Predictivism and the periodic table

This is a comment on the paper by Barnes (2005) and the responses from Scerri (2005) and Worrall (2005), debating the thesis (‘predictivism’) that a fact successfully predicted by a theory is stronger evidence than a similar fact known before the prediction was made. Since Barnes and Scerri both use evidence presented in my paper on Mendeleev’s periodic law (Brush, 1996) to support their views, I reiterate my own position on predictivism. I do not argue for or against predictivism in the normative sense that philosophers of science employ, rather I describe how scientists themselves use facts and predictions to support their theories. I find wide variations, and no support for the assumption that scientists use a single ‘Scientific Method’ in deciding whether to accept a proposed new theory.     

INFORMATION CHARACTERIZATION OF COMMUNICATION CHANNELS FOR SYSTEM IDENTIFICATION

This paper studies identification of systems in which the system output is quantized, transmitted through a digital communication channel, and observed afterwards. The concept of the CR Ratio is introduced to characterize impact of communication channels on identification. The relationship between the CR Ratio and Shannon channel capacity is discussed. Identification algorithms are further developed when the channel error probability is unknown.     

Phylogenetic position of sponges in early metazoan evolution and bionic applications of siliceous sponge spicules

Sponges are the oldest and the simplest but not primitive multicellular animals. They represent the earliest evolutionary metazoan phylum still extant. It was a long and painful scientific process to posi-tion the most enigmatic and mysterious metazoan,the Porifera,into their correct phylogenetic place among the eukaryotes in general and multicellular animals in particular. As living fossils,sponges provide the best evidence for the early evolution of Metazoa. More recently,interest has been focused on the bionic applications of sponges' siliceous spicules,after the discovery of their unique structure and high fiber performance. In this review,the emergence of sponges,evolutionary novelties found in sponges,and the phylogenetic position of sponges in early metazoan evolution are highlighted. In ad-dition,the present state of knowledge on silicatein-mediated "biosilica" formation in marine sponges,including the involvement of other molecules in silica metabolism and their potential application in nanobiotechnology and medicine,is given.     

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.

Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the mucosal surface of the intestine but are normally contained in healthy individuals by the local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs, revealing the presence of hundreds of insertions and deletions compared with the Escherichia coli genome, ranging in size from single genes to large islands. Notably, the genome sequence identifies over two hundred pseudogenes, several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis.     

The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design

The worldwide spread of H5N1 avian influenza has raised concerns that this virus might acquire the ability to pass readily among humans and cause a pandemic. Two anti-influenza drugs currently being used to treat infected patients are oseltamivir (Tamiflu) and zanamivir (Relenza), both of which target the neuraminidase enzyme of the virus. Reports of the emergence of drug resistance make the development of new anti-influenza molecules a priority. Neuraminidases from influenza type A viruses form two genetically distinct groups: group-1 contains the N1 neuraminidase of the H5N1 avian virus and group-2 contains the N2 and N9 enzymes used for the structure-based design of current drugs. Here we show by X-ray crystallography that these two groups are structurally distinct. Group-1 neuraminidases contain a cavity adjacent to their active sites that closes on ligand binding. Our analysis suggests that it may be possible to exploit the size and location of the group-1 cavity to develop new anti-influenza drugs.