Friday, November 6, 2015

“Tree of Life” associations

The term Tree of Life is associated with words such as biodiversity, phylogeny and taxonomy. In the 1970s, Carl Woese and his coworkers began with studies that lead to the reorganization of whatever lives under the biologically grouped kingdoms [1]. Instead of using classifiers based on morphological and physiological data, they employed genetic data to establish relationships between different organisms. In 1977, Woese and Fox proposed eubacteria, archaebacteria and urkaryotes (now bacteria, archaea and eukarya) as the main branches of the tree; defining a three-domain system with various subdomains.

The Tree of Life continues to be rewritten—and refined. There are web sites dedicated to track and incorporate published (sub)trees and to provide information for their twigs and leaves [2,3]. A recent study initiated the automatic assembly and digitalization of published trees into a “complete” Tree of Life [2,4]. This Open Tree of Life can be updated via uploading. The underlying data can be downloaded for homework, analysis and phylogenetic research. The authors of the evolutionary tree study express the following hope [4]:  

This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate, change, agriculture, and genomics.

A supertree to save the world!

References and more to explore
[1] NovaNext: The Man Who Rewrote the Tree of Life [].
[2] Open Tree of Life:
[3] TOLWeb: Tree of Life web project [].
[4] Hincliff, C. E. et al.: Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 2015, 112 (41), DOI: 10.1073/pnas.1423041112.

Friday, October 30, 2015

A twisted, racetrack-shaped torus to generate and confine a plasma: the stellarator

A stellarator is a nuclear-fusion device invented in the early 1950s by American astrophysicist and plasma physicist Lyman Spitzer (1914-1997) [1,2]. The name of this complex device signifies a star machine, referring to the goal of harnessing the energy like a stellar object such as the sun. Therefore, this device is also called by the composed term stellarator-heliotron and the concept behind its design is named the stellarator-heliotron concept [3]—heliotron literally meaning sun automat.

In the plasma physics community a stellarator is also known as the black horse of reactors, since it is very difficult to build. It took 1.1 million construction hours (spent over 19 years, including times of construction setbacks) to built the world's largest experimental stellarator, the W7-X, which currently is ready to be fired up [4].

W7-X is short for Wendelstein 7-X, referring to the Wendelstein mountain in the Bavarian Alps south of Garching, where its predecessor Wendelstein 7-AS was built and tested [5]. The successor W7-X was assembled by researchers and engineers at the Max-Planck-Institut für Plasmaphysik (IPP) in Greifswald, northeast Germany. Now being completed, W7-X—with large modular superconducting coils enabling steady-state plasma operations—is the world's largest fusion device of the stellarator type [5]:
Its objective is to investigate the suitability of this type for a power plant. It will also test an optimised magnetic field for confining the plasma, which will be produced by a system of 50 non-planar and superconducting magnetic coils, this being the technical core piece of the device.
W7-X is expected to generate its first plasma at the end of this year.

References and more to explore
[1]  National Aeronautic and Space Administration: Lyman Spitzer, Jr. [].
[2] Encyclopaedia Britannica: Lyman Spitzer, Jr. [].
[3] Energy technology Network: Stellarator-Heliotron Concept [].
[4] Yahoo!: Germany is about to start up a monster machine that could revolutionize the way we use energy [].
[5] IPP: Wendelstein 7-AS (1988-2002) [].
[6] IPP: Wendelstein 7-X [].

Sunday, October 25, 2015

Frank's introduction to stock market terms

Stock market trading goes back over about two centuries. When telegraphy revolutionized long-distance communication in the 1840s and facilitated stock-market quotations, a new era began for traders, banks and brokerage firms as well as any business relying on their services. As always with novel, growing human activities, an insider language evolved. Today's stock market terminology is super-rich in trading-specific words and phrases [1-3].

Basic trading terms were used then as they are today. Frank Algernon Cowperwood in Theodore Dreiser's financial-world thriller The Financier, published in its first version in 1912,  learned the key terms of trading early along his career path leading to his life as a fiercely ambitious businessman. Even before the telegraph and telephone became commonplace, bears and bulls were fighting and struggling as they do in current markets.

Frank started out under the direction of Mr. Arthur Rivers, the regular floor man of Tighe & Company in Philadelphia. He soon learned that it is useless to try to figure out exactly why stocks rose and fell. Anything can make or break a market. To thrive in the exciting or traumatizing world of uncertainty and constant struggle required knowledge of how to word the flow of virtual money. Frank mastered the stock market lingo with ease [4]:  

Frank soon picked up all the technicalities of the situation. A “bull,” he learned, was one who bought in anticipation of a higher price to come; and if he was “loaded up” with a “line” of stocks he was said to be “long.” He sold to “realize” his profit, or if his margins were exhausted he was “wiped out.” A “bear” was one who sold stocks most frequently he did not have, in anticipation of a lower price, at which he could buy and satisfy his previous sales. He was “short” when he had sold what he did not own, and he “covered” when he bought to satisfy his sales and to realize his profits or to protect himself against further loss in case prices advance instead of declining. He was in a “corner” when he found that he could not buy in order to make good the stock he had borrowed for delivery and the return of which had been demanded. He was then obliged to settle practically at a price fixed by those to whom he and other “shorts” had sold.

The terms within quotes have been text-colored by the author of this post. These terms are mostly elementary words out of the basic English vocabulary that take on a different, context-specific meaning within the financial market domain. 

Keywords: literature, economy, financial world, investment terms, stock market vocabulary.

References and more to explore
[1] Nasdaq: Glossary of Stock Market Terms [].
[2] Value Stock Guide: Stock Market Terminology for Beginners [].
[3] Wise Stock Buyer: Stock Market Terminology [].
[4] Theodore Dreiser: The Financier. Penguin Books Ltd, London, England; Penguin Classics edition with an introduction by Larzer Ziff, 2008.

Friday, September 4, 2015

Connecting with Alfred Russel Wallace

For many, the name Charles Darwin (1809-1882) is synonymous with all observations and thoughts that originated into the theory of evolution by natural selection. Lately, the name of the fourteen-years-younger cofounder of evolution theory is increasingly recognized: Alfred Russel Wallace (1823-1913). The British naturalist  and geographer Wallace is also known as the founder of the science of biogeography; highlighted by the term Wallace Line or Wallace's Line that refers to the boundary line separating Asia-associated and New-Guinea/Australia-associated ecozones.

The September 2015 issue of Natural History—a special commemorative issue as part of the Alfred Russel Wallace Centenary Celebration—honors the outstanding 19th century explorer and biologist. The ARW Online article in the section provides various links to discover Wallace and his world:
ARW Online. Natural History September 2015, 123 (7), page 5.

Thursday, August 27, 2015

An acronym marking the intersection of music and information technology: CCRMA for Center for Computer Research in Music and Acoustics

Computers are frequently employed these days to generate music. Computers are also used to analyze music. Further, they are used to analyze soundscapes of both urban and natural environments. To close the cycle, composers weave environmental sounds, such as animal sounds, into their musical creations.  A composition that incorporates an imitations of a bird song such as a nightingale melody is a case in point.

A natural soundscape is not just a great stimulation for musical compositions, but constitutes a complex acoustical web, which is not fully understood by humans and remains a rich resource for human enjoyment, recreation and (re)connection to the natural world. At the Stanford Center for Computer Research in Music and Acoustics, CCRMA—pronounced “karma” (the first “c” is silent), musicians and researchers are teaming up and exploring computer-assisted technology as an artistic medium and as a research tool [1].

Bernie Krause includes the CCRMA innovators into his review of biophonically inspired composers in Chapter Six “Different Croaks for Different Folks” of his book "The Great Animal Orchestra"[2]. Mentioning the British composer Benjamin Britten, some of whose orchestrations are strongly influenced by the urban and natural soundscapes that Britten experienced at his home in East Anglia and during his travels, Krause continues:

And there are others, including works by a few students at the Center for Computer Research in Music and Acoustics (CCRMA) at Stanford—where composers and innovators such as John Chowning study the intersection of music and information technology using advanced synthesizers as creative media tools through which they express what they discovered. Some of the students have begun to reexamine the potential of natural soundscapes and early instruments as important sources of compositional stimulus.

The oldest musical instrument known today is a Stone Age flute, carved from bone and ivory at least 35,000 years ago [3]. Neither do we know the ancient natural soundscape of southwestern Germany, where the flute was found, nor do we know what tunes were played on it by the early European humans.  But certainly, listining to the soundscape and making sounds (often too many and too loud) is part of human nature and activities.

Keywords: soundscapes, eco-acoustics, biophony, musical science, anthroplolgy.

References and more to explore
[1] Center for Computer Research in Music and Acoustics:
[2] Bernie Krause: The Great Animal Orchestra. Back Bay Books, New York, March 2013; page 150 in first Back Bay paperback edition.
[3] Archaeologists unearth oldest musical instruments ever found:

Sunday, July 19, 2015

Acronym in biology: HHO for Havers-Halberg oscillation

Biological rhythms in animals have fascinated observers of nature for a long time. An example is the circadian rhythm, a diurnal rhythm synchronized with the day/night circle. In mammals, metabolic product rhythms with a twenty-four-hour oscillation pattern are known as the mammalian circadian clock [1]. The concentration of molecular components in body fluids rises and falls on a twenty-four hour cycle.

What about metabolites cycling according to a multidien schedule (multi-day schedule)?  Timothy G. Bromage of the Hard Tissue Research Unit of the New York University College of Dentistry describes findings of his research group showing that certain metabolites in the blood of domestic pigs cycled on a five-day rhythm. Those metabolites belong to two distinct groups: metabolites of one group reached their peak three days later than the other [2,3].

Until recently, such synchronized multi-day rhythms have commonly been overlooked in mammalian chronobiology studies. Most strikingly, the five-day rhythm leaves its marks in enamel and bone structures. The Bromage team found that the pig's teeth show the striae-of-Retzius pattern with a repeat period of exactly five. This evidence suggests a multidien rhythm that regulates growth and body size, which is called the Havers-Halberg oscillation (HHO) by Bromage and his colleagues [2]:

We call this rhythm the Havers-Halberg oscillation (HHO), after Clopton Havers who in 1691 described what we now know are lamellae in bone and striae of Retzius in enamel, and Franz Halberg, father of modern chronobiology. 

Periodic layer structures in hard tissue are documented for various mammal species. Rhythm & stria relationships, which will be similar to the reported correlation between biochemical oscillations and linear marks in pig teeth, can be expected to exist in other mammal species. For humans, the better understanding of such repeat patterns may eventually help to design individual health and healing plans in rhythm with metabolic cycles—think rhythmically tuned diet and medication.    

The English physician Clopton Havers was a pioneer in osteogeny. Anatomists are familiar with Haversian canals traversing compact bone tissue. Havers was born in 1657 in Stambourne, Essex. He is best known for his work on the microstructure of bone. In 1686, he was elected a Fellow of the Royal Society. Havers died in Essex in 1702 [3,4].

Franz Halberg was born in 1919 in Bistriz in Romania. In the 1940s, Halberg performed medicinal research at the University of Innsbruck and became a citizen of Austria. In 1948, he immigrated to the United States, where he continued his inqueries in biology and medicine.  Halberg  founded the fields of  quantitative chronobiolgy, chronomics and chronobioethics. He died in 2013 [5].

The term “Havers-Halberg oscillation” honors two outstanding scientists living in different epochs and gaining insight within until recently unconnected domains, which now find their synthesis in a more holistic view in the science community, deepening and advancing cross-subdiscipline understanding in life science.

Keywords: quantitative chronobiology, biological cycles, chronomics, osteogeny, stria of Retzius, life history.

References and more to explore
[1] Caroline H. Ko and Joseph S. Takahashi: Molecular components of the mammalian circadian clock. Human Molecular Genetics 2006, R271-R277 [].
[2] Timothy G. Bromage: Long in the Tooth: Striation in teeth reveal the pace of life. Natural History June 2015, 123 (5),16-21.
[3] Timothy G. Bromage and Malvin N. Janai: The Havers-Halberg oscillation regulates primate tissue and organ masses across the life-history continuum. Biological Journal of the Linnean Society August 2014, 112 (4), 649-656 [].
[4] Jessie Dobson: Clopton Havers [].
[5] The Blog of Funny Names: Clopton Havers, Bone Master [].
[6] Germaine Cornelissen, Francine Halberg, Julia Halberg and Othild Schwartzkopff: Obituary. Franz Halberg, MD (5 July 1919-9 June 2013) - In Appreciation. Chronobiology International 2013, 1-3 [].

Wednesday, July 8, 2015

Topotaxis: geomagnetically driven orientation and navigation above the ocean floor

The composed noun topotaxis is built from the Greek words topos, meaning place, and taxis, meaning order or responsive movement. The word topotaxis refers to the movement of an animal  from place to place (migration) in response to geographical features the animal is able to sense. The term was coined by the marine biologist and sensory physiologist A. Peter Klimley, who wants to find out if sharks and rays can detect changes in local magnetic underwater topography and use these magnetic-field features as their guiding map—instead of the globally-caused, compass-oriented vector of  Earth's magnetic field, as typically hypothesized [1,2].

Islands, seamounts and subsurface ridges are examples of  geographic formations causing distinct local geomagnetic underwater-landmarks. By diving with the sharks and tagging & tracking them to follow their ocean floor navigation, Klimley explains how is idea of geomagnetic topotaxis has surfaced [3]: 

Our survey of the magnetic field surrounding El Bajo [an volcanic underwater mountain in Mexico's Sea of Cortez rising from the depths of the ocean floor to just 20 meters from the surface] revealed that the outbound and return path of the sharks we were studying coincided with these magnetic ridges and valleys, I hypothesized, therefore, that the magnetic variations in the ocean floor presented the sharks with the equivalent of a route map, and in a 1993 paper in Marine Biology [4], I coined the term topotaxis for an animal's orientation to these magnetic-topographic features.

Understanding navigation and resting behavior of sharks and other marine life—driven by topotactic guidance or other means—will help to design marine sanctuaries, which may protect dwindling shark populations and at the same time provide sites for educational and recreational shark ecotourism.

Keywords: magnetic topography, magnetoreception, travel pattern, migration, Baha California.

References and more to explore
[1] A. Peter Klimley, Director of the Biotelemetry Laboratory, University of California, Davis:
[2] A. Peter Klimley: Experimental Study of Geomagnetic Topotaxis With Elasmobranchs. Grantome:
[3] A. Peter Klimley: Shark Trails of the Eastern Pacific. American Scientist July-August 2015, 103 (4), pp. 276-287 [].
[4] A. P. Klimley: Highly directional swimming by scalloped hammerhead sharks, Sphyrna lewini, and subsurface irradiance, temperature, bathymetry, and geomagnetic field. Marine Biology 1993, 117, pp. 1-22 [].

Monday, July 6, 2015

Acronym in experimental physics: MINOS for Main Injector Neutrino Oscillation Search

Neutrinos are subatomic particles (leptons) with half-integer spin and without electric charge. They come in three types or flavors: electron-neutrino, muon-neutrino and tau-neutrino. The flavor of a neutrino oscillates, while the neutrino is flying through space—for example, after being generated by beta-decay of a radioactive atom. Different neutrino flavors have slightly different masses [1].

Neutrino oscillation has been observed by different experiments.  The oscillation probability of  neutrinos and the exact tiny neutrino masses have not yet been measured with the desired accuracy. The MINOS experiment has the aim to do this: the abbreviation MINOS stands for Main Injector Neutrino Oscillation Search [1-3] .

MINOS is based on two detectors: the first being stationed at the neutrino source at the Fermilab and the second being located 450 miles (735 km) away at the Soudan Underground Mine, a former iron mining site, in norther Minnesota. Frank Close explains the MINOS design in his acclaimed “neutrino cracker” [3]:

A huge 5000 tonne detector was built in a new, bigger, cavern in the Soudan mine. This utises yet another detection method. Charged particles passing through plastic, which had been loaded with small quantities of special chemicals, emit flashes of light (scintillate). These scintillations can be collected and delivered to phototubes which are similar in principle to those used to detect the Cerenkov light in the water detectors. By forming the plastic into narrow strips, sandwiched between plates of steel, the path of the charged particles through the detector can be followed, and by magnetising the steel plates, the curvature of the paths and thus the energy of the produced particles can be measured. From all this information, the details of the neutrino interaction, and in particular its energy, can be reconstructed. Then both the distance travelled (the 735 km from Fermilab) and the neutrino energy are known. A very similar (but smaller) detector was also built at Fermilab, so that by comparing the energy distribution of the neutrinos measured at Fermilab with that measured at Soudan, they could measure how any deficit depended on the energy of the neutrinos. If, as expected, this showed an oscillatory pattern, it would measure the difference in mass between the produced and oscillated neutrino.

What are the special chemicals loaded into the steel-plate-sandwiched plastic strips?

Neutrino mass is not included in the Standard Model of particle physics: neutrinos are assumed to have zero mass. But the phenomenon of neutrino oscillation suggests non-zero masses. MINOS is expected to clarify the neutrino mass conundrum and, thus, add new insight to particle physics and beyond.

Keywordselementary particles, Cerenkov radiation, oscillation pattern, nuclear physics, cosmology.

References and more to explore
[1] Cambridge MINOS Group:
[2] Fermilab: The MINOS Experiment and NuMI Beamline:
[3] Frank Close: Neutrino. Oxford University Press, Oxford, U.K., 2010.

Wednesday, June 24, 2015

Labeling exoworlds: Name an exosolar planet! Try CosmoBlue!

If you want to get involved in naming well-characterized planets that were discovered in exoplanetary systems prior to December 31, 2008, here is your gateway: You may just want to sign up and cast a vote on suggested names as an individual. Community-based, your astronomy-interested club or a public astronomical organization, including planetariums and amateur astronomy groups, will be admitted to submit a naming proposal [1]— ganz offiziell! [2]. The results will be announced in August during a meeting of the IAU (International Astronomical Union) in Honolulu, Hawaii. Daniel Stone writes [3]:

If you've ever wanted to name a planet, now's your chance. The International Astronomical Union (IAU) wants help naming 32 exoplanetsplanets that orbit a star other than our sun. Scientific and cultural organizations were asked to submit potential names. The public can rank finalists at until July 15.

The winning public names will not replace scientific designations (usually consisting of a proper noun or abbreviation, sometimes followed by numbers and always followed by a lowercase letter [4]); but will be IAU-recognized  “with due credit to the organization that proposed it” [1].

What names can we expect, or should we not expect, to win?
Names that are trademark-protected or of a principally commercial nature will not be considered. Also excluded are names of living individuals and pets. Offensive words and terms with politically sensitive associations won't have a chance either. Proposed names should be 16 characters or less in length, preferably one word, pronounceable and “not too similar to an existing name of an astronomical object.”

I guess, CosmoBlue would be a name that fits the above criteria. I know a cat named Cosmo, but she is not blue—so, the pet name violation is circumvented. Further, we need to search—at least—trademark databases and astronomical databases such as the IAU's Minor Planet Center. The latter tells me that it does not have any matching documents for CosmoBlue. The name “CosmoBlue” sounds like a distinctive candidate. Yet, I am not sure if such a promising name should be wasted for a non-habitable planet.

Keywords: astronomy, astronomical nomenclature, exoplanet designation, public naming campaign, Zooniverse.

Rules and references
[1] Name exoworlds: Rules and Privacy. []. 
[2] Jan Hattenbach ( Benennen Sie einen Exoplaneten und das offiziell! [].
[3] Daniel Stone: What should the name be? You Decide. National Geography July 2015, 228 (1), no page number. 
[4] International Astronomical Union: Naming of exoplanets [].

Monday, May 25, 2015

A main-belt asteroid named after forest-canopy scientist Margaret D. Lowman

A Mont-Blanc-size main-belt asteroid, orbiting near Jupiter and discovered by astronomer couple Carolyn S. and Eugene M. Shoemaker at Palomar in 1988, is named after American canopy ecologist Margaret D. Lowman: 10739 Lowman (1988 JB1) [1,2].

The orbit of botanist Margaret Lowman (b. 1953, New York)—known as Canopy Meg—includes Australia, Africa, Peru, Panama, Belize and Florida, where she explores and studies what is happening at the tops of trees [3]. As a pioneer of the science of canopy ecology, Meg is also nicknamed the “real-life Lorax” by National Geographic and “Einstein of the treetops” by Wall Street Journal [4].

Richard Preston writes in his canopy-guided nonfiction page turner The Wild Trees [3]:

In 1978, Margaret D. Lowman, a young American graduate student in botany at the University of Sydney, in Australia, decided to write her dissertation on treetops. She had been anxious about choosing a topic, and she thought that at least nobody had tried this one. Lowman wanted to climb the trees, but she had no idea how to do that. She joined a caving club in Sydney, and the other members taught her how to climb a rope using Jumar ascenders. Lowman sewed a climbing harness for herself made out of seat-belt straps, and welded some pieces of iron together to make a slingshot. She then went into a forest near Sydney and used the slingshot to shoot a fishing line over the branch of a tree, after which she attached a thin nylon cord to the fishing line and dragged the cord over the branch. Then she attached a rope to the nylon cord and pulled it over. Lowman began making solo ascents into the rain-forest canopy of eastern Australia. “When I first started out climbing trees, I had no idea that they held fifty percent of the life on the planet,” Lowman said to me. “We had no clue that the forest canopy is this amazing hot spot for biodiversity.” 
[Richard Preston, 2007]

During an evening tree climb in New South Wales, “Treetop Meg” once slipped and fell off a branch; fifteen feet to the ground in free fall. She got badly bruised, but without suffering any broken bones [2]. It was time to design smart devices and structures that support safe canopy access and observation.

How did the canopy-asteroid connection arise?
Margaret Lowman has designed hot-air balloons for over 30 years.  The balloons advanced the exploration of canopy worlds, but not asteroid belts. This was the realm of planetary scientist Carolyn Shoemaker (b.  1929, Gallup, New Mexico), a leading discoverer of comets and asteroids and co-discoverer of  the to-be-named asteroid. Shoemaker, who “loves to name real estate in outer space after woman whose work I admire” [2], honored Canopy Meg by coining one of “her” asteroids Lowman,  Thus, an outer-space object got named for a woman dedicated to understand life at the delicate interface between outer space and the human landscape—at Earth's fragile and fractal arboreta branching out into the universe.

Keywords: Minor Planet Lowmanastronomy, planetary science, terminology, honoring female scientists, name giving.

References and more to explore
[1] Jet Propulsion Laboratory's Small-Body Database Browser: 10739 Lowman (1988 JB1) [].
[2] Richard Preston: The Wild Trees. Random House Trade Paperbacks, New York, 2008; pp. 53-55.
[3] The Official Web Site Of Margaret D. Lowman, Ph.D., aka: Canopy Meg [].
[4] Oxford Centre for Tropical Forest: Margaret D Lowman, Ph.D. [].

More on naming and classifying orbiting objects in planetary science:

Friday, April 3, 2015

The IUPAC color books: terminology, nomenclature and ontology in chemistry, biochemistry and materials science

Here is a brief overview—hyperlinks included—of those color books by the International Union of Pure and Applied Chemistry (IUPAC) that have accessible online versions [1-3]:

The interactive Gold Book at, and the PDF version Compendium of Chemical Terminology at It is not named for the color or chemical element gold, but to honor the chemist Victor Gold (1922-1985), who initiated its first edition [4,5].

The Green Book: Quantities, Units and Symbols in Physical Chemistry []

The Blue Book: Nomenclature of Organic Chemistry by Advanced Chemistry Development (ACD) []

The Purple Book: Compendium of Polymer Terminology and Nomenclature []

The Orange Book: Compendium of Analytical Nomenclature (website by David S. Moore) []

The Red Book: Nomenclature of Inorganic Chemistry []

The “White Book”: Biochemical Nomenclature and Related Documents []

The Silver Book: Clinical Chemistry is currently under revision (future status of Web availability unknown) [[project_nr]=2007-033-3-700]

Organizationally, the color code gold (in memory of Victor Gold) stands for the combined glossary. As you may have realized by reading the compendium titles, the other colors refer to sub-disciplines or branches of chemistry: green for physical, blue for organic, purple for macromolecular, orange for analytical, red for inorganic, “white” for “biochemical” and silver for clinical [6].

Mark Borkum and Jeremy Frey argue the case for Web-based, machine-accessible representations of these and other IUPAC publications to make them available for reuse by software developers [1]. Further, they urge IUPAC to take immediate measures in promoting a “cohesive vision of chemical terminology, nomenclature and ontology on the Web” by acknowledging and visionarily involving interdisciplinary chemists and software engineers:

There are many fine examples of “chemist-ware” on the Web, but their developers represent an absolutely tiny fraction of the world's chemists, who are presently unable to fully express themselves.
[Mark Borkum and Jeremy Frey, 2015]

Keyterms: cheminformatics, polymer informatics, computer science, e-science infrastructurestandardization, chemical compendia, online resources, open software architectureopen-source mantra.

[1] Mark I. Borkum and Jeremy G. Frey: What's in a Name? Quite a Lot, as it Happens! Chemistry International March-April 2015, pp. 7-9 [].
[2] IUPAC: Nomenclature and Terminology (including IUPAC color books) [].
[3] Wikipedia: IUPAC book [].
[4] W. J. Albery: Victor Gold, 29 June 1922 - 29 September 1985. Biographical Memoirs of Fellows of the Royal Society December 1987, 33, 263 ff. DOI:
[5] Hawaii Book Library: Victor Gold (Chemist) [].
[6] International Union of Pure and Applied Chemistry: Nomenclature Books [].

Monday, March 30, 2015

New Harmony—a small southwestern Indiana town first named Harmonie—considered the birthplace of North American geology

Which small town can say of itself that it is today a scientific center of national significance?  If you can't find a current one, what about one in the past—let's say, in the early nineteenth century. Simon Winchester introduces us to such a community:  New Harmony, now a historic town on the Wabash River in Posey County, Indiana, which was founded in 1814 by a religious group of immigrants from Germany. Beginning as an utopian community and sold to a wealthy industrialist and idealist from Scotland in 1825, this tiny, spiritually minded town—a “Community of Equality”—soon attracted intellectuals, philosophers and naturalists [1-4].

New Harmony's original name is Harmonie, the German-spelled word for harmony. Winchester describes its early development [1]:

The town, first simply named Harmonie, was settled initially by early-nineteenth-century Germans, men and women fleeing to America much as the Pilgrim Fathers had fled two centuries before, to escape religious restrictions back home. Their piety and hard work paid off quickly, and they eventually moved on to larger quarters, selling their tiny settlement to another idealist adventurer, the campaigning Welsh socialist Robert Owen. He, flushed with the success of a millworkers' commune that he had organized outside Edinburgh, planned to establish a utopian beachhead in America, based on socialist ideals. He renamed the former German village New Harmony; and once he had settled during the winter of 1825, he invited like-minded idealists to join him.  

What led to New Harmony's scientific distinction?
Among its inhabitants were no fewer than seven geologists of later fame. Geology played an important role in exploring the American West and in unifying the States. According to Winchester, New Harmony was the place where this realization of geology's importance was born. It is the birthplace of North American geology.

Keywords: geography, history, place name, European immigrants, European American settlement, socialists.

References and more to explore
[1] Simon Winchester: The Men Who United The States. First Harper Perennial edition published 2014.
[2] Country Homes of America: City Data for New Harmony, Indiana [].
[3] Historic New Harmony Newsletter: New Harmony a Magnet for Geologists Past and Present. Fall 2007 [].
[4] Indiana State Museum: Historic New Harmony [].

Thursday, March 26, 2015

Microscopic silica structures in plant tissue: phytoliths and their other names

Phytoliths develop in the tissue of various plant species after take-up of monosilicic-acid-containing groundwater from soil. Silicon dioxide (silica) concretions are then deposited in those plant structures—both intracellular and extracellular structures—through which the water circulates. These plant stones are commonly called phytoliths, but are known under other names as well [1]:
The term is Greek (phyto means plant, lith means stone). Other names that have been used in the past include opaline silica, plant opal, and opal phytoliths, but the most common is simply phytoliths.
Silica phytoliths are a subgroup of biogenic opal [2]. This explains why some synonyms associate phytoliths with opal, a hydrated amorphous form of silica. Phytoliths are composed of mainly noncrystalline silica, enriched in terrigenous metals and other chemical elements such as carbon permitting radiometric dating.

Arguably, the most interesting aspect of phytolithic mineral secretions is their long-time persistence as siliceous plant remains, such as the brown-colored fine dust that Charles Darwin observed at Porto Praya during his voyage on the Beagle [1].

Phytoliths are now systematically studied by multidisciplinary research communities [3-6]. Forensics, archaeology and paleobotany are disciplines naturally interested in the phytolithic fingerprint structures to identify the past occurrences and associations of plant species. Phytolith analysis, including phytolith dating, helps to reconstruct past macro- end microenvironments. The understanding of agricultural development and evolving human dietary patterns based on phytolith tracking is shaping current decisions in health care and nutrition.

Phytolith properties such as mechanical strength, heat absorbability and fungal defense activity makes the broadly accessible phytoliths promising constituents for micro- and nanotechnology applications.

Keyterms: inorganic biochemistry, archaeobotany, biogenic silicaecofact, microfossil, plant opal, opaline silica, [SiOx(OH)4-2x]n.

References and more to explore
[1] Thomas C. Hart: Phytoliths: The Storytelling Stones Inside Plants. American Scientist March April 2015103 (2), pp. 136-143 [].
[2] J. Kamenik, J. Mizera and Z. Řanda: Chemical composition of plant silica phytoliths. Environmental Chemistry Letters 2013. 11 (2), pp. 189-195. doi.: 10.1007/10311-012-0396-9.
[3] Irwin Rovner: Plant Opal Phytolith Analysis: Major Advances in Archaeobotanical Research. Advances in Archaeological Method and Theory 1983, 6, pp. 225-266.
[4] C.A.E. Strömberg et al.: Decoupling the spread of grassland from the evolution of grazer-type herbivores in South America. Nature Communications 2012, 4, article number: 1478. doi: 10.1038/ncomms2508.
[5] Soumya Jain: Biogenic Silica: An Inspiration to Nanotechnology. December 30, 2013 [].
[6] J. Mazumdar and R. Mukhopadhyay: Phytoliths of fern IV: In some aquatic ferns and Chinese Brake fern. Bioresearch Bulletin 2013, 2 (2) [].

Tuesday, February 10, 2015

Weston Beach in the Point Lobos Reserve named in memory of photographer Edward Weston

Weston Beach, south shore in Point Lobos Reserve
Weston Beach in the Point Lobos State Natural Reserve is an inspiring place for family fun activities as well as for exploring intertidal biology and aspects of California geology. Maybe you did come here to take pictures on some of your precious days by the shore. Edward Weston did so for 20 years.

Edward Henry Weston (1886-1958) photographed life, forms and textures around Point Lobos. After him, Weston Beach is named since the United States Board on Geographic Names made this name official in October 1979. Nobody less than the American environmentalist and photographer Ansel Easton Adams (1902-1984) had proposed that this small pebble beach be named in Weston's memory. Adams said that this beach “is sort of synonymous with him” [1].

Edward Weston was born on March 24, 1886, in Highland Park, Illinois, and died on January 1, 1958, in Carmel—just a few miles north of what is now the Point Lobos Reserve. Weston's photography work ranges from natural forms and landscapes to portraits, nudes and close-ups, created in Mexico and California [2,3]. Weston was inducted into the International Photography Hall of Fame and Museum in 1984 [4].

Spontaneous rock art, found at Weston Beach (January 25, 2015)

References and more to explore
[1] How did Weston Beach get its name? Section in the Brochure Weston Beach Tide Pools by Mary Conway, Melissa Gobell and Marie Murphy. California State Parks, Monterey District, 2211 Garden Road, Monterey, CA 93940, USA
[2] Edward Weston Biography [].
[3] Encyclopaedia Britannica: Edward Weston. American photographer [].
[4] International Photography Hall of Fame and Museum: Edward Weston [].

Tuesday, January 20, 2015

Michael D. Thompson Trailhead named after Reno High School graduate and outdoor enthusiast

Trailhead kiosk depiction of Michael D. Thompson

The Michael D. Thompson Trailhead west of Reno in northern Nevada is a gateway to the scenic landscapes of the Truckee River Valley and the Mount Rose Wilderness. This trailhead is a popular meeting place and starting point for short, medium and long hikes to destinations such as the Steamboat Trail Arrow, the two Holes in the Wall and via the Hunter Creek Trail to  Hunter Creek Falls and beyond .

The trailhead is named in honor of  Reno-born Michael David Thompson, who died young and is still remembered by some locals. The trailhead kiosk provides a brief biography:

The land for this trailhead has been given to the citizens of Washoe County in memory of Michael David Thompson. Michael was born in Reno on June 10, 1970, graduating from Reno High School in 1988. He was president of his senior class, a member of the ski team, and an outstanding student. During his twenty years, Michael lived life to the fullest, seeking new challenges and giving back to the community.

Michael loved to do what many Reno residents love to do when outdoors:

Michael loved outdoor adventure whether it was on the ground skiing, hiking, camping, mountain biking, ATV riding, four-wheeling, or flying an airplane 12,000 feet over the Sierra.

The popularity of  the Thompson Trailhead is still growing. Now, it indeed is “a busy place with hikers and bikers ready for the wilderness,” as forecasted in my Hunter Creek Trailhead under construction post in 2009.

Michael D. Thompson Trailhead