Monday, October 31, 2011

A term in biochemistry: anammox for anaerobic ammonium oxidation

Anammox stands for anaerobic ammonium oxidation, a biochemical reaction that combines ammonium and nitrite (or nitrate) to form dinitrogen (N2) gas and water [1-5]. This reaction is performed by aquatic anammox bacteria belonging to the planctomycete group. Using the bacterium Kuenenia stuttgartiensis, it has been shown recently that the reaction pathway involves nitric oxide and hydrazine as intermediates [1,2]: hydrazine is formed via a hydrazine synthase complex and then converted to N2 by a hydrazine dehydragenase enzyme.

The anammox reaction is one of the key biogeochemical processes that leads to the release of geochemically fixed nitrogen as N2 into the atmosphere. Bacteria growth and study of the anammox reaction is typically performed in bioreactors and lab or industrial environments, but evidence for its natural occurrence below the oxic zone of oceans, such as the anoxic deep water in the Black Sea (the world's largest anoxic basin), has been provided [5].

Keywords: chemistry, biogeochemistry, bioreaction, reaction mechanism, cellular organisms, order Planctomycetales, oceanic nitrogen cycle

References and more to explore
[1] J. Kemsley: Making Dinitrogen. Chem & Eng. News, October 10, 2011, 89 (41), page10.
[2] B. Kartal et al.: Molecular mechanism of anaerobic ammonium oxidation. Nature, 2011, published online October 2, 2011. doi
[3] J. G. Kuenen: Anammox bacteria: from discovery to application. Nat. Rev. Microbiol.  April 2008, 6 (4), pp. 320-326 [].
[4] N. Shivaraman and G. Shivaraman: Anammox - A novel microbial process for ammonium removal. Current Science June 25, 2003, 84 (12), pp. 1507-1508 [].
[5] M. M. M. Kuypers et al.: Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature April 10, 2003, 422, pp. 608-611.
doi: 10.1038/nature01472.

Sunday, October 30, 2011

HTML5 <canvas> tag: markup, support and non-support

HTML5 includes the canvas element for display of graphics. Canvas markup is implemented by inserting a <canvas> tag in the desired spot of your HTML document and associating JavaScript code that specifies what to draw and paint [1].
The latest versions of browsers such as Firefox, Opera, Safari, Google Chrome, Konqueror and Internet Explorer support canvas markup.     

Markup should contain alternative content for users of older browser versions or canvas-incompatible browsers; as illustrated with the following syntax:

In those cases where the drawing is going to fail, the animated note of file canvsup_600x490.jpg (shown to the right) would display. If the browser is not image-compatible either, a plain text string with that note would appear.

An image element expects an external source to be uploaded and displayed, while a canvas element uses page-internal instructions (or supplementing js files) to create an image within the capabilities of the client browser.

Canvas-based two-dimensional drawing, for example, is implemented by fetching the canvas element via methods of the JavaScript document object:

var canvas = document.getElementById("my-canvas");
var artist = canvas.getContext("2d");

Drawing instructions are then implemented with methods of the artist object (or whatever  variable name you are coming up with for the context object). Tutorials and examples that explain and show how to use these methods are available online; for example see www.w3schools, basics/opera, developer/mozilla, wikipedia, updates to standard.

[1] Thomas A. Powell: HTML & CSS: The Complete Reference. Fifth Edition. McGraw Hill, New York, 2010.; pages 82 to 101.

Friday, October 28, 2011

A premodifying noun in retail: artisan for hand-crafted—not mass-produced

An artisan is a skilled worker or craftsman [1]. The word has Latin roots: the verb artire means “to instruct in the arts” [2]. Artesanos were craftsmen in Renaissance Italy. With minor transformations the word—and some artesanos, too—made it into France, England and other countries.

Today, retailers of specialty food like to offer their products artisan-style. These days you get artisan sandwiches and bakery items at Starbucks and—in California—at Peet's coffeeshops. And you'll find artisan chocolate, chips, ice cream, pastry, pies, pizza and salads all around. Tom Vierhile, innovation insights director at Datamonitor, says, that the word suggests less likely mass-produced, less processed and perhaps better tasting food [3].

Maybe customers are willing to pay a somewhat higher price for artisan-labeled goods and meals. But is the artisanship always present in the chef's recipe and execution, not just in the word? At your next artisanery visit, make sure that the products, which you get offered or served, are worth the label. Otherwise argue for a rebate and a premodifier drop.

[1]  YourDictionary:
[2] Online Etymology Dictionary:
[3] Bruce Horowitz: But is it Art(isan)? Reno-Gazette Journal October 28, 2011, 9A [].

Thursday, October 27, 2011

A term in computer science and website programming: weblet for individual web page

A weblet was defined by Al Globus and Chris Beaumont at the NASA Ames Research Center as “a highly interconnected portion of the World Wide Web devoted to a particular end, usually maintained by a single individual or organization and located at a single site” [1]. Globus and Beaumont were primarily concerned with educational materials and their access via Internet. For example, the Annotated Scientific Visualization Weblet Bibliography is a listing of weblets maintained by universities, government laboratories, military and commercial sites, providing data, pictures, animations and movies in specific domains of interest [2]. (Remember, this was more than ten years before the YouTube take-off).

Netlingo describes weblet as a techie-speak term that refers to a set of documents accessible via hyperlinks from a starting page [3]. One common feature of a weblet is that it assists site users with in-depth information or demonstrations in connection with a specialized topic. The word microsite may qualify as a synomym for weblet [4]. I guess, my CurlySMILES cluster of pages and subpages present a weblet example—confined to the cheminformatics domain.

References and notes
[1] Al Globus and Chris Beaumont: Spinning a Useful Weblet, 1994 [].
[2] Al Globus:  Annotated Scientific Visualization Weblet Bibliography, 1994  [].
[3] netlingo: Weblet [].
[4] For comparison and further details see Wikipedia sites about  weblet, microsite and minisite.

Thursday, October 20, 2011

A misnomer in chemistry and materials science: β-alumina

Alumina is aluminum(III) oxide (or aluminium(III) oxide) with the formula Al2O3. Alumina occurs in different crystalline forms, for example, α- and γ-alumina [1]. β-Alumina, however, is not another form or polymorph of alumina, as one would assume from the term with a greek-letter prefix. Its name is a misnomer: β-alumina is a ternary oxide of formula xNa2O · nAl2O3, having typical compositions with x between 1.25 and 1.4 and n about 11 [2].

The term β-alumina has also been used to describe a family of compounds of general formula M2O · nX2O3, where n can have values from 5 to 11, M is a monovalent cation and X is a trivalent cation [3] . With M = Na+ and X = Al3+,  the most important member of this family is obtained: sodium β-alumina (compare with formula above). Compositions with other alkali, silver, thallium and ammonium ions for M and gallium(III) and iron(III) ions for X make further members of the β-alumina family [3].

Keywords: solid-state ionics, material structure and composition, ternary oxides, non-stoichiometric compounds 

References and more to explore
[1] Alumina:
[2] Beta-alumina:
[3] Anthony R. West: Solid State Chemistry and its Applications. John Wiley & Sons, Chichester, 1984; page 467.

Fossil turtle Kallokibotion bajazidi named by Franz Nopcsa after his Albanian secretary Bajazid Elmaz Doda

The scientific name Kallokibotion bajazidi refers to a 70-million-year-old fossil turtle that was found in the 1920s in Eastern Hungary (Transylvania), now part of Romania [1-3]. In 1923, openly homosexual Franz Nopcsa,  nicknamed the “Dinosaur Baron,” named the “Transylvanian turtle” in honor of his Albanian secretary and lover Bajazid Elmaz Doda [3]. Franz Nopsca loved fossils and is known for pioneering techniques for fossil analysis and formulating theories about dinosaur evolution and dispersal. To the best of my knowledge, Kallokibotion bajazidi is the only reptile species owing its name to a gay relationship.

Keywords: natural history, paleontology, Uppermost Cretaceous, Austria-Hungary, Romania, Reptilia, Testudines, taxon

[1] Baron Francis Nopsca: On the Geological Importance of the Primitive Reptilian Fauna of the Uppermost Cretaceous of Hungary; with a Description of a New Tortoise (Kallokibotion). Quarterly Journal of the Geological Society 1923, 74, pp. 100-116 [].
[2] Paleobiology Database: Kalokibotion bajazidi Nopsca 1923 (turtle):
[3] Gareth Dyke: The Dinosaur Baron of Transylvania. Scientific American October 2011, 305 (4), pp. 80-83 [].

Wednesday, October 19, 2011

Synonymous terms in solid-state chemistry: “solid electrolyte,” “fast ion conductor” and “superionic conductor”

Chapter 13 with the title “Ionic Conductivity and Solid Electrolytes” in the Solid State Chemistry textbook by Anthony West [1] is a good introduction to the named subject. I found the three terms solid electrolyte, fast ion conductor and superionic conductor mentioned there. Such materials are special salts, composed of ions, with one set of ions able to move around easily.  West describes the materials as having a special crystal structure with open tunnels or layers through which mobile ions may move.

Typical electrical conductivity values of solid electrolytes are between 10-3 and 101 S cm-1, about the range found for common molten salts.  The conductivity of solid electrolytes is higher than that of  “normal” ionic crystals with values from below 10-18 up to 10-4 S cm-1[1].  In contrast to metals (typical conductivity range: 101 to 105 S cm-1), the conductivity of solid electrolytes and ionic crystals increases with increasing temperature. Solid electrolytes are a special class of ionic crystals and—to highlight this relation— the term superionic crystal is used in addition to the above given phrases [2].

Notice that these terms and distinctions refer to phases at low and ambient temperatures—often not well defined. Some materials become appreciable solid electrolytes at elevated temperatures, such as the high temperature oxide ion conductor zirconia (ZrO2, above ~600 °C). However, all salts—unless they evaporate—transform into electrically conductive ionic liquids above their melting point.

Keywords: physics, materials science, solid-state ionics, ionic conductivity, electrical conductivity, temperature dependence

[1] Anthony R. West: Solid State Chemistry and its Applications. John Wiley & Sons, Chichester, 1984; page 453 and others.
[2] Angus Gray-Weale's Research - Superionic conductors:

Wednesday, October 12, 2011

Acronym in mineralogy: CNMMN for Commission on New Minerals and Mineral Names

The Commission on New Minerals and Mineral Names (CNMMN) is part of the International Mineralogical Association (IMA). It was established in 1959 with the task of controlling the introduction of new minerals and mineral names and dealing with nomenclature matters in mineralogy [1]. In July 2006, the CNMMN was merged with the Commission on Classification of Minerals to form the Commission on New Minerals and Mineral Names (CNMMN) [2].

The acronym CNMMN is found in various articles published before the merger. For example, a paper of 1987 discusses the procedure for the submission of a mineral name proposal and provides criteria for selecting a new name based on chemical composition and crystallographic properties, particularly dealing with polymorphs, polytypes, regular interstratifications, adjectival modifiers as well as group and varietal names [3]. Examples of name decision making are provided.

There are mineral classes and subgroups and, accordingly, there are subcommittees for the revision and approval of the nomenclature of material classes. What about the classification and naming of chain silicates such as amphiboles? Yes, there is (or was) a subcommittee on it; and changing nomenclature they did [4]: alkali amphiboles became sodic amphiboles, names like tremolitic horblende (now magnesiohornblende), crossite (now glaucophane or ferroglaucophane or magnesioriebeckite or riebeckite), tirodite (now manganocummingtonite) and dannemorite (now manganogrunerite) were abolished and new amphibole names such as nyböite, leakeite, kornite, ungarettiite, sandanagaite and cannilloite were approved.

Keywords: history of organizations, nomenclature, terms in mineralogy, crystallography, solid state chemistry 

[1] Commission on New Minerals and Mineral Names (CNMMN):
[2] Objectives and officers:
[3] E. H. Nickel and J. A. Mandarino: Procedures involving the IMA Commission on New Minerals and Mineral Names and guidelines on mineral nomenclature. American Mineralogist 1987, 72, 1031-1042 [].
[4] B. L. Leake et al.: Nomenclature of Amphiboles: Report of the Subcommittee on Amphiboles of the International Mineralogical Association, Commission on New Minerals and Mineral Names. The Canadian Mineralogist 1997, 35, 219-246 [].

Sunday, October 9, 2011

Dr. Mises, pseudonym of the German psychologist and philosopher Gustav Theodor Fechner

The German psychologist and philosopher Gustav Theodor Fechner (1801-1887) published satirical and other essays as well as books under the pseudonym, Dr. Mises [1]: Starting out as a physician at the University of Leipzig (where he stayed anchored) in Germany, he developed an aversion to medicine and became interested in subjects of diverse fields including psychology, philosopy, physics and mathematics.  He is often referred to as an experimental psychologist and the founder of psychophysics [2]. Hans G. Fellner and William F. Lindgren point us to Fechner's interest in the fourth dimension [1]: The essays Der Schatten ist lebendig (“The Shadow is Alive”) and Der Raum hat vier Dimensionen (“Space has four Dimensions”) are probably the earliest popular, animating writings going beyond the perception of a three-dimensional world. Both essays have been translated and are printed in [1]. Fechner's writings are original, filled with parodic flair. The world looks flat, if you can't see the higher dimensions!

Keywords: philosophy, mathematics, fourth dimension, physical space, parody, psychology, history

References and more to explore
[1] Hans G. Fellner and William F. Lindgren: Gustav Theodor Fechner: Pioneer of the Fourth Dimension. Mathematical Intelligencer Fall 2011, 33 (3), 126-137. 
DOI: 10.1007/s00283-011-9214-7.
[2] Encyclopedia of World Biography on Gustav Theodor

Saturday, October 8, 2011

A term in mathematics: Meissner body named after Swiss mathematician Ernst Meissner

A Meissner body is a three-dimensional body of constant width, which is generated by rotating the Reuleaux triangle around its axis of symmetry. Bernd Kawohl and Christof Weber recently presented an excellent account on the history and recent developments of  “Meissner's Mysterious Bodies” [1]. They show drawings and plaster models of Meissner bodies and refer to mathematical models produced by the publisher Martin Schilling in 1911, of which Ernst Meissner described said body that became named after him.

Ernst Meissner (also spelled Meißner) was born on September 1, 1883, in Zofingen and died on March 17, 1939 in Zollikon, Switzerland [1,3]. He studied mathematics and physics at the Swiss Polytechnic (Polytechnikum Zürich), later to become the Swiss Federal Institute of Technology (ETH) in Zurich. For two semesters he studied with Klein, Hilbert and Minkowski at the University of Göttingen, Germany, and qualified as a professor (Habilitation) in 1909, after returning to the ETH. Kawohl and Weber describe Meissner's achievements as extraordinarily diverse (see “curriculum vitae of Ernst Meissner” in Appendix of [1]). Meissner's publications cover fields in pure and applied mathematics (number theory, algebra, geometry, Fourier analysis) as well as mechanics (geophysics, seismology, theory of oscillations). 

Keywords: geometry, spheroforms, history

References and more to explore
[1] Bernd Kawohl and Christof Weber: Meissner's Mysterious Bodies. Mathematical Intelligencer Fall 2011, 33 (3), 94-101. 
DOI: 10.1007/s00283-011-9239-y, PDF:
[2] Models: and
[3] Historisches Lexikon der Schweiz - Meissner, Ernst:

Tuesday, October 4, 2011

Climbing terms for descending on a rope: abseil and abseiling

Abseil is a climbing term that means “descending on a rope.” The word “abseil” also occurs in names of canyon wall locations that require abseiling to get down to the canyon creek. In a recent National Geographic article, author Mark Jenkins and photographer Carsten Peter Mark feature the exciting world (underworld) of  slot canyons in the Blue Mountains west of Sydney, Australia [1]. They illustrate the waterfall Danae Falls, which drops and cascades down into Danae Brook Canyon. Along the down-cascading path, you see various pitches with names such as First waterfall (pitch length of 98 ft), Narrow cleft (92 ft) and multiple abseils including Chockstone abseil (92 ft), Waterfall abseil (89 ft), Danae direct abseil (102 ft) and  Slippery log abseil (66 ft, without slipping, I assume). You probably get the idea that it needs some climbing techniques [2,3] and lots of experience—beyond linguistics skills—to manage such abseils.

The noun “abseil” is derived from German Seil. The noun Seil (masculine) translates into rope in English. The German verb seilen means to rope. The prefix ab adds the meaning of down. Abseilen means literally to rope down, but also has the meaning of to disappear or to escape one's duties. Interestingly, the word Abseil does not exist by itself as a German-language noun (not in the Duden anyway), but may occur in composed words, for example Abseilstelle (abseil location) oder Abseilfieber (abseil fever).

Keywords: rock climbing, canyoneering skills, waterfalls, geography, topology, etymology, German-English translation

References and more to explore
[1] Mark Jenkins: Lost in Slot Canyons. National Geographic October 2011, 220 (4),  60-81 [ and].
[2] Climbing Techniques - Abseiling:
[3] Backing Up An Abseil: