I Wear a Coat

We were talking in the lab today about Lonely Island's I'm on a Boat and all the parody's that had been made. I mentioned the I'm in a Pond post from a while back and a labmate told me about I Wear a Coat, a med school parody.

The Evolution of the Geek

I ran across this handy infographic from FlowTown. It chronicles the evolution of the Geek. Click on the image to see a full resulution of the image on FlowTown.

Its What's For Dinner

The tyrannosaurids belong to a group of carnivorous dinosaurs called theropods within the Saurischia ("reptile-hipped") dinosaurs. They lived during the Cretaceous, 85-65 million years ago. They are characterized by massive skulls with short but deep jaws containing large sharp teeth, elongate hindlimbs, small eyes, and highly reduced forelimbs. The Tyrannosauridae taxon includes such creatures as Albertosaurus, Gorgosaurus, Daspletosaurus, Tarbosaurus, and of course Tyrannosaurus rex. These were the dominant large carnivores during the Late Cretaceous in North America and Asia. The T. rex is the last and largest of the terrestrial carnivores. Their fossils are actually relatively common in North America, particularly their teeth. These teeth, with their large banana shape, leave recongnizable markes on the bones of other dinosaurs. You would think that this would make it easy to piece together the feeding habits of these dinosaurs, but it is still difficult to even broadly classify the animal as predator, scavenger, or both. We all grew up thinking of T. rex as a mighty hunter, but the evidence against the predator hypothesis includes the animal's small eyes (most predators have large eyes to help find and follow prey), small arms (difficult to hold struggling prey with dainty little forearms), and large legs (seem fast but are actually slow). Add to it the fact that there is evidence of T. rex teeth scoring bone but not actually killing the prey, bones have healed. Scavaging, however, uses all of these traits as a plus and includes supporting evidence such as large olfactory lobes (smelling foul, dead meat well helps you find it). However, if you look at extant, large predators they are opportunists, scavanging when it is available, and if you look at animals such as birds, sharks, and snakes you will notice that little arms aren't that much of a disadvantage. See how there is some confusion?

In a study published in PLoS ONE this week, palentologists discuss a different type of T. rex feeding habit. During a study of Maastrichtian (latest age of the Late Cretaceous) dinosaurs one of the researchers found a large theropod pedal phalanx (foot/toe bones) that had tooth marks on it that were made by a large carnivorous dinosaur. Considering the geographic region (North America) and the time period, T. rex was the only large carnivore known and so a very likely candidate for inflicting the bone damage. They examined this bone as well as other dinosaur specimens. They found a total of 17 specimens bearing tooth marks made by Tyrannosaurus. The deep U- and V-shaped gouges and shallower scores resemble those found on the pelvis of a Triceratops, and closely resemble the furrowed ‘puncture and pull’ traces that have previously been attributed to T. rex. Four of the examined specimens represent Tyrannosaurus. That's right, we're talking cannabalistic Tyrannosaurus rex!

Figure 2. Tyrannosaurus rex bones bearing
 tooth marks made by Tyrannosaurus rex.

The authors argue that the marks on the bones are the result of feeding rather than fighting. They say that the traces would be difficult to inflict on a live animal, and that, in the case of one bone, the marks are the result of two or three bites. Considering that most animals probably wouldn't sit still while a Tyrannosaur repeatedly bit them, that seems likely. Additional evidence includes where the bites occurred - on the toes (tightly bound in life and not the targets during a fight) rather than the vulnerable head or flanks. Finally, there is no bone remodeling (healing) evidenced, suggesting that the animal died.

Put this together and it gives more evidence to the hypothesis that Tyrannosaurus was an indiscriminate, opportunistic feeder. It didn't just go for herbivorous dinosaurs but also other Tyrannosaurs. The bone marks found in this study were probably the result of scavenging. However, you can't rule out that the Tyrannosaur killed its prey and fed on it over a long period of time.

Cannibalistic Tyrannosaurs, whew, that's a visual right? But, if you think about it, cannibalism isn't all that uncommon in nature. I mean, its been seen in bears, alligators, hyenas, etc. So it seems a good arguement for T. rex as well.

Very cool.

Read more in the paper (its free access):
Longrich Nicholas R., Horner John R, Erickson Gregory M., and Currie Philip J. (2010) Cannibalism in Tyrannosaurus rex. PLoS ONE: 5(10), e13419. (DOI: 10.1371/journal.pone.0013419)

Thesis Insanity



Piled Higher and Deeper

A friend sent me a great webpage called The Five Stages of Grading, which rings so true that it is funny. That reminded me of a little stress-relieving thing I put together while writing my thesis. I call it "Thesis Insanity."

"Significant advances in the understanding and treatment of graduate students in the midst of thesis writing has brought greater recognition to the field of science over the past few decades. The writing of a thesis is a process that results in all different types of mental disorders, including disorders of thought, mood or behavior. These disorders cause distress and result in a reduced ability to function psychologically, socially, occupationally or interpersonally. People that are in this writing process might have trouble handling such things as daily activities, family responsibilities, relationships, or social responsibilities. They can have trouble with one area or all of them, to a greater or lesser degree. And they can have more than one type of these responses at the same time. The symptoms a person experiences and the clinical features that accompany this process are used to identify and classify this disorder. As time goes by and we gain a clearer understanding of how specific genes interact with writers block or other specific behaviors, a much more sophisticated classification system may be developed that is directly linked to a biologic cause, rather than just symptoms. Some disorders with similar symptoms and clinical features, such as the patterns and processes involved in doing research, are very different in terms of their underlying biology. To treat them similarly simply because they share the same symptoms may not be appropriate. Does writer’s block have a biological basis — a problem with the brain's chemistry? Not always. Many serious writer’s block situations do have a strong biological basis but that's not the entire story. Some people, for example, might have an inherited, biological tendency to completely skip over large chunks of pertinent information. They can experience serious revision anxiety even though no specific event triggers it. Others, however, have no known inherited tendency for these exclusions. But if something happens, such as a new publication in a top journal, it can trigger major reorganization. It is not yet known if the underlying neurochemical aspects of these reactions are the same. In other words, one person may have writer’s block because of their nature — their genetic vulnerabilities, their neurochemical functioning. And another person may have a writer’s block because of nurture — a research environment based cause that perhaps then alters their neurochemistry. Most of the time, however, it's probably a complex interaction of both nature and nurture. Manuscript submission might be all that some people need to restore their brain chemistry to a more normal state. But for others, manuscript submission, although effective, doesn't alter the way they cope with the stress that might have contributed to their illness. Graduation and employment can help change coping behaviors and offer strategies to help understand and modify risk factors associated with this disorder. Very often, a combination of graduation and employment is most effective."

Flashy Fins

Figure 1: X-ray image of Pelvicachromis taeniatus

If you recall the Fish-stache story then you will also recall that I explained sexual selection in this way:

"When it comes to sexual selection in the animal world, it is the usually the sex that puts more effort (and has more to lose) into the results that gets to be the choosy sex. Usually this means females get to be picky. After all, eggs are more expensive than sperm and females often end up contributing quite a bit with parental care. This choosiness means that males need to impress females through the evolution of secondary sexual traits. This could be, and usually is, just about anything: elaborate feathers, complicated dances or mating calls, gift giving, etc."

So what happens when you see a highly developed ornament on a female of a species? Usually such ornaments are seen as non-adaptive, they are simply the genetic correlations of male ornaments. But, if you go back to the who "gets to be the choosy sex" argument and apply it to females you may find that females are looking to attract males that give them something that they need in addition to a sperm contribution. Perhaps the male takes care of the female (or "invests in female quality"), or maybe he contributes a significant amount of parental investment (or he's a good baby-daddy). This idea of females evolving ornaments to attract males has gained some ground recently. And that topic is today's article.

There is a species of cichlid fish called Pelvicachromis taeniatus where both sexes have ornamentation. This fish is known to be biparental and socially monogamous. Both sexes develop large, colored pelvic fins that they present to their potential mates during courtship. The pelvic fin of female fish is exceedingly large and differs from the male fin in both color and shape (it is triangular rather than thread-shaped). During courtship, females spread out their violet, triangular pelvic fin and fan it at the males. This behavior enlarges "their violet ventral nuptial projection area," suggesting that the fin and behavior are used to attract males. This study took a look at the allometric relationship of the pelvic fin compared to other fins (anal, caudal, dorsal, and pectoral fin), and then tested male preferences for females showing larger or smaller pelvic fins to determine the effect of fin size on male mate choice.

I would be remiss and probably confuse the heck out of you if I didn't take a sentence, or a few, to explain allometry. The most basic of basic definitions is that allometry is the relationship between size and shape. You define the dimensions of a body part (or trait or character) in relation to the body size, with the scale relating trait size to body size. What you get is an allometric relationship, and these are typically classified in three ways:
(1) Isometry - the ratio of trait to body size is constant
(2) Negative Allometry - large individuals have small traits
(3) Positive Allometry - large individuals have relatively larger traits
This relationship is driven by evolutionary constraints, natural selection, and/or sexual selection. And when you look at those traits driven by sexual selection you usually see option (3) Positive Allometry. Although a positive allometry does not mean the trait was driven by sexual selection.

In the experiment, the researchers took X-ray images of the females so they could analyze trait and body size. Then they conducted mate choice experiments to see which female characters the males preferred. Typically this is achieved by putting a female fish in one tank and a male fish in an adjacent tank and observing the courtship or lack of. Then the trait of interest can be altered (fin clipping, etc) or a substitute used. In this case the researchers used computer animations of females with various pelvic fin sizes. The use of the computer allowed them to standardize the stimuli and eliminate many confounding variables.

The allometry study found that the female pelvic and caudal fins showed isometry in relation to body size, but the anal, dorsal, and pectoral fins showed negative allometry. The females showed a constant ratio of pelvic or caudal fin size to body size, but the other fins were relatively smaller in larger females. They also found that the size of the pelvic and caudal fin is more positively related to body size than the other fins, suggesting that these fins are under selective pressures that the other fins are not. Remember when I said that sexually selected traits usually show positive allometry? This study showed isometry and negative allometry, no positive. The authors hypothesize that when you incorporate viability selection you end up with a more complex relationship between body size and traits, that natural selection and sexual selection "could have synergistic effects on the evolution of traits, thus sexually selected traits may be scaled into isometry or even negative allometry." Perhaps the amount of variation in traits under directional sexual selection may be limited by natural selection, that natural selection is constraining the pelvic fin size of these fish. Basically, a gigantic fin attracts a mate but slows you down and makes it easier for predators to get you. So you find a middle ground, a fin that isn't too big and gets you eaten but isn't too small so that you never attract a mate. This scaling down for the predators is where the isometry and negative allometry are showing themselves.

The mate choice experiment showed that males like large pelvic fins. But why? Could be that the large fin is an indicator to female quality. These indicators may be direct (fertility, fecundity, or maternal investment) or indirect (genetic benefits, parasite resistance, pretty daughters). Translated - If she can carry around that big fin and survive then she must have good behaviors and genes. The researchers found pelvic fin size in females to be positively related to body condition. So it is likely that the indicators are reliable. I haven't discussed much about the violet color of the female pelvic fin, but the fins are colored similar to the ventral violet nuptial belly coloration. The size of this ventral coloration is associated with female quality, indicating the fecundity of the female, her readiness to spawn, and may reveal information about her maternal quality and offspring survival rates. Again, all indicators that tell the male that she's quite a catch (no pun intended).

Anyone who has spent time with a group of females (of any species) knows that there's some competition going on, and you can't rule that out in a study such as this. These cichlid fish show sequential aggressive behaviors towards other females. Before a fight escalates a female will present and fan out her pelvic fin to show off her body condition and body size in the hopes of intimidating and driving off the rival female.

When it comes to fish studies, especially sexual selection studies, there are many. This study is unique in that it is the first to show that male choice might scale the allometry of a female sexual trait. This is important in understanding the scaling relationship of female traits with body size and starting to tease out the selection pressures driving the evolution of these ornaments.

Read the study here:
Baldauf, Sebastian A., et al. (2010) Male mate choice scales female ornament allometry in a cichlid fish. BMC Evolutionary Biology: 10, 301. (DOI: 10.1186/1471-2148-10-301)

The Buzz on the Bees

I was flipping through (or rather, scrolling through) a few popular news sites and noticed that a recent paper published in PLoS ONE has gained some traction. It is a story about honey bees and Colony Collapse Disorder.

The European honey bee (Apis mellifera) is a common pollinator worldwide. You can find them where there are flowers to feed on and suitable hive-building sites. Most of the individuals you see buzzing around your garden collecting pollen are females (workers), the males are significantly bigger and are very few in number. These social insects heat their hives with body heat and cool it by fanning their wings, this way they can live year-round in a place surviving on their honey reserves through the winter.

As you may have guessed by their common name, these honey bees are not native to the western hemisphere. They were brought over by early European colonists for their honey and wax production. Over time, beekeepers have experimented with the about two dozen subspecies, but they've found that Apis mellifera ligustica (a subspecies brought over by early Spanish settlers) is favorable.

Beginning in October 2006, beekeepers started reporting the losses of 30-90% of their hives. Some loss is normal, but this amount is highly unusual. Colony Collapse Disorder (CCD) is the name that has been given to this serious, mysterious die-off of honey bee colonies across the U.S. CCD is characterized by sudden colony death with a lack of adult bees in front of the die-outs. Honey stores and recent brood rearing are often evidenced, and sometimes the queen and a small number of survivor bees remain. Although there have been published incidences of honey bee disappearances - in the 1880's, 1920's, and 1960's - it is unclear if this same phenomena has happened before. Descriptions are similar to CCD but as it is yet unknown what causes CCD it is difficult to tell.

This year, 2010, CCD has once again devastated honey bee colonies in the US, at rates that are potentially higher than the occurrence in 2006-2007. Previous scientific studies, using sensitive genome-based methods, have found small RNA bee viruses and the microsporidia, Nosema apis and N. ceranae in healthy and collapsing colonies alike. However, no single pathogen has been linked to hive losses.

The study published this week in PLoS ONE used mass spectrometry-based proteomics (MSP) to identify and compare proteins from healthy and collapsing honey bee colonies. This particular method revealed two previously unreported RNA viruses, Varroa destructor-1 virus (VDV-1) and Kakugo virus. They also identified an invertebrate iridescent virus (IIV) (Iridoviridae), a DNA virus, and linked it to the CCD colonies. The CCD colonies were found to not only contain  IIV but also Nosema (specifically N. ceranae). The IIV, in particular, is interesting because it was thought until now that small RNA viruses were the cause of bee diseases. The pairing of IIV and N. ceranae and their correlation with CCD colonies suggests that they track each other and they do not occur concurrently in healthy colonies. Laboratory cage trials add more evidence to support this hypothesis.

It is hypothesized that damage to the bees' gut epithelial tissue and other host cells by N. ceranae allows entry to IIV. Or, perhaps, the replication of N. ceranae in honey bee cells may decrease the bees' ability to ward off viral infections. The presence of IIV may prove to be a useful tool in identifying colonies in the early stage of CCD or a possible resistance to the virus in a strong colony. IIV's are not completely unstudied. In fact, a good amount of study has been done on them for use as biopesticides. IIV-3 and IIV-6 have had a complete genome sequencing, and 24 other IIV's have been partially characterized. Viral diseases are currently only manageable rather than curable, with infected bee populations needing culling. Nosema, however, is treatable with current management techniques. Since their pairing suggests increased lethality, disrupting the relationship may be an option to help reduce bee mortality.

You can read the paper here:
Bromenshenk, Jerry J., et al. (2010) Iridovirus and Microsporidian Linked to Honey Bee Colony Decline. PLoS ONE: 5(10): e13181. (DOI: 10.1371/journal.pone.0013181)

Also, here's a NY Times article on the subject:
http://www.nytimes.com/2010/10/07/science/07bees.html

Also, check out these links for more information on Colony Collapse Disorder:
Mid-Atlantic Apiculture Research and Extension Consortium (MAAREC)
United States Department of Agriculture: Agricultural Resource Service
United States Department of Agriculture: National Agricultural Library
The Ohio State University's Agriculture Network Information Center's Bees and Pollination Page

(image from nycgovparks.org)

Colour Canon

I was scrolling through the blog today and noticed that recently most of the posts have been videos rather than articles. I blame that entirely on all the field work that I've been doing recently. Measuring trees all day really just makes me want to shower, eat, and sleep (in that order) when I get home. But, well, excuses excuses right? All that said, I'm going to post another video.

This one is a bit techie, and a commercial (kinda), but its cool enough that I had to post it. The last minute, especially, is pretty sweet.


Canon Pixma: Bringing colour to life from Dentsu London on Vimeo.