Thursday, May 31, 2012

Solar-Powered Sea Slugs!

This is something our guest lecturer touched on...and I thought it was awesome!

Some sea slugs evolved a protective mechanism to “make up” for the lack of a protective shell.  One type of sea slug uses chloroplasts as camouflage and energy! It feeds by slicing or puncturing algal cells and sucking out the cell contents.  All the cell contents are discarded except for the chloroplasts, which are then engulfed phagocytotically into the digestive cells.  Since their digestive tract is just one cell layer beneath the epidermis, the sea slugs blend into the green algal bed and capture light energy to fuel photoautotrophic carbon dioxide fixation.  These sea-slugs can potentially live off of these carbon products for months in the absence of an algal food source!

The paper I read on this calls the relationship between these algal chloroplasts and molluscs symbiotic.  There is debate on whether this qualifies as symbiosis because the symbiont—the chloroplast—is not a free-living organism, just an isolated organelle.  What do you guys think?

Here is the link to the paper:

Coronary risk factors

If you watched the first part of the HBO series below then you learned about the Bogalusa Heart Study -  a 40 year study investigating the early natural history of coronary artery disease and essential hypertension. This type of long term cohort study was pioneered by the Framingham Heart Study which began in1948 and is now on its third generation of participants. Such studies have generated literally thousands of papers and have helped to unravel and quantify the contribution of various risk factors to heart disease.

In class Claudia mentioned BMI (online calculator here). Someone mentioned how broad the categories were (for my height even the normal category covers a 50lb range from 144 to 194lb). Which is a very good point - putting people into three categories: normal, overweight and obese is about the crudest measure we could use. However it is a simple measure that is easy to calculate.

There are other more complicated measures of health that use more information and express the outcome as risk rather than just 'good' and 'bad'. For example one of the classic outcomes of the Framingham heart study has been the development of the Framingham risk score - which expresses your 10-year risk of developing cardiovascular disease. This number can then be compared to the mean for people you age. Your values will all be very low because you are young. If I put my values in I get 2%, which is slightly alarming until you compare it to the average for men 40-49 which is 11%. Yikes.

Other risk score calculations are available at the Framingham Heart Study website.

Wednesday, May 30, 2012

Causes of obesity - part 2

Well if you did your homework and watched the HBO shows you heard quite a bit about fatty liver disease and saw some fatty. I haven't watched the last two shows yet but, so far, there's been no mention of an intriguing new hypothesis that obesity and fatty liver disease in particular may be infectious and therefore treatable with antibiotics. This is not a new suggestion but some of the best evidence to date, from studies of mice, was published in February in Nature:

Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity

"When healthy mice were co-housed with mice that had altered gut microbes, the healthy mice also developed a susceptibility for development of liver disease and obesity."

A number of newspapers and blogs picked up on this fairly dramatic result. Here's part of a blog posting by Suzanne O'Malley at the Huffington Post:

New findings suggest that obesity and liver disease can be caused by proteins that change microbe populations in the stomach, according to a study published in the February 2012 issue of the journal Nature. The Yale immunobiologists' discovery suggests that obesity and non-alcoholic fatty liver disease (NAFLD) may be infectious and treatable with targeted antibiotics. At least that was the case for mice. NAFLD is caused by metabolic syndrome -- diabetes, hypertension, and high blood cholesterol -- which are also risk factors for heart disease. Researchers expanded on an earlier study that showed microbial imbalances in the stomach, caused by the same family of proteins, heightened the risk of intestinal diseases such as colitis. The most extraordinary finding, according to senior author Richard A. Flavell, a Howard Hughes Medical Institute investigator and professor of immunobiology at Yale School of Medicine, was that the changed intestinal environment that led to obesity and liver disease was infectious among the community of mice studied.
The next step, Flavell says, is extending this research to humans and identifying more precisely the bacteria involved in the progression to liver disease.

Tuesday, May 29, 2012

Fastest thing in the world?

I was doing some research on Pilobolus a little while ago, but forgot to post this back then.  So in case anyone doesn't remember, Pilobolus is the fungi we discussed that uses a build up of pressure to launch its sporangium through the air in order continue its life cycle. I found this video (The Fastest Living Thing on the Planet!) which claims that Pilobolus sporangium dispersal is the fastest acceleration of any living organism.  I was extremely impressed until I noticed a couple errors the narrator of the video made which made him lose some credibility.  So I did some more research and found this article on Wired which goes deeper into the physics of the claim. Wired  It seems that saying Pilobolus is the fastest thing in the world is definitely an incorrect statement, but it may take the prize for being the fastest accelerator...that we know of.

And for fun, here's a couple other cool Pilobolus videos:


The video above is the trailer for the show Claudia mentioned. You can watch the four individual parts at the HBO website.

Causes of obesity - part 1

Some of you may have seen this video - check out the numbers, that's nearly 2.5 million YouTube hits! As the New York Times puts it, in a 2011 article 'Is Sugar Toxic?':
'fairly remarkable numbers for a 90-minute discussion of the nuances of fructose biochemistry and human physiology. '

Lustig is a persuasive speaker and he makes some good arguments . It seems like sugar is almost certainly part of the obesity problem - but is it the main part or are there other major causes. In the next post I'll look at some recent evidence for an infectious cause of obesity.

If Lustig is right, then our excessive consumption of sugar is the primary reason that the numbers of obese and diabetic Americans have skyrocketed in the past 30 years. But his argument implies more than that. If Lustig is right, it would mean that sugar is also the likely dietary cause of several other chronic ailments widely considered to be diseases of Western lifestyles — heart disease, hypertension and many common cancers among them.

Monday, May 28, 2012

Nuerobiology Folks Alert! A really neat TED talk

This isn't necessarily my article or research topic but I came across this while doing some personal research on algae and though a few of you would really enjoy this. This is a really neat 2011 TED talk from an MIT research team. The "TL;DR" is basically that because neurons are electrical impulses, they have the potential to be controlled and can possibly be used to treat all kinds of brain disorders like epilepsy, depression, and schizophrenia! "A Light Switch for Neurons"

Undulating Blob Of Flesh

Great title for a story on the NPR site this week: Why Is That Undulating Blob Of Flesh Inspecting My Oil Rig? 
On April 25, somewhere in the ocean off Great Britain, a remotely operated video camera near a deep sea oil rig caught a glimpse — at first it was just a glimpse — of an astonishing looking sea creature. It was a green-gray blob of gelatinous muscle, covered with a finely mesh-like textured skin, no eyes, no tentacles, no front, no back. It moved constantly, floating up to the camera, then it backed off and disappeared. The camera operator tried to find it, and then, suddenly, out of the darkness, back it came.
The original video is above but check out the NPR link for some great video of the beast in question Deepstaria reticulum.

Sunday, May 27, 2012

Painting or photograph?

I keep coming across this photograph on the Interwebs. I think it was originally a photograph of the day at National Geographic about a year ago. Apparently it is not manipulated in any way and simply shows a soaring dune as the backdrop for the long dead camel thorn trees in Namib-Naukluft Park. There's a feature story on the park at the National Geographic site. Did you know Namibia was one of the world’s first nations to write environmental protection into its constitution?

Namibia's civil war started in 1966 and lasted 22 years. In 1990, when Namibia at last gained independence from South Africa, it was one of the first countries in the world to write protection of the environment into its constitution. It was as if Namibians recognized that having fought for the land beneath their feet, they were now profoundly responsible for it.

Saturday, May 26, 2012

Social jetlag

Social Jetlag and Obesity
People who have different sleep patterns at the weekend than they do during the work week may get "social jet lag," according to new research. That shift in our natural sleep patterns is linked to obesity.
For every hour of social jet lag, the risk of being overweight or obese rises about 33%, says researcher Professor Till Roenneberg.

'Social jetlag' is measured as the average midpoint of a person's sleep on weekdays compared to weekends. The difference in those numbers gives the 'social jet lag'. So, a person who goes to bed at 1 am and gets up at 6 am during the working week, and goes to bed at 1 am but only gets up at 9am at weekends for example, would have 1.5 hours of social jet lag.

slime molds are our friends!

Hey everyone! Here's a cool paper on how we can use a chemical from slime molds (DIF-1) to prevent estrogen dependant cancers!

Also, I found a neat summary on the sci Am website if you prefer plain english :)
I'd at least check out the second one!

Wednesday, May 23, 2012

Zombie debates

 It's been cancelled this year.

The 3rd Annual ZOMBIE DEBATES!

The world has been taken over by Zombies!!!! Only one academic subject can survive in the new Human Colony. The question is: Which subject should it be?
Come out to The Hub on Tuesday, May 29th and watch some of your favorite UCSB professors debate this topic and defend their subject!
**Doors open at 7:45pm; the debate begins at 8pm.**
FREE for UCSB students only. You must bring your valid UCSB access card!

Modesty prevents me from saying who won last year but I'll be back this year to defend my title. (Worst prize ever - winner gets to come back next year ?!?). Last year I made a genuine case for biology, this year I'm just going for the cheap shots.

Swim bladders and the "Barry White of the Sea"

Here is the link to the NY Times story I mentioned in class a few lectures ago on vocalizations made by fish using their swim bladders.  The article highlights several cases in which obnoxious noises were assumed to be anything BUT made by fish and those who suggested fish as the culprits were called crazy!  As I mentioned the swim bladder is thought to be evolutionarily homologous to the early lung and both develop as outpockets of the gut (in the early stages of development). A paper by Zheng et al., published in 2011 in PLoSONE looks at some of the evidence for the "homolog" idea, and their results "provide molecular evidence of the relatedness of the fish swimbladder and mammalian lung."

Black drum

Here also is the link to some of the cool sounds fish make, including the "Barry White of the sea", the black drum.

And one more link: this one describing research by SFSU professor Roger Bland on the vocalizations of the toadfish in SF Bay.


Tuesday, May 22, 2012

Dinosaurs had arthritis

Related to both skeletons/bones and immunology is the inflammation of joints or arthritis.  There are many kinds and causes of arthritis and its symptoms can range from irritating to debilitating.  The most common form is osteoarthritis, which mainly affects the elder population, but a significant portion: about 30% of women at age 65 have osteoarthritis.  Apparently we humans have suffered from arthritis throughout our history, having been found even in Egyptian and Peruvian mummies!

Ok, now to the title story....  several studies, including one recent, indicate that dinosaurs, too, had arthritis.  They just didn't get any breaks, huh?

Full citation of the original article:
SASSOON, J., NOÈ, L. F. and BENTON, M. J. (2012), Cranial anatomy, taxonomic implications and palaeopathology of an Upper Jurassic pliosaur (Reptilia: Sauropterygia) from Westbury, Wiltshire, UK. Palaeontology. doi: 10.1111/j.1475-4983.2012.01151.x

How do muscles contract?

I spent a bit too long on immunology and ran out of time to cover muscles. Check out section 48.1 and 48.2 in your textbook which cover this quite clearly.

Note though that this 'sliding filament' model of muscle contraction was only discovered in the 1950's. The key evidence used to construct the model was a series of electron micrographs like those to the right of the picture.

You textbook does a nice job of interpreting the micrographs (figs 48.1 and 48.2) in the context of the theory but it's interesting to consider if you only had the pictures do you think you would have come up with the correct model?

The sliding filament model was actually proposed by two groups working independently and their papers were published together in the same issue of Nature.

 Structural changes in muscle during contraction: interference microscopy of living muscle fibres

Changes in the cross-striations of muscle during contraction and stretch and their structural interpretation 
In 2004 Nature published a special focus to celebrate the papers and look at progress in the subsequent decades on 'one of the most intriguing of biological problems: that of the conversion of chemical energy to mechanical work'.

Monday, May 21, 2012

The Wisdom of Slime

From an op-ed in the New York Times, recently entitled "The Wisdom of Slime." 

An interesting fact about this slime mold is that it is highly intelligent — or at least it behaves as if it is. In locating food in its environment, it builds networks that have been shown to be optimally efficient in transporting the nutrients over the area in question. If placed in a maze, for instance, with a source of food outside the maze, the slime mold will discover the shortest path out. 

The Japanese researcher Toshiyuki Nakagaki and his colleagues have demonstrated that the slime mold’s foraging behavior can be used to perform sophisticated computations, as long as the problems are represented spatially. Problems solved by the slime mold include not only the shortest path out of a maze, but also other complex mathematical challenges (like creating a Voronoi diagram and a Delaunay triangulation). 

Despite its ability to solve an array of problems, the slime mold was designed by evolution to solve just one problem: how to build an optimal transport network (for its nutrients). So we decided to investigate how the slime mold, when presented with the task of connecting the major urban areas of the United States, would design a transport system. Would its design resemble that of the United States highway system, or would the slime mold propose a superior one? 

Here’s how our experiment worked. As we detail in a forthcoming article in the journal Complex Systems, we took a large dish in the shape of the United States and placed rolled oats (a food for the slime mold) in the locations of 20 major urban areas. Then we put the slime mold on the rolled oats representing the New York area. The slime mold propagated out from New York toward the other urban areas and eventually spanned them all with its network of protoplasmic tubes. We performed this experiment a number of times.

Comic Relief!

I'll post my topic in a few days, but this comic that I found on the internet reminded me of this class and I thought you all might find it funny!
Alex Phillips

Sunday, May 20, 2012

Multiple pollen tubes

Going back to last quarter but I thought this paper in Current Biology this month was interesting: Gamete Fusion Is Required to Block Multiple Pollen Tubes from Entering an Arabidopsis Ovule

Plants need to make sure that their female gametes are fertilized but they also need to make sure that only two fertile sperm reach the ovule.

When gamete fusion fails, one of two pollen tube-attracting synergid cells persists, enabling the ovule to attract more pollen tubes for successful fertilization. This mechanism prevents the delivery of more than one pair of sperm to an ovule, provides a means of salvaging fertilization in ovules that have received defective sperm, and ensures maximum reproductive success by distributing pollen tubes to all ovules.

Saturday, May 19, 2012

Not dying sooner

Some confusing headlines this week on the effect of coffee drinking on health.

Most newspapers went with some variation of 'Coffee drinkers live longer', but the truth was a little more complex than that.

The research, published this week in the New England Journal of Medicine, Association of Coffee Drinking with Total and Cause-Specific Mortality, actually reached a slightly different conclusion:
In this large prospective study, coffee consumption was inversely associated with total and cause-specific mortality. Whether this was a causal or associational finding cannot be determined from our data. 

The Washington Post, who have some good science reporters, did well with No, drinking coffee probably won’t make you live longer
The study’s researchers found that coffee drinkers were more prone to engage in a whole host of unhealthy activities. They smoke more, are more likely to consume three or more alcoholic drinks a day and eat more red meat. They exercise less and eat fewer fruits and vegetables.
When the researchers isolated coffee consumption as a single variable, they did indeed see a drop in the risk of premature death. But when they looked at coffee-drinkers who had those bad health habits, the risk of death was actually higher: Coffee-drinkers are actually more likely to die early because of those habits.

and BoingBoing got all wrapped up with Coffee associated with the opposite of death, according to new scientific study
I think what they're trying to tell us is that while drinking coffee does not necessarily cause you to live longer, it is associated with the opposite of dying sooner.

I'll just note that for maximum 'not dyingness' you need to drink six or more cups a day....

Friday, May 18, 2012


Suicide-bags would probably be a good name for a band. If this was the 1970's. Suicide-bags is also a name for the lysosomes found within cells because as well as pathogen destruction they are involved in the natural process of cell organelle recycling and even cell death. This degradation and recycling of ageing and dying cells, or autophagy, is attracting a lot of attention these days because of its links to disease and aging.

The science writter Carl Zimmer wrote an article for the New York Times on this topic, Self-Destructive Behavior in Cells May Hold Key to a Longer Life based on a paper in Trends in Cell Biology: The regulation of aging: does autophagy underlie longevity?
Recent evidence has revealed that autophagic activity is required for lifespan extension in various long-lived mutant organisms, and that numerous autophagy-related genes or proteins are directly regulated by longevity pathways. These findings support the emerging view that autophagy is a central regulatory mechanism for aging in diverse eukaryotic species.

It's an Archosaurian thing

Crocodilians and birds are quite closely related to one another- both belong in the clade Archosauria. Although they seem to not have much in common, researchers from the University of Utah have done tomographic studies of alligator lung anatomy and found some striking similarities to that of its avian relatives. This is interesting because “Conventionally, the avian lung + air sac system is viewed as a cornerstone for the renowned aerobic capacity of birds, and as a very derived and unique respiratory system (Maina, 20002006). However, the discovery of unidirectional airflow in alligator lungs (Farmer, 2010; Farmer and Sanders, 2010) raises the possibility that many features are synapomorphic for archosaurs.” (Sanders+Farmer 2012).  It turns out that Alligator mississippiensis, or the American Alligator, also possesses the unidirectional air sac/lung combination found in birds. It is somewhat more simplistic, which makes sense because the rest of crocodilian anatomy is also less derived from the common archosaurian ancestor. Why would crocodilians have this unique lung structure? According to the authors of this paper, “ It is not clear if unidirectional airflow is an exaptation, initially serving in cardiogenic flow during apnea (Farmer, 2010), an adaptation for expanded aerobic capacity during a time of environmental hypoxia, (Farmer, 2010; Farmer and Sanders, 2010), or if it serves another, unknown function”. Obviously, not much research has been done in this area yet. Perhaps there is more to come. If you want to read the article, click here. Most of the Results section is detailing lung anatomy, and is too dense even for a nerd like me. If you want to learn more, I recommend the “Functional Morphology of the Alligator Lung and Its Relationship With Other Crocodilians” section. Also, for a more detailed description (with diagrams!) of avian respiratory anatomy, click here.

Thursday, May 17, 2012


I mentioned the Triclosan issue today. Take a look at your cleaning products (both human, like soap and shampoo, and household) - I bet that several of them mention being 'antibacterial' and the product is probably Triclosan.

If you google the term you'll see this is quite a hot topic. A google news search throws up this article from 2008, Environmental Group Calls Triclosan a Ubiquitous Menace and this New York Times article from last year: Antibacterial Chemical Raises Safety Issues.

This presentation, Antibacterial Household Products: Cause for Concern by Stuart Levy, from the 2000 Emerging Infectious Diseases Conference in Atlanta, Georgia and on the CDC webpage is a good overview of the resistance issue.

Wednesday, May 16, 2012

Mile high club

Thanks to Wired magazine for that gratuitous headline.

Claudia mentioned some of the issues of altitude for respiration. For a long time athletes have explored the benefits of training at altitude. The key benefit is that prolonged exposure to low oxygen concentrations (it's actually a low pressure but the effect is the same) leads to increased red blood cell concentrations.

However the downside is that it is hard to work your muscles at appropriately high intensities at low oxygen concentrations. One solution that has been around for a while is to 'live high, train low'. This works because the advantages of living at altitude come about from simply being there even if you are just sleeping, eating, working, whatever. But you go to low altitude to train at appropriate intensities. However this is inconvenient to say the least. Hence the development of low oxygen sleeping chambers and even low oxygen offices. These don't mimic the low pressure of altitude but simply reduce the oxygen concentration to induce the same effect.

Looks like it's a pretty big business - Hypoxico are one of the main companies and have an intriguing range of products.

But as anyone who has spent any time at altitude will tell you, there's a downside. From the Wired article:  Mile-High Club: Do Oxygen Tents Boost Athletic Performance?

Crawford discounts anything beyond a placebo effect, claiming that the low-oxygen environment hampers recovery and robs the athlete of sleep, a primary component of any training program. “Why am I starving my athlete of oxygen that he needs to recover?” Crawford asks.

The ethics of the use of these devices by athletes has been discussed by the World Anti-Doping Agency (WADA), which claimed that it could be equivalent to blood doping and therefore they should be banned. Blood doping is the use of hormones such as erythropoietin (EPO) which boost red blood cell production. These were banned  for most sports in 1986. In 2006 the WADA announced that 'the overwhelming consensus of our health, medicine and research committees – was that, at this time, it is not appropriate to do so." Presumably because there would be no mechanism to enforce such a ban

Tuesday, May 15, 2012

Still curious if Tibetians have an evolutionary edge? This article details the discovery of widespread mutation near the so called "super-athelete gene"in Tibetians, and how it affects their respiratory and cardiovascular systems. Enjoy!

A billion heartbeats

One reason I love California is that you can exercise here without being considered weird. In many parts of the country (and world) the active exerciser is considered as a threat to the lifestyle of the sedentary who will go to considerable lengths to explain how exercise is actually bad for you. I have had people stop beside me at traffic lights and lean out of their windows to explain the damage I am doing to my knees by running (not true by the way). But my favorite is the constant heartbeat theory.

This idea is actually quite old - one paper suggests it came to prominence in the late 1800's industrial revolution with the observation that machines that ran fast wore out more quickly. It then became 'supported' by observations across species - bigger animals live longer and also have lower heart rates. Perhaps we all have a finite number of heartbeats and exercising will only use them up faster. Oh noes. However even if this were true (which it isn't) it would not be an argument against exercise because one consequence of being fit is a lower resting heart rate. You don't need to lower it much to have the reduced beats in the 22-23 hours a day you aren't exercising more than compensate for the hour or two you do.

Although the initial theory proposed a constant number of heart beats this became refined to suggest that it's the speed at which an organism processes oxygen that matters. There is evidence, when comparing species, that creatures with faster oxygen metabolisms die younger. Tiny mammals with rapid heartbeats metabolize oxygen quickly and have short lifespans. Tortoises, on the other hand, metabolize oxygen very slowly and have long lifespans. The free-radical theory of ageing provides a potential mechanism that links metabolism to ageing phenomena, since oxygen free radicals are formed as a by-product of oxidative phosphorylation.

The debate rumbles on. One of the complexities is that even if a relationship exists between species we wouldn't necessarily expect it to be the same within a species. When we look within a species it gets very complicated. here's a summary from a 2005 paper in the Journal of Experimental Biology  (Body size, energy metabolism and lifespan):
The observed patterns of association between rates of energy metabolism and the rates of ageing (or lifespans) of animals within species include all the potential patterns of association - positive, negative and not significant. 

So about those giraffes...

I got curious about giraffes after the lecture today about circulations. Here are some sources that I found. I didnt have time to read the longer ones, but I think the summaries and abstracts should have enough info to be satisfactory.

Monday, May 14, 2012

Two free talks this week

Claudia brought two Cambell Hall events this week to my attention. Both are FREE for students

David Eagleman
Monday, May 14 @ 8:00 PM , Campbell Hall
Incognito – The Secret Lives of the Brain

“The Malcolm Gladwell of brain science.” The Independent (U.K.)

“Original and provocative… A smart, captivating book that will give you a prefrontal workout.” Nature

If the conscious mind – the part you consider you – accounts for only a fraction of the brain’s function, what is the rest of it doing? It’s a question neuroscientist David Eagleman has spent years researching and which he’ll explore in a witty and enlightening talk filled with startling new discoveries. Author of the New York Times best-seller, Incognito: The Secret Lives of the Brain, he’ll take us into the depths of the subconscious to illuminate some of our deepest mysteries, such as why is it so difficult to keep a secret? And why does the conscious mind know so little about itself?

Jonah Lehrer
Thursday, May 17, 2012 @ 8:00 PM, Campbell Hall
Imagine – How Creativity Works

Distinguished Visiting Fellow in the College of Creative Studies

Best-selling author of How We Decide and Proust Was a Neuroscientist

“Jonah Lehrer’s new book [Imagine] confirms what his fans have known all along – that he knows more about science than a lot of scientists and more about writing than a lot of writers.” – Malcolm Gladwell

Did you know that brainstorming meetings are a terrible idea? That the color blue can help you double your creative output? In his new book, Imagine: How Creativity Works, Jonah Lehrer takes an exhilarating look at how we can use the latest science to unleash our imaginations – and make our companies and culture more creative. He argues that creativity is not a gift possessed by the lucky few but a variety of thought processes we all can learn to use more effectively. Lehrer is the author of How We Decide and a contributing editor at Wired. Get your tickets early – his talk sold out when he was last here!

Sunday, May 13, 2012

Dragonfly Woman

So, could a diving insect take such a large bubble of air with it that it could, relying on oxygen diffusing into the bubble from the water, stay underwater indefinitely?

Well that's a good question. Let's ignore the problems involved with trapping and holding onto such a bubble for a moment an see whether it is possible.

Unfortunately not because we need to think about the nitrogen as well as the oxygen. But this topic did lead me to the Dragonfly Woman blog of Christine Goforth, a PhD student in Arizona so all is not lost.

Now, it may seem like a physical gill would allow an insect to remain underwater indefinitely, but this is unfortunately not the case.  As the oxygen is consumed by the insect, the concentration of oxygen in the bubble decreases and the gas mixture is thrown out of equilibrium – the ratio of oxygen to nitrogen is no longer the same.  Remember how the bubble wants to remain at equilibrium?  Well, it will do whatever it needs to so that equilibrium is restored.  There are two ways to do it: increase the oxygen in the bubble or decrease the nitrogen in the bubble.  As oxygen is consumed, nitrogen starts to flow out of the bubble to restore the equilibrium.  Oxygen flowing into the bubble from the water slows the loss of nitrogen, but there is so much less oxygen available in water compared to air that consumption of oxygen often outstrips the flow of oxygen into the bubble.  So, nitrogen slowly seeps out of the bubble, making the bubble smaller and smaller until the bug must go to the surface to replace the bubble altogether.

 This is from her Better Breathing Underwater in Aquatic Insects post which is actually a third part of a series of very interesting posts on insect respiration. Part one is Insect Respiration and part two is Aquatic Insect respiration.

Saturday, May 12, 2012

Pushing the limits

If you are interested in diving, human physiology, or simply the limits of what is possibl;e then you may enjoy this CNN photo essay that is currently highlighted on their homepage, documenting a free diving competition off the Cayman Islands:
One deep breath: Pushing the limits of freediving
Off the coast of the Cayman Islands, photographer Logan Mock-Bunting takes a deep breath and descends into the endless blue. He has been freediving for years, swimming long distances underwater without an air tank.
But this time was different. He was there to cover Performance Freediving International’s Deja Blue III, an annual competition that ended Thursday. He would witness iron-lung athletes exploit their bodies to break breath-holding records.

Friday, May 11, 2012

Save your breath....and use it to generate electricity!

You may have thought that inhaling and exhaling held their own intrinsic values and that was plenty.  In with the good air, out with the bad air.... 

But seems there's much more you can do with the CO2 coming out of your nose.  Of course there is the music potential: Nose flutes,   Nose harps...

But now there's even more...  from Science Daily,  "Electricity from the Nose - Engineers Make Power from Human Respiration".  Who knew?  

Thursday, May 10, 2012

Apnea, static and otherwise

Unfortunately (or perhaps fortunately) the static apnea video is no longer available but here's a picture which is very, very similar to the video. I'll paste my earlier description and the much more exciting video with freediving champion William Trubridge below.

Static apnea is floating face down in a swimming pool whilst holding your breath - quite possibly the most boring sport in the world to watch (it makes cricket look exciting) but physiologically quite interesting. For example divers now use glossopharyngeal insuffation - this is a method of pumping additional air into the lungs widely used by reptiles and amphibians (picture a frogs bulging neck) but not by humans. Until a few decades ago when free divers discovered that by using the tongue as a piston an additional liter or so of air can be forced into the lungs. Don't try this at home though, rupturing the lung is a real possibility unless you work up to it.

How long can you hold your breath? A minute? A minute and a half?

What do you think the world record is. Four minutes? Five minutes? Ten minutes? Think again. The static apnea record is ELEVEN AND A HALF MINUTES!

Curiously the techniques involved don't involve keeping the brain alive without oxygen, that's simply not possible, but getting oxygen to the brain even though you aren't breathing.

If you breath oxygen beforehand though the record is much longer - two people have now exceeded TWENTY MINUTES.

(Here's a challenge - using knowledge of physiology and physics could you predict that the record would be almost twice as long using pure oxygen compared to the ~20% oxygen in air?)

Free diving is much more challenging because you must perform physical exercise without breathing (and face the changing pressure at depth.) There are all sorts of categories including 'no limits' where divers use a weighted sled to pull them down and then air bags to ascend. You still have to hold your breath of course... The world record for this is an amazing 214m (over 700 feet). But the purest form of the sport is where the diver swims down and back under his own power without even the benefit of fins. Watch this amazing dive by William Trubridge, who has set further records since this video - currently his record is an amazing 101m. I love how calm and collected he is. Every movement seems perfectly choreographed and he is clearly maximizing efficiency and not speed.

Wednesday, May 9, 2012

Infectious cancer

I don't think anything like this is known in humans but there ARE infectious cancers, and not just the ones caused by viruses. The best known example is the bizarre facial tumors that are threatening the Tasmanian Devil's.

Genome sequences from the infectious tumour were published in February in the journal Cell (Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer), offering clues about how the cancer has spread to devils across the Australian island of Tasmania.

The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations.

Tuesday, May 8, 2012

Teaching and learning evolutionary principles


Thursday, May 10, 2012
3:30-4:30 p.m.
LSB 1001 (Rathmann Auditorium)


Michael Klymkowsky
Professor of Genetics and Director of CU Teach
Molecular, Cellular, and Developmental Biology
University of Colorado Boulder

MCDB Seminar:  Teaching and learning evolutionary principles, Socratically.
Thursday, May 10th at 3:30 pm in LSB 1001

Professor Klymkowsky’s academic research spans a wide range of interests from basic research into the embryonic patterning and gene regulatory networks in Xenopus laevis, at one extreme, to his passion for educational research at the other extreme. In this seminar he will address his recent activates in the realm of STEM education that broadly encompass effective teacher education; coherent biology course and curricular design and delivery; and improving student learning.  His basic mantra is that effective teaching requires awareness and accurate understanding by the instructor of the thinking and implicit assumptions that students bring to the subject to be learned, all of which can be deceptively difficult to assess and respond to with effective pedagogy. Through a multipronged approach untaken in collaboration with other science educators and educational research experts, he is attempting to improve undergraduate introductory biology instruction by identifying and emphasizing fundamental concepts that unite all of biology and, at the same time, measuring student learning gains to validate best instructional practices.

Although his title suggests that the central focus of his seminar will be on teaching evolution, this topic serves as but one of many examples of difficult concepts students encounter in the biology curriculum and that instructors find challenging to teach effectively.  Drawing on the success of the physics concept inventory in terms of revising the curriculum for teaching physics undergraduates the laws of Newtonian mechanics, Mike has helped develop a biology concept inventory along the same lines and he is using it to assess student learning gains and instructor effectiveness in different classroom situations.  In essence, he is driven to ask deep questions like these:  Which concepts do students really need to know for life-long understanding of biology?  Do traditional teaching methods develop student understanding of these concepts in ways that achieve this goal?   Are there more effective ways to promote student learning in these areas?  His efforts to find research-based answers for such questions will be addressed in his seminar.


Oh and this one too about the giant Carboniferous arthropod Arthropleura.

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.

Forbidden experiments

 Mothra's larval form destroying the Tokyo Tower in the movie Mothra from 1961.

Apologies for the repeat but this topic came up today and I thought you'd enjoy

In the Fantastic Four comics Dr Doom was expelled from Empire State University for carrying out 'Forbidden experiments'. The experiment in question involved contacting the dead so maybe that's not that surprising, but I was always amused by the notion that a University might have a big list of 'Forbidden experiments'. Ah yes, item number 147, 'Contacting the Dead', right after number 146 'Reanimating the Dead'.

Anyway, I was reminded of that when I took a quick look for some papers on insect gigantism and came across this recent review paper Atmospheric oxygen level and the evolution of insect body size, where they mention several experiments where people have selected for insect gigantism over many generations under high oxgyen conditions in the lab.

The effects of hyperoxia on growth and body size are less consistent and often nonlinear (Harrison et al. 2009). Body size increases in the giant mealworm, Z. morio (27% O2; Harrison et al. 2009) and in the scarabaeid beetle C. texana (40% O2; Harrison et al. 2009).

I'm pretty sure 'Creating Giant Insects' would also have been on empire State's list. Did Mothra not teach us anything?

But the answer to our question of what other giant insect (and other arthropod) fossils have been found is:

Among insects, gigantism in the Permo-Carboniferous has also been reported for Ephemeroptera, Diplura, Thysanura and the extinct order Paleodictyoptera (Briggs 1985; Kukalova-Peck 1985). Arthropleura, a group related to modern day millipedes, reached upwards of 2 m in length, almost six times the size of any extant millipede. 

So no, no Lepidoptera, you'll just have to make do with Mothra.

Monday, May 7, 2012

Obesity epidemic

We haven't started our physiology section yet but with today's dramatic headlines from the CDC's 'Weight of the Nation' event I thought I'd post a little about obesity.

Obesity is not simply being overweight, it's usually defined as having a Body Mass Index over 30. To put this in perspective I weigh 160lb and have a BMI pretty much in the middle of the normal range. If I put on 70lbs of weight (which would be about two Otto's worth - Otto is the 30+lb cat in the picture who has since lost weight) I would still not be obese (although I would be overweight!) So obesity is not simply a medical term for being overweight - it is a precise medical term for being VERY overweight. We know that at this point obesity causes many serious health problems.

Now in today's headlines we see the shocking news that 36% of American's are now obese (up from 12% in 1990 and 22% in 2000) and by 2030 that is estimated to rise to 42% leading to somewhere around half a TRILLION dollars in extra healthcare costs between now and then (compared to if obesity rates stayed at 2010 levels). This is all based on a paper in the American Journal of Preventive Medicine - Obesity and Severe Obesity Forecasts Through 2030.
About the only good news is that the paper actually results in a lower estimate of future obesity than some previous analyses but that's cold comfort given the conclusions:

The study estimates a 33% increase in obesity prevalence and a 130% increase in severe obesity prevalence over the next 2 decades. If these forecasts prove accurate, this will further hinder efforts for healthcare cost containment.

The paper also provides some estimates for 'severe obesity' (BMI>40 - for me that would be just about doubling my weight to 310lb). These estimates are actually worse than current estimates. By 2030 they predict that 10% of the US population will be severely obese.

Sunday, May 6, 2012

The horror, the horror

Wow. This looks like a video of a projection in a classroom full of kids but that's horrific. I couldn't find the Yakkety Sax video I mentioned. Maybe I was thinking of this white blood cell chasing bacteria.

Saturday, May 5, 2012

ATP parasite

I haven't quite digested this yet but this paper from 2008 describes a Eukaryote that has lost its mitochondria - as I briefly mentioned in class. In this case though the remnant mitochondria, known as a mitosome, actually consumes ATP - that the host cell must absorb from its host. Reversing the usual relationship between mitochondria/mitosome and host cell. Funky.

Thus, uniquely among eukaryotes, the traditional relationship between mitochondrion and host has been subverted in E. cuniculi, by reductive evolution and analogous gene replacement. Instead of the mitosome providing the parasite cytosol with ATP, the parasite cytosol now seems to provide ATP for the organelle.


Only very rarely do I look a the stats for this blog. Usually when I click the wrong button by mistake. Google blogger provides some basic stats and a listing of the search terms that bring people to the site. I won't ask you to guess, because you won't even get close, but the top three search terms of all time that bring people to this site are:

"Voodoo lily"
and "Dragonfly penis"

ccs bio blog (which actually makes sense) is currently number 4.

"Normal heart rate" is number 6 which is worrying.

This is actually all far less puzzling than my disease blog (which gets 1000 visitors on a good day) where 'Kittens" is somewhat mystifyingly one of the top search terms.

Friday, May 4, 2012

Witch trials

Victims of ergotism. Pieter Bruegel painting, Louvre.

Ergot poisoning was certainly common in history, there is no doubt about that. But was it responsible for the events that occurred in Salem and what exactly is the evidence that the fungus was involved?

In 1976 psychology grad student Linnda R. Caporael proposed the ergotism hypothesis, and history professor Mary Matossian elaborated on it in 1982. The core contentions: A cold winter followed by a moist spring and summer prior to the witchcraft hysteria favored the growth of ergot fungus in rye that the colonists were obliged to eat due to crop failure. Ergot contains toxins known to cause convulsions, hallucinations, and other symptoms similar to those reported by the accusers. 

Doubters were quick to raise objections: Evidence of a cold winter and crop failure is dubious, and none of the accusers displayed the full array of symptoms needed to support a diagnosis of convulsive ergotism. More importantly, the symptoms appeared only at opportune moments during the trials, strongly suggesting a psychosomatic origin if not fraud. The counterarguments seem to have persuaded most historians, but a credulous 2001 PBS documentary has helped keep conjecture about ergotism alive. 

A. Woolf in the Journal of  Clinical Toxicology reaches a similar conclusion. Witchcraft or mycotoxin? The Salem witch trials.
The Salem witchcraft trials of 1692 have been studied by many historians looking for the complex social, political, and psychological determinants behind the community-wide hysteria that led to a travesty of justice and the deaths of 20 innocent Puritans. Recently, ergot poisoning has been put forth by some as a previously unsuspected cause of the bizarre behaviors of the young adolescent girls who accused the townsfolk of witchcraft. In this essay the circumstances behind the ergot poisoning theory for this historical event are described. When the evidence is weighed carefully both pro and con, it seems unlikely that ergotism explains much of what went on in colonial Salem.

Read Linnda Caporael's 1976 paper (in Science) and weigh the evidence for yourselves: Ergotism: the satan loosed in Salem?