Monday, December 5, 2011

Native Plant Christmas present

Falling behind on your holiday shopping? Want a local and unique gift for the botanist/gardener/naturalist/outdoor enthusiast in your life? Check out CCBER's Native Plants & Habitats of UCSB Campus field guide!

With funding generously provided by the AS Coastal Fund, the newly-revised 4th edition now contains many new pictures, insets and additional
descriptions to help in your quest to identify the native plants and habitats on our beautiful campus.

If you're interested in purchasing a book, the price is $14.43 each, including tax. Please have exact change or a check payable to the U.C. Regents.

The books are available for purchase at Harder Stadium South, Rm. 1009. The best times to come are Monday - Friday, from 1pm-5pm. For alternative times, please contact and we will try to accommodate your schedule. Sorry, no gift-wrapping available...

Happy Holidays!


Wednesday, October 19, 2011

Sage Center Distinguished Fellow talks

Armand Leroi from Imperial College London is the Sage Center Distinguished Fellow for October and November. He is a developmental biologist and science historian. He is giving a series of lectures over the next few weeks. All talks are at 3 p.m. in Bren 4016

October 24--The Experimental Evolution of Music

People all over the world have very different kinds of music. Why? It seems to me that the diversity of music needs to be studied rather as biologists study the diversity of organisms. In this lecture, I'll talk about several ways in which evolutionary analyses can give insights into the diversity of musical forms.

October 31--Aristotle and The Search for the Soul
Who was the greatest biologist of all times? For most it is Darwin; for me it is Aristotle. Although few read him, his scientific work -- there is no other word for it -- was vast and deep. It is a complete biology. In this lecture I will argue that Aristotle still has things to tell us.

November 7--Mutants — and what to do about them
Should you get yourself sequenced? Should you get someone else sequenced? What then? In this lecture I will discuss the burden of mutation that the human species carries and its implications for the neo-eugenic society.

Wednesday, October 5, 2011

The virtues of waiting, procrastinating and avoiding conflict

Fred Adler will be visiting UCSB next week and giving the EEMB departmental seminar on Monday, Oct 10 at 4 pm in the MSRB Auditorium. The title is "The virtues of waiting, procrastinating and avoiding conflict."

Fred's research spans a huge range of topics in ecology and evolutionary-ecology, much of it relating infectious disease and natural enemies to the behavioral ecology and population dynamics of the interacting species. See  for more information.

Title: The virtues of waiting, procrastinating and avoiding conflict

Ants are among the most successful organisms on earth, not least because they have created an impression of being hard-working automatons who put even graduate students to shame. I will show that ants might
in fact succeed in part through waiting for other individuals to make the hard decisions and by avoiding stressful situations. Unfortunately, I have not quite gotten around to proving these results, but will give a sketch of how they could be demonstrated.

Tuesday, September 20, 2011

Vertebrate Curatorial Internship Fall 2011

Each week throughout the quarter we will focus on a specific area of museum curation, such as the importance of collections, documentation, methods of preservation, taxonomic nomenclature and labeling, and cataloging specimens.  Students will have the opportunity to prepare and process a variety of specimens using several different methods of preservation. Students who complete this introductory internship will be eligible for additional intern positions in vertebrate collection management at CCBER during subsequent quarters.

The class is held weekly from 2:00-5:00 pm unless otherwise noted with an asterisk.  On those dates, students will travel by UCSB van to other museums for the class lesson.  Please allow 3 hours plus travel time of 1 hour each way (approximately 1:30-6:30 pm).

To participate, students must attend the first class orientation and may not add the class after Sept. 28.

ES 192/Geog 193 requirements: Upper division standing, Must have a minimum 3.0 GPA

EEMB 184 requirements: Upper division standing, Must have a minimum 2.5 GPA

CCS students check with department contact

FIRST MEETING: Introduction

Wednesday September 28, 2011 at 2:00 pm

Harder Stadium South, Building 578, Room 1013

Maximum enrollment:  12

CCBER Restoration Internship Fall 2011

Work to restore UCSB campus natural areas for local plants and wildlife through an internship with CCBER for fall quarter 2011. Students will gain valuable hands-on field experience restoring native wetland, coastal sage scrub, grassland and oak woodland habitats. Internship activities include plant propagation, seed collection, planting, weeding, and ecological monitoring. Learn about local plants and animals, earn course credit, meet environmental professionals in your community, and enjoy a beautiful outdoor working environment!

All interns must complete the following for 1 unit of credit: 3 hours of fieldwork per week, creation of a plant collection notebook and restoration journal. To earn course credit, you must be an EEMB, ENVST, GEOG or CCS student and meet the minimum requirements for your department. Once the 10 week internship program has been completed, there may be paid opportunities for the following quarter. Volunteer opportunities are also available in museum curation, wildlife research, and restoration!

ES 192/Geog 193 requirements:  Upper division standing. Must have a minimum 3.0 GPA

EEMB 184 requirements: Upper division standing,Must have a minimum 2.5 GPA

CCS students check with department contact

FIRST MEETING: Introduction and internship/volunteer sign up

Friday September 30, 2011 at 5:00 pm

Harder Stadium South, Building 578, Room 1013

For more information, contact:  Heather Liu-

805- 893-2401

Scuba club

Be there or be terrestrial.

Monday, September 12, 2011

Moorea Bicode

After spending this summer at Gump Station I thought this National Geographic report was interesting...

Monday, August 29, 2011

New Guidebook to Native Plants & Habitats of UCSB

The Cheadle Center for Biodiversity and Ecological Restoration (CCBER) is
proud to announce that the 4th edition of the Native Plants and Habitats
book is for sale!

With funding generously provided by the AS Coastal Fund, the updated book
now contains many new pictures, insets and additional descriptions to help
you in your quest to identify the native plants and habitats on campus.

If you're interested in purchasing one book (or several), the price is
$14.43 each, including tax. Please have exact change or a check payable to U.C. Regents.

The books are available for purchase at Harder Stadium South, Rm #1009. The best times to come are Mon.-Wed and Fri. from 1pm-5pm.

Friday, June 3, 2011

The Power of Poop

This is the podcast I was talking about that discusses a few areas of research into fecal matter transplants.

Thursday, June 2, 2011

Memory "tricks" - what we think we know and what's really happening...

John's post about the invisibile gorilla reminded me to post the video about the "door" examples in which someone initiates a conversation with a subject/bystander and then is switched out in the middle - does the subject notice that he or she is now speaking with a different person?

Check out this video by "psychological magician" Derren Brown who demonstrates examples of "change blindness" or the Person-swap experiment.

Another example is given on the page John listed (the invisible under the heading "The original "door" study" .

Holy Batfish

The Louisiana Pancake Batfish seems like a good image to finish with. Your tour through biology is now over but your adventure IN biology is just beginning. (Mmmm, motivational).

The blog is going into its summer diapause but will be back in the Fall for a new year of fun facts, relevant research and interesting opportunities.

Wednesday, June 1, 2011

National Running Day

Given all the times we've mentioned obesity and our sedentary lives this quarter I would be remiss if I didn't point out that today was National Running Day. It's a bit late today given that it's 11:46pm but there's always tomorrow...

Tuesday, May 31, 2011

Top Ten Evil animals

Time magazine has a 'Top Ten Evil Animals' list, and amidst the usual suspects (rats, bed bugs, tapeworms, humans etc) is the somewhat surprising panda.

The writing made me laugh:

What most people don't realize is that pandas have us duped. They are the one species in the animal kingdom that seem to live outside the realm of Darwinian science. Most creatures in the universe follow German philosopher Friedrich Nietzsche's axiom: a creature "will strive to grow, spread, seize, become predominant... because it is living and because life simply is will to power." Pandas, though, didn't seem to get the memo. They have no will to live or reproduce. To this day, scientists have to perform grotesque procedures to keep the panda population from collapsing into oblivion. Forget about the fact that pandas are mean-spirited, mate-abusing, progeny-mauling, deviant monsters. Forget about the fact that these hoodlum bears have conned humanity with their supposed cuteness. The most evil thing about pandas? The cunning with which they expose the stupidity of us humanoids.

The invisible gorilla

In case you haven't seen this. Sorry if I gave the ending away. I didn't realize that the guys behind this, and similar, experiments have a book - perhaps not surprisingly entitled The Invisible Gorilla - how our intuitions deceive us. The website has a lot more videos. The paperback edition is out on June 7th and I think I'll add that to my summer to do list.

Monday, May 30, 2011

'Duh' Science

In the LA Times today - 'Duh' science: Why researchers spend so much time proving the obvious
Alcohol increases reaction time; obese men have lower odds of getting married. A waste of research money? Not necessarily, scientists say.

It's actually not a bad little article and it does make some interesting points.

Sunday, May 29, 2011

How high?

How high is a normal room?

It's not a trick question. Just estimate the height of a typical room. Okay? Now read on.

Students who struggle to learn mathematics may have a neurocognitive disorder that inhibits the acquisition of basic numerical and arithmetic concepts, according to a new paper. Specialised teaching for individuals with dyscalculia, the mathematical equivalent of dyslexia, should be made widely available in mainstream education, according to a review of current research published in the journal Science - Dyscalculia: From Brain to Education

 But before you decide that this is what you have bear in mind that these are some of the common indicators of dyscalculia:
(i) carrying out simple number comparison and addition tasks by counting, often using fingers, well beyond the age when it is normal, and (ii) finding approximate estimation tasks difficult.

An example of i) is if in calculating which is the larger of two playing cards showing 5 and 8, you count all the symbols on each card. An example of ii) would be if you estimate the height of a normal room as two hundred feet.

Thursday, May 26, 2011

Shocking research

In the news today - sitting on your ass all day can cause you to gain weight. More shocking news at 11.

A new study reveals that the rise in desk jobs over the past 50 years may play a significant role in the obesity epidemic.

Actually, like most of biology, the actual study (in PLoS ONE) is a little more interesting in that they estimate that the

'daily occupation-related energy expenditure has decreased by more than 100 calories (in the last 50 years), and this reduction in energy expenditure accounts for a significant portion of the increase in mean U.S. body weight for women and men over the last 5 decades.'

This is in contrast to previous studies that have largely focused on food consumption.

Also of interest is the note that:

'Our estimation of a reduction of more than 100 calories per day in occupation-related energy expenditure over the last 50 years would have been adequately compensated for by meeting the 2008 federal physical activity recommendations of 150 minutes per week of moderate intensity activity or 75 minutes per week of vigorous intensity activity....when physical activity is assessed with accelerometers the number of Americans that achieve the physical activity recommendations falls to 1 in 20.'

Wednesday, May 25, 2011

Recommended courses

The CCS Biology List of Recommended Courses

This list is intended to supplement, and not replace, advice from your faculty advisors.  I asked, in particular, for recommended upper division courses suitable for Freshmen but there are some additional recommendations here, of breadth courses and others.

Comments have been edited for minor grammar changes and factual information only (eg course names, numbers and instructors). Send additional comments or recommendations to John Latto. This list is only as valuable as you make it.

LOWER DIVISION (especially the less obvious ones)

Memory: Bridging the Humanities and Neuroscience 

MCDB 27 or French 40X or Comparative Literature 27 (3 units)  Kenneth Kosik and Dominique Jullian       Winter
Course summary
Neurosciences now ask some of the same profound questions posed by writers, artists and philosophers for centuries, thus opening
surprising perspectives on memory and morality, dreams and perception, identity and agency. This course explores this emerging concordance.
What CCS students say
The teachers, Kosik and Julien, are wonderful and worked hard to put together a curriculum bridging science and literature. The class is a great lighter addition to a schedule but there is a significant amount of non-scientific reading involved. The class requires little prior knowledge of biology and if taken through the French or Comparative Literature Departments can serve as a breadth course

Biology of Cancer

MCDB 23 (3 units)         David Kohl          Fall
Course Summary
An introduction to developments regarding the etiology and treatment of various cancers. Lectures compare normal cells and tissues with those which have become malignant. Discussion of causes, treatment, and prevention of specific cancers.
What CCS Students say
I would recommend the Biology of Cancer class, I'm sure an incoming CCS freshman could handle it.

Public Speaking

Theater 65 (4 units)          Jody Enders
Course summary
Practical and historical introduction to the art of public speaking in a variety of contexts (legal, political, corporate, artistic, dramatic, educational, etc.). Main lecture focuses on critical and historical analysis of actual speeches; lab offers practical training in performing them.
What CCS students say
While not a biology course, it is great practice for becoming a confident presentation giver--a must if working in a lab...

Introductory Physics

Physics 6A,B,C (3 units each)          Robert Geller (6A and 6B)          Fall, Winter and Spring
Course summary
A. Mechanics.
B. Heat, thermodynamics, electricity, and magnetism.
C. Electromagnetic waves, optics, modern physics.
What CCS Students say
I took Physics 6 series my first year and I would recommend that because even though its not Bio or Chem, there are definitely areas that overlap and Geller is a good teacher and fair grader. Its not too tough and I think its a good idea to have a year of college physics under your belt.


Medical Microbiology

MCDB 139 (4 units)          Diane Eardley          Fall
Course summary
Study of the characteristics of bacteria and viruses, both pathogenic and adventitious, as they are associated with diseases of humans.
What CCS students say
Great for those who feel like they already have a good mcdb intro bio background. I took it with Diane Eardley (this was her last quarter teaching), but Sang Wei (I spelled that wrong) is a good teacher and has a good sense of humor (though I've heard her tests are infernally long.

Group Studies for Advanced Students:  Cell Biology 
Group Studies for Advanced Students:  Regenerative Medicine

MCDB 194X and MCDB 194 ? (2 units)         Kathy Foltz          
What CCS students say
Definitely take a MCDB 194X with Kathy Foltz--Regenerative Medicine and Cell Organelles were both great 

Models and Experiments

CS 101       Claudia Tyler          Fall and Winter
Course summary
Students will carry out individual research projects designed at the end of fall quarter with supervision of the instructor. In addition, we will meet as a group several times during the quarter to census class experiments and to discuss the progress of independent projects. A final written report, PowerPoint presentation, or poster on research findings will be required for all students taking the course for credit.
What CCS students say
I took the models and experiments class for three quarters, it was my best academic college experience so far. I ended up participating in the undergrad research symposium at the end of the year, presenting with my group. I ended up putting a lot of work into the class, but you only get out of it how much you're willing to put in.

Ecology of Running Waters

EEMB148 (4 units)          Tom Even          Winter
Course summary
Review of literature on the physics, chemistry, and biology of running water ecosystems.
What CCS students say
I would recommend taking Stream Ecology (EEMB 148) by Tom Even. He's a very good professor and the material he covers is interesting and accessible to students who have not taken an introduction to ecology class. In Stream Ecology, there are assigned readings for discussions sections for analysis. His exams are straight forward and he tells the students exactly what the tests are like. There may be difficulty getting into the class if they don't sign up during pass 1 because he is a very popular professor.

Applied Marine Ecology

EEMB152 (5 units)          Russ Schmidt and Andy Brooks        
Course summary
Introduction to the application of ecological principles and methods to environmental problems in marine habitats. Focus on problems that are local, regional, and global in scale. Concepts illustrated with case studies.
What CCS students say
For students who are interested in marine subjects because it is an interesting class and really gets students into thinking critically about a subject that they choose for a presentation at the end of the quarter. However, the work load is higher just because the class grade is based on your preparation for a presentation and the presentation itself which is in front of the class in an auditorium.

Tropical Ecology

EEMB159 (4 units)          Tom Even          Winter
Course summary
Examination of ecological processes in terrestrial and aquatic tropical environments.
What CCS students say
I would recommend taking Tropical Ecology by Tom Even. He's a very good professor and the material he covers is interesting and accessible to students who have not taken an introduction to ecology class. The work required in Tropical Ecology is in the discussion sections where there are three (I think) different scenarios to analyze statistically in pairs and produce reports, but it is straight forward.

Conservation Ecology

EEMB 168 (4 units)        John Latto          Fall
Course summary
An introduction to the practical application of biological principles to conserving biodiversity. Covers tools and theory derived from both ecology and evolutionary biology such as metapopulation theory and population viability analysis as applied to real world examples.
What CCS students say
Conservation Ecology is a great class.

Tuesday, May 24, 2011

Multivitamins and pill wranglers take 2

I don't post too many repeats here but I think some of you may be interested in the two posts below. One the one hand there is very little evidence that multivitamins have a beneficial health effect. But on the other hand, why not take them if they might have a beneficial effect?

The first post,  Magic pill, is from 2009

(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 2008.

'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.

Monday, May 23, 2011

Crazy Sex Trick Fuels All-Male Clam Species

When biology makes it to BoingBoing by way of Wired you know that it's going be weird biology.

Nearly all Corbicula clams are clones—physically hermaphroditic but genetically male, just like their forbears. But that's not the fascinating part. Corbicula clams add new genetic material to their portfolio by, essentially, stealing eggs from other clams and dumping the maternal genome after fertilization. Most of the time, all the maternal genes get dumped. But sometimes, a few genes are kept and get incorporated into the all-male Corbicula line.

The original paper is in PNAS this week and is available here: Rare gene capture in predominantly androgenetic species.

Saturday, May 21, 2011

Infectious disease conference

 This is a very generous offer and an awesome opportunity if you are interested in the ecology of infectious disease.

We are hosting the 9th Annual Ecology and Evolution of Infectious Disease Conference at UCSB, June 18-20th:
The conference is FREE for UCSB participants.  But, if you are planning to attend the conference please register at:
(Note this is the Locals Only registration page and there is no link to this page from the main page.)
If you show up without registering:  (a) there will be no nametag for you, and (b) we will run out of programs and coffee!
Please register. We would like to get an accurate count of how many people to expect.

But, there is a $42 charge for the optional banquet/BBQ, Monday evening.
  The only event for which we are requiring UCSB participants to pay is the banquet/BBQ on Monday evening, June 20th, 5:30-8:30pm on the lawn at Manzanita Village.  The cost of the banquet/BBQ is $42 per person (this covers food and drinks).  Payments for the BBQ can be made online at the LocalRegistration page, or directly to me (Cherie Briggs, 2112 Noble Hall) or Kevin Lafferty (2038 MSRB).

Friday, May 20, 2011

Obese is the new normal

Next week Claudia will talk about diet and nutrition, so here is a rather shocking survey I saw today to get you in the mood. Now surveys have all sorts of biases but if you use the same methodology year after year then you can track changes with a degree of accuracy.

According to a survey by the International Food Information Council Foundation, which has been conducted since 2006:
  • Only 8% of Americans consider themselves to be obese even though 35% actually are.
  • The percentage of people who say they don't exercise has risen from 37% to 43% just over the last year.
That finding is interesting for a couple of reasons, Smith Edge says. First, it represents an overall drop in the number of people who think of themselves as being overweight, and second, it shows that many people underestimate how bad their weight problem really is.

Only 57% of participants say they are concerned about their weight this year, down from 70% in 2010 and an all-time low for the survey.

Those who say they are trying to lose or maintain weight is also down, 69% in 2011 compared to 77% in 2010.

“This is a somewhat ominous trend,” says David L. Katz, MD, MPH, founding director of the Yale University Prevention Research Center in New Haven, Conn.
Katz thinks the survey may be picking up signs of a “normalization” of larger body sizes. As friends and families also grow in girth, people feel OK by comparison.
“We might like to be OK at any size, but the simple fact of the matter is that we’re not,” he says. “We are getting diabetes, we are getting heart disease, we are getting preventable cancers, many of them having to do with our size, and that’s not OK. These things are happening in our children, and that’s not OK.”

You can calculate your BMI here if you are curious. 'Obese' is a medical term for those people with a BMI over 30 and is not a value judgement. Changing your weight is not rocket science, it's pretty simple biology. Unfortunately most people are looking for quick fixes and the quick fix is unlikely to last.

Thursday, May 19, 2011

Internship opportunity

If you are going to be around this summer here's a nice little opportunity to get involved with a local conservation project. Note the low time commitment and the convenient location - only about a 10 minute bike ride from campus.

LOCAL INTERNSHIPS: Habitat Restoration Maintenance -- Storke Ranch Vernal Pools

Work with a conservation biologist on this local restoration project sponsored by the Coastal Fund and the Storke Ranch Homeowner's Association.

Interns will participate in invasive plant control (weeding), vegetation surveys, and possibly some photo-documentation, seed collecting, nursery work, and planting.

This is a great opportunity to gain valuable hands-on field experience and obtain skills in plant identification and other aspects of restoration.

Contact Kelly Hildner -- or 685-3621 to request an application.

Hours/week: 2-6

Location: Storke Ranch is an easy bike ride from the university.
Positions: Volunteer internships are available.

Tuesday, May 17, 2011

The dark matter of disease

Interesting, and relevant, article in The Scientist this month:
The dark matter of disease - Scientists are beginning to unravel how non-coding DNA works across long distances of the genome to influence disease

Monday, May 16, 2011

Floral responses to global environmental change

Department of Earth Science Speakers Club May 19th, at 2:00 pm. in Webb 1100.

Cynthia V. Looy
Professor, Integrative Biology
University of California, Berkeley

Floral responses to global environmental change

Understanding patterns and processes of past ecologic crises and biodiversity decline is no longer a matter of purely academic interest. Studies of biotic change related to major extinction events may substantially contribute to predictions of the long-term consequences of the current man-induced "sixth extinction". A major part of the biomass on Earth is sequestered as terrestrial vegetation. Thus, the extensive fossil record of plants can provide insight in how terrestrial ecosystems respond to major environmental transitions. My research primarily focuses on the response of plants, plant communities and floras to environmental change during periods of mass extinction and deglaciation, and possible evolutionary consequences. I will present a botanical perspective of the collapse and recovery of terrestrial ecosystems during the end-Permian biotic crisis (250 Ma ago), and give an update of ongoing and future research on the evolution of Late Paleozoic conifers, against the background of Early Permian deglaciation and related equatorial climate change.

Please go to the following url to view the photograph that accompanies the abstract.

Let Us Eat Fish?

I came across this really awesome ocean science blog, SeaMonster, via a really great Earth Day post from the blog that a friend of mine shared on Facebook: "A letter from your mother on Earth Day"

This blog is run by a group of ocean scientists and journalists. Dr. Steve Gaines, Dean of Bren School Of Environmental Science at UCSB whose lab I work in is a part of the committee of contributors/creators. Here is more about the blog and its creators/contributors.

I meant to post another one of the posts from the blog a while ago and never got around to it. The post was about the process of peer review and might interest any of you who are going to be submitting manuscripts in the near future, or are interested in an insider's look at the peer review process. Check out: "One reason I blog: no peer review"

Those are just a few of the interesting posts on this blog. However, the SeaMonster post that inspired me to make this post on the CCS Bio blog was a very interesting dialogue between some of the leading scientists in the fisheries community (and beyond) that was prompted by an op-ed piece in the New York Times, "Let Us Eat Fish" published April 14, 2011. Though the post "Forum on fish, food, and people" is a long read, it provides a very interesting look into the types of conversations that are taking place among top scientists, the level of uncertainty and lack of unity in hypotheses about future of the Earth's ecosystems, as well as providing a strong argument for how extremely important integration across disciplines is in addressing the impacts of climate change on ecosystems. As someone who eats a 95% vegetarian diet, with the exception being eating some fish and seafood on occasion, I found this debate really interesting and thought you might too.

Enjoy, and check out the blog for more awesome posts daily!

Sunday, May 15, 2011


Although mainly directed at the L&S biology students it is probably worth you signing up for the Biology Undergraduate List (assuming the system doesn't include you already). If you are not receiving the odd e-mail from [Biology-U-L] then you can sign up to receive them here.

Here are two e-mails about eemb courses for Fall quarter I received last week.

Course: EEMB    101
Title: Molecular Evolution
Description  ---
Major concepts in evolutionary biology, presented with a genetic emphasis.
This course provides an introduction to the study of population genetic
processes and   the patterns of genomic evolution, adaptation, and
speciation that result from   these processes.

 Prerequisites: EEMB 2 or MCDB 1A or Geology 3. 

EEMB 101 TR 930-1045, TURNER T.,  SH 1430
58453   F  100- 150   STAFF HSSB 1232
58461   F  200- 250   STAFF HSSB 1232

For those of you interested in applied ecology, aquatic biology, natural resource management, and conservation biology, we alert you to a relatively new course on Applied Freshwater Ecology (EEMB 167) which will be taught in Fall 2011.  This course allows you to apply the theoretical, conceptual, and descriptive information you have acquired in your foundation courses to problems of applied significance.  Because jobs dealing with the management of freshwater resources can be found throughout the nation, this course provides an introduction to problems and their solutions that confront applied biologists, managers, and policy makers every day.  Because clean freshwater is a requirement for all human activities and because freshwater habitats are biodiversity hotspots that are severely threatened by human expansion, this course provides a timely introduction to pressing national and global problems.

The pre-requisites for this course are EEMB 2 and 3.  The course is taught by aquatic ecologists Professor Cooper and Professor Melack and will meet on Tuesdays and Thursdays from 330 to 445 PM in Chem 1171 in Fall Quarter.

 In this course the instructors cover basic principles in ecology and water management that pertain to applied problems, then address such issues as climate change, ozone depletion, acid deposition, land use changes, eutrophication, biocides, metals,  GM crops, nanoparticles, and emerging diseases in lakes, streams, ponds, rivers, and wetlands. They also explore problems associated with species extinctions and invasive species and discuss approaches to these problems associated with conservation biology, natural resource management, and restoration ecology.

TR     330- 445PM   CHEM 1171   
16840   W      400- 450P  PSYCH1805   
16857   W      500- 550P  PSYCH1805    

Friday, May 13, 2011

Biology for the win

It's official - Biology is the most useful subject in the event of a zombie attack. Since the only prize was bragging rights for a year you should use them widely.

Thursday, May 12, 2011

Crytptomycota - a new kingdom

The evolutionary tree of fungi grows a new branch

Fungi found in UK pond could be part of a previously undiscovered — and extremely diverse — phylum.

When a research team started analysing the genetics of microorganisms from their university pond, they might have expected to find a couple of new species. Instead, they discovered a group of fungi that could double the size of that biological kingdom.

Nature news report here and the actual article, Discovery of novel intermediate forms redefines the fungal tree of life, here.

Tuesday, May 10, 2011

Stuttering chains

Jamie Lloyd-Smith, an Assistant Professor from UCLA, will be presenting next Monday's EEMB seminar (Monday, May 16th, 4pm, MSRB auditorium):
"Smallpox eradication, stuttering chains, and the emergence of human monkeypox"

Jamie studies the ecological and evolutionary dynamics of infectious disease in animal and human populations, with emphasis on zoonotic and emerging pathogens.
For more information, visit his website:

Monday, May 9, 2011

Ant rafts

Okay, I'm feeling a little woozy because I just had root canal surgery (which is not as bad as its reputation but I still feel like I got punched in the face), but even so, how can you NOT be a biologist when there are papers like this:
Fire ants self-assemble into waterproof rafts to survive floods

 Why does a single fire ant Solenopsis invicta struggle in water, whereas a group can float effortlessly for days? We use time-lapse photography to investigate how fire ants S. invicta link their bodies together to build waterproof rafts. Although water repellency in nature has been previously viewed as a static material property of plant leaves and insect cuticles, we here demonstrate a self-assembled hydrophobic surface. We find that ants can considerably enhance their water repellency by linking their bodies together, a process analogous to the weaving of a waterproof fabric. We present a model for the rate of raft construction based on observations of ant trajectories atop the raft. Central to the construction process is the trapping of ants at the raft edge by their neighbors, suggesting that some “cooperative” behaviors may rely upon coercion. 

Sunday, May 8, 2011

Zombie debate

I have the somewhat dubious pleasure of taking part in this event this year. Please come along if you'd like to see me defend biology as the only subject worth preserving come the zombocalypse.

AS Program Board Presents…


The world has been taken over by Zombies!!!! Only one academic subject can survive in the new Human Colony. The question is: Which subject should it be?

Come out to The Hub on Thursday, May 12th and watch some of your favorite UCSB professors debate this topic and defend their subject!

**Doors open at 7:45pm; the debate begins at 8pm.**

FREE for UCSB students only. You must bring your access card! 

Thursday, May 5, 2011

Scientific Publishing from the Inside Out

Tomorrow (Friday, May 6, 2011) 11.30-12.30 p.m. in Bren Hall.
Sacha Vignieri, PhD, Associate Editor of SCIENCE
Scientific Publishing from the Inside Out

From the outside, publication in high-impact general-science journals can seem like a mysterious process. A general understanding of the procedures and practices at Science can help unravel the mystery a bit, and contribute to an understanding of what makes a good (or even great) paper a high-impact-journal paper. In particular, while many researchers strive to publish in these journals because of their high impacts, they are fundamentally general-science journals, and understanding this can help authors assess which aspects of their own work will be most successful in such outlets. I’ll discuss some of the inner workings of Science and provide insight for helping authors prepare and assess their own work for consideration in high-impact general-science publications.

The trouble with normal...

Nicole asked what a normal heart rate was. Strangely enough heart rates vary so much that the range considered 'normal' is huge. In most people anything from 60 to 100 could be normal - and if you are fit then even lower, down into the 40's is not just normal but good. But being higher than 60 doesn't mean you are unfit - it might just be normal for you.

Is it bad to have a resting heart rate of, say, 95? Not necessarily - it depends on what your maximum heart rate is. You may have a high maximum heart rate as well - in which case the difference between your resting heart rate and your maximum heart rate (known as your heart rate reserve) could be the same as someone with a resting heart rate of 60.

So why are doctors always taking your pulse if virtually any value can be considered normal? Because changes to your resting heart rate are a very good indicator of potential problems. That's why hospitals track your pulse rate. It's not the value that matters so much as changes to the value. They can indicate something is wrong before you may be aware of it.

In fact some athletes take their resting pulse rate every morning (best immediately after you wake up unless you have a loud and startling alarm clock!). Even small increases to this value are one of the most reliable warning signs of overtraining.

Some people also get very into heart rate training which involves carefully monitoring your heart rate and keeping it within particular ranges for different exercises. Endurance training for example is best done well within the aerobic zone which is around 75% of maximum heart rate. Most people actually need to slow down in order to do this. You can buy chest strap heart rate monitors that send a signal to a wrist watch pretty cheaply these days. Here's an article by Mark Allen on how heart rate training influenced him. Mark Allen is the six times Ironman champion, and (thanks Wikipedia) a biology graduate from UC San Diego.

And a few previous posts you may be interested in checking out:

Tuesday, May 3, 2011

Speaking of giant bugs...

...this story caught my eye. A queen the size of a hummingbird?!

Non-static apnea

Okay maybe floating face down in a swimming pool isn't for everyone. How about free-diving? The problem with this is that there are all sorts of categories including 'no limits' where divers use a weighted sled to pull them down and then air bags to ascend. You still have to hold your breath of course... The world record for this is an amazing 214m (over 700 feet). But the purest form of the sport is where the diver swims down and back under his own power without even the benefit of fins. Watch this amazing dive by William Trubridge, who has set further records since this video. I love how calm and collected he is. Every movement seems perfectly choreographed and he is clearly maximizing efficiency and not speed.

Monday, May 2, 2011

Predator alert

Wait, wait. A COYOTE is running a hotel where he entices naive prairie dogs to rent rooms and then he accuses them of theft before they have even checked in? I think the fox is in on the game. Something is very wrong here. I'm not sure how the mouse preventing the cat getting off the elevator helps anything. I think I may be overthinking this one.

Spider versus ant

Interesting technique by the spider. I wonder how common this is? There's a twist in the end of the tale too..

Saturday, April 30, 2011

Static apnea

On Tuesday we will start our physiology section and Claudia will be talking about respiration. To get you pumped up (pun intended) I thought I'd post this video of what I only just discovered was a sport - static apnea. Basically this is floating face down in a swimming pool whilst holding your breath - quite possibly the most boring sport in the world to watch (it makes cricket look exciting) but physiologically quite interesting. For example if you watch the video you'll notice a demonstration of what I think is glossopharyngeal insuffation - this is a method of pumping additional air into the lungs widely used by reptiles and amphibians (picture a frogs bulging neck) but not by humans. Until a few decades ago when free divers discovered that by using the tongue as a piston an additional liter or so of air can be forced into the lungs. Don't try this at home though, rupturing the lung is a real possibility unless you work up to it.

How long can you hold your breath? A minute? A minute and a half?

What do you think the world record is. Four minutes? Five minutes? TEN minutes? Think again.

Curiously the techniques involved don't involve keeping the brain alive without oxygen, that's simply not possible, but getting oxygen to the brain even though you aren't breathing

Thursday, April 28, 2011

Very different but very cool

Two totally different critters I mentioned today. First up the slime mold.

and then the cephalopod - master of camouflage.

Rock-Paper-Scissors Tournaments Explain Ecological Diversity

Directly relevant to our discussion of ecological diversity, is this hot-off-the-press research co-authored by UCSB ecologist Jonathon Levine.

The mystery of biodiversity –– how thousands of similar species can coexist in a single ecosystem might best be understood as the result of a massive rock-paper-scissors tournament, a new study has revealed.

From the UCSB pub, "Coastlines":

According to classical ecology, when two species compete for the same resource, eventually the more successful species will win out while the other will go extinct. But that rule cannot explain systems such as the Amazon, where thousands of tree species occupy similar ecological niches.

The childhood game of rock-paper-scissors provides one solution to this puzzle, report researchers at UC Santa Barbara and the University of Chicago in the Proceedings of the National Academy of Sciences. A mathematical model designed around the game's dynamics produced the potential for limitless biodiversity, and suggested some surprising new ecological rules. Read the article here.

The link to the original source, published in PNAS is here.

Wednesday, April 27, 2011

Museum event

Bruce forwarded this. It sounds like an interesting

The next Friends of the Santa Barbara Museum Library Lecture is Wednesday, May 11th at 7:00 PM. The evening will feature Curator of Malacology, Paul Valentich-Scott and Elizabeth Garfinkle, a San Roque High School student. Theirs is a unique research story. Read about it below.

Not just your everyday new species How does a small clam from deep water off Baja California end up being a local sensation with a Santa Barbara teenager? Collaborators Paul Valentich-Scott, Curator of Malacology, and Elizabeth Garfinkle, a junior at San Roque High School, will present their recently published research describing a new species of clam. The pair will discuss the initial discovery of the new bivalve and its surprising links to the past of central California.

Elizabeth is one of the few high school students globally who has described a new species. Her achievement has been chronicled in many local media outlets from San Luis Obispo to Los Angeles. She took top honors at the 2011 Santa Barbara County Science Fair for this unique project. Come meet Paul and Elizabeth and learn more about the exciting journey that led to a new species being described in a zoology journal from New Zealand.

Admission is free but you need to make a reservation by e-mailing Terri Sheridan at or (805) 682-4711 ext. 134

Tuesday, April 26, 2011

What is peer review?

I thought this article on peer review was interesting and well written. You may know most of this by now but some of it may surprise you.

For the most part, scientists are not formally trained in how to do peer review, nor given continuing education in how to do it better. And they usually don't get direct feedback from the journals or other scientists about the quality of their peer reviewing. Instead, young scientists learn from their advisors—often when that advisor delegates, to the grad students, papers he or she had volunteered to review. Your peer-review education really depends on whether your advisor is good at it, and how much time they choose to spend training you.

Sunday, April 24, 2011

Time Lapse Fungi

I found this website that contains time lapse movies of fungi, molds, bacteria, slime molds and insects. Its pretty cool to see the time lapse of the Rhizopus on the strawberries and there are a few cool videos of the Pilobolus. This is so related to Thursdays lecture I couldn't help but be intrigued and a little grossed out by how successful these guys are at what they do. If you watch the Pleurotus djamor clip you will never look at an old book the same. Check it out!

Friday, April 22, 2011

Two seminars for Monday 25th April

Next week's EEMB Seminar speaker will be Dr. Stephanie Pau, who is currently a post-doc at NCEAS. Her research incorporates field studies with remote sensing and paleo-ecological methods in order to investigate ecosystem responses to climate variability. Stephanie's talk is titled:
"Investigating diversity and ecosystem function at multiple spatial and temporal scales"
The seminar will take place on Monday April 25 from 4-5pm in the MSRB auditorium.

CCBER is pleased to announce that our Monday evening seminar will feature local botanical expert,
Mary Carroll who will focus on identifying local grasses.
Monday 25th, 6-7pm, Harder 1013.

Thursday, April 21, 2011

Speaking of ecosystems...

By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific.

"We found that the combination of microbes in the human intestine isn't random," says Peer Bork, who led the study at EMBL: "our gut flora can settle into three different types of community -- three different ecosystems, if you like."

Report at ScienceDaily and the paper, Enterotypes of the human gut microbiome, is published in nature this week.

Monday, April 18, 2011


I'm all for education in cartoon format but Slylock Fox always confuses me. As the Comics Curmudgeon points out, if the rules are suspended for half the characters - the fox is a detective, the mouse wears pants and the pig grows tomatoes, why should we assume that in this universe the snake is a carnivore and the raccoon is an omnivore? I hope that the solution to this conundrum would be obvious to any biologist - if the cartoonist has shown their teeth then we could have been confident in the identity of the omnivore.

Sunday, April 17, 2011

Human records

I don't know if anyone watched the London Marathon today. The BBC kindly made it available on the web on demand so you could watch the whole thing at your leisure. The stellar field this year led to a resurgence of interest about whether a sub-2 hour marathon will ever be run. Personally I think people underestimate the significance of the 4 minutes improvement it will take. However watching Emmanuel Mutai storm the second half of the course today led me to believe that maybe I'll see it in my lifetime. He ran the last 12km at a 2:02 pace (and promptly threw up the moment he crossed the line). To run a sub-2 hour marathon would require over 26 consecutive 4:35 miles. That's under 69 seconds for each quarter mile - approximately a lap of a track. Try it. For 69 seconds. Now imagine two hours of it. Humans are, or can be, extraordinarily good distance runners. Why?

Anyway, when we talk about human physiology, which we will shortly, it is always interesting to consider the human superlatives, Haile Gebrselassie or Usain Bolt.

But what is equally interesting is the revolution that is taking place further back in the pack. Virtually unreported in the media was the new world record by Canadian Ed Whitlock in the Rotterdam marathon last week. Whitlock ran 3:25:43. A very nice but utterly unremarkable time you might think. But Ed Whitlock is 80. He beat the old 80-84 world record by almost 15 minutes and Whitlock is not unique. The gains made at older age groups are really amazing. This, of course, is actually much more relevant to most of us - gains made in medical understanding affect both our longevity and also the quality of our life.

For an equally inspiring female example check out this New York Times article on the amazing 91 year old Olga Kotelko: The Incredible Flying Nonagenarian.

When the efforts of medical science converge to simply prolong existence, you envision Updike’s golfer Farrell, poking his way “down the sloping dogleg of decrepitude.” But scientists like Taivassalo and Hepple have a different goal, and exercise — elixir not so much of extended life as extended youthfulness — may be the key to reaching it. James Fries, an emeritus professor at Stanford School of Medicine, coined the working buzz phrase: “compression of morbidity.” You simply erase chronic illness and infirmity from the first, say, 95 percent of your life. “So you’re healthy, healthy, healthy, and then at some point you kick the bucket,” Tarnopolsky says. “It’s like the Neil Young song: better to burn out than to rust.” You get a normal life span, but in Olga years. Who wouldn’t take it? 

Thursday, April 14, 2011

The Song of the Dodo: Island Biogeography in an Age of Extinction

This book deals with many of the studies Claudia talked about in class on Thursday. It may be a bit long to count as a light read, it’s about 600 pages, but the author makes it funny and portrays the information in the form of stories and personal accounts. For anyone who is going into ecology, or is already in ecology, this is kind of a must read. It is a wonderful way to be introduced to some major studies and the people who conducted them. I found it super fun to read and packed full of cool biology facts. The author's other books are also wonderful works of biology writing.

Today's Miscellany

Don't forget next TUESDAY you will be writing about a selected research topic in class (it's on your syllabus).

A few items Claudia mentioned today that are buried here on the blog somewhere.
You may have received an e-mail from Bruce about tomorrow's meeting (Friday noon in room 143) with a CCS bio alum. Brendan Borrell (CCS Biology '99, UC Berkeley PhD in Biology '06 ) will talk about how he made the leap from science to journalism, demystify the logistics of surviving as a freelancer in New York, and share stories of reporting from the Bolivian chaco, the Australian rainforest, and the phosphate mines of Morocco.
    Finally I think Kathy may have also e-mailed you about her summer class but here are the details:

    MCDB 161L: Research Immersion in Molecular Biosciences
    Offered: Summer Session A,  June 20 – July 29,  2011
    Developed as part of the $1,000,0000 UCSB-HHMI initiative, this is an intensive (6 unit) undergraduate laboratory course covering basic approaches to research in molecular biosciences using model systems. In addition to the laboratory techniques, students learn hypothesis building, experimental design, data analysis and interpretation, as well as presentation skills. The 6-week course (Summer Session A) is taught in three modules, each based on current interdisciplinary biomolecular and biomedical research being conducted on the UCSB campus.  This is a unique opportunity for UCSB undergraduate students to obtain practical training that will help them prepare for careers in biomedical research.

    For more information and to apply to enroll in the course, see the attached flyer and the website:

    Kind Regards,
    Kathy Foltz

    Wednesday, April 13, 2011

    Lotusland photo quiz

    Two very nice pictures from Rebecca. Those are ants inside the flower in the second picture, the third picture is just a close up. Speaking of species interactions, which we will, what do you think the ants are doing? ie who is gaining and who is losing in this interaction? More importantly how would you design an experiment to test your hypothesis? What would your treatments be, what would your control be and what would you measure?

    Tuesday, April 12, 2011

    Lotusland redux

    I just unearthed my camera to take some pictures and when I came to download them I found some Lotusland pictures which have just been sat there. I'm sure some of you took some good pictures. Why not post your best ones or send them along for me to post. I rather like the light in the picture above.

    Monday, April 11, 2011

    Biomagnification of Toxins in Marine Food Webs

    The Interdepartmental Graduate Program in Marine Sciences is sponsoring a special seminar that is of potential interest across a broad span of biology (see Abstract). Dr. Trapido-Rosenthal is visiting UCSB for Friday's Symposium honoring Professor Dan Morse (Hank earned his PhD with Dan in 1985).  We hope you can join us for this seminar.

    Special IGP Marine Science Seminar

    Thursday, April 14, 2011
    12 noon
    MSRB Auditorium
    (pizza lunch following, on MSRB 2nd floor balcony)

    Henry (Hank) Trapido-Rosenthal
    Associate Research Scientist
    School of Ocean and Earth Science and Technology
    University of Hawaii

    Biomagnification of Toxins in Marine Food Webs

    Some dinoflagellate algae and cyanobacteria produce toxins that have human health endpoints after being biomagnified as they move upwards through marine food webs. We are studying two of these toxins: (a) ciguatoxin, which is produced by dinoflagellates in the genus Gambierdiscus, and which causes poisoning in humans who eat toxin-containing reef fish; and (b) β-methylaminoalanine (BMAA), a “nonprotein” amino acid which can be produced by some cyanobacteria, and which can have neurotoxic effects on organisms at higher trophic levels after food web biomagnification. In this talk, I will first describe the results of our work with ciguatoxin here in the Hawaiian Islands. I will then describe work being done by ourselves and our international colleagues to address some mysteries associated with the ways in which BMAA is biomagnified and exerts its toxic effects.

    Bienfang, P.K., DeFelice, S.V., Laws, E.A., Brand, L.E., Bidigare, R.R., Christensen, S., Trapido-Rosenthal, H., Hemscheidt, T.K., McGillicuddy Jr., D.HJ., Anderson, D.M., Solo-Gabriele, H.M., Boehm, A.B., and Backer, L.C. (2011) Prominent human health impacts from several marine microbes: History, ecology, and public health implications. Int. J. Microbiol., ID 152815, 15 pages.
    Venn, A.A., Loram, J.E., Trapido-Rosenthal, H.G., Joyce, D.A., and Douglas, A.E. (2008) The importance of time and place: How genetically-different Symbiodinium algae are distributed in a variable coral reef symbiosis. Biol. Bull., 215:243-252.
    Loram, J.E., Boonham, N., O’Toole, P., Trapido-Rosenthal, H.G., and Douglas, A.E.  (2007) Molecular quantification of symbiotic dinoflagellate algae Symbiodinium in corals. Biol. Bull., 212:259-268.
    Loram, J.E., Trapido-Rosenthal, H.G., and Douglas, A.E. (2007) Functional significance of symbiont clade in a coral reef symbiosis. Molec. Ecol. 16: 4849-4857.
    Venn, A.A., Wilson, M.S., Trapido-Rosenthal, H.G., Keely, B.J., and Douglas, A.E. (2006) The impact of coral bleaching on the pigment profile of the symbiotic alga Symbiodinium. Plant, Cell Env. 29:2133-2142.
    Yasuhara-Bell, J., Yang, Y., Barlow, R., Trapido-Rosenthal, H., and Lu, Y. (2010) In vitro evaluation of marine microorganism extracts for anti-viral activity. Virol. Jour. 7: 182-193.
    Anderson, P.A.V., and Trapido-Rosenthal, H.G. (2009) Physiological and chemical analysis of neurotransmitter candidates at a fast excitatory synapse in the jellyfish Cyanea capillata (Cnidaria, Scyphozoa). Invert. Neurosci. 9:167-173.
    Toledo, G., Green, W., Gonzalez, R., Christoffersen, L., Podar, M., Chang, C., Hemscheidt, T., Trapido-Rosenthal, H.G., Short, J.M., Bidigare, R.R., and Mathur, E.J. (2006) High throughput cultivation for isolation of novel marine organisms. Oceanography 19:120-125.
    Owen, R., Mitchelmore, C., Woodley, C., Trapido-Rosenthal, H., Galloway, T., Depledge, M., Readman, J., Buxton, L., Sarkis, S, Jones, R. and Knap, A. (2005) A common sense approach for confronting coral reef decline associated with human activities. Mar. Pol. Bull. 51:481-485.
    Trapido-Rosenthal, H. G., Zielke, S., Owen, R.J., Buxton, L., Boeing, B., Bhagooli, R., and Archer, J.A. (2005) Increased zooxanthellae nitric oxide synthase activity is associated with coral bleaching. Biol. Bull. 208:3-6.