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.     

Membrane guanylate cyclase is a beautiful signal transduction machine: overview

This article is a sequel to the four earlier comprehensive reviews which covered the field of membrane guanylate cyclase from its origin to the year 2002 (Sharma in Mol Cell Biochem 230:3–30, 2002) and then to the year 2004 (Duda et al. in Peptides 26:969–984, 2005); and of the Ca²⁺-modulated membrane guanylate cyclase to the year 1997 (Pugh et al. in Biosci Rep 17:429–473, 1997) and then to 2004 (Sharma et al. in Curr Top Biochem Res 6:111–144, 2004). This article contains three parts. The first part is “Historical”; it is brief, general, and freely borrowed from the earlier reviews, covering the field from its origin to the year 2004 (Sharma in Mol Cell Biochem, 230:3–30, 2002; Duda et al. in Peptides 26:969–984, 2005). The second part focuses on the “Ca²⁺-modulated ROS-GC membrane guanylate cyclase subfamily”. It is divided into two sections. Section “Historical” and covers the area from its inception to the year 2004. It is also freely borrowed from an earlier review (Sharma et al. in Curr Top Biochem Res 6:111–144, 2004). Section “Ca²⁺-modulated ROS-GC membrane guanylate cyclase subfamily” covers the area from the year 2004 to May 2009. The objective is to focus on the chronological development, recognize major contributions of the original investigators, correct misplaced facts, and project on the future trend of the field of mammalian membrane guanylate cyclase. The third portion covers the present status and concludes with future directions in the field.     

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.     

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).     

Two ants (Insecta: Hymenoptera: Formicidae: Formicinae) from the Late Pliocene of Willershausen, Germany, with a nomenclatural note on the genus Camponotites

Two species of the genus Camponotites (Formicidae, Formicinae) are described from the Late Pliocene deposits of Willershausen, Lower Saxony, northern Germany: C. silvestris Steinbach, 1967, and C. steinbachi n. sp. The generic name Camponotites has been established for fossil (Tertiary) ants independently by Steinbach (Bericht der Naturhistorischen Gesellschaft zu Hannover 111:95–102, 1967) and by Dlussky (Trudy paleontologi?eskogo instituta, akademiâ nauk SSSR, 1981), each for materials of different stratigraphical and geographical origin. Though poorly described, Camponotites Steinbach, 1967, and the single included (type) species C. silvestris Steinbach, 1967 (a monotypic species from the Late Pliocene of Willershausen), were based upon indication in the sense of the ICZN. Therefore, both the generic and specific names are valid and available. Camponotites Dlussky, 1981 (and its type species C. macropterus Dlussky, 1981) were certainly introduced correctly and are therefore available, too; but due to its homonymy the generic name is not valid. The revision shows that in this rare case both generic names are not only homonyms but also synonyms.     

Taxonomic review of Kyphosus (Pisces: Kyphosidae) in the Atlantic and Eastern Pacific Oceans

The taxonomy of the Atlantic and Eastern Pacific species of Kyphosus is reviewed with K. bosquii (Lacepède 1802), K. incisor (Cuvier 1831), K. analogus (Gill 1862) and K. elegans (Peters 1869) considered valid, and K. atlanticus sp. nov. newly described. Kyphosus bosquii and K. atlanticus are both characterized by 12 dorsal- and 11 anal-fin soft rays, but differ in the number of longitudinal scale rows along the midbody (61–66, mode 63 vs. 50–56, mode 54). Kyphosus incisor and K. analogus, characterized by 14 dorsal- and 13 anal-fin soft rays, similarly differ from each other in midbody longitudinal scale row counts (57–64, mode 60 vs. 68–74, mode 70 or 72). Kyphosus elegans is characterized by 13 dorsal- and 12 anal-fin soft rays, and 51–57 midbody longitudinal scale rows. Kyphosus bosquii, K. atlanticus and K. incisor are distributed in the Atlantic Ocean, K. analogus and K. elegans occurring in the Eastern Pacific. The holotype of Pimelepterus flavolineatus Poey 1866, here regarded as a junior synonym of K. incisor, was located within a collection of Cuban fishes donated to the Smithsonian Institution by Poey in 1873. A neotype is designated here for K. analogus. Pimelepterus gallveii Cunningham 1910, Kyphosus palpebrosus Miranda-Ribeiro 1919 and K. metzelaari Jordan and Evermann 1927 are recognized as junior synonyms of K. bosquii. Pimelepterus sandwicensis Sauvage 1880 is a junior synonym of K. elegans. Perca saltatrix Linnaeus 1758, together with the replacement name Perca sectatrix Linnaeus 1766, is regarded as nomina dubia.     

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 Macamide N-3-Methoxybenzyl-Linoleamide Is a Time-Dependent Fatty Acid Amide Hydrolase (FAAH) Inhibitor

The Peruvian plant Lepidium meyenii (Maca) has been shown to possess neuroprotective activity both in vitro and in vivo [1–3]. Previous studies have also demonstrated the activity of the pentane extract and its macamides, the most representative lipophilic constituents of Maca, in the endocannabinoid system as fatty acid amide hydrolase (FAAH) inhibitors. One of the most active macamides, N-3-methoxybenzyl-linoleamide [4, 5], was studied to determine its mechanism of interaction with FAAH and whether it has inhibitory activity on mono-acyl glycerol lipase (MAGL), the second enzyme responsible for endocannabinoid degradation [6]. Macamide concentrations from 1 to 100 μM were tested using FAAH and MAGL inhibitor assay methods and showed no effect on MAGL. Tests with other conditions were performed in order to characterize the inhibitory mechanism of FAAH inhibition. N-3-methoxybenzyl-linoleamide displayed significant time-dependent and dose-dependent FAAH inhibitory activity. The mechanism of inhibition was most likely irreversible or slowly reversible. These results suggest the potential application of macamides isolated from Maca as FAAH inhibitors, as they might act on the central nervous system to provide analgesic, anti-inflammatory, or neuroprotective effects, by modulating the release of neurotransmitters.     

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.

ORIUM: Optimized RDC-based Iterative and Unified Model-free analysis

Residual dipolar couplings (RDCs) are NMR parameters that provide both structural and dynamic information concerning inter-nuclear vectors, such as N–H^N and Cα–Hα bonds within the protein backbone. Two approaches for extracting this information from RDCs are the model free analysis (MFA) (Meiler et al. in J Am Chem Soc 123:6098–6107, 2001; Peti et al. in J Am Chem Soc 124:5822–5833, 2002) and the direct interpretation of dipolar couplings (DIDCs) (Tolman in J Am Chem Soc 124:12020–12030, 2002). Both methods have been incorporated into iterative schemes, namely the self-consistent RDC based MFA (SCRM) (Lakomek et al. in J Biomol NMR 41:139–155, 2008) and iterative DIDC (Yao et al. in J Phys Chem B 112:6045–6056, 2008), with the goal of removing the influence of structural noise in the MFA and DIDC formulations. Here, we report a new iterative procedure entitled Optimized RDC-based Iterative and Unified Model-free analysis (ORIUM). ORIUM unifies theoretical concepts developed in the MFA, SCRM, and DIDC methods to construct a computationally less demanding approach to determine these structural and dynamic parameters. In all schemes, dynamic averaging reduces the actual magnitude of the alignment tensors complicating the determination of the absolute values for the generalized order parameters. To readdress this scaling issue that has been previously investigated (Lakomek et al. in J Biomol NMR 41:139–155, 2008; Salmon et al. in Angew Chem Int Edit 48:4154–4157, 2009), a new method is presented using only RDC data to establish a lower bound on protein motion, bypassing the requirement of Lipari–Szabo order parameters. ORIUM and the new scaling procedure are applied to the proteins ubiquitin and the third immunoglobulin domain of protein G (GB3). Our results indicate good agreement with the SCRM and iterative DIDC approaches and signify the general applicability of ORIUM and the proposed scaling for the extraction of inter-nuclear vector structural and dynamic content.     

Plant biotechnology for food security and bioeconomy

This year is a special year for plant biotechnology. It was 30 years ago, on January 18 1983, one of the most important dates in the history of plant biotechnology, that three independent groups described Agrobacterium tumefaciens—mediated genetic transformation at the Miami Winter Symposium, leading to the production of normal, fertile transgenic plants (Bevan et al. in Nature 304:184–187, 1983; Fraley et al. in Proc Natl Acad Sci USA 80:4803–4807, 1983; Herrera-Estrella et al. in EMBO J 2:987–995, 1983; Vasil in Plant Cell Rep 27:1432–1440, 2008). Since then, plant biotechnology has rapidly advanced into a useful and valuable tool and has made a significant impact on crop production, development of a biotech industry and the bio-based economy worldwide.     

Optimized dendritic cell-based immunotherapy for melanoma: the TriMix-formula

Since decades, the main goal of tumor immunologists has been to increase the capacity of the immune system to mediate tumor regression. In this regard, one of the major focuses of cancer immunotherapy has been the design of vaccines promoting strong tumor-specific cytotoxic T lymphocyte responses in cancer patients. Here, dendritic cells (DCs) play a pivotal role as they are regarded as nature’s adjuvant and as such have become the natural agents for antigen delivery in order to finally elicit strong T cell responses (Villadangos and Schnorrer in Nat Rev Immunol 7:543–555, 2007; Melief in Immunity 29:372–383, 2008; Palucka and Banchereau in Nat Rev Cancer 12:265–277, 2012; Vacchelli et al. in Oncoimmunology 2:e25771, 2013; Galluzzi et al. in Oncoimmunology 1:1111–1134, 2012). Therefore, many investigators are actively pursuing the use of DCs as an efficient way of inducing anticancer immune responses. Nowadays, DCs can be generated at a large scale in closed systems, yielding sufficient numbers of cells for clinical application. In addition, with the identification of tumor-associated antigens, which are either selectively or preferentially expressed by tumors, a whole range of strategies using DCs for immunotherapy have been designed and tested in clinical studies. Despite the evidence that DCs loaded with tumor-associated antigens can elicit immune responses in vivo, clinical responses remained disappointingly low. Therefore, optimization of the cellular product and route of administration was urgently needed. Here, we review the path we have followed in the development of TriMixDC-MEL, a potent DC-based cellular therapy, discussing its development as well as further modifications and applications.     

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.     

Manufacturing of peptides exhibiting biological activity

Numerous studies have shown that food proteins may be a source of bioactive peptides. Those peptides are encrypted in the protein sequence. They stay inactive within the parental protein until release by proteolytic enzymes (Mine and Kovacs-Nolan in Worlds Poult Sci J 62(1):87–95, 2006; Hartman and Miesel in Curr Opin Biotechnol 18:163–169, 2007). Once released the bioactive peptides exhibit several biofunctionalities and may serve therapeutic roles in body systems. Opioid peptides, peptides lowering high blood pressure, inhibiting platelet aggregation as well as being carriers of metal ions and peptides with immunostimulatory, antimicrobial and antioxidant activities have been described (Hartman and Miesel in Curr Opin Biotechnol 18:163–169, 2007). The biofunctional abilities of the peptides have therefore aroused a lot of scientific, technological and consumer interest with respect to the role of dietary proteins in controlling and influencing health (Möller et al. in Eur J Nutr 47(4):171–182, 2008). Biopeptides may find wide application in food production, the cosmetics industry as well as in the prevention and treatment of various medical conditions. They are manufactured by chemical and biotechnological methods (Marx in Chem Eng News 83(11):17–24. 2005; Hancock and Sahl in Nat Biotechnol 24(12):1551–1557, 2006). Depending on specific needs (food or pharmaceutical industry) different degrees of peptide purifications are required. This paper discusses the practicability of manufacturing bioactive peptides, especially from food proteins.     

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’).     

Comment on: “root orientation can affect detection accuracy of ground-penetrating radar”

Introduction

In a recent paper, Tanikawa et al. Plant Soil 373:317–327, (2013) reported a considerable impact of root orientation on the accuracy of root detection and root diameter estimation by ground-penetrating radar (GPR).

Methods

In Tanikawa et al. Plant Soil 373:317–327, (2013), buried root samples in a sand box were scanned from multiple cross angles between root orientation and GPR transecting line under controlled conditions. Changes in radar waveform parameter of roots to different cross angles were investigated.

Results

Tanikawa et al. Plant Soil 373:317–327, (2013) clarified that 1) the variation in amplitude area (a signal strength related waveform parameter) to different cross angles fitted a sinusoidal waveform; and 2) the impact of root orientation on root diameter estimation by GPR could be mathematically corrected by applying a grid transect survey. However, we found that the quantitative relationship established in Tanikawa et al. Plant Soil 373:317–327, (2013) between amplitude area and cross angle was incorrect, and the application of a grid transect survey still underestimated root diameter.

Conclusion

The change in amplitude area to cross angle between transecting line and root orientation fits a sinusoidal waveform but different to that reported in Tanikawa et al. Plant Soil 373:317–327, (2013). The polarization of GPR wave may explain such sinusoidal variation in amplitude area to cross angle. The effect of root orientation on GPR-based root diameter estimation remains to be calibrated.     

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.     

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.