Evolutionary connectionism: algorithmic principles underlying the evolution of biological organisation in evo-devo, evo-eco and evolutionary transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions

Bulletin

https://openspace.dmacc.edu/bulletin/1104/thumbnail.jp

PTSD, depression and anxiety among former abductees in Northern Uganda

<p>Abstract</p> <p>Background</p> <p>The population in Northern Uganda has been exposed to extreme levels of traumatic stress and thousands abducted forcibly became rebel combatants.</p> <p>Methods</p> <p>Using structured interviews, the prevalence and severity of posttraumatic stress disorder (PTSD), depression and anxiety was assessed in 72 former abducted adults, 62 of them being former child soldiers.</p> <p>Results</p> <p>As retrospective reports of exposure to traumatic stress increased, anxiety and PTSD occurrence increased (r = .45). 49% of respondents were diagnosed with PTSD, 70% presented with symptoms of depression, and 59% with those of anxiety. In a multiple linear regression analysis four factors could best explain the development of PTSD symptoms: male respondents (sex) living in an IDP-Camp (location) with a kinship murdered in the war (family members killed in the war) and having experienced a high number of traumatic events (number of traumatic events) were more likely to develop symptoms of PTSD than others. In disagreement to a simple dose-response-effect though, we also observed a negative correlation between the time spent with the rebels and the PTSD symptom level.</p> <p>Conclusions</p> <p>Former abductees continue to suffer from severe mental ill-health. Adaptation to the living condition of rebels, however, may lower trauma-related mental suffering.</p

A direct comparison of strategies for combinatorial RNA interference

<p>Abstract</p> <p>Background</p> <p>Combinatorial RNA interference (co-RNAi) is a valuable tool for highly effective gene suppression of single and multiple-genes targets, and can be used to prevent the escape of mutation-prone transcripts. There are currently three main approaches used to achieve co-RNAi in animal cells; multiple promoter/shRNA cassettes, long hairpin RNAs (lhRNA) and miRNA-embedded shRNAs, however, the relative effectiveness of each is not known. The current study directly compares the ability of each co-RNAi method to deliver pre-validated siRNA molecules to the same gene targets.</p> <p>Results</p> <p>Double-shRNA expression vectors were generated for each co-RNAi platform and their ability to suppress both single and double-gene reporter targets were compared. The most reliable and effective gene silencing was achieved from the multiple promoter/shRNA approach, as this method induced additive suppression of single-gene targets and equally effective knockdown of double-gene targets. Although both lhRNA and microRNA-embedded strategies provided efficient gene knockdown, suppression levels were inconsistent and activity varied greatly for different siRNAs tested. Furthermore, it appeared that not only the position of siRNAs within these multi-shRNA constructs impacted upon silencing activity, but also local properties of each individual molecule. In addition, it was also found that the insertion of up to five promoter/shRNA cassettes into a single construct did not negatively affect the efficacy of each individual shRNA.</p> <p>Conclusions</p> <p>By directly comparing the ability of shRNAs delivered from different co-RNA platforms to initiate knockdown of the same gene targets, we found that multiple U6/shRNA cassettes offered the most reliable and predictable suppression of both single and multiple-gene targets. These results highlight some important strengths and pitfalls of the currently used methods for multiple shRNA delivery, and provide valuable insights for the design and application of reliable co-RNAi.</p

The effect of environment on Type Ia supernovae in the Dark Energy Survey three-year cosmological sample

Analyses of Type Ia supernovae (SNe Ia) have found puzzling correlations between their standardized luminosities and host galaxy properties: SNe Ia in high-mass, passive hosts appear brighter than those in lower mass, star-forming hosts. We examine the host galaxies of SNe Ia in the Dark Energy Survey 3-yr spectroscopically confirmed cosmological sample, obtaining photometry in a series of 'local' apertures centred on the SN, and for the global host galaxy. We study the differences in these host galaxy properties, such as stellar mass and rest-frame U - R colours, and their correlations with SN Ia parameters including Hubble residuals. We find all Hubble residual steps to be >3σ in significance, both for splitting at the traditional environmental property sample median and for the step of maximum significance. For stellar mass, we find a maximal local step of 0.098 ± 0.018 mag; ∼0.03 mag greater than the largest global stellar mass step in our sample (0.070 ± 0.017 mag). When splitting at the sample median, differences between local and global U - R steps are small, both ∼0.08 mag, but are more significant than the global stellar mass step (0.057 ± 0.017 mag). We split the data into sub-samples based on SN Ia light-curve parameters: stretch (x1) and colour (c), finding that redder objects (c > 0) have larger Hubble residual steps, for both stellar mass and U - R, for both local and global measurements, of ∼0.14 mag. Additionally, the bluer (star-forming) local environments host a more homogeneous SN Ia sample, with local U - R rms scatter as low as 0.084 ± 0.017 mag for blue (c < 0) SNe Ia in locally blue U - R environments

Women’s experiences of decision-making and informed choice about pregnancy and birth care: a systematic review and meta-synthesis of qualitative research

Background The purpose of this systematic review (PROSPERO Ref: CRD42017053264) was to describe and interpret the qualitative research on parent’s decision-making and informed choice about their pregnancy and birth care. Given the growing evidence on the benefits of different models of maternity care and the prominence of informed choice in health policy, the review aimed to shed light on the research to date and what the findings indicate. Methods a systematic search and screening of qualitative research concerning parents’ decision-making and informed choice experiences about pregnancy and birth care was conducted using PRISMA guidelines. A meta-synthesis approach was taken for the extraction and analysis of data and generation of the findings. Studies from 1990s onwards were included to reflect an era of policies promoting choice in maternity care in high-income countries. Results Thirty-seven original studies were included in the review. A multi-dimensional conceptual framework was developed, consisting of three analytical themes (‘Uncertainty’, ‘Bodily autonomy and integrity’ and ‘Performing good motherhood’) and three inter-linking actions (‘Information gathering,’ ‘Aligning with a birth philosophy,’ and ‘Balancing aspects of a choice’). Conclusions Despite the increasing research on decision-making, informed choice is not often a primary research aim, and its development in literature published since the 1990s was difficult to ascertain. The meta-synthesis suggests that decision-making is a dynamic and temporal process, in that it is made within a defined period and invokes both the past, whether this is personal, familial, social or historical, and the future. Our findings also highlighted the importance of embodiment in maternal health experiences, particularly when it comes to decision-making about care. Policymakers and practitioners alike should examine critically current choice frameworks to ascertain whether they truly allow for flexibility in decision-making. Health systems should embrace more fluid, personalised models of care to augment service users’ decision-making agency

The Dark Energy Survey supernova programme: modelling selection efficiency and observed core-collapse supernova contamination

The analysis of current and future cosmological surveys of Type Ia supernovae (SNe Ia) at high redshift depends on the accurate photometric classification of the SN events detected. Generating realistic simulations of photometric SN surveys constitutes an essential step for training and testing photometric classification algorithms, and for correcting biases introduced by selection effects and contamination arising from core-collapse SNe in the photometric SN Ia samples. We use published SN time-series spectrophotometric templates, rates, luminosity functions, and empirical relationships between SNe and their host galaxies to construct a framework for simulating photometric SN surveys. We present this framework in the context of the Dark Energy Survey (DES) 5-yr photometric SN sample, comparing our simulations of DES with the observed DES transient populations. We demonstrate excellent agreement in many distributions, including Hubble residuals, between our simulations and data. We estimate the core collapse fraction expected in the DES SN sample after selection requirements are applied and before photometric classification. After testing different modelling choices and astrophysical assumptions underlying our simulation, we find that the predicted contamination varies from 7.2 to 11.7 per cent, with an average of 8.8 per cent and an r.m.s. of 1.1 per cent. Our simulations are the first to reproduce the observed photometric SN and host galaxy properties in high-redshift surveys without fine-tuning the input parameters. The simulation methods presented here will be a critical component of the cosmology analysis of the DES photometric SN Ia sample: correcting for biases arising from contamination, and evaluating the associated systematic uncertainty

Supernova host galaxies in the Dark Energy Survey: I. Deep coadds, photometry, and stellar masses

The 5-yr Dark Energy Survey Supernova Programme (DES-SN) is one of the largest and deepest transient surveys to date in terms of volume and number of supernovae. Identifying and characterizing the host galaxies of transients plays a key role in their classification, the study of their formation mechanisms, and the cosmological analyses. To derive accurate host galaxy properties, we create depth-optimized coadds using single-epoch DES-SN images that are selected based on sky and atmospheric conditions. For each of the five DES-SN seasons, a separate coadd is made from the other four seasons such that each SN has a corresponding deep coadd with no contaminating SN emission. The coadds reach limiting magnitudes of order ∼27 in g band, and have a much smaller magnitude uncertainty than the previous DES-SN host templates, particularly for faint objects. We present the resulting multiband photometry of host galaxies for samples of spectroscopically confirmed type Ia (SNe Ia), core-collapse (CCSNe), and superluminous (SLSNe) as well as rapidly evolving transients (RETs) discovered by DES-SN. We derive host galaxy stellar masses and probabilistically compare stellar-mass distributions to samples from other surveys. We find that the DES spectroscopically confirmed sample of SNe Ia selects preferentially fewer high-mass hosts at high-redshift compared to other surveys, while at low redshift the distributions are consistent. DES CCSNe and SLSNe hosts are similar to other samples, while RET hosts are unlike the hosts of any other transients, although these differences have not been disentangled from selection effects

First cosmology results using type Ia supernovae from the Dark Energy Survey: the effect of host galaxy properties on supernova luminosity

We present improved photometric measurements for the host galaxies of 206 spectroscopically confirmed type Ia supernovae discovered by the Dark Energy Survey Supernova Program (DES-SN) and used in the first DES-SN cosmological analysis. For the DES-SN sample, when considering a 5D (z, x1, c, α, β) bias correction, we find evidence of a Hubble residual ‘mass step’, where SNe Ia in high-mass galaxies (>1010M⊙) are intrinsically more luminous (after correction) than their low-mass counterparts by γ=0.040±0.019 mag. This value is larger by 0.031 mag than the value found in the first DES-SN cosmological analysis. This difference is due to a combination of updated photometric measurements and improved star formation histories and is not from host-galaxy misidentification. When using a 1D (redshift-only) bias correction the inferred mass step is larger, with γ=0.066±0.020 mag. The 1D−5D γ difference for DES-SN is 0.026±0.009 mag. We show that this difference is due to a strong correlation between host galaxy stellar mass and the x1 component of the 5D distance-bias correction. Including an intrinsic correlation between the observed properties of SNe Ia, stretch and colour, and stellar mass in simulated SN Ia samples, we show that a 5D fit recovers γ with −9 mmag bias compared to a +2 mmag bias for a 1D fit. This difference can explain part of the discrepancy seen in the data. Improvements in modelling correlations between galaxy properties and SN is necessary to ensure unbiased precision estimates of the dark energy equation of state as we enter the era of LSST