Tuesday, November 27, 2012

An arguable misnomer in physics: the term “quantum mechanics”

Analog or digitaluninterrupted or pixilated, continuity or discontinuity, field or particle? These pairs of opposing adjectives and nouns often occur in texts and discussions about physical reality and theoretical modeling. The periodic table of discrete chemical elements with their characteristic numbers and spectra directs scientists towards a quantum view of matter. As an example: the solution of Schrödinger's equation for the hydrogen atom provides us with quantum numbers (n, l, and m), which are integers [1]. Important: these integers are coming forth from solving an equation formulated with continuous variables for physical quantities that encode electron movement and potential. Thus, quantum mechanics models reality on the basis of continuity. Discrete values result from the approach in which the theoretical model is treated and solved; but may not be nature-inherent.

Intrigued by cosmological challenges and debates over the fundamental laws of the physical world, David Tong—a theoretical physicist at the University of Cambridge—is giving the continuity-discontinuity interrelation a closer look. He writes that the term “quantum mechanics” could said to be a misnomer for a theory that formulates its equations in terms of continuous quantities [2].  He cites Leopold Kronecker's proclamation “God made the integers, all else is the work of man.” and counters with “God did not make the integers. He made continuous numbers, and the rest is the work of the Schrödinger equation.” [3].  Tong explains the latter in detail:

Integers are not inputs of the [quantum] theory, as Bohr thought [Danish physicist Niels Bohr “implemented” discreteness at the atomic scale]. They are outputs. The integers are an example of what physicists call an emergent quantity.  In this view, the term “quantum mechanics” is a misnomer. Deep down, the theory is not quantum. In systems such as the hydrogen atom, the processes described by the theory mold discreteness from underlying continuity. 

Quantum phenomena are these days demonstrated and animated in educational as well as entertaining videos. The Zeitgeist-driven perception: What I simulate and animate, is what I see and believe in. Yet, living in a digital age does not automatically imply living in a digital universe.

Keywords: physics, philosophy, quantum theory, physical world, pointillist universe, emergent integers.

References and more to explore
[1] Quantum Mechanics: Solving Schrödinger's equation [users.aber.ac.uk/ruw/teach/237/hatom.php].
[2] David Tong: The Unquantum Quantum. Scientific American, December 2012, 307 (6), pp. 46-49 [www.nature.com/scientificamerican/journal/v307/n6/full/scientificamerican1212-46.html].
[3] Quoted at axeleratio.tumblr.com: axeleratio.tumblr.com/post/36680758289/god-did-not-make-the-integers-he-made-continuous.

Tuesday, November 20, 2012

A lead-free borosilicate glass, G 702 EJ, named Py-Right, Pie Rite and eventually Pyrex

PYREX® is  is a transparent, lead-free borosilicate glass with a low thermal expansion coefficient—an example of  a material with good heat shock resistance. The excellent thermal properties of Pyrex facilitate its use at high operating temperatures [1].

Pyrex-branded borosilicate glass products were invented and produced at Corning Glass Works in the upstate New York city of Corning, nicknamed Crystal City for its legacy of glass factories and glass cutting shops. In the early 20th century, a hot flame tolerant borosilicate glass, named “fire glass”or  Nonex, was successfully manufactured by the Corning specialty glassmaker and integrated as components in electric lightbulbs and railway signal lamps [2-5]. A borosilicate glass is made by adding borax (sodium tetraborate decahydrate) to the typical glass composition of silica, sodium oxide and lime. By further employing other minor additives, glass properties can be fine-tuned for desired applications.

Pyrex was developed by Corning scientist William Churchill, based on Corning's Nonex know-how. While Nonex released lead when exposed to acids (for example from food), a lead-free borosilicate variation with code G 702 EJ, did not. The latter showed promising properties for being used as ovenware and laboratory glassware.

In 1915, Churchill and Corning made G 702 EJ public under the tradename Pyrex—rhyming with Nonex—after playing with names such as Py-Right and Pie Rite, referring to the first appetizingly prepared cakes and custards in Pyrex dishes. In 1916, these look-right-through dishes were marketed and advertized as ovenware that saves time, labor and fuel [5]: one of the earliest ads further states that Pyrex will not crack, chip nor craze, not be affected by the hottest oven and that “Pyrex is everlastingly sanitary, durable, easy to wash, a constant source of satisfaction in the well-appointed home.”

Keywords: history, materials science, glass research, glass engineering, borosilicates, labware, kitchenware, baking, cooking.

References and more to explore
[1] Pyrex® Borosilicate Glass [www.pgo-online.com/intl/katalog/pyrex.html].
[2] Washington Glass School: Historical Glass Fun Facts: Invention of Pyrex & the Studio Glass Movement [washingtonglass.blogspot.com/2012/01/historical-glass-fun-facts-invention-of.html].
[3] History of Pyrex® [www.classickitchensandmore.com/page_4.html].
[4] William S. Ellis: Glass. Avon Books, Inc., New York, 1998; pp. 49-50.
[5] Regina Lee Blaszczyk: Cooking with Glass. Chemical Heritage Fall 2012/Winter 2013, 30 (3), pp. 8-9 [www.chemheritage.org/discover/online-resources/thanks-to-chemistry/ttc-food-pyrex.aspx].

Crystal City—a pseudonym for Corning, New York

The upstate New York city of Corning is located on the Chemung River in Steuben County. Along the river, the buildings of Corning Glass Works—originally named Corning Flint Glass Works—can be found, where glass and ceramic products for industrial and scientific applications are manufactured.  The Corning Museum of Glass at 1 Museum Way (Corning, NY 14830) calls itself a wonderland of glass, in which master glass-workers demonstrate the making of spectacular glass objects. World-changing innovations in glass can be discovered there [1]. Corning's cornucopia of glass-making arts and technology led to the nickname Crystal City [2], as this picturesque and industrial city often was and still is dubbed in the media.

Physicists and chemists may think of this pseudonym as a misnomer, since glass is an amorphous, non-crystalline material. But its optical transparency and large content of silica (SiO2) may justify the crystal association. Students and hobbyist of glass-working can try their skills by enrolling  in classes at the Corning Museum of Glass, experimenting with phases and facets of non-crystalline matter in the Crystal City [3].

Two articles in a recent Chemical Heritage edition review the collections of the Corning Museum of Glass and feature the history of glass-making in Corning, beginning with Nonex for signaling lamps, Pyrex for lab- and kitchenware and continuing on with fiber optics and touch-screen technology [4,5]. According to the Hot Stuff article by Kelly Tuttle [5], the museum  showcases a Dale Chihuly sculpture in its glass-walled entrance and “houses the largest collection of glass in the world, with over 45,000 objects spanning 3,500 years. In 1868 the Brooklyn Flint Glass Company moved to Corning and bacame the Corning Glass Works. By 1905 upward of 2,500 glass craftspeople had moved into the then industrialized area, which acquired the pseudonym Crystal City.” 

References and more to explore
[1] Corning Museum of Glass [www.cmog.org].
[2] Corning, New York: The Crystal City [lcweb2.loc.gov/diglib/legacies/NY/200003367.html].
[3] William S. Ellis: Glass. Avon Books, Inc., New York, 1998; page 204 (also see www.cmog.org/programs/classes#.UKwALGeAYYs).
[4] Regina Lee Blaszczyk: Cooking with Glass. Chemical Heritage Fall 2012/Winter 2013, 30 (3), pp. 8-9 [www.chemheritage.org/discover/online-resources/thanks-to-chemistry/ttc-food-pyrex.aspx].
[5] Kelly Tuttle: Hot Stuff. Chemical Heritage Fall 2012/Winter 2013, 30 (3), page 46.

Wednesday, October 31, 2012

Acronym in cytology and organogenesis: SFEBq for serum-free floating culture of embryoid body-like aggregate with quick reaggregation

SFEBq stands for serum-free floating culture of embryoid body-like aggregate with quick reaggregation. A complex acronym for a complex process! This cell-aggregation process occurs in three-dimensional culture solutions (instead of  single-layer dish cultures), wherein floating stem cells self-assemble into complex tissue topologies—depending on fine-tuned experimental conditions and supply of chemical precursor compounds. SFEBq technology was developed to explore artificial growth of  protoretina resembling the neural retina in mammalian eyes [1-4].

The successful SFEBq-driven retina growth, including the development of the optic vesicle and its structural collapse to form the optic cup, demonstrates that building and shaping of a retina can occur without support from neighboring tissues such as lens cell. In the words of Yoshika Sasai, a neurobiologist at RIKEN Center for Develiopment Biology in Kobe, Japan [4], “retinal formation, at least in vitro, is a self-organizing phenomenon based on an internal program that resides within these cells.” 

Keywords: molecular neurobiology, organogenesis, neurogenesis, compound tissue, neuroepithelium, mammalian embryogenesis, embryonic stem cells.

References, cell-adhesion figures,  schematic diagram and further reading
[1]  M. Eiraku , N. Takata, H. Ishibashi, M. Kawada, E. Sakakura, S. Okuda, K. Sekiguchi, T. Adachi and Y. Sasai: Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature April 7, 2011, 472, 51-56.
DOI: 10.1038/nature09941.
[2] Kurzweil Accelerating Intelligence: Stem cells used to create retinal tissue. April 7, 2011 [www.kurzweilai.net/stem-cells-used-to-create-retinal-tissue]. 
[3] M. Eiraku and Y. Sasai: Mouse embryonic stem cell culture for generation of three-dimensional retinal and cortical tissues. Nature Protocols 2012, 7, 69-79.
DOI: 10.1038/nprot.2011.429.
[4] Y. Sasai: Grow Your Own Eye. Scientific American November 2012, 307 (5), 44-49.
DOI: 10.1038/scientificamerican1112-44.

Thursday, October 18, 2012

Rhyming in harmony about dinosaur's anatomy

Bert Leston Taylor (1866-1921), using B. L. T. as his initials, was writing humorous columns for newspapers [1-3]. He also engaged in writing comic and delightful verses, which often expose some little-noted wisdom or truth. One of my favorite poems is The Dinosaur, in which B. L. T. referred to the ‘second brain’ (large ganglion in the pelvis) of some dinosaurs [4-6]: 
Behold the mighty dinosaur,
Famous in prehistoric lore,
Not only for his power and strength
But for his intellectual length.

You will observe by his remains
The creature had two sets of brains -
One in his head (the usual place),
The other at his spinal base.

Thus he could reason A priori
As well as A posteriori.
No problem bothered him a bit
He made both head and tail of it.

So wise was he, so wise and solemn,
Each thought filled his spinal column.
If one brain found the pressure strong,
It passed a few ideas along.

If something slipped his forward mind
'Twas rescued by the one behind.
And if in error he was caught
He had a saving afterthought.

As he thought twice before he spoke
He had no judgement to revoke.
Thus he could thing without congestion
Upon both sides of every question.

Oh, gaze upon this model beast,
Defunct ten million years at least.
............>> Bert Leston Taylor <<
With two brains quite distinct, dinosaurs yet went extinct!

Keywords: comparative anatomy, nerve trunk, educational rhyme, poetry, humor, anthropomorphizing.

[1] New York State Literary Tree: Bert Leston Taylor [www.nyslittree.org/index.cfm/fuseaction/DB.PersonDetail/PersonPK/1655.cfm].
[2] Evi: Bert Leston Taylor biography [www.evi.com/q/bert_leston_taylor_biography].
[3] Bert Leston Taylor: The So-Called Human Race. Alfred A. Knopf, New York, 1922 [activefolio.com/files/ET31138.pdf].
[4] Karen's Poetry Spot: The Riddle of The Dinosaur by Bert Leston Taylor. October 16, 2007 [karenspoetryspot.blogspot.com/2007/10/riddle-of-dinosaur-by-bert-leston.html].
[5] The Dinosaur [www.readbookonline.net/readOnLine/50593/].
[6] Richard Dawkins: The Greatest Show on Earth. Free Press, New York, 2009; page 306.

Wednesday, October 10, 2012

An English-American mess: the term ‘turtle’

Do you think you know what a turtle is?

A dictionary definition sounds like this: “any of various chelonian reptiles, especially those of the marine family Chelonidae, having a flattened shell enclosing the body and flipper-like limbs adapted for swimming.” That's for the “English turtle.” US and Canadian turtles are “any of the chelonian reptiles, including the turtoises and terrapins.” [1]

There is a better understandable (and funnier) illustration of this subject in Richard Dawkins' book with the title The Greatest Show on Earth [2]. Quoting George Bernhard Shaw's saying that “England and America are two countries divided by a common language,” Richard Dawkins continues:

In Britain, turtles live in the sea, tortoises live on land and terrapins live in fresh or brackish water. In America all these animals are ‘turtles,’ whether they live on land or in water.  ‘Land turtles’ sounds odd to me, but not to an American, for whom tortoises are the subset of turtles that live on land. Some Americans use ‘tortoise’ in a strict taxonomic sense to refer to the Testudinidae, which is the scientific name for modern land tortoises.In Britain, we'd be inclined to call any land-dwelling chelonian a tortoise, whether it is a member of the Testudinidae or not.

What a mess! In case you wonder, Australians use the word turtle in yet different ways.

Any solution to this linguistic jumble? Zoologists, in their research, use the term chelonian. Broad-based aspects of the conservation and biology of these animals are covered in an international scientific peer-reviewed journal: Chelonian Conservation and Biology [3].

Like the scientific language, the German language has one word for all: Schildkröte for turtle, tortoise and terrapin [4]. Schildkröte literally means shielded toad. A terrapin is a Sumpfschildkröte, Sumpf meaning swamp or bog.

Keywords: languages, terminology, biology, Testudinidae, Chelonidae, nomenclature, taxonomy, classification, confusion.

References and more to explore
[1] Dictionary.com: turtle [dictionary.reference.com/browse/turtle?s=t].
[2] Richard Dawkins: The Greatest Show on Earth. Free Press, New York, 2009.
[3] Chelonian Conservation and Biology [www.chelonian.org/ccb/].
[4] Edmund Launert: Biologisches Wörterbuch. Verlag Eugen Ulmer, Stuttgart, 1998.

Monday, October 8, 2012

One plant genus and 14 plant species named after Francis Guthrie, who first made the graph-theoretical Four-Color Conjecture

In 1852, the English law student Francis Guthrie at the University College of London conjectured that four colors would suffice to color any map, such, that border-sharing regions never come to share the same color [1-3]. The Four-Color Problem, or Four-Color Conjecture, turned into a theorem, when it was proven in 1976 by Kenneth Appel and Wolfgang Haken—a computer-assisted proof, triggering further work in theorem-proving software and strategies.  

Francis Guthrie (1831-1899) developed a strong interest in mathematics and botany. In 1861, Guthrie left England for the Cape Colony, now part of South Africa, where he took up the chair of Mathematics at the Graaff-Reinet College and, in 1878, at the South African College (Zuid Afrikaansche Athenaeum), which became the University of Cape Town in 1918 [2]: Besides mathematics, Guthrie taught botany; inspiring Harry Bolus (1834-1911), who later became a celebrated botanist and illustrator. Honoring his teacher, Bolus named a genus in the plant family Achariaceae after Guthrie: Guthriea Bolus, including the flowering plant Guthriea capensis [4].

Bolus also named plant species after Guthrie. For example, Satyrium guthriei Bolus (1893) in the family Orchidaceae, Gladiolus guthriei Bolus (1917) in the Iris family and Indigofera guthriei Bolus in the family Fabaceae [2,4-6]. 

Keywords: mathematics, graph theory, history, botany, plant species, flowering plants, taxonomy.

References and more to explore
[1] J. J. O'Connor and E. F. Robertson: The four colour theorem. September 1996 [www-groups.dcs.st-and.ac.uk/~history/HistTopics/The_four_colour_theorem.html].
[2] Pieter Maritz and Sonja Mouton: Francis Guthrie: A Colourful Life. The Mathematical Intelligencer 2012, 34 (2), pp. 67-75. DOI: 10.1007/s00283-012-9307-y.
[3] Georges Gonthier: Formal Roof—The Four-Color Theorem. Notices of the AMS December 2008, 55 (11), 1382-1393. PDF: www.ams.org/notices/200811/tx081101382p.pdf.
[4] JSTOR PLANT SCIENCE: Guthriea capensis Bolus [plants.jstor.org/visual/nbgsld0001378], Satyrium Guthriei Bolus [plants.jstor.org/flora/floc014377], Indigofera guthriei Bolus [plants.jstor.org/specimen/nh0005500-0]. 
[5] Victoria Wilman: Gladiolus guthriei F. Bolus [www.plantzafrica.com/plantefg/gladiolusguthriei.htm].
[6] Red List of South African Plants: Indigofera guthriei Bolus [http://redlist.sanbi.org/species.php?species=357-204].

Wednesday, September 26, 2012

Anchiornis, the “nearby bird”

The word Anchiornis defines a dinosaur genus: small, feathered, deinonychosauria (“fearsome claw lizards”) belonging to the family Troodontidae. The genus name Anchiornis is based on the Greek roots anchi and ornis, meaning “nearby” and “bird,” respectively. The name highlights the close relation between these feathered lizards of the Cretaceous period and birds [1].  Anchiornis huxleyi is currently the only known species of this fossil genus—included in the scientific name is an epithet that honors Thomas Henry Huxley (1825-1895), an English biologist, who pioneered research into avian origin.

A recent Keanium article in the journal Chemical Heritage shows a striking artist's rendering of Anchiornis [2]. The article describes how insight in the dinosaur-bird relationship (or evolution of birds) is gained by the study of pigments such as melanin, found in fossil feathers—dino fuzz. Identification and scanning electron microscope-supported analysis of fossilized and surviving melanosomes in proto-feathers of fossil animals from northeastern China allow the reconstruction of dinosaur and early bird's color patterns [3]. While the dinosaur-bird debate is still going on, proto-birds such as Anchiornis already shine in brilliant colors and bring art and science together.

Keywords: paleontology, anatomy, evolution, dinosaurs, birds, feathers, melanin.

References and more to explore
[1] Xu Xing et al.: A new feathered maniraptoran dinosaur fossil fills a morphological gap in avian origin. Chinese Science Bulletin 2008, 54 (3), 430-435. DOI: 10.1007/s11434-009-0009-6.
[2] Sam Kean (artist's rendering by Michael DiGiorgio): Colored In. Chemical Heritage Summer 2012, 30 (2), page 5 [www.chemheritage.org/discover/media/magazine/articles/30-2-colored-in.aspx].
[3] Chris Sloan: Dinosaur True Colors Revealed for First Time. National Geographic January 2010 [http://news.nationalgeographic.com/news/2010/01/100127-dinosaur-feathers-colors-nature/].

Sunday, September 23, 2012

Chompion: champion among strong-biting animals

Which is the hardest-biting land animal ever known? According to recent biomechanical studies, this is Tyrannosaurus rex, which—with a maximum bite force of 12,800 pounds—had a stronger bite than any other known terrestrial animal [1-4]. Only some water-based monsters such as extinct giant sharks and crocodilians had most likely a harder bite. Ouch!

They all made a living by forcefully chomping their prey apart inside their megamouth. T. rex is the chomp champion, chompion, of the land animals. Brian Switek uses this playful portmanteau in his recent Smithsonian article, reporting on the newest results in modeling and estimating bite force of large animals and referring to T. rex as the world chompion [4]. Congratulations!

Keywords: comparative anatomy, biomechanics, paleontology, evolution, biology, bite.

References and more to explore
[1] Jennifer Viegas: T. Rex Had The Toughest Bite. DiscoveryNews, Feb. 28, 2012 [news.discovery.com/animals/t-rex-bite-122802.html].
[2] BBC Nature: Tyrannosaurus rex bite measured [see a video: www.bbc.co.uk/nature/17197633]
[3] Brian Switek: The Tyrannosaurus Rex's Dangerous and Deadly Bite [www.smithsonianmag.com/science-nature/The-Tyrannosaurus-Rexs-Dangerous-and-Deadly-Bite-169806936.html].
[4] Brian Switek: World Chompion. Smithsonian magazine, October 2012, page 14.

Tuesday, September 18, 2012

Donner Summit Bridge and its other names

Donner Summit Bridge is a concrete arch span built during the 1920s. This landmark bridge, as part of the Old Lincoln Highway (Hwy 40), was then an important east-west artery between San Francisco Bay and New England. Now, Interstate 80 takes most of the traffic and the route leading over this bridge, called Hwy 40 Scenic Bypass, is favored by tourists and those who come to the Donner Pass area for hiking, biking, rock climbing, skiing and exploration of natural and Gold Rush history.

Donner Summit Bridge is commonly known as Rainbow Bridge. It also is named Donner Memorial Bridge, reminding visitors to memorize the fateful event of 1846 and 1847, during which many emigrants to California lost their lives. The vista point next to the Rainbow Bridge offers a great overlook of  Truckee's Donner Lake. This view point, as many other locations of interest along the scenic bypass, features informative panels illustrating the local history. More about the Donner history can be learned around the Donner Party Memorial (Pioneer Monument) and in the Emigrant Trail Museum at Donner Memorial State Park at the east end of Donner Lake. 

Keywords: Sierra Nevada, geography, history, landmark name.

Sunday, September 16, 2012

A Scottish-Californian place name: “Loch Leven” means “Lake Eleven”

The Loch Leven Lakes are scenic, subalpine lakes embedded in a granite wilderness of the Sierra Nevada in California. How did they get their name? The Scottish Gaelic word loch for lake gives a clear hint.  J. L. Medeiros, professor emeritus of the Sierra College, suggests that the name came either from the Scottish placename Loch Leven or “from the same moniker given the German brown trout” [1]. Loch Leven is a lake in central Scotland with an island on which a castle ruin, Loch Leven Castle, is located. The German brown trout (Salmo trutta) is also called Behr trout or Loch Leven trout [3].

So far, we have some threads. Jed Welsh nicely connects them for us [4]:
In Scotland there was [a] series of lakes that the Scots simply named lake one, lake two, lake three, etc. The most popular lake was Lake number eleven. The Scottish lingo for the lake was “Loch Leven.” It was from this lake that the Scottish brown trout were planted in the Eastern Sierras. We didn't call it a brown trout we called it Loch Leven. 
By the way, there are different strains of brown trouts: red-and-brown-spotted German and the “real” Loch Leven trout—but neither one is native American [5].

Summary:  North Sierra's Loch Leven Lakes are named after a European trout species nicknamed after a lake named after a number.

Keywords: geography, history, Scotland, Sierra Nevada, North America, toponym, brown trout, natural history, folklore, lingo.

References and more to explore
[1] J. L. Medeiros: A Naturalist's Transect along the I-80 Corridor in California: Rockin to Donner Pass [see Stop #7 in www.sierracollege.edu/ejournals/jscnhm/v2n1/fieldtrip2.html].
[2] Historic Scotland: LochLeven Castle [www.historic-scotland.gov.uk/propertyresults/propertyoverview.htm?PropID=PL_202].
[3] Salmo trutta Linnaeus, 1758 [http://nas.er.usgs.gov/queries/GreatLakes/SpeciesInfo.asp?NoCache=6%2F17%2F2010+1%3A38%3A11+PM&SpeciesID=931&State=&HUCNumber=DGreatLakes/].
[4] George van Zant: Jed Welsh - Brown Trout of the Eastern Sierra [www.bigfishtackle.com/fishing_articles/Featured_Fishing_Authors/George_Van_Zant/Jed_Welsh_-_Brown_Trout_of_the_Eastern_Sierra_338.html].
[5] Lenn Harris: Not All Brown Trout Are German! [www.ultimateoutdoorsradio.com/not-all-brown-trout-are-german-by-lenn-harris/fishing-reports/].

Saturday, September 15, 2012

City of Reno in Nevada named after Jesse Reno (1823-1862), an infantry commander and mathematician born in Wheeling, Virginia

The city of Reno in Nevada was named after Jesse Lee Reno, who was born in 1823 in Wheeling, Virginia [1]. The name Reno is an anglicization of  the French name Reynaud (or was it Renault [2]), which Reno's ancestors from France changed after their arrival in America. Thus, the name of Nevada's second biggest city has french roots.

In 1868 the American railroad executive and founder of the Central Pacific Railroad, Charles Crocker (1822-1888), named the Gold Rush settlement at the Truckee River after Reno. The Union General Jesse Reno, who was killed in the Civil War, was Crocker's friend [3].

This year is the 150th anniversary of  Jesse Reno's death. Reno died September 14, 1862, as an infantry commander at the battle of Fox's Gap in Maryland [4]. He never came to Reno; but he came close to it during the Utah War or Mormon War in 1857—seven years before Nevada became a state.

Even then, battling was not left to good luck: Reno was a Professor of Mathematics at West Point to design artillery [2]. Media are typically focusing on the Reno named after a war hero story. Obviously, Reno is also named after a mathematician; although one that is not in the league of E. T. Bell's Men of Mathematics

The name Reno is often associated with that of its sister city of Sparks and also with nearby Lake Tahoe, to which Reno considers itself as a gateway. For example, Reno's airport is named Reno-Tahoe International Airport. A professional golf tournament,  taking place annually at the Montrêux Golf and Country Club south of Reno, is known as Reno-Tahoe Open.

Keywords: geography, tourism, history, war hero, namesake, eponym, toponym.

References and more to explore
[1] Jesse Lee Reno (1823-1862) [www.thelatinlibrary.com/chron/civilwarnotes/reno.html].
[2] West Virginia Archives & History: Jesse L. Reno [www.wvculture.org/history/civilwar/renojesse01.html]. 
[3] ricklund.com: About the Reno-Sparks Area [http://www.ricklund.com/area.htm].
[4] Emerson Marcus: Reno honors namesake 150 years after death. Reno-Gazette Journal, September 15, 2012; page 3A (also www.rgj.com/article/20120914/NEWS/309140058/Reno-s-namesake-honored-150th-anniversary-his-death) .

Thursday, September 6, 2012

The term “dietary fiber”

Dietary fiber is the preferred spelling in American English. Texts from Canadian, British, Australian, Indian and other non-U.S. publications typically adhere to the spelling dietary fibre. The nouns roughage or ruffage are sometimes used as synonyms.

Dietary fiber is the indigestible portion of  plant parts such as seed husks. Dietary fibers—and their function after eating food containing them—have been described in ancient herb books and medicinal literature up to the recent emergence of the dietary fiber hypothesis, putting forward the idea that indigestible, fibrous residues of seeds and vegetables play a significant role in human nutrition and health [1-3].

AACC International (AACC stands for American Association of Cereal Chemists), a non-profit professional organization of grain scientists, adopted the following definition [4]:

Dietary fiber is the edible parts of plants or analogous carbohydrates that are resistant to digestion and absorption in the human small intestine with complete or partial fermentation in the large intestine. Dietary fiber includes polysaccharides, oligosaccharides, lignin, and associated plants substances. Dietary fibers promote beneficial physiological effects including laxation, and/or blood cholesterol attenuation, and/or blood glucose attenuation.

Instead of merely being a formal definition, this text underlines the nutritional and nutraceutical (a portmanteau of the words nutrition and pharmaceutical) aspects of dietary fibers.

Keywords: biomedical sciences, physiology, gastroenterology, health, food science, macromolecules.

References and more to explore
[1] Steve W. Cui and Keisha T. Roberts. Chapter 13. Dietary Fiber: Fulfilling the Promise of Added-Value Formulations. In  Stefan Kasapis, Ian T. Norton and Johan B. Ibbing (Eds.), Modern Biopolymer Science: Bridging the Divide Between Fundamental Treatise and Industrial Application.(pp. 399-447), London (UK), Burlington (MA) and San Diego (CA): Academic Press, 2009.
[2] Thomas P. Amy: The dietary fiber hypothesis. Am. J. Clin. Nutr. 1981, 34 (3), pp. 432-433 [http://ajcn.nutrition.org/content/34/3/432.full.pdf+html].
[3] Low-Carb for You: The Fiber Hypothesis. May 4, 2010 [lowcarb4u.blogspot.com/2010/05/fiber-schmiber.html].
[4] AACC International: AACCnet > Scientific Initiatives > AACCI Standard Definitions > Dietary Fiber [www.aaccnet.org/initiatives/definitions/Pages/DietaryFiber.aspx].

Friday, August 24, 2012

A term in astronomy: meteorite for a surviving space rock hitting Earth

Meteorites originate from celestial objects such as asteroids or comets that break apart while entering Earth's atmosphere. A penetrating meteorite chemically reacts with atmospheric gases and appears as a fireball—also known as meteor, shooting star or falling star, which typically ends up as dust. Sometimes, however, parts of visible size survive and hit the Earth's surface, where they may be found as space rocks [1] by curious earthlings.

Peter Jenniskens is such a curious human— a meteor astronomer with experience in hunting meteorites in Sudan [2].  He hunts for meteors and meteor showers by surveillance (triangulation of meteor tracks) and by searching the grounds. Interested scientists are invited to participate in the meteor-shower surveillance program [3].

Further naming topics related to astronomical objects:

References and more to explore
[1] Geoffrey Notkin: Have you found a space rock? [geology.com/meteorites/meteorite-identification.shtml].
[2] Filed Notes (as told to Marissa Fessenden): Meteor Hunt. Scientific American September 2012, Volume 307, Number 3, page 23. DOI: 10.1038/scientificamerican0912-23.
[3] NASA Ames Research Center: Cameras for Allsky Meteor Surveillance (CAMS) [cams.seti.org].

Thursday, August 23, 2012

Mayan proper names

A proper name is a designation of a unique item. From the decipherment of various hieroglyphic inscriptions and texts, found at Mayan places like Palenque, formerly Otulum, it is now known that the Maya had proper names not just for people, sites and landmarks, but also for tools and moveable items. In addition to dynastic rulers and scribes, for example, they named pyramids, temples, altars (sculpted stone blocks), stelae, an incense burner as well as jewelry and ceramics [1]:

The ancient Maya liked to name things, and they liked to tell the world who owned these things.

The existence of  Mayan proper names is illustrated, for example, by names for Maya Rulers of Copán [2,3], place names introduced by ut-i [1], and the owner's name carved into a Late Classic vase depicting scenes of assembling gods and acts of creation (page 221 in [1]) .

Keywords: archaeology, epigraphy,  name-tagging, toponyms, patron's name, nomenclature.

References and more to explore
[1] Michael D. Coe: Breaking the Maya Code. Thames & Hudson, New York, Revised Edition 1999; pages 221, 245 and 253-255.
[2] Günther Eichhorn: Maya Rulers of Copán. Travel pictures from Honduras [gei.aerobaticsweb.org/honduras_rulers.html].
[3] Altar Q [users.misericordia.edu//davies/maya/altarq.htm].

Tuesday, August 21, 2012

Otulum, a former name of the Mayan city of Palenque

Otulum is a former place name of the Mayan city of Palenque, a Maya site in the lower foothills of the Sierra de Chiapas—southeast of Villahermosa, today's capital of the state of Tabasco in Mexico [1,2]. The place got its name from the river Otulum running through this site with its Classic Maya architecture, whose stelae, temples and other buildings are richly filled with hieroglyphic inscriptions and texts [3].

Keywords: geography, history, archaeology, toponyms.

References and more to explore
[1] Michael D. Coe: Breaking the Maya Code. Thames & Hudson, New York, Revised Edition 1999; pages 193 and 202.
[2] American Philosophical Society > Native American Collections, Case II, Section Tabular View of the Compared Atlantic Alphabets and Glyphs of Africa & America, by Constantine  Samuel Rafinesque, 1832  [www.amphilsoc.org/library/lobbyexhibit/natam2011/case2].
[3] David Stuart: The Inscriptions from Temple XIX at Palenque. The Pre-Columbian Art Research Institute, San Francisco, 2005 [www.mesoweb.com/publications/stuart/TXIX-spreads.pdf].

Sunday, August 19, 2012

Polyphony versus homophony

The noun polyphony derives from the Greek words polys (many) and phone (voice, sound) and means “variety of sounds” [1]. With the Greek word homos for “same,” the noun homophony means “sameness of sounds” or “monotony of sounds.”

In linguistics, polyphony is a special form of polyvalence, which refers to the assignment of multiple values (meanings) to a written sign. The term polyphony stands for the multiplicity of sounds associated with a hieroglyph, symbol or character (and sequences thereof) belonging to the writing system of a spoken language [2]. For example, the letter combination ow is polyphonic: note its different pronunciation in the words towel, tow and tomorrow.

Homophony is the converse of polyphony. Michael Coe provides a striking example of homophony found in Mayan writing—originally presented by the epigrapher Stephen Houston [2]: Three significantly different looking glyphs, which are the signs for “four,” “snakes” and “sky,” have the same sound can (Yucatec language) or chan (Cholan language). Any of these three homophonic signs may occur as logograph in a phrase whenever this sound is required. This example further demonstrates the phoneticism of the Mayan writing system: although the hieroglyphs may have ideographic or semasiographic roots, they often “evolved” to represent specific sound values.

Keywords: linguistics, language, pronunciation, sign substitution, symbol substitution, glyph interchangeability, Maya homophony, spelling.

References and more to explore
[1] Online Etymology Dictionary: polyphony (n.), polyphonic (adj.) [http://www.etymonline.com/index.php?allowed_in_frame=0&search=polyphony&searchmode=none].
[2] Michael D. Coe: Breaking the Maya Code. Thames & Hudson, New York, Revised Edition 1999; page 235 and Glossary.

Saturday, August 18, 2012

Glottography and semasiography

Glottography is the recording of language-based utterances. To be more precise: the recording of the vocal cords during respiration and phonationthe production of vocal sounds and especially speech [1]. In the context of physics and anatomy, the term recording here refers to the measurement and study of such audible expressions. Linguistically, it refers to the fixation of uttered sounds in the form of symbols or characters, defining a writing system.

In principle, a writing system can be derived from glottographic and non-glottographic origins of symbols or characters [2]. In the latter case, no relation between symbols and sounds is evident. Such a writing system is called semasiographic, formerly ideographic [3]. In semasiography, symbols are constructed by humans who agree upon their meaning. The international road sign system and the ancient quipu of Inca Peru—connected, color-coded cords with tied knots—are examples [4].

The distinction between glottographic and semasiographic writing systems has clearly been made by the British linguist Geoffrey Sampson [3-5]. Michael Coe argues that writing systems are primarily glottographic, but that some degree of semasiography plays a part in all known writing [4]. In his fascinating story of the understanding and decipherment of Maya inscriptions and texts, he emphasizes phoneticism—the glottographic concept—to successfully break hieroglyphic codes based on a once spoken language.   

Keywords: linguistics, typology of writing systems.

References and more to explore
[1] The Free Dictionary: glottography [medical-dictionary.thefreedictionary.com/glottography].
[2] Malcolm D. Hyman: Of Glyphs and Glottography. DRAFT 2006-04-01, to appear in Language & Communication [archimedes.fas.harvard.edu/mdh/glottography.pdf].
[3] Geoffrey Sampson: Writing Systems [www.icosilune.com/2009/01/geoffrey-sampson-writing-systems].
[4] Michael D. Coe: Breaking the Maya Code. Thames & Hudson, New York, Revised Edition 1999; page 18 and others.
[5] Writing Systems by Geoffrey Sampson [www.grsampson.net/BWSys.html].

Friday, August 17, 2012

The word “hieroglyph” means sacred carving

The Greek word hieroglyph originally meant sacred carving or holy carving [1-3]. This noun is now synonymous with logograph: a single written (carved, painted or otherwise displayed) symbol. A hieroglyphic depiction may represent a person, an animal, a plant, a tool or some other object. Often untied from meaning, a hieroglyph stands for a sound or sequence of sounds belonging to the spoken language of a civilization that uses hieroglyphs in their language-based writing system. Hieroglyphs can stand by themselves, but typically compose inscriptions and scripts.

The terms hieroglyph and hieroglyphic go back to the fourth century A.D., when Horapollon, also referred to as Horapollo and Horus Apollus, associated them with Egyptian writing [3,4]. The Hieroglyphics (Hieroglyphica of Horapollo) influenced hieroglyphic decipherment.

Renaissance humanists such as the Jesuit polymath Athanasius Kircher (1602-1680) enthusiastically read the Hieroglyphics [3]. Although Kirchner made the assumption that hieroglyphs were phonetic symbols, he was not very successful in their identification and came to interpret hieroglyphs as symbols used by ancient people largely for ideographic writing. This doctrine of hieroglyphic wisdom delayed the decipherment of scripts such as those of the Maya writing system. Michael Coe [3] writes that “the fallacy that hieroglyphic scripts largely consisted of symbols that communicate ideas directly, without the intervention of language, was held as an article of faith by generations of distinguished Maya scholars, including Seler, Schellhas, and Thompson, as well as the multitude of their lesser followers.”

The understanding that hieroglyphs may simply stand for sounds was critical in deciphering Maya inscriptions and texts. Some hieroglyphs represent a phonetic value only. Often, they incorporate both semantic and phonetic elements. Therefore, one typically speaks of semanto-phonetic writing systems: currently used ones (Chinese, Japanese) and no longer used ones (AkkadianChữ-nôm, Egyptian, Jurchen, Khitan, Linear B, Luwian, Mayan, Sumerian, Tangut) [5].

Keywords: linguistics, writing, documenting, anthropology, history, decipherment, code breaking.

References and more to explore
[1] Encyclopedia Britannica: hieroglyph [www.britannica.com/EBchecked/topic/265009/hieroglyph].
[2] International World History Project: Ancient Egypt, Hieroglyphics [http://history-world.org/hieroglyphics.htm].
[3] Michael D. Coe: Breaking the Maya Code. Thames & Hudson, New York, Revised Edition 1999; page 16, 260, and 288 (Glossary).
[4] The Hieroglyphica of Horapollo. Translated from the Egyptian Tongue and put into Greek by Philip. Now rendered into English [www.masseiana.org/hiero.htm].
[5] Semanto-phonetic writing systems [www.omniglot.com/writing/semanto-phonetic.php].

Tuesday, June 26, 2012

Acronym in fire ecology: WUI for wildland urban interface

In geography and ecology, WUI  stands for wildland urban interface, also written wildland-urban interface” [1]. This is the belt or zone of transition between urban development and unoccupied land, such as forests and wildlife habitats. The WUI itself and adjacent areas on both sides are at high fire risk during dry seasons and conditions of strong winds. 

Wendy Tokuda, a journalist and Oakland hills (California) dweller, writes about efforts of WUI management in the Berkeley-Oakland Hills—an area that is particularly at danger when the dry and warm Diablo winds (named after Mount Diablo, a mountain in Contra Costa County northeast of Danville) are blowing from the east [2,3]. Wildfires can be natural,  but WUI fires are mostly caused by humans; in Tokuda's words [2]:
Almost all of the fires in the so-called “wildland urban interface (WUI or “wooie,” as some call it) are caused by people. Some are outright arson, but others are started inadvertently with cars, power tools, or burning leaves or debris. Either way, the bottom line is people cause fires, and there are a lot of people in California.
And in Colorada, Arizona, Mexico, Spain, Greece, Turkey, India, China, Australia, ...

Keywords: fire prevention, fire hazard, urban landscaping, firefighting, wooies.

References and more to explore
[1] IAFC - International Association of Fire Chiefs: Wildland Urban Interface (WUI) [www.iafc.org/Education/Events.cfm?itemnumber=4640].
[2] Wendy Tokuda: Taming the flames: Wildland fire in the East Bay Hills. Bay Nature July-September 2012, 46-50.
[3] East Bay Parks: Fire Ecology and Management. Part II in “Jul-Sep 2012 Issue Photo/Artwork Needs Bulletin” [baynature.org/about/image-needs].

Wednesday, June 20, 2012

Mt. Erebus and Mt. Terror on Ross Island named after ships of an expedition led by Sir James Clark Ross

The two volcanoes Mt. Erebus and Mt. Terror on Ross Island—a volcanic formation in Antarctica's Ross Sea—were named in 1841 by Sir James Clark Ross after his expedition ships H.M.S. Erebus and H.M.S. Terror, respectively. H.M.S. Erebus was named after the Greek god of primeval darkness [1-3].

Mt. Erebus is an active stratovolcano, 12,448 ft (3,794 m) high. It is the most southerly active volcano on Earth. Although one of the coldest spots on our planet, Mt. Erebus also is a hot spot: literally, considering its lava lake and fumaroles; and research-wise, considering the interesting occurrence of mosses and microbes, whose origin still is debated. Mt. Erebus belongs to the Pacific Ring of Fire. The New Mexico Institute of Mining and Technology maintains the Mount Erebus Volcano Observatory (MEVO) on Ross Island, next to Scott Base, which is operated by New Zealand to support field research [4,5].

Mt. Erebus' smaller companion, Mt. Terror with an elevation of 10,702 ft (3,262 m), is a (dormant or extinct?) basaltic shield volcano, flanked by cinder cones [6].

Both volcanoes have been listed as spectacular skiing destinations with over 10,000 ft (3,000 m) of vertically skiable slopes for downhill enthusiasts [7]. Olivia Judson, in her Erebus article [1] , describes the heavy outfit that researcher on Ross Island wear to protect themselves from extreme weather conditions. What kind of precautions would skiers take?  Thinking of skiing Mt. Terror downslope, I get terrified! 

Keywords:  earth science, geography, locality names, volcanology, mythology, microbiology, history.

References and more to explore
[1] Olivia Judson: Life in an Icy Inferno. National Geographic July 2012, 222 (1), 94-115 [ngm.nationalgeographic.com/2012/07/mount-erebus/judson-text].
[2] Encyclopedia Britannica: Ross Island [www.britannica.com/EBchecked/topic/510133/Ross-Island].
[3] Encyclopedia Mythica: Erebus by Ron Leadbetter [www.pantheon.org/articles/e/erebus.html].
[4] World Organization of Volcano Observatories: Mount Erebus Volcano Observatory [www.wovo.org/1900_02.html].
[5] Antarctica New Zealand: Scott Base [www.antarcticanz.govt.nz/scott-base].
[6] Oregon State/Education: Mount Terror, Ross Island, Antarctica [volcano.oregonstate.edu/vwdocs/volc_images/antarctica/terror.html].
[7] Skiing the Pacific Ring of Fire and Beyond: Mount Erebus [www.skimountaineer.com/ROF/ROF.php?name=Erebus] and  Mount Terror [www.skimountaineer.com/ROF/ROF.php?name=Terror].

Monday, June 4, 2012

From a temporary designator to a recognized chemical element name: ununhexium becomes livermorium

The chemical element with atomic number 116 was until now addressed as ununhexium (Uuh) using the temporary designator and three-letter atomic symbol system recommended by the International Union of Pure and Applied Chemistry (IUPAC).  A few days ago, IUPAC approved the name livermorium to replace the temporary designator ununhexium. The element symbol is Lv.

The name of this synthetic element honors the Lawrence Livermore National Laboratory in California, which, along with the Flerov Laboratory of Nuclear Reactions in Russia, has been involved in the discovery and production of various superheavy elements, including flerovium and livermorium [1].

The most stable isotope known today is livermorium-293, 293Lv, with has a half-life of about 60 ms. Less stable isotopes include 292Lv, 291Lv and 290Lv [2].

Livermorium's “left neighbor” —the element with atomic number 115, ununpentium, with the temporary symbol Uup—is provisionally named eka-bismuth, since it finds its place below the group 15 (Va) element bismuth in the periodic table. Following this Mendeleev-type notation, livermorium can be considered as eka-polonium (its historical name). Livermorium's “next-to-left neighbor ” with atomic number 114 (formerly ununquadium) is flerovium (Fl). The name flerovium also has just been approved officially by IUPAC [see ununquadium becomes flerovium].

[1] Adam Mann: 2 New Elements Named on Periodic Table. May 31, 2012 [www.wired.com/wiredscience/2012/05/flerovium-livermorium].
[2] Scribd: Livermorium [www.scribd.com/doc/95712552/Livermorium].

From a temporary designator to a recognized chemical element name: ununquadium becomes flerovium

The chemical element with atomic number 114 was until now addressed as ununquadium (Uuq) using the temporary designator and three-letter atomic symbol system recommended by the International Union of Pure and Applied Chemistry (IUPAC).  A few days ago, IUPAC approved the name flerovium to replace the temporary designator ununquadium. The element symbol is Fl.

Mistaking Fl as the symbol for fluorine, which simply is F, should be unlikely, since the latter is in use for so long. Further, flerovium will not play any major role in composing compounds and writing their formulae, because it is a radioactive chemical element with isotopes exhibiting half-lifes of only a few seconds or less.

The name of this synthetic element honors the Russian physicist Georgiy N. Flerov and also the Flerov Laboratory of Nuclear Reactions in Russia, a facility named after Flerov and known for its production of  various superheavy elements, including flerovium [1].

Flerovium's “left neighbor” —the element with atomic number 113, ununtrium, with the temporary symbol Uut—is provisionally named eka-thallium (no permanent IUPAC-approved name yet), since it finds its place below the group 13 (IIIa) element thallium in the periodic table. Following this Mendeleev-type notation, flerovium can be considered as eka-lead or eka-plumbum. Flerovium's “next-to-left neighbor ” with atomic number 112 (formerly ununbium) is officially named copernicium (Cn) [see naming history of copernicium].

[1] Adam Mann: 2 New Elements Named on Periodic Table. May 31, 2012 [www.wired.com/wiredscience/2012/05/flerovium-livermorium].

Sunday, June 3, 2012

A bacterium named after chemical transformations that it supports: Dehalococcoides ethenogenes

Dehalococcoides ethenogenes is an anaerobic, Gram-positive bacterium (phylum: Chloroflexi, class: Dehalococcoidetes)  [1].  Its name, Dehalococcoides ethenogenes, hints at the chemical transformations that it can perform: dehalogenation of halogenated ethene compounds to ethene.

Halogenated solvents such as chlorinated ethenes are environmental pollutants, often with a characteristic of long-term persistence. The discovery that D. ethenogenes can help to convert toxic chemicals into less harmful ones is of interest for the treatment of soil and groundwater, when contaminated with such halogenated hydrocarbons. It has been demonstrated, for example, that D. ethenogenes (strain 195)—transferred into an optimized growth medium—completely decomposes tetrachloroethene by reductive dechlorination [2,3].

An interesting question is if D. ethenogenes evolved in contaminated soil environments and developed the metabolic capability to transform chlorinated hydrocarbons for its own benefit. If so, this would be an example for “natural selection on speed” [4].

Keywords: microbiology, bioremediation, metabolic pathway, reductive dehalogenation, terminology.

References and more to explore
[1] Microbe Wiki: Dehalococcoides ethenogenes [microbewiki.kenyon.edu/index.php/Dehalococcoides_ethenogenes].
[2] X. Maymó-Gatell, Y.-t. Chien, J. M. Gossett and S. H. Zinder: Isolation of a Bacterium That Reductively Dechlorinates Tetrachloroethene to Ethene. Science 1997, 276 (5318), pp. 1568-1571. DOI: 10.1126/science.276.5318.1568
[3] X. Maymó-Gatell, T. Anguish and S. H. Zinder: Reductive Dechlorination of Chlorinated Ethenes and 1,2-Dichloroethane by “Dehalococcoides ethenogenes” 195. Applied and Environmental Microbiology 1999, 65 (7), pp. 3108-3113 [aem.asm.org/content/65/7/3108.abstract].
[4] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 248.

Friday, June 1, 2012

A term in aquatic microbiology: picocyanobacteria

Picocyanobacteria (plural of picocyanobacterium) are tiny cyanobacteria—less than two micrometers in size [1].  The prefix pico is derived from the Italian word piccolo for small. The size of picocyanobacteria cells is smaller than that of typical cyanobacteria cells, which ranges from one to forty micrometers [2].

Picocyanobacteria occur in freshwater and marine environments. They are photosynthetic organisms. Their diversity and distribution in dependence on light penetration through water layers and also on other factors is of great interest in ecology. For example, the abundance and composition of picocyanobacterial assemblages has been studied in many lakes of varying trophic state in relation to biomass and dissolved matter [3,4]. A two-year flow-cytometry investigation and in situ experiments in Lake Tahoe revealed seasonal patterns and clear temporal and spatial partitioning between picophytoplankton communities (picocyanobacteria and picoeukaryotes) [4].

Picocyanobacteria are the dominant microbes in the sunlit epipelagic zone of open oceans [5,6]. According to Tim Friend, “these little guys are of tremendous ecological importance” [5].  He informs that various institutions and research centers began sequencing the genomes of marine picocyanobacteria in 2003. Insight in picocyanobacterial metabolisms is critical for our understanding of global environmental and climate changes. Picocyanobacteria species—for example, those in the Synechococcaceae family—have an important role in carbon fixation and nutrient cycling in diverse marine ecosystems [7].

Keywords: marine microbiology, nanobiology, limnology, oceanography, microbial ecology, terminology.

References and more to explore
[1] Wiktionary: picocyanobacterium [en.wiktionary.org/wiki/picocyanobacterium].
[2] Cyanobacteria: huey.colorado.edu/cyanobacteria/about/cyanobacteria.php.
[3] F. R. Pick: The abundance and composition of freshwater picocyanobacteria in relation to light penetration. Limnol. Oceanogr. 1991, 36 (7), 1457-1462 [www.jstor.org/stable/2837651].
[4] Monika Winder:  Photosynthetic picoplankton dynamics in Lake Tahoe: temporal and spatial niche partitioning among prokaryotic and eukaryotic cells. J. Plankton Res. 2009, 31 (11), pp. 1307-1320 [plankton.ucdavis.edu/pdf/Winder_JPR09.pdf].
[5] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 143.
[6] The Darwin Project: Selective pressures on picocyanobacterial nitrogen use [darwinproject.mit.edu/?page_id=16].
[7] S. Huang, S. W. Wilhelm, H. R. Harvey, K. Taylor, N. Jiao and F. Chen: Novel lineages of Prochlorococcus and Synechococcus in the global oceans. The ISME Journal 2012, 6, pp. 285-297. DOI: 10.1038/ismej.2011.106.

Thursday, May 31, 2012

Ignicoccus islandicus, a species of archaea named by Karl Stetter

Ignicoccus islandicus is an archaea species living in marine hydrothermal vents such as those underwater fissures found in the Kolbeinsey Ridge north of Iceland, where this microbe was discovered (hence the epithet islandicus). Ignococci are hyperthermophiles. They are of great interest since they “play” host to even smaller archaea—some of the smallest organisms known: Nanoarchaeum equitans. These nano-sized microbes “sit”as parasites on the surface of ignicocci and also contain copies of parts of their host's genes within their own genome.

The World Register of Marine Species (WoRMS) provides data on the taxonomy of I. islandicus [1]:
Kingdom: Archaea
Phylum: Crenarchaeota
Class: Thermoprotei
Order: Desulfurococcales
Family: Desulfurococcaceae
Genus: Ignococcus
Species: I. islandicus (also in this genus: I. hospitalis, I. pacificus)

Tim Friend describes a presentation by German microbiologist Karl Otto Stetter at a conference in Yellowstone National Park (another hot spot of extremophile discoveries), during which Stetter talked about research on N. equitans, I. islandicus as well as the symbiotic (or parasitic) nanoarchaea-ignicoccus relationship:

Using the two-person research submersible Geo, samples were taken of sandy sediment and vent fluids at temperature around 90 degrees C [at the Kolbeinsey Ridge]. Black smoker samples obtained during a dive made on the submersible Alvin at a vent in in the Pacific also were analyzed. Initially, the samples from the mid-Atlantic ridge [Kolbeinsey Ridge] revealed a new genus and species of archaea, which Stetter named Ignicoccus islandicus. Electron microscopy photos taken at Stetter's lab of an additional Ignicoccus isolate revealed tiny strange spheres attached to its surface. This was shocking. No such thing had been seen on archaea. By culturing the organisms together Stetter was able to isolate Nanoarchaea then look for segments of its RNA. It does not possess the similar ribosomal RNA signature of other archaea. Tim Friend, 2007 [2].

Keywords: microbiology, nanobiology, hyperthermophile, crenarchaeon, nomenclature, taxonomy, history.

References and more to explore
[1] WoRMS taxon details: Ignicoccus islandicus Huber, Burggraf, Mayer, Wyschkony, Rachel & Stetter, 2000:
[2] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pages 121 to 124.

Wednesday, May 30, 2012

An archaeum originally misclassified as bacterium: Sulfolobus acidocaldarius

The microbe Sulfolobus acidocaldarius was isolated from a hot spring in Yellowstone National Park in 1972 and originally misclassified as bacterium [1,2]. Thomas D. Brook and his team described the new genus Sulfolobus as sulfur-oxidizing bacteria with generally spherical cells producing frequent lobes—hence the term Sulfolobus. The isolated microbes were further characterized as acidophilic, living at an optimal pH of 2-3 and optimal temperatures of 70-75 °C—hence the epithet acidocaldarius. Microbes thriving at such temperatures are called hyperthermophiles.

About five years later the archaea domain was proposed by Carl Woese and George Fox. Following detailed genome studies, S. acidocaldarius was then taxonomically classified as belonging to the phylum or kingdom  crenarchaeota in the domain archaea. S. acidocaldarius serves now as a model organism for the Crenarchaeota and is used for many studies in archaeal biology [3,4].

Keywords: microbiology, hyperthermophile, crenarchaeon, nomenclature, taxonomy, history.

References and more to explore
[1] T. D. Brook, K. M. Brock, R. T. Belly and R. L. Weiss:  Sulfolobus: A new genus of sulfur-oxidizing bacteria living at pH and high temperature. Archives of Microbiology 1972, 84 (1), pp. 54-68. DOI: 10.1007/BF00408082.
[2] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pages 110 and 111.
[3]  Microbe Wiki: Sulfolobus acidocaldarius [microbewiki.kenyon.edu/index.php/Sulfolobus_acidocaldarius].
[4] L. Chen et al.: The genome Sulfolobus acidocaldarius, a model organism of the Crenarcheota. Journal of Bacteriology 2005, 187 (14), pp. 4992-4999 [www.ncbi.nlm.nih.gov/pubmed/15995215].

Tuesday, May 29, 2012

Riding the fire sphere: Nanoarchaeum equitans

Nanoarchaeum equitans is one of the smallest living organisms known so far: a nano-sized (about 400 nm in diameter) microbe of the third domain,  named archaea [1-4]. The epithet equitans relates to the Latin nouns equus and equitatus, meaning “horse” and “horse riding,” respectively. N. equitans is too small to ride a horse: it is riding as a symbiont on other archaea in the genus Ignicoccus. Ignicocci (such as I.  islandicus and I. hospitalis) are sphere-shaped hyperthermophiles, (extremophiles, typically growing at 80 °C (176 F), but also at higher temperatures); hence the association that N. equitans is riding the fire sphere.

The symbiotic relationship between these two types of archaea has been described as N. equitans parasites attached to the surface of their Ignicoccus host. The parasites are living off the metabolism of its host. N. equitans lacks genes for its own metabolism, but possesses genes for DNA repair and reproduction. It has a highly compact genome—the smallest microbial genome sequenced to date [3,4].

N. equitans was discovered in 2002 by Karl Otto Stetter of the University of Regensburg (Bavaria, Germany), while exploring hydrothermal vents of the Kolbeinsey Ridge [1,2],  a stretch of the Mid-Atlantic Ridge named after a submarine volcano north of Iceland [5]. Stetter is responsible for the name Nanoarchaeum equitans.
Keywords: microbiology, nanobiology, archaeal kingdom Nanoarchaeota, hyperthermophile, crenarchaeon, nomenclature.

References and more to explore
[1] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007.
[2]  Microbe Wiki: Nanoarchaeum equitans [biowiki.kenyon.edu/index.php/Nanoarchaeum_equitans].
[3] E. Waters et al.: The genome of Nanoarchaeum rquitans: Insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. USA October 2003, 100 (22), pp. 12984-12988 [www.ncbi.nlm.nih.gov/pmc/articles/PMC240731].
[4] K. S. Makarova and E. V. Koonin: Evolutionary and functional genomics of the Archaea. Curr. Opin. Microbiol. October 2005, 8 (5), pp. 586-594 [www.ncbi.nlm.nih.gov/pubmed/16111915].
[5] Global Volcanism Program > Kolbeinsey Ridge: www.volcano.si.edu/world/volcano.cfm?vnum=1705-01=.

Wednesday, May 23, 2012

The adjective postprandial, meaning “after eating a meal”

The adjective postprandial ist derived from the Latin noun prandium meaning “meal” or “breakfast.” Hence, postprandial means “after eating a meal” or “after having breakfast.” The adjective preprandial means the opposite—“before eating a meal.”

This adjective appears in medical terms such as postprandial hyperglycemia (high blood sugar after a meal) and postprandial hypotension (excessive decrease in blood pressure after eating) [1-3].

Your pre- and postprandial states are regulated by the two hormons ghrelin and leptin, telling your brain that you should eat and stop eating, respectively. In her review on the recent research of the bacterial network in human bodies, Jennifer Ackerman explains that the bacterium Helicobacter pylori, which thrives in the acidic stomach environment, is responsible for your ghrelin level: people with H. pylori experience a postprandial decrease in ghrelin, while those lacking the bacterium do not and continue to have appetite [4].  In other words: if you apply antibiotics to reduce H. pylori-induced ulcers, you are going to interfere with your postprandial hormon levels and your appetite and, hence, may gain weight. So, use your postprandial time wisely to plan your future eating and treating habits.

Keywords: Latin, terminology, nutritional planning, human body regulation, physiology, medicine.

References and more to explore
[1] Medical dictionary: postprandial [www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=postprandial]
[2]  Medscape Education: Introduction: Clinical significance of postprandial hyperglycemia [www.medscape.org/viewarticle/491410].
[3] Home Health Handbook: postprandial hypotension [www.merckmanuals.com/home/heart_and_blood_vessel_disorders/low_blood_pressure/postprandial_hypotension.html].
[4] Jennifer Ackerman: The Ultimate Social Network. Scientific American June 2012, 306 (6), pp. 36-43. DOI: 10.1038/scientificamerican0612-36.

Monday, May 21, 2012

A gut bacterium named after Greek letters: Bacteroides thetaiotaomicron

Bacteroides thetaiotaomicron is a Gram-negative anaerobic microbe of the human intestinal tract [1].  The specific epithet of this scientific species name is derived from a combination of the three Greek letters theta, iota and omicron (see example in Names of species section in [2]). Curious about taxonomy, Mark Isaak provides amazing listings of diverse and interesting species and their sometimes odd names, but he admits he does not know why those letters were chosen to denote B. thetaiotaomicron [3].

Jennifer Ackerman writes that this term “sounds like it was named after a Greek sorority or fraternity” [4]. We still wonder why θ, ι and ο? More interesting than its name  is the role this bacterium plays in our intestinal tract. Ackerman reports the latest research results on how microbial genes benefit their human hosts and explains how B. thetaiotaomicron produces enzymes that are not encoded within the human genome. B. thetaiotaomicron “assists” us in digesting complex carbohydrates from plant foods: this bacterium “has genes that code for more than 260 enzymes capable of digesting plant matter, thus providing humans with a way to efficiently extract nutrients from oranges, apples, potatoes and wheat germ, among other food” [4]. B. thetaiotaomicron encodes more enzymes than there are Greek letters for.

Keywords: microbiology, microbial biorealm, nomenclature, terminology.

References and more to explore
[1] Microbe Wiki: Bacteroides thetaiotaomicron [microbewiki.kenyon.edu/index.php/Bacteroides_thetaiotaomicron].
[2] J. P. Euzéby: List of Prokaryotic names with Standing in Nomenclature   [www.bacterio.cict.fr/foreword.html].
[3] Mark Isaak: Curiosities of Biological Nomenclature [www.curioustaxonomy.net/etym/acronyms.html].
[4] Jennifer Ackerman: The Ultimate Social Network. Scientific American June 2012, 306 (6), pp. 36-43. DOI: 10.1038/scientificamerican0612-36.

Friday, May 18, 2012

Ochoa enzyme, named for the Spanish-American biochemist Severo Ochoa

The Ochoa enzyme is named for the Spanish-American biochemist Severo Ochoa (1905-1993), who was awarded the Nobel Prize in Physiology or Medicine 1959, jointly with Arthur Kornberg,  for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid [1-4].

Severo Ochoa was born in 1905 in Luarca, Spain, and died in Madrid in 1993. He worked, researched, taught and inspired others at various prestigious institutions in Spain, Germany and the Unites States [2].

The Ochoa enzyme, polynucleotide phosphorylase, was first isolated from the bacterium Azotobacter vinelandii [3]. The enzyme synthesizes RNA from ribonucleotide triphosphates. The Ochoa enzyme played a critical role in deciphering the genetic code: the American biochemist Marshall Nirenberg and Heinrich Matthaei (a postdoctoral researcher from the University of Bonn in Germany) used the Ochoa enzyme in the enzymatic synthesis of RNA, which they introduced into Escherichia coli [4,5]. Their work resulted  in an understanding of which three-nucleotide codon in a nucleic acid sequence specifies a particular single amino acid. Thanks to the Ochoa enzyme, they achieved the goal of the RNA Tie Club, whose members were corresponding with each other by amino-acid nicknames.

Keywords: history of science, biochemistry, enzymology, synthetic polynucleotides, mRNA sequences, proteins.

References and more to explore
[1] Nobelprize.org - The Official Web Site of the Nobel Prize: The Nobel Prize in Physiology or Medicine 1959 [www.nobelprize.org/nobel_prizes/medicine/laureates/1959].
[2] Ellen Dubinsky: Severo Ochoa (1905-1993). Washington University School of Medicine, Bernard Becker Medical Library [beckerexhibits.wustl.edu/mig/bios/ochoa.html].
[3] Laurence A. Moran: Nobel Laureate: Severo Ochoa. October 1, 2008 [sandwalk.blogspot.com/2008/10/nobel-laureate-severo-ochoa.html].
[4] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 69.
[5] Profiles in Science: The Marshall W. Nirenberg Papers [http://profiles.nlm.nih.gov/ps/retrieve/Narrative/JJ/p-nid/22].

Thursday, May 17, 2012

Corresponding with an amino-acid nickname

Many of us are living and socially interacting with their nicknames. But can you image to use the name of an amino acid as your nickname—or worse, its associated three-letter code? That 's exactly what the members of the RNA Tie Club did  [1-3]: This club was founded in 1954 by the Russian physicist George Gamow, who was interested in the relationship between the molecular RNA structure and protein formation in living cells.

During the 1950s and 1960s it was “hot and hip” (in bioscience and beyond) to speculate about and gain insight into genetic information at the molecular level: the relation between the structure of the DNA strand with its four-letter code and the α-amino acids (see codes and names in different languages) that combine into proteins. Researchers started to realize that RNA, a single-stranded molecule, is playing a key role in this biomolecular translation procedure. To crack the genetic code—now known as the list of amino-acid-encoding three-letter codons of RNA (and DNA)—in a joint effort, the RNA Tie Club was formed. Its members included George Gamow, who was Ala for alanine, Sir Francis Crick (Tyr for tyrosine), James Watson (Pro for proline) and Sydney Brenner (Val for valine).

Each club member received a necktie with the double helix structure and a lapel pin showing his (no females involved) amino acid symbol (hence the club name). The club had 20 members, one for each amino acid of interest (the so-called standard amino acids) and four honorary members representing each nucleotide. Eight members won a Nobel Prize; but not for cracking the code. Ironically, Marshall Nirenberg and Heinrich Matthaei, the scientists who successfully deciphered the genetic code by clever experiments in 1961, were not members of the club. Obviously, the club gentlemen did not participate in the hands-on deciphering race as much as they enjoyed smoking, drinking, tie-binding and hypothesizing.   

 The last time I checked the Wikipedia RNA-Tie-Club page (en.wikipedia.org/wiki/RNA_Tie_Club, also see [2]) I found a table with all club members, their amino-acid designation and their training. Interestingly, only half of them were biologists or chemists, while the others came from a physics and mathematics background.

Keywords: history of science, biochemistry, molecular biology, scientific gentlemen's club, humor, anecdotes.

References and more to explore
[1] Nobelprize.org - The Official Web Site of the Nobel Prize: How the Code was Cracked. What Code? [www.nobelprize.org/educational/medicine/gene-code/history.html].
[2] Power of the Gene > History of Genetics > The RNA Tie Club [powerofthegene.com/joomla/index.php/jistory-of-genetics/the-rna-tie-club]. 
[3] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 68.

Wednesday, May 16, 2012

A term in microbiology: archaea, shortened from archaeabacteria to denote the third domain

In 1977, when Carl Woese and George Fox reformulated the prokaryote-eukaryote grouping as a result of their phylogenetic analysis based upon ribosomal RNA sequencing, they proposed three main branches for the tree of life: eubacteria (typical bacteria), archaebacteria (then only methanogenic bacteria) and urkaryotes that evolved into components of eukaryotic cells [1].  Now these three domains are named bacteria, archaea and eukarya, respectively. Animals, plants and fungi, for example, branch of as subdomains from the latter.

The name archaea was introduced in 1990 by Woese as a short form of the term archaeabacteria [2]. The intention further was to eliminate the bacteria connotation, since archaea significantly differ from “typical” bacteria.

Although the three-domain system finds wide acceptance today, this bacteriocentric scheme has also been critized since it fails to recognize cell symbiogenesis—a five-kingdom scheme has been suggested instead [3].

Archaea are now known to fill many places of our world (at least on Earth). They are thriving in harsh environments, but also in soils, swamps and animal colons. A peer-reviewed, open-access journal with the title Archaea exists in which research and review articles are published that cover topics in archaea biology, ecology and bioinformatics  [4].

Keywords: microbiology, three-kingdom system, phyla of life, taxonomy, nomenclature.

References and more to explore
[1] Carl Wose and George Fox: Phylogenetic structure of the prokarotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. USA November 1977, 74 (11), pp. 5088-5090 [www.pnas.org/content/74/11/5088.full.pdf].
[2] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pp. 60-61 and 86.
[3] Lynn Margulis and Karlene V. Schwartz: Five Kingdoms. Henry Holt and Company, New York, Third Edition 1998.
[4] Hindawi Publishing Corporation: Archaea [www.hindawi.com/journals/arch/].

Tuesday, May 15, 2012

The word “prokaryote” in microbiology: a convenient classification term covering up knowledge gaps

The word prokaryote, sometimes spelled procaryote, is composed of the Greek roots pro and karyon for “before” and for “nut,” “seed” or “grain,” respectively. Within cytology contexts,  “grain” refers to the nucleus of a cell. Prokaryote literally means “before a nucleus,” describing a cell with no nucleus [1]. In contrast, an organisms consisting of cells with a nucleus is called eukaryote. The Greek prefix eu refers to a normal or well-composed condition.

The distinction between eukaryotic and prokaryotic cellular systems was first made in 1937 by the French biologist Edouard Chatton (1883-1947), who significantly contributed to our knowledge of single-celled protoctists such as ciliates and dinoflagellates and of mitotic cytology [2,3].

The paradigm of a simple prokaryote-eukaryote division has now been broken. In his book The Third Domain Tim Friend writes [3]: “Prokaryotes are a fabrication. They do not exist.” Friend reports that microbiologists Carl Woese and Norman Pace, known for their work on microorganism classification based on microbial RNA studies, “wish to rid microbiology entirely of the term prokaryote." This term was created as a matter of convenience and does not reflect how most current biologists depict the tree of life with its three main branches (domains) archaea, bacteria and eukarya (eucarya). Everything “non-eukarya” should not carelessly dumped into the “prokaryote basket”—and it doesn't have to with ever more sophisticated tools for molecular taxonomy becoming available.

Established terms rarely disappear completely.  The Principles of Modern Microbiology by Mark Wheelis [4], for example, surveys “procaryotic microbes” and focuses on the diversity of bacteria and archaea, introducing groups and lineages such as green-sulfur, green-nonsulfur, purple-nonsulfur, aerobic-sulfur and sulfate-reducing bacteria, deinococci, proteobacteria, gram-positive bacteria, cyanobacteria, spirochetes, chlamydia, euryarchaeotes, crenarchaeotes and nanoarchaeotes, just to name a few. Obviously, biodiversity is not a matter of having or not having a cell nucleus.  

Keywords: microbiology, prokaryote-eukaryote dichotomy, cell biology concepts, super-kingdoms, taxonomy, nomenclature.

References and more to explore
[1] wiseGEEK: What Are Prokaryotic Cells? [www.wisegeek.com/what-are-prokaryotic-cells.htm].
[2] Marie-Odile Soyer-Gobillard: Edouard Chatton (1883-1947) and the dinoflagellate protists: concepts and models. International Microbiology 2006, 9, pp. 173-177 [www.im.microbios.org/0903/0903173.pdf].
[3] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pp. 60-61 and 75.
[4] Mark Wheelis:  Principles of Modern Microbiology. Jones and Bartlett Publishers, Sudbury, Massachusetts, 2008; pp.305-321.