Deformations of nearly Kähler instantons

We formulate the deformation theory for instantons on nearly Kähler six-manifolds using spinors and Dirac operators. Using this framework we identify the space of deformations of an irreducible instanton with semisimple structure group with the kernel of an elliptic operator, and prove that abelian instantons are rigid. As an application, we show that the canonical connection on three of the four homogeneous nearly Kähler six-manifolds G/H is a rigid instanton with structure group H. In contrast, these connections admit large spaces of deformations when regarded as instantons on the tangent bundle with structure group SU(3)

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

Technical report on the Bottlenose dolphin (Tursiops aduncus) unusual mortality event within the Swan Canning Riverpark, June-October 2009

This technical report reviews findings from an investigation into the mortalities of six bottlenose dolphins (Tursiops aduncus) in the Swan Canning Riverpark in 2009. The report: (a) describes the epidemiology and pathology of these mortalities; (b) presents background information on the ecology of dolphins in the Swan Canning Riverpark and factors known to affect dolphin health; and (c) discusses the potential role of chemical contaminants in the mortalities. These mortalities were investigated in context of dolphin deaths in the Swan Canning Riverpark prior to 2009 and a series of mortalities of dolphins in the Bunbury area between 2008-10, as well as marine mammal mortality events in other locations

Linkage isomerism in the binding of pentapeptide Ac-His(ALA)3His-NH2 to (Ethylenediamine)Palladium(II): Effect of the binding mode on peptide conformation

The reaction of the pentapeptide Ac-His1-Ala2-Ala3-Ala4-His5-NH2 (AcHAAAHNH2) (1) with [Pd(en)(ONO2)(2)] (en = NH2CH2CH2NH2) in either DMF-d(7) or H2O:D2O (90%:10%) gave three linkage isomers of [Pd(en)(AcHAAAHNH2)](2+) (2), 2a, 2b, and 2c, which differ only in which pair of imidazole nitrogen atoms bind to Pd. In the most abundant isomer, 2a, Pd is bound by N1 from each of the two imidazole rings. In the minor isomers 2b and 2c, Pd is bound by N1(His1) and N3(His5) and by N3(His1) and N1(His5), respectively. The reactions of [Pd(en)(ONO2)(2)] with the N-methylated peptides Ac-(N3-MeHis)Ala-Ala-Ala-(N3-MeHis)-NH2 (AcH*AAAH*NH2) (3), Ac-(N3-MeHis)-Ala-Ala-Ala-(N1-MeHis)-NH2 (AcH*AAAH(#)NH(2)) (4), and Ac(N1-MeHis)-Ala-Ala-Ala-(N3-Me-His)-NH2 (AcH(#)AAAH*NH2) (5) each gave a single species [Pd(en)(peptide)](2+) in N,Ndimethylformamide (DMF) or aqueous solution, 7, 8, and 9, respectively, with Pd bound by the two nonmethylated imidazole nitrogen atoms in each case. These complexes were analogous to 2a, 2b, and 2c, respectively. Ac-(N1-MeHis)-Ala-Ala-Ala(N1-MeHis)-NH2 (AcH(#)AAAH(#)NH(2)) (6) with [Pd(en)(ONO2)21 in DMF slowly gave a single product, [Pd(en)(AcH(#)AAAH(#)NH(2))]21 (10), in which Pd was bound by the N3 of each imidazole ring, The corresponding linkage isomer of 2 was not observed. Complex 10 was also the major product in aqueous solution, but other species were also present. All compounds were exhaustively characterized in solution by multinuclear 1D (H-1, C-13, and, with N-15-labeled ethylenediamine, N-15) and 2D (correlation spectroscopy, total correlation spectroscopy, transverse rotating-frame Overhauser effect spectroscopy (T-ROESY), heteronuclear multiplebond correlation, and heteronuclear single quantum coherence) NMR spectra, circular dichroism (CD) spectra, electrospray mass spectroscopy, and reversed-phase high-performance liquid chromatography. ROESY spectra were used to calculate the structure of 2a, which contained a single turn of a peptide alpha helix in both DMF and water, the helix being better defined in DMF The Pd(en)(2+) moiety was not used in structure calculations, but its location and coordination by one imidazole N1 from each histidine to form a 22-membered metallocycle were unambiguously established. Convergence of the structures was greatest when calculated with two hydrogen-bond constraints (Ala4 pepticle NH center dot center dot center dot OC acetyl and His5 peptide NH center dot center dot center dot OC-His1) that were indicated by the low temperature dependence of these NH chemical shifts. Vicinal HN-CH alpha coupling constants and chemical shifts of alpha-H atoms were also consistent with a helical conformation. Similar long-range ROE correlations were observed for [Pd(en)(AcH*AAAH*NH2)](2+) (7), which displayed a CD spectrum in aqueous solution that suggested the presence of some helicity. Long-range ROE correlations were not observed for 8, 9, or 10, but a combination of NMR data and CD spectroscopy was interpreted in terms of the conformational behavior of the coordinated pentapeptide. Only for the linkage isomer [Pd(en)(AcH*AAAH(#)NH(2))](2+) (8) was there evidence of a contribution from a helical conformation

A metric for phylogenetic trees based on matching

Comparing two or more phylogenetic trees is a fundamental task in computational biology. The simplest outcome of such a comparison is a pairwise measure of similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so tar all suffer from problems varying from computational cost to lack of robustness; many can be shown to behave unexpectedly under certain plausible inputs. For instance, similarity measures based on maximum agreement are too strict, while measures based on the elimination of rogue taxa work poorly when the proportion of rogue taxa is significant: distance measures based on edit distances under simple tree operations (such as nearest-neighbor interchange or subtree pruning and regrafting) are NP-hard; and the widely used Robinson-Foulds distance is poorly distributed and thus affords little discrimination, while also lacking robustness in the face of very small changes-reattaching a single leaf elsewhere in a tree of any size can instantly maximize the distance. In this paper, we introduce an entirely new pairwise distance measure, based on matching, for phylogenetic trees. We prove that our measure induces a metric on the space of trees, show how to compute it in low polynomial time, verify through statistical testing that it is robust, and finally note that it does not exhibit unexpected behavior under the same inputs that cause problems with other measures. We also illustrate its usefulness in clustering trees, demonstrating significant improvements in the quality of hierarchical clustering as compared to the same collections of trees clustered using the Robinson-Foulds distance