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Language of fungi derived from electrical spiking activity
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Abstract
ungi exhibit oscillations of extracellular electrical potential recorded via differential electrodes inserted into a substrate colonised by mycelium or directly into sporocarps. We analysed electrical activity of ghost fungi (\emph{Omphalotus nidiformis}), Enoki fungi (\emph{Flammulina velutipes}), split gill fungi (\emph{Schizophyllum commune}) and caterpillar fungi (\emph{Cordyceps militari}). The spiking characteristics are species specific: a spike duration varies from one to 21 hours and an amplitude from 0.03~mV to 2.1mV. We found that spikes are often clustered into trains. Assuming that spikes of electrical activity are used by fungi to communicate and process information in mycelium networks, we group spikes into words and provide a linguistic and information complexity analysis of the fungal spiking activity. We demonstrate that distributions of fungal word lengths match that of human languages. We also construct algorithmic and Liz-Zempel complexity hierarchies of fungal sentences and show that species \emph{S. commune} generate most complex sentences.
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Oyster fungi Pleurotus djamor generate actin potential like spikes of electrical potential. The trains of spikes might manifest propagation of growing mycelium in a substrate, transportation of nutrients and metabolites and communication processes in the mycelium network. The spiking activity of the mycelium networks is highly variable compared to neural activity and therefore can not be analysed by standard tools from neuroscience. We propose original techniques for detecting and classifying the spiking activity of fungi. Using these techniques, we analyse the information-theoretic complexity of the fungal electrical activity. The results can pave ways for future research on sensorial fusion and decision making of fungi.
As one of the first model systems in biology, the basal metazoan Hydra has been revealing fundamental features of living systems since it was first discovered by Antonie van Leeuwenhoek in the early eighteenth century. While it has become well-established within cell and developmental biology, this tiny freshwater polyp is only now being re-introduced to modern neuroscience where it has already produced a curious finding: the presence of low-frequency spontaneous neural oscillations at the same frequency as those found in the default mode network in the human brain. Surprisingly, increasing evidence suggests such spontaneous electrical low-frequency oscillations (SELFOs) are found across the wide diversity of life on Earth, from bacteria to humans. This paper reviews the evidence for SELFOs in diverse phyla, beginning with the importance of their discovery in Hydra , and hypothesizes a potential role as electrical organism organizers, which supports a growing literature on the role of bioelectricity as a ‘template’ for developmental memory in organism regeneration.
This article is part of the theme issue ‘Basal cognition: conceptual tools and the view from the single cell’.
We recorded extra-cellular electrical potential of fruit bodies of oyster fungi Pleurotus djamor. We demonstrated that the fungi generate action potential like impulses of electrical potential. Trains of the spikes are observed. Two types of spiking activity are uncovered: high-frequency (period 2.6 min) and low-frequency (period 14 min); transitions between modes of spiking are illustrated. An electrical response of fruit bodies to short (5 sec) and long (60 sec) thermal stimulation with open flame is analysed in details. We show that non-stimulated fruit bodies of a cluster react to the thermal stimulation, with a single action-potential like spike, faster than the stimulated fruit body does.
We investigate the properties of a divide-and-conquer Block Decomposition Method (BDM), which extends the power of a Coding Theorem Method (CTM) that approximates local estimations of algorithmic complexity and of logical depth based upon Solomonoff-Levin's theory of algorithmic probability, thereby providing a closer connection to algorithmic complexity. The strategy behind BDM is to find small computer programs that produce the components of a larger, decomposed object. The set of short computer programs can then be artfully arranged in sequence so as to produce the original object and to estimate an upper bound on the greatest length of the shortest computer program that produces said original object. We show that the method provides efficient estimations of algorithmic complexity but that it performs like Shannon entropy when it loses accuracy. We estimate errors and study the behaviour of BDM for different boundary conditions, all of which are compared and assessed in detail. The measure may be adapted for use with more multi-dimensional objects than strings, objects such as arrays and tensors. To test the measure we provide proofs of the algorithmic complexity relations among dual, isomorphic and cospectral graphs. Finally, we introduce a measure based upon the seminal concept of logical depth whose numerical comparisons to CTM and BDM agree with the theoretical expectations. We provide implementations in most major programming languages --Mathematica, Matlab, R, Java, Perl, Python, Pascal, C++, and Haskell-- and a free online algorithmic complexity calculator.
Action potentials (APs) belong to long-distance signals in plants. They fulfill the all-or-none law, propagate without decrement and their generation is limited by refractory periods. The ion mechanism of APs was elaborated in giant Characean algae and extended by another model plant - the liverwort Conocephalum conicum. It consists of an increase in cytoplasmic Ca2+ concentration ([Ca2+]cyt) which activates anion channels responsible for Cl- efflux and for membrane depolarization. Repolarization occurs after the opening of potassium channels and K+ efflux. The resting potential is restored by the electrogenic proton pump. A number of ion channels which may play a role in AP were identified by the patch-clamp technique. APs propagate on the principle of local electrical circuits. They cover whole plants, plant organs or definite tissues, mainly phloem, phloem parenchyma and protoxylem. APs mediate between local stimulation and movements in carnivorous Dionaea muscipula, Aldrovanda vesiculosa, and tigmonastic Mimosa pudica. The role of APs in regulation of respiration, photosynthesis, growth, pollination, fertilization and gene expression is well documented. An AP-coupled increase in [Ca2+]cyt seems to play a central role in signal transduction.
The aim of this paper is to report for the first time the 1000 most common words and lemmas of Modern Greek and some of their quantitative characteristics. The frequency word list produced is based on the Hellenic National Corpus (HNC), a corpus of Modern Greek language consisting of about 13 million words of written texts. In particular, we investigate the application of Zipf’s law in both the 1000 most common words and lemmas. In addition we examine the frequency distribution of the grammatical categories in the 1000 most common words and lemmas as well as the average word length in the whole HNC and the growth of the average word length as a function of the number of the most common words.
As human randomness production has come to be more closely studied and used to assess executive functions (especially inhibition), many normative measures for assessing the degree to which a sequence is randomlike have been suggested. However, each of these measures focuses on one feature of randomness, leading researchers to have to use multiple measures. Although algorithmic complexity has been suggested as a means for overcoming this inconvenience, it has never been used, because standard Kolmogorov complexity is inapplicable to short strings (e.g., of length l ≤ 50), due to both computational and theoretical limitations. Here, we describe a novel technique (the coding theorem method) based on the calculation of a universal distribution, which yields an objective and universal measure of algorithmic complexity for short strings that approximates Kolmogorov-Chaitin complexity.
Dynamics of average length of words in Russian and English is analysed in the
article. Words belonging to the diachronic text corpus Google Books Ngram and
dated back to the last two centuries are studied. It was found out that average
word length slightly increased in the 19th century, and then it was growing
rapidly most of the 20th century and started decreasing over the period from
the end of the 20th - to the beginning of the 21th century. Words which
contributed mostly to increase or decrease of word average length were
identified. At that, content words and functional words are analysed
separately. Long content words contribute mostly to word average length of
word. As it was shown, these words reflect the main tendencies of social
development and thus, are used frequently. Change of frequency of personal
pronouns also contributes significantly to change of average word length. The
other parameters connected with average length of word were also analysed.
We describe an alternative method (to compression) that combines several
theoretical and experimental results to numerically approximate the algorithmic
(Kolmogorov-Chaitin) complexity of all bit strings up to 8
bits long, and for some between 9 and 16 bits long. This is done by an
exhaustive execution of all deterministic 2-symbol Turing machines with up to 4
states for which the halting times are known thanks to the Busy Beaver problem,
that is 11019960576 machines. An output frequency distribution is then
computed, from which the algorithmic probability is calculated and the
algorithmic complexity evaluated by way of the (Levin-Zvonkin-Chaitin) coding
theorem.
In this paper evidence is provided that individual neurons possess language, and that the basic unit for communication consists of two neurons and their entire field of interacting dendritic and synaptic connections. While information processing in the brain is highly complex, each neuron uses a simple mechanism for transmitting information. This is in the form of temporal electrophysiological action potentials or spikes (S) operating on a millisecond timescale that, along with pauses (P) between spikes constitute a two letter “alphabet” that generates meaningful frequency-encoded signals or neuronal S/P “words” in a primary language. However, when a word from an afferent neuron enters the dendritic-synaptic-dendritic field between two neurons, it is translated into a new frequency-encoded word with the same meaning, but in a different spike-pause language, that is delivered to and understood by the efferent neuron. It is suggested that this unidirectional inter-neuronal language-based word translation step is of utmost importance to brain function in that it allows for variations in meaning to occur. Thus, structural or biochemical changes in dendrites or synapses can produce novel words in the second language that have changed meanings, allowing for a specific signaling experience, either external or internal, to modify the meaning of an original word (learning), and store the learned information of that experience (memory) in the form of an altered dendritic-synaptic-dendritic field.
Fungi exhibit action-potential like spiking activity. Up to date, most electrical activity of oyster fungi has been characterized in sufficient detail. It remains unclear if there are any patterns of electrical activity specific only for a certain set of species or if all fungi share the same “language” of electrical signalling. We use pairs of differential electrodes to record extracellular electrical activity of the antler-like sporocarps of the polypore fungus Ganoderma resinaceum. The patterns of the electrical activity are analyzed in terms of frequency of spiking and parameters of the spikes. The indicators of the propagation of electrical activity are also highlighted.
In higher plants at least three different types of electrical long-distance signaling exist: action potential (AP), variation potential (VP), and system potential (SP), all of which have their own characteristics concerning their generation, duration, amplitude, velocity, and propagation. Whereas both AP and VP are due to a transient depolarization of the plasma membrane, the SP is based on hyperpolarization. For more than 100 years the AP is known and described for some specialized plants such as the Venus flytrap. Meanwhile, all three types of electrical signaling have been shown for many common plants, monocots as well as dicots, indicating that the capability to generate long-distance electrical signals is not the exception but a general physiological feature of plants. In spite of this, positive proofs for the involvement of these kinds of electrical signaling in the induction of many different plant responses to (a)biotic stresses or in developmental processes still wait to be established.
"Average durations of 12 vowels of American English measured in bisyllabic nonsense utterances are reported. The vowels occurred in 14 symmetrical consonantal environments and the utterances were produced by 3 male talkers. The consonant environments consisted of the voiced and voiceless versions of 3 stop, 1 affricate, and 3 fricative consonant articulations. 4 determinants of the characteristic durations of stressed vowels are identified and discussed. The hypothesis is advanced that the primary lengthening of vowels in English—that found in tense vowels and in vowels before voiced constants—is a part of the phonology of the language and is learned by speakers of the language, and that the secondary lengthening of vowels in English—that found in open vowels and in vowels before fricative constants—is a function of the articulatory process itself." From Psyc Abstracts 36:01:3GH74H. (PsycINFO Database Record (c) 2012 APA, all rights reserved)
1.1. Potential differences between the two loci of the slime mold (Physarum polycephalum) connected with a single strand of protoplasm were determined successively and the mode of their variation in relation to time was represented graphically.2.2. The electromotive force of the slime mold changes according to a rhythmic pattern, the period of which is the same as that of the cyclic back and forth steaming, and the amplitude of which increases and decreases spontaneously under constant conditions, usually within 10 mv.3.3. The rhythmic change in the potential occurs whether the flow along the connecting strand is allowed to take place freely, or if it is made to stop by means of local blocking of the strand, or by application of a balancing pressure.4.4. Satisfactory results have been obtained in an attempt to represent graphically the simultaneous variation in potential (electroplasmogram or EPG) and the power to flow (dynamoplasmogram or DPG) from one and the same plasmodium with the aid of a double-chamber method.5.5. In addition to the periods of these two curves being the same, a close relationship between them under normal conditions is seen with respect to amplitude, wave form, and polarity.6.6. The phases of the two waves do not coincide with each other, that of the EPG always lagging behind that of the DPG usually by 30–100 sec., or of their period.7.7. The local differences in the bioelectric potential in a plasmodium cannot be regarded as the direct result of the protoplasmic flow or as the streaming potential. Nor is it to be considered as the direct cause responsible for the flow; in other words, the protoplasmic flow is not explained as a phenomenon of electroendosmosis.8.8. Besides the slow cyclic variation mentioned above, there is a quick, transient potential variation which is elicited not only spontaneously at times, but also artificially through use of weak mechanical shocks.
This paper examines data from English, Swedish and German in order to find a theoretical distribution that describes the observed relation between word length and frequency. In Swedish and English, most word tokens consist of three letters only, while shorter or longer words occur less frequently. We found that the equation with the general form fexp = a * Lb * cL (a variant of the so-called gamma distribution) approximates the observed frequencies reasonably well. This formula incorporates both the fact that the number of possible words increases with word length, and the fact that longer words tend to be avoided, presumably because they are uneconomic. To our knowledge this formula has not been proposed to describe word frequency data. We examined frequency distributions of word length in Swedish and English, and explored different variants of the equation by systematically varying the a, b and c parameters. Subsequently, we also applied the formula to the frequency distribution of sentence length in English, and found an almost perfect fit for a corpus consisting of different text genres. Moreover, the data showed that the formula can be used to distinguish between different kinds of text genres.
Electrical currents associiited with the plant-fungus interaction between roots and an arbuscular mycorrhizal
(AM) fungus Gigaspora mtirgarita were measured with a one-dimensional vibrating probe. Uninfected roots of
clover (Trifolium repens L. cv. New Zealand White) and carrot (Daucus carota L. cv. Nantes) had an inwardly
directed positive electrical current at the apical meristen-iatic and elongation zones and an outward flow at the
mature non-growing regions. The current profile of endomycorrhizal colonized roots did not differ markedly in
magnitude or pattern compared with non-colonized roots of an ecjuivalent stage of development. .^ sn-iall current
was measured circulating around and through single mycorrhizal azygospores ot G. mtirgarita. CJerm tubes
emerged within the zone of outward current and an inward current was found at the hyphal tip. When roots were
colonized by the fungus an inward current was induced at the point of hyphal contact with the host root. This
current declined over a period of 6 d. Because hyphal penetration of plant roots by AM fungi does not rupture the
plant host membrane we propose that the host current is not the result of wounding but is induced by fungal
elicitors at the infection court.
In many cellular processes, spontaneous activities are often the basis for their functioning. Paramecium cells change their swimming direction under a homogeneous environment, which is induced by a spontaneous signal generation in the membrane electric potential. For such a spontaneous activity, a theoretical model has been proposed by Oosawa (2007) [Biosystems 88, 191-201.], in which intracellular noise is hierarchically organized from thermal fluctuations to spike-like large fluctuations, which induces a signal to change spontaneously the swimming direction. Our analysis of the model shows that the system is a kind of excitable media, in which a spike is induced by a stochastic fluctuation. We show conditions of channels properties to have a spike train.
Occasional spontaneous "action potentials" are found in mature hyphae of the fungus Neurospora crassa. They can arise either from low-level sinusoidal oscillations of the membrane potential or from a linear slow depolarization which accelerates into a rapid upstroke at a voltage 5-20 mV depolarized from the normal resting potential (near-180 mV). The "action potentials" are long-lasting, 1-2 min and at the peak reach a membrane potential near-40 mV. A 2-to 8-fold increase of membrane conductance accompanies the main depolarization, but a slight decrease of membrane conductance occurs during the slow depolarization. Two plausible mechanisms for the phenomenon are (a) periodic increases of membrane permeability to inorganic ions, particularly H+ or Cl- and (b) periodic decreases in activity of the major electrogenic pump (H+) or the Neurospora membrane, coupled with a nonlinear (inverse signoid) current-boltage relationship. Identification of action potential-like disturbances in fungi means that such behavior has now been found in all major biologic taxa which have been probed with suitable electrodes. As yet there is no obvious function for the events in fungi.
A computer algorithm to identify 'bursts' in trains of spikes is described. The algorithm works by constructing a histogram of interspike intervals, then analyzing the histogram to detect the critical interval value in the distribution that represents the break between short intervals within a burst and the longer intervals between bursts. When such a value is found, it is used as the 'threshold' to determine those intervals in the spike train that lie within a burst and those that lie between bursts and, thereby, to identify the beginning and end of each burst in the train. The validity of the bursts is evaluated with a chi-square test. The performance of the algorithm and how it can be assessed is discussed.
Simultaneous recordings were made from small collections (2-7) of spontaneously active single units in the striate cortex of unanesthetized cats, by means of chronically implanted electrodes. The recorded spike trains were computer scanned for bursts of spikes, and the bursts were catalogued and studied. The firing rates of the neurons ranged from 0.16 to 32 spikes/s; the mean was 8.9 spikes/s, the standard deviation 7.0 spikes/s. Bursts of spikes were assigned a quantitative measure, termed Poisson surprise (S), defined as the negative logarithm of their probability in a random (Poisson) spike train. Only bursts having S greater than 10, corresponding to an occurrence rate of about 0.01 bursts/1,000 spikes in a random spike train, were considered to be of interest. Bursts having S greater than 10 occurred at a rate of about 5-15 bursts/1,000 spikes, or about 1-5 bursts/min. The rate slightly increased with spike rate; averaging about 2 bursts/min for neurons having 3 spikes/s and about 4.5 bursts/min for neurons having 30 spikes/s. About 21% of the recorded units emitted significantly fewer bursts than the rest (below 1 burst/1,000 spikes). The percentage of these neurons was independent of spike rate. The spike rate during bursts was found to be about 3-6 times the average spike rate; about the same for longer as for shorter bursts. Bursts typically contained 10-50 spikes and lasted 0.5-2.0 s. When the number of spikes in the successively emitted bursts was listed, it was found that in some neurons these numbers were not distributed at random but were clustered around one or more preferred values. In this sense, bursts occasionally "recurred" a few times in a few minutes. The finding suggests that neurons are highly reliable. When bursts of two or more simultaneously recorded neurons were compared, the bursts often appeared to be temporally close, especially between pairs of neurons recorded by the same electrode; but bursts seldom started and ended simultaneously on two channels. Recurring bursts emitted by one neuron were occasionally accompanied by time-locked recurring bursts by other neurons.
1. Amoebae can be penetrated by microelectrodes at either end. One records voltage and the other supplies alternating current.
2. Step-like increases in alternating voltage superimposed on potentials recorded by the voltage electrode when in either the pseudopod or rear region demonstrate that low potentials recorded from a pseudopod and high ones from the rear region exist across a discrete impedance barrier. The only structure so far shown to fulfil this function is the plasma membrane.
3. A resistance inserted in the earth path monitors current flowing through the system and confirms observations made when recording with single electrodes that there is a reduction of electrode resistance when the cell is entered.
4. Pronounced depolarization in the rear region is shown when the current-carrying electrode penetrates the pseudopod, but not vice versa.
5. Morphological changes associated with membrane potential reversal are illustrated.
6. Consideration is given to the role of step-like potential changes in movement.
Electrical excitability and signalling, frequently associated with rapid responses to environmental stimuli, are well known in some algae and higher plants. The presence of electrical signals, such as action potentials (AP), in both animal and plant cells suggested that plant cells, too, make use of ion channels to transmit information over long distances. In the light of rapid progress in plant biology during the past decade, the assumption that electrical signals do not only trigger rapid leaf movements in 'sensitive' plants such as Mimosa pudica or Dionaea muscipula, but also physiological processes in ordinary plants proved to be correct. Summarizing recent progress in the field of electrical signalling in plants, the present review will focus on the generation and propagation of various electrical signals, their ways of transmission within the plant body and various physiological effects.
Compressibility of individual sequences by the class of generalized finite-state information-lossless encoders is investigated. These encoders can operate in a variable-rate mode as well as a fixed-rate one, and they allow for any finite-state scheme of variable-length-to-variable-length coding. For every individual infinite sequence x a quantity rho(x) is defined, called the compressibility of x , which is shown to be the asymptotically attainable lower bound on the compression ratio that can be achieved for x by any finite-state encoder. This is demonstrated by means of a constructive coding theorem and its converse that, apart from their asymptotic significance, also provide useful performance criteria for finite and practical data-compression tasks. The proposed concept of compressibility is also shown to play a role analogous to that of entropy in classical information theory where one deals with probabilistic ensembles of sequences rather than with individual sequences. While the definition of rho(x) allows a different machine for each different sequence to be compressed, the constructive coding theorem leads to a universal algorithm that is asymptotically optimal for all sequences.
The language of neurons: theory and applications of a quantitative analysis of the neural code
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