Monday, April 30, 2012

Screeeech on the bridge!

No stroll around Allegheny College's campus would be complete without a visit to the 'rustic bridge'.  Last weekend my parents visited and we were fulfilling this requirement when we were stopped by a tour group listening to the history and legend of the bridge (or rather of the romantic 13th plank).  Instead of barging through and disrupting this magical moment for the prospective students we opted to take a closer look at the trees closest to us.  I am sure glad I did because upon closer inspection we spotted four little, puffy owls trying to catch some shut eye. 

Turns out these small fellas were screech owls, three fledglings and their mother.  And when I say small, I mean it- they appeared to be about as tall as your average banana (about 7 in).  This came as a huge surprise to me without a sense of scale the pictures makes them seem much larger.  Additionally, I haven't seen many owls during the day (and when I did they were always flying by confused) and it was too dark to gauge the size of the few owls I've spotted at night. 

Momma screech

Baby screech- all rights reserved
It is moderately acceptable that I haven't spotted many owls at any time of the day because they are masters of disguise.  Their plumage can take on various overall tones but each of those tones are made up of different complex spots and hues of color.  This coloring provides the perfect camouflage during the day  so that even though humans and animals are constantly walking by their napping site they are not often noticed.  This is also advantageous when it comes to finding a meal.  When the unsuspecting small mammal or bird flies under a screech owls perch it is likely to become dinner before even recognizing its lurking predator.

We were lucky enough to see fledglings because screech owls mate earlier than most other birds.  Few have been fortunate enough to witness the elaborate mating display males put on for females so I was unable to find a video but it sounds pretty neat.  It includes mating calls, head and body bobbing and swiveling AND (if the lady owl is lucky) a slow and deliberate wink that says, "How you doin'?" even better than Joey. 

A last tid-bit on screech owls: surely they must make some dreadful screeching sound that led to their current name... turns out no!  Although they have a variety of calls the most common one is a trill or tremolo.  This somewhat eerie noise is familiar from Maine from Texas.

So there you have it: my last entry provides a little background on the somewhat misnamed screech owl along with the reminder to keep your eyes open!  Countless funky creatures are living in right in your backyard-- go check them out!

Friday, April 27, 2012

The Science of Music. Part 2:

Musical structure resembles the human brain's tendency to make patterns out of sound. Tonal music, like most classical music, establishes a pattern or key that will frame the song then dances around and avoids that key or theme until the end restoring order. The brain desperately desires this structure and constantly tries to recreate this order.

Before that pattern can be desired by the brain, it must play hard to get. Music only excites the brain when it makes the auditory cortex struggle to discover the order. If the pattern is too predictable, the music becomes boring. This is why classical musicians introduce the order at the beginning and are dedicated to avoiding it until the end. The longer we are denied the pattern we expect, the greater the emotional response when that order is restored. Harmony logic is the logic of hide of and seek.

As Leonard Meyer shows in his book Emotion and Meaning in Music, music is defined by its flirtation with and not submission to to expectations of order. Earlier theories of music believed that the emotions we find in music were a result of the way noise refers to real world images and experiences we have previously had. But as Meyer and contemporary neuroscientists argue, the emotions come from the unfolding events of the music itself: the patterns music invokes and then ignores.

"For the human mind, such states of doubt and confusion are abhorrent. When confronted with them, the mind attempts to resolve them into clarity and certainty," wrote Meyer. This nervous anticipation and uncertainty to create feeling. Music makes us uncomfortable and we love it.

Next week I'll get into the biology of the emotional quality of music, primarily its connection with dopamine levels.

Evolution, redefined

If you're reading a biology blog, you're probably aware that Charles Darwin was an important dude, and not just for discovering the plant hormone auxin. He also published the theory of evolution, completely revolutionizing our understanding of the world. However, not until the discovery of DNA and genes was it clear how exactly certain physiological traits could be passed from parent to offspring, and how new traits could emerge through mutations. Now, however, disease-causing particles called prions might be redefining what evolution is and how it works.

Prions are proteins that are usually produced in the human body, but for some reason get misfolded and form aggregates which cause brain tissue to deteriorate. The best-known prion diseases are Mad Cow, Creutzfeld-Jakob, scrapie, and kuru, but there's a prion disease affecting nearly every mammal. Prion diseases are passed by ingesting prion particles. When the normal protein encounters the misfolded prion form, it gets converted into the prion form as well. It's still unclear how exactly this happens, or what causes a previously normal protein to be misfolded into a prion. However, it was previously well-accepted that this prion form was unchangeable. Researchers at Scripps decided to challenge this idea based on a puzzling piece of evidence

They noticed that when you infect mice with a sheep prion, it becomes more virulent over time. An initial spike in virulence from the sheep-to-mouse transfer may have made sense, because it would simply indicate that the mouse brain is more susceptible than the sheep's, but if the prion disease starts killing faster as it infects more mice, this indicates it is adapting to its host to become more successful. So, they decided to test that idea by exposing prions to different conditions and selective pressures, to see if certain variants were more prominent in one situation versus another.

Sure enough, researchers found that different prion particles were present in brain cells versus cell cultures, and that they could get the predominant type to switch if they transferred prions from brain to culture or culture to brain. Also, they exposed prion-infected cells to swainsonine, a compound previously found to have prion-control properties, and found that a drug-resistant form of the prion quickly became the major component of the population. Removing swainsonine returned the population to being mostly susceptible, with less than 1% resistant prions.

The head of the study, Dr. Weissmann, thinks this will have important treatment applications. Because they thought prions couldn't mutate and evolve, the key was going to be finding some way to target the prion and leave the normal, non-problematic cell protein alone. But, if prions can evolve, it's likely that any treatment blocking or removing prions is going to quickly become ineffective, because prion particles resistant to it will quickly take over the population. Instead, Weissmann thinks we should be focusing on finding ways to remove the normal protein from cells, because without a normal protein to convert, the prions will be unable to form large aggregates and cause problems.

Regardless how prion treatments end up looking, it is highly interesting that our ideas of evolution have, once again, expanded. We've been incorrect about a lot of accepted ideas about evolution, for example "silent" mutations. Silent mutations are when there's a mutation, but it doesn't change the protein's building blocks at all, so the rationale was that there was no way that could affect fitness if the protein was the same. However, it turns out that some codes for building blocks are preferable and faster for an organism to make than others, and faster protein assembly may be an advantage. Now, it turns out we might be wrong that the only way a mutation can be passed on is through genetic material, because prions can evolve to fit their environmental conditions better and can pass this along to other members of the population despite being only protein.

Thursday, April 26, 2012

Poop and Destiny

I thought it fitting to spend my last post on this sciencey blog discussing a topic that I first discovered through one of my favorite science communicators, Stephen Jay Gould.  The topic, fitting or not depending on your opinion of my posts, happens to be… guano.  Bird poo.  So come along! 

The species I’d like to discuss is one you may have heard of.  If you have, it’s a name you’re not likely to forget: the Blue-Footed Booby.   

It just fully occurred to me where this post is going, and I’m not sure that I like it.  My apprehension comes not from the mention of “poo” or “Booby,” as you might expect, but rather from the dismal conclusion that could easily be drawn.  Alas, as Dana would attest, writing is about taking leaps, and so I take one now.  I hope to leave you with the notion that nature is both wondrous in its balance and economy, and utterly without human passions, despite what we might hope. 

If you travel to the Galapagos Islands, Blue-Footed Boobies will be among the most obvious of the animals you see.  Not only do they possess, as their name implies, a fairly striking natural pedicure, but many of them seem to be sitting on the bulls-eyes of big, white targets.  Further inspection will reveal that the volcanic landscape has not been modified by a rogue line-painter into some bizarre sporting arena.  Rather, the birds have made the rings themselves – by spraying guano in all directions! 

"This is embarrassing."

The “guano rings,” as it turns out, are part of the homes of these ground-nesting birds.  Each mother sits inside her ring, placidly warming her chicks, apparently oblivious to the gawking tourists who snap photographs mere feet from her face.  When Gould was in the Galapagos, he was surprised enough by the Booby behavior that he decided to do a bit of “research.”  He approached a nest with caution, inching toward the circle while the mother stared into space.  Eventually, he toed the line.  Still no response.  Finally, as his toe moved imperceptibly forward, it reached an invisible line within the circle.  The reaction was immediate: frantic squawking, flapping and pecking.  Every time he repeated the toe experiment the same thing would happen. 

The Boobies operate on a very simple strategy of nest protection: if something lies inside the nest, nurture it.  If it is outside, ignore it.   If it crosses the line, attack.  Unfortunately, this applies even to a bird’s own chicks, which have been observed cheeping helplessly mere inches from a guano ring as their mother sits proudly atop the rest of her clutch.  People who have seen such things are incredulous.  How could she be so cruel?  So Stupid?  They want to put the chick back in the nest, but it is forbidden – things in nature tend to happen for a reason. 

A mother Booby lays between one and three eggs per clutch, one-at-a-time.  They hatch in the order that they are laid, so that the oldest is always biggest.  Often, the mother raises all of her chicks to adulthood without a hitch.  Occasionally though, and this is where the post takes a turn for the appalling, the first-born chick will push his or her younger siblings out of the nest, across the short expanse of rock, and over the invisible line, condemning them to death.  The mother will continue to raise the first-born.  She will pay the others no mind at all. 

When I hear things like this, I feel a physical pain in my gut.  The suffering of little, fuzzy creatures is the worst thing I can imagine.  But the world beyond humanity does not share my concepts of justice, good and evil, right and wrong.  The oldest Booby is not a psychopath; his mother is not deranged.  They are two hungry birds in an environment that does not contain enough food to support two or three nestlings, so one of them does what must be done to prevent the death of the entire clutch.   

I admit I hadn’t intended to leave you with such a sobering meditation on the apathy of nature.  Truth be told, I was hoping to make some poop jokes and leave you with a laugh or two.  Alas, what’s done is done.  Besides, it’s sometimes valuable to remember that life isn’t fair.  It helps us to cope when things go wrong in our personal lives.  It also makes watching that chase scene from Planet Earth a little more bearable.  In any case, I hope you’ve enjoyed this Bio 490 project or ours, and I’m sure many of us hope to keep blogging in the future.  Thanks for reading.

New Genetics

Literature classes can teach students to read between the lines, to understand how prose is built beyond the simple linking of nouns and verbs.  The same critical reading skills are required for geneticists to understand how the genome is more than just a long string of letters called DNA.  Rather than reading between the lines, geneticists read above the line in an emerging field called Epigenetics.

To keep a thread from becoming a knotted mess, a seamstress keeps the strands wrapped around a single, large spool.  To keep DNA from becoming tangled, cells wrap the DNA strand around proteins called histones.  Rather than using one large spool, cells wrap the DNA around multiple histones creating a beaded necklace, with histones as the beads and DNA as the chain.  Those histones are more than just simple spools or decorative beads, though.  The structure of those proteins can be altered through the addition and removal of certain chemical groups.  The presence or absence of these alterations is referred to as the epigenetic code because it is genetic information contained "above" the DNA sequence.  Alterations change which portions of the DNA are easily accessible by the cell and which portions are too tightly wrapped up for the cell to read.  If the cell cannot read, or can too easily read, certain portions of the DNA, then the way the cell uses information written on that portion of DNA will change.

Alterations of histone proteins occur at any stage of an individual's life.  Investigating what sorts of stimuli can create those changes and characterizing the results of those changes is the pursuit of Epigenetics.  Research investigating the role of exposure to environmental toxins during gestation has previously indicated that a component of anti-stick coatings like Teflon is correlated with increased rates of obesity in those children when they become adults.  A separate study linked exposure to that same environmental toxin to changes in the histone modifications of newborn infants.  Additionally, resent research indicates the diet and chemical exposure of mothers before and during pregnancy can alter the epigenetic sequence of her offspring, thereby increasing her children's changes of being diagnosed with obesity-related diabetes.  Combining studies of the health effects of environmental toxins with studies of the epigenetic changes caused by those toxins may help investigators explain why certain toxins have certain effects.

Other elusive biological questions of interest to Epigeneticists include why inheriting a certain gene from one parent rather than the other can produce different effects, the causes of diseases including schizophrenia and colon cancer, and why identical twins are not perfectly identical.

Wednesday, April 25, 2012

Misfolded Proteins

Proteins are present throughout our bodies and are involved in virtually every cell function.  Proteins enable movement by allowing muscle contraction, speed up chemical reactions, and defend against foreign cells.  Proteins are made up of a chain of compounds called amino acids, which interact with each other in a specific way causing the amino acid chain to fold.  The folding of a protein is essential for its function.  However if the protein isn't folded correctly, then they can be destructive to our bodies.  For instance, Huntington's disease, Alzheimer's disease, type 2 diabetes, sickle cell disease and prion disease are all proteopathies, or diseases caused by protein misfolding.

What if these incorrectly folded proteins were capable of replicating themselves to further damage the body?  Well prions do just that.  Prions are defined as infectious agents comprised of a misfolded protein.  Unlike other disease-causing agents like viruses and bacteria, prions contain no genetic material (DNA or RNA); however, they have the ability to convert properly folded proteins into incorrectly folded one like themselves.  The improperly folded proteins then accumulate in tissue causing tissue damage and cell death.  This chain reaction occurs in prion diseases like mad cow disease and its human counterpart, Creutzfeldt-Jakob disease (CJD), the degenerative neurological disorder.

Prion diseases have always been considered untreatable because it is difficult to target these misfolded protein because proteins are all throughout our bodies.  A recent study published in the Journal of Biological Chemistry this month found a way to inhibit their ability to produce more prions.  They used luminescent conjugated polymers (LCPs) to detect the presence of prions in mice brains.  However, they noticed that the number of prions, toxicity, and infectibility decreased in the process.  Most likely, the interaction with the LCP's stabilizes the prions, inhibiting their propagation.  However, LCP's contain many chemical subgroups.  When eight different subgroups were tested, all of them had significant decrease in the toxicity of the prions.

These results are the first that provide the possibility of treating prion diseases.  Also if the LCP's can interact with other misfolded proteins that cause other proteopathies, then the application of these results may be applied to other diseases, like Alzheimer's disease and Huntington's disease.    

Read more about this research here.

Mad Cow Disease in the U.S.

A random test has demonstrated that mad cow disease has infected a cow in California.  This is the first case (out of four, total) of the disease in the United States since 2006 in Alabama.  South Korea, an importer of U.S. beef, is not pleased

Mad cow disease is officially known as Bovine Spongiform Encephalopathy (BSE).  BSE outbreaks in the past have been attribute to feeding cows, which are natural herbivores, with supplements that include the meat and litter of other animals - including cattle. 

BSE is the result of proteins, called prions, becoming misshapen and resistant to degradation.  There are normally prions in the brain, deemed PrP-sen, that do not cause harmful symptoms.  The "broken" prions that cause disease are called PrP-res, for "resistant."  When a PrP-res is passed to a healthy organism, it comes in contact with PrP-sen, and converts the PrP-sen into the dangerous PrP-res.  As the number of PrP-sen grows, the bad prions tend to cluster together, forming amyloid fibers.  The amyloid fibers kill surrounding cells.  As the dead cells are digested, substantial holes are left in the brain, to the detriment of the organism.  Eventually, it will lead to loss of control of the body (ataxia), and subsequent death.

A timeline and explanation regarding prion-based disease can be found here.

Prion diseases like BSE (or the human manifestation called Creutzfeldt-Jakob disease) are incurable once a person is infected with a PrP-res.  As well, due to the nature of PrP-res being a protein and not a living pathogen, meat from a BSE cow cannot be destroyed by heating it. 

Luckily, 40,000 cows per year are selected for BSE checks.  Hopefully, this is the only current case of BSE, and it can be taken care of effeciently.

SciArt Saturday Talks to the Artists

The last SciArt Saturday post went live this past week, and now there's a moment to reflect. 

I only began thinking about the similarities between science and art about a year ago in the middle of a genetics lecture, when I first saw images of the Brainbow --a fluorescent, microscopic imaging technique used to visualize neuron arrangement in brain tissue. I don't remember much of the lecture after that (sorry, Dr. Hersh); I was too busy making notes to learn how cells could be made to appear like beautiful splatters of red, blue and yellow paint across the projector screen. Since that day, I've made it a point to promote the overlap that exists between the two disciplines. And this week I'll be introducing you to others who try to do the same, as I interview artists whose work has appeared in the SciArt Link Roundups.

Today, we meet Nicole Wong, a scientific illustration graduate student at Cal State University, Monterey Bay. SciArt Saturday featured a link to her illustrations earlier this year. Nicole kindly agreed to answer a few questions for The Factual Enquirer about her experiences.  

Southern alligator lizard (Elgaria multicarinata), acrylic
by Nicole Wong

Monday, April 23, 2012

The dangers of a stone-faced fish

I don't know about you but I am always drawn in by those "Top 10 Most [insert adjective and genre]" articles/TV shows. I was recently reading one of these flashy stories on the 10 Scariest Sea Creatures when I came across an animal I had never heard of-- the stonefish, which held its own at spot number eight.

All rights reserved to Erik Schlogl
All rights reserved to Bill and Mark Bell
Although this beauty may soon be in the running for the "Top 10 Ugliest Sea Beings", its claim to scare stems from its powerful venom.  The venom contains a neurotoxin that makes the stonefish the most venomous fish in the world, hence earning it a spot in the countdown.  If a human steps on a stonefish, the venom will be injected from the spines on the back of the fish (difficult to see above) into the foot.  The amount injected will depend on the applied pressure of the unsuspecting and unfortunate being.  Once injected, the venom is known to rapidly cause paralysis and extreme pain; however, it is rarely fatal.  That being said, some victims say the pain is so great that they would rather their affected limb be amputated that cope with it!

Australia has developed an anti-venom to the stonefish venom that can substantially decrease pain and risk of paralysis.  But due to the chance of a severe allergic, or anaphylactic, reaction the anti-venom is only administered in serious cases of injury.

The stonefish may look like something that would only grow on the Flying Dutchman (and match Davy's permanent frown) but it is able live in shallow tropical marine waters throughout the Pacific and Indian Oceans, especially near coral reefs.  It's natural camouflage makes fellow sea creatures and humans enjoying a little R&R blind to its presence rocky habitats.  *Note that the picture above on the right has been removed from its natural habitat to make it's appearance clearer- the picture on the left is a better illustration of what a stonefish can look like in nature.

The best way to protect yourself against these elusive creatures is to wear water shoes, preferably with thick soles, whenever parading around tropical marine areas.  You may miss feeling the water tickling your toes as you scuba dive or snorkel but losing that seems a heck of a lot better than the extreme pain of a stonefish stab.  And believe me, there are tons of other marine beings that are bound to ruin your vacation if you step on them.  If curious check out another "Top 10" here....

That being said, do NOT stop vacationing to tropical islands!  They are gorgeous and often have extremely interesting wildlife. This post was written simply to inform people so they may recognize what creatures actually live in that big blue watery road and protect themselves from some of their dangers.

Sunday, April 22, 2012

Henry David Thoreau and climate change research

Henry David Thoreau, America's original hippie responsible for writings like Walden created primarily to torture high school English classes, was once criticized by his mentor Ralph Waldo Emerson for his lack of ambition and failing to use his intelligence for the greater good. Where Emerson alive now, he might be pleasantly surprised to discover that one of Thoreau's quirks is helping determine the effects of climate change.

As the Smithsonian reports, Thoreau was known for his obsession with plants and migratory birds and their public signalling of spring's arrival. He kept detailed records on over 600 different species of plants, running four to five miles a day to check on a single flower and its blooming time. These records languished in obscurity even long after Thoreau's other works such as Walden gained in popularity. Then, Dr. Primack of Boston University recognized these records' value for demonstrating the effects of climate change.

Upon investigation of the records, made difficult by Thoreau's focus on the beauty of nature and not so much the beauty of his own penmanship, along with collection of current flowering and migratory bird data, Primack and his graduate student Miller-Rushing determined that many native plants are flowering on average three weeks earlier than they did in the 1850s, when Thoreau was collecting his data. Flowering times got earlier with increasing temperature, but bird migration times were not nearly as temperature sensitive.

This is potentially alarming, because spring is a delicate balance between plants flowering, pollinators emerging, and birds carrying seeds at the right times. If plants are changing more in response to climate change than their pollinators or birds, they might be unsuccessful getting pollinated, leading to a loss of biodiversity.

Thoreau really only collected this out of personal interest. He was viewed as an oddity for this meticulous record keeping of seemingly useless information. I can only hope that someday, my pointless hobbies are just as useful.

Saturday, April 21, 2012

SciArt Link Roundup: The Last

Good things come in dozens: flowers, cookies. SciArt Link Roundups.

SciArt Saturday is finally calling it quits in preparation for finals week over here on campus (pay no attention to that girl behind the curtain, because she needs to study study study).

I'm pulling out the big guns, though, for a series of reflection pieces slated for the beginning of next week; I'll be talking to some of my favorite SciArt Saturday artists about their work. Be sure to check back for those soon!

In the mean time, click below to enjoy the last gathering of pretty science things.

Thursday, April 19, 2012

The birds and the bees, for bees

Sex-determination is simple: omitting errors, everyone gets an X chromosome from their mom.  Dad supplies either an X or Y, which makes you either a male or a female, respectively.  End of story… unless you’re not a mammal or a fruit fly or a ginkgo tree (or a few other things).  

Indeed, most of the living world does not share our determination of sex.  In fact, the largest order of insects, which themselves make up a vast proportion of all living things, operates on a sex-determination system wholly foreign to us.  Hymenoptera (ants, bees and wasps) are haplodiploid, meaning some members are diploid, like us, and have two full sets of chromosomes (one from the mother and one from the father), while the rest are haploid and have only one set of chromosomes.   

Here’s how it works:  a male drone fertilizes a female, which becomes a queen.  The queen establishes a colony in one of many possible ways.  Winter becomes spring, spring becomes summer, summer changes back into winter, and winter gives spring and summer a miss and goes straight into autumn.   

Eventually a mature colony is formed.  For utility’s sake, here’s where I’ll begin in earnest.  In a mature colony, the queen mates rarely and stores sperm for long periods of time.  Meanwhile, she constantly produces eggs, sometimes fertilizing them, sometimes not.  Fertilized eggs receive half of her DNA and half of the father’s.  These invariably become females.  Unfertilized eggs still develop into fully functional ants, bees or wasps,  but only contain one set of maternal DNA.  These become the males, known as drones. 

It is the job of drones to fertilize potential queens.  Typically, the meeting of the two occurs away from the hive or colony, and afterward the queen leaves to start anew.  Thus, one queen usually inhabits a hive, and all the workers (female), future queens (female) and drones (male) are her offspring.  Drones and queens get to mate, but workers do not.  Rather, they slave their lives away in service to the queen, living and dying with no hope of passing on their genes. This raises questions in the face of Darwinian evolutionary understanding:  how could such a system evolve?  Why would workers be willing to sacrifice their lives to the queen, in perfect altruism, against the prospect of their own procreation? 

The answer lies in the subtlety of hive-interrelatedness.  Consider the following: 

Males have only one set of chromosomes to contribute when they mate, so they pass on 100% of their DNA to female offspring.  Females, on the other hand, have two sets of chromosomes, so 50% of their DNA passes on to daughters and 50% to sons.  Whether the queen produces daughters or sons, there will be a shared gene proportion of ½ between mother and offspring. 

Now, consider the shared gene proportion between sisters.  Any female Hymenopteran will have 100% of her father’s genes and 50% of her mother’s DNA.  So will her sisters (because most of the time all hive members are of the same parents).  The total relationship between sisters is then the average between 100% and 50%, or 75%.  This means sisters are more closely related to each other than they are to their mother or to any potential offspring.  It is therefore in the best interest of a worker to aid her mother in the production of sisters.  Although she cannot directly transmit her genes to offspring, they can be passed on even more effectively through the success of the queen and of the colony.

In parting, I offer you this image of a wasp wearing a parka, courtesy of

My sister got it for me!

Health and Psychological Benefits of Yoga

The majority of yoga practitioners will attest to the health benefits that it can bring.  Engaging in the physical and mental aspects of the practice can lead to a lower heart rate, increased flexibility and strength, among other advantages that accompany the simple enjoyment of practice.

Yoga has been practiced in times dating back to ancient India. By its sustained popularity alone, it is evident that it has had some profound affect on the health and livelihood of people for quite some time.  Recent studies have demonstrated that yoga can alleviate the symptoms of mental health disorders like anxiety, depression, obsessive-compulsive disorder, and even post-traumatic stress disorder.

An especially interesting case of healing through yoga practice lies in a small population of incarcerated individuals from Washington.  In the journal Psychology of Addictive Behaviors, a study was recently published highlighting the profound affect of meditation and yoga on convicts who had addictions to drugs, including crack cocaine, and/or alcohol and marijuana.  Prison workers had found that typical drug recovery programs were majorly ineffective.  Most addicts tended to resume their drug habits after leaving jail, often perpetuating the incarceration cycle. 

Noting that the current system did not work well, prison officials and a group from the University of Washington instead decided to implement a yoga and meditation program for the recovering addicts.  The program encouraged mindfulness and harnessing one's ability to focus.  Physical exercise was also part of the yoga practice, adding to the newly-found healthy lifestyle.

After the program, the incarcerated population reported decreased negative psychiatric symptoms and enhanced "psychosocial" interactions.  As well, after being released from the prison, the program participants significantly maintained the drug-free habits.

Wednesday, April 18, 2012

Aliens of the Sea

Photo cred:  Flickr account

So much effort and time has gone into space exploration and the search for extraterrestrial life.  However, there is still so much left to be explored on our earth alone.  One extraordinary organism found in the tropical-to-temperate waters of the Atlantic, Pacific, and Indian Oceans is the barreleye or "spook" fish.

With their clear heads exposing their bright green lenses and their black olfactory organs (nostrils), these fish do appear quite spooky!  Barrelfish inhabit the ocean at moderate depths from 400 to 2,500 meters deep, just below the limit of light penetration.  As an adaptation to the limited light source, barreleyes have distinct transparent heads.  Their clear domes allow more light to reach their telescoping eyes, which protrude from their skulls.  Their eyes are thought to mostly point upwards to allow them to detect any prey in the water above.  However when they do spot food, they can rotate their eyes forward so they can coordinate their attack with their toothless mouths.  Although barreleye fish have a rather large field of vision, they can really only detect the silhouettes of their prey because the retinas in their eyes consist of only rod cells and not cone cells.  This is because rods are responsible for detecting images in low lighting and cones operated under high lighting and detect color.    

Not only is this creature's transparent dome useful for viewing objects above it, but it also most likely protects it from the stinging cells of siphonophores, the organism it scavenges food from.  Colonies of siphonophores look similar to jellyfish, and their tentacles house food that the barrelfish can easily steal.

Their unique eyes and transparent dome are obviously a clever product of evolution.  Even though these creatures were first identified in 1939, their mysterious clear heads were not noted until much later because when brought to the surface, their fragile domes collapsed.  If new information is being discovered on identified and new organisms frequently, then one can only imagine what else our Earth holds to uncover!

Watch the video of a live barrelfish below!
Or for more information visit the website here!

An old, familiar sound.

It's a beautiful afternoon-turn-evening, and I'm sitting inside my dorm missing my old blues records. I'd like to hope that even when I grow old enough to forget everything I've learned about cell cycles and photosynthesis, those riffs will still be a soft, familiar hum in my head.

I stumbled today upon the story of Henry Dryer, a 92-year-old dementia patient who lights up after hearing songs from his youth. Music seems to jog the memory in a special way, which allows caretakers to create personalized iPod playlists for Alzheimer patients.

You can watch a clip from the documentary Alive Inside below. Oliver Sacks makes an appearance; Sacks wrote a book about the connection between neuroscience and music just a few years ago.

The remarkable part comes when Henry's caretaker removes his headphones, and Henry remains aware enough to speak briefly about how music affects him. He mentions his favorite singer: Cab Calloway. Between thoughts, he begins to sing Calloway's scat; it's a sweet moment to witness.

Henry's story reminded me also of Floyd Skloot's The Melody Lingers On --published in the Southwest Review back in 2002 --about Skloot's mother who remembers little except for the old melodies she joyfully hums to her son. If you can track down a copy, I highly recommend it.

Alive Inside premiered today in New York City, and it will continue showing through this weekend. If you're in the area, it seems worth checking out.

Bacterial Card Games

Outsourcing as an economic strategy usually reduces costs for a company, making it a strategic business move.  Certain species of bacteria may be next in line for open CEO positions at Fortune 500 companies due to their mastering of this outsourcing technique.  The resume of these organisms was summarized in a March 2012 publication in mBio.

The authors of the recent paper describe this outsourcing technique through a card game analogy, specifically Hearts.  Due to the rules of the game, the black Queen of Spades is usually a card that Hearts players wish to avoid holding.  The authors describe a situation in which performing a particular function is something bacteria wish to avoid.  Species that continue to perform this function are called helpers and species who profit from the help are called beneficiaries.

Tuesday, April 17, 2012

An infinite vacation

Photo credit: thebadastronomer

How would you like to vacation in a land that couldn’t be seen with the naked eye? A land in which no color escaped, time was warped, and that made you suddenly look like the contents in that tube of toothpaste at the bottom of your suitcase?
I couldn’t understand why the Huffington Post would run such an article, “What would happen if you fell into a black hole” but soon found myself equally as interested as the “so many people” that wonder what it would be like to visit one.

Monday, April 16, 2012

How are science and poetry alike? Let me count the ways.

Today's medical students are a busy group. I imagine that most of them spend their spare moments (if such things exist) sleeping and relaxing and definitely not studying Byron, Milton, and Spenser. These students would probably weep if I told them that two centuries ago, young surgeon-in-training John Keats somehow found enough free time to become one of the greatest poets England has ever known before the age of 25.

John Keats, thinking about what
slackers you all are. 

But Keats was bitter about his day job. He expressed his frustration at the "cold philosophy" of science and medicine in his poems:

...Do not all charms fly 
At the mere touch of cold philosophy?
There was an awful rainbow once in heaven:
We know her woof, her texture; she is given
In the dull catalogue of common things. 
Philosophy will clip an Angel's wings,
Conquer all mysteries by rule and line, 
Empty the haunted air, and the gnomed mine --
Unweave a rainbow, as it erewhile made
The tender-person'd Lamia melt into a shade. 

To Keats, science is a prism that "unweaves the rainbow" into lifeless, mechanistic wavelengths, which is to say that science and beauty are made of different stuff. If you've been following this blog for any length of time, you already know that I take issue with that sentiment.

Ancient Nubians, Antibiotics and Beer

You may have heard that among the many talents of ancient peoples was the art of brewing beer.  What you might not know is that an ancient Nubian brew appears to have the ability to fight off bacterial infections.  That's right, antibiotics in beer.
Courtesy of Meganhassler
Bioanthropologist George Armelagos made his way to this discovery by first noting the presence of the antibiotic tetracycline in Nubian skeletons from 350-550 A.D.  Collaboration with the medical chemist Mark Nelson led to the conclusion that tetracycline was not merely present in Nubian bones, but their bones were chock-full of tetracycline.

Tetracycline is produced by bacteria in the Streptomyces genusIt is an antibiotic, which means that Streptomyces produces it for defense from its more pathogenic compatriots.  Antibiotics in humans have the same role as they're used to kill pathogenic bacteria.  About two-thirds of the naturally-derived antibiotics used in medicine today come from Streptomyces, including tetracycline which is currently used as a treatment for skin, genitial, urinary and digestive infections. Assumedly it would have prevented against similar infections in ancient times.

Saturday, April 14, 2012

Science Art Link Roundup #11

Another quick dose of science art for your weekend enjoyment. 

Gender parties: soon to be obsolete?

Back in the good old medieval days, queens had one job: producing heirs, which meant sons. Sons were so important that King Henry invented charges of treason against his second wife, the infamous Anne Boleyn, because she couldn't produce a son. With the discovery of DNA and the Y chromosome, it became clear that Henry had no one to blame but himself: because males have both an X and a Y chromosome, the sperm determines the sex of the child. Females are XX, and thus can only donate an X chromosome to the egg. A very tidy explanation with much vindication for poor Anne Boleyn, but is sperm the whole story?

A recent study from the UK showed that women who had higher caloric intake around the time of conception are more likely to have boys than girls. This sex bias based on environmental conditions has been reported in many other animals, including mammals like horses and cows, but this the first report of it in humans. Granted, it is not a huge difference: 56% of the high calorie group had boys, versus 45% of the low calorie group. The article also does not say if this is a statistically significant result.

I find this interesting because they don't know how it works. Obviously, the male determines the actual sex of the baby, but the mother's womb can favor the development of one sex of fetus over another. Researchers knew from in vitro fertilization treatments that high glucose (simple sugar) levels favors male fetus development and discourages female development, so that might be a link. Fortunately, if they really want to look into the mechanism, human studies will probably be unnecessary. Many mammals change the male: female ratio based on the environment.

Basically, males are a risky evolutionary bet. They can produce more offspring if females are in ample supply, but if there are more males than females, only the best males will reproduce and the rest are left without offspring. Females have a more limited reproductive capacity, but can basically always reproduce (it's just not that hard to find a willing male). So, if the environmental conditions are good, say by having ample food supply, a male child is more likely to grow up strong, fit, and ready to spread some genes around. If there is a low food supply, males are less likely to be successful, and females are a safer bet.

Personally, I'm quite excited to see what the results of a more detailed study are. The glucose explanation makes sense, but how does the uterus determine what chromosomes a fertilized egg contains? Also, 56% is not a large difference, so is this result "real" and what other studies will be done to confirm that?

Linking Exercise and Mutation Rate

Dendrobatidae are a family of frogs, commonly known as poison dart frogs.  They are most famous for their brightly colored skin and toxic secretions.  However, researchers have recently discovered an interesting new quality in these frogs.  The more physically active species of Dendrobatidae accumulate changes to their genetic information faster than frogs species that are less active.

These different species are defined by the fact that they interbreed and are able to produce normally functioning offspring.  The idea that more active cold-blooded animal species would experience faster changing genomes is not new.  Studies in the past have not been able to support this hypothesis; however, they all studied animals while they are resting.  A new study conducted by Juan C. Santos tested animals during periods of activity comparable to activity they would perform in nature.

The study subjected about 50 different frog species to physical exercise (running for four minutes).  Then, their oxygen uptake was measured and compared across the different species.  The results showed that the more active species had a higher oxygen capacity.  They were able to use their oxygen more effectively during the aerobic activity.

He then compared 15 different genes from the different frog species and created a poison dart frog family tree.  This tree showed that more active frog species experienced faster changes in these genes.  One hypothesis for this rate of change difference is that exercise releases molecules that are likely to mutate DNA.  These molecules (called reactive oxygen species) are mainly given off when the body has stopped its physical activity and circulation and oxygen levels are returning to normal.  However, the true mechanism for this difference in mutation rate remains unknown.

Friday, April 13, 2012

The Science of Music. Part One: The Ear

Music moves in waves. Those waves flow through the outer ear [E] and crash up against our eardrum forcing the tiniest three bones in our body to move. These bones are located in the middle ear [M] and press against the fluid-filled membrane of the cochlea, which makes up the bulk of the inner ear [I]. As these bones rock to the beat, their vibrations transfer to waves of salty liquid in the cochlea. 

Photo credit:
Cross section of the ear divided into three regions: [E] the outer ear, [M] the middle ear and [I] the inner ear.
Under these waves, hair cells (so named because they look like microscopic bristles) dance back and forth. This minute movement opens ion channels causing certain cells to swell with electric charges. If the cells are bent at a sharp enough angle for long enough they fire an electrical message onward to the brain. Thus, silence is broken and sound has begun.

The cochlea contains 16,000 neurons. In the noisy day-to-day, they are in fact constantly bent since the air is full of vibrations and every one reverberates inside the echo chamber of the ear. But how exactly do we make sense of the musical cacophony that is constantly assaulting these little hairs in our head?

Thursday, April 12, 2012

Tips from the pros (and almost pros)

We've been talking a lot in our workshop sessions about narrative--choosing a clear story to tell, and ensuring that what you've written tells that story, whether it's about a person (and their scientific life) or an idea, or an experiment.

Carl Zimmer recently shared his thoughts on story, editing, and blogging as they relate to science writing. Avoiding jargon and capturing your readers' attention are critical, according to Ed Yong, who highlights effective writing examples, including one from Zimmer.

If you're in the UK, you can put these suggestions into practice, submitting something to the Wellcome Trust Science Writing Prize 2012 (800 words, due April 25th, 2012). If you're not in the UK, though, you'll have to be content browsing the shortlisted articles and winners of last year's contest for inspiration...

The sky: not as empty as it looks

Rainbows are so commonplace and are known so universally that they barely even elicit awe these days.  Sure, there was that guy on youtube who got pretty excited about one, but that was a double rainbow, for Pete’s sake.  Have we reached the point as a humanity where we need multiple rainbows just to pause Angry Birds and look out on a sunny day once in a while?  I’ll bet you’d look up if this was in the sky:

Wednesday, April 11, 2012

Disgruntled Astronauts & Grumpy Bloggers, Concerning the Equal Time Rule

Persistent debate surrounds the topic of climate change.  At this point, it is widely accepted among scientists and the general public that green house gas levels in the atmosphere have increased, which has affected the climate.  The debate lies in whether humans have had a hand in driving climate change, or whether it is purely a natural change in the Earth's atmospheric composition, or some combination of both.  

Just today, the Huffington Post published an article in which ex-Astronauts challenged the legitimacy of NASA's climate science.  The ex-Astronauts conjecture that NASA's claim that humans contributed to climate change "are not substantiated."  David Freeman, the author of the article, ends the article with a question;  "Is NASA pushing 'unsettled science' on global warming?"

A blogger from Grist (the well-known, notoriously environmentalist, online magazine) responded to HuffPo's article with a critique and a touch of sass.  The blogger, David Roberts, not only disagreed with ex-astronauts' critiques, but labeled the writer as a poor science communicator.

Personally, I found both of these articles to be a slightly irritating.  The HuffPo one challenged whether humans contributed to climate change.  I am tired of this argument because I do not understand the purpose of it.   If we discover that all of the green house gases expelled from human activity into the atmosphere does not, in fact, lead to climate change, what does this prove?  Does it mean, then, that fossil fuels are harmless and should be the main source of fuel forever?  To me, it is evident that we should transition into a society that relies upon less-polluting energy sources, for reasons beyond the impact on the climate.  So, this argument, to me, is becoming tireless, pointless, and is difficult to "prove" either way.

The Grist response by Roberts used unsophisticated conduct while aggressively disagreeing with HuffPo for publishing an article that questioned the human component to global warming.  This made it tedious to read; however, he did make a valuable (albeit vague) point.  A journalist has a responsibility to determine what deserves equal time in an article by doing sufficient background research.  In this case, the HuffPo journalist questioned the legitimacy of NASA's climate science research based on skepticism by a single group and spread this skepticism to his audience.  

Roberts responded as such:

(Freeman, Huffington Post):  What do you think? Is NASA pushing “unsettled science” on global warming?
"Uh. David. I mean no insult to Huffington Post readers when I say that they are probably not the best arbiters of this question. Instead, you might consult, oh, any science academy from any country in the world."

Despite his uncouth demeanor, I agree with Roberts.  There are certainly sources of information that could be consulted to resolve the issue with the ex-Astronauts without planting another seed of uncertainty in the general public mind regarding climate change.

The Ashley Treatment

In January of 2007, a controversial treatment for severely disabled children arose.  This treatment is known as the Ashley treatment, named after the young girl to first undergo this treatment.

Ashley, now 14, was born with a developmental disabilities that has left her unable to walk, speak, and with the cognition of an infant.  Ashley's cognitive ability is expected to remain the same for the rest of her life.  Her parents, concerned with Ashley's quality of life, devised a treatment with doctors at Seattle children's hospital.

In 2006, Ashley underwent surgery to remove her nascent breast buds and a hysterectomy in order to avoid the discomfort of fully developed breasts and menstruation.  She then received high doses of estrogen to induce the closure of her growth plates and halt her growing.  This treatment was developed to improve Ashley's quality of life; her small size will better enable her parents to provide her the care that she needs.  Ashley is now "frozen" in the nine-year old body when she received the treatment.

Tuesday, April 10, 2012