Friday, September 30, 2011

The origin of the words barbecue, canoe, hammock, hurricane and tobacco

The words barbecue, canoe, hammock, hurricane and tobacco are said to have their roots in the culture of Taíno people, who spoke an Arawakan language named after them. Robert M. Poole is tracing the Taíno culture, of which one can still find elements in the current architecture, craftsmanship, farming, fishing and healing practice on Caribbean islands including Cuba, Jamaica, Hispaniola (now Haiti and Dominican Republic), Puerto Rico and the Bahamas [1-4].

The Taíno evolved as a distinct people only after centuries of traveling and merging with other populations in the Antilles [1]. The Taíno almost disappeared after the Spaniards arrived and took hold in the Caribbean. Robert Poole refers to Jorge Estevez, a self-described Taíno from New York City,  who describes the diverse ethnicity of the Taíno. Estevez says that his ancestors were from a plethora of different tribes. He makes an interesting comparison with the ethnicity of Christopher Columbus and his ship crew—a mixture of Spaniards, Moors, Sephardic Jews and Basques.

So, how do we identify indigenous Taíno people or those who have discovered their inner Taíno? Maybe by simply watching out for those who enjoy paddling a canoe, napping in a hammock, savoring a barbecue, smoking tobacco or tracking a hurricane.

A brief glossary based on entries in the Online Etymology Dictionary
barbecue: from Arawakan (Haiti) barbakoa, meaning “framework of sticks,”
canoe: from Arawakan (Haiti) canaoua, meaning “rough-made or dugout boat,”
hammock: from the Taíno word amaca, apparently meaning “fish nets,”
hurricane: from an Arawakan word that appeared as furacan and furacão in 16th-century Spanish and Portuguese texts, respectively;
tobacco: probably from the Taíno word tabaco, said to mean “a roll of tobacco leaves,” but some scholars argue for the origin from the Arabic word tabbaq referring to medicinal herbs.

Keywords: linguistics, Arawakan language, Caribbean islands, etymology, anthropology.

References and more to explore
[1] Robert M. Poole: What Became of the Taíno? Smithsonian Magazine October 2011, 42 (6), 58-70 [].
[2] New World Encyclopedia: Taino:
[3] Welcome to Puerto Rico! - Taino Indians Culture:
[4] The Taino Indians - Native Americans of the Caribbean:

Sunday, September 18, 2011

Morse code, an alphabet of dots and dashes named after American painter and inventor Samuel Finley Breese Morse

Samuel F. B. Morse (1791-1872) was an American history painter. After his hope, to be chosen to paint historic panels for the Rotunda of the Capitol in Washington, was disappointed, Morse eventually gave up painting entirely and focused on work with telecommunication devices, based on  electrical signals, in his New York University studio apartment [1,2]. Together with mechanically skilled partners Leonard Gale and Alfred Vail, Morse developed telegraph models in 1837. At the same time he worked out  his own system for transmitting letters of the alphabet by groups of dots and dashes: the Morse code (see International Morse Code).

Earlier used code system for tracking electronically transmitted letters: The first electromechanical telegraph had been constructed in 1833 by the German physics professor Wilhelm Weber and mathematician Carl Friedrich Gauss in Göttingen, who used a plus-and-minus-sign code system to track signals [3]. The signals were sent over a wire between the Physics Institute and the Astronomical Observatory of the University of  Göttingen. Plus and minus signs were recorded depending on left and right swings of a responding magnet bar. Weber and Gauss used strings of length two, three and four of plus and minus signs to encode letters, which they transmitted in their experiments to demonstrate the feasibility of electromagnetic telegraphy. “Man hat's probiert. Es funktioniert. [It has been tested. It works.] ” was the scientifically minded conclusion by Gauss [3]. Further developments were left to Samuel Morse, his partners and competitors.

Keywords: history of telecommunication, long distance communication, electronic messaging

References and more to explore
[1] David McCullough: Reversal of Fortune. Smithsonian September 2011, 42 (5), 80-88 [].
[2] Internet Archive Wayback Machine: Samuel F. B. Morse [].
[3] Hubert Mania: Gauß Eine Biographie. Rowohlt Taschenbuch Verlag, Reinbeck bei Hamburg, Juli 2009; pages 282 and 324.

Friday, September 16, 2011

Boxdyl: a moiety-in-the-box

Chemical drawings conceptually capture molecular substructures as well as supramolecular structural parts often within a box, omitting compositional and configurational details. I call such a boxed structural part a boxdyl. Its purpose is to formally collapse the structure of certain moieties into a hypernode, hiding their details, but keeping the overall structural connectivity in place.

The chemical language CurlySMILES provides a format to map a molecular sketch, in which molecular-graph-based and boxed parts are present, into a linear notation. A typical boxdyl consists of a metaterm, categorizing the structural part or defining its role. This metaterm is framed by a rectangular, oval or otherwise shaped line. In a CurlySMILES notation the term is assigned as a value to the annotation dictionary key annotation dictionary key box, for example:

C{+Ybox=growth_hormone}c1ccc(cc1)C(C)=N \

This example illustrates the encoding of the modified growth hormone ARX201, as shown in the sketch. The framed term Growth hormone is the boxdyl. The structure of the potential drug ARX201 can formally be divided into three parts: (1) the growth hormone and (2) an oxime-functionalized derivative of an unnatural amino acid to which (3) a polyethylene glycol (PEG) chain is attached. The latter two parts take center stage here, since they are critical to the functionality of the drug, which would fail if PEG had to be attached to another amino acid and there interfer with the hormone's normal activity. To capture this concept, the CurlySMILES notation encodes the latter two parts—an alkoxyamine-functionalized PEG conjugated with the acetyl group of the unnatural amino acid p-acetylphenylalanine—in detail, while collapsing the complex growth hormon part into a boxdyl.

Keywords: cheminformatics, supramolecular drawings, linear notation, molecular graph, super-concepts, metaterms

Tuesday, September 13, 2011

Acronym in chemistry: BIBS for di-tert-butylisobutylsilyl, a protecting group

Di-tert-butylisobutylsilyl, abbreviated as BIBS, is a sterically bulk trialkylsily protecting group. BIBS is useful for protecting acidic hydroxyl molecules such as those of trifluoromethanesulfonic acid (triflic acid, HTf), giving the silyl ether compound di-tert-butylisobutyl silyl triflate (BIBSOTf). The intermediate may then be deprotected with tetrabutylammonium fluoride. The BIBS protecting group offers new routes in synthetic chemistry by obtaining robust protected moieties via Si-O and Si-N bonds. BIBS' bulkiness retards or inhibits hydrolysis in comparison with other commonly employed protecting groups [1,2].

A CurlySMILES notation for BIBS:

Keywords: organic chemistry, organic synthesis, trialkylsilyl group, structural unit, substructure

[1] Science & Technology Concentrates: A More Stable Silyl Ether. Chemical & Engineering News July 25, 2011, 89 (30), page 38.
[2 ] H. Liang, L. Hu and E. J. Corey: Di-tert-butylisobutylsilyl, Another Useful Protecting Group.Org. Lett. 2011, 13 (15), pp.4120-4123. DOI: 10.1021/ol201640y.

Monday, September 12, 2011

BrettPhos, an organic compound and ligand named after Brett Fors of MIT's Buchwald Lab

BrettPhos is named after Brett Fors of  Stephen L. Buchwald's lab at MIT [1]. Spelling and pronunciation of this chemical compound name resembles the spelling and pronunciation of the name of its designer. The word part Phos, substituting for Fors, hints at the phosphorus atom in the molecular structure of  BrettPhos and its formal derivation from phosphane (phosphine). Systematic names for BrettPhos are 2-(dicyclohexylphosphino)-3,6-dimethoxy-2',4',6'-triisopropyl-1,1'-biphenyl and dicyclohexyl-[3,6-dimethoxy-2-(2,4,6-triisopropylphenyl)phenyl]phosphane. The molecular formula is C35H53O2P.

BrettPhos is a promising and effective ligand in metal-catalyzed synthesis including palladium-catalyzed cross-coupling reactions, Suzuki coupling, trifluormethylation reactions and fluorinations [1-3].

A SMILES notation for BrettPhos:  

[1] Profiles from NOS: Brett Fors: The Guy With The Namesake Ligand. Chemical & Engineering News July 11, 2011, 89 (28), page 34 []. 
[2] B. P. Fors, D. A. Watson, M. R. Biscoe and S. L. Buchwald: A Highly Active Catalyst for Pd-Catalyzed Amination Reactions: Cross-Coupling Reactions Using Aryl Mesylates and the Highly Selective Monoarylation of Primary Amines Using Aryl Chlorides. J. Am. Chem. Soc. October 2008, 130 (41), 13552-13554 [].
[3] Patent application by S. L. Buchwald, D. A. Watson, M. Su and G. Teverovskiy: Metal-catalyzed Carbon-Fluorine Bond Formation [].

Friday, September 9, 2011

Eponyms in ichthyology: Malacanthus plumieri, Sicydium plumieri, Haemulon plumieri

The tilefish Malacanthus plumieri (Malacanthidae), the Sirajo goby Sicydium plumieri (Gobiidae), and the white grunt Haemulon plumieri (Haemulidae) are named after the seventeenth-century French monk Charles Plumier (1646-1704), who is known for his compilation of plant and animal records, including his artful and detailed drawings of fish species such as the European perch (Perca fluviatilis), the striated frogfish (Antennarius striatus, then known as “Rana piscatrix ”), the rudd (Scardinius erythrophthalmus) and a grayling (Thymallus thymallus) [1].

Charles Plumier was a traveler, naturalist, botanist and artist. Living and working before Carl Linnaeus was born and dying before he could publish most of his discoveries, Plumier was never given his rightful place among early naturalists [1]. Today, we encounter his name in the binomial nomenclature of the species listed above. The sand tilefish, Malacanthus plumieri, and the Sirajo goby, Sicydium plumieri, were named after him by German naturalist Marcus Bloch (1786) [2,3]; the white grunt, Haemulon plumieri, by French herpetologist and ichthyologist Bernard-Germain-Etienne Lacépède (1801) [5-7].

Keywords: natural history, ichthyology, scientific names.

References and more to explore
[1] Theodore W. Pietsch: Plumier's Passion. Natural History July/August 2011, 119 (7), pp.30-36.
[2] Latintos: Sand tilefish, Malacanthus plumieri, named by German naturalist Marcus E. Bloch after French monk Charles Plumier  [].
[3] Encyclopedia of Life: Sicydium plumieri (Bloch, 1786) [].
[4] Fish Index: White Grunt (Haemulon plumieri)  [].
[5] Smithsonian Marine Station at Fort Pierce: Haemulon plumieri (Lacepede, 1801) [].
[6] Fishwise: Haemulon plumieri (Lacepede, 1801) [].
[7] Bernard-Germain-Etienne Lacépède (1756-1825) [].

Sand tilefish, Malacanthus plumieri, named by German naturalist Marcus E. Bloch after French monk Charles Plumier

The Caribbean sand tilefish, Malacanthus plumieri (Malacanthidae), was in 1786 named by German naturalist Marcus E. Bloch after the French monk, traveler, biologist and artist Charles Plumier (1646-1704) [1-4]. A detailed drawing of the sand tilefish, made by Plumier during his stay in Martinique, can be admired—among other amazing drawings of  fish species and their internal soft parts by Plumier—in a recent Natural History article by Theodore Pietsch [1]. A drawing footnote says that the sand tilefish grows as much as two feet long and makes a burrow in the sand in tropical and subtropical waters of the Western Atlantic.

Most sources refer to Charles Plumier as a botanist. He also deserves the attribute of an early ichthyologist or pioneering fish naturalist.

Keywords: ichthyology,  order Perciformes, tilefishes, eponym.

References and more to explore
[1] Theodore W. Pietsch: Plumier's Passion. Natural History July/August 2011, 119 (7), pp.30-36.
[2] Theodore W. Pietsch: Charles Plumier (1646-1704) and his drawings of French and American fishes. Archives of Natural Historyatural History February 2001, 28 (1), pp. 1-57. DOI: 10.3366/anh.2001.28.1.1.
[3] World Register of Marine Species: Malacanthus plumieri (Bloch, 1786) [].
[4] Pictures: Encyclopedia of Life | Caribbean Reefs | Caribbean Sea - BonaireNotice that Plumier's drawing contains more or different details (color patterns, shapes of body parts) than the photographies!

Thursday, September 8, 2011

An acronym in environmental monitoring: NEON for National Ecological Observatory Network

 In ecology, NEON stands for National Ecological Observatory Network [1,2]. NEON is a public source (, that is going to acquire biological and physical data from plains, forests and lakes, representing different regions of vegetation, landforms, climate and ecosystem performance. The data will be collected and represented in computer spreadsheets, available to scientists, teachers, students, decision makers and the public in general to promote broad ecological literacy.

According to the Nature editorial preceding [1], NEON could be a powerful tool for investigating human pressure on the biosphere: “in an exceedingly difficult fiscal environment, the new ecological network represents a refreshingly forward-looking initiative. Ecologists (and headline writers) everywhere should welcome it.”

Notice the distinction between fiscal environment and ecological environment!

Further, notice that NEON is pronounced in the same way as is the name of the chemical element and rare gas neon. In writing and printing, the two meanings of this term can usually be distinguished by uppercase and lowercase letters.  

References and details
[1] Jeff Tollefson: US launches eco-network. Nature 11. August 2011, 476 (7359), page 135 (also see editorial on page 125) [].
[2] National Science Foundation: Final National Ecological Observatory Network (NEON) Environment Assessment:

Tuesday, September 6, 2011

Lobb's buckwheat (Eriogonum lobbii) named after Cornish plant collector William Lobb

The plant Lobb's buckwheat (Eriogonum lobbii) of the buckwheat family (Polygonaceae) is named after the Cornish plant collector William Lobb, who was born in Cornwall around 1809 and died in San Francisco in 1864 [1,2]. In the 1840s Lobb was collecting plants in South America. He came to North America in 1849, where he continued plant collection in California at the height of the Gold Rush. Lobb's buckwheat, sometimes named granite buckwheat, is found in northern California; for example, on rocky slopes at high elevation along the Sierra Nevada crest.

Keywords: botanist, history, nomenclature, scientific name

[1] Joseph Ewan: William Lobb, plant hunter for Veitch and messenger of the big tree. University of California Press, Berkely, 1973
[2] Plant hunters - William Lobb [].

Friday, September 2, 2011

A term in biology: hyperphagia season

In medical context, hyperphagia is defined as “an increased appetite for and consumption of food, thought to be associated with a lesion or injury in the hypothalamus.” In general, biological terms, hyperphagia simply means over-eating [1]. Hyperphagia season is the season of over-eating. This is the season during which hibernating animals prepare for the cold season by consuming excess food, gaining weight, and putting on fat to be ready for a period of inactivity.

For example, Cheryl Lyn Dybas illustrates the hyperphagia season of black bears (Ursus americanus) in Minnesota [2]: the bears build up their fat reserves for winter by eating their fills of acorns, hazelnuts, chokeberries and other treats. Dybas mentions that during this time bears are more likely to come near people and residential areas, especially if natural foods are scarce. Grizzly bears (Ursus arctos) also increase their food intake as the period of hibernation approaches [3].

References and more to explore
[1] The Free Dictionary:
[2] Cheryl Lyn Dybas: A Frenzy of Bears. Its “hyperphagia season” in Minnesota. Natural History July/August 2011, 119 (7), 22-29 [].
[3] The Grizzly or Brown Bear [].