Thursday, March 31, 2011

Acronym in biochemistry and bacteriology: NDM-1 for New Delhi metallo-β-lactamase

NDM-1 is an enzyme named by Timothy Walsh of Cardiff University in Wales for the city from which a Swedish patient had acquired a Klebsiella pneumoniae strain with a gene producing this bacteria-resistant enzyme : New Delhi metallo-β-lactamase [1-3]. The associated gene is denoted blaNDM-1. The Swedish patient of Indian origin had traveled to New Delhi, India, and acquired a urinary tract infection. Hospitalized in Örebro, Sweden, he was treated by the Swedish physician Christian Giske, who then contacted his acquaintance Timothy Walsh, who runs a lab that unravels the genetics of antibacterial resistance, for consultation concerning the bacterium found in the man's urine.

The NDM-1-producing Klebsiella pneumoniae strain is making headlines since it is resistant to antibiotics including carbapenems, the so-called drugs of last resort [1]. The only drug showing some effect is colistin, which also shows toxic effects on the kidneys.

Keywords: New Delhi metallo-beta-lactamase, NDM-1-producing Enterobacteriaceae, bacterial genes, drug-resistant bacteria, disease control, medicine

[1] Maryn McKenna:
The Enemy Within. Scientific American April 2011, 304 (4), 47-53.
[2] D. Yong et al.:
Characterization of a New Metallo-β-Lactamase Gene, blaNDM-1, and a Novel Erythromycin Esterase Gene Carried on a Unique Genetic Structure in Klebsiella pneumoniae Sequence Type 14 from India. Antimicrobial Agents and Chemotherapy Dec. 2009, 53 (12), 5046-5054.
[3] N. Tijet et al.:
New Delhi metallo-β-lactamase, Ontario, Canada. Emerging Infectious Diseases Feb. 2011, 17 (2), 306-307. PDF.

Tuesday, March 29, 2011

Two names for beetle genera: Batesiana and Erwiniana

The Californian entomologist Terry Erwin, in 1993, was going to give the name Batesiana to a beetle genus to honor Henry Walter Bates, one of his ancestors in neotropical forest expeditions. However, as R. Dunn is telling us in a footnote in his book Every Living Thing, this genus name was already occupied [1]: two scientists at the University of Nebraska found another kind of beetle in their collection that someone else had already given the genus name Batesiana. Two different genera cannot bear the same name. The Nebraska scientists therefore decided to change the name from Batesiana to Erwiniana to honor Erwin.

Keywords: entomology, insects, coleopterology, beetles, nomenclature

References, further reading and watching
[1] Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009; see footnote on page 79.
[2] Henry Walter Bates [].
[3] Terry Erwin about ecology, biodiversity and taxonomy
in an interview by Alida Mercado Cardenas:
[4] Tree of Life web project:

Thursday, March 17, 2011

Aphanus rolandri, a European seed bug species named after Daniel Rolander

Daniel Rolander belonged to the circle of Swedish students, which Linnaeus sent around the world to find new species. In contrast to Christopher Tärnström, a student Linnaeus liked, Daniel Rolander was not one of his favorite students. Linnaeus named a European seed bug species, not to honor, but to insult him: Aphanus rolandri. The Greek word Aphanus stands for ignoble and obscure [1].

Rolander was sent to Suriname in South America, where he grew overwhelmingly terrified and from where he reported about terrible species including thorny trees and bushes, rotting fruit with a stench that can kill and big snakes [anacondas?], lizards, insects and other animals ready to attack. In 2007, Rolander's seven hundred pages of journals (written in Latin), archived in a botanical library at Denmark's Natural History Museum in Copenhagen, were translated and made public [1]. Apparently, he collected many thousands of specimen, which he was not going to hand over to his mentor, when he returned to Uppsala...

Among “Rolander's species” is the carabid beetle Galerita americana, which lives primarily in the tropical forest canopy. On the other hand, the bug species of the family Lygaeidae, which carries Rolander's name, is less exotic, yet a scarce species that is mostly found in the south of England between Cornwall and Kent [2]. It lives in dry, sheltered and well-drained habitats which have a thin covering of leaf litter or stones. With a dark red or orange spot at the base of the wing membrane on its otherwise black body, Aphanus rolandri appears quite beautiful and unique—a distinctive ground bug Daniel Rolander would not have been afraid of.

Keywords: entomology, hemiptera, history, insects, beetles

[1] Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009; pages 62-64 and footnote on page 61.
[2] British Bugs: Aphanus rolandri.
[3] Wikipedia: Daniel Rolander.

Wednesday, March 9, 2011

Plant genus Ternstroemia named after Linnaeus apostle Christopher Tärnström

The plant genus name Ternstroemia refers to the Swedish botanist Christopher Tärnström [1]. He as a student of Carl Linnaeus in Uppsala, Sweden. Rob R. Dunn counts Tärnström was one of the apostles of Linnaeus (there were seventeen), who were to travel around the world and collect plants and other items of interest to natural science. Five of them died of disease and never made it back to Uppsala. Tärnström shared this fate in 1746: he died of a tropical fever in what is now Vietnam—within in a week of his arrival and without collecting a single plant. He was among the best and favorite students of Linnaeus, who immortalized Tärnström by naming a genus of tropical plants with beautiful flowers after him.

Ternstroemia species belong to the Theacea family of flowering plants [2]. Theacea genera are typically evergreens and found in tropical parts of the world including southern and eastern Asia, Africa, New Guinea, and Central and South America, but also the Canary Islands and the southeastern United States.

Keywords: botany, history, expeditions, tropical field research, Vietnam

[1] Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009; in particular, see footnote on page 61.
[2] Kew: Vascular Plant Families and Genera - List of genera in family Theaceae [].

Tuesday, March 8, 2011

Achillea foliis duplicatopinnatis glabris, laciniis linearibus acute laciniatus

Achillea foliis duplicatopinnatis glabris, laciniis linearibus acute laciniatus was the “scientific name” for the common yarrow in pre-Linnaean time. Rob R. Dunn gives this examples in his book with the title “Every Living Thing” to demonstrate how scientists then made names longer and longer to describe and distinguish species. While a rapidly increasing number of new species was discovered by naturalists and explorers around the world—speaking different languages and communicating more frequently —the system of long names became unpractical and non-unique.

In Dunn's words
“Carl Linnaeus would save the common language of science. He would rescue it from the stew of names in which it was brewing.” In 1735 Linnaeus published his new two-name system in his book Systema Naturae. Naming is organizing. Linnaeus approach for plants was to use the male sex organs (stamens), which he thought were more characteristic for plant species than leave forms that typically were (and still are) chosen for classification. For animals, Linnaeus used jawbones and teats. Who said science can't be sexy? Linnaeus, in his time, was accused by his detractors, according to Dunn, of developing a system of classification unsuited to ladies.

By the way, the common yarrow is not named for any sex-organ feature, but for its deeply toothed, fern-like foliage: Achillea millefolium. The adjective
millefolium means thousand-leafed.


Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009.

Monday, March 7, 2011

Camponotus dunni, an ant species of South America named after Rob. R. Dunn

The biologist Rob R. Dunn at North Carolina State University is studying ants, parasites and other species [1]. He has one ant species, Camponotus dunni, named after him. In his book “Every Living Thing” he explains that the entomologist Bill Mackay named the species after him [2]. Dunn found this new species in the Cavinas area of the Bolivian Amazon. The indigenous language in that part of Bolivia is Cavineño. Dunn did explore ants there and the kowledge of the Cavineños about insects, ants in particular. His native guide, he writes, had names for about forty ant species out of the few hundred ant species around Cavinas.

There are over thousand species in the genus Camponotus, also called carpenter ants. A subset of Camponotus species and related references can be found on Wikipedia, but I couldn't locate Camponotus dunni in that list, when I looked on March 7, 2011. Is there any detailed Myrmecopedia?

Keywords: entomology, myrmecology, Amazonian forest in Bolivia, Cavineño

[1] Dee Shore: College Profile: Rob Dunn. North Carolina State University, September 2, 2010 [].
Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009.
Axel Drefahl: Naming and knowing biological species. March 6, 2011.

Sunday, March 6, 2011

Naming and knowing biological species

In the preface to Rob R. Dunn's book Every Living Thing, the biologist and naturalist Edward O. Wilson reminds us of the erroneous conception that most species on Earth are known to science. He ascertains:
Most species on Earth are not yet named. Most named species have not yet been studied.
For example, fewer than 10 percent of fungi and fewer than one percent of microorganisms are known.

Dunn tells us that “naming species is not big science.” He gives us a beautifully written account on the history of naming species. Of course, Linnaeus (of the linden tree) and his students, which he sent around the world, have not been left out in the narrative. Beyond the business of collecting and cataloging, however, there is big science—and some philosophy as well. Dunn introduces us to discoveries in regions, to which most of us don't have access: the deep sea, the deep soil and the extraterrestrial domain. In addition to finding new life forms in new places, there can still species and subspecies be discovered in the microcosm on and in our own body.

At the nano-scale, researchers are confronted with the challenge to distinguish between living species and molecular self-assemblies. And how do we name and classify something with quickly mutating individuality; something that splits into parts, re-assembles or goes endosymbiotically under cover?

Rob R. Dunn: Every Living Thing. First Edition. HarperCollins Publishers, New York, 2009.

Wednesday, March 2, 2011

Petri nets named after German computer scientist Carl Adam Petri

Petri nets are named after Carl Adam Petri, a German mathematician and computer scientist [1-3]. He was born in 1926 in Leipzig, invented Petri nets at the age of 13 and introduced the concept of Petri nets in his dissertation in 1962. Petri died in 2010 [4], but his ideas found places and transitions in various fields including biology and chemistry.

In the Journal Molecular Informatics, Ina Koch has published an instructive review on the history, state-of-the-art and current limitations of Petri nets applied to the modeling of complex systems [3]. Further documentations, work and Petri-net software is available online [5,6].

Petri nets connecting languages:
Dutch: petrinetten
French: réseaux de Petri
German: Petrinetze
Spanish: redes de Petri

[1] IEEE Computer Society: Carl Adam Petri - 2008 Computer Pioneer Award Recipient.
[2] Informationsdienst Wissenschaft: Carl Adam Petri erhält den "Computer Pioneer Award." []
[3] Ina Koch: Petri Nets - A Mathematical Formalism to Analyze Chemical Reaction Networks. Mol. Inf. 2010, 29, pp. 838-843.
DOI: 10.1002/minf.201000086.
[4] Carl Adam Petri dies - his ideas live on.
[5] Petri Nets World []
[6] Inspired by Carl Adam Petri's work, Cornelio Hopmann is working on and blogging/documenting work in progress on mathematical models including Q-Orders and Einstein Spaces