Accurate calibration of beam trajectories in scanning optical imaging systems.

We present a calibration method for finding the coordinates of points in the trajectory of the scanning beam in flying-spot imaging devices. Our method is based on laterally translating the field of view on the imaging object plane by introducing additional beam deflections. We show that laterally translating the field of view provides a series of images whose relative translations are equal to the distances between the points in the scanning pattern to be calibrated. We show how these distances are mapped to the coordinates of the trajectory points. As an example, we demonstrate the calibration of the scanning patterns in an optical system with two independent microelectromechanical system based scanners. Our method profits from a large collection of distance measurements to find the trajectory coordinates, thereby minimizing the effect of random sources of uncertainty in the positions of points in the scanning pattern. We have found that we are capable of finding the coordinates of points in the scanning patterns with accuracy greater than the optical resolution of the imaging system.

Morphological transformation of generalized spirally polarized beams by anisotropic media and its experimental characterization.

We present a generalization of the known spirally polarized beams (SPBs) which we will call generalized spirally polarized beams (GSPBs). We characterize in detail both theoretically and experimentally the streamline morphologies of the GSPBs and their transformation by arbitrary polarization optical systems described by complex Jones matrices. We find that the description of the passage of GSPBs through a polarization system is equivalent to the stability theory of autonomous systems of ordinary differential equations. While the streamlines of the GSPB exhibit a spiral geometry, the streamlines of the output field may exhibit spirals, saddles, nodes, ellipses, and stars as well. Using a novel experimental technique based on a Sagnac interferometer, we have been able to generate in the laboratory each one of the different cases of GSPBs and record their corresponding characteristic streamline morphologies.

Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: a Workshop Report.

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the "bottom up" approach) and (4) how to infer the nature of the last universal common ancestor (the "top down" approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin. We also describe another family of paths motivated by a" circularity" approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.

On-demand tailored vector beams.

We introduce an effective optical system to produce optical beams with arbitrary, inhomogeneous polarization states. Using our system, we are capable of generating vector beams with discretionarily chosen transverse complex fields in a straightforward way. We generate several different instances of well-known vector beams and the less common spirally polarized vector beams, as well as a full Poincaré beam. We visually show the continual transition between azimuthally and radially polarized beams via a collection of spirally polarized beams. We experimentally determine the polarization states of the generated beams and quantitatively assess the performance of our system. We find that the measured polarization distributions accurately coincide with the intended input polarization distributions.

CRISPR as a driving force: the Model T of biotechnology.

The CRISPR system for gene editing can break, repair, and replace targeted sections of DNA. Although CRISPR gene editing has important therapeutic potential, it raises several ethical concerns. Some bioethicists worry CRISPR is a prelude to a dystopian future, while others maintain it should not be feared because it is analogous to past biotechnologies. In the scientific literature, CRISPR is often discussed as a revolutionary technology. In this paper we unpack the framing of CRISPR as a revolutionary technology and contrast it with framing it as a value-threatening biotechnology or business-as-usual. By drawing on a comparison between CRISPR and the Ford Model T, we argue CRISPR is revolutionary as a product, process, and as a force for social change. This characterization of CRISPR offers important conceptual clarity to the existing debates surrounding CRISPR. In particular, conceptualizing CRISPR as a revolutionary technology structures regulatory goals with respect to this new technology. Revolutionary technologies have characteristic patterns of implementation, entrenchment, and social impact. As such, early identification of technologies as revolutionary may help construct more nuanced and effective ethical frameworks for public policy.

The Modern Synthesis in the Light of Microbial Genomics.

We review the theoretical implications of findings in genomics for evolutionary biology since the Modern Synthesis. We examine the ways in which microbial genomics has influenced our understanding of the last universal common ancestor, the tree of life, species, lineages, and evolutionary transitions. We conclude by advocating a piecemeal toolkit approach to evolutionary biology, in lieu of any grand unified theory updated to include microbial genomics.

A Strategy for Origins of Life Research.

Contents 1. Introduction 1.1. A workshop and this document 1.2. Framing origins of life science 1.2.1. What do we mean by the origins of life (OoL)? 1.2.2. Defining life 1.2.3. How should we characterize approaches to OoL science? 1.2.4. One path to life or many? 2. A Strategy for Origins of Life Research 2.1. Outcomes-key questions and investigations 2.1.1. Domain 1: Theory 2.1.2. Domain 2: Practice 2.1.3. Domain 3: Process 2.1.4. Domain 4: Future studies 2.2. EON Roadmap 2.3. Relationship to NASA Astrobiology Roadmap and Strategy documents and the European AstRoMap Appendix I Appendix II Supplementary Materials References.

Convergent evolution as natural experiment: the tape of life reconsidered.

Stephen Jay Gould argued that replaying the 'tape of life' would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution-the independent origination of similar biological forms and functions-which many interpret as evidence against Gould's thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the 'critique from convergent evolution' fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life.

Eukaryotes first: how could that be?

In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such 'eukaryotes first' (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier 'progenotic' period or RNA world. Bacteria and Archaea thus must have lost these complex features secondarily, through 'streamlining'. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic. We ask what this means and how it might be tested.

Introduction: Optical trapping and applications feature issue.

The editors introduce the Biomedical Optics Express feature issue on "Optical Trapping and Applications." The works presented in the papers within this issue include were the focus of the third OTA Topical Meeting that was held on April 14-18, 2013, in Waikoloa, Hawaii.

Treatment outcomes and prognostic factors in mexican patients with endometrial carcinoma with emphasis on patients receiving radiotherapy after surgery: an institutional perspective.

Aim. To analyze the clinical characteristics and treatment outcomes in patients with endometrial carcinoma treated in a Latin American institute with emphasis in patients receiving adjuvant radiotherapy. Methods. A total of 412 patients with endometrial carcinoma admitted to our hospital between 1998 and 2008 were evaluated, retrospectively. The mean age was 55 years (28-87). Two hundred seventy patients received RT following surgery. Stage distribution was as follows: 221 patients (54%) stage I, 86 patients (21%) stage II, and 103 patients (24.5%) stage III and 2 patients (0.5%) stage IVA. Results. Overall survival rate was 95% at 2 years, 84% at 5 years, and 79% at 10 years. By the end of followup, 338 patients (82%) were disease-free, and 13 (3%) were alive with disease. Univariate and multivariate analyses identified age, grade, serosal and adnexial involvement as significant predictors for overall survival. Conclusion. The results of our study suggests that early-stage, low-grade endometrial cancer with no risk factors should not receive external beam radiotherapy, intermediate risk patients should receive only vaginal vault brachytherapy, and the use of chemotherapy with radiotherapy for patients high-risk and advanced-stage carcinoma the addition of radiotherapy is associated with a better survival being an effective therapeutic option.

Tunable optical tweezers for wavelength-dependent measurements.

Optical trapping forces depend on the difference between the trap wavelength and the extinction resonances of trapped particles. This leads to a wavelength-dependent trapping force, which should allow for the optimization of optical tweezers systems, simply by choosing the best trapping wavelength for a given application. Here we present an optical tweezer system with wavelength tunability, for the study of resonance effects. With this system, the optical trap stiffness is measured for single trapped particles that exhibit either single or multiple extinction resonances. We include discussions of wavelength-dependent effects, such as changes in temperature, and how to measure them.

Refractive index measurement through image analysis with an optofluidic device.

We present a novel optical method, to our knowledge, to measure the refractive index of liquids by means of the images produced by an optofluidic lens. In addition we propose a new method to make optofluidic lenses.

Shaped nondiffracting beams.

We demonstrate that nondiffracting beams can be generated with an arbitrary transverse shape. In particular, we show that the azimuthal complex modulation of the angular spectra of Helmholtz-Gauss wave fields constitutes a degree of freedom sufficient to tailor nondiffracting beams with an intensity pattern of choice.

Optofluidic generation of Laguerre-Gaussian beams.

Laguerre-Gaussian (LG) beams have been extensively studied due to their unique structure, characterized by a phase singularity at the center of the beam. Common methods for generating such beams include the use of diffractive optical elements and spatial light modulators, which although offering excellent versatility, suffers from several drawbacks, including in many cases a low power damage threshold as well as complexity and expense. This paper presents a simple, low cost method for the generation of high-fidelity LG beams using rapid prototyping techniques. Our approach is based on a fluidic-hologram concept, whereby the properties of the LG beam can be finely controlled by varying the refractive-index of the fluid that flows through the hologram. This simple approach, while optimized here for LG beam generation, is also expected to find applications in the production of tunable fluidic optical trains.

Phase dynamics of continuous topological upconversion in vortex beams.

The vortex emergence process as an integer order Bessel field progresses continuously onto the contiguous higher order Bessel field is studied in detail. We assess the progressive migration of phase singularities and explain the predicted increase in fractional orbital angular momentum content of the beam in terms of this gradual process.

Direct detection of optical phase conjugation in a colloidal medium.

Degenerate four-wave mixing is demonstrated using an artificial Kerr medium and is evidenced by directly observing the phase conjugation of a vortex signal beam. The nonlinear susceptibility is produced by a refractive index grating created in a suspension of dielectric microscopic particles optically confined in the intensity grating distribution of two interfering laser beams.

Orbital angular momentum transfer in helical Mathieu beams.

We observe the transfer of orbital angular momentum to trapped particles in the azimuthally asymmetric transverse intensity distribution of a helical Mathieu beam. The average rotation rate, instantaneous angular displacement and terminal velocity of the trapped particles are measured experimentally. The angular dependence of these parameters is found to be in good agreement with the variation of the optical gradient force, the transfer of OAM from the wavefield and the Stokes drag force.

Orbital angular momentum transfer in helical Mathieu beams.

We observe the transfer of orbital angular momentum to trapped particles in the azimuthally asymmetric transverse intensity distribution of a helical Mathieu beam. The average rotation rate, instantaneous angular displacement and terminal velocity of the trapped particles are measured experimentally. The angular dependence of these parameters is found to be in good agreement with the variation of the optical gradient force, the transfer of OAM from the wavefield and the Stokes drag force.