Inferential explanations in biology

Among philosophers of science, there is now a widespread agreement that the DN model of explanation is poorly equipped to account for explanations in biology. Rather than identifying laws, so the consensus goes, researchers explain biological capacities by constructing a model of the underlying mechanism.We think that the dichotomy between DN explanations and mechanistic explanations is misleading. In this article, we argue that there are cases in which biological capacities are explained without constructing a model of the underlying mechanism. Although these explanations do not conform to Hempel’s DN model (they do not deduce the explanandum from laws of nature), they do invoke more or less stable generalisations. Because they invoke generalisations and have the form of an argument, we call them inferential explanations. We support this claim by considering two examples of explanations of biological capacities: pigeon navigation and photoperiodism. Next, we will argue that these non-mechanistic explanations are crucial to biology in three ways: (i) sometimes, they are the only thing we have (there is no alternative available), (ii) they are heuristically useful, and (iii) they provide genuine understanding and so are interesting in their own right.In the last sections we discuss the relation between types of explanations and types of experiments and situate our views within some relevant debates on explanatory power and explanatory virtues.     

Statistical analysis of sizes and shapes of virus capsids and their resulting elastic properties

From the analysis of sizes of approximately 130 small icosahedral viruses we find that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed capsid proteins having thicknesses between 2 nm and 4 nm. To investigate whether, in addition to the fairly conserved geometry, capsid proteins show similarities in the way they interact with one another, we examined the shapes of the capsids in detail. We classified them numerically according to their similarity to sphere and icosahedron and an interpolating set of shapes in between, all of them obtained from the theory of elasticity of shells. In order to make a unique and straightforward connection between an idealized, numerically calculated shape of an elastic shell and a capsid, we devised a special shape fitting procedure, the outcome of which is the idealized elastic shape fitting the capsid best. Using such a procedure we performed statistical analysis of a series of virus shapes and we found similarities between the capsid elastic properties of even very different viruses. As we explain in the paper, there are both structural and functional reasons for the convergence of protein sizes and capsid elastic properties. Our work presents a specific quantitative scheme to estimate relatedness between different proteins based on the details of the (quaternary) shape they form (capsid). As such, it may provide an information complementary to the one obtained from the studies of other types of protein similarity, such as the overall composition of structural elements, topology of the folded protein backbone, and sequence similarity.     

Diet and habit explain head-shape convergences in natricine snakes

The concept of ecomorphs, whereby species with similar ecologies have similar phenotypes regardless of their phylogenetic relatedness, is often central to discussions regarding the relationship between ecology and phenotype. However, some aspects of the concept have been questioned, and sometimes species have been grouped as ecomorphs based on phenotypic similarity without demonstrating ecological similarity. Within snakes, similar head shapes have convergently evolved in species living in comparable environments and/or with similar diets. Therefore, ecomorphs could exist in some snake lineages, but this assertion has rarely been tested for a wide-ranging group within a single framework. Natricine snakes (Natricinae) are ecomorphologically diverse and currently distributed in Asia, Africa, Europe and north-central America. They are primarily semiaquatic or ground-dwelling terrestrial snakes, but some are aquatic, burrowing or aquatic and burrowing in habit and may be generalist or specialist in diet. Thus, natricines present an interesting system to test whether snakes from different major habit categories represent ecomorphs. We quantify morphological similarity and disparity in head shape among 191 of the ca. 250 currently recognized natricine species and apply phylogenetic comparative methods to test for convergence. Natricine head shape is largely correlated with habit, but in some burrowers is better explained by dietary specialism. Convergence in head shape is especially strong for aquatic burrowing, semiaquatic and terrestrial ecomorphs and less strong for aquatic and burrowing ecomorphs. The ecomorph concept is useful for understanding natricine diversity and evolution, though would benefit from further refinement, especially for aquatic and burrowing taxa.     

Subjecting the theory of the small‐island effect to Ockham’s razor

Species–area curves from islands and other isolates often differ in shape from sample‐area curves generated from mainlands or sections of isolates (or islands), especially at finer scales. We examine two explanations for this difference: (1) the small‐island effect (SIE), which assumes the species–area curve is composed of two distinctly different curve patterns; and (2) a sigmoid or depressed isolate species–area curve with no break‐points (in arithmetic space). We argue that the application of Ockham’s razor – the principle that the simplest, most economical explanation for a hypothesis should be accepted over less parsimonious alternatives – leads to the conclusion that the latter explanation is preferable. We hold that there is no reason to assume the ecological factors or patterns that affect the shapes of isolate (or island) curves cause two distinctly different patterns. This assumption is not required for the alternative, namely that these factors cause a single (though depressed) isolate species–area curve with no break‐points. We conclude that the theory of the small‐island effect, despite its present standing as an accepted general pattern in nature, should be abandoned.     

On quantitative effects of RNA shape abstraction

Over the last few decades, much effort has been taken to develop approaches for identifying good predictions of RNA secondary structure. This is due to the fact that most computational prediction methods based on free energy minimization compute a number of suboptimal foldings and we have to identify the native folding among all these possible secondary structures. Using the abstract shapes approach as introduced by Giegerich et al. (Nucleic Acids Res 32(16):4843–4851, 2004), each class of similar secondary structures is represented by one shape and the native structures can be found among the top shape representatives. In this article, we derive some interesting results answering enumeration problems for abstract shapes and secondary structures of RNA. We compute precise asymptotics for the number of different shape representations of size n and for the number of different shapes showing up when abstracting from secondary structures of size n under a combinatorial point of view. A more realistic model taking primary structures into account remains an open challenge. We give some arguments why the present techniques cannot be applied in this case.     

Perception of shape-from-motion in macaque monkeys and humans

Motion is one of the most efficient cues for shape perception. We conducted behavioral experiments to examine how monkeys perceive shapes defined by motion cues and whether they perceive them as humans do. We trained monkeys to perform a shape discrimination task in which shapes were defined by the motion of random dots. Effects of dot density and dot speed on the shape perception of monkeys were examined. Human subjects were also tested using the same paradigm and the test results were compared with those of monkeys. In both monkeys and humans, correct performance rates declined when density or speed of random dots was reduced. Both of them tended to confuse the same combinations of shapes frequently. These results suggest that monkeys and humans perceive shapes defined by motion cues in a similar manner and probably have common neural mechanisms to perceive them. Electronic Publication     

Vertebral evolution and the diversification of squamate reptiles

Taxonomic, morphological, and functional diversity are often discordant and independent components of diversity. A fundamental and largely unanswered question in evolutionary biology is why some clades diversify primarily in some of these components and not others. Dramatic variation in trunk vertebral numbers (14 to >300) among squamate reptiles coincides with different body shapes, and snake-like body shapes have evolved numerous times. However, whether increased evolutionary rates or numbers of vertebrae underlie body shape and taxonomic diversification is unknown. Using a supertree of squamates including 1375 species, and corresponding vertebral and body shape data, we show that increased rates of evolution in vertebral numbers have coincided with increased rates and disparity in body shape evolution, but not changes in rates of taxonomic diversification. We also show that the evolution of many vertebrae has not spurred or inhibited body shape or taxonomic diversification, suggesting that increased vertebral number is not a key innovation. Our findings demonstrate that lineage attributes such as the relaxation of constraints on vertebral number can facilitate the evolution of novel body shapes, but that different factors are responsible for body shape and taxonomic diversification.     

Changing the Chevreul illusion by a background luminance ramp: lateral inhibition fails at its traditional stronghold--a psychophysical refutation

The Chevreul illusion is a well-known 19^th century brightness illusion, comprising adjacent homogeneous grey bands of different luminance, which are perceived as inhomogeneous. It is generally explained by lateral inhibition, according to which brighter areas projected to the retina inhibit the sensitivity of neighbouring retinal areas. Lateral inhibition has been considered the foundation-stone of early vision for a century, upon which several computational models of brightness perception are built. One of the last strongholds of lateral inhibition is the Chevreul illusion, which is often illustrated even in current textbooks. Here we prove that lateral inhibition is insufficient to explain the Chevreul illusion. For this aim, we placed the Chevreul staircase in a luminance ramp background, which noticeably changed the illusion. In our psychophysical experiments, all 23 observers reported a strong illusion, when the direction of the ramp was identical to that of the staircase, and all reported homogeneous steps (no illusion) when its direction was the opposite. When the background of the staircase was uniform, 14 saw the illusion, and 9 saw no illusion. To see whether the change of the entire background area or that of the staircase boundary edges were more important, we placed another ramp around the staircase, whose direction was opposite to that of the original, larger ramp. The result is that though the inner ramp is rather narrow (mean = 0.51 deg, SD = 0.48 deg, N = 23), it still dominates perception. Since all conditions of the lateral inhibition account were untouched within the staircase, lateral inhibition fails to model these perceptual changes. Area ratios seem insignificant; the role of boundary edges seems crucial. We suggest that long range interactions between boundary edges and areas enclosed by them, such that diffusion-based models describe, provide a much more plausible account for these brightness phenomena, and local models are insufficient.     

Synaptic modifications depend on synapse location and activity: a biophysical model of STDP

In spike-timing-dependent plasticity (STDP) the synapses are potentiated or depressed depending on the temporal order and temporal difference of the pre- and post-synaptic signals. We present a biophysical model of STDP which assumes that not only the timing, but also the shapes of these signals influence the synaptic modifications. The model is based on a Hebbian learning rule which correlates the NMDA synaptic conductance with the post-synaptic signal at synaptic location as the pre- and post-synaptic quantities. As compared to a previous paper [Saudargiene, A., Porr, B., Worgotter, F., 2004. How the shape of pre- and post-synaptic signals can influence stdp: a biophysical model. Neural Comp.], here we show that this rule reproduces the generic STDP weight change curve by using real neuronal input signals and combinations of more than two (pre- and post-synaptic) spikes. We demonstrate that the shape of the STDP curve strongly depends on the shape of the depolarising membrane potentials, which induces learning. As these potentials vary at different locations of the dendritic tree, model predicts that synaptic changes are location dependent. The model is extended to account for the patterns of more than two spikes of the pre- and post-synaptic cells. The results show that STDP weight change curve is also activity dependent.     

Emergent properties of patch shapes affect edge permeability to animals

Animal travel between habitat patches affects populations, communities and ecosystems. There are three levels of organization of edge properties, and each of these can affect animals. At the lowest level are the different habitats on each side of an edge, then there is the edge itself, and finally, at the highest level of organization, is the geometry or structure of the edge. This study used computer simulations to (1) find out whether effects of edge shapes on animal behavior can arise as emergent properties solely due to reactions to edges in general, without the animals reacting to the shapes of the edges, and to (2) generate predictions to allow field and experimental studies to test mechanisms of edge shape response. Individual animals were modeled traveling inside a habitat patch that had different kinds of edge shapes (convex, concave and straight). When animals responded edges of patches, this created an emergent property of responding to the shape of the edge. The response was mostly to absolute width of the shapes, and not the narrowness of them. When animals were attracted to edges, then they tended to collect in convexities and disperse from concavities, and the opposite happened when animals avoided edges. Most of the responses occurred within a distance of 40% of the perceptual range from the tip of the shapes. Predictions were produced for directionality at various locations and combinations of treatments, to be used for testing edge behavior mechanisms. These results suggest that edge shapes tend to either concentrate or disperse animals, simply because the animals are either attracted to or avoid edges, with an effect as great as 3 times the normal density. Thus edge shape could affect processes like pollination, seed predation and dispersal and predator abundance.     

Multivariate patterns in object-selective cortex dissociate perceptual and physical shape similarity

Prior research has identified the lateral occipital complex (LOC) as a critical cortical region for the representation of object shape in humans. However, little is known about the nature of the representations contained in the LOC and their relationship to the perceptual experience of shape. We used human functional MRI to measure the physical, behavioral, and neural similarity between pairs of novel shapes to ask whether the representations of shape contained in subregions of the LOC more closely reflect the physical stimuli themselves, or the perceptual experience of those stimuli. Perceptual similarity measures for each pair of shapes were obtained from a psychophysical same-different task; physical similarity measures were based on stimulus parameters; and neural similarity measures were obtained from multivoxel pattern analysis methods applied to anterior LOC (pFs) and posterior LOC (LO). We found that the pattern of pairwise shape similarities in LO most closely matched physical shape similarities, whereas shape similarities in pFs most closely matched perceptual shape similarities. Further, shape representations were similar across participants in LO but highly variable across participants in pFs. Together, these findings indicate that activation patterns in subregions of object-selective cortex encode objects according to a hierarchy, with stimulus-based representations in posterior regions and subjective and observer-specific representations in anterior regions.     

Introducing the shape of globe as a predisposing factor for glaucoma

Glaucoma is a common blinding disease worldwide with a number of risk factors such as intraocular pressure, myopia, gender, race and hyperopia. Here we introduce eyeball's shape as a predisposing factor for glaucoma. If the eyeball is a sphere, the stress distribution is homogenous. We assume the eyeball as a non sphere. Then, the distribution of stress will not be homogenous. Different individuals have different eyeball's shapes and different patterns of stress distribution in their eyes. So based on the eyeball's shape deviation from a sphere they will have different risks for glaucoma. The eyeball is routinely considered as a sphere, but some evidences show that the globe is not a sphere. Two empirical observations are consistent with the hypothesis. The first is that ethnicity and sex are established risk factors for glaucoma. On the other hand there are several morphological differences in the body structure among individuals. According to these anatomical differences, eye's shape is different among different races and between two sexes. Secondly, there are some conditions such as myopia and hyperopia in them the shape of the globe has been changed. These conditions are risk factors for glaucoma too. Glaucoma screening program for early detection of high risk individuals is very important. Current diagnostic procedures of glaucoma do not take the shape of eyeball into account. We suggest using eyeball's shape for early glaucoma detection. There are three other factors in addition to eyeball's shape, including thickness of the globe's wall, intraocular pressure, and inner radius that should be measured together for each individual and stress load should be calculated in different points of the globe. Then eyes with more stress load in site of injury are more prone for glaucoma. More accurate measurements of the factors which are contributing in stress value for each case, lead us toward better glaucoma screening.     

Lighting, backlighting and watercolor illusions and the laws of figurality

We report some novel 'lighting' and 'backlighting' effects in plane figures similar to those which induce the 'watercolor illusion', that is, figures made with outlines composed of juxtaposed parallel lines varying in brightness and chromatic color. These new effects show 'illumination' as an emergent percept, and show how arrangements of 'dark and light' along the boundaries of various plane figures model the volume and strengthen the illusion of depth. To account for these various effects we propose several phenomenological 'laws of figurality' to add to the Gestalt laws of organization and figure-ground segregation. We offer a set of meta-laws which are speculative but which serve to integrate and organize the phenomenological laws. These laws indicate how luminance gradient profiles across boundary contours define both the 3D appearance of figures and the properties of the light reflected from their volumetric shapes.     

The role of the Gestalt principle of similarity in the watercolor illusion

The watercolor illusion presents two main effects: a long-range assimilative color spreading (coloration effect), and properties imparting a strong figure status (figural effect) to a region delimited by a dark (e.g. purple) contour flanked by a lighter chromatic contour (e.g. orange). In four experiments, the strength of the watercolor illusion to determine figure-ground organization is directly compared (combined or pitted against) with the Gestalt principle of similarity both of color and line width. The results demonstrated that (i) the watercolor illusion and, particularly, its figural effect won over the classical Gestalt factors of similarity; (ii) the watercolor illusion cannot be due to the coloration effect as suggested by the similarity principle; (iii) coloration and figural effects may be independent in the watercolor illusion, and (iv) the watercolor illusion can be considered as a principle of figure-ground segregation on its own. Two parallel and independent processes as proposed within the FACADE model (Grossberg, 1994, 1997) are suggested to account for the two effects of coloration and figural enhancement in the watercolor illusion.     

Involvement of the Extrageniculate System in the Perception of Optical Illusions: A Functional Magnetic Resonance Imaging Study

Research on the neural processing of optical illusions can provide clues for understanding the neural mechanisms underlying visual perception. Previous studies have shown that some visual areas contribute to the perception of optical illusions such as the Kanizsa triangle and Müller-Lyer figure; however, the neural mechanisms underlying the processing of these and other optical illusions have not been clearly identified. Using functional magnetic resonance imaging (fMRI), we determined which brain regions are active during the perception of optical illusions. For our study, we enrolled 18 participants. The illusory optical stimuli consisted of many kana letters, which are Japanese phonograms. During the shape task, participants stated aloud whether they perceived the shapes of two optical illusions as being the same or not. During the word task, participants read aloud the kana letters in the stimuli. A direct comparison between the shape and word tasks showed activation of the right inferior frontal gyrus, left medial frontal gyrus, and right pulvinar. It is well known that there are two visual pathways, the geniculate and extrageniculate systems, which belong to the higher-level and primary visual systems, respectively. The pulvinar belongs to the latter system, and the findings of the present study suggest that the extrageniculate system is involved in the cognitive processing of optical illusions.     

Visual Adaptation to Thin and Fat Bodies Transfers across Identity

Visual perception is highly variable and can be influenced by the surrounding world. Previous research has revealed that body perception can be biased due to adaptation to thin or fat body shapes. The aim of the present study was to show that adaptation to certain body shapes and the resulting perceptual biases transfer across different identities of adaptation and test stimuli. We designed two similar adaptation experiments in which healthy female participants adapted to pictures of either thin or fat bodies and subsequently compared more or less distorted pictures of their own body to their actual body shape. In the first experiment (n = 16) the same identity was used as adaptation and test stimuli (i.e. pictures of the participant’s own body) while in the second experiment (n = 16) we used pictures of unfamiliar thin or fat bodies as adaptation stimuli. We found comparable adaptation effects in both experiments: After adaptation to a thin body, participants rated a thinner than actual body picture to be the most realistic and vice versa. We therefore assume that adaptation to certain body shapes transfers across different identities. These results raise the questions of whether some type of natural adaptation occurs in everyday life. Natural and predominant exposure to certain bodily features like body shape – especially the thin ideal in Western societies – could bias perception for these features. In this regard, further research might shed light on aspects of body dissatisfaction and the development of body image disturbances in terms of eating disorders.     

Revisiting the question of Neandertal regional variability: a view from the Rhône valley corridor

We compared the dental assemblage of the Rh?ne Valley corridor (RVC) with that of European Neandertals dating to MOIS 7-4 using two linear measurements and three indices. To test if the RVC population was significantly different from Western European Neandertals, we preformed a multi-tiered approached. First, we tested for the normality of the variables using a Shapiro-Wilks test. If the variables were normal, a stepwise Discriminant Function Analysis (DFA) (using Mahalanobis distances) was performed for the normally distributed variables. DFA uses correlation metrics to address weight combinations of variables and emphasizes between group variation while minimizing within group variation. Results show that there is no distinction between the RVC population and other Neandertals except for the Crown Module index of the upper canine. However, the presence of a single significant result does not provide evidence for a local RVC variant within the Neandertal population. These results are supported by evidence from archaeological analysis of this region. We propose that the high genetic control for dental size and shape may account for the reduced ability to distinguish between subpopulation groups based on dental dimensions in groups with small effective size such as the Neandertals.     

Rubber hands feel touch, but not in blind individuals

Psychology and neuroscience have a long-standing tradition of studying blind individuals to investigate how visual experience shapes perception of the external world. Here, we study how blind people experience their own body by exposing them to a multisensory body illusion: the somatic rubber hand illusion. In this illusion, healthy blindfolded participants experience that they are touching their own right hand with their left index finger, when in fact they are touching a rubber hand with their left index finger while the experimenter touches their right hand in a synchronized manner (Ehrsson et al. 2005). We compared the strength of this illusion in a group of blind individuals (n = 10), all of whom had experienced severe visual impairment or complete blindness from birth, and a group of age-matched blindfolded sighted participants (n = 12). The illusion was quantified subjectively using questionnaires and behaviorally by asking participants to point to the felt location of the right hand. The results showed that the sighted participants experienced a strong illusion, whereas the blind participants experienced no illusion at all, a difference that was evident in both tests employed. A further experiment testing the participants' basic ability to localize the right hand in space without vision (proprioception) revealed no difference between the two groups. Taken together, these results suggest that blind individuals with impaired visual development have a more veridical percept of self-touch and a less flexible and dynamic representation of their own body in space compared to sighted individuals. We speculate that the multisensory brain systems that re-map somatosensory signals onto external reference frames are less developed in blind individuals and therefore do not allow efficient fusion of tactile and proprioceptive signals from the two upper limbs into a single illusory experience of self-touch as in sighted individuals.     

Judgments of shape similarity in the barbary dove (Streptopelia risoria)

Sixteen experimentally naive adult Barbary doves (S. risoria) learned a successive discrimination between a simple and a complex shape and were then tested for transfer of training in a generalization test with seven unfamiliar shapes. It was found that the degree of equivalence between shapes was correlated with two physical measures of shape based on contour length and on the number of sides of the shape. These results are in general agreement with other comparative data including those for humans. Results of the generalization test showed an ‘asymmetrical’ response in that judgments of shape similarity were not elicited with equal frequency in all subjects. This was interpreted as evidence for an internal standard in that subjects compared test stimuli to the positive training shape.