On the syntactic structure of protein sequences and the concept of grammar complexity

It is shown that the concepts of grammar complexity and syntactic structure provide a useful mathematical framework for the investigation of some current problems in protein structure. Grammar complexity gives a measure of the degree of aperiodicity of a sequence and also an optimization criterion for evaluating amino acid categorizations. Three systems of amino acid categorization are compared in relation to their value for describing molecular architecture.     

Visual and acoustic communication in non-human animals: a comparison

The visual and auditory systems are two major sensory modalities employed in communication. Although communication in these two sensory modalities can serve analogous functions and evolve in response to similar selection forces, the two systems also operate under different constraints imposed by the environment and the degree to which these sensory modalities are recruited for non-communication functions. Also, the research traditions in each tend to differ, with studies of mechanisms of acoustic communication tending to take a more reductionist tack often concentrating on single signal parameters, and studies of visual communication tending to be more concerned with multivariate signal arrays in natural environments and higher level processing of such signals. Each research tradition would benefit by being more expansive in its approach.     

Transitive inference in non-human animals: an empirical and theoretical analysis

Transitive inference has long been considered one of the hallmarks of human deductive reasoning. Recent reports of transitive-like behaviors in non-human animals have prompted a flourishing empirical and theoretical search for the mechanism(s) that may mediate this ability in non-humans. In this paper, I begin by describing the transitive inference tasks customarily used with non-human animals and then review the empirical findings. Transitive inference has been demonstrated in a wide variety of species, and the signature effects that usually accompany transitive inference in humans (the serial position effect and the symbolic distance effect) have also been found in non-humans. I then critically analyze the most prominent models of this ability in non-human animals. Some models are cognitive, proposing for instance that animals use the rules of formal logic or form mental representations of the premises to solve the task, others are based on associative mechanisms such as value transfer and reinforcement and non-reinforcement. Overall, I argue that the reinforcement-based models are in a much better empirical and theoretical position. Hence, transitive inference in non-human animals should be considered a property of reinforcement history rather than of inferential processes. I finalize by shedding some light on some promising lines of research.     

Visual artificial grammar learning: comparative research on humans, kea (Nestor notabilis) and pigeons (Columba livia)

Artificial grammar learning (AGL) provides a useful tool for exploring rule learning strategies linked to general purpose pattern perception. To be able to directly compare performance of humans with other species with different memory capacities, we developed an AGL task in the visual domain. Presenting entire visual patterns simultaneously instead of sequentially minimizes the amount of required working memory. This approach allowed us to evaluate performance levels of two bird species, kea (Nestor notabilis) and pigeons (Columba livia), in direct comparison to human participants. After being trained to discriminate between two types of visual patterns generated by rules at different levels of computational complexity and presented on a computer screen, birds and humans received further training with a series of novel stimuli that followed the same rules, but differed in various visual features from the training stimuli. Most avian and all human subjects continued to perform well above chance during this initial generalization phase, suggesting that they were able to generalize learned rules to novel stimuli. However, detailed testing with stimuli that violated the intended rules regarding the exact number of stimulus elements indicates that neither bird species was able to successfully acquire the intended pattern rule. Our data suggest that, in contrast to humans, these birds were unable to master a simple rule above the finite-state level, even with simultaneous item presentation and despite intensive training.     

Essay review: Museums: Revisiting sites in the history of the natural sciences

Mary P. Winsor,Reading the shape of Nature: Comparative zoology at the Agassiz Museum (Chacago: University of Chicago Press, 1991); Ronald Rainger,An Agenda for Antiquty: Henry Fairfield Osborn and Vertedrate Paleontology at the American Meseum of Natural History, 1890–1935 (Tuscaloosa: University of Aladama Press, 1991).     

Individual and sex differences in learning abilities of ravens

Behavioral and physiological characteristics of individuals within the same species have been found to be stable across time and contexts. In this study, we investigated individual differences in learning abilities and object and social manipulation to test for consistency within individuals across different tasks. Individual ravens (Corvus corax) were tested in simple color and position discrimination tasks to establish their learning abilities. We found that males were significantly better in the acquisition of the first discrimination task and the object manipulation task, but not in any of the other tasks. Furthermore, faster learners engaged less often in manipulations of conspecifics and exploration of objects to get access to food. No relationship between object and social manipulation and reversal training were found. Our results suggest that individual differences in regard to the acquisition of new tasks may be related to personalities or at least object manipulation in ravens.     

Ultrasonic vocalizations and social learning of food preferences by female Norway rats

We examined whether ultrasonic vocalizations facilitate social learning of food preferences in female Norway rats, Rattus norvegicus. Females produced ultrasonic vocalizations at higher rates when they were reunited with a familiar conspecific if one member of the reunited pair had eaten an unfamiliar food while the pair members were separated. However, the influence of demonstrator rats on food choices of their observers was as great in pairs of rats that had been devocalized surgically as it was in sham-operated controls. The latter result is not consistent with the hypothesis that ultrasonic vocalizations facilitate social learning of food preferences in Norway rats.     

On the value of information: studying changes in patch assessment abilities through learning

Little is known about how animals acquire and use prior information, particularly for Bayesian patch assessment strategies. Because different patch assessment strategies rely upon distinct capabilities to obtain information, we analyzed whether foragers can alter their foraging strategy when they exploit predictable patches with periodic renewal. For this, we evaluated if learning contribute to increase foraging efficiency by improving patch assessment abilities in degus (Octodon degus), a diurnal caviomorph rodent from central Chile. Single degus exploited pairs of depleting patches that were renewed daily. During the initial two days of the experiment, degus exploited patches in agreement with a fixed‐time strategy, i.e. at the population level, giving‐up densities (GUD) were not distinguishable from density‐independence (i.e. consumption proportional to initial patch densities), and richer patches were under‐exploited. After day five, degus improved significantly their assessment strategy, showing agreement with Bayesian information updating. However, on day 15 and afterwards, degus foraged patches in agreement with a prescient strategy, because GUDs across patches indicated positive density‐dependence and equalization of GUDs. Although highly variable, the GUD ratio between rich and poor patches decreased significantly throughout time. Within‐subject data showed that as subjects learned patch qualities they showed a tendency toward GUD equalization and differentiation from density‐independence. By the end of the experiment, degus allocated more time to richer patches during the initial period of each trial, and allocated similar amounts of time by the end of trials. Further, the first visit of a session was significantly biased toward the rich patch by the final days of the experiment. The results suggest that assessment abilities can change when exploiting novel but predictable patches. When degus can incorporate adequate environmental information, prior and current information may become accurate enough to make animals exploit patches efficiently.     

On the pursuit of the brain network for proto-syntactic learning in non-human primates: conceptual issues and neurobiological hypotheses

Songbirds have become impressive neurobiological models for aspects of human verbal communication because they learn to sequence their song elements, analogous, in some ways, to how humans learn to produce spoken sequences with syntactic structure. However, mammals such as non-human primates are considered to be at best limited-vocal learners and not able to sequence their vocalizations, although some of these animals can learn certain 'artificial grammar' sequences. Thus, conceptual issues have slowed the progress in exploring potential neurobiological homologues to language-related processes in species that are taxonomically closely related to humans. We consider some of the conceptual issues impeding a pursuit of, as we define them, 'proto-syntactic' capabilities and their neuronal substrates in non-human animals. We also discuss ways to better bridge comparative behavioural and neurobiological data between humans and other animals. Finally, we propose guiding neurobiological hypotheses with which we aim to facilitate the future testing of the level of correspondence between the human brain network for syntactic-learning and related neurobiological networks present in other primates. Insights from the study of non-human primates and other mammals are likely to complement those being obtained in birds to further our knowledge of the human language-related network at the cellular level.     

Preface: to the special issue: photochemistry and electrochemistry of natural and artificial photosynthesis

Photosynthesis Research -     

On the lack of evidence that non-human animals possess anything remotely resembling a 'theory of mind'

After decades of effort by some of our brightest human and non-human minds, there is still little consensus on whether or not non-human animals understand anything about the unobservable mental states of other animals or even what it would mean for a non-verbal animal to understand the concept of a ‘mental state’. In the present paper, we confront four related and contentious questions head-on: (i) What exactly would it mean for a non-verbal organism to have an ‘understanding’ or a ‘representation’ of another animal''s mental state? (ii) What should (and should not) count as compelling empirical evidence that a non-verbal cognitive agent has a system for understanding or forming representations about mental states in a functionally adaptive manner? (iii) Why have the kind of experimental protocols that are currently in vogue failed to produce compelling evidence that non-human animals possess anything even remotely resembling a theory of mind? (iv) What kind of experiments could, at least in principle, provide compelling evidence for such a system in a non-verbal organism?     

Social learning in animals: comparative analysis of different forms and levels

Social learning as one of the key concepts of cognitive ecology includes different forms of behavioural displays from relatively simple, such as "social release" and "stimulus enhancement" up to "teaching" and "cultural transmission" in animal communities. Rapid development of this fields resulted in some contradictions in methods and terminology. In this review different forms and levels of social learning are analyzed. Ecological aspects of social learning are connected with diet shaping, fear of predators and mate choice. The first aspect is the most studied but still discussible. Social learning being an intricate component of feeding behaviour matches with innate behaviour, imprinting as well as early associative learning. Investigation of cognitive aspects of social learning going back to Thorndike's crucial question "Do apes ape?" are now developing into series of questions including even: "Do ants ape?". Elaboration of universal methods of comparative studying of social learning such as "artificial fruit" and "two ways/one outcome" has essentially enlightened these questions and made comparative analysis possible. Large continuum of displays of cognitive skills in social learning has been revealed in non-primate species. One of the discussible issues in the role of social learning is distribution of innovations. Many authors have investigated this intriguing aspect of animal behaviour in different ways, such as long field observations as well as laboratory experiments based on "artificial innovators" that is specimens specially taught by experimentalists. Many impressive results were obtained; in particular it turned out in contradiction with some mathematical models that individuals in groups are rather different in their psychophysiological predisposition to innovative behaviour. Role of teaching in such different forms of behaviour as shaping of species-specific behavioural patterns and spread of innovations is considered. Although the majority of animals in wild populations are not good teachers and pupils, some cultural aspects of behaviour were recently revealed, mostly in primates. At the same time some classical results concerning cultural transmission of new patterns (for example, bottle-opening in tits) were experimentally revised. Many problems still remain unsolved, in particular, how spread of innovations may favour prosperity of populations; to what degree behavioural peculiarities of local groups may be determined by processes of social learning; which internal and external factors and under what circumstances invest into social learning in natural environment.     

Biological and bionic hands: natural neural coding and artificial perception

The first decade and a half of the twenty-first century brought about two major innovations in neuroprosthetics: the development of anthropomorphic robotic limbs that replicate much of the function of a native human arm and the refinement of algorithms that decode intended movements from brain activity. However, skilled manipulation of objects requires somatosensory feedback, for which vision is a poor substitute. For upper-limb neuroprostheses to be clinically viable, they must therefore provide for the restoration of touch and proprioception. In this review, I discuss efforts to elicit meaningful tactile sensations through stimulation of neurons in somatosensory cortex. I focus on biomimetic approaches to sensory restoration, which leverage our current understanding about how information about grasped objects is encoded in the brain of intact individuals. I argue that not only can sensory neuroscience inform the development of sensory neuroprostheses, but also that the converse is true: stimulating the brain offers an exceptional opportunity to causally interrogate neural circuits and test hypotheses about natural neural coding.     

Darwin's use of the analogy between artificial and natural selection

Conclusion The central role played by Darwin's analogy between selection under domestication and that under nature has been adequately appreciated, but I have indicated how important the domesticated organisms also were to other elements of Darwin's theory of evolution-his recognition of the constant principle of change, for instance, of the imperfection of adaptation, and of the extent of variation in nature. The further development of his theory and its presentation to the public likewise hinged on frequent reference to domesticates.We have seen that Darwin's reliance on the analogy between domesticated varieties and wild species was a bold and original step, in light of contemporary views on the nature of domesticates. However, as Darwin undoubtedly foresaw, his reliance on the analogy created difficulties as well as solving problems, and these began with his Malthusian codiscoverer of the principle of natural selection, Alfred Russel Wallace. Wallace's paper On the Tendency of Varieties to Depart Indefinitely from the Original Type, presented to the Linnean Scoiety along with the first public unveiling of Darwin's theory, states: We see, then, that no inferences as to varieties in a state of nature can be deduced from the observation of those occurring among domestic animals. The two are so much opposed to each other in every circumstance of their existence, that what applies to the one is almost sure not to apply to the other. Domestic animals are abnormal, irregular, artificial; they are subject to varieties which never occur and never can occur in a state of nature.⁶² Much has been made of the similarity of views of Darwin and Wallace, but this quotation surely reveals how utterly different their views were on what to Darwin was an important matter. Several critics of the Origin saw Darwin's reliance on the domesticates as his Achilles heel. As Young has pointed out, Samuel Wilberforce included the following passage in his attack on the Origin: Nor must we pass over unnoticed the transference of the argument from the domesticated to the untamed animals. Assuming that man as the selector can do much in a limited time, Mr. Darwin argues that Nature, a more powerful, a more continuous power, working over vastly extended ranges of time, can do more. But why should Nature, so uniform and persistent in all her operations, tend in this instance to change? Why should she become a selector of varieties?⁶³ Another critic, Fleeming Jenkin, found the analogy a weakness in Darwin's theory because of the limited extent of variation in any one direction in domestic animals and plants.⁶⁴ We have already seen that Darwin had confided a similar view to his notebook thirty years earlier, but changed his mind as a result of his profound study of domesticates. De Beer's reference to an English country gentleman's knowledge of domestic plants and animals and their breeding⁶⁵ fails totally to recognize the originality and depth of Darwin's knowledge of domesticates.Why did Darwin, against the currents of his time, rely so heavily on mankind's experience with domesticated organisms to shape his theory about species in nature? On reason is that only with domesticates was an approach that came close to experimental verification possible. Darwin fully realized the inadequacies of the experiment, as is emphasized by his repeated contrasting of selection under nature and selection by man. Yet the extensive experience and data of plant and animal breeders offered the only reliable base against which Darwin could continually challenge his views. As he wrote in the introduction to Variation, with domestication, man ... may be said to have been trying an experiment on a gigantic scale.⁶⁶ Given Darwin's high opinion of the quantitative work of Malthus and Quetelet (as emphasized by Schweber),⁶⁷ and his unremitting efforts to secure data by which to test his theories, it was inevitable that he should attach high significance to domesticated varieties. John Tyndall, in his Belfast address of 1874, said: The strength of the doctrine of Evolution consists, not in experimental demonstration (for the subject is hardly accessible to this mode of proof), but in its general harmony with scientific thought.⁶⁸ Darwin would have agreed with the latter thought, but I think he would have challenged the preceding one on the grounds that long experience with domesticated varieties did provide an element of experimental demonstration. It gave him confidence in his theory, and he used his vast knowledge of artificial selection boldly and creatively.