Physics of Life Reviews

Physics of Life Reviews 7 (2010) 260–261 www.elsevier.com/locate/plrev Comment The use of codes to connect mental and material aspects of brain function Comment on: “Natural world physical, brain operational, and mind phenomenal space–time” by A.A. Fingelkurts, A.A. Fingelkurts and C.F.H. Neves Walter J. Freeman Department of Molecular & Cell Biology, University of California at Berkeley, Berkeley, CA 94720-3206, USA Received 29 April 2010; accepted 29 April 2010 Available online 15 May 2010 Communicated by L. Perlovsky Keywords: Electrocorticogram (ECoG); Neural codes; Perception The authors propose the hypothesis that the brain’s “operational space–time” connects “subjective space–time” to “physical space–time reality”. They pose the major challenge of explaining the neural mechanisms that so rapidly transpose stimulus energies to abstract concepts – from the specific to the generic, from the material to the mental. They describe and use three levels of explanations, which I conceive in terms of neural codes [1]. As neurobiolo- gists they connect the microscopic properties of conditioned stimuli to intervals and frequencies in trains of action potentials evoked by stimuli and carried by topographically organized axons. As cognitivists they connect mesoscopic symbolic codes to bursts of action potentials from hierarchically organized feature-detector neurons that represent phonemes, lines, odorants, pressures, etc., which object-detector neurons bind into images of stimuli. As dynami- cists they connect perceptions of the world to continuous spatial patterns of oscillatory fields of dendritic activity, which self-organize and evolve on trajectories through high-dimensional brain state spaces. This macroscopic code is expressed in landscapes of chaotic attractors. Unlike other scientific codes such as those of DNA and the Periodic Table, these neural codes have no alphabets or syntaxes. They are epistemological metaphors that neurobiologists require to measure neural activity and that engineers use to design models of higher brain functions such as recognition, prediction, decision and intentional action (summarized with references in [1]). Their hypothesis posits two sets of ‘connections’ between three states: that of the world (including the body), the brain activity, and thoughts. Thoughts take time and are shallow or deep, wide or narrow, so ‘connections’ can be posited without risk of getting mired in the Cartesian swamp or the ‘hard problem’ of qualia. My data show DOI of original article: 10.1016/j.plrev.2010.04.001. E-mail address: dfreeman@berkeley.edu. 1571-0645/$ – see front matter © 2010 Elsevier B.V. All rights reserved. doi:10.1016/j.plrev.2010.04.010

This is just an invited commentary to the article of: Fingelkurts, Fingelkurts & Neves "Natural world physical, brain operational, and mind phenomenal space–time". Physics of Life Reviews, 7, 252-253.

In a review article in this journal (Phys. Life. Rev. 10: 351-370, 2013), I discussed the feasibility of lightning-triggered electroporation and electrofusion acting as purely (bio)physical mechanisms of horizontal gene transfer and thus contributing to biological evolution, particularly among the prokaryotes. I would like to thank the authors of all commentaries on this article, and here I try to address the most important issues raised in them.

Physical processes leading to horizontal gene transfer.Electroporation induced abiotic horizontal gene transfer.Freezing induced abiotic gene transfer.

Proteins of all living organisms including plants, animals, and humans are made up of amino acid monomers that show identical stereochemical L-configuration. Hypotheses for the origin of this symmetry breaking in biomolecules include the absolute asymmetric photochemistry model by which interstellar ultraviolet (UV) circularly polarized light (CPL) induces an enantiomeric excess in chiral organic molecules in the interstellar/circumstellar media. This scenario is supported by a) the detection of amino acids in the organic residues of UV-photo-processed interstellar ice analogues, b) the occurrence of L-enantiomer-enriched amino acids in carbonaceous meteorites, and c) the observation of CPL of the same helicity over large distance scales in the massive star-forming region of Orion. These topics are of high importance in topical biophysical research and will be discussed in this review. Further evidence that amino acids and other molecules of prebiotic interest are asymmetrically formed in space comes from studies on the enantioselective photolysis of amino acids by UV-CPL. Also, experiments have been performed on the absolute asymmetric photochemical synthesis of enantiomer-enriched amino acids from mixtures of astrophysically relevant achiral precursor molecules using UV-circularly polarized photons. Both approaches are based on circular dichroic transitions of amino acids that will be highlighted here as well. These results have strong implications on our current understanding of how life's precursor molecules were possibly built and how life selected the left-handed form of proteinogenic amino acids.

In this review we concentrate on a grounded approach to the modeling of cognition through the methodologies of cognitive agents and developmental robotics. This work will focus on the modeling of the evolutionary and developmental acquisition of linguistic capabilities based on the principles of symbol grounding. We review cognitive agent and developmental robotics models of the grounding of language to demonstrate their consistency with the empirical and theoretical evidence on language grounding and embodiment, and to reveal the benefits of such an approach in the design of linguistic capabilities in cognitive robotic agents. In particular, three different models will be discussed, where the complexity of the agent's sensorimotor and cognitive system gradually increases: from a multi-agent simulation of language evolution, to a simulated robotic agent model for symbol grounding transfer, to a model of language comprehension in the humanoid robot iCub. The review also discusses the benefits of the use of humanoid robotic platform, and specifically of the open source iCub platform, for the study of embodied cognition.

This note presents a brief commentary to a paper by Verbeni et al. concerning flux limited interpretation of morphogenetic actions. After a concise excursus on nonlinearity in diffusion phenomena, the commentary focuses on the derivation of macroscopic tissues equations from the underlying description at the cellular scale.

A central question in biology is how secreted morphogens act to induce different cellular responses within a group of cells in a concentration-dependent manner. Modeling morphogenetic output in multicellular systems has so far employed linear diffusion, which is the normal type of diffusion associated with Brownian processes. However, there is evidence that at least some morphogens, such as Hedgehog (Hh) molecules, may not freely diffuse. Moreover, the mathematical analysis of such models necessarily implies unrealistic instantaneous spreading of morphogen molecules, which are derived from the assumptions of Brownian motion in its continuous formulation. A strict mathematical model considering Fick's diffusion law predicts morphogen exposure of the whole tissue at the same time. Such a strict model thus does not describe true biological patterns, even if similar and attractive patterns appear as results of applying such simple model. To eliminate non-biological behaviors from diffusion models we introduce flux-limited spreading (FLS), which implies a restricted velocity for morphogen propagation and a nonlinear mechanism of transport. Using FLS and focusing on intercellular Hh-Gli signaling, we model a morphogen gradient and highlight the propagation velocity of morphogen particles as a new key biological parameter. This model is then applied to the formation and action of the Sonic Hh (Shh) gradient in the vertebrate embryonic neural tube using our experimental data on Hh spreading in heterologous systems together with published data. Unlike linear diffusion models, FLS modeling predicts concentration fronts and the evolution of gradient dynamics and responses over time. In addition to spreading restrictions by extracellular binding partners, we suggest that the constraints imposed by direct bridges of information transfer such as nanotubes or cytonemes underlie FLS. Indeed, we detect and measure morphogen particle velocity in such cell extensions in different systems.

Perception is interpreted as a set of capabilities that facilitate two functions necessary for survival; learning about the environment and controlling real-time behavioral interactions with it. Perceptual capabilities evolve in the context of an organism and its environment, adapted to an organism's ecological niche. The relation between embodied perception and action can be studied in the context of the only muscles that serve only to enable perception--the eye muscles. The only eye movements under cognitive control are saccades, the rapid jumps of binocular fixation from one target to another. The world is perceived as stable while the retinal image, and the corresponding projections inside the brain, are displaced with each saccade. This space constancy forms the stable platform for all other visual functions and requires an explanation that involves visual short-term memory. This memory, and the change detection that it makes possible, is enhanced when there is a physical interaction between the observer and the visual stimulus. Perception is something you do, not something that happens to you.