Kamis, 24 Maret 2011

Living with Invasive Species

What should be done when non-native species introduced into an ecosystem begin to outcompete native species? Should such invasive species, as they are called, be eradicated before they do serious damage to an ecosystem and lead to a loss of biodiversity? The traditional answer is yes, according to many conservationists. But the sad fact is that that most invasive species eradication efforts haven’t been very effective.

More recently, some conservationists are beginning to rethink the problem of invasive species. Perhaps invasive species should be viewed as a more normal part of the constant change that has been shaping our world since life began. Containment rather than eradication seems to be the new buzzword. Ecologists who study the effect of invasive species on ecosystems say that over time, native species begin to compete more effectively against invasive species. It may take decades or even centuries, but eventually a new ecosystem balance is likely to be achieved, with or without human intervention.

Jumat, 11 Maret 2011

The Simeons Therapy Diet Fad

The New York Times published an article this week on the latest diet fad; a daily food intake of just 500 calories a day combined with daily injections of human chorionic gonadotropin (hCG). It’s known as the Simeons therapy, and it’s been around since 1964.

Frankly, the New York Times article stirs up an old “controversy” that shouldn’t still exist. Anyone who can stick to a 500 calorie-per-day diet will lose weight. Weight loss accomplished on the Simeons therapy diet has nothing to do with the added hCG, according to a well-documented review written in 1995.

The FDA has warned that non-injectable “homeopathic” forms of hCG available over the counter cannot be labelled as having have weight-loss properties. But there’s a long-standing tradition of allowing physicians to decide what is best for each patient (in consultation with the patient, of course). Therefore, physicians can legally prescribe injectable hCG as part of a diet plan if they wish, whether or not it works. And of course, they are free to charge whatever they like for the consultation/evaluation prior to writing the prescription.

Acquaint yourself with the facts, and then don’t waste your money on this diet.

Kamis, 10 Maret 2011


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

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.

Full Article:

Rabu, 09 Maret 2011

More dates for your calendar

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.


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.


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.


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

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.

Selasa, 08 Maret 2011

Zombie taxa

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.

Senin, 07 Maret 2011

Redefining Evolutionary Relationships

The evolutionary tree of life may undergo a makeover in the next decade or so.

In the past, the primary sources of information about the evolutionary relationships between organisms came from the fossil record or from comparative anatomy, physiology, or biochemistry. But now a new scientific field called phylogenomics (the study of the evolutionary history of organisms based on genetics) has emerged, thanks to the increased availability and cheap cost of sequencing DNA.

How does comparative DNA sequence data tell us anything? By tracing specific differences in the nucleotide sequences of the genes of closely related species, phylogeneticists can tell just how closely related two species are and when they most likely split from a common ancestor. That’s because when a mutation (a change in nucleotide sequence) occurs by random chance in a common ancestor, that mutation should still be present in all subsequent descendants of that ancestor. So when exactly the same mutation appears in the same gene in two species, the mutation most likely occurred before the two species split from a common ancestor – i.e. the two species are related to each other by a common ancestor.

The DNA sequences of a wide variety of species are now known, and more are being determined every day. We can expect challenges to the current tree of life (also called the phylogenetic tree) as the data are analyzed and debated.

Save the date

The Department of Molecular, Cellular and Developmental Biology at  UCSB cordially invites all faculty, staff and students to attend:
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).

Minggu, 06 Maret 2011

Career opportunities

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...

Sabtu, 05 Maret 2011


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.

Jumat, 04 Maret 2011

The Sixth Mass Extinction

Over about 3.5 billion years, evolution (descent of species over time, with genetic modification) has produced the astonishing variety and number of life forms found on Earth today. Punctuating this natural evolutionary process of speciation have been five mass extinctions – periods characterized by the rapid (compared to evolutionary processes) loss of over 75% of all species. Past causes of mass extinctions include major changes in ocean and atmospheric chemistry, changes in climate, periods of volcanic activity, and an impact with an asteroid.

According to a recent review article in Nature, we may be about to enter a sixth mass extinction, meaning that over the next 300 to several thousand years we can expect that over 75% of all current species will become extinct. Somewhat disturbing is the suggested cause – humans. Won’t THAT be an interesting and contentious debate over the next 300 years or so!

This is a well-referenced review in a high-quality journal. It’s worth reading if you’re interested in this subject. The notion that the next mass extinction may be caused by humans is only a small part of it.

Lotusland 2011

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. 

Kamis, 03 Maret 2011

Early earth tectonics

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.

Rabu, 02 Maret 2011

Repairing Damaged Heart Muscle

After a heart attack, the best one can generally hope for is that the area of damage becomes scar tissue that is sufficiently strong to withstand the high blood pressures generated in the heart. That’s because in adult mammals, cardiac muscle does not rebuild or repair itself after an injury. And yet, adult frogs, newts, and some fish still do have the ability to rebuild functional heart tissue after injury – what’s the difference?

One hypothesis is that the general ability of heart muscle to regenerate in essentially all embryos is switched off shortly after birth in higher mammals. In support of this hypothesis, researchers have now shown that mouse hearts do undergo structural and functional regeneration, but only if the damage occurs within the first week after birth. These findings raise the possibility that if we could understand the process of heart muscle regeneration in a newborn mouse, we might be able to induce the process again in adult mammals if necessary. Ultimately this could lead to new approaches for the treatment of victims of heart attacks.

Biomimicry for the Future

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

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.

Selasa, 01 Maret 2011


Cuttlefish eye, close-up
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 :)

More epigenetics

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

    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."
    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...
    A fossil of Diania cactiformis.
    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.
    Illustration of Hallucigenia.
    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...

    Senin, 28 Februari 2011

    Pitcher Plants

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

    Minggu, 27 Februari 2011

    It's not just the genes...

    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.

    Sabtu, 26 Februari 2011

    Competing sinks?

    Just because two plants are sufficiently closely related to graft them together doesn't necessarily mean it's a good idea to graft them together.

    I must confess that, beyond the novelty value, I don't quite get the amazing tomato-potato.

    It seems more sensible from a plant physiology point of view to just plant a tomato next to a potato and have two sets of leaves each providing for one sink rather than have two large sinks competing for the same resources. I initially wondered if maybe the potatoes ripened first and then maybe the tomatoes but the inset photograph seems to show them both ripe together.

    Given that tobacco is also in the Solanaceae family I wonder how long it will be before we see tomacco for real? Oh wait someone already did that.

    Taxol and Repair of Spinal Cord Injuries

    One of the challenges in facilitating repair of the spinal cord after spinal cord injuries has been to get axons to re-grow through the damaged area. Usually the process of axonal re-growth is inhibited by the formation of scar tissue.

    But now researchers have discovered a potential new weapon in the treatment of spinal cord injuries – taxol, the same drug that is currently used to inhibit the growth of certain cancers. It turns out that taxol produces “stabilization” of microtubules in damaged areas of the spinal cord, which in turn reduces scarring and reduces the production of certain factors which normally inhibit axonal regeneration. The result is that axons tend to grow more readily through taxol-treated lesion sites.

    So far, taxol has only been shown to work in rats. Nevertheless, these encouraging results could pave the way for future clinical trials in humans. Perhaps some day taxol will become part of the normal treatment regimen for spinal cord injuries.

    Jumat, 25 Februari 2011

    Walking with dinosaurs

    Natasha's post below, and the topic of some forthcoming lectures, reminded me of the BBC's fondness for dinosaur simulations.

    I think it all started with a show called 'Walking with dinosaurs' that was , at the time, the most expensive documentary ever made. Using computer simulation and animatronics to create a 'realistic' wildlife show - but one with dinosaurs. You should check these out if you haven't seen them. I think they are available on Netflix and Veoh online.

    Then there's Prehistoric Park, made by the same company, which now includes a 'time portal' and a narrator. Wikipedia calls it 'docu-fiction'. I almost posted a clip from this earlier in the quarter because they have a nice segment with one of those giant Carboniferous arthropods - Arthropleura.

    Finally, keep the time portal and the dinosaurs but add in ludicrous characters, creatures from the future and the stupidest plotlines you can imagine and you have Primeval. Check out episode two of the first series for Arthropleura in the London Underground.

    Choose your own level of prehistoric incredulity.

    CCS Bio Sweatshirts!

    Hey guys!

    I was thinking it would be cool to have a CCS bio sweatshirt so I decided to create a design, but I want your input on a few things. One, do you like it? Two, do you prefer the blue or yellow? If you would prefer like a cat or something please don't message me but if you have something constructive to add to the design definitely let me know. The yellow looks brighter and more legible as a computer image but they'll both look good when printed. Also, its only going to cost $20 hooray! My email is ellabc@gmail.com or you can find me on facebook if you have a question or suggestion. I'll bring all this to class on Tuesday and we can talk more about it. Have a good weekend ; )

    Ella Bendrick-Chartier

    Ground sloths and mastodons

    Life in prehistoric Los Angeles was more perilous than you ever thought.

    Kamis, 24 Februari 2011

    Oh that's what it was...

    Even though you didn't see them I added the slides from today's class so you can work out what my scribbles meant. This material is also well covered in chapters 34-36 in your textbook which has some excellent illustrations.

    On an unrelated note next Monday's EEMB seminar is by Professor Mary Power of UC Berkeley. Her title is still listed as TBA but Mary works on food webs in rivers and their watersheds. She has been the president of the Ecological Society of America and usually gives a pretty enthusiastic talk.

    Rabu, 23 Februari 2011

    Angel's trumpet poisoning

    I looked up some information on the toxic compounds in Brugmansia. The plant contains an unhealthy brew of the alkaloids atropine, scopolamine and hyoscyamine.

    Because these can cause hallucinogenic effects they are often ingested by those seeking just such an effect. When combined with alcohol the effects can be rapid. Although the plant can be eaten or smoked the most popular method of ingestion is to prepare a tea from the flowers and seeds.

    Unfortunately because the levels of the alkaloids vary widely from season to season it is very easy to overdose and it is estimated that 'teas prepared from as few as 10 flowers could be extremely toxic if not fatal'. Angel's trumpet ingestion produces the classic symptoms of anticholinergic poisoning, so classic that they have their own mnemonic: 'hot as a hare, dry as a bone, blind as a bat, red as a beet and mad as a hatter.'

    This paper, Ingestion of Angel's Trumpet: An increasingly Common Source of Toxicity, reports a ten fold increase in Brugmanisa poisoning in Florida in 1994. They failed to locate a particular reason for this (ie reference to Brugmania use in a movie) and suggest the idea was simply spread by word of mouth. And then the internet came along...

    Selasa, 22 Februari 2011

    Night Bloomers

    If anyone wants their garden to be as much of a night owl as they are, here are some amazing plants.
    Night Blooming Cereus, made kind of famous in the book The Bean Trees by Barbara Kingsolver, the lovely Moon Flower, and according to this website you can watch a video of it blooming, our lovely deadly and possibly hallucinogenic flower from class, the Angel's Trumpet and for those of you who really want to plant stuff right now, The Evening Garden is a great book.
    On another note, Wicked Plants is a great book on all kinds of nasty plants you don't want to run into. It's got amazing illustrations and stories for most of the plants.


    Haplodiploidy is a  mechanism of sex determination that is common in the hymenoptera but also found in some other groups. In this system sex is determined by the number of sets of chromosomes an offspring receives. Fertlized eggs develop as females, and unfertilized eggs develop as males. This means that the males have half the number of chromosomes that a female have - hence the name haplodiploidy for this system. In this system males have no father and cannot have sons, but have grandfathers and can have grandsons (think about it). Also because males are already haploid all the sperm they produce is identical.

    Haplodiploidy has important consequences that seem to affect social behavior. Here's a nice description form an online Animal Behavior textbook:
    1. If a queen mates only once, her daughters are highly related to each other (called supersisters), because the father's sperm are all identical.
    2. A female is more related to her sisters (on average, 75% similar) than she is to her own daughters (on average 50% similar).
    3. A female is more related to her son (50 % similar) than she is to a brother (on average, 25% similar).
    These three factors combine to create a condition in which it may be more advantageous, evolutionarily speaking, for a female to help her mother produce sisters (to the female in question) than to produce her own daughters. Thus haplodiploidy opens the way for the evolution of a worker caste, devoted to helping their mother. If workers evolve under these conditions, then we would expect:
    • That all workers will be female (males have no special pattern of relatedness in a haplodiploid system that would make working advantageous to them
    • That workers will help their mother to lay and rear females, but
    • That workers would prefer to lay their own male offspring, rather than rear brothers
    In fact, Hymenoptera workers are uniformly female and conflict between the queen and the workers over who lays the males eggs in a nest is common. The role of haplodiploidy in the evolution of worker Hymenoptera fits into an overall theory of how genetic similarity affects social behavior called kin selection which was developed by Bill Hamilton.

    Deciphering Local Diversity

    Next quarter CCBER will present a series of talks on local biodiversity with a focus on developing observational and identification skills.You can take this as a class or simply attend any talks you are interested in.

    CCBER Conservation and Restoration Seminar (RE 188/288) - Deciphering Local Diversity

    Monday evenings, 6-7pm, Rm 1013 Harder South
    • March 28th – Introduction – Lisa Stratton
    • April 4th – Dan Fontaine – Interpreting animals signs
    • April 11th – Mark Holmgren – Raptor ID and Behavior
    • April 18th – John Bleck – Differentiating Succulents
    • April 25th – Mary Carroll – Differentiating Sedges
    • May 2nd – Marc Kummel – The story behind local Oak Galls
    • May 9th – Mary Carroll – Learning the key to Grass Identification
    • May 16th – Lisa Stratton – Local vernal pool hydrology and flora
    • May 23rd – Scott Cooper – Below the surface of Vernal Pools: Invertebrate lifecycles
    Contact Lisa Stratton if you have questions.

    Senin, 21 Februari 2011

    Seed Plant Phylogeny

    You may be surprised to find out that the relationship between the angiosperms and the gymnosperm groups is still subject to much debate. One of the perennial questions is the position of the gnetophytes.

     One of the reasons for this debate is that the Gnetophytes (one of the gymnosperm taxa we discussed) show several features that are typically associated with the angiosperms, including double fertilisation and vessel elements in their vascular tissue. Do these indicate a close relationship and that the gnetophytes are a sister taxa to the angiosperms or are they the results of parallel evolution?

    Wikipedia actually has a nice clear discussion of the alternative hypotheses or for a meatier discussion there's this paper from 2009 in the American Journal of Botany:
    Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data

    Minggu, 20 Februari 2011

    Lymph Node Surgery for Breast Cancer

    For decades, the standard treatment for women who have been diagnosed with early-stage breast cancer has been to perform a biopsy on a nearby lymph node, called a “sentinal” lymph node, to see if the cancer has metastasized beyond the breast. If it has, then the usual recommendation is surgery to remove some or most of the thirty axillary (armpit) lymph nodes as well, to try to halt the spread of cancer. The surgery is extensive, and recovery is painful and slow.

    A new study published in the Journal of the American Medical Association reports that removal of armpit lymph nodes may not be necessary any more, given the current effectiveness of post-surgical radiation therapy and chemotherapy. In the study, 891 women who had undergone a lumpectomy for early stage breast cancer were randomly assigned to just sentinal node removal, or removal of at least 10 of the axillary lymph nodes. There were no differences in survival rates or disease-free survival rates between the two groups for the entire eight years of the study.

    The authors recommend that physicians consider carefully whether more radical axillary node surgery is really necessary in most patients. Some cancer centers are already starting to change their cancer treatment protocols as a result of these new findings.

    The Birds and the Bees and the Flowers and the Trees

    Given that about 5% of angiosperms are dioecious but only a few cases of sex chromosomes have been discovered this raises the question of how sex is determined in the rest of these species. I found this nice review in the journal Genetics last year:
    The Birds and the Bees and the Flowers and the Trees: Lessons from Genetic Mapping of Sex Determination in Plants and Animals

    Sex determination is an important area of study in developmental and evolutionary biology, as well as ecology. Its importance for organisms might suggest that sex determination is highly conserved. However, genetic studies have shown that sex determination mechanisms, and the genes involved, are surprisingly labile.

    Sabtu, 19 Februari 2011

    Trees, photosynthesis and weasels

    Any questions?

    Jumat, 18 Februari 2011

    The Evolution of Sex Chromosomes

    Sex chromosomes have arisen independently in many taxonomic groups. It is an interesting question whether the same mechanisms were involved each time.

    Sex chromosomes are an oddity in flowering plants. They are limited to dioecious species and only a few examples are known. The genus Silene, which includes the White Campion, includes both dioecious and hermaphrodite species and three of the dioecious species, Silene dioica, S. latifolia, and S. diclinis,  have an X-Y sex-determination system where Y specifies maleness.
    Although the X-Y system evolved quite recently in Silene (less than 10 million years ago) compared to mammals (about 320 million years ago), our results suggest that similar processes have been at work in the evolution of sex chromosomes in plants and mammals, and shed some light on the molecular mechanisms suppressing recombination between X and Y chromosomes.

    Ref:  Nicolas M, Marais G, Hykelova V, Janousek B, Laporte V, et al. (2005) A Gradual Process of Recombination Restriction in the Evolutionary History of the Sex Chromosomes in Dioecious Plants. PLoS Biol 3(1).

    There's a synopsis of the article in the same issue: Evolution of Sex Chromosomes: The Case of the White Campion.

    Kamis, 17 Februari 2011

    The plant in you (and vice versa)

     From: Double-fertilization, from myths to reality, a review from 2007 -

    It is becoming gradually clear that although plant and animal kingdoms diverged more than 1 billion years ago, similar mechanisms govern sexual reproduction in both kingdoms. The review by Márton and Dresselhaus (2008) outlines some of these parallels. The current idiosyncratic nomenclature used to designate plant reproduction has obscured the parallels that now become apparent between plants and animals. It is likely to be the time to rethink the designation of each actor of the reproductive process such that the literature in the field becomes relevant to a broader readership working in the field of reproductive biology.
    The  Márton and Dresselhauspaper referred to is A comparison of early molecular fertilization mechanisms in animals and flowering plants.

    Rabu, 16 Februari 2011

    The Vaccinations-Cause-Autism Fraud

    Anyone who still persists in believing that childhood vaccinations have anything to do with the development of autism should read the three well-documented articles by investigative reporter Brian Deer published recently in the prestigious British Medical Journal. The first article is presented here. For those who don’t have the time, here’s a brief synopsis:

    The original research article allegedly showing a causal link between vaccinations and autism was later shown to be a deliberate fraud. The paper, published in 1998 by the Lancet, was retracted in 2010 after it was shown to contain numerous misrepresentations. The paper’s author, Dr. Andrew Wakefield, was investigated by the UK General Medical Council and ultimately lost his license to practice medicine. Records released during the investigation show that Dr. Wakefield was paid nearly $700,000 by a British lawyer who was preparing a class-action lawsuit against vaccine-makers.

    Since 1998, study after study has failed to validate Dr. Wakefield’s work and failed to show any causal link between childhood vaccinations and autism. And yet, some parents of autistic children still believe in that there may be a causal link. Actress Jenny McCarthy, herself a mother of an autistic child, is one of them. Ms. McCarthy has appeared on the Oprah Winfrey show to promote the vaccination-autism “cause” and has written several books about autism. I have yet to see an admission from her that she may have been wrong about vaccines.

    Sorry, Ms. McCarthy, you lose on this one. Give it up before you look even more foolish than you already do.

    (Topic for debate: Why do some people continue to believe in something despite overwhelming evidence in favor of just the opposite? What does that continued belief do for them?)

    Fractal ferns

    Most species of ferns have pinnate fronds.  The term pinnate describes the arrangement of leaflets arising at multiple points along a common axis. A fern may be simply pinnate or may be bipinnate if the leaflets are divided again, or tripinnate or even tetrapinnate depending how many levels of division the fronds have.

    Because this is a simple mathematical process, simple algorithms can make surprisingly lifelike ferns. Check out the Fractal fern page if you are interested in math.

    Can you tell which of these ferns is real and which is computer generated?

    Selasa, 15 Februari 2011

    Undergraduate Research Colloquium

    If you have any research to present then you should present it at this year's Undergraduate Research Colloquium. This is a fantastic opportunity to practice preparing and presenting a poster. 

    Every year the College of Letters and Science celebrates undergraduate research at UCSB by sponsoring a colloquium where students from all over campus may come together to showcase their research activities.  I am
    writing to invite you to attend this event to be held on Thursday, May 19, 2011, in the Corwin Pavilion.  All presentations will be in poster form (poster size 2 ft by 3 ft portrait style).  The event will run from 11:30
    to 2:00 p.m.

    Students interested in sharing their research efforts should submit the two-part entry application (entry and abstract submission forms) found on the URCA web site, www.ltsc.ucsb.edu/urca/colloquium.php, by Wednesday, April 6.  Questions should be referred to the URCA Coordinator, urca@Ltsc.ucsb.edu.


    I posted about REU's before. The posting below is from just one of the dozens of opportunities available. If you want a summer research adventure then now is the time to be checking them out and applying.

    Texas A&M is offering a summer Research Experiences for Undergraduates program, which will be held from June 1 to August 5 in College Station.  The theme is Interdisciplinary Research on Imaging and Biomarkers.  The application can be found at:  http://etidweb.tamu.edu/hsieh/REU and the flyer is attached.
    Activities will include joining a research group led by a faculty mentor, completion of a 10-week research project, and participation in weekly faculty seminars, field trips, and career development workshops.  Students will write a report and present their research to their REU cohort and at an REU poster session on campus. They will also be strongly encouraged to polish their reports after completing the program, with a view toward presenting at a national conference and/or publishing in an academic journal.
    Each participant will receive a stipend of $450/week for ten weeks. Other benefits include allowances for housing, meals and round trip travel to College Station; 1.0 credit hour of undergraduate course credit; and full access to university recreational facilities.
    Criteria for selection include: 
    • Desire to participate in research as evidenced by application responses and faculty recommendation;
    • Completion of at least the sophomore year of the curriculum for an academic major in engineering, computer science, or the life sciences;
    • GPA of 3.00 or above (exceptions may be made based on review of an applicant's last 60 hours of coursework);
    • Citizen or permanent resident of the U.S. or its possessions;
    • Plan to graduate no earlier than December 2011.
    Students who have limited opportunities to participate in research on their home campuses or who are from groups traditionally underrepresented in engineering and science are highly encouraged to apply.

    Senin, 14 Februari 2011

    Manipulative microbes

    In the spirit of this divisive holiday, here is an intriguing article about how bacteria in your gut may be secretively manipulating your deepest emotions. A study done in fruit flies showed that fruit flies preferred mating with other flies that had been put on the same diet (either malt sugar or starch). The intriguing part is that when the flies were treated with an antibiotic, this preference disappeared.


    Who is the culprit? Lactobacillus plantarum, a Gram-positive bacterium found in dairy products and other fermented foods. It is thought - researchers are not entirely certain - that the bacteria alter the flies' pheromone levels, making them more attractive and attracted to similar members of the opposite sex. The question arises...how much of this actually applies to humans?

    An important concept put forth by the researchers is the holobiont. Rather than considering just the parts directly connected to an organism, we should take into account all its "normal flora" - the diverse hordes of microbes that inhabit the body, from our skin to our gut. Although it's initially mildly disturbing to think that 90 percent of the cells in our body are not our own, we should take into account the host of tasks they perform for us. When our normal flora are destroyed - for instance, by a long-term antibiotic - we too are destroyed, unable to digest food and plagued by infections that our normal flora would have otherwise caught.

    So the holobiont theory certainly applies to humans. What about the influence on mating preferences? Hard to say. But if our resident bacteria can chew our food for us and protect us from hostile (albeit microscopic) strangers, I think I'll trust their judgment in choosing a suitable mate.

    Dating tips

    Not only is it adorably left wing but the Guardian newspaper in England actually sometimes has some decent science reporting. I enjoyed their Valentine's Day dating tips from lovestruck scientists. It even includes a list of references at the end - a very welcome trend. Here's an example, 
    Tip #4: Cross a scary bridge

    Here's another very simple tip for the ladies: frighten him. No, seriously. In 1974, University of British Columbia psychologists were studying human attraction using two bridges that crossed a local river. One bridge was solid, allowed firm footing, and was made of heavy cedar. It was only ten feet above the river, and had steady handrails. The other bridge was a five-foot-wide, 450-foot-long suspension bridge made of wire cables threaded through the ends of wooden boards. It would tilt, sway, and wobble as people tried to cross, 230 feet above the river.
    Men who had just crossed one of the bridges were approached by an attractive female experimenter who asked them to complete several questionnaires. The men who had crossed the anxiety-inducing suspension bridge were more likely to attempt further contact with the experimenter than were the men who had crossed the stable bridge. The researchers suggest that it's as if the men misunderstood their anxiety-induced physiological arousal – elevated heart rate, sweaty palms, and so on – interpreting it as sexual attraction and desire.
    Moral of the story: scare the crap out of him and he might just make a move.

    Oh and don't forget - CCBER tomorrow.

    Minggu, 13 Februari 2011

    Debating Darwin

    I only just heard about this conference which is going on next weekend right here ar UCSB. It's free to attend but they do request that you register: http://www.philosophy.ucsb.edu/conferences/

    UC Santa Barbara Department of Philosophy Announcesa Steven Humphrey Fund for Excellence in Philosophy ConferenceDebating Darwin: Philosophical Issues in Evolution and Natural Selection
    February 18-20, 2011
    Friday, February 18
    5:00 - 7:00 PM Peter Godfrey-Smith (Harvard), "Origin Explanations" 
    7:00 - 9:00 PM Reception/Buffet, UCSB Faculty Club

    Saturday, February 19
    9:30 - 11:30 AM Elisabeth Lloyd (Indiana), "Adaptationism in Action"
    11:30 - 1:00 PM Lunch, Graduate Student Association Lounge
    1:00 - 3:00 PM Paul Griffiths (Sydney), "How Evolution Tracks Truth"
    3:00 - 3:15 PM Break
    3:15 - 5:15 PM Jerry Fodor (Rutgers), "From the Darwin Wars"

    Sunday, February 20
    9:30 - 11:30 AM Mohan Matthen (Toronto), TBA
    11:30 - 1:00 PM Lunch, UCSB Faculty Club
    1:00 - 3:00 PM Richard Boyd (Cornell), "Evolutionary Theory as Methodological Anesthesia: Methodological and Philosophical Lessons from Evolutionary Psychology"
    3:00 - 3:15 PM Break
    3:15 - 5:15 PM Alex Rosenberg (Duke), "How Jerry Fodor Slid Down the Slippery Slope to Anti-Darwinism, and How We Can Avoid the Same Fate"
    Location: All talks will be in Theater & Dance 1701

    Altruism for the Win!

    Ants and the Buggers from Ender's Game have one important thing in common: The ability to selflessly commit their lives to the good of the colony. Social ants build nests, collect food, and defend the colony. Most ants don't reproduce, but will spend their lives helping raise non-descendant young. Their altruistic social behaviors have clearly paid off, as there are estimated to be over 20,000 species and 10,000,000,000,000,000 (that's 10 quadrillion!) individual ants in the world.

    Researchers have found yet another way in which ants selflessly sacrifice their lives for the good of the colony, this time literally. Temnothorax unifasciatus ant workers infected by a fungal pathogen leave the nest hours or even days before an imminent death, to die in isolation far from the colony in order to prevent the spread of infection as well as the waste of resources. The life-span of ants who left the nest to die in isolation can be up to days shorter, further proving the altruistic nature of the worker. While some species of ants have specialized workers (evolved with special resistance to fungal disease, cool!) who dispose of sick and dying ants, T. unifasciatus ants voluntarily leave the colony.
    Because of the immense (no kidding) amounts of inter-relatedness within a colony, susceptibility to disease is a very limiting factor within colonies. In order to cope with this, ants have developed a social evolution (!!!) which has allowed them to extend colony success and growth. While there are many other ways in which ants have socially evolved to compensate for this danger, T. unifasciatus ants have developed a method of altruistic sacrifice which reflects a desire for the success of a colony over the success of an individual, and... is truly inspirational.
    Happy Sunday:)

    Analyzing and Storing Genomics Data

    In just the last 10 years, the cost of sequencing a million DNA base pairs has dropped from $10,000 to just $1. A single modern DNA sequencing machine can generate more data in a single day than could once be generated in a decade. Consequently, genomics researchers now face a looming problem, according to an article in Science - the speed and efficiency with which DNA sequence data can be produced will soon outstrip the ability of most computers to analyze and store the data! That’s right; despite huge gains in computer speed and storage capacity over the years, the computers are now lagging behind.

    To combat this growing problem, bioinformatics specialists are increasingly turning to “cloud computing”, whereby data are analyzed and even stored on networks of computers off-site. But cloud computing raises complex new issues of data security, particularly when that data involves human subjects.

    Perhaps if the cost of sequencing DNA continues to fall it may not even be necessary to store the data long-term; it could just be regenerated as needed.

    Sabtu, 12 Februari 2011

    Gymnosperm Reproduction

    Anything that happens in 3-d is just crying out for a video. When it comes to Gymnosperm reporoduction I rather like these videos The first one is very short and a little obvious but I liked the second and third ones a lot. I thought they really helped in visualizing what is going on.

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