Predicting Horizontal Gene Transfers with Perfect Transfer Networks

Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and species trees. However, it is well-known that sequences have difficulty identifying ancient transfers since mutations have enough time to erase all evidence of such events. In this work, we ask whether character-based methods can predict gene transfers. Their advantage over sequences is that homologous genes can have low DNA similarity, but still have retained enough important common motifs that allow them to have common character traits, for instance the same functional or expression profile. A phylogeny that has two separate clades that acquired the same character independently might indicate the presence of a transfer even in the absence of sequence similarity. We introduce perfect transfer networks, which are phylogenetic networks that can explain the character diversity of a set of taxa. This problem has been studied extensively in the form of ancestral recombination networks, but these only model hybridation events and do not differentiate between direct parents and lateral donors. We focus on tree-based networks, in which edges representing vertical descent are clearly distinguished from those that represent horizontal transmission. Our model is a direct generalization of perfect phylogeny models to such networks. Our goal is to initiate a study on the structural and algorithmic properties of perfect transfer networks. We then show that in polynomial time, one can decide whether a given network is a valid explanation for a set of taxa, and show how, for a given tree, one can add transfer edges to it so that it explains a set of taxa

Quantum Gravity and Taoist Cosmology: Exploring the Ancient Origins of Phenomenological String Theory

In the author’s previous contribution to this journal (Rosen 2015), a phenomenological string theory was proposed based on qualitative topology and hypercomplex numbers. The current paper takes this further by delving into the ancient Chinese origin of phenomenological string theory. First, we discover a connection between the Klein bottle, which is crucial to the theory, and the Ho-t’u, a Chinese number archetype central to Taoist cosmology. The two structures are seen to mirror each other in expressing the psychophysical (phenomenological) action pattern at the heart of microphysics. But tackling the question of quantum gravity requires that a whole family of topological dimensions be brought into play. What we find in engaging with these structures is a closely related family of Taoist forebears that, in concert with their successors, provide a blueprint for cosmic evolution. Whereas conventional string theory accounts for the generation of nature’s fundamental forces via a notion of symmetry breaking that is essentially static and thus unable to explain cosmogony successfully, phenomenological/Taoist string theory entails the dialectical interplay of symmetry and asymmetry inherent in the principle of synsymmetry. This dynamic concept of cosmic change is elaborated on in the three concluding sections of the paper. Here, a detailed analysis of cosmogony is offered, first in terms of the theory of dimensional development and its Taoist (yin-yang) counterpart, then in terms of the evolution of the elemental force particles through cycles of expansion and contraction in a spiraling universe. The paper closes by considering the role of the analyst per se in the further evolution of the cosmos

Spartan Daily, September 3, 1992

Volume 99, Issue 5https://scholarworks.sjsu.edu/spartandaily/8290/thumbnail.jp

Conversation with Robert Brandom

In this broad interview Robert Brandom talks about many themes concerning his work and about his career and education. Brandom reconstructs the main debts that he owes to colleagues and teachers, especially Wilfrid Sellars, Richard Rorty, and David Lewis, and talks about the projects he’s currently working on. He also talks about contemporary and classical pragmatism, and of the importance of classical thinkers like Kant and Hegel for contemporary debates. Other themes go deeper into the principal topics of his theoretical work – in particular, his later understanding of expressivism, his take on the debate between representationalists and anti-representationalists in semantics, the main open problems for his wide inferentialist project, and his methodological preference for the normative vocabulary in his account of discursive practice. Finally, Brandom touches on the epistemic role of perception and on his views about the importance of the phenomenological aspects of perceptual experience

Feeding behavior of crayfish snakes (Regina) : allometry, ontogeny and adaptations to an extremely specialized diet

Dietary specialists are often predicted to have specialized and stereotyped behaviors that increase the efficiency of foraging on their preferred prey, but which limit their ability to feed on nonpreferred prey. Although there is support for various aspects of this prediction, a number of studies suggest that specialists should not be characterized in such a simplified way. The purpose of this study was to describe the prey selectivity, prey handling behavior, and chemosensory behavior of crayfish snakes (Regina, Colubridae), which are extreme dietary specialists, and determine the effects of prey type, feeding experience and ontogeny. Museum specimens and field captured snakes, together with published data, were used to determine the effect of predator and prey size on prey selectivity in each species of Regina. Snakes were videotaped feeding on different prey to determine the effects of prey type and size on prey handling behavior, its efficiency and stereotypy. Finally, snakes born in captivity were raised on different diets to determine the effect of prey availability and prey type on the ontogeny of chemosensory behavior. This study confirmed the dietary specializations of Regina grahamii, R. septemvittata and R. alleni, and found that R. rigida, like R. alleni, includes odonate larvae in their diet as juveniles. Snake size and prey availability determines prey selection by R. alleni and R. rigida. This study also demonstrated that the relationships between dietary and behavioral specialization can be complex and depend on the characteristics of both the predator and its prey. For example, behavioral specializations in prey handling behavior were correlated with prey type rather than degree of dietary specialization. Hard crayfish required complex prey handling techniques, while soft crayfish did not. In R. alleni and R. rigida, such specialization appears to have permitted dietary expansion rather than restriction. Also, experience improved both prey handling efficiency and stereotypy irrespective of prey type consumed. As predicted the chemosensory response of each Regina species was greatest toward species characteristic prey. However, prey availability and type influenced these responses. In particular, R. septemvittata increased its chemosensory response toward hard crayfish (nonpreferred prey) when not permitted to eat soft crayfish

The Evolution Of Coral Snake Mimicry

Scientists have regarded mimicry as one of the most amazing examples of the power of natural selection. Early observations by naturalists of the mimetic association between venomous New World coral snakes of the genus Micrurus and harmless mimics has stimulated an intense debate about the causes and consequences of mimicry that persists today. Despite its medical, evolutionary and historical importance our understanding of evolution within the genus Micrurus is negligible. My dissertation explores the evolution of mimicry within South American coral snakes and their mimics using a multi-scale framework involving macroevolutionary (Chapter I), geographic/morphological concordance (Chapters II and III), behavioral (Chapter IV), and phylogeographic (Chapter V) approaches. I show that warning coloration is widespread, liable and positively correlated with speciation rates. I found that Micrurus species behave as Müllerian mimics. Oxyrhopus guibei is a potential mimic of the genus Micrurus and mimetic precision is independent of model’s species richness but dependent on which part of the snake’s body is being studied. I also demonstrate that social interactions might be an underappreciated factor on the evolution of mimicry. Finally, I explore the phylogeographic history of M. surinamensis and M. lemniscatus and provide an interpretation of their distinct patterns of evolution with implications for Micrurus’ taxonomy