Biology subjects

Alex Gomez-Marin

Publications and source records attributed to Alex Gomez-Marin.

6 recordsLinked to original sources

bioRxiv2016

Reproducibility and replicability of rodent phenotyping in preclinical studies

The scientific community is increasingly concerned with cases of published \"discoveries\" that are not replicated in further studies. The field of mouse behavioral phenotyping was one of the first to raise this concern, and to relate it to other complicated methodological issues: the complex interaction between genotype and environment; the definitions of behavioral constructs; and the use of the mouse as a model animal for human health and disease mechanisms. In January 2015, researchers from various disciplines including genetics, behavior genetics, neuroscience, ethology, statistics and bioinformatics gathered in Tel Aviv University to discuss these issues. The general consent presented here was that the issue is prevalent and of concern, and should be addressed at the statistical, methodological and policy levels, but is not so severe as to call into question the validity and the usefulness of model organisms as a whole. Well-organized community efforts, coupled with improved data and metadata sharing, were agreed by all to have a key role to play in identifying specific problems and promoting effective solutions. As replicability is related to validity and may also affect generalizability and translation of findings, the implications of the present discussion reach far beyond the issue of replicability of mouse phenotypes but may be highly relevant throughout biomedical research.

Scientific Communication and Education↗

bioRxiv2016

The velocity-curvature power law in Drosophila larval locomotion

We report the discovery that the locomotor trajectories generated by crawling fruit fly larvae follow the same power law relationship between speed and curvature previously found in the human motor control of hand-drawing, walking, eye movements and speech. Using high resolution behavioral tracking of individual flies in different sensory environments, we tested the power law by making maggots trace different trajectory types in naturalistic conditions, from reaching-like movements to scribbles. In all these conditions, we found that the law holds, and also that the exponent of the larval scaling law approaches 3/4, rather than the usual 2/3 exponent found in almost all human situations. This is consistent with recent findings on humans drawing ellipses on water, where dynamic effects related to medium viscosity have been shown to increase the exponent that would emerge from purely kinematic-geometric constraints. To our knowledge, the speed-curvature power law has only been studied in human and non-human primates, our work then being the first demonstration of the speed-curvature scaling principle in other species. As there are still different competing hypotheses for the origin of such law in humans (one invoking complex cortical computations in primates; another postulating its emergence from the coupling of viscoelastic muscle properties with simple central pattern generation) our findings in the larva demonstrate that the law is possible in an animal with a nervous system orders of magnitude simpler than that of humans, thus supporting the latter view. Given that our discovery is in Drosophila (amenable to precise genetic manipulations, electron microscopy reconstruction of neural circuits, imaging in behaving animals, electrophysiology, and other techniques) this opens great potential for uncovering the mechanistic implementation of the velocity-curvature power law. Such scaling laws might exist because natural selection favors processes that remain behaviorally efficient across a wide range of contexts in distantly related species. Our work is an effort to search for shared principles of animal behavior across phyla.

Animal Behavior and Cognition↗

bioRxiv2016

Expanding perspectives on cognition in humans, animals, and machines

Over the past decade neuroscience has been attacking the problem of cognition with increasing vigor. Yet, what exactly is cognition, beyond a general signifier of anything seemingly complex the brain does? Here, we briefly review attempts to define, describe, explain, build, enhance and experience cognition. We highlight perspectives including psychology, molecular biology, computation, dynamical systems, machine learning, behavior and phenomenology. This survey of the landscape reveals not a clear target for explanation but a pluralistic and evolving scene with diverse opportunities for grounding future research. We argue that rather than getting to the bottom of it, over the next century, by deconstructing and redefining cognition, neuroscience will and should expand rather than merely reduce our concept of the mind.

Animal Behavior and Cognition↗

bioRxiv2015

Shared generative rules of locomotor behavior in arthropods and vertebrates

The discovery of shared behavioral processes across phyla is an essential step in the establishment of a comparative study of behavior. We use immobility as an origin and reference for the measurement of locomotor behavior; speed, direction of walking and direction of facing as the three degrees of freedom shaping fly locomotor behavior; and cocaine as the parameter inducing a progressive transition in and out of immobility. In this way we expose and quantify the generative rules that shape part of fruit fly locomotor behavior, bringing about a gradual buildup of freedom during the transition from immobility to normal behavior and a precisely opposite narrowing down during the transition into immobility. During buildup the fly exhibits enhancement and then reduction to normal values of movement along each degree of freedom: first, body rotation in the horizontal plane, then path curvature and then speed of translation. Transition into immobility unfolds by narrowing down of the repertoire in the opposite sequential order, showing reciprocal relations during both buildup and narrowing down. The same generative rules apply to vertebrate locomotor behavior in a variety of contexts involving transition out and into immobility. Recent claims for deep homology between the arthropod central complex and the vertebrate basal ganglia provide an opportunity to examine whether the generative rules we discovered also share common descent. Neurochemical processes mediating the buildup of locomotor behavior in vertebrates could guide the search for equivalent processes in arthropods. The measurement methodology we use prompts the discovery of candidate behavioral homologies.\n\nSignificance StatementDo flies and mice share the same behavior? By defining immobility as an intrinsic reference point for locomotor behavior we show that the rules that generate the transition from immobility to full blown normal behavior, and from full blown behavior to immobility are shared by fruit flies and mice. These rules constitute a much desired aim of evolutionary biology: the discovery of behavioral homologies across distant phyla. The methodology we use facilitates the discovery of cross-phyletic behavioral homologies, shedding light on the problem of the evolution of behavior.

Animal Behavior and Cognition↗

bioRxiv2015

Hierarchical compression of C. elegans locomotion reveals phenotypic differences in the organisation of behaviour

Regularities in animal behaviour offer insight into the underlying organisational and functional principles of nervous systems and automated tracking provides the opportunity to extract features of behaviour directly from large-scale video data. Yet how to effectively analyse such behavioural data remains an open question. Here we explore whether a minimum description length principle can be exploited to identify meaningful behaviours and phenotypes. We apply a dictionary compression algorithm to behavioural sequences from the nematode worm Caenorhabditis elegans freely crawling on an agar plate both with and without food and during chemotaxis. We find that the motifs identified by the compression algorithm are rare but relevant for comparisons between worms in different environments, suggesting that hierarchical compression can be a useful step in behaviour analysis. We also use compressibility as a new quantitative phenotype and find that the behaviour of wild-isolated strains of C. elegans is more compressible than that of the laboratory strain N2 as well as the majority of mutant strains examined. Importantly, in distinction to more conventional phenotypes such as overall motor activity or aggregation behaviour, the increased compressibility of wild isolates is not explained by the loss of function of the gene npr-1, which suggests that erratic locomotion is a laboratory-derived trait with a novel genetic basis. Because hierarchical compression can be applied to any sequence, we anticipate that compressibility can offer insight into the organisation of behaviour in other animals including humans.

Animal Behavior and Cognition↗

bioRxiv2014

Big Behavioral Data: Psychology, Ethology and the Foundations of Neuroscience

Behavior is a unifying organismal process through which genes, neural function, anatomy and environment converge and interrelate. Here we review the current state and sketch the future impact of accelerating advances in technology for behavioral studies, focusing on rodents as an exemplar. We frame our analysis in three dimensions: (1) degree of experimental constraint, (2) dimensionality of data, and (3) level of description. We argue that ethomics, fueled by \"big behavioral data\", presents challenges proportionate to its promise and describe how these challenges might be met through opportunities afforded by the two rival conceptual legacies of 20th century behavioral science, ethology and psychology. We conclude that although \"ethomes\" are not the goal, big behavioral data has the potential to transform and unify these two disciplines and to solidify the foundations of others, including neuroscience, particularly if the data is as open as it is copious and quantitative.

Animal Behavior and Cognition↗