How does cognition evolve? Phylogenetic comparative psychology.

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

DNA-Directed DNA Polymerases Evolve From Reverse Transcriptase

Scientists have been debating for decades the origin of life on earth. A number of hypotheses were proposed as to what emerged first RNA or DNA; with most scientists are in favour of the "RNA World" hypothesis. Assuming RNA emerged first, it fellow that the RNA polymerases would've appeared before DNA polymerases. Using recombinant DNA technology and bioinformatics we undertook this study to explore the relationship between RNA polymerases, reverse transcriptase and DNA polymerases. The working hypothesis is that DNA polymerases evolved from reverse transcriptase and the latter evolved from RNA polymerases. If this hypothesis is correct then one would expect to find various ancient DNA polymerases with varying level of reverse transcriptase activity. In the first phase of this research project multiple sequence alignments were made on the protein sequence of 32 prokaryotic DNA-directed DNA polymerases originating from 11 prokaryotic families against 3 viral reverse transcriptase. The data from such alignments was not very conclusive. DNA polymerases with higher level of reverse transcriptase activity were non-confined to ancient organisms, as one would've expected. The second phase of this project was focused on conditions that may alter the DNA polymerase activity. Various reaction conditions, such as temperature, using various ions (Ni2+, Mn2+, Mg2+) were tested. Interestingly, it was found that the DNA polymerase from the Thermos aquatics family can be made to copy RNA into DNA (i.e. reverse transcriptase activity). Thus it was shown that under appropriate conditions (ions and reactions temperatures) reverse transcriptase activity can be induced in DNA polymerase. In the third phase of this study recombinant DNA technology was used to generate a chimeric DNA polymerase; in attempts to identify the region(s) of the polymerase responsible for RNA-directed DNA polymerase activity. The two DNA polymerases employed were the Thermus aquatic us and Thermus thermophiles. As in the second phase various reaction conditions were investigated. Data indicated that the newly engineered chimeric DNA polymerase can be induced to copy RNA into DNA. Thus the intrinsic reverse transcriptase activity found in ancient DNA polymerases was localized into a domain and can be induced via appropriate reaction conditions.

Faster techniques to evolve wavelet coefficients for better fingerprint image compression

In this article, techniques have been presented for faster evolution of wavelet lifting coefficients for fingerprint image compression (FIC). In addition to increasing the computational speed by 81.35%, the coefficients performed much better than the reported coefficients in literature. Generally, full-size images are used for evolving wavelet coefficients, which is time consuming. To overcome this, in this work, wavelets were evolved with resized, cropped, resized-average and cropped-average images. On comparing the peak- signal-to-noise-ratios (PSNR) offered by the evolved wavelets, it was found that the cropped images excelled the resized images and is in par with the results reported till date. Wavelet lifting coefficients evolved from an average of four 256 256 centre-cropped images took less than 1/5th the evolution time reported in literature. It produced an improvement of 1.009 dB in average PSNR. Improvement in average PSNR was observed for other compression ratios (CR) and degraded images as well. The proposed technique gave better PSNR for various bit rates, with set partitioning in hierarchical trees (SPIHT) coder. These coefficients performed well with other fingerprint databases as well.

Working memory and working attention: What could possibly evolve?

The concept of “working” memory is traceable back to nineteenth century theorists (Baldwin, 1894; James 1890) but the term itself was not used until the mid-twentieth century (Miller, Galanter & Pribram, 1960). A variety of different explanatory constructs have since evolved which all make use of the working memory label (Miyake & Shah, 1999). This history is briefly reviewed and alternative formulations of working memory (as language-processor, executive attention, and global workspace) are considered as potential mechanisms for cognitive change within and between individuals and between species. A means, derived from the literature on human problem-solving (Newell & Simon, 1972), of tracing memory and computational demands across a single task is described and applied to two specific examples of tool-use by chimpanzees and early hominids. The examples show how specific proposals for necessary and/or sufficient computational and memory requirements can be more rigorously assessed on a task by task basis. General difficulties in connecting cognitive theories (arising from the observed capabilities of individuals deprived of material support) with archaeological data (primarily remnants of material culture) are discussed.

How will organic carbon stocks in mineral soils evolve under future climate? Global projections using RothC for a range of climate change scenarios

We use a soil carbon (C) model (RothC), driven by a range of climate models for a range of climate scenarios to examine the impacts of future climate on global soil organic carbon (SOC) stocks. The results suggest an overall global increase in SOC stocks by 2100 under all scenarios, but with a different extent of increase among the climate model and emissions scenarios. The impacts of projected land use changes are also simulated, but have relatively minor impacts at the global scale. Whether soils gain or lose SOC depends upon the balance between C inputs and decomposition. Changes in net primary production (NPP) change C inputs to the soil, whilst decomposition usually increases under warmer temperatures, but can also be slowed by decreased soil moisture. Underlying the global trend of increasing SOC under future climate is a complex pattern of regional SOC change. SOC losses are projected to occur in northern latitudes where higher SOC decomposition rates due to higher temperatures are not balanced by increased NPP, whereas in tropical regions, NPP increases override losses due to higher SOC decomposition. The spatial heterogeneity in the response of SOC to changing climate shows how delicately balanced the competing gain and loss processes are, with subtle changes in temperature, moisture, soil type and land use, interacting to determine whether SOC increases or decreases in the future. Our results suggest that we should stop looking for a single answer regarding whether SOC stocks will increase or decrease under future climate, since there is no single answer. Instead, we should focus on improving our prediction of the factors that determine the size and direction of change, and the land management practices that can be implemented to protect and enhance SOC stocks.

A methodology for in-situ and remote sensing of microphysical and radiative properties of contrails as they evolve into cirrus

Contrails and especially their evolution into cirrus-like clouds are thought to have very important effects on local and global radiation budgets, though are generally not well represented in global climate models. Lack of contrail parameterisations is due to the limited availability of in situ contrail measurements which are difficult to obtain. Here we present a methodology for successful sampling and interpretation of contrail microphysical and radiative data using both in situ and remote sensing instrumentation on board the FAAM BAe146 UK research aircraft as part of the COntrails Spreading Into Cirrus (COSIC) study.

Do phytoplankton communities evolve through a self-regulatory abundance-diversity relationship?

A small group of phytoplankton species that produce toxic or allelopathic chemicals has a significant effect on plankton dynamics in marine ecosystems. The species of non-toxic phytoplankton, which are large in number, are affected by the toxin-allelopathy of those species. By analysis of the abundance data of marine phytoplankton collected from the North-West coast of the Bay of Bengal, an empirical relationship between the abundance of the potential toxin-producing species and the species diversity of the non-toxic phytoplankton is formulated. A change-point analysis demonstrates that the diversity of non-toxic phytoplankton increases with the increase of toxic species up to a certain level. However, for a massive increase of the toxin-producing species the diversity of phytoplankton at species level reduces gradually. Following the results, a deterministic relationship between the abundance of toxic phytoplankton and the diversity of non-toxic phytoplankton is developed. The abundance–diversity relationship develops a unimodal pathway through which the abundance of toxic species regulates the diversity of phytoplankton. These results contribute to the current understanding of the coexistence and biodiversity of phytoplankton, the top-down vs. bottom-up debate, and to that of abundance–diversity relationship in marine ecosystems.

Geotechnical systems that evolve with ecological processes

Geotechnical systems, such as landfills, mine tailings storage facilities (TSFs), slopes, and levees, are required to perform safely throughout their service life, which can span from decades for levees to “in perpetuity” for TSFs. The conventional design practice by geotechnical engineers for these systems utilizes the as-built material properties to predict its performance throughout the required service life. The implicit assumption in this design methodology is that the soil properties are stable through time. This is counter to long-term field observations of these systems, particularly where ecological processes such as plant, animal, biological, and geochemical activity are present. Plant roots can densify soil and/or increase hydraulic conductivity, burrowing animals can increase seepage, biological activity can strengthen soil, geochemical processes can increase stiffness, etc. The engineering soil properties naturally change as a stable ecological system is gradually established following initial construction, and these changes alter system performance. This paper presents an integrated perspective and new approach to this issue, considering ecological, geotechnical, and mining demands and constraints. A series of data sets and case histories are utilized to examine these issues and to propose a more integrated design approach, and consideration is given to future opportunities to manage engineered landscapes as ecological systems. We conclude that soil scientists and restoration ecologists must be engaged in initial project design and geotechnical engineers must be active in long-term management during the facility’s service life. For near-surface geotechnical structures in particular, this requires an interdisciplinary perspective and the embracing of soil as a living ecological system rather than an inert construction material.

How language did not evolve

accepted for presentation

Can we predict which patients will evolve to chronic kidney disease after nephrectomy for cortical renal tumors?

Introduction: While some studies show that patients submitted to radical nephrectomy have a higher risk of developing chronic kidney disease (CKD), some studies report that carefully selected living kidney donors do not present a higher risk for CKD. Here, we aim to study predictive factors of CKD after radical nephrectomy. Materials and Methods: Between January 2006 to January 2010, 107 patients submitted to radical nephrectomy for cortical renal tumors at our institution were enrolled in this study. Demographic data were recorded, modified Charlson-Romano Index was calculated, and creatinine clearance was estimated using abbreviated Modification of Diet in Renal Disease (MDRD) study equation. Pathological characteristics, surgical access and surgical complications were also reviewed. The end-point of the current study was new onset estimated glomerular filtration rate (eGFR) less than 60 and less than 45 mL/minute/1.73 m(2). Results: Age, preoperative eGFR, Charlson-Romano Index and hypertension were predictive factors of renal function loss, when the end-point considered was eGFR lower than 60 mL/minute/1.73 m(2). Age and preoperative eGFR were predictive factors of renal function loss, when the end-point considered was eGFR lower than 45 mL/minute/1.73 m2. Moreover, each year older increased 1.1 times the risk of eGFR lower than 60 and 45 mL/minute/1.73 m(2). After multivariate logistic regression, only age remained as an independent predictive factor of eGFR loss. Conclusion: Age is an independent predictive factor of GFR loss for patients submitted to radical nephrectomy for cortical renal tumors.