Computational protein function prediction: Are we making progress?

The computational prediction of gene and protein function is rapidly gaining ground as a central undertaking in computational biology. Making sense of the flood of genomic data requires fast and reliable annotation. Many ingenious algorithms have been devised to infer a protein's function from its amino acid sequence, 3D structure and chromosomal location of the encoding genes. However, there are significant challenges in assessing how well these programs perform. In this article we explore those challenges and review our own attempt at assessing the performance of those programs. We conclude that the task is far from complete and that a critical assessment of the performance of function prediction programs is necessary to make true progress in computational function prediction.     

Kant on anatomy and the status of the life sciences

This paper contributes to recent interest in Kant's engagement with the life sciences by focusing on one corner of those sciences that has received comparatively little attention: physical and comparative anatomy. By attending to remarks spread across Kant's writings, we gain some insight into Kant's understanding of the disciplinary limitations but also the methodological sophistication of the study of anatomy and physiology. Insofar as Kant highlights anatomy as a paradigmatic science guided by the principle of teleology in the Critique of the Power of Judgment, a more careful study of Kant's discussions of anatomy promises to illuminate some of the obscurities of that text and of his understanding of the life sciences more generally. In the end, it is argued, Kant's ambivalence with regard to anatomy gives way to a pessimistic conclusion about the possibility that anatomy, natural history, and, by extension, the life sciences more generally might one day become true natural sciences.     

Taming theory with thought experiments: Understanding and scientific progress

I claim that one way thought experiments contribute to scientific progress is by increasing scientific understanding. Understanding does not have a currently accepted characterization in the philosophical literature, but I argue that we already have ways to test for it. For instance, current pedagogical practice often requires that students demonstrate being in either or both of the following two states: 1) Having grasped the meaning of some relevant theory, concept, law or model, 2) Being able to apply that theory, concept, law or model fruitfully to new instances. Three thought experiments are presented which have been important historically in helping us pass these tests, and two others that cause us to fail. Then I use this operationalization of understanding to clarify the relationships between scientific thought experiments, the understanding they produce, and the progress they enable. I conclude that while no specific instance of understanding (thus conceived) is necessary for scientific progress, understanding in general is.     

Predation on eggs of Schneider’s dwarf caiman,Paleosuchus trigonatus (Schneider, 1807), by armadillos and other predators

Nests of Schneider’s dwarf caiman, Paleosuchus trigonatus, were located in the forests around three streams that drain into the Xingu River, Brazilian Amazonia, in October 2014. Camera traps were installed at the edge of four nests to document predators and female parental care. At two nests, females unsuccessfully defended their nests against one or more giant armadillos, Priodontes maximus, and nine-banded armadillos, Dasypus novemcinctus. Both armadillo species responded to the attack by fleeing and returning on the opposite side of the nest by going around the tree under which the nest was located. Giant armadillos have never before been recorded consuming caiman eggs and their diet has been described as consisting mostly of ants and termites. Another species of armadillo, Cabassous unicinctus, was also registered digging into a nest and probably consuming eggs, though it is generally considered to be primarily insectivorous. A tayra (Eira barbara), lizard (Tupinambis teguixin) and coati (Nasua nasua) were also registered taking eggs from nests during the day, but we obtained no registers of nest defence by caimans during the day. The three nests were attacked after 60 days of incubation, when the eggs were well developed.     

New findings of Hexalona-branch representatives in Brazil,with a description of Prenda gen. nov. (Crustacea: Anomopoda: Aloninae)

Altogether, Coronatella and Hexalona-branches are considered the main lineages of Aloninae – a subfamily of common bottom-dwelling microcrustaceans in freshwater environments. Although the taxonomic features of Brazilian members of the Hexalona-branch have been summarised for species from the costata-group and affinis-group, a revision of other widely distributed species in the world is still lacking in this country. The aim of this paper was to study the morphology of Brazilian populations from the guttata-group and intermedia-group, and to describe a new genus from the Hexalona-branch. The parthenogenetic females of Alona cf. guttata from Brazil have similar morphology when compared to data from the literature, but the armature of the terminal claw of its males seems to be different from those of Alona guttata sensu stricto, Alona barbulata and Alona werestschagini. The intermedia-group is formed by Alona elisae sp. nov., which seems to be endemic to the Cerrado of Brazil Central, and Alona isabellae sp. nov., which is widely distributed in Brazil; this species has a labral keel armed with 2–4 setulae, and postabdomen with setulae of lateral fascicles longer than the level of marginal denticles, morphological traits that differentiate it from Alona elisae sp. nov. Another endemic species from the Hexalona-branch is Prenda arvensis gen. nov. and sp. nov., which has two main head pores, a reduced seta on endite 1 of the first limb, sixth limb is a wide lobe. The potential of biodiversity from the Hexalona-branch from Brazil is still underestimated, and a global revision of the guttata-group and intermedia-group is very important for the progress of Aloninae taxonomy and systematics.

http://zoobank.org/urn:lsid:zoobank.org:pub:0A2E4A30-0C9C-43E8-8E72-1DEDA6AFF3C3     

Cryptic subarctic diversity: a new bumblebee species from the Yukon and Alaska (Hymenoptera: Apidae)

It is nearly 90 years since a bumblebee species has been described for the first time from Canada or the USA that was previously unrecognised by science. We describe and illustrate Bombus(Alpinobombus) kluanensis sp. nov. and begin to map its distribution. This species was discovered through analysis of Cytochrome c Oxidase subunit I barcodes and had been unsuspected on the basis of morphological and colour characteristics. So far, 247 female specimens considered to belong to this species are known from the subarctic mountains associated with the Denali Fault running from the Alaska Range (Alaska, USA) to Kluane in the Saint Elias Mountains (Yukon, Canada). A checklist of all species of the subgenus Alpinobombus worldwide is provided.

http://zoobank.org/urn:lsid:zoobank.org:pub:78D524DD-FFBA-4BC4-8D39-3EF4F6BDD39E