Paradoxical fusion of two images and depth perception with a squinting eye.

Some strabismic patients with inconstant squint can fuse two images in a single eye, and experience lustre and depth. One of these images is foveal and the other extrafoveal. Depth perception was tested on 30 such subjects. Relief was perceived mostly on the fixated image. Camouflaged continuous surfaces (hemispheres, cylinders) were perceived as bumps or hollows, without detail. Camouflaged rectangles could not be separated in depth from the background, while their explicit counterparts could. Slanted bars were mostly interpreted as frontoparallel near or remote bars. Depth responses were more frequent with stimuli involving inward rather than outward disparities, and were then heavily biased towards "near" judgements. All monocular fusion effects were markedly reduced after the recovery of normal stereoscopic vision following an orthoptic treatment. The depth effects reported here may provide clues on what stereoscopic pathways may or may not accomplish with incomplete retinal and misleading vergence information.

Last but not least. Flashing lines.

In a periodic pattern of horizontally and vertically aligned quadrangles, two sets of illusory lines are seen to pulsate at orthogonal orientations, corresponding to the directions of knight's moves on a chessboard. The illusion seems to be governed by subtle rules of long-range interactions between parallel and non-parallel orientation filters.

Illusory defects and mismatches: why must DNA repair always be (slightly) error prone?

There is growing evidence that recombination is mu;tagenic and that some forms of DNA repair synthesis are error prone. DNA synthesis in mismatch repair might also be error prone. DNA-repair systems detect structural defects in DNA with high efficiency but they occasionally also strike at normal sections of DNA. Considering the diversity of local DNA structure, some DNA sections with complementary sequences are bound to act as preferential false targets for a repair system (i.e. as "illusory defects"). However, if the repair system never changes the sequence upon repair, it will be solicited again and again by the illusory defect, a potentially harmful situation. It is therefore advantageous for a repair system to be, to some extent, error prone. Strong illusory defects may arise at the decanucleotide level and could be the cause of local increases in mutation levels. They might be used to initiate somatic hypermutation pathways.

Variations on the Hermann grid: an extinction illusion.

When the white disks in a scintillating grid are reduced in size, and outlined in black, they tend to disappear. One sees only a few of them at a time, in clusters which move erratically on the page. Where they are not seen, the grey alleys seem to be continuous, generating grey crossings that are not actually present. Some black sparkling can be seen at those crossings where no disk is seen. The illusion also works in reverse contrast.

Curvature biases in stereoscopic vision: a nasotemporal asymmetry.

The reliability of curvature judgments for linear elements was studied, with stereograms that contained a binocular arc with curvature in depth, and either a binocular frontoparallel arc or a monocular one, on a background representing a hemiellipsoid. The subjects made about 15% errors on binocular arcs with curvature in depth, and 60%-80% of these occurred when both the hemiellipsoid and the arc were convex, the arc being perceived as concave, by transparency through the hemiellipsoid. There were also about 15%-30% errors on frontoparallel arcs, but spread among all situations, with a small prevalence of concave judgments. Curvature in depth was assigned to the monocular stimuli in more than 60% of the cases. There was a curvature bias when the monocular arcs were on the nasal side, and were viewed against a concave background. Assuming parallel viewing, nasal ingoing arcs were usually perceived as concave, and nasal outgoing arcs usually perceived as convex, in agreement with geometrical likelihood. Nasal-side elements captured by one eye are, in general, those with the highest likelihood of having matching elements in the other eye. Then the observed nasal bias effect suggests that the matching process in stereopsis could be driven from the nasal sides of the projections in the two cerebral hemispheres.

Characterisation of the misalignment and misangulation components in the Poggendorff and corner-Poggendorff illusions.

In the Poggendorff illusion, two colinear segments abutting obliquely on an intervening configuration (often consisting of two long parallel lines) appear misaligned. We report here the results of a component analysis of the illusion and several of its variants, including in particular the 'corner-Poggendorff' illusion, and variants with a single arm. Using a nulling method, we determined an 'orientation profile' of each configuration, that is, how the illusions varied as the configuration was rotated in the plane of the display. We were able to characterise a pure-misalignment component (having peaks and dips around the +/- 22.5 degrees and +/- 67.5 degrees orientations of the arms) and a pure misangulation component of constant sign, having peaks at the +/- 45 degrees orientations of the arms. Both these components were present in both the classic and the corner-Poggendorff configurations. Thus, the misangulation component appears clearly in the classic Poggendorff illusion, once the misalignment component is partitioned out. Similarly, the corner-Poggendorff configuration, which essentially estimates a misangulation component, contains a misalignment component which becomes apparent once the misangulation is nulled. While our analysis accounts for much of the variability in the shapes of the profiles, additional assumptions must be made to explain the relatively small misangulation measured in the corner-Poggendorff configuration (1.5 degrees, on average, at peak value), and the relatively large illusion measured in the configurations with a single arm (above 6 degrees, on average, at peak values). We invoke the notion that parallelism and colinearity detectors provide counteracting cues, the first class reducing misangulation in the corner-Poggendorff configuration, and the second class reducing the illusion in the Poggendorff configurations with two arms.

Acquisition of shape information in working memory, as a function of viewing time and number of consecutive images: evidence for a succession of discrete storage classes.

The capacity of visual working memory was investigated using abstract images that were slightly distorted NxN (with generally N=8) square lattices of black or white randomly selected elements. After viewing an image, or a sequence of images, the subjects viewed couples of images containing the test image and a distractor image derived from the first one by changing the black or white value of q randomly selected elements. The number q was adjusted in each experiment to the difficulty of the task and the abilities of the subject. The fraction of recognition errors, given q and N was used to evaluate the number M of bits memorized by the subject. For untrained subjects, this number M varied in a biphasic manner as a function of the time t of presentation of the test image: it was on average 13 bits for 1 s, 16 bits for 2 to 5 s, and 20 bits for 8 s. The slow pace of acquisition, from 1 to 8 s, seems due to encoding difficulties, and not to channel capacity limitations. Beyond 8 s, M(t), accurately determined for one subject, followed a square root law, in agreement with 19th century observations on the memorization of lists of digits. When two consecutive 8x8 images were viewed and tested in the same order, the number of memorized bits was downshifted by a nearly constant amount, independent of t, and equal on average to 6-7 bits. Across the subjects, the shift was independent of M. When two consecutive test images were related, the recognition errors decreased for both images, whether the testing was performed in the presentation or the reverse order. Studies involving three subjects, indicate that, when viewing m consecutive images, the average amount of information captured per image varies with m in a stepwise fashion. The first two step boundaries were around m=3 and m=9-12. The data are compatible with a model of organization of working memory in several successive layers containing increasing numbers of units, the more remote a unit, the lower the rate at which it may acquire encoded information.

The evolutionary design of error-rates, and the fast fixation enigma.

Genetic and non-genetic error-rates are analyzed in parallel for a lower and a higher organism (E. coli and man, respectively). From the comparison of mutation with fixation rates, contrasting proposals are made, concerning the arrangement of error-rates in the two organisms. In E. coli, reproduction is very conservative, but genetic variability is high within populations. Most mutations are discarded by selection, yet single mutational variants of a gene have, on average, little impact on fitness. In man, the mutation rate per generation is high, the variability generated in the population is comparatively low, and most mutations are fixed by drift rather than selection. The variants of a gene are in general more deleterious than in E. coli. There is a discrepancy in the published mutation rates: the rate of mutation fixations in human populations is twice or four times higher than the individual rate of mutation production, a feature which is not consistent with current population genetics models. Two, not mutually exclusive, hypotheses may explain this 'fast fixation enigma': (i) Mutation rates have substantially decreased in recent human evolution and (ii) A substantial fraction of the fixed mutations were generated in a process-such as gene conversion-that violates the principle of independence of mutation events.

Time to detect the difference between two images presented side by side.

The time to locate a difference between two artificial images presented side by side on a CRT screen was studied as a function of their complexity. The images were square lattices of black or white squares or quadrangles, in some cases delineated by a blue grid. Each pair differed at a single position, chosen at random. For images of size N x N, the median reaction time varied as cN2, from N = 3-15, with c being around 50 ms in the absence of grid (i.e., when the quadrangles were associated into continuous shapes). For N < or = 9, when the lattice was made irregular, performance did not deteriorate, up to a rather high level of irregularity. Furthermore, the presence of uncorrelated distortions in the left and right images did not affect performance for N < or = 6. In the presence of a grid, the reaction times were on average higher by 20%. The results taken together indicate that the detection of differences does not proceed on a point-by-point basis and must be mediated by some abstract shape analysis, in agreement with current views on short-term visual memory (e.g., Phillips, W.A., On the distinction between sensory storage and short-term visual memory, Percept. Psychophys., 16 (1974) 283-290 [13]). In complementary experiments, the subjects had to judge whether two images presented side by side were the same or different, with N varying from 1 to 5. For N < 3, the same and the different responses were similar in all their statistical aspects. For N > or = 4, the "same" responses took a significantly larger time than the "different" responses and were accompanied by a significant increase in errors. The qualitative change from N = 3 to N = 4 is interpreted as a shift from a "single inspection" analysis to an obligatory scanning procedure. On the whole, we suggest that visual information in our simultaneous comparison task is extracted by chunks of about 12 +/- 3 bits, and that the visual processing and matching tasks take about 50 ms per couple of quadrangles. In Section 4, we compare these values to the values obtained through other experimental paradigms.

Gene conversion as a focusing mechanism for correlated mutations: a hypothesis.

Ways of producing complex mutational events without substantially raising the primary mutation rate are explored. If the small amount of DNA that is resynthesised through the action of the mismatch DNA repair system is not subject to further repair, the incidence of double mutations can increase by a factor of 100, while single mutations would increase by only 30%. Such a boost in the incidence of double mutations seems insufficient to meet the needs of higher organisms. For them, an alternative strategy would be to produce complex events by a succession of single mutations occurring in a correlated manner over several sexual generations. It is proposed that gene conversion may fulfill this role. Assuming that the resynthesis of DNA that occurs during gene conversion produces mutations in the conversion tract, one predicts a tendency for close mutations in corresponding sequences in the two homologous chromosomes, to promote, during conversion, further mutations in their vicinity. Semiquantitative calculations suggest that such a mechanism can be quite effective, provided the divergence between two paired chromosomes is around 10(-4) or less. Such a mechanism might constitute an adaptive mutation strategy acting at the population level.

The half-Zöllner illusion.

The Zollner figure contains stacks of short parallel segments oriented obliquely to the direction of the stack. Adjacent parallel stacks of opposite polarity seem to diverge where their top segments form an arrowhead. To probe whether or not the opposite polarities are necessary to the illusion, three 'half-Zollner' configurations were designed, containing stacks of a single polarity. The 'orientation profile' of these configurations was studied, that is, the way the strength of the perceived illusion varies with the orientation of the stacks. The subjects had to align two stacks or align stacks with target segments situated at a slight distance from them. All three half-Zollner configurations produced errors that could be assimilated to global-orientation misjudgments. These errors were of opposite sign for the two types of stacks and varied with the orientation of the stacks as in the standard Zollner illusion. A further study was conducted in which the effect of several configurational parameters was explored for a single observer. The standard Zollner illusion increases with the separation of the stacks. The illusion is also increased when the orientations of the segments in different stacks are orthogonal, independently of the particular longitudinal orientations of the stacks. When the ends of the short segments are curved so that at their endpoints they become precisely perpendicular to the axis of the stacks, the standard and half-Zollner illusions are reduced, but not abolished. Therefore, they cannot be entirely accounted for by a mechanism of alignment of illusory contours generated at these endpoints. The results are consistent with the existence of a single common mechanism at work in both the standard and the half-Zollner illusion. It is suggested that the illusion itself is not a rotation of the stacks but either a shear deformation in which the segments of a stack slide with respect to one another, or an expansion of the stacks orthogonally to the segments.

Processing of linear elements in stereopsis: effects of positional and orientational distinctiveness.

The stereoscopic processing of small linear elements is probed through the comparative analysis of stereograms containing needles or crosses, differing in the local spatial arrangement and orientation of the elements, and the presence or absence of slant. Depending upon the details of the textural design, depth analysis may proceed faster with crosses than with needles, or the reverse. It proceeds faster with vertical than with horizontal needles, except in the case of unslanted regularly-spaced needles. On the whole the data suggest that the elements to be matched in a stereogram are first processed along a common pathway, in which positional regularity has a detrimental effect. In the presence of small linear elements, orientation-tuned neurons would be recruited and their participation would lead either to an inhibition effect when the elements are all similarly oriented, or to a facilitation effect when there is sufficient orientational diversity among the elements. Here, slant plays an indirect role, by widening the orientation spectrum in otherwise regularly oriented textures. Positional irregularity is useful to suppress false matches, while orientational diversity helps to stabilize the perceived surfaces.

Connections between translation, transcription and replication error-rates.

The analysis of published data from E coli suggests that in all three processes of translation, transcription, and replication, a minority of errors are produced by sub-classes of error-prone components. These add to the basal level of errors a noise of about 10 to 30%. Each one of the three processes contributes to the noisiness of the two others in a loose manner: a large increase in one error-rate produces a moderate increase in another error-rate. The strongest influence is that of transcription on translation errors. There it is possible that a majority of the misacylation errors are produced during the encounter of a correct amino acyl-tRNA ligase with a mistranscribed tRNA. Extreme mutator mutants are expected to produce a moderate increase in translation errors.

Transient mutators: a semiquantitative analysis of the influence of translation and transcription errors on mutation rates.

A population of bacteria growing in a nonlimiting medium includes mutator bacteria and transient mutators defined as wild-type bacteria which, due to occasional transcription or translation errors, display a mutator phenotype. A semiquantitative theoretical analysis of the steady-state composition of an Escherichia coli population suggests that true strong genotypic mutators produce about 3 x 10(-3) of the single mutations arising in the population, while transient mutators produce at least 10% of the single mutations and more than 95% of the simultaneous double mutations. Numbers of mismatch repair proteins inherited by the offspring, proportions of lethal mutations and mortality rates are among the main parameters that influence the steady-state composition of the population. These results have implications for the experimental manipulation of mutation rates and the evolutionary fixation of frequent but nearly neutral mutations (e.g., synonymous codon substitutions).

The revised genetic code.

Recent findings on the genetic code are reviewed, including selenocysteine usage, deviations in the assignments of sense and nonsense codons, RNA editing, natural ribosomal frameshifts and non-orthodox codon-anticodon pairings. A multi-stage codon reading process is presented.

String analysis and energy minimization in the partition of DNA sequences.

Two approaches to the understanding of biological sequences are confronted. While the recognition of particular signals in sequences relies on complex physical interactions, the problem is often analysed in terms of the presence or absence of literal motifs (strings) in the sequence. We present here a test-case for evaluating the potential of this approach. We classify DNA sequences as positive or negative depending on whether they contain a single melted domain in the middle of the sequence, which is a global physical property. Two sets of positive "biological" sequences were generated by a computer simulation of evolutionary divergence along the branches of a phylogenetic tree, under the constraint that each intermediate sequence be positive. These two sets and a set of random positive sequences were subjected to pattern analysis. The observed local patterns were used to construct expert systems to discriminate positive from negative sequences. The experts achieved 79% to 90% success on random positive sequences and up to 99% on the biological sets, while making less than 2% errors on negative sequences. Thus, the global constraints imposed on sequences by a physical process may generate local patterns that are sufficient to predict, with a reasonable probability, the behaviour of the sequences. However, rather large sets of biological sequences are required to generate patterns free of illegitimate constraints. Furthermore, depending upon the initial sequence, the sets of sequences generated on a phylogenetic tree may be amenable or refractory to string analysis, while obeying identical physical constraints. Our study clarifies the relationship between experts' errors on positive and negative sequences, and the contributions of legitimate and illegitimate patterns to these errors. The test-case appears suitable both for further investigations of problems in the theory of sequence evolution and for further testing of pattern analysis techniques.

Nucleotide excision by E. coli DNA polymerase I in proofreading and non-proofreading modes.

Escherichia coli DNA polymerase I exists in at least two distinct kinetic forms. When it binds to a template, the proofreading activity is usually switched off. As the enzyme progresses along the template, it becomes more and more competent for excision. This phenomenon introduces a link between fidelity and processivity. Processivity is best studied when the chain-length distributions of synthesized polymers are stationary. Even then, however, one cannot avoid multiple initiations on a given template by the same molecule of the enzyme. When synthesis is initiated with primers of lengths 15 or 20, a strange phenomenon is observed. It seems that the polymerase starts by hydrolyzing the primer down to a length of 7-10 nucleotides and only then starts to add nucleotides. It does so in a low-accuracy mode, suggesting that, while the exonuclease is clearly active, it does not contribute to proofreading. The warm-up of the proofreading function is therefore reinterpreted as a switch between two modes of behaviour: a mode 1 of low accuracy in which the 3'----5' exonuclease, while active, is uncoupled from the polymerase and does not contribute to proofreading, and a mode 2 of high accuracy in which the exonuclease is kinetically linked to the polymerase activity.

Speed and accuracy of 3D interpretation of linear stereograms.

Stereograms belonging to 10 different textural types were constructed. Each stereogram represented five hemi-ellipsoids, either as bumps or hollows (+, -) and elongated either along the horizontal, or the vertical direction (H, V). The ease with which these stereograms could be interpreted was tested on 70 subjects. The two criteria of speed and accuracy were correlated. The main factors contributing to the ease of interpretation, in the case of the +/- character were: (i) diversity in the orientations of the matching stimuli; (ii) other factors reducing matching ambiguity; (iii) the presence of discontinuous elements; and, to a much lesser extent (iv) the presence of monocular cues. The last two factors exerted a stronger influence on the appreciation of the H-V character. Of the four kinds of objects, the H- and V+ hemi-ellipsoids appeared to be the least and the most error-prone ones respectively. The results further suggest that: (i) stereoscopic interpretation does not proceed from small to large disparities; (ii) the edge detectors of the visual cortex, when activated, speed up interpretation, but are easily saturated; (iii) large surfaces are reconstructed by correlation of horizontal rather than vertical patches.

[A model of localized iconic memory, replicable and associative, using time sharing and 3 neuronal communication modes]. / Modèle de mémoire iconique localisée, réplicable et associative, utilisant le temps partagé et trois modes de communications neuronales.

A model is proposed for the functioning of an iconic memory involving several layers of neurones. A small group of neurones in one layer project their terminations over the terminations of a single neurone of the superior layer. According to the communication mode (emission or reception), a neurone in one layer can memorize the state of the terminations of a neurone of the superior layer, or impose on the latter the state of its own terminations. In the comparison mode, an emitting neurone compares its state to another emitting neurone and, in case of sufficient similarity, switches to the reception mode (associative recall). The first layer, corresponding to short-term memory, communicates with the cells involved in the representation of the perceived image. This model makes possible the establishment of a correspondence between a percept and a neurone, the replication of memorized configurations, the restructuration of memory and, starting with a percept or a memorized item, the integral associative recall of all similar memorized items.

Variations with position of replication errors due to exonuclease warm-up.

A.A mismatch errors occurring during poly(dA) replication with the Klenow fragment of E. coli DNA polymerase I have been quantified. The A/T ratio measured for chains extended by 1-25 nucleotides decreases by a factor of at least 15 from beginning to end. The deduced true error rate may decrease by a factor of 2.5 at each successive nucleotide addition. When ddATP is used instead of dATP, the ddA/T ratio indicates little variation of the misincorporation probability with position. Thus, the accuracy improvement in the first case is due to a warm-up of the proofreading function.