German for casual travelers: Schon 'was zum Pennen?

“Schon 'was zum Pennen?” is short for “Schon etwas zum Pennen?”
The vocabulary:

• schon: already
• etwas: something
• zum: to 
• pennen: to nap or to sleep

The question “...schon 'was zum Pennen?” is asking you, if you have found a place to stay overnight.  Painting and question are found at the south-facing wall of the Zollhaus Bremen, Am Kaffee-Quartier 1, Walle, 28217 Bremen.

This former custom-house (Zollhaus) in Bremen's  harbor district has been turned into a hostel (www.zollhaus-bremen.de). With the slogan “Meet and sleep in Bremen,” the Zollhaus invites easy-going travelers to stay at this affordable hotel. Bremen's city center, the Weser river walk and biking promenade, the still developing harbor city (Überseestadt) as well as coffee shops, bistros, restaurants, pubs and other hang-outs are nearby—a short walk or bike ride away. Lots to do and not much time “zum Pennen.”

Keywords: German slang, tourism, city of Bremen, harbor district.

English-German word play: “umfairteilen” sounds like “umverteilen”

The adjective fair can take on various meanings in English, including the meaning of being honest, impartial and just—as in the phrase fair play. When used in German, fair has that meaning. The word fair sounds like the German prefix ver, giving rise to the word play of the trade-union banner above, where the verb umfairteilen is used instead of umverteilen. The meaning of the latter should become clear by comparing the meaning of the simple verb teilen with those of the composita that are derived by employing the prefixes ver and um:

• teilen: divide
• verteilen: distribute or share
• umverteilen: redistribute

The verb umfairteilen has cleverly been constructed to ask for a fair redistribution of wealth. The text umfairteilen - Reichtum besteuern, displayed over the entrance of the Gewerkschaftshaus Bremen (trade union building in Bremen in northern Germany), calls for the redistribution of wealth via adjusted tax regulations. The noun Reichtum means riches or wealth and the verb besteuern means to tax.

Keywords: Wortspiel, word play;  Steuern, taxes; Politik, politics;  soziale Gerechtigkeit, social justice.

Detailed information on Germany's Umfairteilen activities and demands is given at de.wikipedia.org/wiki/Umfairteilen.

Mastigostyla woodii in the iris family named in honor of British botanist John Wood

 Mastigostyla woodii, a Bolivian plant in the iris family (Iridaceae) with blue-purple flowers, was named in honor of the British botanist John R. I. Wood [1-3]. The genus name is based on the greek words mastigos and stylos, meaning “whip” and “style,” respectively. The conservation status and distribution of M. woodii and the three related species M. cardenasii, M. chuquisacensis and M. torotoroensis in the arid mountains and valleys of the eastern Andes in Boliva has recently been described [4].

John Wood, an Honorary Research Associate at Kew, collected plant specimens from around the world, including habitats in Yemen, Bhutan, Columbia and Bolivia. Wood collected more than 30,000 plant specimens over 40 years and encountered various inconveniences during his search for remote places and rare species. He had malaria twice, Dengue fever once, and is today celebrated as an elite field botanists—a discoverer and science-driven gatherer from an era that is drawing to a close [3].

Taxonomy of Mastigostyla woodii Huayalla & Wilkin [1]
Class: Equisetopsida
Subclass: Magnoliidae
Superorder: Lilianae
Order: Asparagales
Family: Iridaceae
Note that the above organization is based on the Angiosperm Phylogeny Group (APG) system, while the Cronquist, Takhtajan or Thorne system treat Iridaceae as part of the order Liliales, Iridales or Orchidales, respectively.

Keywords: botany, systematics, nomenclature, plant collecting.

References and more to explore
[1] Kew Royal Botanical Gardens: Mastigostyla woodii [www.kew.org/plants-fungi/Mastigostyla-woodii.htm].
[2] Encyclopedia of Life: Mastigostyla woodii [eol.org/pages/31921821/details].
[3] John Whitfield: Rare Specimens. Nature April 25,  2012, 484, pp. 436-438 [www.nature.com/news/superstars-of-botany-rare-specimens-1.10498].
[4] Hibert Huaylla, Paul Wilkin and Odile Weber: Mastigostyla I. M. Johnst. in Bolivia: three new species and new data on M. cardenasii R. C. Foster. Kew Bulletin June 2010, 65 (2), pp. 241-254. doi: 10.1007/s12225-010-9199-y.

Molecular-modeling terms in pharmacology: ADMET, ADME and ADME-Tox

The acronym ADMET stands for absorption, distribution, metabolism, elimination, and toxicity. The word elimination may be swapped for excretion. This acronym is typically used in the context of drug design, where the relationship between the molecular structure and properties of chemical substances with pharmacokinetic, metabolic and toxicological endpoints is key in finding promising candidates to be further explored and tested as drugs. Toxicity—seen as a result of the other for processes or phenomena—is sometimes considered separatedly and the acronym ADME without a final T for toxicity is then used. Or, the notation ADME-Tox (also: ADME/Tox) is employed, visually separating the role of toxicity from the four physiological functions.

A short introduction and important links to ADMET-integrated research and associated software tools have recently been posted online. 

An acronym in genetics: SNP for single nucleotide polymorphism

In genetics, the acronym SNP stands for single nucleotide polymorphism. SNP is pronounced “snip” [1-4] .

SNPs are recognized by comparing aligned sequences of DNA. A single location along a pair of “matching” sequences, at which two nucleotides differ, constitute a SNP. In the above example, the swap of thymine (T) for adenine (A) is such a SNP.

SNPs are biological markers in the genome of humans and other life forms. SNP comparison—by using human genomes from distinct populations around the world—helps to understand genetic diversity of humans and, for example, regiospecific disease patterns and human adaption to different environments.

A recent article by Gary Styx illustrates the role of SNP in studying the historical path of human migration around the globe all the way to contemporary human diversity [5].

Keywords: bioinformatics, evolutionary anthropology, ancestry, DNA building blocks, diversity of DNA

References and more to explore
[1] An earlier SNP post on Latintos: http://golatintos.blogspot.com/2010/10/acronym-in-genomics-snp-for-single.html.
[2] Genetics Home Reference: What are single single nucleotide polymorphisms (SNPs)? [ghr.nlm.nih.gov/handbook/genomicresearch/snp].
[3] SNPedia: Single Nucleotide Polymorphism [snpedia.com/index.php/Single_Nucleotide_Polymorphism].
[4] National Human Genome Research Institute/Francis S. Collins: Single Nucleotide Polymorphisms (SNPs) [www.genome.gov/Glossary/index.cfm?id=185].
[5] Gary Styx: Traces of a Distant Past. Scientific American Winter 2013, 22 (1), 60-67.

An acronym in genetics: HAR1 for human accelerated region 1

A recent Special Collector's Edition of Scientific American is entitled What Makes Us Human. The missing question mark suggests that some knowledge exists today on what makes humans evolutionary different from closely related hominids and also from other mammals—despite nearly identical DNA blueprints. A key finding concerning this difference is presented in an exciting article by Katherine Pollard, entitled What Makes Us Different? [1]. Notice the question mark here! The discussed difference: the evolutionary change of a DNA sequence of 118 bases known as human accelerated region 1, HAR1 for short [1-4].

The name for this stretch of letters (bases) refers to the rapid change of letters (18 out of the 118 bases) in the human sequence that occurred over the last 6 million years relative to the conforming chimpanzee sequence. In contrast, comparison of this sequence between chimps, chickens and other vertebrate species over the past 300 million years reveals extremely slow changes (two out of 118 letters differing in the chimp and chicken sequence). Conclusion: the HAR1 genome region remained almost unchanged during most of the vertebrate evolution, while—throughout the dawn of humanity—it quickly acquired new and significant functions in humans, relative to the offsprings of their common chimp-like ancestors.

HAR1 does not directly encode proteins, but RNA. HAR1 is the first documented example of an RNA-encoding sequence that might have undergone positive selection (directional selection), a special mode of natural selection. Recent research suggests that HAR1 has a significant role in the development of a healthy cerebral cortex, the wrinkled outermost brain layer [1].

Many other accelerated genome regions have been predicted and identified, including HAR2, which drives limb (wrist and thumb) development and may be responsible for human dexterity [1,4], as well as a sequence within the FOXP2 gene, which is associated with speech and language development [1,5]. 

Keywords: biology, biostatistics, bioinformatics, mammalian genome, genome scanning, human-specific brain features, evolutionary anthropology.

References and more to explore
[1] Katherine S. Pollard: What Makes Us Different? Scientific American Winter 2013, 22 (1), 30-35.
[2] Katherine S. Pollard et al.: An RNA gene expressed during cortical development evolved rapidly in humans. Nature 2006, 443, 167-172. DOI: 10.1038/nature05113.
[3] Artemy Beniaminov, Eric Westhof and Alain Kroi: Distinctive structures between chimpanzee and human in a brain noncoding RNA. RNA 2008, 14, 1270-1275.
DOI: 10.1261/rna.1054608.
[4] Jeffrey Norris: What Makes Us Human? Studies of Chimp and Human DNA May Tell Us. June 28, 2010 [http://www.ucsf.edu/news/2010/06/5993/what-makes-us-human-studies-chimp-and-human-dna-may-tell-us].
Note: this post also features Katie Pollard, a biostatistician at the University of California in San Francisco, who played an important role in creating mathematical algorithms and software for comparative genomics.
[5] FOXP2: A genetic window into speech and language. [http://www.yourgenome.org/sis/evbbi/evbbi20.shtml].

An arguable misnomer in physics: the term “quantum mechanics”

Analog or digital,  uninterrupted or pixilated, continuity or discontinuity, field or particle? These pairs of opposing adjectives and nouns often occur in texts and discussions about physical reality and theoretical modeling. The periodic table of discrete chemical elements with their characteristic numbers and spectra directs scientists towards a quantum view of matter. As an example: the solution of Schrödinger's equation for the hydrogen atom provides us with quantum numbers (n, l, and m), which are integers [1]. Important: these integers are coming forth from solving an equation formulated with continuous variables for physical quantities that encode electron movement and potential. Thus, quantum mechanics models reality on the basis of continuity. Discrete values result from the approach in which the theoretical model is treated and solved; but may not be nature-inherent.

Intrigued by cosmological challenges and debates over the fundamental laws of the physical world, David Tong—a theoretical physicist at the University of Cambridge—is giving the continuity-discontinuity interrelation a closer look. He writes that the term “quantum mechanics” could said to be a misnomer for a theory that formulates its equations in terms of continuous quantities [2].  He cites Leopold Kronecker's proclamation “God made the integers, all else is the work of man.” and counters with “God did not make the integers. He made continuous numbers, and the rest is the work of the Schrödinger equation.” [3].  Tong explains the latter in detail:

Integers are not inputs of the [quantum] theory, as Bohr thought [Danish physicist Niels Bohr “implemented” discreteness at the atomic scale]. They are outputs. The integers are an example of what physicists call an emergent quantity.  In this view, the term “quantum mechanics” is a misnomer. Deep down, the theory is not quantum. In systems such as the hydrogen atom, the processes described by the theory mold discreteness from underlying continuity. 

Quantum phenomena are these days demonstrated and animated in educational as well as entertaining videos. The Zeitgeist-driven perception: What I simulate and animate, is what I see and believe in. Yet, living in a digital age does not automatically imply living in a digital universe.

Keywords: physics, philosophy, quantum theory, physical world, pointillist universe, emergent integers.

References and more to explore
[1] Quantum Mechanics: Solving Schrödinger's equation [users.aber.ac.uk/ruw/teach/237/hatom.php].
[2] David Tong: The Unquantum Quantum. Scientific American, December 2012, 307 (6), pp. 46-49 [www.nature.com/scientificamerican/journal/v307/n6/full/scientificamerican1212-46.html].
[3] Quoted at axeleratio.tumblr.com: axeleratio.tumblr.com/post/36680758289/god-did-not-make-the-integers-he-made-continuous.