Theory of degenerate coding and informational parameters of protein coding genes

The theory of degenerate coding is presented in a way enabling further application to molecular biology. There are two kinds of redundancy of a degenerate code. The first is due to the excess in codon length and the second to the code degeneracy. If the code is asymmetrically degenerate, the second kind of redundancy can be profitable for control of error rate. This control can be performed just by selective synonymous codon usage. Utilisation of the genetic code is partially influenced by this theoretical possibility. In particular the degree of error protectivity is well correlated with deviation from equiprobability in synonymous codon usage. The biological significance of this fact is discussed.     

Volume coding for BBA-Biomembranes

Photoconductivity changes in lipid bilayers containing magnesium-octaethylporphyrin were measured in KCl solutions. Light flashes increase the total current to at least twice the dark current under anaerobic conditions. Under aerobic conditions the photocurrent decreases to less than a third of the dark current and approaches zero as the oxygen concentration is increased. ESR measurements on liposomes containing magnesium-porphyrin are used to show that magnesium-octaethylporphyrin is converted to a cation, accompanied by oxygen consumption.     

The DNA-protein coding problem

The DNA-protein coding problem is given a general algebraic formulation, the consequences of which are then explored by standard mathematical methods. To keep the treatment self-contained, the mathematical techniques to be used are explained in detail. It is demonstrated that there exista priori a countably infinite number of different abstract DNA-protein codes, thereby showing that inductive attempts to construct such a code will most likely be fruitless. A notion of ergodicity is then introduced, which imposes a number of restrictions on the admissible codes, and, in fact, these considerations enable us toderive a small portion of a code which, if our hypothesis of ergodicity is correct, must occur in nature. Finally, we discuss briefly the problem as to whether there can exist more than one DNA-protein code in nature.     

Theory of epigenetic coding

The logic of genetic control of development may be based on a binary epigenetic code. This paper revises the author's previous scheme dealing with the numerology of annelid metamerism in these terms. Certain features of the code had been deduced to be combinatorial, others not. This paradoxical contrast is resolved here by the interpretation that these features relate to different operations of the code; the combinatiorial to coding identity of units, the non-combinatorial to coding production of units. Consideration of a second paradox in the theory of epigenetic coding leads to a new solution which further provides a basis for epimorphic regeneration, and may in particular throw light on the "regeneration-duplication" phenomenon. A possible test of the model is also put forward.     

Context-dependent persistency as a coding mechanism for robust and widely distributed value coding

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Neural dynamics of envelope coding

We consider the processing of narrowband signals that modulate carrier waveforms in sensory systems. The tuning of sensory neurons to the carrier frequency results in a high sensitivity to the amplitude modulations of the carrier. Recent work has revealed how specialized circuitry can extract the lower-frequency modulation associated with the slow envelope of a narrowband signal, and send it to higher brain along with the full signal. This paper first summarizes the experimental evidence for this processing in the context of electroreception, where the narrowband signals arise in the context of social communication between the animals. It then examines the mechanism of this extraction by single neurons and neural populations, using intracellular recordings and new modeling results contrasting envelope extraction and stochastic resonance. Low noise and peri-threshold stimulation are necessary to obtain a firing pattern that shows high coherence with the envelope of the input. Further, the output must be fed through a slow synapse. Averaging networks are then considered for their ability to detect, using additional noise, signals with power in the envelope bandwidth. The circuitry that does support envelope extraction beyond the primary receptors is available in many areas of the brain including cortex. The mechanism of envelope extraction and its gating by noise and bias currents is thus accessible to non-carrier-based coding as well, as long as the input to the circuit is a narrowband signal. Novel results are also presented on a more biophysical model of the receptor population, showing that it can encode a narrowband signal, but not its envelope, as observed experimentally. The model is modified from previous models by stimulus reducing contrast in order to make it sufficiently linear to agree with the experimental data.     

Sparse coding of sensory inputs

Several theoretical, computational, and experimental studies suggest that neurons encode sensory information using a small number of active neurons at any given point in time. This strategy, referred to as 'sparse coding', could possibly confer several advantages. First, it allows for increased storage capacity in associative memories; second, it makes the structure in natural signals explicit; third, it represents complex data in a way that is easier to read out at subsequent levels of processing; and fourth, it saves energy. Recent physiological recordings from sensory neurons have indicated that sparse coding could be a ubiquitous strategy employed in several different modalities across different organisms.     

Olfactory coding by lepidopterous larvae

Extracellular electrophysiological recording from olfactory receptors in the antennae of tobacco hornworm larvae (Manduca sexta (Johan.)) has revealed that cells respond differentially to different odors by changing latency, rate of increase of frequency of firing, rate of adaptation, and alternation of frequency increase and decrease. The resulting temporal patterns of spike activity could function as a code to allow for discrimination among various plant odors.

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Zusammenfassung Extrazelluläre elektrophysiologische Erregungsableitungen von Geruchsrezeptoren in den Antennen von Tabakschwärmer-Raupen (Manduca sexta (Johan.)) ergaben, daß die Zellen auf verschiedene Duftstoffe unterschiedlich mit Änderung der Latenzzeit, der Zunahmerate der Erregungsfrequenz, der Anpassungsrate sowie der Änderung der Frequenz-Zunahme und-Abnahme reagieren. Die sich daraus ergebenden Zeitmuster der Spike-Aktivität könnten als Code dienen und so die Unterscheidung zwischen verschiedenen Pflanzendüften ermöglichen.

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This research was supported by National Science Foundation Grant GB-1472.