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G Mitchison

Publications and source records attributed to G Mitchison.

18 recordsLinked to original sources
PubMed1999

Is there a phylogenetic signal in prokaryote proteins?

Using the sequence information from nine completely sequenced bacterial genomes, we extract 32 protein families that are thought to contain orthologous proteins from each genome. The alignments of these 32 families are used to construct a phylogeny with the neighbor-joining algorithm. This tree has several topological features that are different from the conventional phylogeny, yet it is highly reliable according to its bootstrap values. Upon closer study of the individual families used, it is clear that the strong phylogenetic signal comes from three families, at least two of which are good candidates for horizontal transfer. The tree from the remaining 29 families consists almost entirely of noise at the level of bacterial phylum divisions, indicating that, even with large amounts of data, it may not be possible to reconstruct the prokaryote phylogeny using standard sequence-based methods.

Arginine-tRNA Ligase↗
PubMed1995

Maximum discrimination hidden Markov models of sequence consensus.

We introduce a maximum discrimination method for building hidden Markov models (HMMs) of protein or nucleic acid primary sequence consensus. The method compensates for biased representation in sequence data sets, superseding the need for sequence weighting methods. Maximum discrimination HMMs are more sensitive for detecting distant sequence homologs than various other HMM methods or BLAST when tested on globin and protein kinase catalytic domain sequences.

Algorithms↗
PubMed1995

Maximum entropy weighting of aligned sequences of proteins or DNA.

In a family of proteins or other biological sequences like DNA the various subfamilies are often very unevenly represented. For this reason a scheme for assigning weights to each sequence can greatly improve performance at tasks such as database searching with profiles or other consensus models based on multiple alignments. A new weighting scheme for this type of database search is proposed. In a statistical description of the searching problem it is derived from the maximum entropy principle. It can be proved that, in a certain sense, it corrects for uneven representation. It is shown that finding the maximum entropy weights is an easy optimization problem for which standard techniques are applicable.

Amino Acid Sequence↗
PubMed1993

The neural representation of stereoscopic depth contrast.

Stereoscopic vision provides examples of contrast phenomena broadly analogous to those seen with brightness. Several authors have suggested that lateral inhibition between disparity-tuned neurons might underlie these phenomena. This type of lateral inhibition would differ from the more familiar kind which occurs with retinal ganglion cells, where an inhibitory surround has essentially a linear subtractive effect. Lateral inhibition by disparity-tuned units would introduce the nonlinearity of the tuning curve. I argue here that the evidence nonetheless suggests that a linear subtractive mechanism operates in the stereo realm--in fact, that there is a stereo equivalent of the classical centre-surround. This seems at first sight implausible, partly because of the occurrence of the nonlinearity mentioned above, but also because disparity is only provided at certain locations in the retinal field, namely those where appropriate features are matched. I show that both objections can be easily overcome, the first because Laplacian-like centre-surrounds can be constructed from disparity-tuned cells, the second because interpolation can fill in between features, and can provide precisely the quantitative dependence upon disparities of neighbouring features which matches the experimental data.

Attention↗
PubMed1992

Axonal trees and cortical architecture.

In modern computer design considerable care is taken to arrange the components in such a way that wiring is kept to a minimum. Certain features of cortical structure--the mappings, stripes and blobs within areas, and areas themselves--are somewhat reminiscent of the layout of computer components, and suggest that the cortex may also be organized so as to economize on neuronal 'wiring'. One important difference between the brain and a computer is that the wiring in the brain takes the form of elaborate branched structures, namely axonal trees. In this article, it is argued that an assessment of the efficiency of cortical wiring must take account of the branching rules of these trees.

Animals↗
PubMed1991

Neuronal branching patterns and the economy of cortical wiring.

Keeping the volume of connections in the cortex as low as possible may be an important evolutionary constraint on the design of the brain. Much as an engineer tries to arrange the components of a computer in such a way as to give efficient wiring, so the brain may have evolved a layout of neuronal types which gives an economical use of axonal 'wiring'. One key difference between computer and brain is that connections in the brain take the form of elaborate branching structures. It is argued here that certain features of cortical mapping, such as the stripes and patches seen within cortical areas, may be adaptations which allow efficient wiring by such structures. Some simple calculations are given to support this, using as models for axonal arbors certain branching patterns which give a low volume of wiring. In particular, it is shown that a pattern of stripes can give economical wiring when axon diameters follow a law dp = dp1 + dp2 with p greater than 4, where d1 and d2 are the diameters of the daughter branches and d that of the parent.

Animals↗
PubMed1990

A dimension reduction framework for understanding cortical maps.

We argue that cortical maps, such as those for ocular dominance, orientation and retinotopic position in primary visual cortex, can be understood in terms of dimension-reducing mappings from many-dimensional parameter spaces to the surface of the cortex. The goal of these mappings is to preserve as far as possible neighbourhood relations in parameter space so that local computations in parameter space can be performed locally in the cortex. We have found that, in a simple case, certain self-organizing models generate maps that are near-optimally local, in the sense that they come close to minimizing the neuronal wiring required for local operations. When these self-organizing models are applied to the task of simultaneously mapping retinotopic position and orientation, they produce maps with orientation vortices resembling those produced in primary visual cortex. This approach also yields a new prediction, which is that the mapping of position in visual cortex will be distorted in the orientation fracture zones.

Animals↗
PubMed1988

Planarity and segmentation in stereoscopic matching.

The matching of stereograms which contain periodic patterns suggests ways in which the stereo correspondence problem may be solved in human vision. The stereograms seem to be segmented by coarse-scale features. Within each segment a set of matches approximating a plane is chosen. In regions with periodic patterns there may be many such planar sets, and the disparity of coarse-scale features seems to guide the choice of a particular set. This emphasis on planarity may reflect the occurrence of correlation-like operations in cortical neurons. An attractive possibility is that segmentation effectively delimits areas of the visual field within which disparities are likely to be slow changing (eg local tangent planes to surfaces) so that the correlation sums evaluated in a segment can give the best estimate of depth. A mechanism of this kind cannot account for all of stereo matching, since not all visual objects are well described by ensembles of planes. But it is likely to be a component of the matching system which is particularly important where images are 'noisy' and averaging is needed to extract reliable disparities.

Algorithms↗
PubMed1982

Long axons within the striate cortex: their distribution, orientation, and patterns of connection.

Rockland and Lung [Rockland, K. S. & Lung, J. S. (1982) Science 215, 1532-1534] have recently observed that an injection of horseradish peroxidase into the striate cortex of the tree shrew produces a patchy distribution of label adjacent to the injection site. They proposed that this pattern might be due to populations of neurons with long-range cortico-cortical connections that are interspersed with populations having no such connections. We suggest here an alternative explanation. We can account for the pattern by supposing that the label is carrier by a system of oriented axons. We suppose that these axons link cells with similar orientation preferences and make their connections within a narrow strip of cortex whose direction is related to the orientation of the cells in question. We suggest that such connections could be involved in generating complex receptive fields from simple ones. Other possibilities are that they are used to generate very elongated receptive fields, inhibitory flanks, or end-stopping. We suggest a number of experimental tests of these ideas.

Animals↗
PubMedDate not supplied

REM sleep and neural nets.

The broad features of rapid eye movement (REM) sleep are reviewed. Memory storage in the brain is probably quite unlike that in a digital computer, being distributed, superimposed and robust. Such memory systems are easily overloaded. If the stored memories share common features, random stimulation often produces mixed outputs. Simulations show that such overloading can be reduced by a process we call 'reverse learning'. We propose that this process is what is happening in REM sleep and that it explains in an unforced manner the condensation commonly found in dreams. Evidence for and against the proposed theory is discussed and several alternative theories are briefly described. The absence of REM sleep in the Enchidna and in two species of dolphins (that have relatively large brains) suggests that REM may allow the brain to be smaller than if REM were lacking.

Animals↗
PubMedDate not supplied

The function of dream sleep.

We propose that the function of dream sleep (more properly rapid-eye movement or REM sleep) is to remove certain undesirable modes of interaction in networks of cells in the cerebral cortex. We postulate that this is done in REM sleep by a reverse learning mechanism (see also p. 158), so that the trace in the brain of the unconscious dream is weakened, rather than strengthened, by the dream.

Cerebral Cortex↗