New Hampshire Motor Transport Association v. Rowe: Federal Preemption of Maine\u27s Attempt to Regulate Internet Sales of Tobacco to Minors

In New Hampshire Motor Transport Ass\u27n v. Rowe, trade associations sought a declaratory judgment that the Federal Aviation Administration Authorization Act of 1994 (FAAAA) preempts a Maine law enacted to facilitate collection of state taxes and restrict the delivery of tobacco products to minors (the Tobacco Delivery Law). The district court granted the plaintiffs\u27 second motion for summary judgment in part, finding that a single provision of little independent consequence escaped preemption, and enjoined enforcement of the preempted provisions. The state appealed to the United States Court of Appeals for the First Circuit, which held that most of Maine\u27s Tobacco Delivery Law is preempted. Maine argued that its efforts to protect the health and welfare of its minor citizens and collect unpaid tobacco taxes cannot be characterized as components of an artificial regulatory structure. To the contrary, the state maintained that its law (1) is foremost a legitimate exercise of Maine\u27s police power that advances a vested interest of the state as a consumer of federal grants and a provider of health-related anti-smoking services for minors, and (2) was duly enacted pursuant to its concurrent jurisdiction-as provided by federal law-to enforce proscriptions on trafficking in contraband cigarettes. Is it possible that Maine over-reached by combining in a single enactment a revenue collection provision and a citizen health provision? Should simpler mechanisms be employed to forestall a future adverse preemption ruling based on a finding of “forbidden significant effect” of state law on interstate carriers? Does New York\u27s law-which proscribes all delivery of cigarettes to consumers-represent a viable model? Congress should clarify the inherent authority of the states to control the importation of harmful tobacco products across their borders. Only by affirming the jurisdiction of states in the quasi-regulation of instrumentalities of interstate commerce-when those instrumentalities choose to deal in notoriously harmful consumer goods-can the seemingly intractable issues raised by the N.H. Motor Transport litigation be put to rest

Mapping the Space of Genomic Signatures

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to $k$ (herein $k=9$) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence homology and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information.Comment: 14 pages, 7 figures. arXiv admin note: substantial text overlap with arXiv:1307.375

Identifying and explaining large-scale genome sequence convergence

Recently it has been shown that convergent sequence evolution can happen in nature at unexpectedly large scales, systematically misleading methods of phylogenetic reconstruction. For this reason, among others, there has been growing interest in sequence convergence in recent years. Although various techniques for detecting sequence convergence, such as site-specific log-likelihood support and ancestral sequence reconstruction, have been used, there does not yet exist a general statistical procedure for reliably distinguishing between random convergence and convergence resulting from parallel selective pressures or time-heterogeneous evolutionary processes. Here, I intend to further our understanding of sequence convergence by creating a new algorithm for detecting, quantifying and understanding non-random sequence convergence in a principled and unbiased manner. I design and implement a new approach for detecting convergence across entire phylogenies, making it amenable to a wider variety of datasets than was previously possible. Finally, I investigate the role of effective population size in contributing to sequence convergence, where I show for the first time that time-heterogeneity in effective population sizes can be sufficient to cause large-scale episodes of convergent sequence evolution. This surprising finding suggests an apparently non-adaptive mechanistic explanation since it can occur without changes to the underlying fitness landscape and is instead driven by lineages with increased effective population sizes becoming enabled to climb higher on the same adaptive peaks. As a result, we believe this phenomenon to be of adaptive significance even though it does not require adaptation to a changing environment per se. These finding suggest that time-heterogeneous evolutionary processes must be integrated into the models used for phylogenomic reconstruction and in comparative genomics more broadly

New Hampshire Motor Transport Association v. Rowe: Federal Preemption of Maine\u27s Attempt to Regulate Internet Sales of Tobacco to Minors

In New Hampshire Motor Transport Ass\u27n v. Rowe, trade associations sought a declaratory judgment that the Federal Aviation Administration Authorization Act of 1994 (FAAAA) preempts a Maine law enacted to facilitate collection of state taxes and restrict the delivery of tobacco products to minors (the Tobacco Delivery Law). The district court granted the plaintiffs\u27 second motion for summary judgment in part, finding that a single provision of little independent consequence escaped preemption, and enjoined enforcement of the preempted provisions. The state appealed to the United States Court of Appeals for the First Circuit, which held that most of Maine\u27s Tobacco Delivery Law is preempted. Maine argued that its efforts to protect the health and welfare of its minor citizens and collect unpaid tobacco taxes cannot be characterized as components of an artificial regulatory structure. To the contrary, the state maintained that its law (1) is foremost a legitimate exercise of Maine\u27s police power that advances a vested interest of the state as a consumer of federal grants and a provider of health-related anti-smoking services for minors, and (2) was duly enacted pursuant to its concurrent jurisdiction-as provided by federal law-to enforce proscriptions on trafficking in contraband cigarettes. Is it possible that Maine over-reached by combining in a single enactment a revenue collection provision and a citizen health provision? Should simpler mechanisms be employed to forestall a future adverse preemption ruling based on a finding of “forbidden significant effect” of state law on interstate carriers? Does New York\u27s law-which proscribes all delivery of cigarettes to consumers-represent a viable model? Congress should clarify the inherent authority of the states to control the importation of harmful tobacco products across their borders. Only by affirming the jurisdiction of states in the quasi-regulation of instrumentalities of interstate commerce-when those instrumentalities choose to deal in notoriously harmful consumer goods-can the seemingly intractable issues raised by the N.H. Motor Transport litigation be put to rest

The Power of Nondeterminism in Self-Assembly

We investigate the role of nondeterminism in Winfree's abstract tile assembly model, which was conceived to model artificial molecular self-assembling systems constructed from DNA. By nondeterminism we do not mean a magical ability such as that possessed by a nondeterministic algorithm to search an exponential-size space in polynomial time. Rather, we study realistically implementable systems that retain a different sense of determinism in that they are guaranteed to produce a unique shape but are nondeterministic in that they do not guarantee which tile types will be placed where within the shape. We show a "molecular computability" result: there is an infinite shape S that is uniquely assembled by a tile system but not by any deterministic tile system. We show a "molecular complexity" result: there is a finite shape S that is uniquely assembled by a tile system with c tile types, but every deterministic tile system that uniquely assembles S has more than c tile types. In fact we extend the technique to derive a stronger (classical complexity theoretic) result, showing that the problem of finding the minimum number of tile types that uniquely assemble a given finite shape is Σ^(P)_(2)-complete. In contrast, the problem of finding the minimum number of deterministic tile types that uniquely assemble a shape is NP-complete [5]

CGR images for three DNA sequences.

<p>(a) <i>Homo sapiens sapiens</i> mtDNA, 16,569 bp; (b) <i>Homo sapiens sapiens</i> chromosome 11, beta-globin region, 73,308 bp; (c) <i>Polypterus endlicherii</i> (fish) mtDNA, 16,632 bp. Observe that chromosomal and mitochondrial DNA from the same species can display different patterns, and also that mtDNA of different species may display visually similar patterns that are however sufficiently different as to be computationally distinguishable.</p

Molecular Distance Map of class Amphibia and three of its orders.

<p>The total number of mtDNA sequences is 112, the average DSSIM distance is 0.8445, and the MDS <i>Stress-1</i> is 0.18. Note that the shape of the amphibian cluster and the (<i>x</i>, <i>y</i>)-coordinates of sequence-points are different here from those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119815#pone.0119815.g004" target="_blank">Fig. 4</a>. This is because MDS outputs a map that aims to preserve pairwise distances between points, but not necessarily their absolute coordinates.</p

Molecular Distance Map of three classes: Amphibia, Insecta and Mammalia.

<p>The method successfully clusters taxonomic groups also at the Class level. Gaps and spaces in clusters, in this and other maps, may be due to sampling bias. A topic of further exploration would be to understand the cluster shapes and nature of the distribution of sequences in this figure. The total number of mtDNA sequences is 790, the average DSSIM distance is 0.8139, and the MDS <i>Stress-1</i> is 0.16.</p

Molecular Distance Map of all represented species from (super)kingdom Protista and its orders.

<p>The total number of mtDNA sequences is 70, the average DSSIM distance is 0.8288, and the MDS <i>Stress-1</i> is 0.26. The sequence-point #1466 (red) is the unclassified <i>Haemoproteus</i> sp. jb1.JA27, #1935 (grey) is <i>Babesia bovis T2Bo</i>, and #3173 (grey) is <i>Theileria parva</i>. The annotation shows that all these three species belong to the same taxonomic groups, Chromalveolata, Alveolata, Apicomplexa, Aconoidasida, up to the order level.</p