Monday, January 30, 2012

Things Darwin didn't say

It's probably safe to say you've made a significant impact on science when people write whole articles on what you didn't say.  In the case of Darwin this isn't actually as odd as it sounds since many people believe he said a lot of things he didn't and still manage to underestimate the importance of what he did say. I think this article from the Guardian (A British Newspaper) is a nice piece of popular science writing.

It ain't necessarily so ...Darwin was no atheist, he didn't say humans came from monkeys, and 'survival of the fittest' - that was someone else's idea. John van Wyhe clears up some myths

Saturday, January 28, 2012

Human height

The data on human height I mentioned in class was taken from this fascinating article from the New Yorker on changes in human height, subtitled 'Why Europeans are getting taller and taller—and Americans aren’t.' There is some great writing here and some wonderful images which I confess I shamelessly stole for class.

"Charlemagne was well over six feet; the soldiers who stormed the Bastille a millennium later averaged five feet and weighed a hundred pounds. “They didn’t look like Errol Flynn and Alan Hale,” the economist Robert Fogel told me. “They looked like thirteen-year-old girls.”

Friday, January 27, 2012

Ocean acidification

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.

Thursday, January 26, 2012

American degeneracy

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.

Wednesday, January 25, 2012

Not ready for prime time

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

Tuesday, January 24, 2012

Rapid evolutionary innovation

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. 

Monday, January 23, 2012

Run and twiddle

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!

Sunday, January 22, 2012

Chlamydia pneumoniae - no smoke without fire?

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.

Saturday, January 21, 2012

Meet the Clostridiums

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

Friday, January 20, 2012

Biodiversity bonanza

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.

Thursday, January 19, 2012


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.

Wednesday, January 18, 2012

Endogenous retroviruses

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?

Tuesday, January 17, 2012

Cool Article On Multicellular Evolution

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
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."

Monday, January 16, 2012

Gray Whale Count

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, UCSB Scott 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:

Get to the Point in 2012.

Saturday, January 14, 2012

Facial color patterns in primates

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."

Friday, January 13, 2012


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.

Thursday, January 12, 2012

Sample size >>1

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 

Wednesday, January 11, 2012

Stem cell seminar tomorrow (Jan 12th)

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

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.

Tuesday, January 10, 2012

Experiment Exploded ! ! !

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.