Friday, March 30, 2012

Altering behavior: Another viral trick?

Mosquito (Aedes aegypti)
Photo by USDA

Dengue virus (DENV) is one of the world’s fastest growing health problems.  Each year, about 500,000 dengue infected people are admitted to the hospital with life-threatening symptoms, including gastrointestinal bleeding, seizures, and slow heart rate.  More alarmingly, no vaccine or treatment is available for those infected.  DENV is spread by mosquitoes, much like malaria and West Nile virus.  Therefore, controlling the mosquito vector remains the primary defense against dengue.  While DENV causes illness in humans, researchers have uncovered different effects in the mosquito that may impact viral transmission.

In order to be transmitted to a human host, DENV must first infect a female mosquito’s salivary glands.  These glands contain compounds that help the insect feed.  It would be in the virus’ best interest to encourage the presence of these compounds to increase transmission rates.  Therefore, scientists wanted to investigate any changes in the salivary glands during DENV infection. 

To detect any changes, researchers screened the entire genome looking for differences in expression of individual genes in DENV infected mosquitoes compared to healthy mosquitoes.  They found a total of 147 genes being regulated by DENV.  Most of these genes were involved in the immune response, food digestion, and metabolism.  However, there were a few surprising genes being regulated by DENV.  These genes are actually involved making proteins that bind odorant, allowing the insect to detect odors.  Scientists engineered mosquitoes that could never express these specific odor binding protein genes.  These insects took significantly longer to find and bite their host. 

This suggests that by increasing the expression of these odor binding proteins, the insects will be able to detect their hosts more quickly, resulting in better transmission of the virus.  This is the first hint that human pathogens may be able to increase their transmission by affecting the behavior of their vector animal.

Supreme Court throws out BRCA patent

America has been fixated upon the Supreme Court's upcoming decision regarding President Obama's healthcare plan, so much so that we appear to have missed another crucial ruling in the healthcare field. On Monday, the Supreme Court ruled to revoke Myriad Genetics Inc.'s patents on the BRCA-1 and BRCA-2 genes. Gene patents have been a controversial topic since the first gene was patented in 1982. The precedent was set way back in 1906, when the Supreme Court ruled that purified adrenaline could be patented because its purified state was more useful than its natural state. The BRCA patents have been the lightening rod for the entire gene patenting issue because Myriad is the only company that can produce a test for mutant BRCA genes. This test can help inform women how aggressive of treatment to choose. For example, one of the women who filed the original lawsuit tried to get the BRCA test from Myriad when she was diagnosed with breast cancer to see if she had one of the really bad BRCA mutations, which would increase her risk of ovarian cancer by 50%. However, her insurance did not cover the $3000 Myriad test, and since no one else was allowed to offer it, she was out of options. This situation prompted her and other women to sue Myriad, with the assistance of the ACLU. And now, they've won, which does not mean that Myriad immediately loses its BRCA patents, but rather that the decision gets handed back to the district courts for new action.
Personally, I'm not sure what to make of this decision. If all gene patents are tossed out, the face of pharmaceutical research will change dramatically. Companies claim that without patent protection on the genes, there is no way for them to make a profit on potential therapies, because the cost of discovery is so high, but the idea of patenting something contained within every humans' cells seems wrong. In any case, it should be interesting to see how the issue of gene patents plays out: will pharmaceutical research grind to a halt without patent protection? Or would continued gene patenting slow scientific process and doom consumers to prohibitively expensive tests and treatments? Probably neither, but the changes in healthcare and pharmaceuticals resulting will nonetheless be interesting to watch.

America gets poor marks for science.

Quick! What's the easiest way to identify what elements are likely to chemically react with chlorine?

Right. Google it. OR you could consider the electron configuration of chlorine and the number of valence electrons necessary to complete its valence shell and then determine what elements are likely to give up that number of electrons to drop down to a full valence level.

If you didn't understand all that, don't worry. You are not alone.

A majority of US states' standards of science education remains, "mediocre to awful" according to a new comprehensive study by the Thomas B. Fordham Institute. Needless to say by Fordham's standards we didn't pass the science standard pop-quiz.

The institute analyzed the science standards of all 50 states and the District of Columbia for grades K-12 and gave each state a grade based on "Content & Rigor," "Scientific Inquiry & Methodology," "Physics" and "Chemistry." The average grade allotted was a very low C. More than half of the states went home with a D or lower and were promptly scolded by their parents even though only six states total got a smiley sticker for earning an A.

Thomas B. Fordham Institute

Thursday, March 29, 2012

The Garden of Otherworldly Delights

The island I'm about to show you is often described as "an alien island" or "the most alien place on Earth," so I'm going to be admittedly unoriginal when I portray it as such.  Before I even go on, let me show you a few pictures so you'll forgive my conterfeit comparison:

Understanding is Joyous

"Our species needs, and deserves, a citizenry with minds wide-awake and a basic understanding of how the world works."- Carl Sagan

Carl Sagan -- astrophysicist, author, science communicator, renowned ambient techno artist?

Sagan is one of the best science communicators of our time.   As quote above indicates, Sagan believed that approaching science openly would shape us into a more reasonable and peaceful culture.  He promoted science not as challenging bits of knowledge that one need "learn," but rather, as a way of inquiring about the "awesome machinery of nature" with a willingness to learn.

One medium through which Sagan thrived is the book, both fiction and nonfiction.  He wrote the fictional Contact, which was later made into a movie.  His nonfiction may be even more reputable, with pieces like Pale Blue Dot.  Sagan's literature attracted scientists and non-scientists alike.  His writing was eloquent and poetic; the scientific descriptions were succinct and often delivered from a philosophical perspective.

"Consider again that dot. That's here. That's home. That's us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. The aggregate of our joy and suffering, thousands of confident religions, ideologies, and economic doctrines, every hunter and forager, every hero and coward, every creator and destroyer of civilization, every king and peasant, every young couple in love, every mother and father, hopeful child, inventor and explorer, every teacher of morals, every corrupt politician, every "superstar", every "supreme leader", every saint and sinner in the history of our species lived there - on a mote of dust suspended in a sunbeam."

Perhaps Sagan is most well-known for the series, Cosmos.  (Note: Neil DeGrasse Tyson, among others, is working on a new version of the series!  see hereCosmos is a documentary series (made into a book later) in which Sagan touched upon various scientific disciplines.  For each, he described the inspiration behind the prominent scientists, the history of their discoveries, and current applications of the sciences.

"The cosmos is full beyond measure of elegant truths; of exquisite interrelationships; of the awesome machinery of nature."  (Cosmos: The Shores of the Cosmic Ocean)

Sagan lectured and researched at numerous universities, and was a full-time faculty member at Cornell.  He even co-wrote a paper on the origin of life with the well-known H.C. Urey.

Although Sagan passed away, his message still continues to reach many.   In fact, a new medium has promoted Sagan's science -- music videos.  John D. Boswell's Symphony of Science makes music by autotuning science clips, like TED talks and Cosmos, and creates a musical montage.  The project was made to "deliver scientific knowledge and philosophy in musical form."  The videos feature other prominent science figures, like Neil DeGrasse Tyson, Stephen Hawking, Richard Dawkins, and Richard Feynman.

Whether it be through his films, books, lectures, or tunes, Sagan continues to reach a broad audience due to his ability to frame science as inspirational and wondrous rather than tedious. 

"The brain is like a muscle. When it is in use we feel very good. Understanding is joyous."

Wednesday, March 28, 2012

Common Cliché for a Chicken

Writers have been taught time and time again to avoid common expressions and clichés like bark up the wrong tree, cut to the chase, and go back to the drawing board.  These phrases should be avoided because they have been used so frequently that the actual phrases lose meaning.  In fact these expressions may lose the ability to conjure up images at all.

Many of us understand the meaning of a phrase like "running around like a chicken with its head cut off," but may never have actually seen how a chicken acts after it is beheaded.  I hadn't until I recently "youtubed" it (I wouldn't recommend it).  During a time when most people raised their own livestock, this expression was probably a good way to describe frantic, aimless running around.  However for the people of Fruita, Colorado, the expression, "running around like a chicken with its head cut off," has special meaning.

Tuesday, March 27, 2012

Whooping Cough and Its Vaccine

The list of bacterial infections becoming ever more difficult to cure due to development of multi-drug resistant forms of the pathogens may now include a new name.  Strains of the bacterium responsible for the childhood disease Whooping Cough have developed new genetic identities capable of evading the vaccine currently used to prevent the disease.

Monday, March 26, 2012

Immortal Devil: The Problem of Transmissible Cancer

The Tasmanian Devil made his first Looney Tunes appearance alongside Bugs Bunny in 1954. Warner Brothers, afraid of Taz's violent image, axed him after only a few episodes. But the grumpy, spinning character was so popular among viewers that producers scrambled to bring him back to the screen.

The real Tasmanian devils are small, feisty marsupials with the most powerful bite of any living mammal. In confrontations, blood rushes to the ears to turn them a glowing red. The sound of a fight is unsettling --shrieks and growls that seem to alternate between throaty screams and deep, gasping breaths. And, of course, there is biting. Lots of it. Unfortunately for the devils, biting is part of the reason that the species could become extinct in the near future. And unlike Taz's situation, no amount of fan mail will bring them back once they're gone.

The real Taz, whose species is now threatened with extinction.
Photo credit: David Boon

Advances in sickle cell treatment

Production of fetal hemoglobin as an adult is a form of treatment for people with sickle cell disease.  Scientists have identified a protein that represses the production of fetal hemoglobin in adults.  If this protein can be targeted and reduced it could serve as a powerful treatment for patients with sickle cell disease.

Scientists identified that the protein BCL11A prevents the production of fetal hemoglobin in adults.  If the amount of BCL11A in individuals with sickle cell disease can be decreased, fetal hemoglobin levels in these individuals can increase while the amount of red blood cell produced by the body is unaffected.  This fetal hemoglobin can then substitute for the diseased adult hemoglobin and alleviate symptoms associated with sickle cell disease.

Researchers and physicians have been studying sickle cell disease, specifically sickle cell anemia, since the early 1900s.  The disease occurs because of a single mutation in the gene that codes for the adult hemoglobin protein.  The mutation changes the shape of adult hemoglobin, which in turn changes the shape of the red blood cell that contains the misshapen hemoglobin.  Normal adult hemoglobin is a robust, flexible disc shape but when it contains the mutation for sickle cell the shape changes to a rigid, crescent or "sickle".  This sickle shape decreases hemoglobin's ability to transport oxygen/collect carbon dioxide and makes the red blood cell more 'sticky'.  The stickiness is a problem because allows diseased red blood cells to adhere to the walls of blood vessels as well as other normal and sickle red blood cells, which can cause blood clots.

Sickle red blood cell above normal red blood cells; credit to wellcome images of Flickr.

Saturday, March 24, 2012

SciArt Link Roundup #8

Hyacinths are the only things blooming in my backyard, for now.  

It's the first week of spring (magnolia blooms are out!). You know what that means. SciArt Saturday botany special. And lucky for you, this week is a very good one for science art.

Thursday, March 22, 2012

Scurvy Dogs, Landlubbers, and the Hi-C Mystery

If you’ve ever been on an expedition to circumnavigate the globe, you may have noticed, perhaps near San Pablo Island or the Cape of Good Hope, that you were lethargic, jaundiced, and losing a few teeth here and there.  Haven’t you always wondered why?  Well, you had scurvy, of course – a deadly condition brought on by severe lack of vitamin C!

If you had any livestock on the ship with you, which you undoubtedly did, you may have found yourself wondering why they seemed to be getting along just fine, even as you suffered from general edema, neuropathy, and violent convulsions.  Were they simply deteriorating at a different rate?  Were they making their own vitamin C in secret?  Was some sort of sinister “Rime of the Ancient Mariner” thing going on?  Actually, it’s the second one.  Almost all animals are capable of synthesizing vitamin C on their own.  Humans, most other primates, some passerine birds, and guinea pigs are among the few that cannot.

But wait, you might say.  Aren’t humans supposed to be at the top of the evolutionary tree?  We’re clearly the best at this whole “survival of the fittest” thing, right?  Are you telling me a lowly vole or a sea cucumber can go forever without supplementary vitamin C and I can’t?

First of all, there is no “top” of the tree.  The tree is the history of life on Earth, and the branch tips are all the currently existing species.  Each one is suited to its own particular niche, and although we are more intelligent than sea cucumbers, we are not “better” than they are.  We can’t survive in their environment and they can’t survive in ours.  We are each adapted to our own surroundings.

Adapted.  That word always arises in these discussions of evolution.  We associate it with novel traits that give various animals advantages in their environments: giraffes’ necks are adapted for reaching lofty leaves, and zebras’ stripes are adapted for savannah camouflage.  Adaptations are genetic changes that allow organisms to compete better and reproduce more than their cohorts.  By the same token, if a mutation in a gene makes an organism less fit, it should be rooted out by natural selection.  Similar organisms without that negative mutation will survive longer, find mates more effectively, produce more offspring, or otherwise pass on their genes better than the one with the unfortunate disadvantage.

If a trait is universal in a species (if it has reached “fixation,” that is), or across several species, it is likely that trait got to where it is by being advantageous.  A moose’s antlers, then, although they are cumbersome and ridiculous looking, must provide an advantage, or they wouldn’t be on every single male moose!  It is possible for minimally disadvantageous traits to reach fixation despite natural selection acting against them, but this possibility rapidly subsides to nothing as population size increases into substantial numbers.

Alright, then.  We are nearing the big resolution.  But first, I must add another twist: Primates and a few other haphazardly chosen species cannot make vitamin C, sure, but that’s not the end of it.  You see, our ancestors could make it.  We still have the genes, albeit non-functional versions of them, that code for vitamin C synthesis.  So do guinea pigs and all the others.  This can only mean that on several occasions throughout evolutionary history individual organisms lost the ability to provide themselves with a substance essential to life and somehow not only survived, but performed better than their competitors to the point where inability to produce that substance reached fixation!  No way, right?  There must be an argument for Creationism in here somewhere!

Hold your horses.  Seriously.  I’m not going to leave you hanging.

Long ago, when the ancestors of guinea pigs and men and Saffron-breasted Whitestarts were all living comfortably on balmy, equatorial shores, vitamin C flowed like sunshine.  Every day was a Sunny-D commercial.  Citrus fruits were everywhere, and of course all the monkeys were constantly gorging themselves.  But back then, they didn’t even need to - they could still synthesize all the C they would ever need.  That was all about to change.  One day, a rebel monkey was born.  We’ll call him “Cheeto.”  Cheeto, unlike his parents, couldn’t make any vitamin C because of a few misplaced nucleotides in his vitamin C-making gene.  The world held its breath.  Cheeto ate a banana.  Then he had some berries.  Years passed.  Cheeto was getting along just fine, it seemed.  He was getting more than enough C from all the fruit, and all the excess he consumed was just excreted in his urine, so his condition passed unnoticed.  In fact, since he wasn’t wasting energy making a substance he didn’t need, and since all the others were still monkeying around with unnecessary metabolic pathways, Cheeto and his offspring thrived.  The same thing happened with Randolf the guinea pig and Clarence the Yellow-rumped Eremomela. 

Eventually, Cheeto’s and the others’ genes achieved fixation in their respective species.  And they’d have gotten away with it too, but humans had to move to areas without ample fruit and attempt crazy voyages with inadequate lime stores.  Nowadays, if you live on a latitude greater than 25 degrees or so, your inability to make vitamin C is no longer an advantage.  Now, we must make sure to eat from all the food groups and get 4-6 servings of fruit or something per day.  If we follow the recommendations of the dieticians, we only get enough vitamin C to avoid scurvy.  Some schools of thought recommend much more.

So if we could lose our "C" genes, can we get them back?  Unfortunately it's much easier to "break" a gene than to "fix" it.  If it makes you feel any better though, there are attempts being made to artificially restore the gene.  -In mice that have previously been genetically manipulated, that is.  Don't expect this any time soon:

Saturday, March 17, 2012

SciArt Link Roundup #7

A stained clover stalk, Trifolium pratense
By  Eckhard Völcker 

In case you aren't content to spend St. Patrick's Day hunting the clover fields for a lucky recessive trait, I recommend checking out this week in science art (mostly because you'd have to beat this guy).

Friday, March 16, 2012

Drosophila Drink the Pain Away too

Let's play with some stereotypes here: females who have been recently are about half the reason Ben and Jerry's exists. The other half is probably dumped guys, but they won't admit it, making proving my entirely invented statistics hard to do. The stereotypical male behavior breakup behavior is to go to a bar and get schwasted. Turns out, they might be sitting next to some Drosophila melanogaster at the bar doing the exact same thing.

A recent study out of the University of California by Dr. Shohat-Ophir showed that male fruit flies whose sexual advances got rejected were about 20% more likely to drink a food supply containing alcohol. They also drank 4 times as much as their progenitor-producing peers. To make sure these flies couldn't catch a break, the unlucky flies were placed in a vial with a female who had already mated, so she would continually reject the male's advances. The lucky flies were placed in vials containing 20 virgin female flies to 4 virgin males, ensuring they mated multiple times.

Naturally, these results raised questions of what in the flies' neurobiology was stimulating this desire for ethanol. They took the rejected male brains and measured how much neuropeptide F (NPF) there was, as NPF has been previously linked to alcohol preference. The levels of NPF were inversely related to alcohol desire: mated flies had higher levels of NPF than the unmated flies. In order to verify this, they lowered levels of NPF in mated males and, sure enough, saw the mated males drinking more alcohol. This proved that NPF is sufficient to dictate alcohol preference in fruit flies.

Humans have a similar protein, called neuropeptide Y (NPY). In depressed people and those experiencing post-traumatic stress disorder, NPY levels are indeed decreased, and certain alternate versions of NPY have been linked to alcoholism in humans. However, in both fruit flies and humans, how social cues like rejection are translated into NPF/Y levels is unknown, and how NPF/Y affect alcohol consumption is a black box as well.

Triceratops Identity Crisis

A) Triceratops skull    B) Torosaurus skull

Photo credit: Nicholas R. Longrich and Daniel J. Field

In recent years, paleontologists have proposed that the well-known and beloved dinosaur Triceratops was actually a juvenile form of a different dinosaur, Torosaurus.  The three horned dinosaurs, also known as Ceratopsidae, have been extremely hard to identify and catagorize because their skull and frill tend to morph with maturity.  This may have been to distinguish adult dinosaurs (those ready to reproduce) from immature juveniles. There are so many morphological differences in Ceratopsidae fossils that these dinosaurs were originally catagorized into 10 different genera.  Today, there are only two, Triceratops  and Torosaurus.  Now, some paleontologists are calling for a merge between these two genera, while others maintain that Triceratops  and Torosaurus are two distinctly different dinosaurs.

Traditionally, Triceratops is classified by its short, solid frill.  Torosaurus has a longer frill that contains two large holes.  One hypothesis is that as the dinosaur matured, changes in a Triceratops' short frill caused it to elongate and become the open skull that is normally associated with Torosaurus.  To support this hypothesis both types of dinosaur fossils must be found in overlapping geographic locations.  Dinosaurs with longer, open frills should also be more mature than those with a short, solid frill.  Lastly, there should be intermediate fossils that would depict the maturation of the dinosaur overtime.
Paleontologists agree that the first condition is supported.  Fossils from both types of three horned dinosaurs have been discovered across modern day Western United States and Canada.  These fossils all seem to be from the same time period as well (the late Maastrichtian period). 

The evidence for the second condition is more controversial.  Researchers analyzed these dinosaurs’ development by looking at bone remodeling.  More mature animals would have more bone remodeling because their skeleton (specifically their skull) would have morphed as they aged.  However, there are very few fossils that are intact enough to accurately make this analysis.
The third condition is just as difficult to support for the same reasons.  There are few fossils that are complete enough to determine if the physiological characteristics are intermediates between Triceratops and Torosaurus.  One fossil of a Triceratops seemed to have indentations in its frill, which could have been the beginnings of the holes that are found in Torosaurus frills.  However, some paleontologists argue that the indentations are not in the expected location to develop into a Torosaurus frill.

Though unsolved, this controversy has definitively affected the way paleontologists identify dinosaur genera and species.  They must take into account the way that the animal’s morphology developed and changed over its lifetime.  Currently, new systematic approaches are being developed to explain and characterize fossils, helping to clarify dinosaur diversity.  Overall, more caution is being taken when identifying new species (or eliminating old ones).

Thursday, March 15, 2012

An attempt to explain why the word "heart" is in every song, ever.

            Sometimes school is a wonderful place.  My friends are close-by, my food is prepared for me, and… hmm.  Well, I’m sure there are more reasons.  On the other hand, school can be pretty stressful.  In this desk wedged in the corner of a tiny, messy room, my potential future paths are paved or demolished with each new assignment.  That’s why, although it is precariously placed and makes my space even more cramped, I always have my guitar with me, back in this corner against the wall.  It rests upright on the floor, leaning over just slightly.  Whenever a task overwhelms me and I feel my temperature rise, I drop my pen or remove my hands from the keyboard and play some songs until I’ve calmed down enough to move on.  It’s carried me through some tough times.

            That may not be surprising to you.  I assume most anyone can agree that music alters moods.  In general, reggae evokes joy, jazz causes relaxation, rock triggers excitement, and Ke$ha induces uncontrollable, projectile vomiting.  It’s so familiar that it seems to be intuitive, but there’s no obvious reason for a harp to put me to sleep while an electric guitar makes me throw myself mindlessly around in a stagefront pit and punch people (I have never done this.).

            To illuminate the effects of music on the human body, a University of Maryland study monitored cardiovascular changes in ten volunteers as they listened to several musical genres.  Each participant was starved of their favorite tunes for a week before the test.  They each selected one genre that made them happy (which turned out to be country for most participants – Something tells me not to comment on this.), and one that made them anxious.  Humorous videos were also included in the test.

Wednesday, March 14, 2012

Frogs and the City

A new frog species, Rana sp. nov, or "new frog species" has been discovered on the streets of New York City.

Once thought to be the common leopard frog, the new species sounded a unique croak.  The "short, repetitive croak" made scientists suspicious, as the leopard frogs usually emit "rapid chuckles."  Upon doing a bit of research, it was clear that there were genetic differences between the leopard frog and this hot frog in the city. [source]

Courtesy Bill Curr

The news of the emergence of an urban frog species caused me to consider the extensive nature of evolution.  New York City lacks natural space, barring Central Park, and seems uninhabitable for many animal species.  A new frog species has evolved, as its close relative adapted to the conditions of the city.  This new species now thrives.

In fact, these frogs thrive particularly well in and around Yankee Stadium [source].

Jeremy Feinberg, the doctoral candidate from Rutgers University, discovered the frog by its croak.  Naming rights have been left to him.  What would you name the new frog species?  Some suggestions I have enjoyed include "Commuter Frog," as they are often spotted in tunnels, and "Yankee Doodle Froggy."

Targeting RNA for Mitochondrial Mutation Repair

Mitochondrial diseases affect 1,000 to 4,000 newborn children each year in the US1.  These diseases often result in loss of muscle coordination, muscle weakness, poor growth, visual and hearing problems, learning disabilities, neurological disorders and dementia.  They are most often caused by mutations in the mitochondrial DNA.

Mitochondrial DNA is more susceptible to mutation than nuclear DNA because its repair functions are less robust and are more vulnerable to oxidative damage due to its proximity to the respiratory chain.  Researchers have identified a protein that may be key in developing a gene therapy for mitochondrial disease.

In 2010, Teitell and Koehler identified the protein called polynucleotide phosphorylase (PNPASE), which is involved in the regulation of transporting RNA into the mitochondria.  The importation of RNA into the mitochondria is necessary for the replication, transcription, and translation of the mitochondrial genome.  Therefore, with the decreased expression of PNPASE, the import of RNA into the mitochondria also reduces and ultimately leads to the halt of cell growth.  A subsequent study, "Correcting human mitochondrial mutations with targeted RNA import," explores the use of PNPASE to import specific RNA molecules into the mitochondria, which express the production of other proteins capable of repairing the mutated mitochondrial genome.

Geng Wang and colleagues developed a method to pinpoint and import specific RNA molecules into the mitochondria to regulate proteins essential for the repair gene mutations.  The reparative RNA molecules that Wang was targeting exist in the nucleus of the cell.  First a series of export sequences were engineered to direct the reparative RNA out of the nucleus and into the mitochondria.  Once inside the mitochondria, the targeted RNA were able to repair mutated mitochondrial DNA as was demonstrated in two different human cell line models of mitochondrial disease.

Researchers are now hopeful that this strategy for correcting mitochondrial mutations can be demonstrated in animal models.  If successful this method could also be applied to the development of regenerative medicine therapies by repairing mitochondrial mutations in stem cells.

Persons: Ethical, Legal, and Scientific

This month's celestial events may seem quite grounded in comparison to the ethical musings of some researchers at the annual meeting of the American Association for the Advancement of Science, the organization responsible for publishing Science.  A session focusing on the possibility of defining certain animals as non-human persons publicized a topic blending ethics, laws, and science that emerged no later than the 1960s.

Follow-up or cover-up, when is extensive coverage excessive coverage

Last Wednesday night, the LA Times tweeted this headline: “Massive solar flare ripples sun’s surface, storms speed to Earth”. 

The following day, another headline: “Solar storm is a bit of a dud -- but wait, there’s more to come.”

And on Friday: “Solar storm that seemed to fizzle gains new strength.”
After today’s class discussion surrounding the New York Times piece on arsenic, I thought this was an interesting find.
A solar flare from 2011, courtesy of phunk_ee

Monday, March 12, 2012

Just a reminder: French Creek is pretty neat!

I've heard many students grumble about the lack of things to do here in Meadville, PA.  My best combat to this self-inflicted boredom is to check out something that Meadville offers year round and never goes out of style: the great outdoors!  The crown-jewel of interesting outdoor aspects in Crawford county has to be French Creek, which is nationally renowned for its biodiversity and support of many endangered species.  French Creek is home to the largest (and coolest!) salamander in PA, as well as the greatest diversity of fish and freshwater mussels in PA.

All rights reserved to Todd Pierson
All rights reserved to Brian Gratwicke.
Pennsylvania's biggest salamander (and should-be mascot of Allegheny College) gets its Mr. Cool reputation in good part because of its name: hellbender!  In addition to the unruly name, hellbenders look downright funky.  Their head and tail give look as though they have been flattened by a canoe, their stubby legs give way to paddle-like 'feet' with four tiny 'toes' on each end, they appear anciently wrinkled and they can grow to be over two feet long (a hefty salamander).  These attractive beings live primarily off of crayfish and can only survive in relatively unpolluted streams.  This leads to a gold star to French Creek for staying 'clean' enough to support this slimy fellow!

In addition to Mr. Cool, there are approximately 80 different species of fish living in French Creek, 15 of which are on PA's list of endangered/threatened species.  Some of these species are considered indicator species because they are sensitive to polluted water conditions; this means that their presence in French Creek indicates unpolluted water.  For instance, the brook trout is native to western PA but has disappeared in many nearby streams because it cannot survive in polluted (or warm) water.  However, can still be found in French Creek and its tributaries!  And if you ever see one, my, it is a pretty fish.  Here's a young male showing off his colors during breeding season.

All rights reserved to The Express photographer
 Many mussel species are also indicator species because polluted water disrupts their feeding regime.  They are filter feeders so they eat food by sifting, or filtering, water for food particles.  When ambient water carries pollutants, the pollutants can clog or damage mussels' siphons.  Mussels respond by closing their siphons, which prevents pollutants from entering.  This defense strategy also prevents food from entering so it doesn't work forever.  But guess what?  French Creek has these too!  There are 25 different species of mussels in French Creek, 15 of which are on the endangered/threatened list in PA, so this creek is (pretty) clean! 

There you have it: a brief overview of some of the neat organisms that reside in French Creek.  Meadville has a beautiful stream right in its backyard so the next time you're feeling bored (or blue or angry or chipper) take a stroll along the creek to see what you can see!  Oh and I think the French Creek Conservancy would appreciate me saying that the more you see of this fine stream, the more you'll strive to preserve its fineness.  

Science Writing Top 5

Nearly every surface of my room is covered by newspaper --clippings taped to the walls, old issues piled high on desks or splayed open mid-article, curled edges poking out of drawers. This is fortunate for the art student across the hall*, whose papier-mâché dreams were realized when two months of New York Times back issues finally made it into the recycling bin.
*Not quite as fortunate for my roommate; sorry, Sara. 

The time Orson Welles stopped by my room to chat.

No surprise, I have read a lot of articles. But there are only a few that I've remembered through the years. These pieces have left lasting impressions on my own writing style; all are excellent examples of science writing and literary journalism. Today, I sit down to think about how each piece has held my attention for so long. And because I am borrowing a friend's tablet, my thinking entails a lot of unnecessary doodling...

Saturday, March 10, 2012

SciArt Link Roundup #6

Adapted from BioDivLibrary

This week, SciArt Saturday features scientific illustration archives, excellent photojournalism, and more Muppets than you might expect.

A Small (but Promising) Pilot Study: Reducing Organ Rejection

Your immune system is responsible for recognizing and fighting off invaders that cause illness.  However, what if you needed your immune system to make an exception for particular foreign cells?  This is the challenge that organ transplant recipients face.  If their body rejects their new organ, they face a repeat transplant or possibly death.  To prevent this rejection, doctors attempt to find a donor organ that matches the recipient’s original organ, so that their immune system is less likely to detect the new organ cells as unfamiliar.  Recipients also have to follow a very expensive, strict drug regimen for the rest of their lives to suppress this potentially devastating reaction to the new organ.  A new pilot study may reveal a different treatment for organ recipients that would decrease the rejection rate and relieve recipients of a lifelong reliance on anti-rejection drugs.

Friday, March 9, 2012

Green eggs have got biologists juiced.

Sam I Am and David Albertini of the University of Kansas Medical Center have something in common... a passion for green eggs.

Lo and behold:

Credit: Vincent Center for Reproductive Biology 
This past August, Hurricane Irene hit the United State with a ferocity not seen since Hurricane Katrina. While Irene was much less devastating, she still shut down masses of airports, flooded roads, destroyed homes and business, and killed at least 21 people. Even now, the aftermath lingers in the form of a political battle in North Carolina.
        Highway 12 connects the Outer Banks, North Carolina's chain of barrier islands and highly popular tourist destination, to the rest of the state. The highway provides the primary access to and from the islands. However, because the barrier islands themselves are unstable, and due to Highway 12's proximity to the coast, large portions of it were ruined in the hurricane (see this link for cool before and after photos, scroll down to the bottom). This NYTimes article focuses on Hatteras Island, one of the most popular destinations and one that has no access other than Highway 12.
Image courtesy of Damage to Highway 12 following Hurricane Irene
Critics are saying that NC should not be focusing so much money on repairing a highway that is bound to get a similar treatment in the next hurricane. Dr. Young, a coastal scientist, sums up the situation very succinctly: They can engineer that bridge so well that it can withstand a Category 3 or 4 hurricane...The barrier island it is connected to cannot.” Professor Stanley Riggs, another coastal scientist who wrote "The Battle for North Carolina's Coast", claims Highway 12 "will bankrupt the state".  His book claims that between 1983 and now, NC has spent at least $93 million on Highway 12 maintenance. The NYTimes says that in 2011 alone, the Outer Banks brought in $2.6 billion through tourism. That doesn't sound like bankrupting to me, instead that sounds more like the state making $250,700,000. Is it ecologically sound? No. Economically? Sure seems like it. Young and Riggs do have a point that it is not environmentally sound policy to build ontop of sand that is supposed to shift with waves, but they need to start using arguments beyond how much money Highway 12 costs in order to be convincing.

Thursday, March 8, 2012

Primate Power and Potential

Classical biology was basically a bunch of British guys sailing around the world and sticking pins through any moving thing they found. Animal "specimens" from lowly insects to birds and primates were all subject to the same, often brutal treatment. Concepts like "animal welfare" weren't supported with substantial legislation until the late 20th century. It was Jane Goodall's work with chimpanzees in the 1960s that taught humanity it wasn't a lone island of intelligence in a sea of soulless animal automatons. Since then we’ve been surprised, amazed, and even surpassed by some of our ingenious animal cousins. 

Meet Kanzi the bonobo.   


The Great Ape Trust has deemed him “the world’s undisputed ape-language superstar.”  He understands over 600 words, many of which he communicates to researchers via a large keyboard.  The keys correspond to various nouns, verbs and adjectives, which the machine then speaks in English, but no key’s symbol is related to the thing it represents.  Kanzi is the first ape to have learned human language simply by observing people, namely his adoptive mother, Dr. Sue Savage-Rumbaugh, who has been his primary teacher and researcher.  He is able not only to identify items and answer simple questions, but to synthesize his own words and phrases from the ones on his keyboard.  To identify pizza, he said, “bread, cheese, tomato,” and when his home-state of Iowa was flooded during a storm he said, “big water.”  Kanzi has been observed collecting and breaking wood for a fire, lighting the fire with matches, and roasting marshmallows.  He’s also an accomplished craftsman.  He learned to make stone knives which are sharp enough to cut leather. 

Altruistic, fermentative, and leavening

What is in bread, beer, and is willing to sacrifice itself to save the others? 
Hint: Altruistic, fermentative, willing to leaven

Wednesday, March 7, 2012

Little Boy Blue and the Man in the Moon

Photo Cred to Kaptain Kobold flickr account

Have you ever gone on a late night stroll and got the eerie feeling that someone was watching you?  As you gaze up into the night sky, you realize the eyes that have been haunting you belong to the "man in the moon."  No matter what time of night or where you are in the world, the "man in the moon" is peering down at you.  Have you ever wondered why?

Oded Aharonson, a professor of planetary science at the California Institute of Technology, has set out to explain exactly why the earth only sees one side of the moon.  As the earth is orbiting around the sun and spinning around its axis, the moon is also orbiting around the earth and spinning around its axis.  It so happens that the moon rotates once around its axis every time it rotates around the earth.  Mere coindidence?  Aharonson and team think not!

Tuesday, March 6, 2012

Eyes Like an Athlete

The portion of athletic prowess that may be innate and the portion that is learned through practice were investigated through a study of the eyes of college baseball players.  The eye movements of eight players and eight college-aged, male non-athletes revealed the players have learned how to track a fast moving object by moving their eyes rather than having better image processing abilities in the eye itself.

Monday, March 5, 2012

Taking a bite out of the emerald ash borer

To combat the destruction of ash trees in North America, scientists suggest the release of three wasps that are native predators to the emerald ash borer (EAB). 

The EAB was first identified in the US in 2002, when people in southern Michigan realized a sudden decrease in ash tree vigor and an increase in the mortality.  Nobody knows for certain how the EAB got into North America but the best guess is that it was present in ash wood cargo that was transported into the US from Russia, China, Japan or Korea. That northeastern region of Asia is the EABs native habitat and although there are ash trees present in this region, they have co-evolved with the EAB to have increased resistance against this beetle.  Over on the other side of the world, North American ash trees (which are pretty hardy specimens against native pests) are left completely defenseless against the introduced EAB.  Since 2002 EAB has spread into 14 states in the upper mid-west and northeast and killed over 60 million ash trees.

In addition to ash trees in northeastern Asia having a greater resistance to EAB there are also several native predators of EABs including three species of parasitic non-stinging wasps: Oobius agrili, Spathius agrili and Tetrastichus planipennisi.  Each of these wasps has a different strategy for feeding on the EAB .  Oobius agrili lays its eggs inside previously laid EAB eggs, then uses the EAB eggs as food to grow to their adult form.  Spathius agrili deposits its eggs on EAB larvae and simultaneously injects a paralyzing venom.  This doesn't make for a very fair fight as it allows Spathius agrili to feed on the EAB larvae without any attempt at victim escape.  Tetrastichus planipennisi also feeds on EAB larvae, but they are the real gladiators: they eat EAB larvae that are alive and active.

O. agrili; All rights reserved to Deborah Miller

S. agrili; All rights reserved to Tracy Ayer
T. planipennisi; All rights reserved to David Cappaert 

Look'd up in perfect silence at the stars, but the stars weren't there.

The Meadville sky at night is a little sickly looking in the space above the parking lots. There are hardly any stars to find in the strange pink haze that stretches across campus and toward a dotted cluster of lights in town. It is 11 PM, and I can still see the dim white outlines of clouds.

That cluster of lights in the distance is a problem. The town, with all its lampposts and security floodlights, casts a continuous glow upward that lingers in the atmosphere and washes out the pitch of nighttime. This loss of darkness is called light pollution, and I’m not the only one noticing it. 

Light pollution creeping up the mountains of the Canary Islands, Spain.
(Significantly prettier than downtown Meadville; sorry Meadville)
Photo credit: Cestomano

Saturday, March 3, 2012

SciArt Link Roundup #5

Robert Oppenheimer leaps for joy --and for
Philippe Halsman's iconic Jump book. 

Happy Leap Week! You've gained an extra day; why not spend it looking at science art?

Friday, March 2, 2012

Here today, gone tomorrow, here again the day after tomorrow

 Australia is, in my opinion, one of the weirdest places on Earth. In the good old Northern Hemisphere, marsupials are a minor annoyance you sometimes squish with your car, while in Australia, marsupials can land you in the hospital. In America, our large mammals stroll sedately across our amber waves of grain; in Australia they bounce across vast deserts. Here in PA, we have solid, dependable native species like earwigs, bumblebees, and ladybugs. Australia contains an insect so massive its nickname is "tree lobster". This insect and another, Nothomyrmecia, both have both played peek-a-boo with scientists over the years, but their discovery stories couldn't be more different.
             In 1918, British soldiers had to crash-land on Howe's island, losing one crewmember to the sea and several black rats to the island. Unfortunately, these rats thrived off of the tree lobsters, and quickly ate them into presumed extinction by 1920. In 1960 though, some climbers on nearby island Ball's Pyramid claimed to have see a few recently dead tree lobsters. As exciting as the reemergence of an extinct species was, it wasn't until 2001 till scientists actually went to look at Balls Pyramid, because the insects are nocturnal and the climb is dangerous at night. Their daring paid off: Nick Carlile and a local ranger found 24 tree lobsters on one bush. After a prolonged fight with the authorities, four were removed to start a breeding program at the Melbourne Zoo which now has over 700 individuals (for the full story of the breeding program's struggles, see here). Now, the triumphant tree lobsters faces trouble from Howe Island residents on its reintroduction. Rats still live on the island, causing concerns that history will just repeat itself. Also, look at these things.
Tree lobster, courtesy of Wikipedia
I wouldn't suddenly want this introduced into my backyard either.
             Nothomyrmecia is a different story. It had a slightly later discovery time, 1931. And discovery is perhaps a generous term: a couple specimens were collected by amateur naturalists in West Australia and shipped off to England, but they didn't bother record their collection site, which was quite a bother when Nothomyrmecia turned out to be a living link in the evolution of ants from wasps.
Nothomyrmecia (courtesy of Wikipedia), kicked out of both the ant and wasp family portraits

In fact, Nothomyrmecia wasn't rediscovered until 1977, when Dr. Bob Taylor launched an expedition to Western Australia in a last-ditch effort to find the ant again. Their truck had mechanical problems and broke down near Poochera, where they were forced to camp for the night. As only a true scientist would in these circumstances, Dr. Taylor did a little insect survey around their campsite that night and found: Nothomyrmecia crawling on a tree trunk, over one hundred miles and 46 years from its original collection site. To this day, Nothomyrmecia have never been seen in Western Australia.
      To me, the most interesting part of these Australian insect stories is the contrast in human involvement. Tree lobsters rose and fell with humans: without us, they would never have been eaten to almost extinction, but nor would their numbers have rebounded through a heroic breeding program effort. In contrast, we wander in and out of Nothmyrmecia's life. We don't even really know where their range is, what their numbers are, or how their population has changed over time, just vaguely that they do exist in Australia.

Eliminating the Annual Flu Shot


Every October signs to remind you to get your annual flu shot pop up in your local drug store.  Each year new vaccine becomes available to offer protection against the seasonal flu bug.  The influenza virus is very good at adapting from year to year, making the previous year's vaccine obsolete.  Because each new year brings a slightly different virus and a slightly different vaccine, you need to get your flu shot each year to prevent infection.  However, a new type of flu vaccine is in the works, and it may eliminate the idea of an annual flu shot.

Vaccines are designed to show your immune system particular germ characteristics .  Once your body recognizes these characteristics as foreign, it can recognize the real thing when being invaded by an actual germ.  The characteristics that are normally targeted for vaccine production are present on the surface of the virus or bacterium.  This is because if the characteristic is on the surface, then it will be easily identified by your immune system.  The only problem is that these are the characteristics that evolve the fastest in viruses and bacteria.  Therefore, the vaccine for last year's flu is now out of date because the virus has changed.  Your body can't identify this year's virus because its surface characteristics are different, so it looks different to your cells.

There are other characteristics that do not change as rapidly, which are the targets for universal vaccines.  A closer look at how we actually respond to flu virus infection showed that our immune cells can respond to more than surface characteristics.  T-cells, a type of white blood cell capable of killing viruses, are able to recognize characteristics associated with internal viral structures.  Because these internal characteristics evolve more slowly, they are also more common among various flu viruses.  A universal vaccine would provide protection for more types of flu virus, and would therefore protect you for a longer span of time.

Now that we know that vaccines can be made to target these internal structures, the next step is to decide which ones become part of the vaccine.  There are different advantages and disadvantages to the various choices, but the options are narrowing with more and more research.  A universal vaccine may be available within the next couple of years. 

Thursday, March 1, 2012

Evolutionary branch tips merge in animal-algae combo-creature

When running with the cross country team here at school, often for an hour or more, it's essential to maintain conversation lest we die of boredom.  Frequently this is done with bizarre, acontextual questions like, "what would be your ideal superpower?"  This question always gets answers along the lines of "invisibility," "flight" and "teleportation," but recently one of the blokes proposed something original and intriguing: photosynthesis.

Imagine - you could go into the wilderness for weeks with no food supplies and be fine; you could sunbathe for dinner!  You would never have to pay for a meal again!  But let's not entertain such frivolous thoughts.  Photosynthesis has always been, and will always be, reserved for plants (and algae and some bacteria), right? 

Of course not.  Why would I be writing this article, then?

Behold, the solar-powered sea slug:

Elysia chlorotica is the first animal known to perform photosynthesis. A single algal meal shortly after birth gives it the chloroplasts it needs to survive for a whole lifetime of about a year with no food at all.