Friday, April 30, 2010

Horizontal gene transfer

A couple of recent papers are providing good evidence for the horizontal transfer of genetic material between species.

In the Journal Nature this week: A role for host–parasite interactions in the horizontal transfer of transposons across phyla.

The horizontal transfer (HT) of genetic material between non-mating species, common in bacteria, is increasingly being recognized as a significant force in eukaryotic evolution. Most instances of HT described so far in metazoans involve mobile genetic elements — mainly transposons — but the mechanisms enabling this exchange between widely divergent species are unknown. Gilbert et al. now show that transposable elements spread between disparate species by hitch-hiking in the genomes of parasites shared by these species. Specifically, Rhodnius prolixus, an insect that feeds on the blood of tetrapods and which is the vector of Chagas disease in humans, carries four distinct transposon families in its genome that can invade the genomes of a range of tetrapods including the opossum and squirrel monkey. One of these transposon families is also present in the pond snail Lymnaea stagnalis, a vector of trematodes infecting many vertebrates.

A paper in Nature earlier this year revealed that horizontal gene transfer has also been important in the evolution of virulence in Fungi: Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Fungi of the genus Fusarium are important plant pathogens, causing various blights, root rots and wilts. While some species have a wide host range, others are more selective. Comparative genomics of three Fusarium fungi with broad and narrow host range, two newly sequenced, provide clues as to what drives these differences. Experimental follow-up shows that simply by mixing two strains on standard growth medium, transfer of two whole chromosomes from a Fusarium oxysporum tomato pathogen turns a nonpathogenic strain into a pathogenic one. These findings shed light on the evolution of host range and pathogenicity.

Thursday, April 29, 2010


I hope that some of you are exploring the past posts on the blog. After all there are, quick check, 530 of them! Even I'm forgetting what I've already written about. Here's a few posts about topics we covered today that might interest you.

Wednesday, April 28, 2010

Shoestring rot

The giant fungus I mentioned in class is an individual Armillaria bulbosa, or honey mushroom. I've posted about this study before so check that out for further details on the 'pulsating mass of fungus'.

A subsequent study in Oregon revealed an even larger individual of another species in the same genus, Armillaria ostoyae or 'Shoestring rot' . This fungus attacks the sapwood of a variety of tree species and is able to travel great distances under the bark or between trees in the form of black rhizomes.

A question in class about why individuals are able to get so big is possibly answered by this comment by the author of the study I found on a BBC news report:

The huge size of this fungus may be related to the dry climate in eastern Oregon, Dr Dreisbach said. Spores have a hard time establishing new organisms, making room for the old-timers to spread.

This is the original paper, Coarse-scale population structure of pathogenic Armillaria species in a mixed-conifer forest in the Blue Mountains of northeast Oregon,

Tuesday, April 27, 2010

Clinton Global Initiative

Forwarded from Bruce. The deadline is rather close but it's an interesting looking program.

Apply now to fund your student project! The Clinton Global Initiative University's 2010 Outstanding Commitment Awards, sponsored by Walmart, will award anywhere from $1,000 - $10,000 to support student-led projects in the areas of Education, Environment & Climate Change, Peace & Human Rights, Poverty Alleviation, and Public Health. The deadline for these awards has been extended to Friday, April 30th.

The CGI U Outstanding Commitment Awards were launched in 2008 to provide financial support to innovative, student-driven initiatives. To view a map of previous award winners and their projects:

Take advantage of this funding opportunity by submitting an application today:

Monday, April 26, 2010

..and now for something completely different.

After years of neglect it appears that microbial art is making something of a come back. Because we'll be talking about Fungi tomorrow here's a Fungus made out of bacteria by Niall Hamilton . Hmm, that's just wrong.

For all your microbial art needs there is the MicrobialArt website. You can see more from Niall Hamilton, and many more.
From an interview at MycoRant:

Hamilton uses both fungi and bacteria in his creations, and each no doubt has its own advantages and disadvantages. “I have to say I’m rather envious of other artists’ work with bioluminescent bacteria or slime molds,” he offers, adding, “both of which I think are very visually impressive. But, I haven’t had the opportunity to work with them (simply because I haven’t isolated them). Bacteria I like for the fast growth and clean edges, but they generally are a lot more limited in range of color and texture than the fungi.”

Sunday, April 25, 2010

Complexity and Diversity

In Science this week: Complexity and Diversity
The mechanisms for the origin and maintenance of biological
diversity are not fully understood. It is known that frequency-dependent selection, generating advantages for rare types, can maintain genetic variation and lead to speciation, but in models with simple phenotypes (that is, low-dimensional phenotype spaces), frequency dependence needs to be strong to generate diversity. However, we show that if the ecological properties of an organism are determined by multiple traits with complex interactions, the conditions needed for frequency-dependent selection to generate diversity are relaxed to the point where they are easily satisfied in high-dimensional phenotype spaces.

"When you model one trait at a time--in isolation--you often find that ecological interactions aren't strong enough to drive divergence. But with many traits acting in concert, even very weak interactions can generate diversity. Our approach mirrors the complexity of reality more closely--if you think about it, all living organisms have at least dozens, if not hundreds, of ecologically relevant traits," says Doebeli.

Thursday, April 22, 2010


Campus point is a very convenient place to see some nice intertidal species and some good zonation. What it lacks is some good tidepools where you can spend a whole day hunting for those more elusive creatures - sea hares, nudibranchs (pictured is the Spanish Shawl nudibranch, Flabellina iodinea), octopus etc.

Any tide below 0 is sufficient to reveal interesting tidepools and critters and with lows in the negative range the viewing is probably good for an hour or two before and after low tide. You can pick up printed tide tables at bait shops, boat supply places etc or access them online (there are apps for your phone and gadgets/widgets for pc's and apples ) or use Saltwater Tides.

There are several good local spots for tidepooling. Some require a bit of planning but all are accessible by bike and you should check them all out.

Devereux Point (Coal Oil Point) and the area between there and IV is the most convenient spot for most of you. The point itself has some decent sized rocks and is easy to get to from campus. Straight down Del Playa and keep going on the path along the bluffs when DP runs out. Or just follow the surfers. The flat area of rock that is exposed at a low tide between Coal Oil Point and IV is good for tidepooling.

A better spot is the reef between Elwood Bluffs and Haskell's Beach (now better known as the beach by the Bacara resort). For a weekend outing you could cycle (or drive) west on Hollister until just before it crosses the railway and ends at the Freeway. Take the well signposted turn to Bacara resort. Go about half a mile down here to the public parking lot (free). You can leave your bike here and walk a hundred meters down to the beach. Turn left (East) and at a low tide you can walk for miles, largely in solitude heading back towards campus. The tidepools start getting really good just past the two stubby piers you can see and keep getting better and better. If you get a friend to drop you off you could walk all the way back to campus. I think it would be about 4 miles from Bacara back to campus.

Or for a summer adventure check out the Naples coast. Follow the instructions above to Haskells beach at the Bacara resort but head West on the beach (ie turn right away from campus). You'll go past the prominent pier used to ferry workers to and from the oil platforms. Then past a pleasant beach with, as you will see, the appropriate name Driftwoods. There's a surf break here so you'll see the odd surfer. As you leave this beach you may not see anyone again for several hours because there is no further public access until you get to El Capitan State Beach. At a low tide there is then several miles of fabulous tidepooling. You'll also see lots of seals, cormorants and other critters. About 3 miles from Bacara you'll come to Dos Pueblos Canyon, with a somewhat incongruous trailer almost on the beach. That's a good point to turn around if you don't want to get cut off by the tide! You need to time this one right, I usually hit the oil pier by Bacara about an hour and a half before low tide and turn around at low tide (assuming a -1 low). It's 3 miles from Bacara to Dos Pueblos Canyon.

You can find some maps of this part of the coast at the SaveNaples website (scroll down this document for cool aerial photographs/maps). This beautiful part of the Gaviota coast is under imminent threat of development although it looks like the current financial situation has both affected the developer and reduced demand for the proposed luxury homes.

Let us know what you find, or better, post some pictures. There's a really nice tide pool website at Santa Barbara City College with a great many of the beautiful pictures taken right by UCSB campus so these are the plants and animals you will see. Check out the 'Treasures' page. These are some of the organisms you might catch sight of.

Wednesday, April 21, 2010


Meanwhile, in less fart related news.... (Seriously, read the article below, it's got some interesting physiological facts.)

1) Don't forget that we will be heading for the beach tomorrow. Wear something warm and some shoes you don't mind getting wet. The weather looks like the worst of the rain and any chance of thunderstorms will have passed.

2) Shortly we will move into our physiology lectures. All hearts and muscles and skeletons and gas exchange. To see them in action come join the fun at the 3rd annual Gaucho Gallop 10k race on Saturday. You can sign up online (ends 5pm today) or on the day. The weather looks like it will be much nicer on Saturday.


Alright, this is quite off-topic from the community ecology we have been talking about in class, but I thought it was interesting and worth sharing. If you can get past the fact that this is an article by Vice (and with that comes their obvious attempt at humor), there's some pretty interesting information from when they interviewed a proctologist who had some pretty good stories. Check it out.

Tuesday, April 20, 2010

Competition Drives Big Beaks Out of Business

The Darwin's Finch story I briefly mentioned is a fascinating part of a long term study by husband and wife team Peter and Rosemary Grant. They now have an amazing 37 year data set on these small birds on the Galapagos.

One of the latest parts of the story to be revealed was published in Science in 2006 as Evolution of Character Displacement in Darwin's Finches. It's also included in their news summary as Competition Drives Big Beaks Out of Business.

I think the fascinating part of this story is that it is the interaction of environment and competitors that drives evolution. Whilst resources are plentiful competition is weak but during the drought the effects of competition became severe.

Here we report that a Darwin's finch species (Geospiza fortis) on an undisturbed Galápagos island diverged in beak size from a competitor species (G. magnirostris) 22 years after the competitor's arrival, when they jointly and severely depleted the food supply. The observed evolutionary response to natural selection was the strongest recorded in 33 years of study, and close to the value predicted from the high heritability of beak size. These findings support the role of competition in models of community assembly, speciation, and adaptive radiations.

Monday, April 19, 2010

The Psychological Immune System

We won't get to the immune system for a little while yet, but we will get there this quarter. However I thought this was interesting:

Is it good for your health to see me coughing, sneezing and blowing my runny nose? Believe it or not, recent research suggests that the answer might be: Yes.

Of course, it's not good for your health if I sneeze right into your face. You're better off not being exposed to all those disease-causing microbes in the first place. But if you are exposed to those microbes, your immune system is going to have to fight them off; and it may fight them off more aggressively if you've just been looking at people who look diseased. That's the implication of some new results published by scientists at the University of British Columbia.

Check the full story in Psychology Today - The Psychological Immune System. Why seeing me sneeze makes you healthier for an interview with the authors and the explanation for the picture above. The actual paper, in Psychological Science this month, is available here: Mere Visual Perception of Other People’s Disease Symptoms Facilitates a More Aggressive Immune Response

Sunday, April 18, 2010

Weekend squirm

Most people could do without the discovery of a new species of leech that specializes on the mucus membranes, including eyes, urethras, rectums, and vaginas.

The new species—dubbed Tyrannobdella rex, or "tyrant leech king" was discovered in the remote Peruvian Amazon region

The full report is in PLoS ONE this week: Tyrannobdella rex N. Gen. N. Sp. and the Evolutionary Origins of Mucosal Leech Infestations and National Geographic also has a write up with a catchier title: "Tyrant King" Leech Discovered, Attacks Orifice- Toothy new T. rex saws into eyes, rectums ... and so on.

"As Douglas Adams would say: Do we want a planet that is only full of panda bears and pine trees?" he said. "The loss of any species is going to make this planet colder and lonelier."

Hmm. I'm not convinced that most people would see the argument this way. I could be wrong but I suspect most people would rather live on a planet without orifice invading leeches. I'm a card carrying bleeding heart liberal tree hugger and I'm in two minds about this one so I don't see Mr and Mrs Middle America caring too much for the Tyrant Leech King. I believe that conservationists need to get their story straight, or at least consistent. Why should we care about the tremendous diversity of life on the planet? Because we might get valuable products from it? Because it provides invaluable ecosystem services? Because we have a moral responsibility to do so?

Friday, April 16, 2010


Vaccine-autism claims, "Frankenfood" bans, the herbal cure craze: All point to the public's growing fear (and, often, outright denial) of science and reason, says Michael Specter. He warns the trend spells disaster for human progress.

of the TED talks. This one raises interesting point about scientific literacy. The time machine question in the first few moments is really rather intriguing. I'd like to see the results from a large sample of people especially if the answers were broken down by age and sex. Actually I'd like to see them broken down by political affiliation too. Oh, and maybe by religious beliefs.

Thursday, April 15, 2010

Eutrophication and Recovery

The classic whole lake experiments Claudia referred to were published in Science as Eutrophication and Recovery in Experimental Lakes: Implications for Lake Management. The lead author, David Schindler, was elected to the National Academy of Sciences in 2006 and they have a nice profile of him that explains some of the background to the experiments and their impact.

Aerial photographs captured the dramatic results: the phosphorous-treated half of the lake had become green and murky because of algal blooms, whereas the other half of the lake remained clear. Pictures can speak a thousand words, and the stark contrast of the two sides of Lake 226 caught the public's eye and policymakers' collective ear.

Wednesday, April 14, 2010

Summer REU positions

From Susan Mazer - a Professor in EEMB:

This a great (and well-paying) opportunity for two motivated and NSF is particularly interested in funding students from under-represented groups.

Check here for further details: (pdf file).

Evolutionary Genetics, Ecological and Physiological Research: The Mazer lab recently received a five-year grant from the National Science Foundation to study the evolution of different pollination mechanisms (or “mating systems”), along with the evolution of physiological performance and life history in a group of California native wildflower species (in the genus Clarkia). This group of wildflowers is unusual in that the ability to self-fertilize (that is, to produce seeds without the assistance of crosspollinating insects) has evolved multiple times from insect-dependent, outcrossing relatives. Two subspecies of the species Clarkia xantiana (shown above) illustrate the kind of floral trait that is associated with the evolution of the ability to self-fertilize: smaller flowers with pollen that is “dumped” right onto the adjacent stigma. Our research group develops and tests a variety of genetic and ecological predictions and hypotheses concerning the causes and the consequences of the evolution of selffertilization. If you are selected as an REU student for the summer of 2010, you would help us to measure the physiological stress responses (anti-oxidant production) that these plants exhibit throughout the flowering season. Much of the activity would be conducting chemical assays in our lab at UCSB, but you would also have the opportunity to assist with field work in June and July, visiting our remote and rugged field sites in the southern Sierra Nevada.

Tuesday, April 13, 2010

Mutualism.... Or just really cute?

Had a friend send this to me... Looks like both species are benefiting from this relationship :)!Wisdom/OrangutanAndHound.html

Sea Otters: Cute lil critters or sex crazed maniacs?

Claudia showed some cute sea otter pictures but sea otters always look cute - they probably look cute even when they are practicing necrophilia or trying to rape baby harbor seals.

Without even trying too hard sea otters can reach almost lethal levels of cuteness. Anyone remember this viral video from a few years back (check out the number of hits - almost 14 million!). At about 1:20 into this video the cuteness level gets dangerously high.

Monday, April 12, 2010

Population Prospects

Here's an interesting statistic that I ran across recently that is related to the last class.

Which is the only country in the world where mandatory contraceptive courses are required for both men and women before a marriage license can be obtained?

No, it isn't China.
Highlight the answer if you are curious--> Iran

For the most up to date information on population trends the 2008 revision of the UN's World Population Prospects is available here. The Population division website has links to lots more data.

Saturday, April 10, 2010

REU opportunity in Bermuda

The Bermuda Institute of Ocean Sciences has received National Science Foundation Research Experiences for Undergraduates (REU) funding to support 8 fellowships for undergraduate student research at BIOS during the 2010 fall semester (DATES: arrive on September 1, 2010 - depart on November 24, 2010). Students will design and conduct independent projects under faculty supervision within several research areas including:
  • Biology, chemistry and physics of the open ocean
  • Biology, physiology and biochemistry of reef building corals and reef ecosystems
  • Aspects of the molecular biology of marine organisms
  • Environmental chemistry of Bermuda's atmosphere and inshore waters
  • Effects and consequences of global environmental change
See their website for further details

Initial selection begins May 30 which is the unofficial deadline for applications.
Students who have completed at least two years of undergraduate study and will still be undergraduates in the fall of 2010 are eligible to apply.

Friday, April 9, 2010

Study finds sexism rampant in nature

One of the millions of lionesses trapped in an abusive relationship.

How come nobody posted this? If I read the Onion more than you do then something is very, very wrong in the world. From a few weeks ago: Study Finds Sexism Rampant In Nature.

"The sexist attitude that child-rearing is 'women's work' is prevalent throughout nature and has been for generations, probably since reptiles first developed mammalian characteristics in the Triassic period," Tannen said. "Sadly, most creatures never pause to challenge these woefully outdated gender roles."

Thursday, April 8, 2010

Anaerobic metazoan

Sandwiched between 'Earliest known Led Zeppelin recording' and 'Evolutionary Psychology Bingo' on BoingBoing is A multicellular organism that lives without oxygen.

This is based on a paper in BMC Biology entitled The first metazoa living in permanently anoxic conditions.

This is the first evidence of a metazoan life cycle that is spent entirely in permanently anoxic sediments. Our findings allow us also to conclude that these metazoans live under anoxic conditions through an obligate anaerobic metabolism that is similar to that demonstrated so far only for unicellular eukaryotes. The discovery of these life forms opens new perspectives for the study of metazoan life in habitats lacking molecular oxygen.

Wednesday, April 7, 2010

Primate sperm competition: speed matters

Sperm cells from the sexually promiscuous chimpanzee and rhesus macaques swim faster and with greater force than those of gorillas. The surprise was how fast human sperm cells swim.

Tuesday, April 6, 2010

Our Planet our Problem


This conference will bring influential members in the climate change arena to UCSB in order to provoke critical thought about the dilemma at hand. This full day event, featuring three panels addressing grassroots, business, and legislative solutions, respectively, comes in the wake of the UN Climate Conference in Copenhagen, Denmark. The event has been organized by students, and was conceived by a group of 23 undergraduates who were inspired to bring change to their campus community after attending the UN summit in December of 2009. By integrating grassroots, business, and government efforts, the event will empower the nation's youth to seek a greener future.


Sponsored by the Associated Students Environmental Affairs Board, UCSB Environmental Studies Program, the College of Letters & Sciences Critical Issues in America series, the Institute for Energy Efficiency, Campus Progress / Center for American Progress, the League of Women Voters of Santa Barbara, the Community Environmental Council, Office of the Chancellor, Office of the Vice Chancellor for Student Affairs, Collegiate Panhellenic Council, Office of the External Vice President for Local Affairs, and the Green Campus Program

10:00AM - 12:00PM
Global Climate, Local Change
Corwin Pavilion

Presenter/Speaker Info
Dave Davis, CEO & Executive Director, Community Environmental Council
Jason Mark, Author, Building the Green Economy: Success Stories from the Grassroots; Director, Alemany Farm
Kandi Mosset, Tribal Campus Organizer, Indigenous Environmental Network
Alec Loorz, Founder, Kids vs. Global Warming
Moderator: Natasha Joyce Weidner, Sustainable Foods Chair, Environmental Affairs Board

Panel Description
This panel will demonstrate the power of individuals to tackle climate issues in their communities at the grassroots level. Unique approaches on a local level are a crucial element to achieving a climate solution. The passionate work of average citizens around the United States continues to build even when the government and business fail to act. We invite members of the Santa Barbara community to come learn what is being done now to reduce our climate impact.

Refreshments served

12:00 - 1:30 PM
Student Film Screening: Navigating Copenhagen
Corwin Pavilion

Movie Description: 23 UCSB students attended the 2009 United Nations Climate Conference in Copenhagen, Denmark. This film catalogues their experiences and perspectives on the international deliberations as well as the grassroots activism outside of the official conference.

Presenter/Speaker Info
Students from UCSB Copenhagen delegation
Moderator: Corie Radka, External Affairs Chair, Environmental Affairs Board

1:30 - 3:30 PM
The Green Economy: Moving Beyond Business as Usual
Corwin Pavilion

Presenter/Speaker Info
Jim Dehlsen, Founder & Chairman, Clipper Windpower
Brent Constantz, CEO, Calera Corp.
John Fielder, President, Southern California Edison
Moderator: David Auston, Associate Director, Institute for Energy Efficiency

Panel Description
This panel will highlight the integral role of business innovation in reconciling society and climate. For global capitalism to function properly in the 21st century, new solutions must take hold that minimize our impact on the environment. Science, technology, and industry are mobilizing to advance a new, green economy. It will take forward-thinking ideas to reshape society, create jobs, and usher in a new era of sustainability.

4:00 PM - 6:00 PM
The Power of Politics: Legislative Measures that Work
Corwin Pavilion

Presenter/Speaker Info
Fran Pavley, California State Senator
Mary Nichols, CA Air Resources Board Chairman
Moderator: Robert Wilkinson, Professor, Environmental Studies

Panel Description
This panel will explore legislative solutions to climate change at the international, domestic, and sub-national levels, with particular emphasis on measures that work. Panelists will address the audience with a focus on solutions, and will speak to the potential of youth and activists to effect change in the policy arena.

6:00 PM - 7:00 PM
Reception in the MultiCultural Center

Monday, April 5, 2010

Bigger testes and semen displacement

A paper in PLoS One last month: Genetic Patterns of Paternity and Testes Size in Mammals

Also the subject of a news article in National Geographic: Bigger Testes Can Offer a Competitive Edge

When competition for females is fierce, males of some species have evolved bigger testes to trounce their rivals, a new study has confirmed.

Specifically, the research shows that testicle size matters in highly competitive animal societies in which females mate with many males or in which females live in groups ruled by an alpha male that must constantly defend his harem.

But that doesn't mean that females seek out more endowed males. Rather, the rivalry occurs after mating, as sperm battle inside the female.

Not surprisingly, males with larger testes produce more sperm—giving the male, so to speak, more bang for his buck.

Just how much all this applies to humans is always interesting to consider. Here's a curious paper with a lot more speculation than data: Semen Displacement as a Sperm Competition Strategy in Humans

We examine some of the implications of the possibility that the human penis may have evolved to compete with sperm from other males by displacing rival semen from the cervical end of the vagina prior to ejaculation. The semen displacement hypothesis integrates considerable information about genital morphology and human reproductive behavior, and can be used to generate a number of interesting predictions.

Saturday, April 3, 2010

Something for the weekend

I briefly mentioned some of the work of University of Manchester researchers Robin Baker and Mark Bellis. Their work on sperm competition in humans has attracted quite a number of popular articles.
Here's one from New Scientist: The subtle side of sex and one from the somewhat dubiously entitled Sperm competition and the Kamikaze Sperm Hypothesis.

Both are well written and interesting articles with the latter article from 2007 being a little more critical of the kamikaze sperm hypothesis in humans than the earlier 1993 article.

Thursday, April 1, 2010

I googled dragonfly penis so you don't have to....

There are numerous articles on this topic (people love to read about freaky animal sex). National Geographic's is pretty good but, sadly, does not include any pictures of the 'rigid, spoonlike, and sometimes spiky' penis. The picture to the left is from Jonathan Waage's seminal (pun intended) paper Dual Function of the Damselfly Penis: Sperm Removal and Transfer

Grab, shake, bite, gouge, puncture, split, punch: It's enough to put anyone off sex.

In a brilliant experiment some years ago, Jonathan Waage of Brown University discovered the Rosetta stone to this strange mating behavior. Waage studied the jewelwing damselfly Calopteryx maculata. First he examined the sperm-storage organ of females after a couple of matings to determine whether sperm from a second mating was added to sperm from the first. He was surprised to find that the amount of sperm hadn't changed. Then he dissected pairs in the midst of copulation and studied their sex organs under an electron microscope. The experiment revealed that a male dragonfly uses his penis not just to transfer sperm to the female, but also to remove sperm left in her storage organ from previous matings. When he curls into that wheel position and begins his energetic genital thrusting, he's actually using his rigid, spoonlike, and sometimes spiky, penis to scrape out rival sperm before he deposits his own.

Such a ploy is necessary, Corbet says, because of female choice and sperm competition. A female nearly always mates with more than one male; it's in her interest to "upgrade" her fertilizations if she can, thereby exercising choice over the paternity of her offspring. Males want their sperm alone to prevail, so they have evolved strategies for purging other sperm and for discouraging mates from copulating with rivals. In this game of sexual chess, the last sperm into the female's storage organ wins by fertilizing her eggs.