Neither touch nor vision: sensory substitution as artificial synaesthesia?

Block (Trends Cogn Sci 7:285–286, 2003) and Prinz (PSYCHE 12:1–19, 2006) have defended the idea that SSD perception remains in the substituting modality (auditory or tactile). Hurley and Noë (Biol Philos 18:131–168, 2003) instead argued that after substantial training with the device, the perceptual experience that the SSD user enjoys undergoes a change, switching from tactile/auditory to visual. This debate has unfolded in something like a stalemate where, I will argue, it has become difficult to determine whether the perception acquired through the coupling with an SSD remains in the substituting or the substituted modality. Within this puzzling deadlock two new approaches have been recently suggested. Ward and Meijer (Conscious Cogn 19:492–500, 2010) describe SSD perception as visual-like but characterize it as a kind of artificially induced synaesthesia. Auvray et al. (Perception 36:416–430, 2007) and Auvray and Myin (Cogn Sci 33:1036–1058, 2009) suggest that SSDs let their users experience a new kind of perception. Deroy and Auvray (forthcoming) refine this position, and argue that this new kind of perception depends on pre-existing senses without entirely aligning with any of them. So, they have talked about perceptual experience in SSDs as going "beyond vision". In a similar vein, MacPherson (Oxford University Press, New York, 2011a) claims that “if the subjects (SSD users) have experiences with both vision-like and touch-like representational characteristics then perhaps they have a sense that ordinary humans do not” (MacPherson in Oxford University Press, New York, 2011a, p. 139).     

How to Start a Wet Forest Ablaze: Perspectives on the Question of the Origins of Human Mindedness

This paper is a methodological and theoretical meditation on how some research has approached the question of the evolution of human cognitive traits. I discuss views that explicitly or implicitly endorse a view of human cognition as originating from a cause that can be singled out. Following Ross and Ladyman (2010), I suggest that this “singling-out” strategy correlates with a “container” metaphor that doesn’t fit with the interactive process-ontology of modern physics (Campbell 2009). Instead, Ross and Ladyman as well as Campbell recommend the metaphor of ‘emergence’. The logic and ontology of emergent systems finds resonance with developmental systems theory in biology. I suggest in agreement with Stotz (Phenomenology and the Cognitive Sciences 9(4), 2010) that we view the origins of human mindedness within such a framework.     

A dynamical systems perspective on the relationship between symbolic and non-symbolic computation

It has been claimed that connectionist (artificial neural network) models of language processing, which do not appear to employ “rules”, are doing something different in kind from classical symbol processing models, which treat “rules” as atoms (e.g., McClelland and Patterson in Trends Cogn Sci 6(11):465–472, 2002). This claim is hard to assess in the absence of careful, formal comparisons between the two approaches. This paper formally investigates the symbol-processing properties of simple dynamical systems called affine dynamical automata, which are close relatives of several recurrent connectionist models of language processing (e.g., Elman in Cogn Sci 14:179–211, 1990). In line with related work (Moore in Theor Comput Sci 201:99–136, 1998; Siegelmann in Neural networks and analog computation: beyond the Turing limit. Birkhäuser, Boston, 1999), the analysis shows that affine dynamical automata exhibit a range of symbol processing behaviors, some of which can be mirrored by various Turing machine devices, and others of which cannot be. On the assumption that the Turing machine framework is a good way to formalize the “computation” part of our understanding of classical symbol processing, this finding supports the view that there is a fundamental “incompatibility” between connectionist and classical models (see Fodor and Pylyshyn 1988; Smolensky in Behav Brain Sci 11(1):1–74, 1988; beim Graben in Mind Matter 2(2):29--51,2004b). Given the empirical successes of connectionist models, the more general, super-Turing framework is a preferable vantage point from which to consider cognitive phenomena. This vantage may give us insight into ill-formed as well as well-formed language behavior and shed light on important structural properties of learning processes.     

Leges sine moribus vanae: does language make moral thinking possible?

Does language make moral cognition possible? Some authors like Andy Clark have argued for a positive answer whereby language and the ways people use it mark a fundamental divide between humans and all other animals with respect to moral thinking (Clark, Mind and morals: essays on cognitive science and ethics. MIT Press, Cambridge, MA, 1996; Moral Epistemol Nat Can J Philos Suppl XXVI, 2000a; Moral Epistemol Nat Can J Philos Suppl XXVI, 2000b; Philosophy of mental representation. Oxford University Press, Oxford, pp 37–43 and discussion, 44–61, 2002). I take issue with Clark’s view and argue that language is probably unnecessary for the emergence of moral cognition. I acknowledge, however, that humans unlike other animals seem to posses what Haugeland in Philosophy of mental representation. Oxford University Press, Oxford (2002) terms ‘norm-hungriness’: an idiosyncratic need or desire to create and abide by a multitude of norms. Our peculiar norm-hungriness, I suggest, depends on what can be called florid control rather than on language.     

Homology, female orgasm and the forgotten argument of Donald Symons

The ‘byproduct account’ of female orgasm, a subject of renewed debate since Lloyd (The case of the female orgasm, Harvard University Press, Cambridge, 2005), is universally attributed to Symons (The evolution of human sexuality, Oxford University Press, Oxford, 1979). While this is correct to the extent that he linked it to the adaptive value of male orgasm, I argue that the attribution of the theory as we understand it to Symons is based on a serious and hitherto unrecognised misinterpretation. Symons had a different explanation of why women can orgasm, and beneath this explanation lies an obscure line of argument, including a particularly obscure use of the word ‘homologous’.     

Phenomenology of Psychoanalytic Data. A Biosemiotic Framework

In my continuing efforts to build a bridge between psychoanalytic findings and biosemiotics here, as in previous works, ‘biosemiotic’ refers to the hierarchy of meaning-forms (from biological to semiotic-organizations) underlying an updated psychoanalytic model of mind. Within this framework I present a broad range of bio-semiotic phenomena, processes, dynamics, defenses, and universal and unique internalized interpersonal patterns, that in psychoanalysis all commonly fall under the broad heading of the “Unconscious.” Reconceptualized as interpretive data within the purview of a psychoanalytic discourse-semantic this biosemiotic framework posits an epigenetic continuum of human meaning-organizations originating at basic organic levels, moving upward through biological, psycho-somatic and affective expression, proto-semiotic transmissions, represented forms, and finally to explicit linguistic signs and complex symbol systems. In addition to assuming an uninterrupted epigenetic continuum crystallizing in hierarchic organization, this framework accentuates the multilayered and increasingly condensed quality of higher more elaborate organizations of meaning in human communication, drawing attention to persisting biological undercurrents in implied sense, intent, and motivation, all of which impact on repressive/defensive mechanisms. Drawing from previous works (Aragno 1997, 2005, 2008a, b, Psychoanalytic Inquiry 29(1):30–47, 2009, Biosemiotics 3:57–77, 2010, 2011a, Signs 5:71–74, 2011b, Journal of the American Psychoanalytic Association, Centennial Paper, Special Centennial Issue 59(2):239–288, 2011b, Signs 5:29–70, 2011c) in which I labored to update and revise Freud’s first topographical theory of mind, this paper presents the phenomenology of unconscious ‘data’ for the purpose of introducing a diverse range of non-linguistic signifying forms from which psychoanalysts infer mental processes and ‘interpret’ meanings. An important underlying premise regarding psychoanalytic data and its relation to the basic biosemiotic ‘agenda’ is that until grounded in an updated developmental theory of mind inclusive of pre- and proto-semiotic-forms, that is evolutionarily plausible, epistemologically based, and correlates with contemporary neuroscience, the term “sign” is merely an abstract linguistic ‘label’ rather than a mental act with antecedent developmental stages manifesting meanings through different forms and modes of expression. Drawn from the yields of the psychoanalytic method and semantic this revised metatheoretical approach provides insights into the sensory-emotive, bodily origins of unconscious layers of non-linguistic signification thereby expanding our understanding of the formative stages of the ‘semiotic function’ in human evolution. This being the third in a series of papers integrating the yields of psychoanalytic methodology with the underlying premises of ‘Biosemiotics,’ some familiarity with the background knowledge provided in the previous two is strongly recommended.     

A comment on Farwell (2012): brain fingerprinting: a comprehensive tutorial review of detection of concealed information with event-related brain potentials

In a recent issue of Cognitive Neurodynamics Farwell (Cogn Neurodyn 6:115–154, 2012) published a comprehensive tutorial review of the use of Event Related Brain Potentials (ERP) in the detection of concealed information. Farwell’s review covered much of his own work employing his “brain fingerprinting” technology. All his work showed a 100 % accuracy rate in detecting concealed information. We argue in this comment that Farwell (Cogn Neurodyn 6:115–154, 2012) is misleading and misrepresents the scientific status of brain fingerprinting technology.     

An analysis of a ‘community-driven’ reconstruction of the human metabolic network

Following a strategy similar to that used in baker’s yeast (Herrgård et al. Nat Biotechnol 26:1155–1160, 2008). A consensus yeast metabolic network obtained from a community approach to systems biology (Herrgård et al. 2008; Dobson et al. BMC Syst Biol 4:145, 2010). Further developments towards a genome-scale metabolic model of yeast (Dobson et al. 2010; Heavner et al. BMC Syst Biol 6:55, 2012). Yeast 5—an expanded reconstruction of the Saccharomyces cerevisiae metabolic network (Heavner et al. 2012) and in Salmonella typhimurium (Thiele et al. BMC Syst Biol 5:8, 2011). A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2 (Thiele et al. 2011), a recent paper (Thiele et al. Nat Biotechnol 31:419–425, 2013). A community-driven global reconstruction of human metabolism (Thiele et al. 2013) described a much improved ‘community consensus’ reconstruction of the human metabolic network, called Recon 2, and the authors (that include the present ones) have made it freely available via a database at http://humanmetabolism.org/ and in SBML format at Biomodels (http://identifiers.org/biomodels.db/MODEL1109130000). This short analysis summarises the main findings, and suggests some approaches that will be able to exploit the availability of this model to advantage.     

Animals on Drugs: Understanding the Role of Pharmaceutical Companies in the Animal-Industrial Complex

In this paper I revisit previous critiques that I have made of much, though by no means all, bioethical discourse. These pertain to faithfulness to dualistic ontology, a taken-for-granted normative anthropocentrism, and the exclusion of a consideration of how political economy shapes the conditions for bioethical discourse (Twine Medicine, Health Care and Philosophy 8(3):285-295, 2005; International Journal of Sociology of Agriculture and Food 16(3):1-18, 2007, 2010). Part of my argument around bioethical dualist ontology is to critique the assumption of a division between the “medical” (human) and “agricultural” (nonhuman) and to show various ways in which they are interrelated. I deepen this analysis with a focus on transnational pharmaceutical companies, with specific attention to their role in enhancing agricultural production through animal drug administration. I employ the topical case of antibiotics in order to speak to current debates in not only the interdisciplinary field of bioethics but also that of animal studies. More generally, the animal-industrial complex (Twine Journal for Critical Animal Studies 10(1):12-39, 2012) is underlined as a highly relevant bioethical object that deserves more conceptual and empirical attention.     

On the ‘transmission sense of information’

In order to illuminate the role of information in biology, Bergstrom and Rosvall (Biol Philos 26:159–176, 2011a; Biol Philos 26:195–200, 2011b) propose a ‘transmission sense of information’ which builds on Shannon’s theory. At the core of the transmission sense is an appeal to the reduction in uncertainty in receivers and to etiological function. I explore several ways of cashing out uncertainty reduction as well as the consequences of appealing to function.     

Mitochondrial complex I inhibitors, acetogenins, induce HepG2 cell death through the induction of the complete apoptotic mitochondrial pathway

The development of new anti-neoplastic drugs is a key issue for cancer chemotherapy due to the reality that, most likely, certain cancer cells are resistant to current chemotherapy. The past two decades have witnessed tremendous advances in our understanding of the pathogenesis of cancer. These advances have allowed identification new targets as oncogenes, tumor supressor genes and the possible implication of the mitochondria (Fulda et al. Nat Rev Drug Discov 9:447–464, 2010). Annonaceous Acetogenins (ACGs) have been described as the most potent inhibitors of the respiratory chain because of their interaction with mitochondrial Complex I (Degli Esposti and Ghelli Biochim Biophys Acta 1187:116–120, 1994; Zafra-Polo et al. Phytochemistry 42:253–271, 1996; Miyoshi et al. Biochim Biophys Acta 1365:443–452, 1998; Tormo et al. Arch Biochem Biophys 369:119–126, 1999; Motoyama et al. Bioorg Med Chem Lett 12:2089–2092, 2002). To explore a possible application of natural products from Annonaceous plants to cancer treatment, we have selected four bis-tetrahydrofuranic ACGs, three from Annona cherimolia (cherimolin-1, motrilin and laherradurin) and one from Rollinia mucosa (rollinianstatin-1) in order to fully describe their mechanisms responsible within the cell (Fig. 1). In this study, using a hepato-carcinoma cell line (HepG2) as a model, we showed that the bis-THF ACGs caused cell death through the induction of the apoptotic mitochondrial pathway. Their potency and behavior were compared with the classical mitochondrial respiratory chain Complex I inhibitor rotenone in every apoptotic pathway step.

A radically non-morphemic approach to bidirectional syncretism

This paper addresses the question of how certain kinds of overlapping syncretisms in inflectional paradigms can be accounted for that Baerman et al. (Language 80:807–824, 2005) refer to as convergent/divergent bidirectional syncretisms (based on earlier work by Stump, Inflectional morphology, 2001). Bidirectional syncretism strongly resists accounts in terms of standard rules of exponence (or similar devices) that correlate inflection markers with (often underspecified) morpho-syntactic specifications (such rules are used in many morphological theories; e.g., Anderson, A-morphous morphology, 1992; Halle and Marantz in The view from building, pp. 111–176, 1993; Aronoff, Morphology by itself, 1994; Wunderlich in Yearbook of morphology 1995, pp. 93–114, 1996; and Stump, Inflectional morphology, 2001). The reason is that it is difficult to capture overlapping distributions by natural classes. In view of this, rules of referral have been proposed to derive bidirectional syncretism (Stump, Inflectional morphology, 2001; Baerman et al. (Language 80:807–824, 2005)). In contrast, I would like to pursue the hypothesis that systematic instances of overlapping syncretism ultimately motivate a new approach to inflectional morphology—one that fully dispenses with the assumption that morphological exponents are paired with morpho-syntactic feature specifications (and that therefore qualifies as radically non-morphemic): First, rules of exponence are replaced with feature co-occurrence restrictions (FCRs; Gazdar et al., Generalized Phrase Structure Grammar, 1985). For phonologically determined natural classes of exponents, FCRs state incompatibilites with morpho-syntactic feature specifications. Second, marker competition is resolved by a principle of Phonology-driven Marker Selection (PMS). PMS takes over the role of the Specificity (Blocking, Elsewhere, Panini) Principle of standard analyses. Empirically, the main focus is on Bonan declension; the analysis is subsequently extended to Gujarati conjugation and Latin o-declension, with further remarks on bidirectional syncretism in other inflectional paradigms.     

The Effects of Sweep Numbers Per Average and Protocol Type on the Accuracy of the P300-Based Concealed Information Test

In the first of two experiments, we compared the accuracy of the P300 concealed information test protocol as a function of numbers of trials experienced by subjects and ERP averages analyzed by investigators. Contrary to Farwell et al. (Cogn Neurodyn 6(2):115–154, 2012), we found no evidence that 100 trial based averages are more accurate than 66 or 33 trial based averages (all numbers led to accuracies of 84–94 %). There was actually a trend favoring the lowest trial numbers. The second study compared numbers of irrelevant stimuli recalled and recognized in the 3-stimulus protocol versus the complex trial protocol (Rosenfeld in Memory detection: theory and application of the concealed information test, Cambridge University Press, New York, pp 63–89, 2011). Again, in contrast to expectations from Farwell et al. (Cogn Neurodyn 6(2):115–154, 2012), there were no differences between protocols, although there were more irrelevant stimuli recognized than recalled, and irrelevant 4-digit number group stimuli were neither recalled nor recognized as well as irrelevant city name stimuli. We therefore conclude that stimulus processing in the P300-based complex trial protocol—with no more than 33 sweep averages—is adequate to allow accurate detection of concealed information.     

The (Paleo)Geography of Evolution: Making Sense of Changing Biology and Changing Continents

During the voyage of the H.M.S. Beagle, Charles Darwin quickly realized that geographic isolation led to significant changes in the adaptation of local flora and fauna (Darwin 1859). Genetic isolation is one of the well-known mechanisms by which adaptation (allopatric speciation) can occur (Palumbi, Annu Rev Ecol Syst 25:547?C72, 1994; Ricklefs, J Avian Biol 33:207?C11, 2002; Burns et al., Evolution 56:1240?C52, 2002; Hendry et al., Science 290:516?C8, 2009). Evolutionary changes can also occur when landmasses converge or are ??bridged.?? An important and relatively recent (Pliocene Epoch) example known as the ??Great American Biotic Interchange?? allowed for the migration of previously isolated species into new ecological niches between North and South America (Webb 1985, Ann Mo Bot Gard 93:245?C57, 2006; Kirby and MacFadden, Palaeogeogr Palaeoclimatol Palaeoecol 228:193?C202, 2005). Geographic isolation (vicariance) or geographic merging (geodispersal) can occur for a variety of reasons (sea level rise, splitting of continents, mountain building). In addition, the growth of a large supercontinent (or breakup) may change the climatic zonation on the globe and form a different type of barrier for species migration. This short review paper focuses on changing paleogeography throughout the Phanerozoic and the close ties between paleogeography and the evolutionary history of life on Earth.     

A model of direction selectivity in the starburst amacrine cell network

Displaced starburst amacrine cells (SACs) are retinal interneurons that exhibit GABA _A receptor-mediated and Cl ^? cotransporter-mediated, directionally selective (DS) light responses in the rabbit retina. They depolarize to stimuli that move centrifugally through the receptive field surround and hyperpolarize to stimuli that move centripetally through the surround (Gavrikov et al, PNAS 100(26):16047–16052, 2003, PNAS 103(49):18793–18798, 2006). They also play a key role in the activity of DS ganglion cells (DS GC; Amthor et al, Vis Neurosci 19:495–509 2002; Euler et al, Nature 418:845–852, 2002; Fried et al, Nature 420:411– 414, 2002; Gavrikov et al, PNAS 100(26):16047–16052, 2003, PNAS 103(49):18793–18798, 2006; Lee and Zhou, Neuron 51:787–799 2006; Yoshida et al, Neuron 30:771–780, 2001). In this paper we present a model of strong DS behavior of SACs which relies on the GABA-mediated communication within a tightly interconnected network of these cells and on the glutamate signal that the SACs receive from bipolar cells (a presynaptic cell that receives input from cones). We describe how a moving light stimulus can produce a large, sustained depolarization of the SAC dendritic tips that point in the direction that the stimulus moves (i.e., centrifugal motion), but produce a minimal depolarization of the dendritic tips that point in the opposite direction (i.e., centripetal motion). This DS behavior, which is quantified based on the relative size and duration of the depolarizations evoked by stimulus motion at dendritic tips pointing in opposite directions, is robust to changes of many different parameter values and consistent with experimental data. In addition, the DS behavior is strengthened under the assumptions that the Cl^? cotransporters Na^?+?-K^?+?-Cl^?? and K^?+?-Cl^?? are located in different regions of the SAC dendritic tree (Gavrikov et al, PNAS 103(49):18793–18798, 2006) and that GABA evokes a long-lasting response (Gavrikov et al, PNAS 100(26):16047–16052, 2003, PNAS 103(49):18793–18798, 2006; Lee and Zhou, Neuron 51:787–799, 2006). A possible mechanism is discussed based on the generation of waves of local glutamate and GABA secretion, and their postsynaptic interplay as the waves travel between cell compartments.     

Neural Crest and Olfactory System: New Prospective

Sensory neurons in vertebrates are derived from two embryonic transient cell sources: neural crest (NC) and ectodermal placodes. The placodes are thickenings of ectodermal tissue that are responsible for the formation of cranial ganglia as well as complex sensory organs that include the lens, inner ear, and olfactory epithelium. The NC cells have been indicated to arise at the edges of the neural plate/dorsal neural tube, from both the neural plate and the epidermis in response to reciprocal interactions Moury and Jacobson (Dev Biol 141:243?C253, 1990). NC cells migrate throughout the organism and give rise to a multitude of cell types that include melanocytes, cartilage and connective tissue of the head, components of the cranial nerves, the dorsal root ganglia, and Schwann cells. The embryonic definition of these two transient populations and their relative contribution to the formation of sensory organs has been investigated and debated for several decades (Basch and Bronner-Fraser, Adv Exp Med Biol 589:24?C31, 2006; Basch et al., Nature 441:218?C222, 2006) review (Baker and Bronner-Fraser, Dev Biol 232:1?C61, 2001). Historically, all placodes have been described as exclusively derived from non-neural ectodermal progenitors. Recent genetic fate-mapping studies suggested a NC contribution to the olfactory placodes (OP) as well as the otic (auditory) placodes in rodents (Murdoch and Roskams, J Neurosci Off J Soc Neurosci 28:4271?C4282, 2008; Murdoch et al., J Neurosci 30:9523?C9532, 2010; Forni et al., J Neurosci Off J Soc Neurosci 31:6915?C6927, 2011b; Freyer et al., Development 138:5403?C5414, 2011; Katoh et al., Mol Brain 4:34, 2011). This review analyzes and discusses some recent developmental studies on the OP, placodal derivatives, and olfactory system.     

Constructions and headedness in derivation and compounding

The ??traditional?? distinction of compounds into endocentric (Eng. doorknob) and exocentric (pickpocket) is based on the presence or absence of a head constituent (Bloomfield, Language, Holt, New York, 1933); since the early eighties, the syntactic notion of ??head?? has been extended also to derivation, claiming that English derivational suffixes, as e.g. -ness, are heads, either in an absolute sense or in a categorial sense (see Williams Linguist Inq 12:245?C274, 1981; Lieber On the organization of the lexicon, Indiana university Linguistics Club, Bloomington, 1981; Lieber, in Yearbook of morphology 1989, Foris, Dordrecht, 1989; among others). In this paper, we shall first review some key issues in the morphological notion of head, illustrating well-known problematic cases, and then we shall discuss the Construction Morphology approach to headedness in derivation and compounding (Booij in The Oxford handbook of compounding, Oxford University Press, Oxford, 2009; Booij, in Cross-disciplinary issues in compounding, John Benjamins, Amsterdam, 2010a, 2010 Booij, Construction morphology, Oxford University Press, Oxford, 2010b). The stipulation of a hierarchical lexicon with subschemas expressing intermediate generalizations is a powerful theoretical device in accounting for a phenomenon as headedness variation, as we shall show with a Vietnamese case study; also, inconsistencies in word-class assignment in derivation will be dealt with in a constructionist perspective. Moreover, we shall discuss the consequences of a constructionist approach to the distinction between compounding and derivation.     

Feature extraction from spike trains with Bayesian binning: ‘Latency is where the signal starts’

The peristimulus time histogram (PSTH) and its more continuous cousin, the spike density function (SDF) are staples in the analytic toolkit of neurophysiologists. The former is usually obtained by binning spike trains, whereas the standard method for the latter is smoothing with a Gaussian kernel. Selection of a bin width or a kernel size is often done in an relatively arbitrary fashion, even though there have been recent attempts to remedy this situation (DiMatteo et al., Biometrika 88(4):1055–1071, 2001; Shimazaki and Shinomoto 2007a, Neural Comput 19(6):1503–1527, 2007b, c; Cunningham et al. 2008). We develop an exact Bayesian, generative model approach to estimating PSTHs. Advantages of our scheme include automatic complexity control and error bars on its predictions. We show how to perform feature extraction on spike trains in a principled way, exemplified through latency and firing rate posterior distribution evaluations on repeated and single trial data. We also demonstrate using both simulated and real neuronal data that our approach provides a more accurate estimates of the PSTH and the latency than current competing methods. We employ the posterior distributions for an information theoretic analysis of the neural code comprised of latency and firing rate of neurons in high-level visual area STSa. A software implementation of our method is available at the machine learning open source software repository (www.mloss.org, project ‘binsdfc’).