Computational validity: using computation to translate behaviours across species

We propose a new conceptual framework (computational validity) for translation across species and populations based on the computational similarity between the information processing underlying parallel tasks. Translating between species depends not on the superficial similarity of the tasks presented, but rather on the computational similarity of the strategies and mechanisms that underlie those behaviours. Computational validity goes beyond construct validity by directly addressing questions of information processing. Computational validity interacts with circuit validity as computation depends on circuits, but similar computations could be accomplished by different circuits. Because different individuals may use different computations to accomplish a given task, computational validity suggests that behaviour should be understood through the subject's point of view; thus, behaviour should be characterized on an individual level rather than a task level. Tasks can constrain the computational algorithms available to a subject and the observed subtleties of that behaviour can provide information about the computations used by each individual. Computational validity has especially high relevance for the study of psychiatric disorders, given the new views of psychiatry as identifying and mediating information processing dysfunctions that may show high inter-individual variability, as well as for animal models investigating aspects of human psychiatric disorders. This article is part of the theme issue ‘Systems neuroscience through the lens of evolutionary theory’.

The Name of Grim: Tracing the Character of Grim the Collier in Sixteenth- and Seventeenth-Century English Theatre

Grim the Collier is a curious comic character who receives little critical attention. Grim appears in three key plays, sixteenth- and seventeenth-century pamphlets, herbals, and ballad culture. This article examines, and rejects, Grim as a potentially useful figure for environmental awareness. I dispel legends about the basis of this character, and examine how the labile significance of the name ‘Grim’ implicates it in networks of superficial similarity between devils, colliers, and racialized black skin. These networks link to the proverb that underlies most early modern depictions of Grim: ‘like will to like quoth the devil to the collier’.

Taxonomic revision of the Savanna Nightjar (Caprimulgus affinis) complex based on vocalizations reveals three species

Background The Savanna Nightjar (Caprimulgus affinis) is a widespread, polytypic species which was previously treated as two or three species. It is currently treated as a single species based on superficial similarity of their songs but no detailed comparisons of the songs in this complex have been made. Methods A total of 15 acoustic variables were measured for the songs of 86 individuals representing 8 of the 10 subspecies in the complex. Results Three major groups can be distinguished based on univariate and multivariate analyses: a northern group consisting of the subspecies C. a. monticolus, C. a. amoyensis and C. a. stictomus; a southern group consisting of C. a. affinis, C. a. kasuidori, C. a. timorensis and C. a. propinquus; and a third group in the Philippines consisting of C. a. griseatus. Conclusions It is here argued that these groups are best treated as species, and that Franklin’s Nightjar (C. monticolus) and Kayumanggi Nightjar (C. griseatus) are reinstated as separate species.

Functional ecological convergence between the thylacine and small prey-focused canids

Background Morphological convergence is a fundamental aspect of evolution, allowing for inference of the biology and ecology of extinct species by comparison with the form and function of living species as analogues. The thylacine (Thylacinus cynocephalus), the iconic recently extinct marsupial, is considered a classic example of convergent evolution with the distantly related placental wolf or dog, though almost nothing is actually known regarding its ecology. This lack of data leads to questions regarding the degree of convergence with, and the similarity of, the functional ecology of the thylacine and the wolf/dog. Here, we examined the cranium of the thylacine using 3D geometric morphometrics and two quantitative tests of convergence to more precisely determine convergent analogues, within a phylogenetically informed dataset of 56 comparative species across 12 families of marsupial and placental faunivorous mammals. Using this dataset, we investigated patterns of correlation between cranial shape and diet, phylogeny, and relative prey size across these terrestrial faunivores. Results We find a correlation between cranial, facial, and neurocranial shape and the ratio of prey-to-predator body mass, though neurocranial shape may not correlate with prey size within marsupials. The thylacine was found to group with predators that routinely take prey smaller than 45% of their own body mass, not with predators that take subequal-sized or larger prey. Both convergence tests find significant levels of convergence between the thylacine and the African jackals and South American ‘foxes’, with lesser support for the coyote and red fox. We find little support for convergence between the thylacine and the wolf or dog. Conclusions Our study finds little support for a wolf/dog-like functional ecology in the thylacine, with it instead being most similar to mid-sized canids such as African jackals and South American ‘foxes’ that mainly take prey less than half their size. This work suggests that concepts of convergence should extend beyond superficial similarity, and broader comparisons can lead to false interpretations of functional ecology. The thylacine was a predator of small to mid-sized prey, not a big-game specialist like the placental wolf.

The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis

The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on earth and is metabolized by bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolises SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden-Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase and sulfofructose-1-phosphate (SFP) aldolase. Our data shows that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by 3D structures of each enzyme, which reveal the presence of conserved sulfonate-binding pockets. We show that SQ isomerase acts preferentially on the β-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a transcriptional regulator for the transcriptional repressor CsqR that regulates SQ-utilization. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex modulation by the metabolites AMP, ADP, ATP, F6P, FBP, PEP, and citrate, and we show that SFP aldolase reversibly synthesizes SFP. This body of work provides fresh insights into the mechanism, specificity and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.

British Project in Palestine: Colonial “National Home”

Mandatory Palestine proved to be a unique example of an attempt to create a “national home” within the framework of the colonial system. The present article aims to analyse the combination of the national and the colonial in the implementation of the “home for the Jewish people” in Palestine, as well as the role of cultural-religious narratives in the mindset of both the British administrators and the Zionist settlers. The research is based on British official documents and archive materials, as well as on the memoirs of Jewish settlers in Eretz Yisrael, some of which are introduced into the Russian academic circulation for the first time. Many British politicians viewed the return of the Jews to their historical homeland as a specific noble mission, which fit both into the framework of “Christian Zionism” and the notion of the civilizing nature of imperial colonialism. Palestine, along with its religious and cultural significance, was at the same time playing a thoroughly practical strategic role, and in that sense served as a highly convenient “foothold”. The British politicians and administrators perceived the Zionists as loyal agents of European colonial influence in the Middle East region. Based on the conducted research, the author reached the following conclusions. Even before ethnic confrontation in mandate Palestine intensified, some representatives of the British Empire anticipated that the Jews would not be a loyal minority, always ready to act in the Empire’s interests to the full extent. The main finding of the research is that despite the superficial similarity between the outlooks of the European Zionists and the official representatives of the British Empire, their perceptions of Palestine and their aims and purposes there were fundamentally different. On the one hand, the notions of the leaders of the Zionist movement about Eretz Yisrael were indeed in many respects close to the positions of British politicians and administrators. Jewish nationalism emerged under the influence of European ideas and concepts, and even orientalism influenced it to a certain degree. On the other hand, the Zionists perceived the Europeans as situational allies, therefore their interests coincided only in the short-term perspective. The idea of the national revival of the people of Israel in its historical homeland played a key role for them. This laid the foundation of the new Jewish identity, which also included multiple elements of religious traditions and legal bases of Judaism.

The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis

The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on earth and is metabolized bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolises SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden-Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase and sulfofructose-1-phosphate aldolase. Our data shows that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by 3D structures of each of these enzymes, which reveal the presence of conserved sulfonate-binding pockets. We show that SQ isomerase acts preferentially on the b-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a transcriptional regulator for the transcriptional repressor CsqR that regulates SQ-utilisation. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex allosteric modulation by the metabolites AMP, ADP, ATP, F6P, FBP, PEP, and citrate. This body of work provides fresh insights into the mechanism, specificity and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.

The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis

The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on earth and is metabolized bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolises SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden-Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase and sulfofructose-1-phosphate aldolase. Our data shows that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by 3D structures of each of these enzymes, which reveal the presence of conserved sulfonate-binding pockets. We show that SQ isomerase acts preferentially on the b-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a transcriptional regulator for the transcriptional repressor CsqR that regulates SQ-utilisation. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex allosteric modulation by the metabolites AMP, ADP, ATP, F6P, FBP, PEP, and citrate. This body of work provides fresh insights into the mechanism, specificity and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.

The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis

The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on earth and is metabolized bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolises SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden-Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase and sulfofructose-1-phosphate aldolase. Our data shows that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by 3D structures of each of these enzymes, which reveal the presence of conserved sulfonate-binding pockets. We show that SQ isomerase acts preferentially on the b-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a transcriptional regulator for the transcriptional repressor CsqR that regulates SQ-utilisation. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex allosteric modulation by the metabolites AMP, ADP, ATP, F6P, FBP, PEP, and citrate. This body of work provides fresh insights into the mechanism, specificity and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.

Regularity ≠ symmetry: A comment on Makin, Rahman, and Bertamini (2020)

Previous studies have shown that the perceived duration of symmetrical visual patterns is longer than that of asymmetrical ones. In a different context, regular visual stimuli have been found to be judged as lasting longer than irregular ones. A recent replication study reported that the effect of symmetry on time perception might not be robust; however, the study jumbled the effects of regularity and symmetry. The stimuli used in our previous study on the effect of regularity were qualitatively and quantitatively different from those used in the study addressing symmetry. Moreover, the hypothesized underlying mechanisms involved in the effects of regularity and symmetry were completely different. Taken together, the present commentary claims that combining these findings based on the superficial similarity of these phenomena would lead to flawed scientific discussions.