that float around in the bloodstreams of people and almost all animals. Antibodies keep a sort of "memory" of all the diseases, allergens and other foreign invaders your body has come into contact with. If the same infiltrator shows up again, the antibodies can match it up with their stored records and immediately know how to fight it.
      For a while now, scientists have used genetically altered antibodies to help ID and treat specific diseases. But these techniques always ran into a common problem: Antibodies were just too delicate to be of much use outside a lab or hospital setting. Enter the llama.

      According to news stories about the research, llamas have extraordinarily tough and hardy antibodies, capable of sustaining exposure to temperatures as high as 200 degrees F. This discovery gave the researchers the idea to develop sensors, based on llama antibodies, that could be distributed to soldiers in a war, or around cities back home. Modified to be specifically on the lookout for likely-to-be-weaponized diseases, these sensors could pick up signs of a biochemical attack before victims started arriving at the hospital.

      Thursday, April 23, 2009

      Job Seminar

      Jessica Tyler from the  Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine - and a faculty recruitment candidate  - will be speaking today (Thursday) at 3:30  in the Rathmann Auditorium in LSB on:

      "Epigenetic Regulation of Gene Expression, DNA repair, aging and cancer"

      Wednesday, April 22, 2009

      Robot Scientist

      If you've been in a research lab you can't have failed to notice not only how much expensive looking equipment there often is, but how much of it is linked together these days. Lots of machinery either comes with a computer or is later linked to one in the lab to automate data entry.

      It's only a couple of steps from there to linking together all your equipment, adding in some simple algorithms for how the scientific process works, and you can go hang out on a beach whilst your lab equipment does its own experiments.

      Sounds a bit futuristic? Nope, a recent paper in Science entitled 'The Automation of Science' describes just such a scenario. Scientists in England developed a robot named Adam to identify genes involved in yeast metabolism. Adam formulates hypotheses about the origins of enzymes for which scientists have been unable to identify the encoding genes. The robot then plans and executes experiments to test its hypotheses--selecting yeast mutants from a collection, incubating cells, and measuring their growth rates. Adam came up with 20 hypotheses about genes encoding 13 enzymes, 12 of which it confirmed.

      There's a commentary on the paper in Science, the story was picked up by the media, but the best comment is in a New Scientist report:

      'Will Bridewell, an artificial intelligence researcher at Stanford University in Palo Alto, California, says Adam is operating only at the level of a graduate student. '

      Tuesday, April 21, 2009

      Oliver Sacks

      Don't forget that we will meet for class at 8.30 on Thursday and that we will be in room 136 in CCS.

      We will finish at ~9.50 so that you can attend Oliver Sack's talk in the Old Little Theater.

      If you haven't read any of is work, take a look around his website and check out a couple of interesting recent articles, one in wired magazine on hallucinations, one from the New Yorker about music and amnesia, and an interview in Discover magazine: Your Brain on Music, Magnets, and Meth.

      Monday, April 20, 2009

      Spatial and Temporal trends in global malaria

      The UCSB brown-bag forum on spatial thinking Presents:
      Kevin D. Lafferty, US Geological Survey
      Marine Science Institute, University of California, Santa Barbara
      Spatial and Temporal trends in global malaria: How do climate change and economics interact?
      Ellison Hall 6824, 12:00 p.m. Wednesday, 22 April 2009

      Abstract. Malaria is the most important infectious disease facing humans. Although it is largely a concern in tropical developing countries, a century ago its distribution extended well into upper latitudes presently occupied by developing countries. Because temperature and precipitation affect mosquito vectors and the plasmodium disease agent, transmission depends on climate. Projected climate changes may therefore alter where malaria will be a problem in the future. The discussion will briefly describe the ways that geographers have used spatial data to project future climate envelopes for infectious disease. It will then consider the relative importance of covariates that help explain a portion of the variation in transmission. By analogy, a paper by Kuhn (PNAS 2002) shows that wetland destruction and cattle farming do a better job explaining historical temporal variability in malaria in Britain than does climate variability. The main purpose of the discussion will be to pose the question of how to partition the effects of climate and economics on the spatial and temporal variation in malaria at the global scale. Knowing the relative roles of these factors would greatly help explain current patterns of transmission as well as identify future challenges and opportunities for diseases control.