A term in biology: constructive neutral evolution

The rise and evolution of novel, complex structures and operations in biological organisms is typically explained by processes involving random mutations followed by natural selection: complexity is emerging from environmentally driven, essentially non-random processes discovered by Charles Darwin and illustrated, for example, by Richard Dawkins in his book The Blind Watchmaker [1].

But is evolution completely directed by natural selection or do non-Darwinian factors (non-selective factors: chance, neutral changes, bio-molecular side effects) play a significant role? Currently, the possibility of constructive neutral evolution (CNE) is discussed [2-5]. The CNE idea opens additional routes in biological inquiry that allow the development of neutral models, which can anchor molecular-evolution studies—designed to explain complexity as well as biodiversity—on grounds free of a priori adaptionist explanations. The scheme of CNE will supplement or may revolutionize our understanding of the origin, direction and meaning of life. 

Carl Zimmer instructively put the origin of the term “constructive neutral evolution” into context [4]:

In the 1990s a group of Canadian biologists started to ponder the fact that mutations often have no effect on an organism at all. These mutations are, in the jargon of evolutionary biology, neutral. The scientists, including Michael Gray of Dalhousie University in Halifax, proposed that the mutations could give rise to complex structures without going through a series of intermediates that are each selected for their help in adapting an organism to its environment. They dubbed this process “constructive neutral evolution.”

Keywords: life science, evolutionary theory, neutral theory, neo-Darwinian thinking, evolutionary genetics, bio-molecular complexity.

References and more to explore
[1] R. Dawkins: The Blind Watchmaker. Penguin Books, London, England, reprinted (from the 1986 Longman publication) with an appendix 1991.
[2] A. Stoltzfus: On the possibility of constructive neutral evolution. J. Mol. Evol. August 1999, 49 (2), pp. 169-181 [www.ncbi.nlm.nih.gov/pubmed/10441669].
[3] A. Stoltzfus: Constructive neutral evolutionary theory: exploring evolutionary theory's curious disconnect. Biology Direct 2012, 7:35. doi: 10.1186/1745-6150-7-35. 
[4] C. Zimmer: The surprising origins of life's complexity. Sci. Am. August 2013, 309 (2), pp. 84-89 [www.scientificamerican.com/article.cfm?id=the-surprising-origins-of-evolutionary-complexity].
[5] Entropic Existence: Selection, Neutrality, and the Appearance of Design. April 23, 2010 [entropicexistence.blogspot.com/2010/04/selection-neutrality-and-appearance-of.html].

Talus, meaning “rock debris” or “slope of rock debris”

The word talus refers to rock debris at the base of a cliff, crag or valley shoulder. This word may also specify a slope covered with such rock debris [1,2]. In the latter case, one often speaks of a talus slope. A good example are the talus slopes below the south-facing cliffs of Castle Peak in the Sierra Nevada northwest of Truckee, California. The picture above shows Castle Peak seen from nearby Andesite Peak: concave talus slopes are skirting the cliffs keeping vegetation away from the upper mountain belt. The lower, less steep areas have some single conifers (survivors of rock slides). The forest begins where the slopes turn into a saddle and plateau topography, on the surface of which the impact of rolling rocks is becoming less powerful.   

Talus is created by weathering and fracturing of granite and other types of rock. Talus accumulates through periodic rockfall. F. J. Smiley, in 1915, briefly described the degrading process of Sierran mountain walls—while studying the Lake Tahoe region—and pointed out “the immense heaps of angular talus, which skirts the bases of Mt. Tallac, Maggie's Peaks and Castle Peak” [3]. 

A talus slope is always ready for a slide—triggered by an earthquake, an animal or a reckless mountaineer. Needless to say that a talus slope is dangerous terrain to walk across or to climb up or down on.

In addition to its meaning in topography and geology, the word talus means ankle or ankle bone in anatomy [1,2]. How the word and its meanings derived, is not completely clear. Old French, Latin or Celtic origins are typically mentioned. The plural form of talus is tali. Another word for talus is scree, probably from Old Norse skridha, meaning landslide [4].

Keywords: geology, etymology, synonyms.

References
[1] Merriam-Webster: talus [www.merriam-webster.com/dictionary/talus].
[2] The Free Dictionary: talus [www.thefreedictionary.com/talus]. 
[3] F. J. Smiley: The Alpine and Subalpine Vegetation of the Lake Tahoe Region. Botanical Gazette April 1915, 59 (4), pp. 265-286 [www.jstor.org/stable/2468057].
[4] The Free Dictionary: scree [www.thefreedictionary.com/scree].

Acronym in scent detection and civil security: EDC for explosive detection canine

Explosive-sniffing dogs are trained and employed to detect hidden reactive substances with a destructive potential. Such dogs are called bomb dogs,  or—more formal—explosive detection canines (EDCs) [1,2]. They are becoming best friends of security officials and safety personal who are in charge of protecting public places and controlling conflict zones.

EDCs do not smell bombs. But they can be trained to be highly alert to the ingredients of explosive materials. At the MSA Security Training Academy, for example, odors of chemical vapors are imprinted on the olfactory cortex of the dog's brains—Pavlov-style by task repetition and reward [2]:

MSA's dogs begin building their vocabulary of suspicious odors working with rows of more than 100 identical cans laid out in a grid. Ingredients from the basic chemical families of explosives—such as powders, commercial dynamite, TNT, water gel and RDX, a component of the plastic explosives C4 and Semtex—are placed in random cans. In addition, urea nitrate and hydrogen peroxide—primary components of improvised explosive devices—have joined the training regime.

EDCs learn not to scratch a potentially threatening material or device (avoiding a possible blow-up), but to respond by just sitting down when they sense one. Today, EDCs at airports, train stations, stadiums, fairs and banks are not even noticed by travelers and visitors; and if, they are greated with a friendly look or smile. The simple presents of EDCs hopefully keeps people safe and threats away. 

Keywords: threat protection, chemistry, sensory system, dog's nose, Canis lupus.

References and more to explore
[1] MSA Security: Bomb Dogs [www.msasecurity.net/bomb-dogs/].
[2] Joshua Levine: The education of a bomb dog. Smithsonian July-August 2013, 44 (4), pp. 72-78 [http://www.smithsonianmag.com/ideas-innovations/The-Education-of-a-Bomb-Dog-213881241.html#Bomb-Dogs-explosive-detection-canine-training-1.jpg].

Silicene: a honeycombed, atom-thick sheet of silicon named to recall similarly structured graphene

Silicene sheets can be epitaxially grown on a close-packed silver surface, Ag(111), via silicon atomic flux under ultrahigh vacuum conditions [1]. The condensed atoms arrange themselves within a two-dimensional honycomb lattice, geometrically resembling the structure of carbon atoms in graphene sheets. Chemists like to indicate structural and functional similarity of compounds in the ending of their names:  hence, the name silicene, which rhymes with graphene.

Equal or similar topology, however, does not necessarily imply property similarity. So far, many silicene properties have been predicted rather than measured, since the graphen-like form of silicon proves hard to handle [2].  Whereas graphene is very stable, silicene is reacting with other molecules and materials in its neighborhood. Silicene sheets also show a tendency to crinkle. Yet, the interest in silicene, its properties and potential applications is rapidly growing [3-5].

And to continue with the analogy of chemical elements of the carbon group (Group IV or Group 14), germanene—the planar, hexagonal germanium allotrope—could then be the next thin sheet.   

The CurlySMILES notation for silicene is [Si]{alall=silicene}, in which the square bracket code (SQC) for silicon is annotated with al for atomic layer and all for allotrope. The analogous linear notation for graphene and germanene are [C]{alall=graphene} and [Ge]{alall=germanene}, respectively.

Keywords: inorganic chemistry, material science, nanotechnology, epitaxy, spontaneous organization, honeycomb lattice, allotropes.

References and more to explore
[1] B. Lalmi et al.: Epitaxial growth of a silicene sheet. Appl. Phys. Lett. 2010, 97, pp. 223109-223110. doi: 10.1063/1.3524215.
[2] G. Brumfiel: Sticky problems snares wonder material. Nature March 14, 2013, 495, pp. 152-153. doi: 10.1038/495152a.
[3] B. Feng et al.: Evidence of Silicene in Honeycomb Structures of Silicon on Ag(111). Nano Lett. 2012, 12 (3), pp. 3507-3511. doi: 10.1021/nl301047g.
[4] Z. Ni et al.: Tunable Bandgap in Silicene and Germanene. Nano Lett. 2012, 12 (1), pp. 113-118. doi: http://dx.doi.org/10.1021/nl203065e.
[5] Foresight Institute: Silicene: silicon's answer to graphene [www.foresight.org/nanodot/?p=5642].

Translating the names of chemical compounds and compound classes

Chemists are typically not trained as translators. The latter, on the other hand, often do not have a background in chemistry and materials science. The translation of chemical compound and class names can easily turn into a non-trivial task.

In some cases translation is a simple matter of dictionary knowledge and look-up. For example, the names of the so-called “standard amino acids, ” a set of  α-amino acids, display overall name consistency across languages (one-word names with the exceptions of aspartic acid and glutamic acid [1]): for a given molecular structure the linguistic root of an amino acid name is recognizable—language-specific names are just spelled differently based on language character. As “trivial names ” they have not been derived by employment of a nomenclature scheme.

Generally, for complex chemical structures and nanoscale architectures, it can be a challenge to correctly translate a chemical compound name or chemical class name, which commonly is constructed from prefixes, suffixes, locants and (sub)structure (functional group) names. Bernardo Herold emphasizes a basic two-step approach, to which one should adhere, when translating a chemical term from English into a target language (or vice versa) [2]:

1. Establish the required rules of nomenclature in the target language.
2. Translate a name based on the vocabulary and rules of the target language.

Language-specific spelling is the main reason why composed chemical names cannot always be translated successively name-part by name-part. In particular, the spelling of the names of certain chemical groups varies between languages, giving rise to different alphabetical ordering—for example, phenyl in English and German becomes phényle in French, fenyl in Dutch and fenil in Italian, Portuguese and Spanish. Herold demonstrates how the English-language name 3-methyl-5-phenylpyridine is correctly translated—according to IUPAC rules—into the Romanic-language name 3-fenil-5-metilpiridina [2].

In addition to language-adjusted nomenclature application, the understanding of the language-specific grammar is important. It determines features such as word order and word concatenation: potassium bromide in English is Kaliumbromid (one word) in German and  bromuro de potasio  (change of word order and insertion of preposition) in Spanish.  

Chemical nomenclature books are available in several languages [3].

Keywords: multilingual collaboration, linguistics, chemical terminology, IUPAC naming, disambiguation.

References and more to explore
[1] Latintos: Amino acids in English, French, German, Italian, Portuguese and Spanish [golatintos.blogspot.com/2010/02/amino-acids-in-english-french-german.html].
[2] Bernardo Herold: Why Translate Nomenclature? Chemistry International May-June 2013, 35 (3), pp. 12-15 [www.iupac.org/publications/ci/2013/3503/5_herold.html].
[3] International Union of Pure and Applied Chemistry - Nomenclature Books: www.chem.qmul.ac.uk/iupac/bibliog/books.html. 

Synonyms for sand corn, the common name of a flowering plant native to the western United States and parts of New Mexico

Sand corn is a flowering plant found in dry habitats of the western United States; for example in northwest Nevada. It has two accepted scientific names: Zigadenus paniculatus (Nutt.) S. Watson and  Toxicoscordion paniculatum (Nutt.) Rydb. [1-5].  Its scientific classification: order Liliales. In the literature, sand corn is taxonomically grouped either into Lilliaceae (lily family) or Melanthiaceae, the latter not unanimously recognized as a family and sometimes considered as part of the lily family.

Sand corn, also written sand-corn, is often referred to by its other common name: foothill deathcamas (also written: foothill death camas). This name indicates the poisonous character of the plant, which becomes relevant, when sand corns are growing on rangeland: intoxication of livestock may result from their alkaloid components such as zygacine [3].

Another synonym, panicled death camas [4], makes a reference to the often bending or nodding panicle with sometimes over fifty flowers (see Thomas Creek plant)—each having six small tepals with yellow-green splotch at base and showy, yellow anthers [5].

Keywords: botany, taxonomy, nomenclature, scientific name.

References and more to explore
[1] USDA Plants Profile: Zigadenus paniculatus (Nutt.) S. Watson [plants.usda.gov/java/profile?symbol=ZIPA2].
[2] Kew Royal Botanic Garden: Toxicoscordion paniculatum (Nutt.) Rydb., Bull. Torrey Bot. Club 30: 272 (1903) [apps.kew.org/wcsp/namedetail.do?name_id=289937].
[3] K. D. Welch et al.: The acute toxocity of the death camas (Zigadenus species) alkaloid zygacine in mice, including the effect of methyllycaconitine coadministration on zygacine toxity. J. Anim. Sci. 2011, 89 (5), pp. 1650-1657.  
doi: 10.2527/jas.2010-3444.
[4] Calflora Taxon Report 8367:  Zigadenus paniculatus [www.calflora.org/cgi-bin/species_query.cgi?where-taxon=Zigadenus+paniculatus].
[5] Laird R. Blackwell: Tahoe Wildflowers. Morris Book Publishing, LLC, Guilford, Connecticut, 2007; page 37.

A term in microbial ecology: disappearing microbiota hypothesis

Occurrences of certain medical conditions and diseases such as asthma, food allergies, hay fever, eczema, diabetes, obesity and celiac disease are dramatically going up. The physician and director of the Human Microbiome Program, Martin Blaser at New York University's School of Medicine is hypothesizing that the disappearance of microbiota from the human body is to blame. This loss of  microbiome species is largely caused by our obsessive use of antibacterial soaps and lotions as well as frequent treatments with antibiotics [1,2]:

Though they have always known that antibiotics kill “good” bacteria as well as “bad,” doctors generally assumed the body's microbial community was resilient enough to bounce back. But new studies show that the microbiome struggles to recover from repeated assaults, and may lose species permanently. Blaser suspects that diversity loss is cumulative, worsening from one generation to the next. He calls it “the disappearing microbiota hypothesis.” [boldface by author]

How clean should we be, without cleaning out the good microbes—or disturbing the balance between good, bad and neutral ones—that live behind our ears, in our armpits and in our gut and mouth?

Keywords: microbial diversity, microbiome, microbiology, medicine, hygiene, human health.

References and more to explore
[1] Martin J. Blaser, M. D. [http://www.med.nyu.edu/biosketch/blasem01/research].
[2] Richard Conniff: The Body Eclectic. Smithsonian May 30, 2013, 44 (2), pp. 40-47 [www.smithsonianmag.com/science-nature/Microbes-The-Trillions-of-Creatures-Governing-Your-Health-204134001.html].