CCS Bio Blog

Ocean acidification

2012-01-27T16:23:00.000-08:00

A paper out this week in Nature Climate Change confirms that CO₂ emissions over the last 100 to 200 years have raised ocean acidity far beyond the range of natural variations. Like atmospheric climate change the issue of ocean acidification is complicated by seasonal, regional and various long term trends. However direct observations of pH in the oceans only go back 30 years and so various techniques need to be used to estimate ocean pH in the past. Detecting regional anthropogenic trends in ocean acidification against natural variability

The picture is the cover of a report on Ocean Acidification released in 2010 by Oceana, an international organization working to protect the world's oceans.

American degeneracy

2012-01-26T21:27:00.000-08:00

Every time I hear the phrase 'American exceptionalism' I think of Buffon and his theory of American degeneracy. Jefferson's instructions to Lewis and Clark - to seek out Mastodon in the American interior - were provoked by Buffon who had been mocking America as a degenerate continent

"In America, therefore, animated Nature is weaker, less active, and more circumscribed in the variety of her productions; for we perceive, from the enumeration of the American animals, that the numbers of species is not only fewer, but that, in general, all the animals are much smaller than those of the Old Continent."
George Louis Leclerc, comte de Buffon (1707-1788)

The Academy of Natural Sciences has a nice series of webpages entitled 'Buffon's Degeneracy' that descibe this interesting, but often forgotten period in history.

The anteater with a splendid classical background is from Buffon's Histoire naturelle, thirty-six volumes of which were completed during his lifetime and another eight published after his death from material he had prepared.

(Some of this post has been recycled from a post in 2009. I just think it's worthy of repeat.

Not ready for prime time

2012-01-25T15:18:00.000-08:00

Seawater from the Southern Ocean (left) and seawater collected from a patch in the Southern Ocean after scientists enriched it with iron to create a phytoplankton bloom (right).

It's been fascinating to follow the rise and fall of ocean fertilization over the last few years.

2007 - The business view
Recruiting Plankton to Fight Global Warming
Can plankton help save the planet?

2008 - The environmental backlash
Planktos Dead in the Water
A highly effective disinformation campaign waged by anti-offset crusaders has provoked widespread opposition to plankton restoration in the environmental world, and has caused the company to encounter serious difficulty in raising the capital needed to fund its planned series of ocean research trials.

2008 - A view from the ivory tower
2008 Ocean Iron Fertilization--Moving Forward in a Sea of Uncertainty
It is premature to sell carbon offsets from ocean iron fertilization unless research provides the scientific foundation to evaluate risks and benefits.
The bottom of the Science paper links to some more recent articles that cited it.

Here's one last article, from the more popular press, that seems to cover the debate in a fairly even handed way
Seeding the Sea: Will releasing iron into the oceans to combat climate change help — or harm — the planet?

Rapid evolutionary innovation

2012-01-24T13:56:00.000-08:00

Inspired by Nate's question I was looking up some research on the evolution of aerobic respiration and I found this really interesting paper in Nature from last year about a narrow window of genetic expansion between about 3.3 and 2.8 billion years ago, called the Archaean expansion, during which 27% of the largest modern gene families arose.The paper is called: Rapid evolutionary innovation during an Archaean genetic expansion and there is also a commentary on the paper: Evolution: Old genes

During the Great Oxidation Event about 2.4 billion years ago, the surface of the Earth tipped irrevocably into an oxygenated state, as free molecular oxygen began to accumulate in the oceans and atmosphere. But the first whiffs of oxygen began to appear at least 300 million years earlier, as organisms capable of producing the gas through photosynthesis evolved. As the Earth's chemistry changed, so too must have the microbes that lived on its surface. But the rock record leaves only hints of the ecosystem, primarily in the form of isotopic fractionation of the elements — including iron and sulphur — that presumably fuelled the bacteria.

To assess the evolution of these metabolisms, Lawrence David and Eric Alm of the Massachusetts Institute of Technology looked to the genetics of extant organisms. They re-examined existing gene families using a technique that accounts for both the evolution of new genes, and the transfer of genes between different species.

The paper is interesting not just because of the results but because it gives you an insight into the techniques you need to use to address these sorts of questions.

Run and twiddle

2012-01-23T23:02:00.000-08:00

Bacterial chemotaxis is a subject that has attracted considerable attention over the last couple of decades. I came across this review in PNAS that gives an overview of the progress over the last 30 years:
Bacterial chemotaxis and the question of gain

I like the fact that the authors are still so excited about their topic they can'r resist sneaking an exclamation point in:
E. coli is able to sense aspartate over a range of at least 5 orders of magnitude in concentration by using just one molecular species of receptor!

Chlamydia pneumoniae - no smoke without fire?

2012-01-22T23:37:00.000-08:00

There are two species of Chlamydia that are of particular concern to humans. The sexually transmitted Chlamydia trachomatis I mentioned in class and the intriguing Chlamydia pneumoniae. You won't be surprised to hear that this is one of many organisms that can cause pneumonia but you may be surprised to hear that infection with Chlamydia pneumoniae has been linked to both coronary heart disease and obesity. The evidence for the former is stronger than the evidence for the latter but there is enough evidence in both cases to make it clear something is going on. We don't think of obesity as an infectious disease but there is mounting evidence that some obesity may be caused by infectious agents.

C. pneumoniae was thought to solely a human pathogen but more recent evidence suggests that C. pneumoniae is able to infect a wide range of species, including horses, frogs and koalas. Yet another reason to be wary of Koalas. They may look cuddly but they have very sharp claws and if you are holding one and they are startled they can rip your scalp open as they dig in. This actually happened to the wife of a friend who worked at San Francisco zoo. I think they stopped with the Koala show and tell after that.

So not only can koalas maul you but they can give you pneumonia, and possibly make you fat and lead you to have a heart attack. Move over pandas there's a new evil animal in town.

Meet the Clostridiums

2012-01-21T23:24:00.000-08:00

I'm copying this from a post I made to the blog for my Disease Ecology class but in terms of microbial biodiversity it's not a bad idea to take a closer look at one particular group of microbes. Clostridium is a group of low-GC gram-positive bacteria. There are only about 100 species but several of importance to humans.

The worst is Clostridium perfringens, the causative agent of gas gangrene - a major cause of death in World War 1, the US Civil War and many wars prior to the invention of antibiotics. Near the top of the list for 'ways not to die' although sadly many soldiers did.

You might also have heard of Clostridium botulinum, or at least of the disease it causes - botulism. Botulism is a paralytic food poisoning that is fortunately rare. The bacteria grow on food and cause harm in people as we digest a toxin produced by the bacteria. The neurotoxin is one of the most powerful toxins known to man, a single microgram is lethal. It is also used (in minute doses!) in the cosmetic treatment known as Botox.

Clostridium tetani is the causative agent of tetanus. The symptoms, muscle spasms and difficulty swallowing are caused by a neurotoxin produced by the bacteria. Infection generally occurs through wound contamination, and often involves a cut or deep puncture wound. Infection can be prevented by immunization, and this is often successful even if given after the wound occurs. Which is why it's a good idea to get a tetanus shot after a deep cut or puncture wound. If you wait to see if an infection develops it is too late for immunization to be much use.

The final member of our bad boys is Clostridium difficile. C. difficile, or just C. diff. is the latest, greatest threat in nosocomial infections and there have been numerous outbreaks lately. Try a google news search on Clostridium difficile to see where the latest outbreak is. C. diff is an interesting bacteria because it is found as a natural part of the gut flora in a small fraction of people, usually with no problems. But if the usual gut flora is eradicated with broad spectrum antibiotics C.diff can greatly increase in numbers and release toxins that cause severe diarrhoea and death in some cases. Some new strains appear to be producing much more toxin. Hospitals are very good places to find people taking broad spectrum antibiotics and, apparently, are good at spreading C.diff around as well.

On the positive side, non-pathogenic strains of Clostridium may help in the treatment of diseases such as cancer. Some strains of Clostridium can selectively target cancer cells and Clostridium could be used to deliver therapeutic proteins to tumours

Biodiversity bonanza

2012-01-20T23:18:00.000-08:00

Most wildlife photographers strive to capture their subjects in the field in as a natural setting as possible. Joel Sartore has been taking a different approach and has been traveling around the country photographing animals in zoos and wildlife parks against stark black or white backgrounds. The crisp, sharp pictures are more reminiscent of fashion shoots than wildlife photographs and I think he is achieving his aim:

This black-and-white background technique gives all species equal weight and importance. A tiny beetle is as interesting as a lion, and a two-toed sloth as cuddly as a panda bear. The clean background, combined with nice light, allows the viewer to look every species in the eye, the window to the soul. I hope these portraits will connect with viewers and get them to understand that all creatures have at least a consciousness as well as a basic right to exist.
For more pictures, and a nice video, check out this National geographic article or visit Joel's website.

Seminar alert

2012-01-19T14:51:00.000-08:00

Two more job talks coming up next week plus the regular Monday EEMB seminar sounds of fairly general interest.

MONDAY 23rd - EEMB seminar

Prof. Dick Zimmer from UCLA is the EEMB seminar speaker for Monday, Jan 23rd (4 pm, MSRB auditorium). Dick is a marine ecologist who focuses on the role of chemical signaling in the environment in relation to species interactions, population and community dynamics, and a variety of other ecologically important processes and phenomena. As such, Dick’s work involving the molecular basis for behavior of marine organisms integrates across many scales of biological organization – from molecules to ecosystems. Last year Dick finished a two-year term as an NSF Rotator in Biological Oceanography and next Monday he will present results of his new research on ‘Keystone Species and Molecules of Keystone Significance.’

TUESDAY 24th - MCDB job candidate

3:30-4:30 P.M. in the Marine Science Auditorium, MSRB 1302
Dr. Yi Xing, University of Iowa, Carver College of Medicine
"Global insight into post-transcriptional regulation and evolution"
The long-term goal of my research is to elucidate the regulation of post-transcriptional RNA processing and understand how genomic and environmental variation of post-transcriptional networks impacts cellular functions, phenotypic traits, and diseases. Post-transcriptional regulatory processes, including alternative splicing and alternative polyadenylation, generate enormous functional and regulatory complexity in eukaryotes. We are developing computational and statistical tools for global analysis of post-transcriptional regulation using high-throughput sequencing technologies. Through the use of integrated genomic, computational, and molecular approaches we are investigating the variation and dynamics of alternative splicing and post-transcriptional regulatory networks between species, within populations, and in response to cellular and environmental signals. In this talk, I will discuss two projects in which we study post-transcriptional gene regulation in evolution and development. In the first project, we combine RNA sequencing (RNA-Seq) with computational and molecular studies to investigate the regulatory impact of de novo exon creation during primate and human evolution. In the second project, we utilize multiple high-throughput sequencing technologies (RNA-Seq, DRS, SELEX-Seq) to delineate the complete spectrum of a cell-type-specific post-transcriptional regulatory network during the epithelial-to-mesenchymal transition, which plays a critical role in development and cancer metastasis.

The next candidate for the EEMB Biological Oceanographer position search, Dr.Michael Lomas, Bermuda Institute of Ocean Science, will be visiting on Jan 26-27. I don't have the talk details yet but I'm guessing Wednesday at noon again. Dr Lomas isa biological oceanographer who’s primary focus is to improve our understandingof the marine carbon cycle by studying the inherent taxonomic and physiologicalvariability of marine phytoplankton.

MicrobeWiki

2012-01-19T14:18:00.000-08:00

For researching topics and also for some good old fashioned random browsing I recommend MicrobeWiki. For example there was a question about whether the sulfur oxidizing chemoautotrophs I mentioned at the base of hydrothermal food webs were bacteria or achaea - turns out they are both and there is a really nice article at the MicrobeWiki site about Chemotrophy Along Seafloor Hydrothermal Vents.

Endogenous retroviruses

2012-01-18T14:30:00.000-08:00

Although we encourage you to read primary literature I think it is also important to read about science in the more popular literature to see how it is presented to a very different audience. Good science writing is often hard to come by but there was great article in the New Yorker a few years back on endogenous retroviruses. It describes their discovery and their potential influence on human evolution as well as links to AIDS and the recreation of the so called Phoenix virus in Thierry Heidmann's lab. I've been very impressed with science articles I have read in the New Yorker, I wonder if they could ever be persuaded to put out a Science textbook?

Another faculty recruitement seminar

2012-01-17T13:30:00.000-08:00

TODAY!!! TUESDAY, JANUARY 17, 2012

3:30-4:30 P.M.

Marine Science Auditorium, MSRB 1302 Host: Kathy Foltz

Dr. Lucy O’Brien, UC Berkeley

“Supersize Me: Stem cells as agents of adult organ adaptation”

Animals live in dynamic environments where external conditions vary at cyclic or irregular intervals. When faced with environmental change, an individual’s physiological fitness requires its organ systems to functionally adapt. One type of adult organ adaptation is function-enhancing growth in response to increased physiological demand. However, the mechanistic origins of adaptive flexibility and responsiveness in adult tissues are largely mysterious. I have established the Drosophila intestine as tractable, stem-based model to study adaptive growth. When dietary load increases, local insulin secretion by intestinal tissues triggers gut stem cells to activate a reversible growth program. The growth response hinges on two synergistic shifts in stem cell behavior: accelerated division rate and symmetric daughter fate. Stem cell-driven adaptive remodeling reveals how adult tissues exploit their renewal programs to adapt to environmental change.

Cool Article On Multicellular Evolution

2012-01-17T00:08:00.001-08:00

Test Tube Yeast Evolve Multicellularity

By watching evolution in progress, scientists reveal key developments in the evolution of complex life and put evolutionary theories to the test

By Sarah Fecht | January 16, 2012 | 7

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Image: William Ratcliff

The transition from single-celled to multicellular organisms was one of the most significant developments in the history of life on Earth. Without it, all living things would still be microscopic and simple; there would be no such thing as a plant or a brain or a human. How exactly multicellularity arose is still a mystery, but a new study, published January 16 inProceedings of the National Academy of Sciences, found that it may have been quicker and easier than many scientists expected.

"This is a significant paper that addresses one of the most fundamental questions in evolutionary and developmental biology," says Rick Grosberg, an evolutionary biologist at the University of California at Davis, who was not involved with the research.

Since evolution acts on individual cells, it pays off for a cell to be selfish. By hogging resources and hindering neighbors, a cell can increase the odds that more of its own genes get passed into the next generation. This logic is one of the reasons it has been challenging to imagine how multicellularity arose; it requires the subjugation of self-interest in favor of the group’s survival.

"Traditional theories make this out to be a difficult transition because you have to somehow turn off selection on the individual cells and turn it on for the collective," says Carl Simpson, a paleobiologist at the Museum für Naturkunde in Berlin, Germany, who also was not involved in the research. "The big result here is that these transitions can be super easy."

In the new paper, researchers at the University of Minnesota at Minneapolis used a simple but elegant technique to artificially select for multicellularity in yeast. They dumped unicellular yeast into a tube of liquid food and waited a few minutes for the cells to settle. Then they extracted the lowest fraction of the liquid and allowed whatever cells it contained to form the next generation. Because the cells had to cluster together in order to sink to the bottom and survive, the artificial selection made it more advantageous for yeast to cooperate than to be solitary.

After just 60 generations, all of the surviving yeast populations had formed snowflake-shaped multicellular clusters. "Hence we know that simple conditions are sufficient to select for multicellularity," says biologist Michael Travisano, who led the research.

But at what point do the yeast become something more than a cluster of cells? When do they begin behaving as one organism?

In a true multicellular organism, such as a rabbit, evolution acts upon the rabbit and not upon each of the billions of cells that build it. So the researchers set out to determine whether artificial selection would act upon the snowflake yeast as if they too were multicellular organisms. To test it, one batch of the multicellular yeast was allowed only five minutes to settle in a tube (representing a strong selection pressure), while another batch was given 25 minutes (a weaker selection pressure). After 35 generations, the yeast that were exposed to stronger selection evolved to have larger cluster sizes, while those in the weak selection group actually shrank in size. This indicated that each cluster of cells was evolving as one organism.

In addition, time-lapse photography [video below] revealed that, in order to reproduce, the multicellular yeast divides itself into branches that develop into the multicellular form as well. The daughter clusters did not create their own offspring until they had reached a similar size as their parents. The presence of this juvenile stage shows that the snowflake yeast had adopted a multicellular way of life, says William Ratcliff, a postdoctoral student in Travisano’s lab.

The researchers also found evidence of rudimentary division of labor, which is an essential characteristic for more complex multicellular life forms. In a human, for example, some cells may differentiate into blood cells, others may differentiate into immune cells, but only select egg or sperm cells help form the next generation.

In the multicellular yeast, the division of labor was more subtle. Although the experiment's artificial selection favored large clusters, a large cluster required more time to grow before it could reproduce. That meant that smaller clusters, which divide in half more quickly, could soon outnumber the larger clusters. But after many generations of selection, the large clusters evolved a solution: non-reproductive cells which served as points where offspring could break away from the parent cluster. By providing more break points, these specialized cells allowed the clusters to break into more pieces, to produce a greater number offspring quickly.

“The discovery that there are cells specialized to die in order for the structure to reproduce is suggestive of the first steps toward cellular differentiation,” Grosberg says.

Although researchers agree that the yeast clusters could indeed be considered multicellular organisms, they remain relatively simple. "The researchers are not going to evolve sponges with this approach, but it's amazing what they’re able to do so quickly," Simpson says.

The fast evolution was not all that surprising to Grosberg, who has written papers arguing that multicellularity should be relatively easy to evolve; other researchers have estimated that multicellularity has arisen independently on at least 25 different occasions throughout the history of life. Yet nobody really knew how it originated, or what steps were involved in the process. By watching evolution in progress, the new research uncovered experimental evidence for these theories and revealed one possible scenario of how multicellularity may have evolved.

"We had hypotheses about how multicellularity could evolve, but until now, no one has really been able to test them,” Ratcliff says. "Now that we have this experimental system, we can ask lots of really exciting questions."

Gray Whale Count

2012-01-16T22:04:00.000-08:00

2012: coming to the Channel near you ...whales, dolphins, seals, sea lions, and the occasional sea otters.This is your opportunity to be something special ... to Count!

We have scheduled an exceptional presentation on campus: Tuesday evening, January 17, 2012 @ 7 PM Marine Science Institute Auditorium, UCSBScott Simon, Manager of MSI's Research Experience and Education Facility (REEF) will talk about opportunities for students and the university community in the the new building going up adjacent to MSI, the Outreach Center for Teaching Ocean Sciences (OCTOS).Michael Smith will then detail immediate opportunities for students to participate in Gray Whales Count 2012 as interns — sponsored by the Coastal Fund — training to supervise the survey from Counter Point or as volunteer observers, monitoring whales, dolphins, otters, and pinnipeds just off our shore.

Gray Whales Count conducts an annual survey of the northbound migration of Gray whales through the nearshore of the Santa Barbara Channel. From February through mid-May, the fifteen-week survey is conducted from land at Counter Point (above Devereux and Sands) in the Coal Oil Point Reserve by community volunteers, including students from UCSB. Since 2006, UCSB's Coastal Fund has supported the project with funding for student internships and special equipment needs.There are three choices for UCSB students. Most participate as volunteer observers with a scheduled two-hour shift, ideally each week through the Count. Interns make a much bigger commitment, training to be supervisors or the research and education. Interns will learn to identify and distinguish marine mammals in the Santa Barbara Channel with one of the most abundant and diverse populations of marine mammals in the world. Interns commit to a four-hour shift a week through the Count, fifteen weeks. Most first-year interns are volunteers, but there are a few stipends available for need and exceptional qualifications. Experienced interns returning to the Count are eligible for a stipend.All stipends are funded by the Coastal Fund. We are very grateful for their dedication and support.To learn more about these opportunities please visit our web site: www.GrayWhalesCount.org.

Get to the Point in 2012.

EEMB job candidate

2012-01-15T22:53:00.000-08:00

Those of you who were in the CCS Biology Colloquium may remember that I mentioned EEMB would be hiring a new faculty member this quarter in the field of Biological Oceanography. Well the job ad went out, the applications were scrutinised and the short list was made. Over the next few weeks six candidates will visit campus and give a job talk. These are all open to the campus community and are a great chance to see someone give, hopefully, a great talk. These talks are generally pitched at a level that general biologists can understand whilst also trying to give some idea of the candidates depth in their specific field.

The first of these will be this Wednesday at noon in the MSI auditorium (ground floor of the MSI building) by Dr. Ian Hewson of Cornell University with the title:

Foe or friend? Newperspectives on aquatic viral diversity and roles in host ecology enabled bycommunity genomics

Viruses in aquatic ecosystems play crucial roles inmicrobial food webs, where they influence the abundance, productivity, anddiversity of hosts. While most viruses are believed to infect bacteria, theymay also infect other organisms, from other viruses to whales. Despite a growing appreciation for theirimpacts on bacterio- and phytoplankton, there is little information on thediversity and activities of viruses arising from allochthonous sources, orthose associated with aquatic metazoa. Theorigin, decay and infectivity of allochthonous viruses was investigated inaquatic habitats. These studies have revealed that viruses move and infect hostsacross biomes, and that their decay rates are similar to viruses originatingfrom native hosts. Investigations ofviruses associated with sea fans, marine copepods and freshwater cladoceranshave shown that viruses are widespread in aquatic metazoa, and that they mayinfluence host population dynamics. The wide diversity of viruses in planktonand associated with metazoa in the absence of apparent disease raisesinteresting questions about the role of viruses in host ecology. Moreover,these studies have provided new perspective on the ecological significance ofviruses in aquatic ecosystems.

Facial color patterns in primates

2012-01-14T23:13:00.000-08:00

Monkeys - excellent.
Facial hair - amusing
Monkeys with facial hair and strangely colored faces - priceless.

An entertaining paper in Proceedings of the Royal Society this week - Adaptive evolution of facial colour patterns in Neotropical primates.

It reaches the somewhat surprising conclusion that species that live in larger groups have less complex facial patterns that those that live more solitary lives.

The author's explain in a ScienceDaily report:

The researchers' finding that faces are more simple in larger groups came as a surprise.
"Initially, we thought it might be the opposite," Santana said. "You might expect that in larger groups, faces would vary more and have more complex parts that would allow one individual to identify any member of that group. That is not what we found. Species that live in larger groups live in closer proximity to one another and tend to use facial expressions more than species in smaller groups that are more spread out. Being in closer proximity puts a stronger pressure on using facial expressions."
"This finding suggests that facial expressions are increasingly important in large groups," said co-author Jessica Lynch Alfaro, associate director of the UCLA Institute for Society and Genetics. "If you're highly social, then facial expressions matter more than having a highly complex pattern on your face."

REU

2012-01-13T14:38:00.000-08:00

It's not too early to start thinking about next summer. If you are looking for both some travel and an exciting research experience then you should investigate the NSF's REU program - Research Experience for Undergraduates.

NSF funds a large number of research opportunities for undergraduate students through its REU Sites program. An REU Site consists of a group of ten or so undergraduates who work in the research programs of the host institution. Each student is associated with a specific research project, where he/she works closely with the faculty and other researchers. Students are granted stipends and, in many cases, assistance with housing and travel. Undergraduate students supported with NSF funds must be citizens or permanent residents of the United States or its possessions. An REU Site may be at either a US or foreign location.

You apply via the individual institutions but NSF maintains a website where you can search through all the sites by location, discipline or keyword. There are lots of them in the biological sciences and CCS students are successful every year. Now is the time to be making plans. Deadlines vary but are typically in February.

Sample size >>1

2012-01-12T13:33:00.000-08:00

A few years ago we had not identified a single planet outside our solar system. Today the estimate is up to 100,000,000,000 (give or take a few). In fact the study of exoplanets is hot stuff at the moment with Nature papers generating headlines about exoplanets both yesterday and today.

Here's today's paper from Nature:
One or more bound planets per Milky Way star from microlensing observations
and one, of many, news reports - this one from the BBC: More planets than stars?

Yesterday's paper was about the recent discovery of several new planets that orbit multiple suns,
Transiting circumbinary planets Kepler-34 b and Kepler-35 b.
Was there a press report that didn't mention Tatooine? Real-Life Tatooine: Planets With Two Suns Found

Stem cell seminar tomorrow (Jan 12th)

2012-01-11T21:16:00.000-08:00

January 12th, 3:30-4:30 p.m.
LSB 1001 (Rathmann Auditorium)
Hosted by: Tony De Tomaso

A Doreen J. Putrah Cancer Foundation Research Lecture

Speaker: Dr. Leanne Jones, Associate Professor, Salk Institute
Title: "Mechanisms regulating aging of stem cells and the niche"

The Jones lab is using fruit fly Drosophila melanogaster as a model system to establish paradigms for how stem cell behavior is controlled. Adult stem cells can be easily located in the fly intestine and testis, and the stem cells that maintain these tissues are remarkably similar to their mammalian counterparts. Therefore, it is possible to study these cells in the context of their normal environment without destroying the tissue. Being able to study the behavior of stem cells in vivo allows us to begin to ask questions about how the niche can control stem cell self-renewal and survival and how the relationship between stem cells and the niche evolves during development, as a consequence of aging, and during tumor initiation and progression. Importantly, lessons learned from the study of stem cells in fruit flies has already told us much about how stem cell behavior is regulated in more complex tissues in mammals.

Start the quarter with a bang

2012-01-11T14:52:00.000-08:00

I thought I was going to have to skip my traditional opening to the Winter blog because YouTube had taken this down but it's back. Also this is an opportunity to remind you that as we go through the course you can click on the labels at the bottom of the posts to review past postings. For example as well as my yearly version of this post the Abiogenesis label has a small, but interesting, collection of posts

For everyone who has ever wondered what it would be like when a 500km diameter asteroid crashes into the earth here's a simulation. Asteroids of this size would have impacted the earth during the late heavy bombardment I mentioned. If you go to YouTube to watch it you can click a little link to watch it in high def. (highly recommended). You might also want to wait until you can crank up the speakers. The perfect soundtrack to the end of the world.

Experiment Exploded ! ! !

2012-01-10T13:42:00.000-08:00

Here's the link to the Miller-Urey experiment simulator I mentioned in class. Not only is this a fun little simulation but it is also a snapshot of how the internet looked 10 years ago with tiny videos in mpg format!

Still fun though. See how many goes it takes you to actually simulate the experiment correctly.

Native Plant Christmas present

2011-12-05T22:43:00.001-08:00

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

With funding generously provided by the AS Coastal Fund, the newly-revised4th edition now contains many new pictures, insets and additional
descriptions to help in your quest to identify the native plants andhabitats 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 theU.C. Regents.

The books are available for purchase at Harder Stadium South, Rm. 1009. Thebest times to come are Monday - Friday, from 1pm-5pm. For alternativetimes, please contact cliu@ccber.ucsb.edu and we will try to accommodateyour schedule. Sorry, no gift-wrapping available...

Happy Holidays!

CCBER Staff

Sage Center Distinguished Fellow talks

2011-10-19T22:38:00.000-07:00

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.

The virtues of waiting, procrastinating and avoiding conflict

2011-10-05T12:07:00.000-07:00

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

Fred'sresearch spans a huge range of topics in ecology andevolutionary-ecology, much of it relating infectious disease andnatural enemies to the behavioral ecology and population dynamics ofthe interacting species. See http://bioweb.biology.utah.edu/adler/ for more information.

Title: The virtues of waiting, procrastinating and avoiding conflict

Abstract:
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.

Vertebrate Curatorial Internship Fall 2011

2011-09-20T22:53:00.000-07:00

Each week throughout the quarter we will focus on a specific area of museumcuration, such as the importance of collections, documentation, methods ofpreservation, taxonomic nomenclature and labeling, and catalogingspecimens. Students will have the opportunity to prepare and process avariety of specimens using several different methods of preservation.Students who complete this introductory internship will be eligible foradditional intern positions in vertebrate collection management at CCBERduring subsequent quarters.

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

To participate, students must attend the first class orientation and maynot 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

2011-09-20T22:47:00.000-07:00

Work to restore UCSB campus natural areas for local plants and wildlifethrough an internship with CCBER for fall quarter 2011. Students will gainvaluable hands-on field experience restoring native wetland, coastal sagescrub, grassland and oak woodland habitats. Internship activities includeplant propagation, seed collection, planting, weeding, and ecologicalmonitoring. Learn about local plants and animals, earn course credit, meetenvironmental professionals in your community, and enjoy a beautifuloutdoor working environment!

All interns must complete the following for 1 unit of credit: 3 hours offieldwork per week, creation of a plant collection notebook and restorationjournal. To earn course credit, you must be an EEMB, ENVST, GEOG or CCSstudent and meet the minimum requirements for your department. Once the 10week internship program has been completed, there may be paid opportunitiesfor the following quarter. Volunteer opportunities are also available inmuseum 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- cliu@ccber.ucsb.edu

805- 893-2401

Scuba club

2011-09-20T22:40:00.000-07:00

Be there or be terrestrial.

Moorea Bicode

2011-09-12T11:32:00.000-07:00

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

http://news.nationalgeographic.com/news/2011/02/110223-biodiversity-moorea-biocode

New Guidebook to Native Plants & Habitats of UCSB

2011-08-29T22:30:00.000-07:00

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.

The Power of Poop

2011-06-03T17:48:00.001-07:00

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

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

2011-06-02T16:46:00.000-07:00

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 gorilla.com) under the heading "The original "door" study" .

Holy Batfish

2011-06-02T14:55:00.000-07:00

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.

National Running Day

2011-06-01T23:50:00.000-07:00

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...

Top Ten Evil animals

2011-05-31T23:23:00.000-07:00

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

2011-05-31T15:41:00.000-07:00

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.

'Duh' Science

2011-05-30T17:16:00.000-07:00

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.

How high?

2011-05-29T23:01:00.000-07:00

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.

Shocking research

2011-05-26T23:19:00.000-07:00

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.'

Recommended courses - Add your own!

2011-05-25T14:13:00.000-07:00

On the right hand side, under 'Useful Links' is a list of course comments and recommendations by CCS students. This is designed to be an informal guide that adds to, but does not replace, advice from your faculty advisors.

This post, which I will periodically bump up to the top, and is also linked to under the recommendation list, is designed to solicit your input to this resource. You can either e-mail them to me or you can simply add it as a comment on this page. Just click on the bottom where it says '# Comments'. Note that you do not need to be registered or logged in to leave a comment. Simply choose anonymous of you wish. Periodically I will add any comments to the list. Why not try it now?

(Thanks to whoever suggested we add this to Bruce, who passed on the suggestion to me.)

Multivitamins and pill wranglers take 2

2011-05-24T11:57:00.000-07:00

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.

Crazy Sex Trick Fuels All-Male Clam Species

2011-05-23T16:08:00.000-07:00

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.

Infectious disease conference

2011-05-21T23:30:00.000-07:00

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: http://www.eeidconference.org/
The conference is FREE for UCSB participants. But, if you are planning to attend the conference please register at: http://www.eeidconference.org/LocalRegistration/
(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).

Obese is the new normal

2011-05-20T23:44:00.000-07:00

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.

Internship opportunity

2011-05-19T11:45:00.000-07:00

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 -- Kelly@dock.net 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.

The dark matter of disease

2011-05-17T12:52:00.000-07:00

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

Floral responses to global environmental change

2011-05-16T10:51:00.000-07:00

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

Title:
Floral responses to global environmental change

Abstract:
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.
http://www.geol.ucsb.edu/news/speakers_club.php

Let Us Eat Fish?

2011-05-16T00:58:00.000-07:00

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!

Courses

2011-05-15T22:29:00.000-07:00

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.

1/
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

2/
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

Biology for the win

2011-05-13T11:03:00.000-07:00

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.

Crytptomycota - a new kingdom

2011-05-12T12:34:00.000-07:00

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.

Stuttering chains

2011-05-10T22:20:00.000-07:00

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: http://www.eeb.ucla.edu/Faculty/lloydsmith/

Ant rafts

2011-05-09T21:51:00.000-07:00

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.

Zombie debate

2011-05-08T22:28:00.000-07:00

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…

ZOMBIE DEBATES!

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!

Scientific Publishing from the Inside Out

2011-05-05T14:49:00.000-07:00

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...

2011-05-05T14:21:00.000-07:00

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:

Speaking of giant bugs...

2011-05-03T23:32:00.001-07:00

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

http://www.bbc.co.uk/news/science-environment-13269302

Non-static apnea

2011-05-03T16:05:00.000-07:00

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.

Predator alert

2011-05-02T22:35:00.000-07:00

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

2011-05-02T14:08:00.000-07:00

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

Static apnea

2011-04-30T22:09:00.000-07:00

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

Very different but very cool

2011-04-28T13:20:00.000-07:00

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

2011-04-28T13:07:00.000-07:00

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.

Museum event

2011-04-27T14:47:00.000-07:00

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 tsheridan@sbnature2.org or (805) 682-4711 ext. 134

What is peer review?

2011-04-26T23:14:00.000-07:00

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.

Time Lapse Fungi

2011-04-24T11:30:00.000-07:00

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!

Two seminars for Monday 25th April

2011-04-22T12:11:00.000-07:00

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.

Speaking of ecosystems...

2011-04-21T22:48:00.000-07:00

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.

Omnivore

2011-04-18T22:41:00.000-07:00

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.

Human records

2011-04-17T23:26:00.000-07:00

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?

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

2011-04-14T15:05:00.000-07:00

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

2011-04-14T14:30:00.000-07:00

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:
http://hhmi.mcdb.ucsb.edu/course/mcdb161

Kind Regards,
Kathy Foltz

Lotusland photo quiz

2011-04-13T14:04:00.000-07:00

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?

Lotusland redux

2011-04-12T21:41:00.000-07:00

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.

Biomagnification of Toxins in Marine Food Webs

2011-04-11T14:22:00.000-07:00

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

ABSTRACT
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.

PUBLICATIONS
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.

Rebecca Skloot

2011-04-11T12:32:00.000-07:00

The last CCS Distinguished Visiting Fellow for 2011 will be Rebecca Skloot, author of 'The Immortal Life of Henrietta Lacks'. Ms. Skloot will be available for a special question and answer session Tuesday morning , April 12th 10:00 - 11:00 AM in the CCS Art Gallery. This event is open to CCS Students and Faculty.

In order to generate lively discussion, Ms. Skloot requests that you attend the Campbell Hall Lecture the prior evening (4/11 8PM Campbell Hall) to avoid duplicating Questions & Answers raised there. The CCS special engagement on April 12th is specifically for Rebecca to go deeper into the discussion of the book with students and faculty. In preparation, it is also asked that you acquaint yourself with the FAQ page on Rebecca's website:

A limited number of free tickets are available for the event at Campbell Hall. Please see Casey in Room 102 CCS (casey.moreau@ccs.ucsb.edu). These will be available on a first come, first served basis.

Cool Endosymbiotic Algae in a vertebrate!

2011-04-09T14:35:00.000-07:00

This article discusses a pretty interesting case of endosymbiosis, the first of its kind seen in vertebrates. I am very curious about how the algae actually gets in their cells and if there is some bizarre vertical transmission mechanism as mentioned in the article.

Don't worry it's short, no TLDRs!

Original paper is here.

Proteus

2011-04-08T14:06:00.000-07:00

Kathy sent this on:

Chasing Haeckel - A documentary centered on Ernst Haeckel's drawings of radiolarians sets the unity of art and science in motion

Selections from the the film Proteus, a documentary concerning the life, work, and philosophy of Ernst Haeckel, a 19th century naturalist. The film tells of the man's character and influences while using his detailed engravings of Radiolaria, single celled marine organisms, to make animated progressions

Awesome summer opportunity

2011-04-07T14:37:00.000-07:00

Awesome opportunity. Get involved in research, see beautiful places, get fit, and help save a declining amphibian species. What more could you ask?

Andrea needs help with back-country field work studying disease dynamics in mountain yellow legged frogs. The work will involve hiking, backpacking, catching frogs and testing them for chytrid infection, and collecting water samples. Contact Andrea directly if you are interested: andrea.jani@lifesci.ucsb.edu

How to post to the Blog

2011-04-07T13:24:00.000-07:00

This information will be archived as one of the links on the right hand side.

HOW TO SIGN UP TO POST TO THE BLOG
You all received an invitation to join the blog at the start of the Winter quarter. If you need me to send a new invite just let me know.
The invite comes as an e-mail from google with the heading: 'You have been invited to contribute to John Latto's blog'
This will contain a link. (The information that follows is what I think happens but if it is different just follow the instructions). If you click on the link you will have two choices:
If you already have a Google account just log in with your username and password and follow the instructions.
If you don't have a Google account then click the link to sign up for an account. This requires very little in the way of information - just a valid e-mail, the password you want, and the name you want to use. I think you will then get sent an e-mail with a link to click on to validate your account.
If you haven't received that e-mail then check your spam folder since it is an automated e-mail it may have been filtered out as spam.

HOW TO POST
Adding posts is really easy. Starting from scratch you would go to:
http://www.blogger.com
and sign in at the top with your Google username and password.

You should then see the dashboard with the EEMB40 Blog. Click on 'New Post' and a simple word processor type screen will come up. Adding a text only post is as simple as typing it and hitting 'Publish Post'. You will probably also want to add links though (the whole point of the blog really) and adding links is very easy. Just highlight the text you want linked and click the word 'link' on the toolbar at the top of
the entry form. Just cut and paste the link in directly from your browser, including the http://.

Further buttons at the top allow you to format the text, add pictures, spell check and, usefully, remove all the formatting from any section. You can preview posts before publishing them if you wish. Oh and the spellcheck is automatic and very easy to use but comes up with some very strange and amusing corrections for words it doesn't know. It is a good idea to test any links after you have posted to make sure they work (and work as you expect).

Let me know if you have any questions. Rather than give a big long tutorial on how to use the blog publisher I suggest you just play with it and then ask questions. It is very easy to delete posts, and preview them before you publish, so you can practice without messing anything up.

E.O. Wilson on saving life on Earth

2011-04-05T14:21:00.000-07:00

What great opportunities to see E. O. Wilson: this Thursday at CCS from 4-5 in the art gallery (free), and/or at Campbell Hall at 8pm ($15). Hope you will take advantage.

To inspire you, here is his biography. And here is an interview of E. O. Wilson on “Bill Moyers Journal”

And finally, in 2007 he won the prestigious TED prize.

See his TED talk and what he wants to do with his $100,000 prize money:

Voodoo Lily

2011-03-31T11:42:00.000-07:00

Voodoo Lilly in Bloom today only

Very smelly plant attracts flies. This is NOT Mr. Stinky from a few years ago but impressive.

There is also The Stanhopea in bloom in Bay 4 come down and see it.

Bay 4 open now until 1:30 today.

This is in the glasshouses to the west of Noble Hall.

One more for the diary

2011-03-11T23:04:00.001-08:00

EO Wilson is now scheduled to talk in CCS on Thursday afternoon (April 7) at 4:00pm.

Carniverous Plants (Venus Flytrap)

2011-03-10T17:41:00.000-08:00

I found these videos on youtube of the Venus Flytraps in action along with some other carniverous plants.

http://www.youtube.com/watch?v=ktIGVtKdgwo

http://www.youtube.com/watch?v=uJpgMDOZInA&feature=fvwrel

The videos have some great information about the plants. Such as did you know that Carniverous plants can get "indigestion"? Check them out they are cool.

Storytelling

2011-03-10T14:40:00.000-08:00

Thank you to everyone for an interesting end to the quarter. I really do enjoy seeing what has grabbed your imagination.

As well as a (relatively) unstressful opportunity to practice public speaking, this is also a fantastic opportunity for you to see almost 30 brief talks in rapid succession. Which ones did you find most memorable? Why? Think about that for a moment.

Good luck with your finals. Have a safe Spring Break and we will see you in the same place (but an earlier time slot) next quarter. Please sign up for the class if you haven't done so already, our numbers will probably be tight again.

I'm going to take a brief break from daily blogging, although I may still make the odd post if any seminars or research opportunities come across my desk.

Anyway, back to the talks. One of the keys to giving a good talk, whether it is one minute or one hour, is to tell a story. There is something very primal in humans in the way we even respond to the word 'story'. I assume this dates back to the tens of thousands of years when the only means we had to entertain ourselves were sitting around campfires and telling stories (songs are also stories).

Consider yourself in a lecture room. You have come to see a talk because the topic sounded interesting. You don't know much about the speaker but you want it to be a good talk. The speaker steps up to the podium, looks out at the audience and starts their talk. Consider how your brain responds to their first few words:

Today I'm going to teach you about... (oh well, at least I might learn something. I wonder what I should have for dinner...)
Today I'm going to tell you about cytopathological infection of the mammalian gastrointestinal tract... (err okay. Oh look a squirrel!)
Today I'm going to tell you a story... (Cool. I hope its a good story.)

So, regardless of length, think of any talk as a story. Which talks today did you remember? I'm guessing the ones that told a story rather than presented a collection of facts. I'm also guessing that for the talks that were structured as a story you could recall much more of the talks.

A couple of other tips. If you are telling a story then be interested in your story. Enthusiasm is what makes or breaks any oral presentation.

And finally, again regardless of length, have an ending! Always have a well rehearsed final sentence. If you run out of time (which of course you never should) you skip right to your final sentence but you never omit it. Unfortunately many of you had to leave but our final talk for the day had the best final sentence. A fitting note to end on.

New breakthrough in fighting malaria

2011-03-10T00:53:00.000-08:00

Malaria affects hundreds of millions of people every year. It is spread by mosquitoes carrying a parasite that, once introduced to your body, multiplies by manipulating signaling pathways in your liver and red blood cells. The parasite's ability to quickly develop resistance to drugs has hindered attempts to find an effective treatment for the disease. However, it was recently discovered that certain drugs used for chemotherapy can also cure malaria. By disabling the host cells' signaling pathways, these "kinase inhibitors" effectively kill the malaria parasite since it can no longer proliferate. This discovery presents an entirely new method of curing malaria in which we target the host cell environment rather than the parasite itself. This method has several benefits: 1. it is effective against all strains of malaria, 2. the parasite won't be able to develop drug resistance, and 3. since there are already many chemotherapy drugs that have been deemed relatively safe and that could potentially be effective against malaria, it might not be necessary to develop a whole new drug. This breakthrough is a huge step toward a much more effective and permanent treatment of this disease.

Overview:

http://www.sciencedaily.com/releases/2011/03/110308084743.htm

Full Article:

http://onlinelibrary.wiley.com/doi/10.1111/j.1462-5822.2011.01582.x/abstract;jsessionid=A579C344505613F5582C1E83691A00DC.d01t01

More dates for your calendar

2011-03-09T23:18:00.000-08:00

Going to the Extremes -- from the Blue Holes of the Bahamas to Parasitic Ecosystems to Edge of the Universe -- at the Santa Barbara Museum of Natural History

Santa Barbara, CA -- Explore the extremes through the eyes of scientific explorers at the Santa Barbara Museum of Natural History. This lecture series brings Dr. Kenneth Broad (environmental anthropologist), Dr. Kevin Lafferty (ecologist) and Dr. Lynn Rothschild (evolutionary biologist/astrobiologist) who will share their compelling and inspiring tales about the frontiers of science -- from the Blue Holes of the Bahamas to parasitic ecosystems to the edge of the universe. All presentations will be held in Fleischman Auditorium and will conclude with a lively conversation between speaker and audience, as well as an opportunity to meet the scientist. The lectures are weekly on Thursdays (March 10, 17 and 24) and each lecture begins at 7:30 PM. Tickets are available online at www.sbnature.org/tickets or at the door (Museum Members $8; Non-members $10). Parking is free. For more information call 805-682-4711 ext. 170.

EXTREME EXPLORER

Blue Holes of the Bahamas: Caves, Climate, and Cognition

by Dr. Kenneth Broad

Thursday, March 10

7:30 PM

Largely unexplored, and considered among the most hazardous places to dive, the flooded caves, or "blue holes" of the Bahamas, are a potential treasure trove of scientific knowledge. Dr. Broad will speak on the findings of his recent cave diving expeditions to the Blue Holes of the Bahamas which were featured on the cover of the August 2010 issue of National Geographic. Discoveries from the Blue Holes are significant to the fields of microbiology, paleontology and climate science. He will also discuss cave exploration in terms of risk perception.

To quote National Geographic, "Inland blue holes are the scientific equivalent of Tut's tomb. From a diver's perspective, they're on par with Everest or K2, requiring highly specialized training, equipment, and experience. Even more than high-altitude mountaineers, cave divers work under tremendous time pressure. When something goes wrong, if they don't solve the problem and make it back to the cave entrance before their gas runs out, they're doomed."

Dr. Broad is an environmental anthropologist who studies the relationship between humans and their environment. Kenny has led or participated in extreme expeditions around the globe - from dangerous urban slums to the deepest caves on the planet - to gather information and samples that shed light on little known environmental and cultural subjects. He is an associate professor at the Rosenstiel School of Marine and Atmospheric Science and is Director of the University of Miami's Abess Center for Ecosystem Science. He also Co-directs the Center for Research on Environmental Decisions at Columbia University. Broad received the 2006 Emerging Explorer Award and was elected a Fellow National of the Explorers Club in 2009. He received his PhD in anthropology from Columbia University in 1999.

EXTREME PASSENGERS

Parasites Rule! Castration, Mind Control, and Human Culture

by Dr. Kevin Lafferty

Thursday, March 17

7:30 PM

Parasitism is the most popular lifestyle on earth and parasites have evolved insidious and fascinating ways to complete their life cycles. Dr. Lafferty will discuss how parasites quietly affect entire ecosystems and human culture, noting that parasites are normal part of a functioning food web.

Dr. Kevin Lafferty is an ecologist with the US Geological Survey and adjunct faculty at UCSB, specializing in parasites. He's lived in Santa Barbara for 30 years and travelled the world in search of the parasites he admires. He and his wife, Cristina Sandoval, the director of Coal Oil Point Reserve, are actively engaged in local conservation issues.

EXTREME ENVIRONMENTS

Life at the Edge: Life in Extreme Environments on Earth and the Search for Life in the Universe

by Dr. Lynn Rothschild

Thursday, March 24

7:30 PM

Lynn Rothschild has gone from the Bolivian Andes to the Rift Valley of Kenya searching for the hardiest of organisms in the most extreme environments for life. By getting to know life forms on Earth that can occupy the most hostile niches, we can begin to understand the survival requirements for life in general. She describes her quest for "life at the edge" and how such discoveries will shape our search for life in the Solar System and beyond.

Dr. Lynn Rothschild is an evolutionary biologist/astrobiologist at NASA Ames, and Professor at Stanford and Brown University, where she teaches Astrobiology and Space Exploration. She has broad training in biology, with degrees from Yale, Indiana University, and a Ph.D. from Brown University in Molecular and Cell Biology. Since arriving at Ames in 1987, her research has focused on how life, particularly microbes, has evolved in the context of the physical environment, both here and potentially elsewhere. Field sites range from Australia to Africa to the Andes, from the ocean to 100,000 feet on a balloon. In the last few years Rothschild has brought her expertise in extremophiles and evolutionary biology to the field of synthetic biology, addressing on how synthetic biology can enhance NASA's missions. Rothschild is a Fellow of the Linnean Society of London, the California Academy of Sciences and the Explorers Club.

Great research opportunity

2011-03-09T00:02:00.000-08:00

Andrea, a grad student in my wife's lab is looking for good undergrads to help with summer research (and possibly to pair up with to apply for a grant for grad-undergrad research teams).

This is a fantastic opportunity to get involved in a very exciting research project. The Briggs lab works on a number of research areas but much of the current focus is on the frog-killing Chytrid Fungus in the California Sierra Nevada.

Like most folks in the lab Andrea will be doing some back-country field work, but also does a lot of molecular biology (genotyping chytrid strains and characterizing bacterial communities that are symbiotic on the skin of frogs). The general idea is to understand how bacterial community composition and chytrid strain contribute to the outcome of infection (persistence or die-off of populations).

Let me know asap if you are interested and I'll put you in touch with Andrea. Cherie has had lots of great CCS students in her lab and I'd like to continue that tradition.

Zombie taxa

2011-03-08T13:52:00.000-08:00

The dinosaurs all died out at the end of the Mesozoic, about 60 million years earlier. Or did they...

Numerous dinosaur teeth have actually been found in much more recent rock formations, well into the Paeleogene. There are a number of explanations for this.

One explanation is that we are entirely wrong about the extinction of the dinosaurs. They did not go extinct at the end of the Cretaceous and persisted much longer, perhaps to the modern day! But for some mysterious reason their bones stopped being preserved and they just left teeth and claws.

An entirely different explanation, and dare I say a much more plausible one, is that in some taxa fossil structures may be eroded out of one layer and then re-deposited in a younger layer. Given that our fossil record of dinosaurs post-Cretaceous consists of just the sort of a structures (teeth) we'd expect to be washed out and re-preserved the evidence is consistent with this hypothesis.

This hypothesis also predicts that even today we would find structures like dinosaur teeth washed out of sediments and being preserved in brand new depositions. Yes, yes we do. Such taxa are known as zombie taxa.

Save the date

2011-03-07T21:41:00.000-08:00

The Department of Molecular, Cellular and Developmental Biology at UCSB cordially invites all faculty, staff and students to attend:
MORSE SYMPOSIUM
Honoring Dan Morse and his ongoing contributions to the UCSB campus and the at-large research community

Friday, April 15, 2011
100 PM - 530 PM
Loma Pelona Center, UCSB Campus

DRAFT SCHEDULE (speakers confirmed):
100 PM -- coffee/tea/cookies
115 PM -- Opening Remarks hosted by Dr. Joel Rothman, Chair, MCD Biology
130 PM -- Talk #1 (Dr. Bernie Degnan)
230 PM -- Talk #2 (Dr. Jen Cha)
315PM -- BREAK (refreshments)
330 PM -- Talk #3 (Dr. Angela Belcher - Giving Life to Materials for Energy, the Environment and Medicine)
415 PM -- Closing Remarks
430-530 PM -- RECEPTION (libations, hors d'ouevres)

A final schedule will be posted on the MCDB website
(http://www.lifesci.ucsb.edu/mcdb/ ).

Angela Belcher is one of CCS Bio's more famous alumni, director of the Biomolecular Materials Group at MIT and a 2004 MacArthur Fellow (aka the Genius award).

Career opportunities

2011-03-06T15:05:00.000-08:00

Who knew that panda impersonator was even a valid career option?

From a Time Photo-story: Giant Panda People - scientists don costumes for good cause.

In 1980, the Chinese government teamed up with the World Wildlife Fund to establish the China Conservation and Research Center for giant pandas. Since then, with 100,000 visitors a year, it has become the most popular place on the planet to see giant pandas in their habitat. The reserve's mission is to observe, study and breed the endangered species to increase their chances of survival. So far the reservation has successfully bred 66 panda cubs.

Part of the reserve's mission includes placing the pandas it has bred back into the wild. Because previous attempts to reintroduce captive pandas into the wild have been largely unsuccessful, the researchers have developed the novel technique of dressing as the animals to acclimate them to the wild.

I think we need one more picture but you should check them all out at the Time website.

Is the 'panda' on the left eating bamboo? That seems to be taking method acting a bit too far...

Dilemma

2011-03-05T14:38:00.000-08:00

The world’s largest set of shark jaws is going up for auction. The jaws, which once belonged to a megalodon, will be placed up for bid in Dallas, Texas in June at the Heritage Auction Galleries. The asking price is set at $625,000. The previous owner, the late Vito Bertucci, spent 16 years gathering the right shaped teeth to fit the jaw. So paleontologically this may be a specimen of many parts but realistically it is just awesome.

Magalodon is an extinct species of shark that lived roughly about 25 to 1.5 million years ago, during the Cenozoic Era.

It is thought that megalodon looked like a bigger version of the great white shark. Much bigger.

Furthermore a paper in 2008 suggested that Magalodon had the most powerful bite that has yet been discovered.

Personally I think this would look awesome placed around my front door. Assuming it doesn't go for much more than the asking price I guess I could sell my house and buy it but then I wouldn't have a front door... It's a pity CCS doesn't have a large slush fund or a generous benefactor because these jaws would also look great as the entrance to CCS. I'm not sure if they would send the right message but they'd look fantastic.

Lotusland 2011

2011-03-04T18:54:00.000-08:00

Unlike last year when it rained we had beautiful weather this year. The rain did lead to some great pictures last year though. Check out the posts here and here for some photos of the gardens last year in the sun and rain.

Post some pictures from this year if you took some good ones (when you click the photo icon in the posting screen this will give you the option to upload a photo).

Here are two articles about the Lotusland gardens and their founder, Ganna Walska, Forget About Rubies – She Wanted Cycads from the Christian Science Monitor and What The Diva Wrought, published in the Wall Street Journal. Both are short and well worth a read. The second article is hosted at the Lotusland website so click the links on the left for further information about Lotusland.

Early earth tectonics

2011-03-03T14:07:00.000-08:00

This National Geographic video showing plate tectonics during the early earth covers a surprisingly large number of topics we have mentioned in this class - from the surprisingly early appearance of life before the end of the massive asteroid bombardment, to the generation of heat via radioactivity within the earth and the movement of the continents. Notice that they go much further back than Pangaea. Evidence for these early super continents is much weaker than the evidence for Pangaea.

'Here's how it might have happened...'

The UC Museum of Paleotology at Berkeley has some neat animated gifs of Plate tectonics, I like this one that ends with the present day. Check out India smashing into the rest of asia.

Biomimicry for the Future

2011-03-02T21:17:00.000-08:00

This is an amazing short talk on how biomimicry could be utilized to reduce waste products and carbon footprints in modern designs.

Also, this is the Eden Project he references and the seawater greenhouse.

Research Ethics Talk

2011-03-02T12:22:00.000-08:00

And now for something completely different.

*Date and location*: Mon, March 7, 4-6pm, Girvetz 1004

*Speaker*: Prof. Herbert Kroemer

*Abstract*: In early 2002, Bell Labs physicist Hendrick Schoen was considered a rising star in the field of molecular electronics. A little older than 30, Schoen had already authored 90 publications and received a series of prestigious awards. In April 2002, he was being considered for the directorship of the Max Planck Institute for Solid State Research in Stuttgart. In September 2002, he was fired by the Bell Labs and his most prominent papers were withdrawn from publication. What happened? In this talk, Prof. Kroemer will tell us about his role in the investigation on scientific misconduct and discuss issues and repercussions of unethical conduct in research.

To whet your appetite for this talk check out The Rise and Fall of a Physics Fraudster in Physics World. Although this example is from the world of physics the implications for scientific research are very general.

I used to joke with my friends in the physics community that if you want to cleanse your discipline of the worst scientists in it, every three or four years, you should have someone publish a bogus paper claiming to make some remarkable new discovery — infinite free energy or ESP, or something suitably cosmic like that. Then you have it published in a legitimate journal ; it shows up on the front page of the New York Times, and within two months, every bad scientist in the field will be working on it. Gary Taubes.

CUTTLEFISH!!!!

2011-03-01T20:22:00.000-08:00

Cuttlefish are amazing animals! They can change their color faster than a chameleon because they have chromatophores which are special cells. They can change their pigment to complicated shapes to fit their background, and amazingly enough most cuttlefish are color blind!

Cuttlefish are color blind and yet they are masters of camouflage. Scientists don't know how they read colors, which they can do in the dark, perhaps something about their skin.

A strange fact about the cuttlefish is that it can adopt the female coloration along one side of the body as well as retain the male coloration on the other side. Male cuttlefish are extremely alert when it comes to the females, especially if she is laying the eggs. The male will guard aggressively over the female and this is when another approaching male will use his ability to have a dual look to access the female and trick the male.

Here are some cool links about the cuttlefish :)

http://www.answersingenesis.org/creation/v19/i2/cuttlefish.asp

http://www.stopdown.net/bio%20camouflage%20cuttlefish.htm

http://news.discovery.com/videos/animals-cuttlefish.html

http://www.youtube.com/watch?v=2x-8v1mxpR0

More epigenetics

2011-03-01T14:24:00.000-08:00

The Scientist magazine (the magazine of the Life Sciences) March issue has a special Focus on epigenetics.

I haven't had time to read these yet but there's a whole bunch of interesting looking articles:

and, in case you thought this wasn't relevant to today's lecture:

The Footprints of Winter - Epigenetic marks laid down during the cold months of the year allow flowering in spring and summer.

Many plants that grow in climates with a cold winter require growth for several months at low temperatures—a process called vernalization—to promote flowering in spring, when days lengthen and temperatures increase. Without this period of cold, plants would grow leaves in the spring, but would fail to flower. This phenomenon, familiar to every horticulturist, was difficult to explain with genetics alone; something occurred during those cold months that left a mark, which, in effect, released a switch that permitted flowering in spring. In recent years, the field has looked beyond the genome and found that vernalization is controlled by a wide range of epigenetic mechanisms.

Cactus Walking On 20 Legs Found In China

2011-03-01T11:10:00.001-08:00

Cactus Walking On 20 Legs Found In China

http://www.npr.org/blogs/krulwich/2011/03/01/134138005/cactus-walking-on-20-legs-found-in-china

There was a wild period — roughly 520 million years ago — when life, for no obvious reason, burst into a crazy display of weird new fantastic forms — producing creatures in shapes never seen before or since. Consider this animal, the newest fossil discovery from Jianni Liu in China. She calls it "the walking cactus."

Nature

This is not a plant, not a sculpture. It was a live animal, with no eyes, what may or may not be a head, mostly a gaggle of limbs, armor-plated, covered in thorns, attached to a stomach.

What is it? Taxonomically, Jianni Liu thinks it's a lobopodian, a group of animals described as "worms with legs." Lobopodians are about the craziest looking critters that ever lived. A whole zoo of them appear in the rocks around Chengjiang, China. Here's what the walking cactus looks like in a rock...

Nature

A fossil of Diania cactiformis.

Jianni Liu has found three well-preserved walking cactus fossils, but previously discovered lobopodians are even weirder. Hallucigeni, so named because of its "bizarre and dreamlike quality" (said the scientist who described it) is another walking worm that has what looks like a head-like blob on one side, but with no mouth, no eyes, no sensory organs, so it probably isn't a head.

Mary Parrish/Smithsonian Institution

No one can quite figure out if those projections are walking legs or feeding tentacles. We're not sure which side is up, which is down, but we know it lived in shallow seas and so the folks at the Field Museum in Chicago have imagined it taking a walk on a sunny day...moving something like this...

Pitcher Plants

2011-02-28T23:34:00.001-08:00

The usual stunning photography reveals the complex ecology of a pitcher plant.

It's not just the genes...

2011-02-27T21:56:00.000-08:00

Increasingly we are realizing that it isn't just the genes that are important but how those genes are expressed.

This was nicely illustrated in a Science paper this week where they looked at the role of the Agouti gene in pattern development: The Developmental Role of Agouti in Color Pattern Evolution.

Agouti, ... governs color patterns in deer mice, the most widespread mammal in North America. This gene, found in all vertebrates, may establish color pattern in a wide variety of species, a process that has been poorly understood at both the molecular and the evolutionary level.

Agouti had previously been known to affect the type of pigment found in vertebrate fur, feathers, and scales: Little expression of the gene in adults results in the production of dark pigments, while robust Agouti activity generally yields light pigment production. But Manceau and Hoekstra found that subtle changes in the gene's embryonic activity can also make a profound difference in the distribution of pigments across the entire body.

"During embryogenesis, Agouti is expressed in the belly, where it delays maturation of the cells that will eventually produce pigments," says Hoekstra, John L. Loeb Associate Professor of the Natural Sciences at Harvard. "This leads to a lighter colored belly in adults, which is the most common color pattern across a wide variety of vertebrates, from fish to antelope."

Even small changes in Agouti gene expression can establish a completely new color pattern. In deer mice, natural selection drives changes in the amount and place of Agouti expression, which in turn results in new color patterns that can camouflage animals from visual predators in habitats including dark forests and light sandy beaches.

"It is hard not to speculate that Agouti plays a role in generating more complex patterns -- from stripes to spots -- in a diversity of vertebrates," Hoekstra says.

Looking for a picture of a leopard to add I found this cool picture of a black panther (panthers are just black leopards). Notice how you can see the pattern of spots in the fur even though the fur is all black.