Invasion science, ecology and economics : seeking roads not taken

As members of the editorial board of Neobiota who, for various reasons, didn’t get our names on the original editorial (Kühn et al. 2011), we would like to add a coda to it. Even though there were 38 bullet points listing areas in invasion science where more work is needed, we would like to mention additional areas that we hope would be addressed in future issues of Neobiota. Like the other editors, we would like this innovative and exciting new journal to lead the way in all areas of invasion science. As the graphs in Gurevitch et al. (2011) and Kühn et al. (2011) show, the literature on invasions has been increasing almost exponentially since the early 1980s and so we cannot expect any list of areas of interest to stay complete and up to date for very long. Three areas that we would like to stress are the interaction between invasion science and economics and the role that invasion science should play in advancing pure ecology in two areas, population dynamics and ecosystem ecology. Neither ecology nor economics appears as a word in the original bullet list, but many of the topics are obviously ecological while none are obviously economic. For economics, we want to point out its relevance to invasion science and the feedback between the two disciplines, particularly in a rapidly changing world with powerful new emerging economies. For ecology, we want to emphasise not what ecology tells us about invasions but what invasions reveal about ecology and evolution at two scales

Reuse of Neural Modules for General Video Game Playing

A general approach to knowledge transfer is introduced in which an agent controlled by a neural network adapts how it reuses existing networks as it learns in a new domain. Networks trained for a new domain can improve their performance by routing activation selectively through previously learned neural structure, regardless of how or for what it was learned. A neuroevolution implementation of this approach is presented with application to high-dimensional sequential decision-making domains. This approach is more general than previous approaches to neural transfer for reinforcement learning. It is domain-agnostic and requires no prior assumptions about the nature of task relatedness or mappings. The method is analyzed in a stochastic version of the Arcade Learning Environment, demonstrating that it improves performance in some of the more complex Atari 2600 games, and that the success of transfer can be predicted based on a high-level characterization of game dynamics.Comment: Accepted at AAAI 1

The polar expression of ENSO and sea-ice variability as recorded in a South Pole ice core

An annually dated ice core recovered from South Pole (2850 m a.s.l.) in 1995, that covers the period 1487–1992, was analyzed for the marine biogenic sulfur species methanesulfonate (MS). Empirical orthogonal function analysis is used to calibrate the high-resolution MS series with associated environmental series for the period of overlap (1973–92). Utilizing this calibration we present a ~500 year long proxy record of the polar expression of the El Niño–Southern Oscillation (ENSO) and southeastern Pacific sea-ice extent variations. These records reveal short-term periods of increased (1800–50, 1900–40) and decreased sea-ice extent (1550–1610, 1660–1710, 1760–1800). In general, increased (decreased) sea-ice extent is associated with a higher (lower) frequency of El Niño events

Language Model Crossover: Variation through Few-Shot Prompting

This paper pursues the insight that language models naturally enable an intelligent variation operator similar in spirit to evolutionary crossover. In particular, language models of sufficient scale demonstrate in-context learning, i.e. they can learn from associations between a small number of input patterns to generate outputs incorporating such associations (also called few-shot prompting). This ability can be leveraged to form a simple but powerful variation operator, i.e. to prompt a language model with a few text-based genotypes (such as code, plain-text sentences, or equations), and to parse its corresponding output as those genotypes' offspring. The promise of such language model crossover (which is simple to implement and can leverage many different open-source language models) is that it enables a simple mechanism to evolve semantically-rich text representations (with few domain-specific tweaks), and naturally benefits from current progress in language models. Experiments in this paper highlight the versatility of language-model crossover, through evolving binary bit-strings, sentences, equations, text-to-image prompts, and Python code. The conclusion is that language model crossover is a promising method for evolving genomes representable as text

A 700 year record of Southern Hemisphere extratropical climate variability

Annually dated ice cores from West and East Antarctica provide proxies for past changes in atmospheric circulation over Antarctica and portions of the Southern Ocean, temperature in coastal West and East Antarctica, and the frequency of South Polar penetration of El Niño events. During the period AD 1700–1850, atmospheric circulation over the Antarctic and at least portions of the Southern Hemisphere underwent a mode switch departing from the out-of-phase alternation of multi-decadal long phases of EOF1 and EOF2 modes of the 850 hPa field over the Southern Hemisphere (as defined in the recent record by Thompson and Wallace, 2000; Thompson and Solomon, 2002) that characterizes the remainder of the 700 year long record. From AD 1700 to 1850, lower-tropospheric circulation was replaced by in-phase behavior of the Amundsen Sea Low component of EOF2 and the East Antarctic High component of EOF1. During the first phase of the mode switch, both West and East Antarctic temperatures declined, potentially in response to the increased extent of sea ice surrounding both regions. At the end of the mode switch, West Antarctic coastal temperatures rose and East Antarctic coastal temperatures fell, respectively, to their second highest and lowest of the record. Polar penetration of El Niño events increased during the mode switch. The onset of the AD 1700–1850 mode switch coincides with the extreme state of the Maunder Minimum in solar variability. Late 20th-century West Antarctic coastal temperatures are the highest in the record period, and East Antarctic coastal temperatures close to the lowest. Since AD 1700, extratropical regions of the Southern Hemisphere have experienced significant climate variability coincident with changes in both solar variability and greenhouse gase

Solar Forcing of the Polar Atmosphere

We present highly resolved, annually dated, calibrated proxies for atmospheric circulation from several Antarctic ice cores (ITASE (International Trans-Antarctic Scientific Expedition), Siple Dome, Law Dome) that reveal decadal-scale associations with a South Pole ice-core Be-10 proxy for solar variability over the last 600 years and annual-scale associations with solar variability since AD 1720. We show that increased (decreased) solar irradiance is associated with increased (decreased) zonal wind strength near the edge of the Antarctic polar vortex. The association is particularly strong in the Indian and Pacific Oceans and as such may contribute to understanding climate forcing that controls drought in Australia and other Southern Hemisphere climate events. We also include evidence suggestive of solar forcing of atmospheric circulation near the edge of the Arctic polar vortex based on ice-core records from Mount Logan, Yukon Territory, Canada, and both central and south Greenland as enticement for future investigations. Our identification of solar forcing of the polar atmosphere and its impact on lower latitudes offers a mechanism for better understanding modern climate variability and potentially the initiation of abrupt climate-change events that operate on decadal and faster scales

Gene Expression Profiling Reveals Reproducible Human Lung Adenocarcinoma Subtypes in Multiple Independent Patient Cohorts

PURPOSE: Published reports suggest that DNA microarrays identify clinically meaningful subtypes of lung adenocarcinomas not recognizable by other routine tests. This report is an investigation of the reproducibility of the reported tumor subtypes. METHODS: Three independent cohorts of patients with lung cancer were evaluated using a variety of DNA microarray assays. Using the integrative correlations method, a subset of genes was selected, the reliability of which was acceptable across the different DNA microarray platforms. Tumor subtypes were selected using consensus clustering and genes distinguishing subtypes were identified using the weighted difference statistic. Gene lists were compared across cohorts using centroids and gene set enrichment analysis. RESULTS: Cohorts of 31, 72, and 128 adenocarcinomas were generated for a total of 231 microarrays, each with 2,553 reliable genes. Three adenocarcinoma subtypes were identified in each cohort. These were named bronchioid, squamoid, and magnoid according to their respective correlations with gene expression patterns from histologically defined bronchioalveolar carcinoma, squamous cell carcinoma, and large-cell carcinoma. Tumor subtypes were distinguishable by many hundreds of genes, and lists generated in one cohort were predictive of tumor subtypes in the two other cohorts. Tumor subtypes correlated with clinically relevant covariates, including stage-specific survival and metastatic pattern. Most notably, bronchioid tumors were correlated with improved survival in early-stage disease, whereas squamoid tumors were associated with better survival in advanced disease. CONCLUSION: DNA microarray analysis of lung adenocarcinomas identified reproducible tumor subtypes which differ significantly in clinically important behaviors such as stage-specific survival