L.I. Vorobiova,Propionibacteria, Kluver Academic Publishers,Dordrecht–Boston–London, 1999

Applied Biochemistry and Microbiology -     

Recommendations for the Role of Publishers in Access to Data

As appeals for public access of research data continue to proliferate, many scholarly publishers—alongside funders, institutions, and libraries—are expanding their role to address this need. Here we outline eight recommendations and a set of suggested action items for publishers to promote and contribute to increasing access to data. This call to action emerged from a summit that brought together data stewardship leaders across stakeholder groups. The recommendations were subsequently refined by the community as a result of public input gathered online and in meetings.     

The Geometric Increase in Meta-Analyses from China in the Genomic Era

Meta-analyses are increasingly popular. It is unknown whether this popularity is driven by specific countries and specific meta-analyses types. PubMed was used to identify meta-analyses since 1995 (last update 9/1/2012) and catalogue their types and country of origin. We focused more on meta-analyses from China (the current top producer of meta-analyses) versus the USA (top producer until recently). The annual number of meta-analyses from China increased 40-fold between 2003 and 2011 versus 2.4-fold for the USA. The growth of Chinese meta-analyses was driven by genetics (110-fold increase in 2011 versus 2003). The HuGE Navigator identified 612 meta-analyses of genetic association studies published in 2012 from China versus only 109 from the USA. We compared in-depth 50 genetic association meta-analyses from China versus 50 from USA in 2012. Meta-analyses from China almost always used only literature-based data (92%), and focused on one or two genes (94%) and variants (78%) identified with candidate gene approaches (88%), while many USA meta-analyses used genome-wide approaches and raw data. Both groups usually concluded favorably for the presence of genetic associations (80% versus 74%), but nominal significance (P<0.05) typically sufficed in the China group. Meta-analyses from China typically neglected genome-wide data, and often included candidate gene studies published in Chinese-language journals. Overall, there is an impressive rise of meta-analyses from China, particularly on genetic associations. Since most claimed candidate gene associations are likely false-positives, there is an urgent global need to incorporate genome-wide data and state-of-the art statistical inferences to avoid a flood of false-positive genetic meta-analyses.     

The Era of Management Is Over

The management paradigm fails when confronted with complex problems where there are no clearly defined objectives and a plethora of mutually contradictory approaches, each of which is plausible in a particular frame of reference. The notion of the disinterested expert cannot withstand scrutiny, and putative experts must earn public trust. Scientists must be prepared to share their advisory and decision-making roles with a variety of interested parties and participate with them on an equal footing. Received 6 September 2000; accepted 31 May 2001.     

Photosynthesis in the Archean Era

The earliest reductant for photosynthesis may have been H₂. The carbon isotope composition measured in graphite from the 3.8-Ga Isua Supercrustal Belt in Greenland is attributed to H₂-driven photosynthesis, rather than to oxygenic photosynthesis as there would have been no evolutionary pressure for oxygenic photosynthesis in the presence of H₂. Anoxygenic photosynthesis may also be responsible for the filamentous mats found in the 3.4-Ga Buck Reef Chert in South Africa. Another early reductant was probably H₂S. Eventually the supply of H₂ in the atmosphere was likely to have been attenuated by the production of CH₄ by methanogens, and the supply of H₂S was likely to have been restricted to special environments near volcanos. Evaporites, possible stromatolites, and possible microfossils found in the 3.5-Ga Warrawoona Megasequence in Australia are attributed to sulfur-driven photosynthesis. Proteobacteria and protocyanobacteria are assumed to have evolved to use ferrous iron as reductant sometime around 3.0 Ga or earlier. This type of photosynthesis could have produced banded iron formations similar to those produced by oxygenic photosynthesis. Microfossils, stromatolites, and chemical biomarkers in Australia and South Africa show that cyanobacteria containing chlorophyll a and carrying out oxygenic photosynthesis appeared by 2.8 Ga, but the oxygen level in the atmosphere did not begin to increase until about 2.3 Ga.