Tuesday, December 21, 2010

A Terrible Life Choice

I saw this on The Simpsons a long time ago. Talk about hitting the nail on the head! LOL.

On Thin Ice

When it comes to charismatic megafauna, polar bears are right up there in terms of cute stuff people like to like. Lately they have also been the poster-bear against climate change. That makes sense, considering that polar bears (Ursus maritimus) occur only in the Northern Hemisphere and are dependent on sea ice for access to their marine mammal prey, mainly seals. Declines in summer sea ice have been associated with declining physical stature, declining physical condition, poorer survival rates, and declining population sizes for these bears. This sea ice decline has been linked to these declines.

A new paper this week in Nature uses projections of twenty-first century global mean surface air temperature (GMAT) and data from the Community Climate System Model (CCSM3) to test the hypothesis that a tipping point will lead to irreversible loss of seasonal ice habitat as GMAT increases. Basically, that there are some elements/variables within a system that, when changed enough, cause habitats that support cold-dependent species to disappear abruptly and irreversibly. Namely when a particular GMAT is exceeded.
In a nutshell, they tested whether mitigating the rise in greenhouse gases could improve the outlook for polar bears.
Now, a USGS study in 2007 concluded that two-thirds of the world's polar bears could disappear by 2050 if atmospheric temperatures continue to increase due to greenhouse gases. Their model was a general circulation model (GCM) that projected losses of Arctic sea ice based on the Special Report on Emissions Scenarios (SRES) and a "business as usual" greenhouse gas emissions scenario, where emissions continue to increase and the carbon dioxide concentration reaches 689 parts per million (ppm) by the end of the century. However, they did not consider the possible benefits of greenhouse gas mitigation. Think about that in terms of tipping points. If you mitigate too little and/or too late then you get no conservation benefits for polar bears as their ice would already be gone. If you mitigate more and/or soon enough then you save the ice and the bears. That's the thought anyway. So the researchers modeled 5 different scenarios that ranged from "business as usual" all the way to aggressive cuts that reduce carbon dioxide concentrations to 368 ppm, those seen in the year 2000.
The study concludes that mitigating the rise in greenhouse gases will result in substantially more sea ice habitat being retained. The business-as-usual-model shows a 50% loss of sea ice by 2050 whereas the aggressive-mitigation-model shows only a 20% loss. They also show that this habitat retention, in turn, will allow polar bears to persist throughout the century in greater numbers and in more areas. The business-as-usual-model shows a 50-80% chance of polar bears disappearing from these habitats whereas the aggressive-mitigation-model shows only a 25-50% chance. However, the models did not give the thresholds or tipping point values that will lead to irreversible ice loss. They found that sea ice will decline at a steady rate as global mean annual temperature rises.
The paper also addresses positive feedback in this system. Its all about albedo, or how strongly a surface reflects light. Its really a quite logical scenario. Ice reflects light very well, warmer temperatures cause ice to melt, retreating ice means less reflective surface, retreating ice also means more exposed water, the darker water absorbs more sunlight, more absorbed light increases temperatures, increased temperatures melt more ice. And so on and so on. In this paper they test models that might counter this feedback mechanism. They specifically refer to rapid ice-loss events (RILEs). These rapid freezes result from going from open water to cold conditions reappearing in the Fall, and these compensate for the effects that are working to provide the potential tipping points.
Polar bears are not out of the woods yet. After all, we are still running the business-as-usual-model. And, in the past, models predicting sea ice loss have fallen short. But this paper shows us some good news, that with proper mitigation we can potentially slow down the decline.
Here's the paper:
Amstrup, Steven C. et al. (2010) Greenhouse gas mitigation can reduce sea-ice loss and increase polar bear persistence. Nature: 468, 955-958. (DOI: 10.1038/nature09653)

Additionally, I suggest reading this paper on polar bear and grizzly hybridization:
Kelly, Brendan P., Andrew Whiteley, and David Tallmon (2010) The Arctic Melting Pot. Nature: 468, 891. (DOI:  10.1038/468891a)
Story links:
(image from metro.co.uk)

Rapping, Ecology Style

I don't know about you, but that's how I measure DBH.

Monday, December 20, 2010

Footprints in the Sand

This story is about tracks, specifically dinosaur tracks. Footprints can be very informative, giving so much more information than just the shape of the foot. They provide information on species, body posture, locomotor ability, sociality, preferential environments, and stratigraphic and geographic faunal diversity.

As you might guess, it isn't always easy to identify fossilized dinosaur tracks. Sure, some species are easier than others like sauropods, stegosaurs, and ceratopsians. The difficulty arises in distinguishing bipedal theropods (carnivores walking on two legs) and ornithopod dinosaurs ("bird-hipped" dinos, grazers walking/running on two legs). You can see how they might look pretty similar.

A new, in press, paper in Cretaceous Research takes a look at the Dinosaur Stampede National Monument at Lake Quarry Conservation Park in central-western Queensland, Australia. This monument contains thousands of fossilized footprints of dozens of dinosaurs from the mid-Cretaceous. Since the 1970's, the popular hypothesis regarding this area is that an Allosaurus-sized dinosaur chased a mixed herd of small-bodied dinosaurs, causing a stampede. Previous studies have identified this "predatory protagonist" as a large tridactyl (three-toed) dinosaur, a theropod (likely a Tyrannosauropus). This particular taxon has a bit of a checkered history, scientists have argued about it since the early 1920's. It has also been proposed that the tracks on the monument are attributable to a hadrosaurid ornithopod (a duck-billed dinosaur that walked on two legs).

Figure 1. The Winton Formation at Lark Quarry.
These authors applied a multivariate analysis to discriminate between theropod and ornithopod tracks in order to identify the track maker. Multivariate analysis allows you to analyze more than one statistical variable at a time and therefore you are able to test multiple dimensions while taking into account several variables. Why mention the statistical test used? Some people like statistics. No really, I mentioned it because this is the first time that multivariate analysis has been used to identify tracks on this valuable piece of biological history. To perform this analysis the researchers measured all of the tracks using published line drawings, catalogued photographs, latex peels, museum casts, and actually measured the real ones themselves. The variables for the analysis included track length and width, total digit lengths, basal digit length and width, middle digit widths, and the distance from heal to the interdigital (hypex) point.

The results showed that a majority of these measurements fell within the threshold expected for ornithopod dinosaurs. In fact, the authors conclude that of the known types of theropods from this region, none of the body fossils adequately match the measurements and analyses that they did.

So what type of ornithopod was the track maker? Well, the footprints are slightly longer than they are wide, they have symmetrical toes, have claws, and have a V-shaped central digit. Of the known large Cretaceous ornithopods, previous studies have concluded that it could be either Ambyldactylus, Caririchnium or Iguanodonipus. Of these, only the iguanodontian dinosaur, Amblydactylus, shares the distinctive features exhibited in the Lark Quarry tracks. The tracks are remarkably similar to ornithopod tracks from Canada named Amblydactylus gethingi and so the authors suggest re-naming the Lark Quarry tracks Amblydactlyus cf. A. gethingi. In all likelihood, the footprints were made by a large ornithopod standing approximately 2.5 meters tall at the hips, likely a more primitive member of the group, probably similar to Muttaburrasaurus langdoni. This species specifically because it has been found in similarly aged rocks only a few hundred kilometers from Lark Quarry. The stampede of the smaller dinosaurs also represented in these rocks was probably due to the approach of this larger dinosaur. A large herbivore spooking a group of smaller dinosaurs is not exactly as exciting as a predator chasing them down but, in this case, is more accurate.

The authors state that if this identification is correct then it removes any published evidence that a large theropod dinosaur existed in the Australian Cretaceous. However, I do recall posting an article about a new theropod discovered in Australia from 110 million years ago - which I'm pretty sure is the Cretaceous period (144 to 65 million years ago?) - so I'm not sure about this wiping out all evidence thing. Just sayin'.

This is the paper:
Romilio, Anthony and Steven W. Salisbury (2010). A reassessment of large theropod dinosaur tracks from the mid-Cretaceous (late Albian-Cenomanian) Winton Formation of Lark Quarry, central-western Queensland, Australia: A case for mistaken identity. Cretaceous Research: in press. (DOI: 10.1016/j.cretres.2010.11.003)

And here's some more reading material on the subject:

Body by Google

Google. Love Google. It does so much, including powering this blog. They are known for their great mapping technologies such as Google Earth. Now they tackle a new mapping challenge: The human body. Last Thursday marked the release of Body Browser.

Body Browser uses 3D graphics application programming interface WebGL running within a browser to create a three-dimensional model that allows users to zoom in and out of the human body, remove layers, and generally explore. It is searchable and clickable, giving all sorts of info on how the body is put together.

Body Browser doesn't require Java or Flash, but you will need a browser that supports WebGL. Google recommends using the most recent version of Chrome, but Safari and Firefox/4.0b1 work as well. Body Browser is still in beta and has not been officially released, but users are able to try it out and report problems and bugs. So keep an eye out for this program to become fully operational.


Here's the Body Browser site: http://bodybrowser.googlelabs.com/






Wednesday, December 15, 2010

A Year in Reviews

 No kidding, three people sent this one to me today. I can see why. It's fantastic. It's a review of peer reviews. Here are a few of my favorites:
  • Alfachetoglutarate
  • Season's Greetings! I apologise for my slow response but a roast goose prevented me from answering emails for a few days.
  •  I started to review this but could not get much past the abstract.
  • I suppose that I should be happy that I don't have to spend a lot of time reviewing this dreadful paper; however I am depressed that people are performing such bad science.
  •  I feel like a curmudgeon, but I still have problems with this paper.
  • Preliminary and intriguing results that should be published elsewhere.
  • Reject – More holes than my grandad's string vest!

Read the complete list here:
Referees' quotes - 2010. (2010) Environmental Microbiology: 12(12), 3303-3304. (DOI: 10.1111/j.1462-2920.2010.02394.x) or click HERE

Having so thoroughly enjoyed this list I looked to see if there were any more. As it turns out the same journal publishes this type of list annually. I freely admit that I like the negative reviews best, you gotta admit they are the funniest. Here are a few of my favorites from years past, and at the end is the references/links so you can read the complete lists.

From 2009:
  • Some self citations may be easily taken out without harming the paper.
  • The peaceful atmosphere between Christmas and New Year was transiently disrupted by reading this manuscript.
  • Ribosomes do not contain DNA.
  • Page 3, line 28 –‘arqueobacteria’?
  • I am afraid this current version looks too much like another manuscript saying ‘gee whiz we looked in a strange place and found some new microbes’.
  • The writing style is flowery and has an air of Oscar Wilde about it.
  • The trees are crap but, besides this, excellent work.
From 2008:
  • Mouldy bread. Unfortunately there are too many technical flaws in this one. Too bad because the potential was high.
  • Great organism. Great scientists. Terrible manuscript.
  • I am fed up with people ignoring totally the instructions for authors.
  • The Abstract describes results that I could not find in the Results section.
  • I wonder if you and I do not have better things to do than help people who can't help themselves.
  • They were not the first to have done this, but they don't seem to know that.
  • I have found this ms. boring to death.
  • ‘Hijacked’ is a very dramatic word; maybe the bacteria are more polite with their biosynthesis.
  • Page X, line Y claims both ‘rare’ and ‘unusual.’ Madonna and Tony Blair might use both in the same sentence.
From 2007:
  • I felt like I was teaching my grandmother to suck eggs. Accept with minor revision.
  • The paper is full of wild speculation linked by a few random experiments.
  • A bad paper containing a good idea.
  • Hundreds of commas are missing!
  • A highly relevant, beautifully and concisely written cross-disciplinary report that unfortunately comes with a dull abstract.
  • Use of the term remarkably borders on dramatization.
  • For this crucial initial step, authors behaved like a cook who is in charge of preparing an ‘haute cuisine’ meal for the 40th wedding anniversary for 100 guests and consults the first cookbook for kiddies to get some idea.
  • I nearly said reject. But then I recalled that I have a hangover and I am feeling grumpy.
 From 2006:
  • I have taken out my earlier comment that the authors retake Chemistry 101, that is probably not allowable.
  • The authors assume. . . . All assumptions are wrong.
  • The authors need to remember that adverbs in English tend to end in -ly.
  • The work is basically sound but unfortunately the presentation is a bit of a dog's breakfast.
  • This is an essentially unreadable paper sent to the wrong journal.
  • Fig. 1a looks a bit hand-drawn, 1b has more axes than display area.
  • There is no apparent study concept other than ‘we went out to the campus pond one day and took 2 samples for sequencing’.
From 2005:
  • This is depressing! So much work with so little science.
  • They have no clue what they write about.
  • The authors are quite creative in using different statistical approaches.
  • This paper is the very expression of what happens when one tries to chop up one piece of work into as many publications as possible.
  • Why don’t the percentages . . . add up to 100%?
  • Almost all references used by the authors are from the last century.

Since I'm only posting a subset of each list I went ahead and looked at 5 years. There are more, and they get addictive once you start reading. So if you like them then look up some more, they are always published in the last issue of December. Have fun!

Referees' quotes - 2009. (2009) Environmental Microbiology: 11(12), 3309-3310. (DOI: 10.1111/j.1462-2920.2009.02120.x) or click HERE

Referees' quotes - 2008. (2008) Environmental Microbiology: 10(12), 3425-3426. (DOI: 10.1111/j.1462-2920.2008.01813.x) or click HERE

Referees' quotes - 2007. (2007) Environmental Microbiology: 9(12), 3153-3154.(DOI: 10.1111/j.1462-2920.2007.01484.x) or click HERE

Referees' quotes - 2006. (2006) Environmental Microbiology: 8(12), 2233-2234. (DOI: 10.1111/j.1462-2920.2006.01157.x) or click HERE

Referees' quotes - 2006. (2005) Environmental Microbiology: 7(12), 2036. (DOI: 10.1111/j.1462-2920.2005.00953.x) or click HERE

(image from cellbiochem.ca)

Monday, December 13, 2010

And We Have Liftoff!

This video is really long, but at the same time really interesting. It is a narrated video from NASA showing the best of the ground-based Space Shuttle motion imagery from STS-114, STS-117, and STS-124 missions. Such imagery is taken during each mission in order to visually identify off-nominal events and conditions requiring corrective action to ensure mission safety and success. So celebrate 30 years of the Space Shuttle Program by learning a little more about the Space Shuttle Program.

Saturday, December 11, 2010

Pitch Perfect

Once again, I'm going to ask you to close your eyes and picture this: your perfect mate. If you were to describe him/her to me how would you do so? Hair, eyes, and skin color? Height and build? Think about it while we go through a short sexual selection primer.

Natural selection produces changes in the genetic composition of a population from one generation to the next. These changes occur as traits become more or less common in a population due to effects on the survival and reproduction of the individuals within that population/species. There's all kinds of mechanisms and processes involved in natural selection, but we are going to focus on sexual selection. Sexual selection is a special case or adjunct to natural selection. This type of selection acts on an organism's ability to successfully attract a mate. One of the key words being "successfully". After all, you can't pass on a trait if you don't produce offspring. Sexual selection acts on the "attractiveness" of an individual to the opposite sex. I put that word in quotes because attractiveness is different in each species. In many species this type of selection leads to sexual dimorphism, where one sex looks different from the other, often as a result of ornamentation or primary sexual characteristics. In some cases a trait will go so extreme that natural selection acts upon it -- if your trait decreases your survival ability to the point where you do not live long enough to reproduce then that extreme trait gets removed from the population. The attractive trait doesn't necessarily have to be some type of bodily ornamentation. It can be courtship dances, nuptial gifts, building elaborate structures/nests, territoriality, combat skills, or any other of a host of things.  The overall point is that you have to have or do something that attracts the opposite sex in such a way that it makes you the most attractive of all while still allowing you to survive to reproduce. As with most scientific theories, it gets much more complicated than that, but I think you get the point.

So now let's go back to that picture-this-scenario and add some information based off of what we know about sexual selection and the attractiveness of the human face. We know that facial features that increase a person's attractiveness serve as subconscious cues of biologically important variables such as health. We also know that human faces show marked sexual shape dimorphism, men's faces are different shapes than women's faces. Yeah, I know, a "duh" moment right. Well, just hang with me for this one. It has been found that attractiveness for female faces is related to signs of youth, symmetry, and averageness (an odd term, I know, but basically meaning 'not weird looking'), and that these features signal health, femininity, and fertility. Male faces are considered to be more attractive with increased symmetry and averageness. But as many women will tell you, greater masculinity does not always go hand-in-hand with greater attractiveness. In this instance, I'm using the word "attractive" to relate to facial features rather than an overall impression - thing pretty boy vs. tough guy. However, many women will also tell you that both the pretty boy and the tough guy can be attractive, just not necessarily in the same way.

The shapes of the human faces themselves are also important. Highly feminine faces tend to have relatively large eyes, smaller brow ridges, smaller jaws, and fuller lips. Attractive male faces tend to have longer and wider jaws, relatively smaller top halves and eyes, and more prominent brow ridges. Those descriptions I'm taking right from the article even though they tend to conjure up a rather funny looking person in my mind's eye. Anyway, its all related to genes and hormone levels during puberty. A topic better left for another post. For this particular study it is also important to note that humans show marked height dimorphism as well. Men, in general, are taller than women.

So far I've been relaying information (mostly) from a study I came across recently, published in the journal Evolutionary Psychology, about the evolutionary origin of the shape dimorphism in human faces and how that is related to height dimorphism. In layman's terms, does the angle or tilt at which you see someone's face make them more or less attractive?

Now, picture your perfect mate not just as a set of handsome/pretty characteristics but those characteristics on a person standing right in front of you. What do you see now?

This study had participants complete two tasks designed to measure the masculinity/femininity of a face as well as rate their attractiveness. They used a 3D face modeling program that manipulated the portrayed pitch of a model - untilted (straight), tilted slightly upwards, further upwards, slightly downwards, and further downwards - while using "examples of unattractive, real, attractive, and average" faces of the sexes.

They found that the pitch of the face directly influences its perceived masculinity/femininity and affects its perceived attractiveness. They found that an upward tilted face is judged to be more masculine (or less feminine in female faces) and downward faces judged to be more feminine (or less masculine in male faces). Sure, that makes sense, especially when you factor in the height dimorphism. Think about it: A male is taller than a female, the male viewing the female from above perceives her face as tilting down, the female viewing the male from below perceives his face as tilting up. Remember those funny sounding descriptions of the attractive faces (jaws, brow ridges, etc.)? Why those shaped features? Perhaps they are due to divergent sexual selection pressures that resulted in the selection for male and female faces that had these pitch perspective differences as part of their typical proportions. Or maybe they are more related to behavior. The authors draw a parallel between the dominance/appeasement displays of other species - stretching/rearing vs. crouching/bowing. Upward tilting faces are more dominant than downward tilting faces. I gotta say, the little feminist voice in my head cringes at that one.

So, was your picture-this perfect mate tilting their head upward or downward?

Guess maybe I should practice my coy look.

Here are your links:
Burke, Darren and Danielle Sulikowski (2010) A new viewpoint on the evolution of sexually dimorphic human faces. Evolutionary Psychology: 8(4), 573-585. (link)


Wednesday, December 8, 2010

Harry Potter and the Question of Heritability

I just saw the new Harry Potter movie and so decided to type the general search term "Harry Potter" into a few science literature search engines just to see what got conjured up. One of the first topics was all about the heritability of magic!

A correspondence in Nature suggests that magical ability is inherited in a Mendelian fashion, with the wizard allele (W) being recessive to the muggle allele (M). The recessive part makes since considering there are so many more muggles, those without magical abilities, than there are witches/wizards. That means that those with magical ability must have two copies of the wizard allele (W W). Take this up the family tree and it means that purebloods will have both parents that are W W while half-bloods and mudbloods will have one or both parents with W M. Although, Harry does have a W W genotype he is not considered pureblood since his mother was muggle-born. Later published comments point out some interesting flaws in this particular hypothesis.

Craig, Jeffrey M., Renee Dow, and MaryAnne Aitken (2005) Harry Potter and the recessive allele. Nature: 436(7052), 776. (DOI: 10.1038/436776a)

Dodd, Antony N., Carlos T. Hotta, and Michael J. Gardner (2005) Harry Potter and the prisoner of presumption. Nature: 437(7057), 318. (DOI: 10.1038/437318d)

Another paper, published in BMJ, discusses in more detail the evidence for a genetic basis to magic. As we discussed above the books, and the movies, to some degree, class people as either muggles, squibs, mudbloods, or purebloods. Most of the world is made up of muggles, a minority of people are witches/wizards, those with magical abilities, and a very small fraction of the magic community are squibs (non-magical people from an otherwise magical family). This suggests that there is some heritability to the trait that is magical ability. Additionally, the environment Harry was raised in, a very non-magical muggle home, further supports that this is a genetic trait, one leaning more towards the nature rather than the nurture.

This particular paper prefers the idea of magical ability not as a dichotomous trait but rather a quantitative attribute that ranges in its ability with some individuals having an exceptional proficiency and others a relative ineptitude. Individual magical skills such as parseltongue (ability to talk to snakes), clairvoyance, metamorphmagus (ability to change physical appearance) are all likely skills that seem to be conferred by specific genes. The authors argue that the best explanation for the inheritance of magic in the world of Harry Potter is best explained by a multilocus model with a dominant gene for magic, the function of which is controlled epistatically by one or more loci, possibly recessive in nature. The genotypes influence total magical abilities with the allele frequencies differing significantly between populations with magical abilities and those without.

Ramagopalan, Sreeram V., Marian Knight, George C. Ebers, and Julian C. Knight (2007) Origins of magic: review of genetic and epigenetic effects. BMJ: 335, 1299. (DOI:10.1136/bmj.39414.582639.BE)

This is a fun topic to get all sciency over. Check out another set of papers on the origins of Harry Potter's headaches:

Sheftell Fred, Steiner Timothy J., and Thomas Hallie (2007) Harry Potter and the curse of headache. Headache 47, 911-916. (DOI: 10.1111/j.1526-4610.2007.00665.x)

Hagen, Knut. Harry Potter's Headache. (2007) Headache: 48(1), 166. (DOI: 10.1111/j.1526-4610.2007.00985.x)
Lewis, Donald and Andrew Hersheym (2007) Harry Potter's Headaches. Headache: 48(1), 167. (DOI: 10.1111/j.1526-4610.2007.00986.x)

(image from blog.syracuse.com)

Its a squid, its a worm, its a squidworm!

The Celebes Sea is a deep basin (approx. 6200 m) located between the Philippines and Indonesia, at the center of the Coral Triangle. Since its formation in the Eocene (44-42 million years ago) it has been isolated from surrounding deep water by relatively shallow sills. Due to density differences in the water in this basis in relation to the water around it, the water is thought to have long residence times. This area is considered to be a biodiversity hotspot because of the high diversity and endemism of shallow-water corals and fishes as well as being the center of geographical distributions and diversity of lanternfish, hatchetfish, dragonfish, and anglerfish. Considering the high diversity of these shallow water creatures it stands to reason that the deep water fauna may be equivalently diverse even though animal density typically decreases with increasing ocean depth. Finding and studying the creatures found that these depths can be very difficult as they are few and far between and because it is just plain difficult to get down that far.

Meet Teuthidodrilus samae, the squidworm:

This is a new and unusual genus and species of swimming polychaete (marine annelid or segmented worms) recently described in a paper in Biology Letters. T. samae belongs to Acrocirridae as a member of the swimming clade and sister to the "bomb"-bearing clade. As you can see from the picture, it sports a series of 10 large appendages near its head. Hence the likeness to a squid. It is slow moving and found in these very deep waters, and it is likely that similar species can be found in this unique region of the ocean.

Osborn, Karen J., Laurence P. Madin, and Greg W. Rouse (2010) The remarkable squidworm is an example of discoveries that await in deep-pelagic habitats. Biology Letters: published online. (DOI: 10.1098/rsbl.2010.0323)

Here's the ScienceShot:

(Image Credit: Laurence Madin/WHOI, image from ScienceShot via Science Magazine)

Tuesday, December 7, 2010

Falling with Style

Its been a little while since I've posted anything. I suppose that's what the "semi-frequent" part of my blog description really means. So for the next couple of posts not only am I going to post them in rapid succession but they will also be slightly older stories. But, I figure, cool science is always cool science and so will allow myself to get away with it.

This story caught my eye because (1) I attended a talk by this researcher when I was in grad school and (2) it is about flying snakes.

You didn't know there were flying snakes? Well, then you are in for a treat, my friend, a real treat. Flying snakes or flying tree snakes belong to the genus Chrysopelea (family Colubridae) which can be found in Southeast Asia, India and southern China. Despite its name the snake doesn't actually fly. When they launch themselves off a tree they flatten their bodies and undulate to glide to their destination. Basically its body becomes like a big wing ideal for gliding.

The Paradise Tree Snake (Chrysopelea paradisi) is the most commonly studied of this genus. This snake is brightly colored, with a black body covered from head to tail with a yellow spotting pattern that at times can look stripped and has 5 yellow (sometimes orange) bars that span its width. It is native to the tropical forests of southern Thailand, Peninsular Malaysia, the Philippines, Singapore, and Indonesia. The vegetation in these forests can be quite diverse, including tropical broadleafed species and evergreens with little to no understory. Its diet consists of arboreal reptiles and amphibians (lizards, frogs, etc.) as well as small birds and even bats. Add together habitat and hunting and you can probably start see why this snake needs to fly.

A Virginia Tech researcher, John Socha, studies the kinematics of these snakes. He published a short article in Nature in 2002 (and a similar one in The Journal of Experimental Biology in 2005) where he looked at the full three-dimensional gliding trajectory of these snakes. First, in an open field, he built a 10 meter high tower/platform with a horizontal branch extending from the top. Then he carried his snakes to the top of the platform and videotaped and photographed them jumping off the branch and gliding to the ground. Besides the flying snake (which is obviously so very cool) my favorite part is the undergrad let's-call-them-lackeys running to get the escaping snake once it reaches the ground.

Anyway, he found that the snake prepares for take-off by hanging the front part of its body off the branch looped into a J-shape. When the snake jumps it accelerates up and way from the branch, straightening its body and flattening it by stretching out its ribs. The body width of the snake actually doubles and the stretching of the ribs curves the belly into a concave shape. Because the snake is falling it will gain speed and as it does that it will pitch its body downwards and curve into an S-shape. Then the snake starts undulating from side-to-side, starting at the front and moving down the body. This creates lift and allows it to go a further horizontal distance rather than falling straight down to the ground. C. paradisi is very adept at aerial manoeuvring, being able to turn without banking. It can even out-glide other gliders like flying squirrels (Petaurista petaurista) and flying frogs (Rhacophorus nigropalmatus).

Recently there have been some articles in various major news outlets about Socha's new research presented at the American Physical Society Division of Fluid Dynamics meeting in Long Beach, California and a paper accepted for publication in the journal Bioinspiration & Biomimetics. He explains in further detail the gliding motion of these snakes, having developed a mathematical model that explains how they travel such long distances. Basically it takes the gliding description above and explains it mathematically as well as explaining the gliding techniques of other species (mammals, frogs, lizards, etc.). The U.S. Pentagon and the Defense Advanced Research Projects Agency (DARPA) has had a big interest and funded a lot of this research, although they have yet to explain their big interest in the work.

Here is Socha's kinematics paper:
Socha, J.J. (2002) Kinematics: Gliding flight in the paradise tree snake. Nature: 418 (6898), 603–604. (DOI:10.1038/418603a)

This is Socha's flying snake page. It includes some great images and videos of his experiments as well as a fantastic links page to find out more about these snakes. I highly recommend checking it out!

News stories:

Wednesday, November 24, 2010

What If

What would happen if you put your hand in front of the beam at the Large Hadron Collider? Find out...

Saturday, November 20, 2010

Science Scouts

This falls squarely in the I-wish-I'd-thought-of-that category. It is the badge directory of the "Order of the Science Scouts of Exemplary Repute and Above Average Physique" from The Science Creative Quarterly. They are "for the propagation of an ideal where science communicators can meet firstly, for drinks; secondly, for communicating; and ultimately, for networking."

Which badges would you get?

Go to the website and compile your list:  Badge Directory

Here's my list:
1. "Talking Science"
2. "MacGuyver"
3. "Arts and Crafts"
4. "I'm confident around an open flame"
5. “I may look like a scientist but I’m actually also a ninja”
6. “Will glady kick sexual harasser’s ass”
7. “Has frozen stuff just to see what happens” (LEVEL I,II,III)
8. “Inordinately fond of invertebrates”
9. “I know what a tadpole is”
10. “Science has forced me to seek medical attention”
11. “Statistical linear regression”



Want to take part in a cool, real scientific study? Of course you do. Check out the bodyLAB! This project explores the evolution of human body shapes and our ideas of attractiveness. Basically, they try to quantify the judgments and decisions that we make about the attractiveness of others. They are trying to understand how all the traits that make up a human body combine to influence attractiveness.

In September 2010 the first results were published in the Journal of Experimental Biology (perhaps I'll review it in a future post). But this paper isn't the end of the study, it is ongoing, with the "population" of bodies refreshed every month. Recently, they've also added a facial attractiveness test. So visit the site more than once.

Wednesday, November 17, 2010

Chemical Party

Let's go to a chemical party...

Earth as Art

MSNBC has put up some wonderful pictures on their Earth as Art 2010 page. As you can see, these pictures are gorgeous! Look at lots more at the link below.


Leonid Meteor Showers

In the pre-dawn hours on the mornings of November 17th and 18th take a trip outside and look up. It is the time of year for the Leonid meteor shower. This meteor shower is due to the Comet Temple/Tuttle. As the comet makes its way around the Sun it loses some of its material as a debris tail, and when that tail crosses Earth's path we see the debris streaking through our atmosphere. Because that debris is not always uniform between years you may see a light shower or an especially heavy one, its difficult to say.

The shower will be visible through the constellation Leo (hence the name). For all observers Leo is along the ecliptic plane. This year is expected to be good, with about 15-30 (average of 20) meteors per hour, and you don't even need a telescope to see the show.

So set your alarm a little early, grab a lawn chair and some hot coffee, and find a nice dark place with little obstruction to watch the sky.

Read more about the Leonids here, including some good information on how to locate the constellation Leo:

Sunday, November 14, 2010

The New Post-Climate Change Society

Tripod is an Australian musical comedy act. They specialize in improv, parody, and satire. The group is composed of three members: Scod (Scott Edgar), Yon (Simon Hall) and Gatesy (Steven Gates). Here, Tripod performs on The Sideshow ABC-TV about the aftermath of climate change.

The Aftermath of the Snowball

Our planet covered in ice from one pole to the other. Doesn't really seem possible does it? Well, a controversial hypothesis called Snowball Earth posits that our planet was indeed covered with a thick sheet of ice for a period of its history. This thick sheet of ice lasted for millions of years and may have occurred more than once. The most severe likely occurred around 750-580 million years ago.

When an entire planet is covered in ice it is bound to have effects. A new(ish) paper in Nature takes a look at one of these effects and its relationship to life. But let's step back for a second...

Nutrients are chemicals that an organism needs to survive and grow, usually because they are vital to various metabolic and other bodily processes. What do we know about the kinds of nutrients that life needs to survive? Well, we know that life needs water (its inorganic but still counts), and if we're talking about a big melting ice sheet then we can check that one off our list. What about organic molecules? Sure. After all, we are organic and need building blocks, if you will, to help us live and grow. These building blocks, or nutrients, come in the form of carbohydrates, fats, and proteins (or amino acids), as well as various vitamins. Certain chemical elements are also important. These include carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, calcium, etc. Of course, what type of organism you are will expand or narrow this list and vary the concentrations of these various nutrients.

The Nature paper zeros in on phosphorous. In most modern marine aquatic systems you will find that phosphorous and bioavailable nitrogen are the limiting factors. Usually when we are talking about nutrient limitations we're talking not about one being completely gone from the system but, rather, an imbalance of the nutrients. In the case of nitrogen and phosphorous you should see a nitrogen to phosphorous ratio of 16:1. It is generally thought that phosphorous limits productivity on a geologic timescale, and so it is particularly interesting to scientists to find the concentrations of this chemical over time.

In the aftermath of Snowball Earth, these researchers have found that the oceans were rich in phosphorus. Now, how in the world do you go about measuring that one? Well, these scientists looked at the rocks and sediments on the sea floor - about 700 samples of iron-oxide-rich rocks. They tracked phosphorus concentrations by analyzing the composition of iron-rich chemical precipitates which accumulated on the sea floor and took up phosphorus from the seawater. This analysis showed a spike in marine phosphorus levels in the mid-Neoproterozoic (from ~750 to ~635 million years ago). We know that the ice sheet melted right? Then it stands to reason that there was quite a bit of erosion and weathering going on at that time. These processes could explain the high concentrations of phosphorus in the seawater.

Let's take it another step, and link together what we know. Life likes phosphorus, there was lots of phosphorous in the seawater, therefore we should see more life in the oceans. Makes sense. Keep going. More life in the oceans means there's more oxygen production via photosynthesis, the oxygen is released into the atmosphere, atmospheric oxygen is available for other organisms. OK, good. Let's keep going. Oxygen is another of those molecules that life needs/likes, more oxygen availability, more animals using it and multiplying, throw in a little mutation and subsequent evolution, and bang! the emergence of more complex life on Earth.

Alright, alright, I agree, that's a lot of steps. Steps that all start at a single there-was-lots-of-phosphorus point. On their side, there is evidence that links marine phosphorus concentrations and the levels of atmospheric oxygen. And the authors aren't saying that this is definitely what happened. They are simply saying there was more oceanic phosphorus at that time and that it could have paved the way for the evolution of complex organisms and their diversification.

On a purely let's-look-at-the-chemicals level, until now scientists believed that the conditions of an iron-rich ocean would lead to low phosphorus levels. The fact that these researchers found the opposite after the Snowball Earth events is quite significant. We're talking about the finding of a possible nutrient driver behind one of the big explosions of life. Pretty neat.

Here's the source:
Planavsky, Noah J., Olivier J. Rouxel, Andrey Bekker, Stefan V. Lalonde, Kurt O. Konhauser, Christopher T. Reinhard, and Timothy W. Lyons (2010) The evolution of the marine phosphate reservoir. Nature: 467(7319): 1088 (DOI: 10.1038/nature09485)


(image from geos.ed.ac.uk)

Saturday, November 13, 2010

Evolution Rocks

The video just speaks for itself, in a really good way.

Cone of Silence

Genus Conus LINNAEUS, 1758. Not really a taxa that many people give much though to, but cone shells (or cone snails) are ubber cool. There are about 500 extant species of Conus, that's the largest genus of marine invertebrates. These mollusks are found between latitude 40° North and the 40° South parallel. That means you can find them in tropical and subtropical oceans including the Indo-Pacific, Panamic, Caribbean, West African, South African, Peruvian, Patagonic, and Mediterranean Seas. You can find a few other species outside of this region but they tend to be localized in South Africa, Southern Australia, and Southern Japan. Cone snails live in the intertidal muds and sandflats, areas where the high and low tides alternate, but you can also find some offshore or in deep waters.

When picturing the structure of a cone shell, think of something like an underwater snail. They have a strong, muscular foot with a flat sole that is truncated or widely rounded at the front and pointed at the back. The foot can be striped or pimpled, but the coloring is really variable, not just due to genetics but environmental factors as well. On each side of the head they have an eye on a stalk, stalks that are wide at the bottom and narrow at the end. The mouth of this animal is very elastic and includes sharp and often hooked teeth, allowing the cone shell to swallow large prey. Being a cone shell, they are covered by a shell. This shell is spiral shaped and can have interesting patterns, and they are very desirable to shell collectors.

Most people, including me, find the cone snails' venom to be its most interesting feature. We're talking venom that is often fatal, or at the very least causes temporary paralysis, respiratory trouble, or swelling and inflammation (depending on the species). The composition of this venom varies depending on the species, the individual, or even between injections by the same individual. The active components are small, disulfide-rich peptides called conotoxins or conopeptides, and they cause paralysis in the victim. The specific paralytic components include alpha-, omega- and mu-conotoxins which all prevent neuronal communication, each targeting a different aspect of the process. Alpha-conotoxins target the nicotinic ligand gated channels, omega-conotoxins target the voltage-gated calcium channels, and the mu-conotoxins target the voltage-gated sodium channels. These toxins are particularly interesting to scientists, especially neurobiologists and medical researchers, because they can be used to identify specific ion channels.

To be effective the venom must be delivered from the cone shell to the prey. The cone shell itself is relatively slow and unable to swim, and yet it hunts other, faster marine organisms such as fish. The venom is synthesized in the epithelial cells of a long, convoluted venom gland and stored in the gland's lumen. When the cone snail zeros in on its prey it extends it's proboscis which is loaded with venom and tipped with a specialized radula tooth that functions as both a harpoon and hypodermic needle. The snail then shoots it (by a ballistic mechanism, we're talking around 400 miles per hour) into the prey to deliver the venom. It is known that the distal end of the venom gland dilates into an oval structure called the venom bulb and it has been suggested the this bulb functions in venom transport, perhaps like a peristaltic pump. If you look at other animals that use jet propulsion, like scallops and squid, you see that the closing of their valves requires a burst contraction of the adductor muscle. This muscle shows high levels of glycolytic enzymes as well as arginine kinase (a type of phosphagen kinase).

Figure 1 showing the venom apparatus of cone snails.
Also, Figure 1A is probably the best figure I've ever seen in a peer reviewed paper.
 A study in the Journal of Proteome Research takes a closer look at the Australian cone species Conus novaehollandiae and Conus victoriae in order to shed some light on the role of the venom bulb, or pump. Specifically they look at the levels of enzymes and kinases integral to pump function. In terms of methods they did a protein extraction and 2-dimensional gel electrophoresis, a one dimensional gel electrophoresis of the venom gland and bulb proteins, a cDNA (complementary DNA) isolation and identification of arginine kinase and BIP (immunoglobulin binding protein), and an in situ hybridization of the venom bulb using an arginine kinase specific probe.

After lots of tables and graphs, some colorful and pretty and some not-so-much, they found that the venom bulbs contain high concentrations of arginine kinase. The presence of this kinase enables the venom bulb to contract very rapidly and repeatedly. That means that the cone snail can quickly force the venom through the venom duct and out through the proboscis and into the harpooned prey. In addition to the kinase, morphological examination of the bulb showed the organ to be highly muscularized. Three distinct muscle layers are separated by a tunic-like collagen sheet and the outer muscle layer, in particular, contains radially, spirally organized collagen fibers. Ok, cool. Layered muscle. What does that matter? Well, if we go back to the squid comparison you see that squids have inner and outer surfaces of muscle lined with collagen tunics. These tunics are stronger than the muscles and prevent the muscle from stretching longitudinally during contraction. This restriction and contraction allows the squid to propel water through it's jet at very high speeds. Now, the cone's venom bulb is less complex but it is likely that the function is similar. So rather than just holding the venom, these researchers found that the venom bulb is an active participant in the injection event itself. Previous studies have shown that the venom is pressurized before injection. This study shows that repeated burst contractions of the venom bulb in combination with the relaxation of the proboscis leads to a sudden ballistic discharge of the radula tooth, where it is shot into the prey and the pressurized venom pumped in by ongoing, repeated burst contractions of the venom bulb (you got an image of that in your head right? Wow!).

Read more in the article:
Safavi-Hemami, Helena , Neil D. Young, Nicholas A. Williamson, Anthony W. Purcell (2010) Proteomic Interrogation of Venom Delivery in Marine Cone Snails: Novel Insights into the Role of the Venom Bulb. Journal of Proteome Research: 9(11), 5610–5619. (DOI: 10.1021/pr100431x)

Learn more about cone shells at these links:

Thursday, November 11, 2010

I'm Bringin' Stickleback

I just love sciency song parodies. Here's a "Sexyback" parody about sticklebacks. Awesome.

Saturday, November 6, 2010

We Are Star Stuff

Happy Carl Sagan Day!

Carl Sagan was born on November 9th, 1934, and to celebrate the anniversary of his birth there will be an event held today in Broward County Florida (that's in South Florida, folks). The event will be held to increase public involvement in the amazing field that is astronomy and space exploration.

Carl Sagan was the David Duncan Professor of Astronomy and Space Sciences and Director of the Laboratory for Planetary Studies at Cornell University, and you can visit his gravesite in Ithaca, New York to this day. He played an important role in the American space program starting in the 1950's as a consultant and advisor to NASA. He was involved in almost every level, even briefing the Apollo astronauts before their trip to the Moon. He was also a key player in the Mariner, Viking, Voyager, and Galileo missions. His own work focused on planetary atmospheres, planetary surfaces, the history of Earth, and exobiology, solving questions that we almost take for granted now: Why is Venus so hot (answer: massive greenhouse effect), what causes the seasonal changes on Mars (answer: windblown dust), and what is the reddish haze that can be seen on Titan (answer: complex organic molecules)?

Needless to say, he was an extremely productive and influential scientist. He was also known as an extraordinary communicator. Some of his speeches and books are still recognized for their accuracy, foresight, and eloquence. His book The Dragons of Eden: Speculations of the Evolution of Human Intelligence won him the Pulitzer Prize and his book Cosmos became the bestselling science book ever published in English. The lay person probably knows him best from his Emmy winning television show Cosmos, which was watched by people all over the world. Oh, yeah, and have you seen the movie Contact? You can thank Carl for that one too.

So take the day to celebrate Carl, or at least a few minutes to remember all of the amazing contributions he made to science.

Also, take a look at the website for Carl Sagan Day, it has live streaming from some of the events:

Learn all about the life and works of Carl Sagan here:

Scroll through these websites as well:

p.s. No one could rock a turtleneck and jacket like Carl Sagan.

Tuesday, November 2, 2010

Votes From Space

Here in the U.S. its Election Day. If you live here, have you voted today?

It never really occurred to me that you need special rules or laws for astronauts. Apparently you do. In 1997 the state of Texas passed a bill allowing astronauts to vote from orbit, and as most astronauts are stationed in Houston that means that they can cast their vote on election day.

All three of the Americans currently on board the International Space Station have cased their votes. Their votes came via complex, secure e-mail system from orbit, 220 miles above us. The six space shuttle astronauts currently on their way to the space station voted last week as they are scheduled to lift off tomorrow.

Live in the U.S.? Haven't voted? What's your excuse?


Sunday, October 31, 2010

Dress to Impress

Have you gotten your Halloween costume all picked out? What are you going to be this year?

I was interested in journal articles about Halloween practices and so did a quick literature search. Mostly I came up with articles about whether and how we should inspect and X-ray the candy kids get when they go trick-or-treating. Instead of choosing that necessary but creepy topic, I picked a study on the partying habits of college students on Halloween.

If you've been to college, lived around a college, or just know anything about college students then you know that many students use...how shall I put it?...mind altering substances. In 1988, 90% of 18 to 25 year olds had tried alcohol, 65% were considered current alcohol users, 56% had tried marijuana, and 15% were considered current marijuana users. This same age group also reported having tried or used other drugs such as cocaine (20%), stimulants (11%), and sedatives (5%). This study was published in 1993 and so, admittedly, its stats from 1988 were newer then and probably have changed some since then, and vary considerably. But, because we are discussing this paper specifically, let's go with it.

Halloween is a major party opportunity for students. It is also an opportunity to dress in costume. This study took a look at the behavior of college students and the role that Halloween costumes play in whether students masquerade with a group and if these factors relate to alcohol and drug use. Why should wearing a costume make such a difference? Well, it has to do both with the relationship between dress behavior and self as well as the disguise of identity.

The study looked at a total of 1,253 students from two colleges in upstate New York and included both sexes across all age ranges and class years. A questionnaire called "Halloween Activities" was administered to the students to gauge their Halloween partying practices. The questionnaire revealed dressing in costume to be associated with alcohol use, in fact, 85% of those who partied on Halloween used alcohol. There was no relationship between wearing a costume and drug use, though. They asked students if they used costumes to hide or disguise their identity and related that to alcohol use, and they found no significant association. On the topic of "masquerading with a group" they found an association between drugs and groups, but of those who used these substances a greater number did not masquerade with a group.

The study advises educators to "emphasize that dressing in costume can be a positive social experience - one that allows for creative expression of the self - and that alcohol and other drugs are not necessary to enhance this experience," that students could dress "for both fun and fantasy when wearing a costume."

Here's the paper:
Miller, Kimberly A., Cynthia R. Jasper, and Donald R. Hill (1993) Dressing in costume and the use of alcohol, marijuana, and other drugs by college students. Adolescence: Spring 1993; 28(109), 189-198. (PMID: 8456608)

It's Alive!

Happy Halloween! The next couple of posts are going to be Halloween inspired. This first one was sent to me by a friend, and I'm going to quote most of it to keep it simple. It is a story about the science that inspired Mary Shelley to write Frankenstein.
"Written in 1818, the book was influenced by a scientific feud that ushered in the first battery and our modern understanding of electricity.

The story begins in the mid-18th century. Electricity had captured the imaginations of many of Europe's top scientists, and at that time very little was understood about the nature of electricity. Scientists could generate static electricity using spinning machines, but it was not until Benjamin Franklin's famous kite experiment in 1752 that they proved that lightning was of the same essence.

At the Univ. of Bologna in Italy, noted surgeon Luigi Galvani was investigating the effects of electricity on animals. It was not an unusual line of inquiry. Researchers knew electrical shocks produced violent spasms and speculated that electricity might cause muscular contractions.

On January 26, 1781, while dissecting a frog near a static electricity machine, Galvani's assistant touched a scalpel to a nerve in its leg, and the frog's leg jumped. Galvani repeated this and several other experiments, observing the same violent muscle spasms. He also noticed that frog legs occasionally twitched when they were hung from a brass hook and allowed to touch an iron trellis, so Galvani joined a length of each metal together to form a brass and iron arc that made the leg muscles contract when touched.

But where did the electricity come from?
Galvani, who called it 'animal electricity,' believed it resided in the frog itself. He thought that the bimetallic arc merely conducted the electricity from one part of the frog to the nerve, causing the leg to jump. He published his findings in 1791 and, as the story goes, came to be known as the frog dancing master.

One of Galvin's earliest readers was Italian physicist Alessandro Volta. Volta already had earned an imposing reputation as the discoverer of electrical capacitance, potential, and charge, and also discovered and was the first to isolate methane gas. He replicated Galvani's experiments and helped popularize his work.

Yet Volta reached very different conclusions. He believed the electricity came from the two metals used in the arc, and that the frog was acting as the conductor. Within the year, he replaced the frog's leg with brine-soaked paper, detected a current, and challenged Galvani.

The scientific world divided into two camps, animal electricity versus dissimilar metals. The feud became bitter. At one point, Volta wrote to a friend that his opponents wanted him dead. 'I'll be damned if I'll oblige them,' he added.

In 1799, Volta invented the voltaic pile, a stack of discs of two different metals separated by brine soaked paper. The galvanic or voltaic cell was the world's first battery, and the progenitor of automotive lead-acid batteries.

Today, we know that Volta's stack worked because dissimilar metals transferred electrons in an oxidation-reduction reaction, and the frog legs moved because electricity plays a role in muscular contractions. Of course it would take many decades to work out the details to reach this level of understanding.

So how did this influence a young Mary Shelly and lead her to compose one of the most widely read novels of all time, 'Frankenstein; or, The Modern Prometheus'?

Galvani's nephew, Giovanni Aldini, was a fierce partisan of animal electricity, yet he did not ignore Volta's pile. Aldini used it to tour the capitals of Europe and demonstrate the medical benefits of electricity -- or not. His demonstrations involved jolting corpses with electricity and making decapitated criminals sit upright.

Aldini's most famous exhibition took place in 1803 at the Newgate Prison in London, U.K. He inserted metal rods into the mouth and ear of the recently executed corpse of murderer George Foster. 'The Newgate Calendar,' a book about the criminals of Newgate Prison, described what happened next: 'On the first application of the process to the face, the jaws of the deceased criminal began to quiver, and the adjoining muscles were horribly contorted, and one eye was actually opened. In the subsequent part of the process the right hand was raised and clenched, and the legs and thighs were set in motion.'

Not surprisingly, some observers thought Aldini was bringing Foster back to life.

Mary Shelley knew all about Galvani, Volta and Aldini. Humphry Davy and William Nicholson -- the era's leading electrical researchers -- were friends of her father. In 1816, at age 19, she spent the summer in Geneva, Switzerland with Lord Byron and her future husband, Percy Shelley. The season was cold and rainy, and they spent many evenings around the fire, reading German ghost stories and discussing electricity's potential to reanimate corpses.

It must have seemed like she was merely peering into the near future to imagine that one day, a Victor Frankenstein might succeed in reanimating an assembly of body parts."
You can see the actual story I quoted here:

Because of Halloween and the popularity of Frankenstein, this story has been making its way around the Internet. And, granted, has been appearing verbatim on many credible news sources and websites. But I usually try to verify a story before posting it, if I can. This one, however, was a bit more difficult to track down. I did find some interesting information posted by Sherry Ginn of Wingate University on a University of Florida website. The information there seems to support the above story, as do some other sources, and so I'm pretty confident that it is authentic. You can read that entry and more about Mary Shelley's life here :

And here is some additional info about Mary Shelley and the writting of her book:

Friday, October 29, 2010

Know Your Nerds

Threadless is a tee shirt website that has an ongoing open call for tee shirt design submissions. Here is a great one that was posted on to how know the different types of nerds. Excellent.

Feel Useful

This is a really creative ad that I think you'll enjoy:

Monday, October 25, 2010

On the Spot

Have you ever looked at a leopard and wondered why it has spots and not stripes or why it is patterned and not plain? A new study in the Proceedings of the Royal Society B looks at just that question.

The patterns themselves come in a large variety even within the wild cats, and previous studies have suggested that they are for camouflage in these predominantly ambush predators. It is known that hunts are more successful when an attack is initiated from shorter distances. Makes sense. And smaller cats are probably camouflaged for both a hunting advantage and protection from predators. Other studies have also found spots to be significantly associated with arboreality (the presence of trees or a forest or movement within the trees) with dark spots, in particular, associated with closed habitats and predators that prey on ungulates (hooved animals). The conclusions about stripes have been a little less than clear.

The researchers collected images of 35 species of Felidae from the Internet from various wildlife photography resources. They then picked 6 of the best images from each species, images where the animal was shown in profile, full view, free of distortions and occlusions, in focus, in dry weather, and in natural lighting. Then they took rectangular crops of the images using the base of the neck and tail. They then had to classify the images according to the type of pattern they were seeing.

So how do you go about measuring the influence of spots? I mean, consider the jaguar vs. the clouded leopard vs. the serval. All of them have spots, but none of them have the same kinds of spots. So in order to study the evolution of pattern you need to come up with a better way than just calling something spotted. The method used in this study was inspired by reaction–diffusion theories of biological pattern formation. I'm not so much up on those kinds of theories, but here is how the paper describes it:
"Human observers classified standard examples of felid flank patterns to the closest matching comparison pattern in this multidimensional space. The values of variables in the underlying equation that generated the chosen pattern and distribution of observers' classification decisions parameterize the important properties of each standard image. The five dimensions can be conceptualized as: (i) patterned versus plain, (ii) pattern irregularity, (iii) pattern complexity, (iv) pattern element size and (v) the anisotropy (directionality) of pattern elements."
One the measures were characterized they were tested against ecological variables that have been proposed to drive the evolution of pattern phenotypes. These variables include habitat, locomotion, activity time, social systems, prey size, body size, and weight.

After lots of images and lots and lots of stats what did they find? Basically that flank patterns function as camouflage. Okay, not really a new finding, just the same finding with a different method (but the more support for a hypothesis the better right?). They also found that evolution has generally paired plain (unpatterned) cats with relatively uniformly colored, textured, and illuminated environments. Patterned cats were paired with environments that are "full of trees and bushes and stripy, speckly, patchy-blatchy shadows." It is likely that the pattern on the cat resembles the background pattern of the habitat in which it lives or hunts. The cat species living in closed environments and who move around in the trees are more likely to have complex patterns than those who live in open environments and move around on the ground. Felids that have especially irregular patterns live in tropical areas and tend to be nocturnal hunters, preferring to hunt in the trees.

On the topic of stripes, as with previous studies, these authors found no evidence to support the proposition that vertical stripes are associated with grasslands. Considering that the tiger was the only one to be classified as having vertical stripes and its favored habitat is not a grassland, that seems pretty plausible to me.

It wouldn't be a scientific study if you didn't have some outliers to speculate upon. For example, the cheetah (Acinonyx jubatus). This cat has a pattern and yet lives and hunts in a grassland/savanna habitat. Similar outliers include servals (Caracal serval) and black-footed cats (Felis nigripes). On the other side of the coin there are those species who have plain coats but live in closed environments, such as the bay cat (Pardofelis badia) and flat-headed cat (Prionailurus planiceps). Its possible that these outliers could be utilizing different microhabitats within the categories used by this study. Perhaps plain and patterned cats have instances in which the (non-)pattern works and some where it doesn't. Or maybe they are constrained genetically or developmentally. Its difficult to say.

Here's the paper:
Allen, William L., Innes C. Cuthill, Nicholas E. Scott-Samuel and Roland Baddeley (2010) Why the leopard got its spots: relating pattern development to ecology in felids. Proceedings of the Royal Society B: published online. ( DOI: 10.1098/rspb.2010.1734)

If you want to take a look at some of these cats and here patterns then look here:

And here are some story links:

(image from webshots.com)

Thursday, October 21, 2010

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.

Wednesday, October 20, 2010

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.

Sunday, October 17, 2010

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)
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