Friday, December 31, 2010

Materpiscis attenboroughi, a fish fossil named in honor of British nature presenter David Attenborough

John A. Long describes his Eureka! moment, which he had while examining an extraordinarily preserved fish fossil he and his team found at the site of the tropical shallow-sea Devonian Gogo reef in now-dry northwestern Australia [1-3]. The excitement came with the discovery of a fossilized umbilical cord belonging to an embryo in the ancient fish. After in-depth analysis using scanning electron microscopy (SEM) the researchers soon were convinced that they were studying an 375-million-year-old expectant mother fish and the oldest vertebrate embryo on record. They named the newly discovered ptyctodontid placoderm Materpiscis attenboroughi, meaning “Attenborough's mother fish,” after the British nature presenter David Attenborough, who introduced the Gogo fossil sites to the world in the 1979 documentary series Life on Earth [1].

The fossilized Gogo specimen is critical in dating the beginning of copulation, fertilization, childbearing and birth giving. Is it time to celebrate 375 million years of sexual intercourse or is the origin of this form of intimate vertebrate reproduction going even further back in time? And what was (is) the evolutionary advantage over spawning—still practiced by many aquatic animals today?

References and fun by exploring more
[1] John A. Long:
Dawn of the Deed. Scientific American January 2011, 304 (1), pp. 34-39. Excerpt.
[2] Sarah Clarke: Aussie scientists find world's oldest fossil mum. ABC News.
[3] J. A. Long, K. Trinajstic, G. C. Young and T. Senden: Live birth in the Devonian period. Nature 29 May 2008, 453, pp. 650-652.
DOI: 10.1038/nature06966.

Sunday, December 26, 2010

Acronym in quantum chromodynamics: CQM for constituent quark model

In physics, CQM stands for constituent quark model, which has its origin in the quark hypothesis proposed in 1964 by Murray Gell-Mann and George Zweig to account for the plethora of subatomic particles discovered in cosmic ray and accelerator experiments [1]. Constituent quark means massive quark [2]. The CQM concentrates on valence quarks, which are constituents of hadrons such as protons and neutrons. Timothy Paul Smith illustrates the application of the CQM in a highly recommended article about the properties and inner dynamics of the neutron [3].

The “complex life” inside a neutron—a “quark-sea” of quark-antiquark pairs that quickly come and go—is fully described by quantum chromodynamics (QCD). The valence quark model confines description to the “permanent quarks” of a hadron: a proton is made up of two up-quarks and one down-quark, whereas a neutron is made up of two down-quarks and one up-quark. Hence, the notation uud and udd for for the proton and neutron, respectively [3].

[1] Bill Carithers and Paul Grannis: Discovery of the Top Quark. PDF.
[2] Dmitri Diakonov:
Foundations of the Constituent Quark Model.
[3] Timothy Paul Smith: The Anatomy of a Neutron. American Scientist November-December 2010, 98 (6), pp. 478-485. Abstract.

Wednesday, December 22, 2010

Size-defining prefixes: mega, macro, meio and micro

Size-defining prefixes are in common use. Words like megabyte and microchip come immediately to mind. The prefix meio is somewhat different. It means less and makes only sense in relation with other prefixes denoting superior categories of size.

As an interesting application of these prefixes, I came upon a classification scheme for deep-sea fauna [1]:
  • megafauna: fish, crabs, lobster, starfish, urchins, sea cucumbers, sponges and corals
  • macrofauna: small polychaete worms, crustaceans and mollusks
  • meiofauna: forams, copepods and nematodes
  • microfauna: bacteria
In fact, the term microfauna is not used in the scheme—just bacteria. But since bacteria are subjects of microbiology, which typically require a microscope to be seen, this term should be appropriate and nicely fits into the line of this terminology.

There is an inverse relationship between animal size and depth. Craig McClain refers to the findings of Hjalmar Thiel of the University of Hamburg in northern Germany, who observed that the deep sea is a habitat mostly populated by small organisms [1]:
Thiel's specific findings were that megafauna and macrofauna decrease more rapidly with depth than do meiofauna or bacteria. In fact, with increased depth meiofauna and bacteria become increasingly more dominant. Thus, at depth greater than 4 kilometers on the vast abyssal plains where food is extremely limited, there is a shift toward diminutive size.
The term meiofauna is specifically used for aquatic organisms. Worms and nematodes living in the soil are grouped as mesofauna. The prefix meso, meaning middle or intermediate, defines size in relative terms like meio—somewhere between micro and macro.

Deep-sea reference
[1] Craig McClain:
An Empire Lacking Food. American Scientist November-December 2010, 98 (6), pp.470-477.

Tuesday, December 21, 2010

Ein Frosch sitzt im Schnee...

Ein Frosch sitzt im Schnee.
Der Frost tut ihm nicht weh;

Denn er ist eine Skulptur
Und wartet auf Neujahr nur.

Mehr zu diesem Frosch und seiner Umgebung:
On the sculpture trail: frog in the snow

A frog is sitting on a wall ...

A frog is sitting on a wall,

while the snow continues to fall.
Snow makes him disappear.
He'll still sit there next year.

Find out more about this frog and his surroundings:
On the sculpture trail: frog in the snow

Saturday, December 18, 2010

Unexplained unexpectedness: deus ex machina

The expression deus ex machina denotes a sudden solution to a plot or problem, which comes as a surprise to those who merely know the plot in the way it was presented. Deux ex machina literally means “god from the machine.” Sounds modern, but has its origin in ancient Greek drama [1].

Alan J. Cain nicely demonstrates the concept of deus ex machina (or lack of it) in mathematical proof, using the proof of Morley's Theorem as a case in point [2]. The deus seems to be a smart trick to short-cut a proof. He or she (dea ex machina) is disappearing as one receives retrospective explanation and reasoning. In science as well as in fiction, deus is sort of a mental construct deriving from the order or chronology in which facts and facets are presented. In a play or movie, deus may just be a redeemer from over-length.

How can the Latin phrase deus ex machina be replaced by an expression in English? If you are more attracted to the magic than to the divine, you perhaps like “out of the hat.” If you are looking for a less vivid, neutral phrase, “surprisingly, but inevitably” might work, while the inevitability leaves room for arguments.

[1] The Literary Encyclopedia: Deus ex machina.
[2] Alan J. Cain: Deus ex Machina and the Aesthetics of Proof. The Mathematical Intelligencer Fall 2010, 32 (3), pp. 7-11. PDF.

Sunday, December 12, 2010

A dinosaur named Sinosauropteryx, meaning “Chinese lizard wing”

Modern birds are descendants of Maniraptoran dinosaurs, according to the current knowledge in paleontology. The evolutionary path from dinosaurs to birds, however, has many branches with dead-ends, representing species such as non-avian dinosaurs that went extinct long ago. One such dinosaur is Sinosauropteryx, a dinosaur with feathers and a bird-like skull found by a Chinese farmer in August 1996 in Sihetun village [1]. It was concluded by dating of radioactive elements in the fossil-encasing sediments, that this dinosaur lived around 125 million years ago.

Sinosauropteryx means “Chinese lizard wing.” The latter two word parts are immediately recognized by anybody with an interest in paleontology, as saur occurs in the word dinosaur and opteryx in archaeopteryx, the name of the “first bird,” flying around 150 million years ago.

Reference with tree of birds and non-avian dinosaurs:
[1] Richard Stone: Dinosaurs' Living Descendants. Smithsonian December 2010, 41 (8) , pp. 54-62.

Friday, December 10, 2010

Encyclia dickinsoniana, an orchid named after Chicago native Stirling Dickinson

Stirling Dickinson from Chicago lived and traveled in Mexico in the last century. He is known for helping the old silver mining town San Miguel de Allende 166 miles northwest of Mexico City to turn into an international art center [1]. Dickinson is said to have had three passions: art, baseball and orchids. In the 1960s he explored the Chiapas highlands in southern Mexico and discovered an orchid species there, which in 1971 was named after him. Both the binomial name, Encyclia dickensoniana, and the common name, Dickinson's Encyclia [2], honor the discoverer. Another synonym can be found: Epidendrum dickinsonianum Withner 1970 [3]. Like any orchid flower, dickensoniana flowers look like pieces of art.

Keywords: botany, Orchidaceae, epiphyte, scientific name, eponym

[1] Jonathan Kandell: Under the spell of San Miguel de Allende. Smithsonian December 2010, 41 (8) , pp. 74-83.
Encyclia dickinsoniana (Withner) F. Hamer:
[3] Encyclia dickinsoniana (Withner) Hamer 1985: Photo.

Thursday, December 9, 2010

Frasera ackermanae, a flowering plant in the Gentianaceae family named after geologist Diane Ackerman

Species of the genus Frasera (sometimes considered part of the genus Swertia) are flowering plants in the Gentianaceae family. Clayton Newberry and Sherel Goodrich have described a new species, Frasera ackermanae, sp. nov., collected in Uintah County, Utah [1]. They report a narrow endemism for F. ackermanae and compared this species with the similar Frasera pahutensis plant.

Newberry and Goodrich named the new species in honor of geologist Diane Ackerman, who first spotted the plant and brought it to their attention. Diane Ackerman is a plant enthusiast. She has worked for the National Park Service at Fossil Butte National Monument near Kemmerer, Wyoming. She now lives in Utah.

Keywords: botany, perennial herb, scientific name, order Gentianales, asterids, clay hillsides

[1] C, Newberry and S. Goodrich: A new species of Frasera (Gentianaceae) From Uinta Basin, Utah. Western North American Naturalist October 2010, 70 (3), pp. 415-417.
: 10.3398/064.070.0315.

Monday, December 6, 2010

English: graphene; German: Graphen or Graphén

Graphene is a single carbon layer within the structure of the carbon allotrope graphite or—in separated form— a planar, one-atom-thick honeycomb lattice of carbon atoms. The term graphene describes such a carbon layer in analogy to a polycyclic aromatic hydrocarbon (PAH) of quasi infinite size [1]. Note that names for planar PAH molecules such as anthracene, pyrene and ovalene end with the suffix -ene. To reflect the structural analogy in the name for the “unlimited PAH”, the word graphene is derived by stemming the word graphite and appending the suffix -ene.

The German name is Graphen. Since this word also happens to be the plural form of the noun Graph (although pronounced differently), meaning graph as in molecular graph, the spelling Graphén is alternately used. Another possible, sound-conserving spelling would be Grapheen. Either way, the suffix identity with German names for PAHs is compromised: anthracene, for example, is Anthracen (or Anthrazen, when I went to school), but not Anthracén or Anthraceen.

Instead of playing with its name, chemists and material scientists like to play with its structure. Already in the 1960s graphene derivatives were produced by reduction of graphite oxide [2]. Stoichiometric graphene derivatives such as fluorographene have been obtained and characterized recently [3].

Continuing the name game: CurlySMILES encoding of graphene and stoichiometric derivatives.

Keywords: carbon chemistry, structural similarity, chemical nomenclature, structural encoding, linear notations, translation

References and further reading
[1] IUPAC Gold Book: graphene layer.
[2] H.-P. Boehm: Graphen - wie eine Laborkuriosität
äußerst interessant wurde. Angewandte Chemie 2010, 122 (49), pp. 9520-9523. DOI: 10.1002/ange.201004096.
[3] R. R. Nair et al.: Fluorographene: A Two-Dimensional Counterpart of Teflon. Small 2010. DOI: 10.1002/smll.201001555

Friday, December 3, 2010

Nantucket from Native American, Nattick, meaning far away land

Nantucket Island and the waters around it are the birthplace of “modern” whaling, but Nattick Indians had foraged there for whales in the centuries before the first Europeans arrived [1]. As Philip Hoare tells us, “the word [Nantucket] is Native American, Nattick, meaning far away land; and from far away, its wharves once stank so much that visitors could smell the island before they saw it.”

Today, visitors from far away and nearby come here for recreation including kayaking, seal cruising and whale watching. What to look for on Nantucket? Weathervanes in the shape of whales.

Residents of Nantucket are called Nantucketers.

[1] Philip Hoare: The WhaleIn Search of the Giants of the Sea. HarperCollins Publishers, New York, 2010; see Chapter V Far Away Land.

Thursday, December 2, 2010

The minke whale, named after a sailor and whaler with a differently spelled name

Most sources agree that the minke whale is named after a sailor and whaler. Details, however, depend on which references you consult. The sailor is alternatingly German or Norwegian and his name varies from Miencke, Meincke to Meineke. Fortunately, the common name for the whale is consistently given as minke, pronounced “minky.” Use of the short plural form minkes instead of minke whales is common.

The scientific name is Balaenoptera acutorostrata, meaning “winged whale with a sharp-pointed snout.” This whale is found in oceans worldwide. And as it is often the case for such “ubiquitous species,” debates on whether there are just one, two or more species evolve. Distinctions between a northern-hemisphere species, B. acutorostrata, and a southern-hemisphere species, B. bonaerensis, have recently been made.

Minke whale names and synonyms in various languages

Dutch: dwergvinvis
English: minke whale
French: baleine de Minke (also: petit rorqual)
German: Zwergwal (also: Minkwal or Minkewal)
Italian: balenottera minore (also: balenottera rostrata)
Portuguese: baleia-de-minke
Spanish: rorcual aliblanco

Interestingly, the Norsk and German names do not make any reference to a sailor with a Norwegian or German name. Let's assume that this Mr. Miencky never lived or, at least, never hunted a whale. Then, he really deserves to be honored by having a whale species named after him.

Keywords: cetology, Mysticeti, Balaenopteridae, marine mammals, taxonomy


[1] Philip Hoare: The WhaleIn Search of the Giants of the Sea. HarperCollins Publishers, New York, 2010; see Chapter XI The Melancholy Whale.
[2] Save the whales: Minke Whale, Balaenoptera acutorostrata (Lacepéde 1804).
[3] NOAA Fisheries, Office of Protected Resources: Minke Whale (Balaenoptera acutorostrata).