No Such Thing as ‘Attorney Estoppel’: Ethical Conflicts and Attorney Prior Publications

Law school graduates today are increasingly freighted with Internet-accessible and readily searchable publication records. Can these publications create actionable conflicts of interest for attorneys later on? Assessing the relevance of attorney publications requires balancing clients’ entitlement to adequate and zealous representation against the rights of lawyers to express opinions and participate freely in social discourse. The Model Rules offer little guidance, and academics have largely skirted the issue. This paper presents the Publication Conflicts test, a framework for inquiry to assess the impact of prior publications. Then, informed by interviews with judges, ethics experts, law professors and practitioners, this paper presents the view that in general, an attorney’s prior publications lie outside the ‘bounded exclusivity’ that attorneys owe their clients, and thus, do not amount to meaningful conflicts of interest

Getting Started in Text Mining: Part Two

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Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae

Transposons are widely employed as tools for gene disruption. Ideally, they should display unbiased insertion behavior, and incorporate readily into any genomic DNA to which they are exposed. However, many transposons preferentially insert at specific nucleotide sequences. It is unclear to what extent such bias affects their usefulness as mutagenesis tools. Here, we examine insertion site specificity and global insertion behavior of two mini-transposons previously used for large-scale gene disruption in Saccharomyces cerevisiae: Tn3 and Tn7. Using an expanded set of insertion data, we confirm that Tn3 displays marked preference for the AT-rich 5 bp consensus site TA[A/T]TA, whereas Tn7 displays negligible target site preference. On a genome level, both transposons display marked non-uniform insertion behavior: certain sites are targeted far more often than expected, and both distributions depart drastically from Poisson. Thus, to compare their insertion behavior on a genome level, we developed a windowed Kolmogorov–Smirnov (K–S) test to analyze transposon insertion distributions in sequence windows of various sizes. We find that when scored in large windows (>300 bp), both Tn3 and Tn7 distributions appear uniform, whereas in smaller windows, Tn7 appears uniform while Tn3 does not. Thus, both transposons are effective tools for gene disruption, but Tn7 does so with less duplication and a more uniform distribution, better approximating the behavior of the ideal transposon

Uncovering trends in gene naming

A survey of unusual gene names reveals trends underlying their choice

Publishing perishing? Towards tomorrow's information architecture

Scientific articles are tailored to present information in human-readable aliquots. Although the Internet has revolutionized the way our society thinks about information, the traditional text-based framework of the scientific article remains largely unchanged. This format imposes sharp constraints upon the type and quantity of biological information published today. Academic journals alone cannot capture the findings of modern genome-scale inquiry. Like many other disciplines, molecular biology is a science of facts: information inherently suited to database storage. In the past decade, a proliferation of public and private databases has emerged to house genome sequence, protein structure information, functional genomics data and more; these digital repositories are now a vital component of scientific communication. The next challenge is to integrate this vast and ever-growing body of information with academic journals and other media. To truly integrate scientific information we must modernize academic publishing to exploit the power of the Internet. This means more than online access to articles, hyperlinked references and web-based supplemental data; it means making articles fully computer-readable with intelligent markup and Structured Digital Abstracts. Here, we examine the changing roles of scholarly journals and databases. We present our vision of the optimal information architecture for the biosciences, and close with tangible steps to improve our handling of scientific information today while paving the way for an expansive central index in the future