Wednesday, October 10, 2012


Rep. Paul Broun (R-GA) at the Liberty Baptist Church Sportsman's Banquet on September 27, 2012, in Hartwell, Georgia, denying evolution, embryology, and the Big Bang Theory, saying that they are lies from the "pit of Hell".

Rep. Broun chairs the House Science Committee on Investigations and Oversight. Which, as Bruce points out, is a good reminder that Your Vote Matters and that our elected officials determine science policy in this country. Get registered and vote.

Friday, June 8, 2012

It might not be cancer...

Good job with the presentations on Thursday. Lots of fascinating stuff. Thanks for those who posted here and there's still time to do so if you didn't already. 

I'm personally taking a brief hiatus from posting (at least until summer session starts) and this particular blog will be going into hibernation until our new cohort starts up in the Fall. Feel free to check back in for a whole new fun year of blog posts for Introductory Biology in the Winter and Spring.

Fun story - I got home on Thursday and my dog is all over me, sniffing like crazy. Now he hasn't been trained to sniff out cancer but it was still a little alarming after hearing about that. Only after about 10 minutes did I find the slice of banana bread I'd forgotten in my pocket.

Sleeping > Studying ( some extent)

Good morning all! I hope your studying is going well - I thought that this article was particularly relevant to finals week. In brief, sleep is highly beneficial, possibly essential, for remembering things. You probably already know this - but seriously take it into consideration. Don't underestimate sleep, especially REM sleep. (If you're curious about the complex electrical signaling which causes sleep to help you remember things, the article is "Sleep to Remember" (Born, Rasch, and Gais 2006), which can be found here:

Do you need a place to live?

I stumbled upon an article a while back and you can take a look at their official site here:

They seem to have it fully planned out to send out a group of people to Mars by he year 2023, which if you think about it, isn't all that far away. They'll start out by sending a group of four people to "colonize" the planet, then every two years they'll send another four more people.

A co-founder said:  "By sending a new crew every two years, Mars will have a real, growing settlement of humans -- who would not like to follow that major event in human history?"
Personally, I wouldn't. And to me, that statement seems to actually mean: "There must be at least four people willing to go..."

The mission itself will provide us with invaluable scientific and social knowledge that will be accessible to everyone, not just an elite select few.

So... would you move to Mars? You know... for science?

Thursday, June 7, 2012

Oskar the Blind Cat

Here is the channel with videos of Oskar.

Some videos will show close ups of his face so you can really see that he actually has no eyes, but he can navigate pretty well without them.

Hummingbird Hovering

I thought this was a very good video about hummingbird flight. It is pretty amazing how hummingbirds have so much dexterity and maneuverability in the air. They can even fly backwards and upside down!

At about 1:35 scientists are performing the same experiment as in the paper I read, where they attach a string with weights on it to a hummingbird and see how many weights the hummingbird can lift.

If this link doesn't work, the video is called NATURE | Hummingbirds: Magic in the Air | Hovering | PBS

Natural Selection

Natural selection is fairly lazy, in my opinion, because it doesn't want to put energy into developing something new. If it absolutely has to create something new, though, it will do so at the expense of something else. Never will it just decide to make changes for the fun of it. For instance, we humans have five senses (sight, hearing, touch, taste, smell) and at one point during human evolution (approx. 23 mya), natural selection decided that trichromatic color vision would be very beneficial to humans. But because this would be such a huge expense (in time and energy spent), something else would have to be diminished. 

In one study, they found that the deterioration of the human olfactory repertoire was probably due to the development of trichromatic color vision. Olfactory receptor (OR) genes provide a basis for our sense of smell and human genomes possess more than 1,000 of these genes. But ~60% of these genes are pseudogenes, meaning that they are "turned off" and don't contribute to the phenotype. This is why we can't smell things as well as a dog. Most of dogs' OR genes are "turned on", allowing them to smell more things than we can.
Is there a reason why most OR genes are turned off in humans? The answer is yes, because natural selection does things for specific reasons, and for humans it seems to have deemed trichromatic color vision as more important than a great sense of smell.


So I took a class about oncogenesis (cancer growth), and we had been talking about possible causes for gene mutations. That is when I realized that nearly anything that is supposedly good for you (sunlight, legumes, sunscreen, wheat, etc) actually can cause gene mutations. And you can't simply say "well I'm just going to avoid these things altogether. That'll help me avoid cancer" because if you avoid sunlight altogether, you can become vitamin D deficient, which a lot of the population already is, or you can miss out on the benefits that certain food bring you. And realistically, avoid everything that could cause you to have oncogenic gene mutations would be basically to avoid life. Everything causes some kind of mutation. some mutations you are born with. I believe that basically, we all just need to realize that cancer is a likely thing to happen, and try to be as aware of it as possible to be able to catch it before it kills us.

 About the contagious cancer in tasmanian devils : It's caused by a virus which just so happen to insert its genetic code into a part of the host's genome which is too close to an important functional gene.

Wednesday, June 6, 2012

Lungless Frog

In class we learned about lungless salamanders. The only other four-limbed lungless creature is Barbourula kalimantanensis, the lungless frog! This species has been found on very few occasions. 
How does it get its oxygen, you ask? The frog respires through its skin and lives in cold waters, which hold more oxygen than warmer waters. It also has a low metabolic rate so it doesn't need as much oxygen. 

This article has more info on this badass little frog.

I was a rocket ship

TED is now getting into the education game - check out TEDEd.

There's not a huge amount there yet, just 85 videos compared to the TED site with over 900 talks, but it's new and I'm sure it will grow rapidly.

Tuesday, June 5, 2012

I found a pretty cool article related to my current research online that investigates the differing degrees of gene regulation of gene duplications in DNA-methylating species vs. those that do not methylate their DNA and how this causes differences in evolution of new gene functions of those respective species. I couldn't get the whole article to show up here, but here is the abstract:

Gene duplication is commonly regarded as the main evolutionary path toward the gain of a new function. However, even with gene duplication, there is a loss-versus-gain dilemma: most newly born duplicates degrade to pseudogenes, since degenerative mutations are much more frequent than advantageous ones. Thus, something additional seems to be needed to shift the loss versus gain equilibrium toward functional divergence. We suggest that epigenetic silencing of duplicates might play this role in evolution. This study began when we noticed in a previous publication (Lynch M, Conery JS [2000] Science 291:1151-1155) that the frequency of functional young gene duplicates is higher in organisms that have cytosine methylation (H. sapiens, M. musculus, and A. thaliana) than in organisms that do not have methylated genomes (S. cerevisiae, D. melanogaster, and C. elegans). We find that genome data analysis confirms the likelihood of much more efficient functional divergence of gene duplicates in mammals and plants than in yeast, nematode, and fly. We have also extended the classic model of gene duplication, in which newly duplicated genes have exactly the same expression pattern, to the case when they are epigenetically silenced in a tissue- and/or developmental stage-complementary manner. This exposes each of the duplicates to negative selection, thus protecting from "pseudogenization." Our analysis indicates that this kind of silencing (i) enhances evolution of duplicated genes to new functions, particularly in small populations, (ii) is quite consistent with the subfunctionalization model when degenerative but complementary mutations affect different subfunctions of the gene, and (iii) furthermore, may actually cooperate with the DDC (duplication-degeneration-complementation) process.

On a lighter note, here is a duck:

I've had an awesome time in the CCS Bio classes with you all, hopefully we will have a similar class in the future!
This is a pretty popular video that had spread around a while ago and it seems rather baffling. Legadema kills a mother baboon and while dragging its prey away, finds the baby of the baboon still alive. Seemingly, its maternal instincts kick in and out of curiosity or care, it takes care of the baby for the rest of the day not even caring about its previous kill. Was this a truly altruistic act imparted by a Leopard mother caring for the helpless or had it not a clue of what it was doing.  Whether it was raising it as its own or preparing it for a meal, no one will know as the baby baboon died over night.

Adverse reaction

Some fascinating research coming out at the moment on the potential negative effects of exercise. Since this goes counter to what we are all told such studies warrant close examination but certainly should not be simply dismissed because they don't fit the dominant paradigm.

First up, from the Mayo Clinic Proceedings this month: Potential Adverse Cardiovascular Effects From Excessive Endurance Exercise
where they review some of the evidence that long-term excessive endurance exercise can induce pathologic structural remodeling of the heart and large arteries.

Physically active people are much healthier than their sedentary counterparts. Exercise is one of the most important things you need to do on a daily basis,” he explains. “But what this paper points out is that a lot of people do not understand that the lion’s share of health benefits accrue at a relatively modest level. Extreme exercise is not really conducive to great cardiovascular health. Beyond 30-60 minutes per day, you reach a point of diminishing returns.

Second, and of more general relevance to the general population, a paper in PLoS ONE this week : Adverse Metabolic Response to Regular Exercise: Is It a Rare or Common Occurrence?

The review of six previous studies on exercise found that working out worsened at least one measure of heart risk — blood pressure, insulin level or levels of HDL cholesterol or triglycerides — for about 10% of people. About 7% of people declined on at least two measures.
For a scientist this doesn't seem that surprising after some reflection - although, on average, exercise may lead to a favorable outcome there may be a range of responses from individuals that span a range from very favorable all the way down to an unfavorable change.

Unfortunately I think you can imagine the headlines:
For those looking for an excuse to avoid exercise, here's one 
Can Exercise Actually Be Bad For You?
Exercise could be, er, bad for your heart, study says

Oh, and tomorrow is National Running Day...

Your inner fish

A repeat, but since Claudia mentioned it I thought I'd bump it up. I have the book sat in my office. If anyone wants to borrow it as long as you give it back so someone else can borrow it.

I just finished reading Neil Shubin's book 'Your Inner Fish.' It is a very easy and highly recommended read. We tend to focus on those areas where we have 'improved' on our fish-like ancestors (walking upright, doing pushups, inventing calculus etc) but what I found fascinating, and relevant to class today, was a discussion of olfaction (smelling) and how it's all been downhill since our aquatic past.

The human genome only contains about 23,000 protein-coding genes - which itself is an amazing fact. The other 98.5% of our genome consists of non-coding genes, regulatory sequences, introns and endogenous retrovirus sequences.

About 1,000 of those 23,000 protein-coding genes code for different odor receptors but less than half of them are functional in modern humans. Which says a lot about the importance of different senses in the evolution of humans from an aquatic ancestor (smell) to a terrestrial life (vision). Our evolutionary history is revealed in our genes.

Why Spinner Dolphins spin

The spinner dolphin is known for its incredible leaps out of the water during which they can spin up to seven times.  Until 2005 no studies should evidence explaining why the dolphins spun in the air, but it had been proposed that the spinning could possibly help with the removal of unwanted remoras.  In 2005 Frank E. Fish, Anthony J. Nicastro, and Daniel Weihs conducted an experiment that supported this hypothesis.  Using mathematical models they showed that spinning would be extremely helpful in the removal of remoras.

Normal jumping does not move the remoras because they are still parallel to the dolphins body causing them to feel minimum drag upon reentry into the water.  However, spinning causes the remora to become perpendicular to the dolphins body thus causing a significant increase in drag upon reentry.  This resulting drag is the force that dislodges the remora.

Monday, June 4, 2012

Strange Nervous System Adaptations in Reptiles

Strange Nervous System Adaptations in Reptiles

It is by coincidence that I am simultaneously learning about animal nervous systems in both this class and in herpetology.  I found out today that some reptiles, most notably the sea snake, can detect ultraviolet light through photoreceptors in their skin.  For the olive sea snake, the photoreceptors are present on the tail.  Sea snakes live in crevices in reefs, and cannot tell by plain sight or feel whether they are completely hidden from predators or not.  The ability to sense light with their tails lets them know that their tails are still exposed, prompting them to move them out of sight. It's almost like seeing with your skin!

Link to a related paper:

Little wing

This fossil insect wing (Stephanotypus schneideri) from the period about 300 million years ago when insects reached their greatest sizes, measures 19.5 centimeters (almost eight inches) long. The largest species of that time were even bigger, with wings 30 centimeters long. For comparison, the inset shows the wing of the largest dragonfly of the past 65 million years. (Credit: Photo by Wolfgang Zessin.)

Insects got bigger as oxygen levels rose during the late Carboniferous and early Permian. But around the end of the Jurassic and beginning of the Cretaceous period, about 150 million years ago, all of a sudden oxygen goes up but insect size goes down.

Blame the birds. In PNAS this week:

Environmental and biotic controls on the evolutionary history of insect body size.

Maximum insect size decreased even as atmospheric pO2 rose in the Early Cretaceous following the evolution and radiation of early birds, particularly as birds acquired adaptations that allowed more agile flight. A further decrease in maximum size during the Cenozoic may relate to the evolution of bats, the Cretaceous mass extinction, or further specialization of flying birds. The decoupling of insect size and atmospheric pO2 coincident with the radiation of birds suggests that biotic interactions, such as predation and competition, superseded oxygen as the most important constraint on maximum body size of the largest insects.
Tibetan Altitude Tolerance Mutations:

The people of Tibet, who have survived for thousands of years in extremely high altitude conditions, show distinct phenotypic adaptations to life in the mountains, of which the genetic basis is unknown.  Many groups, including mountain climbers, endurance athletes, and pharmaceutical companies, would love be able to use the evolutionary products of the Tibetan respiratory system to give other people an advantage at altitude.  This study scanned the genome of a sample of Tibetans and compared it to the genome of lower-elevation populations in the area, and analyzed where the two differ.  The two genes hypothesized to be most likely to contribute are EGLN1 and PPARA, which are known to be associated with the decreased hemoglobin phenotype expressed in Tibetans.  This study sheds light on the origin of Tibetan altitude tolerance, but more research is necessary to determine the exact pathway by which the phenotype is actually carried out.

Link to the paper:;329/5987/72

Sunday, June 3, 2012

Insect eyes

Here's a large collection of macro photographs of insect eyes and lots of other bugs and stuff.

Saturday, June 2, 2012

Communication is Key

Communication and contact are key to the preservation of a species. Despite this, humans have evolved to learn that the use of too many words can often make our intended messages unclear. Well, maybe its time we take things down a notch in communicational complexity and learn a lesson or two from Caenorhabditis elegans, a free-living nematode that knows how to get straight to the point when communicating with its peers.
C. elegans is used as a model system for understanding social behaviors such as foraging, population density sensing, mating and aggregation. Like many other eusocial species, C. elegans utilize the effectiveness of chemical signaling for efficient intra- and inter-specific interactions. However, unlike most eusocial species C. elegans has produced an assortment of 150 different chemical pheromones, which are secreted from the nematode’s skin, and can induce and prohibit specific behavioral activities among its fellow nematodes.
Recent observations and analyses have shown that C. elegans use small molecule signals – called indole ascarosides – to regulate behaviors such as population density sensing and mating. These indole ascarosides are able to receive input from two major metabolic pathways, amino acid catabolism and lipid beta-oxidation, which suggests that C. elegans communicate metabolic status through the use of a modular code of small molecule signals.

86 million year old lunch box

In a tenuous link to the previous posts on obesity I was drawn to the following news article on NPR:
Ancient Deep-Sea Bacteria Are In No Hurry To Eat

The Science paper the report is based on isn't quite as catchy:
Aerobic Microbial Respiration in 86-Million-Year-Old Deep-Sea Red Clay

 but the observations and the implications are pretty interesting:

They left the surface 86 million years ago with one lunch box, and they're still eating out of it. It's like they're splitting a pie, and they keep splitting in half and in half and in half, but nobody ever eats the last crumble. It's quite remarkable.
One reason scientists are interested in this extreme lifestyle is because it provides clues about the absolute minimum conditions required to sustain life. Andreas Teske, a marine microbiologist at the University of North Carolina, Chapel Hill, says that's useful for people looking beyond our planet for signs of life.

Friday, June 1, 2012

Thick and thin

If you played around with Framingham risk score calculator I posted yesterday you may have reached an erroneous conclusion. If you enter your age rather than  my age then you can enter some pretty unhealthy values for blood pressure and cholesterol and it still won't raise your ten year risk of heart disease much. It will probably still say <1%.

So does it not matter what you do? It's obesity - poor diet and lack of exercise that lead to high cholesterol and high blood pressure but if it doesn't raise your risk of death then why worry about it? Well the problem is that increasing evidence suggests that each year lived with obesity increases your chances of death (from both heat disease and cancer) way down the road -more than ten years down the road in your case. A recent study in the International Journal of Epidemiology actually quantified this: The number of years lived with obesity and the risk of all-cause and cause-specific mortality. Using data from, you guessed it, the Framingham heart study, they showed that the risk of dying increased 7% for every two years a person was obese, and for every ten years lived with obesity, the risk of heart disease and cancer mortality more than doubled. The researchers suggest counting "obese years" - similar to "pack years" for cigarette smokers - in order to better estimate health risks. 

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.