Thursday, April 28, 2011

Synonyms in mathematics and string theory: originally called octaves, now known as octonions or Cayley numbers

Octonions build an eight-dimensional number system— the largest of the four sets of numbers of normed devision algebra [1,2]. Baez and Huerla (both with first name John) describe how they were discovered by John Graves (another John!), who called them octaves [3]. Graves communicated his findings to the Irish mathematician William Rowan Hamilton. Although Hamilton was not interested in these numbers, he reported them at the Irish Royal Society. Without any written publication, Arthur Cayley, one of the Invariant Twins [4], rediscovered the octonions and beat Graves to publication. Thus, octonions are also known as Cayley numbers—and not as Graves numbers

Octonions are the elements in a Cayley algebra [5]. Like the multiplication of quaternions, the multiplication of octonions is noncommutative: order matters. Multiplication of octonions is not even associative. But they have two “very good properties” [2]: every nonzero octonion has a multiplicative inverse, and two nonzero octonions never multiply together to give zero. John Graves amateur interest (he was a lawyer) in algebra and his imagination of numbers with supernatural properties remains striking, especially, when considering their growing importance in explaining the universe and modeling the matter and forces therein.  

Keywords:  multidimensional systems, vector space, supersymmetry, spinors

References and further reading
[1] John C. Baez: The Octonions [].
[2] Timothy Gowers (Editor): The Princeton Companion to Mathematics. Princeton University Press, Princeton, New Jersey, 2008; pp. 275 to 279.
[3] John C. Baez and John Huerta: The Strangest Numbers in String Theory. Sci. Am. May 2011, 304 (5), pp. 60-65 [].
[4] Chapter 20 “Invariant Twins” in Men of Mathematics by E. T. Bell. Simon & Schuster, New York,  1937.
[5]  Wolfram MathWorld: Octonion [].

Saturday, April 23, 2011

The Indonesian mimic octopus (Thaumoctopus mimicus), named for its diverse mimicry displays

The Indonesian mimic octopus (Thaumoctopus mimicus, Octopodidae family) is named for its ability to mimic various marine species including sea snakes, lionfish and flatfish [1,2]. The mimic octopus is relatively small in comparison to other octopus species. It normally shows dark and white stripes around its arms, but the pattern and depth of color changes depending on whether it attempts to blend in with its surroundings or mimic the appearance of other creatures.

In a recent ‘Natural History’ article in the journal Scientific American, Peter Forbes offers examples of animal mimicry, studied in butterfly and moth populations—and the mimic octopus [3]. He describes, how Thaumoctopus mimicus, in addition to its coloration tricks, mimics movement behavior of other species within its habitat. For example, it masquerades as a flounder by holding its arms together to copy the flounder's shape and to replicate the flounder's mode of swimming by undulating.  Among humans, we call this impersonation. Considering octopus-flounder mimicry, my term of choice is flounderation. For an octopus, this means not fun or show time (or maybe it does, too), but irritation and deception of predators and probably also disguise of its own predating activity.

Keywords: marine biology, Cephalopoda, Octopoda, camouflage, tropical seas of South East Asia

References and more to explore
[1] The Indonesian Mimic Octopus (Thaumoctopus mimicus) Sulawesi [].
[2] Roger T. Hanlon, Lou-Anne Conroy and John W. Forsythe: Mimicry and foraging behavior of two tropical sand-flat octopus species off North Sulawesi, Indonesia. Biol. J. Linn. Soc. January 2008, 93 (1), 23-38. DOI: 10.1111/j.1095-8312.2007.00948.x.
[3] Peter Forbes: Masters of Disguise. Sci. Am. May 2011, 304 (5), pp.80-83 [].

Friday, April 22, 2011

Lorquin's admiral, a Californian butterfly named after gold-seeker Pierre Lorquin

Lorquin's admiral (Limenitis lorquini, Nymphalidae family) is a butterfly species named after Pierre Joseph Michel Lorquin, who came from France to California during the gold rush in the 1850s [1]. In search of gold, he found and got interested in butterflies instead [2]: No field notes (if any taken) or letters survived; but he is said to be California's first lepidopterist.

Lorquin's admiral resembles the California Sister (Adelpha bredowii) of the brushfoot family [2-4]: both species have upperwing patterns of white diagonals on a dark background and an orange spot on each tip of their forewings. But Lorquin's admiral is smaller and its orange spots extend to the forewing edges. The admiral is found in scrub and oak woodland and riparian habitat of the Coast Ranges and Sierran valleys up to 8000 feet, where Pierre may have observed and flirted with his namesake, forgetting about the gold nuggets. 

Keywords: lepidopterology, history, taxonomy, North American West Coast

References and more to explore
[1] Arthur M. Shapiro: Field Guide to Butterflies of the San Francisco Bay and Sacramento Valley Region. UC Press [].

[2] Joe Eaton: The Color of Flight - Falling for Butterflies in the East Bay. Bay Nature April-June 2011, pp. 16-20 [].
[3] Peter Alden and Fred Heath: Field Guide to California. Chanticleer Press, Inc and Alfred A. Knopf, Inc., New York, Seventh Printing 2007; page 214.
[4] Art Shapiro's Butterfly Site: Limenitis lorquini [].

Thursday, April 21, 2011

Acronym in biodiversity and intellectual property context: MGR for marine genetic resource

In the context of global genetic resource management, the acronym MGR stands for marine genetic resource [1]. MGRs are part of the most biodiverse habitat on Earth and include species of macro- and micro-organisms, many of which are living in complex symbiotic relationships [2]. Although the understanding of MGRs and their interrelationships is incomplete, knowledge of selected marine organisms and parts thereof is growing and available on various scales, often on molecular level. Marine molecules, for example thermostable enzymes from deep-sea, hydrothermal vent organisms, are of increasing interest in drug discovery and biotechnology. With respect to their potential market value, patent claims associated with MGRs are on the rise.

A raw natural material cannot be claimed per se, but isolated and purified extractions therefrom can. According to a recent article, ten countries account for 90% of patent claims associated with marine genes [1]. The authors of that article identify a broadening gap in oceanographic and biotechnological capacities among countries, discuss legal gaps concerning international waters and also weigh possibilities for a future governance framework for MGRs.

For those of us, who just want to learn what is there, the Census of Marine Life is a resourceful harbor, containing, among many other discovery gadgets, a Census Resources and Media Resources menu.

Keywords: oceanography, marine biology, bioprospecting, patentability, international consensus

References and resources
[1] S. Arnaud-Haond, J. M. Arrieta and C. M. Duarte: Marine Biodiversity and Gene Patents. Science March 25, 2011, 331 (6024), pp. 1521-1522. 
DOI: 10.1126/science.1200783. 
[2] L. Evens-Illidge: Towards a practical knowledgebase for marine genetic resources [].

Monday, April 11, 2011

Three-letter atomic symbols for chemical elements

Known chemical elements have one- or two-letter atomic symbols. Predicted chemical elements typically occur in the scientific literature with three-letter symbols until they receive a permanent name and symbol from the International Union of Pure and Applied Chemistry (IUPAC). The temporary designators for new chemical elements are systematically derived from their atomic number. For example, the element 114 is named ununquadium and its symbol is Uuq. The name is composed from the numerical roots un and quad for digits 1 and 4. The symbol is derived from the corresponding first letters of these roots. The element with atomic number 112 occurred in the literature as ununbium (bi for 2), having symbol Uub, before it was officially named copernicium (Cn).

In the context of data mining and cheminformatics applications, atoms, isotopes and nuclidic isomers of temporary-designator elements can be encoded in linear notation using the grammar and format options of the CurlySMILES language: an atomic node wild card with an MDAM annotation {!a} including a dictionary entry with key nuc and ila.

Lutetium, lutecium, cassiopeium—different names and spellings for the same chemical element

Lutetium (pronounced ‘loo-tee-shi-uhm’) is a metallic chemical element—the last member of the lanthanide series. The name derives from Lutetia, the ancient name for Paris [1], where it was discovered (in not so ancient times) in 1907 by G. Urbain. Independently, it was discovered by C. James at the University of New Hampshire, USA [2] and by Carl Auer von Welsbach in Austria [3]. Lutecium is an older spelling, which was changes to lutetium in 1949.

The atomic number of lutetium is 71 and the atomic symbol is Lu. However, one may also find the symbol Cp in the (older) literature and table works. Cp derives from cassiopeium, the name given by von Welsbach in reference to the northern-sky star constellation Cassiopeia. The element was called cassiopeium by German-speaking chemists during the first half of the twentieth century and frequently occurs in its traditional German spelling: Kassiopeium.

The key isotopes of lutetium are 175Lu and 176Lu with natural abundance values of 97.4% and 2.59% [2], respectively. Compare these values with the relative abundance given in a German-language publication [4]: 175Cp:176Cp=100:2,58±0.07 (notice the use of symbol Cp and of a comma as decimal point).

Keywords: chemistry, history, nomenclature, rare-earth elements (German: Seltene Erden)

References and museum tour
[1] Handbook of Chemistry and Physics, 88th Edition, 2007-2008; Section 4:
the elements.
[2] John Emsley:
The Elements. Third Edition. Oxford University Press, Oxford, UK, 1998.
Dr. Carl Freiherr Auer von Welsbach:
[4] J. Mattauch and H. Lichtblau:
Ein bemerkenswertes Isotop des Cassiopeiums. Z. Phys. A 1938, 111 (7-8), pp. 514-521. DOI: 10.1007/BF01329513.

An abbreviation in physics: SUSY for supersymmetry

In particle physics, the term SUSY (pronounced ‘Susie’) is a short form for supersymmetry [1-3]. Supersymmetry is a theory: an extension of the Standard Model. SUSY—often addressed as an elegant theory—provides a framework for attempts to unify electromagnetic, weak, strong, and gravitational interactions.

A key feature of SUSY is the prediction of superparticles. The Large Hadron Collider (LHC) [4] at the French-Swiss border near Geneva has the capability to recreate conditions that existed a split second after the Big Bang, during which superparticles should have been created and lasted for a very short time in the nanosecond range. However, particle physicists at LHC, so far, have not been able to detect any superparticles, casting doubt on the theory of supersymmetry. Whatever happens to the theory, the abbreviation SUSY will stay!

Keywords: particle physics, super particles, Large Hadron Collider (LHC)

References and more
[1] Geoff Brumfiel:
Beautiful theory collides with smashing particle data. Nature, March 3, 2011, 471 (7336), pp. 13-14.
[2] BackRe(Action):
[3] Rice University Physics & Astronomy:
[4] The Large Hadron Collider:

Saturday, April 9, 2011

A new name for tiny species, whose existence is still hotly debated: nanons

The term nanons has been given as a short-hand for nanobacteria by a group of French scientists led by Didier Raoult at the Unité des Rickettsies, Centre National de la Recherche Scientifique [1]. The group members think they have experimentally confirmed the existence of nanobacteria.

The respective singular nouns are nanon and nanobacterium. The name indicates that the associated (proposed) life-forms are tiny: about 200 nanometers and even lower. In physical and chemical research within materials science, the nano-scale viewpoint is commonplace, considering instrumental/analytical resolution and techniques based on supramolecular templating and molecular self-assembly. Also, the size of prions and viruses falls within this range. But the status of cellular organisms within this size range is still controversial [2].

Nanons are real. But are they really life-forms? Or to ask the question in a more differentiated form: what kind of life do they live? It comes down to the definition of life. And once again, we got an example demonstrating that our human languages, derived to name and communicate objects at larger scales, lack “natural words” to adequately phrase facts beyond that scope.

Keywords: nanoscience, biology, bacteriology, mcrobes, origin of life, philosophy

References and further reading
[1] Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009; page 221.
[2] John D. Young and Jan Martel: The Rise and Fall of Nanobacteria. Sci. Am. Jan. 2010, 302 (1), pp.52-59; also see Bions, biologically related and structurally similar ion complexes.

Thursday, April 7, 2011

Term in oceanography: marine snow for sinking organic matter

We all know snow as crystallized water, precipitating within the atmosphere of the Earth. This is airborne snow, whereas marine snow is waterborne, precipitating or falling through sea water [1]. Marine snow is decaying material that derives from dead or dying organisms and fecal matter, but also may include sand, soot and other inorganic dust [2].

The amount of forming sea or marine snow range as high as 1000 meters per year [3]: While most of it is consumed or recycled in the surface waters, some continues to sink all the way down to the ocean floor, bringing food/energy from the light-rich upper layers to the dark deep-sea zone, where bottom dwellers will be eager to break down some of the arriving snow.

Keywords: oceanography, decaying materials, organic detritus, vertical food chain

References, viewing and reading
[1] Marine snow video:
[2] National Ocean Service: Marine snow is a shower of organic material falling from upper waters to the deep ocean [].
[3] Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009; page 170.

Wednesday, April 6, 2011

Methanocaldococcus jannaschii, a deep-sea archaeon named for Holger Jannasch

Holger Windekilde Jannasch was a microbiologist at the Woods Hole Oceanographic Institution [1]: He was born in 1927 in Holzminden, Germany, and died in 1998 in Woods Hole after a long battle with cancer. His research in marine biology includes areas such as microbial growth kinetics in seawater, effects of low temperature and high pressure, and processes at hydrothermal vents. Holger's name became synonymous with deep-sea microbiology after new areas or research opened up in 1977, when the deep-sea hydrothermal vents were discovered.

Holger Jannasch was honored in 1996, when a thermophilic archaeon was named for him: Methanocaldococcus jannaschii. Rob Dunn describes the joint project of Craig Venter and Carl Woese, in which the genome of Methanocaldococcus jannaschii was sequenced [2]: This archaea species turned out to be very different from any bacteria species ever sequenced. But, according to Dunn, it showed some resemblance to Holger Jannasch, who had long, thick hair, a few pieces of which always waving about like the flagella cascading off one end of the Methanococcus cell in the photomicrographs published by Carl Woese.

One also finds the scientific name Methanococcus jannaschii in the (older) literature, since Methanocaldococcus was formerly known as Methanococcus. The name Methanocaldococcus emphasizes the thermophilicity of some species of this genus. The majority are mesophiles.

In case you want to turn into a “methanococcophile”, here are the family, order and class terms: Methanocaldococcaceae, Methanococcales, and Methanococci.

Keywords: microbiology, oceanography, archaea, methanogens, extreme thermophiles, taxonomy

References and further reading
[1] Media Relations Office of Woods Hole Oceanographic Institution: In Memoriam: Holger W. Jannasch [].
[2] Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009; pages 175- 179.
[3] P. J. Haney, J. H. Badger, G. L. Buldak, C. I. Reich, C. R. Woese and G. J. Olsen: Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl. Acad. Sci. USA March 1999, 96, pp. 3578-3583 [].

Monday, April 4, 2011

The terms symbiogenesis, endosymbiosis and endosymbiogenesis

The term symbiogenesis refers to the genesis of a new species or kind of life through the merger of two or more existing species. This term has been coined by scientists Merezhkovsky and Margulis.

Endosymbiosis refers to the symbiogenetic process and the resulting state, in which one partner (species) lives inside another [1,2]; for example, a chloroplast in an eukaryote. Such a the symbiotic relationship, including the hypothesized process leading to it, “blurs” the concept of species (biologist disagree on the definition of the term ‘species’ [3], anyway), making species distinction time-dependent. In the chloroplast case, a species turned into an organelle.

Endosymbiogenesis refers to the origin of a new lineage—a sequence of species that forms a line of descent.

The terms symbiogenesis, endosymbiosis and endosymbiogenesis belong to the vocabulary of evolutionary biology. They define hypothetical processes thought to explain the origin of species in addition to the inertwined processes of random mutation and natural selection. Recent advances in molecular biology and systematics provide experimental support for symbio-diversity thinking and reasoning.

Keywords: cytology, theoretical biology, molecular biology, theory of evolution, symbiosis

References and further reading
[1] Virtual Fossil Museum: Endosymbiosis - the Origin of Domain Eukarya [].
[2] Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009; see Chapter 7 and 10.
[3] Marc Ereshefsky: Species. Stanford Encyclopedia of Philosophy 2010 [].

Sunday, April 3, 2011

Symbiogenesis, a term in biology coined by scientists Lynn Margulis and also Konstantin S. Merezhkovsky

The key concepts of evolution (theory) are random mutation and non-random cumulative natural selection. In addition, genetic variation and the formation of new species may be driven by symbiotic merger: American scientist Lynn Margulis and Russian scientist Constantin Merezhkovsky (1855-1921), also spelled Konstantin Mereschkovsky, coined the term symbiogenesis to describe this evolutionary process [1-3].

Charles Darwin's evolutionary biology originated from exploring the macroworld: collecting and comparing species around the world. The idea of symbiogenesis stems from observing the microworld: the study of species (bacteria) and cells through the microscope.

While studying cells, biologists Lynn Margulis became to believe that chloroplasts in plant cells as well as mitochondria in all eukaryote cells were bacteria. Cells were engulfing each other, so she argued, and extended this assumption to cilia, flagella and centrioles. Lichens were hypothesized and finally became known to be multiple organisms: a symbiosis between an algae and fungus. Merezhkovsky “extrapolated” and speculated about trees: the forest a world of ancient cyanobacteria held up by trees in every leaf.

Merezhkowsky ended his life by suicide in 1921. Besides his interest in early evolution, he had troubling views, including his eugenics and racist writings [2]. In contrast, Lynn Margulis' ideas and research is merging, in parts, towards acceptance and into mainstream biology within the rRNA-supported tree-of-life framework. Rob R. Dunn writes (page 163 in [1]):
If Margulis were right that our mitochondria had once been free-living microbes, their rRNA would be more similar to that of other microbes than it is to the rRNA in our nucleus. And it was. Here was almost unassailable support for Margulis. The mitochondria and even chloroplasts could be mapped onto [Carl] Woese's tree of life, as easily as if they were still free-ling microbes living in the ground.

Keywords: cytology, theoretical biology, molecular biology, ribosomal ribonucleic acid (rRNA), theory of evolution, beyond Charles Darwin, philosophy, symbiosis

References and further reading
[1] Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009; pages 138 and 144.
[2] J. Sapp, F. Carrapiço and M. Zolotonosov: Symbiogenesis: the hidden face of Constantin Merezhkowsky [].
[3] San Jose STS: Dr. Lynn Margulis [ Jose 04-05/MargulisSaganSJ.html].

Saturday, April 2, 2011

Neivamyrmex sumichrasti, an army ant bearing the name of French naturalist François Sumichrast

The army ant Neivamyrmex sumichrasti was first documented in the 1860s by the French naturalist François Sumichrast, who worked at that time in Mexico. There he observed, collected and documented the ant that would later bear his name [1]. Interestingly, the “Eponym Dictionary of Mammals” lists a Swiss naturalist with the name Adrien Jean Louis François Sumichrast (1828-1882), who is commemorated in the names of species such as Sumichrast's Vesper Rat (Nyctomys sumichrasti), Sumichrast's Harvest Mouse (Reithrodontomys sumichrasti), Sumichrast's Wren (Hylorchilos sumichrasti) and Sumichrast's Garter Snake (Thamnophis sumichrasti), which all are found between Mexico and Panama [2]. Ants are not mammals and Neivamyrmex sumichrasti cannot be expected to be included in this list. Yet, I am wondering whether all names refer to the same naturalist? Maybe he was French-Swiss and both sources are right? I didn't succeed in finding a clearly linking cross-reference and I am still looking for an eponym dictionary of insects. For now, I am staying with the world of ants:

Keywords: entomology, myrmecology, army ants, Ecitoninae, nomenclature

References and further reading
[1] Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009; pages 120 and 121.
[2] Bo Beolens, Michael Watkins and Michael Grayson: The Eponym Dictionary of Mammals. The Johns Hopkins University Press, Baltimore, Maryland, 2009.
[3] John T. Longino (The Evergreen State College, Olympia, WA): Neivamyrmex sumichrasti (Norton 1868)