Topic: Coevolution

Energy landscapes, order and disorder, and protein sequence coevolution: From proteins to chromosome structure

In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. A theoretical model for chromatin (the minimal chromatin model) explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data is presented. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. This model was generalized by utilizing a neural network to infer these chromatin types using epigenetic marks present at a locus, as assayed by ChIP-Seq. The ensemble of structures resulting from these simulations completely agree with HI-C data and exhibits unknotted chromosomes, phase separation of chromatin types, and a tendency for open chromatin to lie at the periphery of chromosome territories. Although this theoretical methodology was trained in one cell line, the human GM12878 lymphoblastoid cells, it has successfully predicted the structural ensembles of multiple human cell lines. Finally, going beyond Hi-C, our predicted structures are also consistent with microscopy measurements. Analysis of both structures from simulation and microscopy reveals that short segments of chromatin make two-state transitions between closed conformations and open dumbbell conformations. For gene active segments, the vast majority of genes appear clustered in the linker region of the chromatin segment, allowing us to speculate possible mechanisms by which chromatin structure and dynamics may be involved in controlling gene expression. * Supported by the NSF

Analogy as a Catalyst for Cumulative Cultural Evolution

Analogies, broadly defined, map novel concepts onto familiar concepts, making them essential for perception, reasoning, and communication. We argue that analogy-building served a critical role in the evolution of cumulative culture, by allowing humans to learn and transmit complex behavioural sequences that would otherwise be too cognitively demanding or opaque to acquire. The emergence of a protolanguage consisting of simple labels would have provided early humans with the cognitive tools to build explicit analogies and to communicate them to others. This focus on analogy-building can shed new light on the coevolution of cognition and culture, and addresses recent calls for better integration of the field of cultural evolution with cognitive science. This talk will address what cumulative cultural evolution is, how we define analogy-building, how analogy-building applies to cumulative cultural evolution, how analogy-building fits into language evolution, and the implications of analogy-building for causal understanding and cognitive evolution.

Coevolutionary processes in the adaptive immune system