Single-neuron theory of consciousness

By most accounts, the mind arises from the integrated activity of large populations of neurons distributed across multiple brain regions. A contrasting model is presented in the present paper that places the mind/brain interface not at the whole brain level but at the level of single neurons. Specifically, it is proposed that each neuron in the nervous system is independently conscious, with conscious content corresponding to the spatial pattern of a portion of that neuron's dendritic electrical activity. For most neurons, such as those in the hypothalamus or posterior sensory cortices, the conscious activity would be assumed to be simple and unable to directly affect the organism's macroscopic conscious behavior. For a subpopulation of layer 5 pyramidal neurons in the lateral prefrontal cortices, however, an arrangement is proposed to be present such that, at any given moment: (i) the spatial pattern of electrical activity in a portion of the dendritic tree of each neuron in the subpopulation individually manifests a complexity and diversity sufficient to account for the complexity and diversity of conscious experience; (ii) the dendritic trees of the neurons in the subpopulation all contain similar spatial electrical patterns; (iii) the spatial electrical pattern in the dendritic tree of each neuron interacts non-linearly with the remaining ambient dendritic electrical activity to determine the neuron's overall axonal response; (iv) the dendritic spatial pattern is reexpressed at the population level by the spatial pattern exhibited by a synchronously firing subgroup of the conscious neurons, thereby providing a mechanism by which conscious activity at the neuronal level can influence overall behavior. The resulting scheme is one in which conscious behavior appears to be the product of a single macroscopic mind, but is actually the integrated output of a chorus of minds, each associated with a different neuron.     

Using process diagrams for the graphical representation of biological networks

With the increased interest in understanding biological networks, such as protein-protein interaction networks and gene regulatory networks, methods for representing and communicating such networks in both human- and machine-readable form have become increasingly important. Although there has been significant progress in machine-readable representation of networks, as exemplified by the Systems Biology Mark-up Language (SBML) (http://www.sbml.org) issues in human-readable representation have been largely ignored. This article discusses human-readable diagrammatic representations and proposes a set of notations that enhances the formality and richness of the information represented. The process diagram is a fully state transition-based diagram that can be translated into machine-readable forms such as SBML in a straightforward way. It is supported by CellDesigner, a diagrammatic network editing software (http://www.celldesigner.org/), and has been used to represent a variety of networks of various sizes (from only a few components to several hundred components).     

Coding of distributed, topographic and non-specific representations within the brain

This article explores the theoretical basis of coding within topographic representations, where neurons encoding specific features such as locations, are arranged into maps. A novel type of representation, termed non-specific, where each neuron does not encode specific features is also postulated. In common with the previously described distributed representations [Rolls, E.T., Treves, A., 1998. Neural Networks and Brain Function. Oxford University Press, Oxford], topographic representations display an exponential relationship between stimuli encoded and both number of neurons and maximum firing rate of those neurons. The non-specific representations described here display a binomial expansion between the number of stimuli encoded and the sum of the number of neurons and the maximum firing rate; therefore groups of non-specific neurons usually encode less stimuli than equivalent topographic layers of neurons. Lower and higher order sensory regions of the brain use either topographic or distributed representations to encode information. It is proposed that non-specific representations may occur in regions of the brain where different types of information may be represented by the same neurons, as occurs in the prefrontal cortex.     

Sensory representation abnormalities that parallel focal hand dystonia in a primate model

In our hypothesis of focal dystonia, attended repetitive behaviors generate aberrant sensory representations. Those aberrant representations interfere with motor control. Abnormal motor control strengthens sensory abnormalities. The positive feedback loop reinforces the dystonic condition. Previous studies of primates with focal hand dystonia have demonstrated multi-digit or hairy-glabrous responses at single sites in area 3b, receptive fields that average ten times larger than normal, and high receptive field overlap as a function of horizontal distance. In this study, we strengthen and elaborate these findings. One animal was implanted with an array of microelectrodes that spanned the border between the face and digits. After the animal developed hand dystonia, responses in the initial hand representation increasingly responded to low threshold stimulation of the face in a columnar substitution. The hand-face border that is normally sharp became patchy and smeared over 1 mm of cortex within 6 weeks. Two more trained animals developed a focal hand dystonia variable in severity across the hand. Receptive field size, presence of multi-digit or hairy-glabrous receptive fields, and columnar overlap covaried with the animal's ability to use specific digits. A fourth animal performed the same behaviors without developing dystonia. Many of its physiological measures were similar to the dystonic animals, but receptive field overlap functions were minimally abnormal, and no sites shared response properties that are normally segregated such as hairy-glabrous combined fields, or multi-digit fields. Thalamic mapping demonstrated proportionate levels of abnormality in thalamic representations as were found in cortical representations.     

Processing of frequency-modulated stimuli in the chick auditory cortex analogue: evidence for topographic representations and possible mechanisms of rate and directional sensitivity

Summary Responses of units in the auditory forebrain (field L/hyperstriatum ventrale-complex) of awake domestic chicks were studied to frequency-modulated (FM) signals and isointensity tone bursts, presented to the ear contralateral to the recording sites. FM signals, linear frequency sweeps in the range of 50 Hz to 10.25 kHz, differed in the rate of change of frequency (RCF) and in the direction of modulation. The majority of RCF response functions obtained could be classified as predominantly ascending and bell shaped. Best rates of change of frequency (BRCFs), assigned to these functions, covered a range of nearly 3 orders of magnitude. BRCFs of the same units for upward (positive BRCFs) and for downward modulations (negative BRCFs) were correlated. The lowest BRCF encountered among all units for a given isointensity ON-response bandwidth (F _on ) increased as a function of F _on . F _on was derived from the responses to tone bursts of various frequencies at 70 dB SPL. As F_ON tended to increase with the best frequency (BF) of units the lowest BRCF encountered among all units for a given BF also increased as a function of BF. Positive and negative BRCFs of a unit were also correlated with the slopes of onset latency-frequency relationships below and above BF, respectively. FM responses were optimal, when the frequency-specific latency differences at a given unit were compensated by the direction and rate of frequency change in the signal. FM-directional sensitivity varied with BF. Most units with BFs below about 2 kHz preferred upward modulations, while those with BFs above 2 kHz preferred downward modulations. Directional preference and sensitivity correlated with asymmetric distributions of inhibitory sidebands around BF, as derived from the analysis of OFF-responses. Maximum directional sensitivity for a given BRCF increased with BRCF. BRCF and FM-directional sensitivity were topographically organized on neuronal planes harboring units with similar BFs (isofrequency planes). Highest BRCFs were observed in the input-layer L₂ of field L. BRCF declined along a rostrocaudal isofrequency axis in all 4 subdivisions of the auditory forebrain. Similarly, response strength shifted from rostral to caudal as a function of RCF. FM-directional sensitivity was organized in a subdivision-specific fashion. Units in the input-layer of field L (L₂), and even more so in the hyperstriatum ventrale, were fairly insensitive to the direction of modulation, whereas units in the postsynaptic layers of field L (L₁ and L₃) exhibited higher degrees of directional sensitivity. Directional sensitivity also declined along the rostrocaudal isofrequency axis of field L. Two simple models of connectivity in the chick auditory forebrain are presented, which could be sufficient to explain these results. One is based on a tonotopic arrangement of afferent synapses on dendrites and somata of units in L₂, the other on local lateral inhibition in the postsynaptic layers of field L.Abbreviations BF best frequency (kHz) - BRCF best rate of change of frequency (kHz/s) - DS index of FM-directional sensitivity - F _on ON-response bandwidth (kHz) - F _off OFF-response bandwidth (kHz) - FM frequency modulation - RCF rate of change of frequency (kHz/s)     

Early thalamocortical tract guidance and topographic sorting of thalamic projections requires LIM-homeodomain gene Lhx2

The thalamocortical tract is the primary source of sensory information to the cerebral cortex, but the mechanisms regulating its pathfinding are not completely understood. LIM-homeodomain (LIM-HD) gene Lhx2 has been proposed to participate in a combinatorial "code" to regulate dorsal thalamic patterning and also the topography of thalamocortical projections. Here, we report that Lhx2-/- embryos exhibit a gross disruption in the early development of the thalamocortical tract, such that thalamic axons are unable to enter the ventral telencephalon. A possible cause for this deficit is a severe reduction of "pioneer" cells in the mutant ventral telencephalon that constitutes a putative mechanism for guiding the entry of the thalamocortical tract into this structure in vivo. However, in vitro, the thalamocortical tract is able to enter the ventral telencephalon, and this permitted an examination of whether thalamocortical topography is normal in the Lhx2 mutant. Contrary to hypotheses that proposed a cell-autonomous role for Lhx2 in the thalamus, Lhx2-/- thalamic explants generate a normal topography of projections in control ventral telencephalic preparations. This is consistent with our findings of normal patterning of the Lhx2 mutant dorsal thalamus using a wide array of markers. In the reverse experiment, however, control thalamic explants display aberrant topography in Lhx2-/- telencephalic preparations. This perturbation is restricted to projections from caudal thalamic explants, while rostral and middle explants project normally. Thus Lhx2 is required for multiple steps in thalamocortical tract pathfinding, but these functions appear localized in the ventral telencephalon rather than in the dorsal thalamic neurons. Furthermore, the absence of Lhx2 in the ventral telencephalon selectively disrupts a subset of thalamic axon topography, indicating a specific rather than a general perturbation of cues in this structure.     

Cultivated plant remains of the late Neolithic Michelsberg Culture at Heilbronn-Klingenberg (southwest Germany) - a comparison of different features, find assemblages and preservation conditions relating to the representation of archaeobotanical remains

A large area investigation was undertaken of the plant remains from a Michelsberg Culture (late Neolithic) settlement. The charred macroscopic remains and imprints in pieces of daub were expected to show both the spectrum of the cultivated plants there, and also the degree of their cultivation and use. The loess covered hill-top lies in a landscape with favourable climatic and soil conditions and is blocked off by two parallel ditches running in an arc. Ditches and pits filled with different sediments were investigated. The daub, unearthed in several pits, had been deliberately mixed with chaff of the glume wheats einkorn and emmer to temper it when it was originally made. The investigated imprints and charred plant remains give hints of spatial distribution of crop processing activities. To determine the amounts of the crops that were cultivated and used, it is necessary to study the charred remains. The degree of ubiquity (frequency of occurrence) of grains in the pit sediments seems to be the best indicator of the representation of cereals. Four main cereals were found: Triticum monococcum, T. dicoccum, T. aestivum/T. durum and Hordeum vulgare var. nudum. Pisum sativum also was an important cultivated plant, much more than Lens culinaris. The role of Linum usitatissimum and Papaver somniferum is less clear.     

How to build a mammalian super-predator

Questions surrounding the biology of large fossil predators that differ markedly from living forms have long intrigued palaeobiologists. Among such taxa few have excited more interest than sabertooth cats, whose distinctive hypertrophied canines are suggestive of killing behaviors and feeding ecologies that may have departed widely from those of extant carnivores. Moreover, considerable variation among sabertooth species is further suggestive of intriguing differences within the group. Behavior and ecology in another large, extinct mammalian carnivore, the Australian marsupial lion (Thylacoleo carnifex), has also proven contentious. In this study, we assemble a wide range of cranio-dental and postcranial indices in a dataset including machairodont sabertooths, T. carnifex and an extensive sample of extant taxa in order to examine the palaeobiology of these charismatic fossil carnivores. Results of multivariate analyses point to significant relationships between behavior and overall body proportions in extant mammalian carnivores. Postcranial morphologies of two American dirk-tooth species of sabertooth (Smilodon) depart greatly from those of living felids and group most closely with bears among living placentals. Scimitar-tooth species of Homotherium and Machairodus cluster with modern pantherine cats. The marsupial lion groups with Smilodon. If these latter two phylogenetically disparate clades do represent a specialized, robust ecomorph adapted to predation on large prey, then it is a body plan that might be effectively identified on the basis of a handful of ‘bear-like’ postcranial features in combination with a more typically ‘felid-like’ carnassialization of the cheektooth row.     

How to build a grid cell

Neurons in the medial entorhinal cortex fire action potentials at regular spatial intervals, creating a striking grid-like pattern of spike rates spanning the whole environment of a navigating animal. This remarkable spatial code may represent a neural map for path integration. Recent advances using patch-clamp recordings from entorhinal cortex neurons in vitro and in vivo have revealed how the microcircuitry in the medial entorhinal cortex may contribute to grid cell firing patterns, and how grid cells may transform synaptic inputs into spike output during firing field crossings. These new findings provide key insights into the ingredients necessary to build a grid cell.     

Absence of Intraspinal Sprouting in Dorsal Root Axons Caudal to a Partial Spinal Hemisection: A Horseradish Peroxidase Transport Study

Primary afferent sprouting in the spinal cord was evaluated by comparing the central projection of horseradish peroxidase (HRP)-labeled sciatic nerve afferent axons in nonlesioned control rats, and in rats subjected to acute or chronic partial spinal hemisections as adults. The lesions were performed at various levels from T₁₀ to L₃, and removed supraspinal and varying amounts of descending propriospinal afferents to lumbar segments receiving the maximal sciatic projection. The hemisections typically involved all but the dorsal column, although in some cases a portion of the dorsal column, including the corticospinal tract, was also transected.

The distribution pattern and density of spinal HRP reaction product was not significantly different in experimental and control preparations in any segment below the lesion, regardless of the quantity of denervation, or the density of the normal sciatic projection in a given terminal region. These results, together with our previous finding concerning an absence of primary afferent sprouting following long-term dorsal root ganglionectomies, suggest that current concepts concerning collateral sprouting as a factor in functional plasticity in the mature mammalian spinal cord warrant re-evaluation.     

Using cellular automata to generate image representation for biological sequences

Summary. A novel approach to visualize biological sequences is developed based on cellular automata (Wolfram, S. Nature 1984, 311, 419–424), a set of discrete dynamical systems in which space and time are discrete. By transforming the symbolic sequence codes into the digital codes, and using some optimal space-time evolvement rules of cellular automata, a biological sequence can be represented by a unique image, the so-called cellular automata image. Many important features, which are originally hidden in a long and complicated biological sequence, can be clearly revealed thru its cellular automata image. With biological sequences entering into databanks rapidly increasing in the post-genomic era, it is anticipated that the cellular automata image will become a very useful vehicle for investigation into their key features, identification of their function, as well as revelation of their fingerprint. It is anticipated that by using the concept of the pseudo amino acid composition (Chou, K.C. Proteins: Structure, Function, and Genetics, 2001, 43, 246–255), the cellular automata image approach can also be used to improve the quality of predicting protein attributes, such as structural class and subcellular location.     

Extended Newick: it is time for a standard representation of phylogenetic networks

Background  

Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutionary events such as recombination, hybridization or lateral gene transfer, the lack of a standard format for their representation has hindered the publication of explicit phylogenetic networks in the specialized literature and their incorporation in specialized databases. Two different proposals to represent phylogenetic networks exist: as a single Newick string (where each hybrid node is splitted once for each parent) or as a set of Newick strings (one for each hybrid node plus another one for the phylogenetic network).     

OURCIN: a tool to build expert systems

OURCIN is a tool to build expert systems, which was developed by a joint team from INRIA and SEMA. We emphasized developing on this system the ergonomic features which make Expert Systems a comfortable and interesting approach for knowledge engineering.     

Theoretical approaches to holistic biological features: Pattern formation,neural networks and the brain-mind relation

The topic of this article is the relation between bottom-up and top-down, reductionist and “holistic” approaches to the solution of basic biological problems. While there is no doubt that the laws of physics apply to all events in space and time, including the domains of life, understanding biology depends not only on elucidating the role of the molecules involved, but, to an increasing extent, on systems theoretical approaches in diverse fields of the life sciences. Examples discussed in this article are the generation of spatial patterns in development by the interplay of autocatalysis and lateral inhibition; the evolution of integrating capabilities of the human brain, such as cognition-based empathy; and both neurobiological and epistemological aspects of scientific theories of consciousness and the mind.     

Using effective subnetworks to predict selected properties of gene networks

Background

Difficulties associated with implementing gene therapy are caused by the complexity of the underlying regulatory networks. The forms of interactions between the hundreds of genes, proteins, and metabolites in these networks are not known very accurately. An alternative approach is to limit consideration to genes on the network. Steady state measurements of these influence networks can be obtained from DNA microarray experiments. However, since they contain a large number of nodes, the computation of influence networks requires a prohibitively large set of microarray experiments. Furthermore, error estimates of the network make verifiable predictions impossible.

Methodology/Principal Findings

Here, we propose an alternative approach. Rather than attempting to derive an accurate model of the network, we ask what questions can be addressed using lower dimensional, highly simplified models. More importantly, is it possible to use such robust features in applications? We first identify a small group of genes that can be used to affect changes in other nodes of the network. The reduced effective empirical subnetwork (EES) can be computed using steady state measurements on a small number of genetically perturbed systems. We show that the EES can be used to make predictions on expression profiles of other mutants, and to compute how to implement pre-specified changes in the steady state of the underlying biological process. These assertions are verified in a synthetic influence network. We also use previously published experimental data to compute the EES associated with an oxygen deprivation network of E.coli, and use it to predict gene expression levels on a double mutant. The predictions are significantly different from the experimental results for less than of genes.

Conclusions/Significance

The constraints imposed by gene expression levels of mutants can be used to address a selected set of questions about a gene network.     

Beyond Profiling: Using ADMET Models to Guide Decisions

ADMET Models, whether in silico or in vitro, are commonly used to ‘profile’ molecules, to identify potential liabilities or filter out molecules expected to have undesirable properties. While useful, this is the most basic application of such models. Here, we will show how models may be used to go ‘beyond profiling’ to guide key decisions in drug discovery. For example, selection of chemical series to focus resources with confidence or design of improved molecules targeting structural modifications to improve key properties. To prioritise molecules and chemical series, the success criteria for properties and their relative importance to a project's objective must be defined. Data from models (experimental or predicted) may then be used to assess each molecule's balance of properties against those requirements. However, to make decisions with confidence, the uncertainties in all of the data must also be considered. In silico models encode information regarding the relationship between molecular structure and properties. This is used to predict the property value of a novel molecule. However, further interpretation can yield information on the contributions of different groups in a molecule to the property and the sensitivity of the property to structural changes. Visualising this information can guide the redesign process. In this article, we describe methods to achieve these goals and drive drug‐discovery decisions and illustrate the results with practical examples.