For the pet lovers

Although this is a bit off topic I couldn't help but post this for all of the dog kissers in class. If you just happen to have $100,000 laying around and a pet you can't stand to loose the DNA of then you can have you pooch cloned!

here's the link

Seminars next week

More gems coming up next week. The Monday and Friday seminars are particularly relevant to the topics we have been discussing in class.

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Monday June 2, 2008. EEMB Seminar 4:00pm MSI Auditorium (MSB 1302)
Lauren Buckley.
Reptile range dynamics in changing environments: linking traits to energetics and population dynamics

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Thursday June 5, 2008 PhD Seminar. 2:00 p.m. Marine Science Auditorium, MSB 1302
Crow White, Ecology, Evolution and Marine Biology UC Santa Barbara
Populations Connectivity and the Management of Coastal Fisheries

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Thursday June 5, 2008. MCDB Seminar 3:30 Rathmann Auditorium (LSB 1001)
James Thomson, University of Wisconsin Madison/UC Santa Barbara
Induced Pluripotent Stem Cells

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Thursday, June 5, 2:00pm ESB 2001
Georg Seelig, California Institute of Technology
Nucleic acid logic circuits for programming biology

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Friday, June 6, 2008. PhD Seminar 1:00 p.m. Marine Science Auditorium, MSB 1302
Katie Arkema, Ecology, Evolution and Marine Biology, UC Santa Barbara
Consequences of kelp forest structure and dynamics for epiphytes and understory communities

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HSS

As promised here's a link to the Hairston, smith and Slobodkin paper and, just for fun, a reply by UCSB's own Professor Bill Murdoch. Don't miss the reply to the reply by HSS at the end of the reply.

Leonard Cohen's March Of The Penguins

As you've doubtless noticed (if anyone is even reading this anymore), I try to post every day. The reason for this is that if I didn't then, well, I wouldn't. There's a life lesson there. But sometimes it gets close to midnight and I'm tired and there is still much to do. My wife suggested I should have repeats from blog postings past. I try to avoid this but it's been a long day. So I bring you my favorite blog posting that was very loosely related to life history strategies.


Penguin's - adorable flightless comedians of the Antarctic. Leonard Cohen - the adorable flightless poet from Canada. Put them together and you get something truly disturbing.

Seminar next Monday

This sounds like a good illustration of how the hardest part of ecology is measuring the parameters of interest. You may already be aware that bones in the fish ear, otoliths, accumulate yearly growth rings (just like trees) and so can be used to age fish but I didn't know you could get more information from them.

Monday, June 2, 2008
10:00 a.m.
Marine Science Building Auditorium, MSB 1302

*Julie Standish*
Ecology, Evolution and Marine Biology
UC Santa Barbara

Use of otolith trace-elemental signatures to identify larval 
connectivity and dispersal patterns in a temperate marine fish

Advisor:  Robert Warner

Life in a seed

I love stuff that ties together different lectures. Here's some ecology (plant-insect interaction) and plant biology (seed development) in action.

Some species of insects complete their entire development in seeds. Protected by the seed coat and nourished by the seed's food supply a developing insect has everything it needs. However these reserves only normally accumulate in fertilized ovules - requiring female insects that wish to lay eggs inside the seeds to either wait until ovules are fertilized (and be able to discriminate), or to lay their eggs earlier and risk many being laid in unfertilized seed. A paper in the Proceedings of the Royal Society in 2005 describes how a host-specific insect, the chalcid Megastigmus spermotrophus that lays its eggs in ovules of Douglas fir has managed to evolve a solution to this problem. This insect lays its eggs before fertilization has taken place in the plant and ovipoisiton of eggs not only prevents the expected degeneration and death of unfertilized ovules, but it induces energy reserve accumulation. Ovules that would otherwise develop as empty seed are redirected in their development by the insect to provide food for the developing larvae. This is the first report of this type of insect-host relationship.

Piled Higher and Deeper

If you don't read PhD Comics, well you probably should. Especially if you think you might end up in grad school. Do not start reading the archive though unless you've got some spare time. Like a holiday weekend.....

Chaos

For an introduction to chaos theory the Wikipedia article isn't bad although I prefer this New Scientist article by Ian Stewart. The best introduction though is the book Chaos: Making a New Science by James Gleick which somehow manages to explain everything with very little actual math. I'm sure the library will have copies you can borrow. Even after 20 years this is still considered one of the best reads on the subject.

Elephants in Space

Actually that's a NASA headline, not mine. It turns out they aren't currently planning to put any elephants in space. In fact elephants are waaaay back in the queue - just ahead of whales, poison ivy, ferrets and killer bees.

The article and the NASA project concerns the viewing of elephants from space. The Wildlife Conservation Society (the people who run the fabulous, conservation oriented, Bronx Zoo amongst other things) have been collaborating with NASA to see if wildlife counts from space would be feasible. High definition photographs were taken of the Bronx Zoo itself by the Quickbird satellite, 450km vertically overhead. The advantage of taking photos of the Zoo for testing is that these could be ground truthed by taking photographs at ground level at the same time (see images above and below with 3 items: a clearing, a tree and a fence labeled in each).

The advantages are obviously many, from less disturbance of the animals to cheaper research.

Imagine being able to monitor a herd of elephants in the Serengeti, or a flock of endangered flamingos in Bolivia, from a lab in New York. This technology may allow us to do just that.
Dr. Eric Sanderson, WCS landscape ecologist

Satellite imagery resolutions are continuously improving. Typical resolutions today are about 1m (i.e. each pixel represents a square 1m on a side) and 0.5m resolution is probably close. Military satellites almost certainly have better resolution - perhaps as good as 5 or 10cm. With this sort of resolution you could spot, but not definitively identify, some of the world's biggest insects! (But not if they were hiding under a leaf of course). I think ecologists will need to be out there in the field for a long time to come......

Population growth, population decline

We talked about how populations can respond to release from predators or competition with exponential growth. We can also consider the opposite scenario: population growth/decline when a novel predator or parasite is introduced/added to the system. Unfortunately we have many examples and the results aren’t pretty. Today on NPR’s program “Day to Day” they aired a short segment on the Emerald Ash Borer – a species of beetle accidentally introduced from China only about a decade ago. In that relatively short time, the beetles have killed over 25 MILLION (!) Ash trees in the US Midwest. Good-bye baseball bats? Anyway, today’s story was of added interest in that one of the attempts to stop the local extinction of ash trees is to employ genetic engineering techniques – inserting DNA from beetle-resistant ash species into the native ones.

Limits on Adaptation of Drosophila species

Check out this article in Science, Low Potential for Climatic Stress Adaptation in a Rainforest Drosophila Species

http://www.sciencemag.org/cgi/content/full/301/5629/100

The article discusses recent interest in resistance evolution in Drosophila birchii. What's interesting here is the limit on evolved resistance, after 30 years of "intense selection" for desiccation resistance. Here is a little abstract of the article. I found it very interesting and ever so slightly related to what we're studying in class / in the text. 

The ability of sensitive rainforest species to evolve in response to climate change is largely unknown. We show that the Australian tropical rainforest fly Drosophila birchii exhibits clinal variation in desiccation resistance, but the most resistant population lacks the ability to evolve further resistance even after intense selection for over 30 generations. Parent-offspring comparisons indicate low heritable variation for this trait but high levels of genetic variation for morphology. D. birchii also exhibits abundant genetic variation at microsatellite loci. The low potential for resistance evolution highlights the importance of assessing evolutionary potential in targeted ecological traits and species from threatened habitats.

Centre for Environmental Stress and Adaptation Research, La Trobe University, Bundoora, Victoria 3086, Australia.

The trouble with chasing a bee....

Here's an interesting article on tracking bees that has some very amusing images in the first few paragraphs.

"Running behind a bee doesn't help very much," he says. Racing along, an observer can keep a tiny spot against the sky in sight for a good distance, but sooner or later the person glances away from the bee for a second. "If you have lost it from sight, you will never find it again," says Menzel.

One athletic student could keep up for record distances of some 50 meters, "but he was falling down a lot," Menzel recalls. So, Menzel gave up on runners and instead maximized conditions for stationary observers to track the bee. "We had lots of students lying on the ground, following it with their fingers," he says.

This wonderfully low tech biology is then superseded by radar and transponders. Interesting article.

The amazing Lyre bird

This really needs no introduction. Just watch the amazing video. But since I'm here, I'll just point out that for most of my childhood England had 3 TV stations, and no-one really watched one of them (I'm talking about you BBC2). This meant that the whole country watched anything of remote interest on the other two and so now they seem to have endless Top 10 moments, which is a lame excuse for a clip show, but at least everyone remembers the shows they reminisce about. Last time I was back in England I watched the Top 100 TV comedy moments and despite not living in England for over a decade I recognized almost all of them. Anyway, this is obviously from the top ten Attenborough moments and makes me want to see the rest. Not only is it amazing but it's also profoundly depressing with the poor bird mimicking the sounds of its own destruction. You can get most of the Attenborough nature documentaries on DVD here, they are, without exception, worth watching. The quality is simply remarkable. FYI, for some reason most Americans don't seem to realize David Attenborough is the younger brother of Richard Attenborough who is an equally distinguished actor (you probably saw him in Jurassic Park as the developer John Hammond) and director (A Bridge too Far, Gandhi and Cry Freedom amongst others).

Microwaves

Here's some information on the ballast water treatment method that James mentioned. The paper is called Design and Implementation of a Continuous Microwave Heating System for Ballast Water Treatment, and is getting some press coverage as a possible solution to the ballast water spread of invasive species.

Press reports are a little contradictory on the cost although the paper itself says 'implementation of this system by itself would be prohibitively expensive' so it looks like the 'low operating costs' are only when compared to conventional heating methods which are even more expensive.

'Boldor noted that the high heating rates, low operating costs, and effectiveness in hazy water distinguish it from conventional heating methods.' From Science Daily

and

'Given the amount of energy it takes to heat the water, the system’s operating costs are currently impractically high. But it may someday be useful in conjunction with other, cheaper methods, Dr. Boldor said, killing organisms that those technologies cannot.' From the NY Times

But even so, it's good to have options. I'm curious what 'prohibitively expensive' actually means since ship owners have been getting away with doing nothing for, well, ever. I presume any cost seems like a lot. Suck it up ship-owning dudes (or, more likely, pass the cost on).

Something for everyone

Lots of seminars in Biology next week covering a wide range of Biology at a rate of one per day. If you haven't been to a seminar this quarter then week 8 is the perfect time to start.

EEMB Seminar, Monday May 19, 2008. 4:00pm MSB Auditorium (1302)
Bill Nelson, Department of Biology, Queen's University
Evolution in Stage Structured Populations
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MCDB Seminar, Tuesday May 20, 2008. 3:30pm. Rathmann Auditorium (LSB 1001)
Elliot Meyerowitz, Caltech,
Computational Morphodynamics: Live Imaging and Computational Modeling of Plant Stem Cells in the Shoot Apical Meristem
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BMSE Seminar, Wednesday May 21, 2008. 11:00am. MRL 2053
William D. Hunt, Professor of Bioengineering & Microelectronics/Microsystems
School of Electrical and Computer Engineering, Georgia Tech
Clues from digital radio regarding biomolecular recognition or why I believe God is probably an IEEE fellow
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MCDB Seminar, Thursday May 22, 2008. 3:30 Rathmann Auditorium (LSB 1001)
Philip Schwartz, Children's Hospital of Orange County Research Institute
The Potential of Stem Cell Therapies of Neurological Diseases
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Ph.D. Seminar Friday, May 23, 2008. 1:00 p.m. Marine Science Building Auditorium, MSB 1302
Nathan Silva. Interdepartmental Graduate Program in Marine Science UC Santa Barbara
An Assessment of the Level of Genetic Polymorphism on the Ascidians of Santa Barbara, California
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Can I eat the scorpion now mom?

Perhaps surprisingly there is little evidence for teaching in nonhuman animals. In a 2006 study published in the journal Science, by researchers at the University of Cambridge in England, adult meerkats in the Kalahari were shown to teach their pups how to deal with scorpions and other prey.

After all if part of your diet consists of deadly scorpions and you are born clueless it might be a good idea to get some pointers from an experienced relative. Meerkats are social animals that live in groups of around forty. Some of the teaching is carried out not by the parents but by helpers. These helpers are likely to be closely related to the pups they are teaching so this is a nice example of kin selection at work. There is a good summary of the research at the National Geographic website.

Stomatopods and their specialized vision

I know this isn't directly linked to the stuff we've been looking at in class but it has both ecological and physiological relevance. Stomatopods are of group of shrimp-like crustaceans, which you are familiar with if you know what a Mantis shrimp is. Mantis shrimps are known by many as 'thumb splitters' because they can produce that much force when striking prey and the reaction time for it is quite possibly the fastest in the animal kingdom. However what I find even more fascinating is the complexity of their vision. Unlike us, stomatopods in general are able to see 12 'primary colors' and pick up on circular polarization. Circular polarization refers to the slight directional shifts that can be noted (well we actually need fancy technology, or have to be clever enough to design a mechanism that shows quantum noise with a pointer's laser) as light spirals. It is believed that such sensitivity aids the crustacean in finding food, fleeing, combat and finding mates. You thought our optical system was advance.

Of course this makes one wonder what kind of environment would drive this kind of evolution. Why is it that they're so complex in comparison to other crustaceans?

The links at the bottom are to the actual websites where you can see the articles. The Science daily ones are very user friendly, the other two are VERY physics intensive.

[Edited to add links]
http://www.sciencedaily.com/releases/2008/03/080320120732.htm

http://www.sciencedaily.com/releases/2008/05/080513210456.htm

Physics intensive:
http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0002190

http://www.current-biology.com/content/article/abstract?uid=PIIS09

Spite

What is it that makes us uniquely human? Is it our intelligence, no, dolphins and monkeys are plenty smart. Is it our capacity for self-awareness? Nope, apes, dolphins and elephants have been shown to be self-aware. Mourning the dead? Nope, elephants do that. In fact we could go through a pretty long list of traits that we might think are uniquely human, only to find one or more animal species that also show this trait. So its a relief to find a recently published study that allows us to hold on to the one trait that, so far at least, remains uniquely human - spite. (Incidentally there are very few scientific experiments I'd want to watch on video but I'd make an exception for this one. Chimps and collapsing tables of food sound like a great combination).

Also, published just last year, the first evidence of an unusual form of altruism, termed 'generalized reciprocity': Generalized Reciprocity in Rats. In the first example of general cooperation in any animal, rodents helped by unfamiliar rats are found to help strangers themselves.

What is Ecology?

A couple of years ago now the Journal of Applied Ecology had an interesting article entitled:
The identification of 100 ecological questions of high policy relevance in the UK. Ecologists wanted the list to have a major impact on both science and policy and in the press release they liken the list to the 23 mathematical problems David Hilbert posed at the Second International Congress of Mathematicians in Paris in 1900. This list had a major impact on mathematics throughout the twentieth century.

The list is interesting to browse through (the link above takes you to the complete paper) because it really does help to highlight how little we know in ecology. It is also interesting to speculate what fraction of the questions will have general answers and what fraction will have answers that vary from system to system.

Although a few questions are rather UK specific most are equally relevant to the US.

Pavlov's bacteria

In this week's Science:

Could bacteria learn to match a signal that didn't occur regularly to a probable future event? If so, the bacterium could improve its chances of survival by turning on a preemptive response.

Because E. coli gets warmer when it enters a human mouth and then must soon contend with low oxygen levels as it passes into the large intestine, the team reasoned that the bacterium might use temperature as a cue to prepare for the upcoming lack of oxygen. Indeed, when the researchers turned up the heat in a dish of E. coli, the bugs dialed down activity in genes that normally operate in high-oxygen conditions. But the true test came when the team flipped the normal association, growing the bacteria in conditions in which high oxygen levels followed temperature increases. Less than 100 generations later, the bacteria stopped turning on their low-oxygen response after exposure to high temperatures, suggesting that they had evolved to break the association.

The study is the "first convincing demonstration" that bacteria can use environmental cues to anticipate events, says Michael Travisano, an evolutionary biologist at the University of Minnesota, Twin Cities. The work could open up new ways to explain puzzling behavior of microbial pathogens, which might use predictive signals to change their cell surfaces and avoid a host's impending immune attack.

Ah….ah….ah…. ACHOO (autosomal-dominant compulsive helio-ophthalmic outbursts of sneezing)!!!!

Check out this Scientific American article on the photic sneeze reflex (PSR) or the ACHOO syndrome, which describes sneezing that occurs in response to bright light. Apparently this type of sneeze reflex has a genetic component, and occurs in 18-35% of the population. Though I can’t answer James’ question (“why does it feel good to sneeze?”), maybe it’s good enough to suggest that if you can’t get that lurking sneeze out, try looking at a bright light. But don’t look directly into the sun…
“Looking at the Sun Can Trigger a Sneeze: For some people, bright lights mean big sneezes”

Saturdaze

(Seems like a good program but the name sucks - it sounds like a low budget Saturday morning kids TV show)

Saturdaze has partnered with the Santa Barbara Museum of Natural History and has funded a scholarship to encourage research that helps to explain one or another "entangled bank". The Saturdaze Scholarship for Natural History Research rewards exceptional students attempting to discover interactions in nature. Saturdaze and the Museum share the goal of "inspiring a passion for the natural world".
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Scholarship amount: $2,000 and $500 annual awards

Application deadline: 15 June

Award date: 15 July

Application website: http://www.sbnature.net/scholarship/index.htm

Use of scholarship award : unrestricted

Scope of Saturdaze Scholarships: Awarded to undergraduates involved in research in natural history and majoring in a biological sciences major. Research area must be within one or more of the following geographic areas: San Luis Obispo County, Santa Barbara County, and/or northern Channel Islands

Applicant field: Applicant must be an undergraduate student at one of the colleges or universities within San Luis Obispo or Santa Barbara Counties: Santa Barbara City College, Cuesta College, Allan Hancock, University of California Santa Barbara, Westmont College, Cal Poly San Luis Obispo

>From the Saturdaze Scholarship website . . .

Natural History is the broadest study of science and attempts to tie together observations of the natural world into a single interwoven fabric. As such, the knowledge base of natural history has grown beyond a single category of study and has been divided into smaller and smaller and more and more isolated disciplines. It is not uncommon that professional biologists study a single organism in a laboratory, far removed from its natural habitat. The Saturdaze Scholarship for Natural History Research supports the broader view.

Natural History is accessible to all who love and enjoy observing nature. In his essay on the Origin of Species, Charles Darwin, as a naturalist, wrote that . . .

"It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us."

Who among us has not contemplated nature and been inspired to learn about the connectedness within diversity? In this sense, natural history has attracted not only the scientist, but the artist and poet; natural history has become the romantic science. The romance of natural history stems from our desire to relate to the natural world, to regain a connectedness to it, and to preserve its diversity.

Saturdaze has partnered with the Santa Barbara Museum of Natural History and has funded a scholarship to encourage research that helps to explain one or another "entangled bank". The Saturdaze Scholarship for Natural History Research rewards exceptional students attempting to discover interactions in nature. Saturdaze and the Museum share the goal of "inspiring a passion for the natural world".

The problem of the burping cows

As mentioned briefly in class, herbivores’ digestion is impacted by the fact that cellulose is the principle organic compound in their diets BUT most herbivores cannot produce cellulases, the enzymes that hydrolyze cellulose. Cud chewing herbivores (i.e., ruminants) like cows and sheep rely on endosymbiotic microorganisms living within their digestive tracts to digest cellulose for them.

This is a cool arrangement, except for maybe two things. First it’s a bit of a raw deal for some of the individual microorganisms that, in spite of their service to the cow, get digested themselves. I think I mentioned that ruminants can derive more than 100 g of protein per day from digestion of their endosymbiotic microorganisms.

The other problem, from the more global perspective, is the amount of burping, etc. that cows do because of this association. About 17 percent of the methane in the atmosphere comes from cows and other ruminants as they digest food. This greenhouse gas is formed as their stomach microbes metabolize carbon dioxide into methane, which is “vented” to the atmosphere.

There is research underway to try to reduce the amount of methane Bessie produces, including making “burpless grass” and trying to introduce less burpy microbes into cow guts (from kangaroos, which have more microbes with better manners).

You can read about the efforts to create “burpless” grass in this article from Sciencedaily.com

And listen to an NPR interview about the Australian researcher working on transfer of microbes from roos to cows.

It’s a bit older, but there is a nice NPR story on greenhouse gas production from sources (like cows) other than big industry. This was aired on Ira Flatow’s show, “Science Friday”. I recommend tuning into the show when you can; it airs on, well, Fridays - locally on KCLU (102.3) from 1-2pm. It’s also online at http://www.sciencefriday.com/

Beetle damage

Going back to last semester but I thought this was interesting:

A team from Brigham Young University (BYU) in Provo, Utah, has examined thousands of dinosaur bones from the Jurassic and Cretaceous periods and found that flesh-eating bugs devoured them by the mouthful, erasing part of the fossil record in the process.

Sea Hare

Good tide pooling this morning. Find of the day was the California Brown Sea Hare - Aplysia californica. Each sea hare is both male and female, but they cannot fertilize their own eggs. Dozens pile up for sea hare orgies. They mate in lines and circles: each is male to the one in front and female to the one behind, so each is both a mother and a father. That is one x-rated gastropod....

For all things sea slug check out the sea slug forum at the Australian Museum.

Muscle Energetics

The Monday EEMB departmental seminar at 4pm in the Marine Science Building auditorium, entitled "Evolution of Muscle Energetics", will be presented by Chris Moyes, a professor at Queens University in Canada. Much of the data to be presented will be about fish, although there may be some mention of other species, possibly even humans. Chris Moyes works in the field of comparative biochemistry and physiology and has done research on diverse subjects including the bioenergetics of exercise, biochemical adaptation to temperature, metabolic scaling, and the genetic regulation of mitochondrial content in muscles. He is the coauthor (with Patricia Schulte) of a highly-regarded and widely used textbook of animal physiology.

You walk wrong

I mentioned this New York magazine article briefly at the start of class but it might be an interesting article to many of you and it does tie in to human physiology and biomechanics.

For a scientific analysis of whether those fancy athletic shoes are worth it here's a nice study 'Hazard of deceptive advertising of athletic footwear' that you still see cited although it doesn't seem to have dented the expensive athletic shoe market much, or stopped their deceptive advertising.

'This study tested the hypothesis that deceptive advertising creates a false sense of security with users of expensive athletic shoes, inducing attenuation of impact moderating behaviour, increased impact, and injury.'

Blood guns?

Roger Bannister achieved world fame in 1954 at the age of 25 by becoming the first person to break 4 minutes for the mile. What many people don't know about Bannister is that he was a medical student at the time and was already carrying out experiments, using himself and friends as subjects, to investigate the effects of inhaling oxygen enriched air on the physiological response to maximum exercise.

I read an interesting article describing the conditions of these experiments on inclined treadmills in the 1950's.

You had to breath from great gasbags and they had blood guns which sprang a blade into your finger to measure lactic acid levels as you labored on. You poured sweat, your spine turned to rubber, and driving up the incline there was the most extraordinary effect on your chin and knees meeting in front of you. Near the end, there was blood all over, and when you broke, you staggered and rolled off onto a mattress, trying to hit the off switch as you went down. Roger himself ran to breaking point on at least 11 occasions. Compared to that, the 4-minute mile was like a day off.

Sir Roger Bannister went on to become an eminent neurologist and retired in 2001. He will be 80 next year. The current mile record for men is 3:43 set by Hicham El Guerrouj of Morocco and it has stood since 1999.

Would you like your books back?

Hopefully many of you followed the Kitzmiller v Dover Area School District trial in 2005 that was the first direct challenge in federal court against a school district requiring the presentation of 'intelligent design'. If you didn't or are still unsure what it was all about and why it was important then you should watch the PBS 'Judgement Day' special. Cameras were not allowed in the courtroom so there are 'dramatic recreations'. You can watch the whole thing online.

A decision was made early on by the plaintiff's legal team to make the evolution of the immune system their key example. Given the complexity of the immune system this was a bold move but the key defense witness, Michael Behe, had made particularly dramatic claims about the evolution of the immune system:

"We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system." (Darwin's Black Box, p. 138)

A key moment in the trial came as Behe was literally surrounded by a mounting pile of papers and books that demonstrated the massive amount of research there is on the evolution of the vertebrate immune system.

The National Center for Science Education who provided much of the research for the plaintiffs have a nice website on the trial which, because it focuses on the immune system, now provides a nice, up to date annotated bibliography on the evolution of the vertebrate immune system.

If you'd like to hear how this was used in the trial read the transcript of day 12. Wikipedia has links to all the trial documents here.

Mutant Swan in UCSB Lagoon!!!!!

This weekend I decided to show my mother who was visiting from Colorado the pristine scenery of UCSB. We were walking around the lagoon and I was describing the one swan who normally occupies the lagoon in all his majesty when we spotted this monstrosity. Is it the same swan? Is it a mutant swan? Is that a third leg? Or perhaps just the second bent at an obscure and uncomfortable angle? Should I worry about walking so close to Lagoon water? Please help me solve this mystery.

Off the couch again - another public service announcement

Well we saw some exercise in action today and heard about the wonderful benefits of a fitness regime for your heart, lungs and longevity. As students here you have some great facilities right on campus but getting motivated and finding the time can be difficult with all the other demands on your time. One thing that works for lots of people, especially as you get older, is to participate in community events. This gives you a target to aim for regardless of whether your goal is simply to complete the event or beat some particular time. Here are some events going on in the Santa Barbara area in the near and long term that might motivate you.

Nite Moves happens every Wednesday night from Leadbetter beach in downtown Santa Barbara over the summer. There's an ocean swim, a 5k run, or both, followed by food, beer and music. It's downtown but you can hang around for dinner. It started last week and runs through to the end of August.

A fairly unique Santa Barbara event is the June State Street Mile. A fast, downhill mile through the center of Santa Barbara run as a series of heats according to age, ability and presence/absence of a dog. Borrow a fast dog and try the dog mile...

If you are here in the summer there's free ice cream at the McConnell's Ice Cream endurance events on August 17th. Events occur right by campus at Goleta Beach: 5k, 10k, Biathlon and Ocean Swim.

Santa Barbara Triathlon is also in August and has both long and sprint courses.

Santa Barbara half marathon in November attracts a couple of thousand people to a nice oceanfront course.

It is rumored that a Santa Barbara Marathon will return in Late 2009 after an absence of several years. No details yet but someone has bought the domain name and put some nice photographs up. Should be long enough for you to train....

For details on all these events and more the Santa Barbara Athletic Association keeps a handy calendar.

Diving Physiology

Those of you that are interested in marine biology and diving should take this opportunity to look into the diving physiology of marine mammals which, to be quite honest make humans look pretty shabby. The Weddell seal for example can dive to over 1000' and remain there for up to an hour. Elephant seals dive down over a mile and stay down for two hours (what is this a competition?). These mammals tend to store their oxygen in blood and muscle rather than in their lungs, which would cause buoyancy problems. The Weddell seal also stores a huge amount, over 50 pints, of oxygenated blood in its spleen. The spleen contracts after a dive begins fortifying the blood with oxygenated cells. As this paper explains animals also use physiological tricks to extend their time underwater

Lactate threshold

At Berkeley I was associated with both the Environmental Science program and the Department of Integrative Biology. IB was an interesting department that included ecologists, evolutionary biologists, biomechanics, sports physiologists and others. Inevitably you learn a bit about what other people in a department do and I remembered this study from a couple of years back that may become relevant to our class, our lab session on Monday, or just for general interest or edification. But first a bit of background....

As you may know we have two modes of energy use - aerobic and anaerobic. Over short distances or time periods we can perform (run, swim, cycle etc) at high rates for short periods of time but this involves the build up of lactic acid. Sooner or later this will limit your ability to perform anaerobically and you switch to aerobic mode. The bad news is that your aerobic capacity is largely inherited and training can only increase it by 10-15%. The good news is that this so called 'lactate threshold' which is the pace or work rate when lactic acid begins to accumulate can be improved quite dramatically by training. So if you do interval training or other types of training to improve your lactate threshold you are improving your ability to clear lactate and your ability to work at a high level for longer. If you run, then a 5k or 10k pace should be slightly above your lactate threshold. That's why pacing is so important in these shorter races because if you go out too fast you are way above your lactate threshold and will never clear it. The aim is to slowly accumulate a manageable amount of lactic acid by the end of the race, and because the race is relatively short you won't have it for long. In longer races (half marathon and above) you cannot afford to have any lactate accumulation.

Anyway, what I thought was interesting was that in 2006 George Barlow at Berkeley showed that the much demonized lactic acid is actually used as a fuel and isn't just a waste product. This doesn't really alter any training advice but it's interesting and just goes to show you should always question the things that 'everyone knows'.

The high life

Here is a link to a nice article in Audubon magazine about the bar-headed goose – a species that migrates OVER Mt. Everest. The article also mentions some other animals with superb respiratory efficiency and/or other adaptations that allow them to survive at high altitudes.

Another excuse, I mean reason, to sunbathe?

....or drink that glass of milk. We talked about the importance of adequate levels of Vitamin D to ensure normal bone formation, but Vitamin D may also be related to cardiovascular health. Recent research indicates that people with low vitamin D levels may face an increased risk for peripheral artery disease (PAD). Remember that humans make vitamin D (through skin exposure to sunlight) but it can also be obtained through foods such as fish and fortified dairy products, or vitamin supplements.

Where's my pill wrangler?

'Kurzweil does not believe in half measures. He takes 180 to 210 vitamin and mineral supplements a day, so many that he doesn't have time to organize them all himself. So he's hired a pill wrangler, who takes them out of their bottles and sorts them into daily doses, which he carries everywhere in plastic bags.'

From an article on Ray Kurzweil in Wired magazine. If you need to know more about Kurzweil the Wikipedia article is pretty thorough. From Wikipedia:

'Kurzweil believes that radical technological advances will be made throughout the 21st century, and that many of those advances will benefit the field of medicine. This will ultimately culminate with the discovery of the means to reverse the aging process, cure any disease, and repair presently unrepairable injuries, which together translate into medical immortality. Kurzweil has thus focused himself towards following a maximally healthy lifestyle to heighten his odds of living to see the day when science can make him immortal.'