Phylogenetic mixture models can reduce node-density artifacts

We investigate the performance of phylogenetic mixture models in reducing a well-known and pervasive artifact of phylogenetic inference known as the node-density effect, comparing them to partitioned analyses of the same data. The node-density effect refers to the tendency for the amount of evolutionary change in longer branches of phylogenies to be underestimated compared to that in regions of the tree where there are more nodes and thus branches are typically shorter. Mixture models allow more than one model of sequence evolution to describe the sites in an alignment without prior knowledge of the evolutionary processes that characterize the data or how they correspond to different sites. If multiple evolutionary patterns are common in sequence evolution, mixture models may be capable of reducing node-density effects by characterizing the evolutionary processes more accurately. In gene-sequence alignments simulated to have heterogeneous patterns of evolution, we find that mixture models can reduce node-density effects to negligible levels or remove them altogether, performing as well as partitioned analyses based on the known simulated patterns. The mixture models achieve this without knowledge of the patterns that generated the data and even in some cases without specifying the full or true model of sequence evolution known to underlie the data. The latter result is especially important in real applications, as the true model of evolution is seldom known. We find the same patterns of results for two real data sets with evidence of complex patterns of sequence evolution: mixture models substantially reduced node-density effects and returned better likelihoods compared to partitioning models specifically fitted to these data. We suggest that the presence of more than one pattern of evolution in the data is a common source of error in phylogenetic inference and that mixture models can often detect these patterns even without prior knowledge of their presence in the data. Routine use of mixture models alongside other approaches to phylogenetic inference may often reveal hidden or unexpected patterns of sequence evolution and can improve phylogenetic inference.

Visual representations as 'artifacts of knowing'

How does the manipulation of visual representations play a role in the practices of generating, evolving and exchanging knowledge? The role of visual representation in mediating knowledge work is explored in a study of design work of an architectural practice, Edward Cullinan Architects. The intensity of interactions with visual representations in the everyday activities on design projects is immediately striking. Through a discussion of observed design episodes, two ways are articulated in which visual representations act as 'artefacts of knowing'. As communication media they are symbolic representations, rich in meaning, through which ideas are articulated, developed and exchanged. Furthermore, as tangible artefacts they constitute material entities with which to interact and thereby develop knowledge. The communicative and interactive properties of visual representations constitute them as central elements of knowledge work. The paper explores emblematic knowledge practices supported by visual representation and concludes by pinpointing avenues for further research.

The impact of an intelligent classroom on pupils' interactive behaviour

Purpose – The purpose of this research is to determine whether new intelligent classrooms will affect the behaviour of children in their new learning environments. Design/methodology/approach – A multi-method study approach was used to carry out the research. Behavioural mapping was used to observe and monitor the classroom environment and analyse usage. Two new classrooms designed by INTEGER (Intelligent and Green) in two different UK schools provided the case studies to determine whether intelligent buildings (learning environments) can enhance learning experiences. Findings – Several factors were observed in the learning environments: mobility, flexibility, use of technology, interactions. Relationships among them were found indicating that the new environments have positive impact on pupils' behaviour. Practical implications – A very useful feedback for the Classrooms of the Future initiative will be provided, which can be used as basis for the School of the Future initiative. Originality/value – The behavioural analysis method described in this study will enable an evaluation of the “Schools of the Future” concept, under children's perspective. Using a real life laboratory gives contribution to the education field by rethinking the classroom environment and the way of teaching.