Thursday, December 31, 2015

2015: A Quick Recap



2015 was a terrific year for THE ‘SCOPE! We showed you some of the science behind The Martian, The Avengers, Star Wars, and the Last Man On Earth. We tackled monsters as well as superheroes. We had a series on Star Trek tech that is becoming reality. We discussed the science of love, pop music, vaccination, near death experiences, and – of course – competitive eating. We brought you up to speed on allergies, CRISPR, cancer, the microbiome, giant viruses, a beetle that eats nothing but coffee, and much more. We amassed over 107,000 pageviews and look forward to reaching more eyes in 2016. Thanks to all of our hard-working contributors:  Mark Lasbury, Julia van Rensburg, Sarah Deffit, Don Byrd, and Jason Organ.

If you are interested in contributing to THE 'SCOPE, please email us.

Tuesday, December 15, 2015

Wookiees Are Primates. Or Are We Barking Up The Wrong Tree?

The latest installment in the Star Wars franchise, The Force Awakens, opens on December 18, and is expected to be the movie event of the year! To get the hype machine running at hyper speed, the merchandizing onslaught has begun. New Star Wars merchandise is everywhere: lightsabers, bed sheets, shower curtains, action figures, r/c droids, breakfast cereals, flamethrowers (okay… no flamethrowers).


My personal favorite is the menu of Star Wars-themed sandwiches sold by a local food truck, including the ever-so-delectable Chuebakka. And as I sat eating my Chuebakka for lunch, I couldn’t help wonder – as only a science geek would – if Chewbacca would eat this sandwich in the same way that I do.

Chewbacca meets the "Chuebakka"
Chewbacca is a wookiee from the jungle planet Kashyyyk. Wookiees are known for their high intelligence, brute strength, unwavering loyalty, and short tempers. According to Wookieepedia, George Lucas took his inspiration to create Chewbacca (and the rest of the wookiees) from his dog, Indiana, who would ride shotgun in his car. As revealed in an episode of Animal Planet’s Animal Icons (“Star Wars Creatures”), orangutans and other suspensory primates also inspired Lucas’ creation. And the link to primates, whether living, extinct, or legendary, is undeniable. They are a species of tall, human-like bipeds (i.e., they walk one two legs) with forward-facing eyes, a keen sense of smell, sharp teeth, and opposable thumbs. Because they are a species of tree-climbers, they also possess a number of mammalian anatomical specializations that enable them to live an arboreal lifestyle, including disproportionately high strength for their body size, well-developed back and calf muscles, and retractable claws.

The phylogeny or evolutionary relatedness among animal groups can be ascertained by examining their shared ancestral traits relative to their shared derived traits. For example, primates and dogs are both considered mammals because they share a number of derived traits. Among the most well known of these is the presence of mammary glands that produce milk for newborns to suckle. Additional traits include the presence of hair, sebaceous (oil) glands in the skin, and rearranged accessory bones of the jaw, including those that became the bones of the middle ear: incus, stapes, and malleus.

Evolution, and the paleontology through which it is interpreted, is a historical science. This means that the inferences one can make about the relatedness of one species to another are rooted in the fact that life on Earth has changed over time and the different species that make up Earth’s biodiversity share common ancestry.

Phylogeny of the vertebrates. Each node connecting two branches represents the common ancestor of the two descendent taxa. Major character transformations are indicated on the stems leading up to the nodes. For example, this phylogeny indicates that amniotic eggs evolved in the common ancestor of primates, rodents/rabbits, crocodiles, and dinosaurs/birds; hair, however, evolved sometime after amniotic eggs but prior to the common ancestor of primates and rodents/rabbits. Figure taken from University of California Museum of Paleontology's Understanding Evolution (http://evolution.berkeley.edu).
In the 19th century, geologist Charles Lyell recognized that processes that alter the Earth’s landscape are gradual, and he postulated that these processes are uniform through time. This idea has since been validated, as we know that plate tectonics alter the shape of the Earth’s crust by small amounts each year, and that over vast stretches of time (millions of years), these small incremental changes leave the landscape looking profoundly different. Lyell’s understanding of the geologic record is known as the Principle of Uniformitarianism, and it was profoundly influential to the writings of Charles Darwin as he formulated his thoughts on biological descent with modification (the underpinning of natural selection) while he sailed around the world aboard the HMS Beagle.

Assuming that the principle of uniformitarianism can be applied a long time ago in a galaxy far, far away, we are presented with an opportunity to examine whether wookiees are in fact more dog-like or more primate-like by looking closely at the morphological traits that unite them relative to their own uniquely derived traits. And of course, whether they are more dog-like or primate-like has important implications for whether Chewbacca would eat a Chuebakka like I do. (Truth be told, my behavior is probably better described as more pig-like than primate-like when I eat this sandwich, even though my anatomy is undoubtedly primate).

The genera and species of the mammalian order Primates (pronounced pry-may-tees) are defined morphologically by the possession of large brains relative to body size, stereoscopic vision (forward facing with overlapping visual fields), reduced sense of olfaction (smell) compared to other mammals, and prehensile hands and feet, which includes opposable thumbs and big toes in most species. The reduced sense of smell in primates is considered an evolutionary tradeoff of having a large brain and stereoscopic vision; primates are more reliant on their sense of vision than their sense of smell in order to find food and avoid predators. Most primates also have nails instead of claws on all or most of their digits, and the ones that retain claws on a digit or two use them primarily for grooming.

Dogs are members of the family Canidae, which belongs to the mammalian order Carnivora. Within Carnivora, there are two distinct suborders: Caniformia, which includes those animals that are more dog-like: bears, weasels, badgers, raccoons, and pinnipeds (seals, sea lions, and walruses); and Feliformia, which includes those animals that are more cat-like: cats, hyenas, aardwolves, civets, genets, and mongooses. The defining characteristics of the Canivora include a number of very specific morphologies of the skull, like how and where certain bones of the skull are fused to the rest of the skull. Among the Caniformia, the canids exhibit highly developed senses of smell, as evidenced by extensive sensory mucosa covering a series of intricate turbinal bones in the nasal cavity (as mentioned above, this is significantly less developed in primates), and their claws are most definitely non-retractable. Like most carnivorans, canids have specialized shearing blades, also called carnassials, on their lower first molars and upper fourth premolars, which are highly effective at slicing tough food objects like meat.

So, looking back on the descriptions of wookiee anatomy detailed at Wookieepedia (the definitive authority, after all), it appears that wookiees possess a mosaic of derived traits that align them with both primates and dogs. This is not surprising as both of these groups inspired Lucas’ imagination when he created Chewbacca. However, the preponderance of evidence suggests that wookiees are more similar in morphology to primates than they are to dogs. On the one hand/paw, they are arboreal, bipedal, and have stereoscopic vision – all primate characteristics. On the other hand/paw, they have a strong sense of smell, sharp pointed teeth, and claws instead of nails – all canid features. Yet, wookiee claws are retractable, which is a shared, derived trait present only in the carnivoran family Felidae (cats, Feliformia), and so it is not a canid trait. With the majority of evidence suggesting a closer link to primates than to canids, the wookiee retractable claw is clearly a derived trait, as they are not present in any canid common ancestors, at least as we understand mammalian evolution on Earth. Obviously Kashyyyk would have a completely different evolutionary history…but hey, who’s counting?

So then, operating within the context that wookiees are more primate-like than dog-like, it is now possible to examine whether or not Chebacca’s chuebakka would undergo the same process of ingestion and deglutition (swallowing) as mine. Spoiler alert: probably not!

Primate vocal anatomy and physiology have been described in greater detail in a previous entry at The 'Scope. But a brief review here is in order. In the neck, there are two passageways: one for air and one for food. The airway (yellow line/arrow) begins in the nose and mouth and ends after traveling through the pharynx by passing anteriorly to the laryngeal cartilages and into the trachea and lungs. The foodway (blue line/arrow) begins in the mouth and ends after also traveling through the pharynx by passing posteriorly to the esophagus and into the stomach. Notice that the two passageways cross each other. And then remember that it “could be bad” when the streams are crossed.

During a normal swallow, the hyoid bone and larynx move closer to the base of the skull (higher in the neck), while the epiglottis attached to the top of the thyroid cartilage (larynx) folds/flips backward to direct food toward the esophagus (digestive tract) rather than into larynx (respiratory tract).

In most living mammals, including non-human primates, the hyoid and larynx are positioned high in the neck (very close to the head) throughout postnatal development, as are their connections to most of their contiguous structures such as the tongue, pharyngeal constrictor muscles, and the supra- and infra-hyoid strap musculature that moves the hyolaryngeal complex during swallowing. This configuration enables the epiglottis (blue structure) to form a seal with the soft palate (pink structure), safeguarding against accidental aspiration of a bolus of food. This means that most mammals can swallow and breathe at the same time without choking. In humans, these structures are positioned similarly high in the neck at birth (diagram on left), but they descend gradually during postnatal development (diagram on right), reaching a unique position further down in the neck than in any other mammal (and perhaps wookiees?).

The caudal position of the human hyoid and larynx creates a supralaryngeal vocal tract, which forms two dynamically functioning and equal sized "tubes" – a horizontal tube extending from the posterior pharyngeal wall to the lips, and a vertical tube extending from the vocal folds to the soft palate. The ontogenetic descent of the hyoid and larynx in humans, along with the ability of the tongue to alter the cross-sectional area of both of these “tubes”, enables production of a wide range of vocalizations necessary for the evolution of quantal speech (which we know wookiees cannot produce). However, this adaptation comes at an expense to the swallowing function, as the lower position of the hyo-laryngeal complex in the neck prevents the epiglottis from forming a seal with the soft palate. Thus, the risk of aspirating a food bolus increases markedly in humans, making coordination between respiration and swallowing even more critical to survival.

So back to the original question… would Chewbacca have ingested and processed his Chuebakka in the same manner that I do? Well… it seems unlikely. It is well-documented (again on Wookieepedia) that wookiees speak a number of dialects that do not require vocal nuance, and due to their unique vocal apparatus, they are incapable of speaking Galactic Basic Standard, the most prevalent and most used language in the galaxy. If wookiees have a hyo-laryngeal complex that is situated high up in the neck near the base of the skull, morphology shared by all non-human primates, it would suggest that they are capable of swallowing and breathing simultaneously. This in turn would suggest that while I would have to wait to swallow chuebakka before alerting the world (or those immediately nearby) about how great it tastes, Chewbacca himself could swallow and breathe and presumably roar. At. The. Same. Time. And this makes me insanely jealous.

Contributed by:  Jason Organ, Ph.D.
Follow Jason on Twitter.


Laitman JT, & Reidenberg JS (1993). Specializations of the human upper respiratory and upper digestive systems as seen through comparative and developmental anatomy. Dysphagia, 8 (4), 318-25 PMID: 8269722

Laitman JT, & Reidenberg JS (1997). The human aerodigestive tract and gastroesophageal reflux: an evolutionary perspective. The American journal of medicine, 103 (5A) PMID: 9422615

Lieberman DE, McCarthy RC, Hiiemae KM, & Palmer JB (2001). Ontogeny of postnatal hyoid and larynx descent in humans. Archives of oral biology, 46 (2), 117-28 PMID: 11163319

Crompton AW, German RZ, & Thexton AJ (2008). Development of the movement of the epiglottis in infant and juvenile pigs. Zoology (Jena, Germany), 111 (5), 339-49 PMID: 18387794

Tuesday, November 24, 2015

Gobble Up Some Facts About Turkeys

Just in time to impress your family at dinner (or to divert them from the annual inquisition), here are some juicy turkey facts to have on hand...

1. The Jurassic Park centerpiece at your Thanksgiving table.

See it now?
Like other birds, turkeys are descendants of dinosaurs. The dinosaur on your Thanksgiving table is about 150 million years in the making, branching off from their close relatives, the pheasant, about 11 million years ago. So even if you’re served a dry bird this year, it may become more palatable when you remember that it is a saurischian dinosaur, related to Tyrannosaurus and Velociraptor.

Ben Franklin was a big admirer of the turkey. In fact, he favored the turkey over the bald eagle to be the US National Bird. He is quoted as saying, "For in truth, the turkey is in comparison a much more respectable bird, and withal a true original native of America" - more on that below...

2. Taming the turkey:  how the turkey was won.

Wild turkeys (Meleagris gallopavo) are indigenous to wilderness regions of North America and grew to larger sizes after migrating to Central America where there were fewer predators. About 800 BC, Olmec farmers in this region were the first people believed to have used the turkey on a wide scale, harnessing the meat and eggs for food and the feathers and bones for tools and decoration. By the time of the Aztecs, who called the bird “huehxolotl”, the turkey was domesticated.

The larger size of domesticated turkeys has severely compromised their ability to run fast and fly like their wild turkey counterparts, which is another benefit for the farmer since a turkey’s eyes are on the sides of its head. This ocular arrangement coupled with a flexible neck gives the turkey a 360-degree field of vision, good enough to spot a suspicious axe-wielding farmer lurking nearby.


3. What does a turkey have in common with a peacock?

Male turkeys puff their feathers, strut and gobble loudly, and fan out their tail like a peacock in an effort to win over a female companion, who will produce up to 18 eggs per mate. The courtship rituals for both turkeys and peacocks are risky, as these flamboyant displays may draw the attention of predators (and TMZ). But this is how the ladies select their men – they don’t have the benefit of DNA-based matchmaker sites to find suitable mates. According to evolutionary psychologists, many species rely upon courtship signals as a metric for strength and intelligence. If the male can produce such a display and get away with it, he must be strong and smart enough to outwit predators – those are genes that you would want in your pool.

Turkeys evolved to blend into the wilderness. Males, however, stand out when they fan their tail, gobble, and dance. Male turkeys do this to attract females, who have tails that are comparatively boring and speak with gentle clucks rather than obnoxious gobbles.
4. The name “turkey” is based on a mistake.




English settlers arriving on the East Coast of North America around 1500 mistook the turkey (right) to be Guinea fowl (left), a bird that the English imported from Turkey at the time (incidentally, Turkish merchants acquired the fowl from West Africa). However, as indicated above, this is wrong – turkeys are not from Turkey. Despite the error, the name has stuck and shows no sign of ever being changed - "pass the huehxolotl and gravy" just doesn’t have a nice ring to it.




5. Does eating turkey make you sleepy?

Some people have claimed that the tryptophan in turkey meat makes us feel sleepy after Thanksgiving dinner. You can get the scoop on tryptophan in a previous post found here. 



Contributed by:  Bill Sullivan, Ph.D.


Russo, E., Scicchitano, F., Citraro, R., Aiello, R., Camastra, C., Mainardi, P., Chimirri, S., Perucca, E., Donato, G., & De Sarro, G. (2012). Protective activity of α-lactoalbumin (ALAC), a whey protein rich in tryptophan, in rodent models of epileptogenesis Neuroscience, 226, 282-288 DOI: 10.1016/j.neuroscience.2012.09.021

Bruce KR, Steiger H, Young SN, Kin NM, Israël M, & Lévesque M (2009). Impact of acute tryptophan depletion on mood and eating-related urges in bulimic and nonbulimic women. Journal of psychiatry & neuroscience : JPN, 34 (5), 376-82 PMID: 19721848

Wednesday, November 11, 2015

Where Do All Those Leaves Come From?!



I wanted to link my leaf raking drudgery to some scene
in a famous movie. No go. Raking leaves is so mundane
that I could only find one movie that showed someone
raking leaves – Disney’s The Odd Life of Timothy Green.
And heck, he sprang up from a garden, all those leaves
are his cousins!
It’s Fall if you hadn’t noticed. Apple cider, football, pumpkin, wonderful colors….. and raking leaves. I spent last weekend with a rake in my hand and hate in my heart.

Maybe that’s a little strong. But when you spend time trying to put the little beggars in piles and then have to watch the wind scatter them and blow more leaves off the trees – well, you know it’s exasperating.

My efforts resulted in seven 50 gallon bags stuffed with botanical death. All told, more than 400 pounds of biomass. I stare up at the bare branches and wonder, “where did all that matter come from?”

Matter is made of atoms, so the leaves in the trash bags represent literally trillions upon trillions of atoms joined together in specific molecules. So the question is really, what was the source(s) of those particular atoms?

The tree made the leaves, but it didn’t get smaller due to its effort to produce leaves, so the material in leaves didn’t come from the mass of the tree. They were certainly organized by the tree into those biomolecules (proteins, carbohydrates, DNA and RNA, and fats) that make up the leaves, but they didn’t come from the tree originally.

The tree has roots in the soil and pulls water and nutrients into its trunk via those roots. Could the soil be where all the mass comes from? Consider this. If you have a potted plant, do you have to add soil to it every year? Nope.



Jan Baptiste van Helmont was a successful scientist, even
though it may not look like it at first. He was wrong about
digestion’s stages, but did include a description of
something that sounds a lot like the enzymes we have.
He said that trees didn’t get there mass from the soil, but
said they did get it from water – wrong. However, he said
air was involved and proposed that air was made of gas –
a word he coined.
Six hundred years ago, a scientist named Jan Baptist von Helmont measured this more carefully. He grew a tree in 200 pounds of soil from a seed until it weighed 190 pounds. Then he weighed the soil again. He found all his original dirt except for 2 ounces. I very much doubt that 190 pounds of tree mass came from two ounces of soil.

Everyone knows that trees need water. During a drought, your trees die and your grass turns brown. If water is that crucial, maybe my 400 hundred pounds of dead leaves came from water.

Water is made up of hydrogen and oxygen (H2O).  Can all the leaves be made from just water? No way; trees (and every other living thing on Earth) are carbon based. The proteins sugars, lipids, and nucleic acids are all built on a backbone of carbon atoms, with oxygen, hydrogen, and nitrogen atoms in some specific spots.

Carbon, hydrogen, oxygen, and nitrogen are the main elements of life. You can’t change one atom into another (with the exception of radioactive elements) so all the mass in my bags of leaves couldn’t have come from just water. Certainly some of the mass came from water, after all, living things are mostly water, but there’s no way the carbon came from water.

When a tree uses sugars to make energy, some water is produced. This is called metabolic water, and we do it too. You can prove this by breathing on a mirror. See that condensation? Much of that is metabolic water. Metabolic water is important in producing the molecules of life, so important that some animals, like the kangaroo rat, can live only on metabolic water, they never drink!


Kangaroo rats can live their lives without drinking even
though they live in Death Valley. Another fun fact – they
have fur-lined cheek pouches for carrying seeds back to
their den. No drinking and fur in their oral cavity – worst
case of dry mouth ever!
So a bit comes from water, even less from soil, and none of the leaf mass springs from the tree itself. What do we have left? Only one choice comes to my mind - and your breathing it right now. 

Air? Really? How could 400 hundred pounds of leaves come from the air? It seems silly, but it’s the basis of life on Earth. Air is 78% nitrogen (N2), 21% oxygen (O2), and 0.00397% carbon dioxide (CO2) – plus some water vapor. This is almost everything a growing tree needs, except for some trace minerals that can be found in that 2 ounces of disappeared soil that von Helmont measured 600 years ago. 

Basically, those things we humans breathe out (CO2, H2O, O2, and N2) are exactly what plants need to grow. We actually use only a small portion of the oxygen that we breathe in, but we do add some carbon dioxide to the air when we exhale. This is a big reason why talking to your plants makes them grow better; you're increasing the concentration of carbon dioxide in their immediate vicinity.

Plants take carbon dioxide from the air, and using the energy of sunlight, turn it into carbohydrates – this is photosynthesis. But they don’t just use the carbs for energy. The sugars are the carbon basis for synthesizing every biomolecule the plant will need in order to build leaves and wood.

We have covered carbon (from CO2), hydrogen (from rain and metabolic water), oxygen (from carbon dioxide and metabolic water), but what about the nitrogen in DNA and proteins? Believe it or not, that comes from the air too.

N2 in the air is hard to tear apart so the nitrogen can be used in building biomolecules. Plants can “fix” carbon themselves, turning gaseous carbon to solid carbon during photosynthesis, but they can’t fix nitrogen. To turn nitrogen into a form they can use, plants rely on nitrogen fixing bacteria in the soil.

Many plants form a symbiotic relationship with nitrogen fixing bacteria, letting them live inside nodules of their roots. Therefore, the nitrogen the trees use comes from the air, even if it passes through the bacteria first.



The top image is from art student Melchiorri. He claims
that the silk mesh stabilizes the chloroplasts and lets them
produce oxygen via photosynthesis even though they aren’t
in a cell. There are problems here, like chloroplasts don’t live
very long. The bottom image is of an artificial leaf that can
produce hydrogen and oxygen gases from water in the
presence of light. Leaves use 1% of available light; this “leaf”
already uses 7x as much of the light.
Most trees don’t harbor nitrogen-fixing bacteria in their roots, they rely on the nitrogen that the bacteria spread around and leave in the soil, or that nitrogen that comes from dead plant material. One exception is the black locust tree. It is estimated that a black locust stand of trees (and their bacteria) can add 40-60 kg (88 –133 lb.s) of nitrogen to the soil every year.


Now I can rake my leaves confident in the knowledge that I'm raking up a true miracle. They can’t weigh too much, they’re basically nothing but air, water vapor and a bit of bacterial waste. So why does my back hurt so much?

Soon, we may have artificial leaves to deal with. One recent project by art school graduate Julian Melchiorri has used chloroplasts embedded in silk protein mesh in order to carry out photosynthesis. These can be used in space, where plants have a harder time growing in zero gravity. This might be our source of oxygen on the way to Mars.

In addition, new research describes a synthetic leaf made form metal films on either side of a silicon mesh can be used to split water as occurs in photosynthesis. These synthetic leaves might be helpful in producing hydrogen and oxygen for use in fuel cells. I just hope we don’t have to rake them up.



Contributed by Mark E. Lasbury, MS, MSEd, PhD
As Many Exceptions As Rules

Pijpers, J., Winkler, M., Surendranath, Y., Buonassisi, T., & Nocera, D. (2011). Light-induced water oxidation at silicon electrodes functionalized with a cobalt oxygen-evolving catalyst Proceedings of the National Academy of Sciences, 108 (25), 10056-10061 DOI: 10.1073/pnas.1106545108