Oren Kolodny | The Hebrew University of Jerusalem (original) (raw)
Papers by Oren Kolodny
Creativity is a central phenomenon in human life. World-famous scientists and artists are praised... more Creativity is a central phenomenon in human life. World-famous scientists and artists are praised for their creative genius. Schools and universities seek to educate creativity in students and many employers want to hire creative personnel. However, the measurement of creativity is difficult up to the present day. Standard creativity tests typically require human expertise in the evaluation of test responses. This evaluation is often more time-intensive than taking the test itself. Moreover, creativity tests are still regularly conducted in a pen-and-paper format, rendering the data analysis all the more tedious. In this article, we propose a digital game for assessing creativity. It can be hosted online. The data analysis can be automated and conducted in real-time. The test is implemented as a tower defense game ("Immune Defense"). We submit that a video game constitutes a natural setting, as opposed to a formal testing scenario, and provides an opportunity to test real-...
One of the outstanding questions regarding the human gut microbiota is how interventions designed... more One of the outstanding questions regarding the human gut microbiota is how interventions designed to manipulate the microbiota may influence host phenotypic traits. Here, we employed a dietary intervention to probe this question in the context of lactose intolerance. To assess the effects of dairy elimination and reintroduction on the microbiota and host phenotype, we paired fecal 16S rRNA amplicon sequencing with a clinical assay for lactose intolerance, the hydrogen breath test. We studied 12 self-reported mildly lactose intolerant adults, each with tri-weekly collection of fecal samples over a 12-week study period (2 weeks baseline, 4 weeks of dairy elimination, 6 weeks of gradual milk reintroduction) and a hydrogen breath test before and after each phase. We found that although none of the subjects experienced a change in clinically defined status of lactose intolerant or tolerant, most subjects were qualitatively better able to tolerate dairy products with minimal symptoms at t...
Philosophical Transactions of the Royal Society B: Biological Sciences
In the last decade, we have witnessed a major paradigm shift in the life sciences: the recognitio... more In the last decade, we have witnessed a major paradigm shift in the life sciences: the recognition that the microbiome, i.e. the set of microorganisms associated with healthy animals (including humans) and plants, plays a crucial role in the sustained health and fitness of its host. Enabled by rapid advances in sequencing technologies and analytical methods, substantial advances have been achieved in both identifying the microbial taxa and understanding the relationship between microbiome composition and host phenotype. These breakthroughs are leading to novel strategies for improved human and animal health, enhanced crop yield and nutritional quality, and the control of various pests and disease agents. This article is part of the theme issue ‘The role of the microbiome in host evolution'.
Philosophical Transactions of the Royal Society B: Biological Sciences
Host-associated microbiomes influence their host's fitness in myriad ways and can be viewed a... more Host-associated microbiomes influence their host's fitness in myriad ways and can be viewed as a source of phenotypic plasticity. This plasticity may allow the host to accommodate novel environmental challenges and thus influence the host's evolutionary adaptation. As with other modalities of phenotypic plasticity in phenomena such as the Baldwin effect and genetic assimilation, the microbiome-mediated plasticity may influence host genetic adaptation by facilitating and accelerating it, by slowing it down, or even by preventing it. The dynamics involved are likely more complex than those of previously studied phenomena related to phenotypic plasticity, and involve different processes on each time scale, such as acquired recognition of newly associated microbes by the host's immune system on single- and multiple-generation time scales, or selection on transmission dynamics of microbes between hosts, acting on longer time scales. To date, it is unclear if and how any of th...
Open Biology
The course of infection by SARS-CoV-2 frequently includes a long asymptomatic period, followed in... more The course of infection by SARS-CoV-2 frequently includes a long asymptomatic period, followed in some individuals by an immune dysregulation period that may lead to complications and immunopathology-induced death. This course of disease suggests that the virus often evades detection by the innate immune system. We suggest a novel therapeutic approach to mitigate the infection's severity, probability of complications and duration. We propose that priming an individual's innate immune system for viral attack shortly before it is expected to occur may allow pre-activation of the preferable trajectory of immune response, leading to early detection of the virus. Priming can be carried out, for example, by administering a standard vaccine or another reagent that elicits a broad anti-viral innate immune response. By the time that the expected SARS-CoV-2 infection occurs, activation cascades will have been put in motion and levels of immune factors needed to combat the infection wi...
Proceedings of the National Academy of Sciences
Van Vliet & Doebeli (1) (henceforth VVD) present a multi-level selection framework simulating hos... more Van Vliet & Doebeli (1) (henceforth VVD) present a multi-level selection framework simulating host-microbiome evolutionary dynamics. The model explores the conditions under which the association between hosts and their “helper” microbiome – microbes that developed a trait that provides a benefit to the host at a cost to themselves – is strong enough to allow for selection at the holobiont level. The model is an important contribution to the holobiont debate, making the notion quantifiable and highlighting the involved parameters.In the study, VVD conclude that the parameter space in which selection occurs at the level of the holobiont is extremely restricted (Fig 1). Here we show that this result stems from specific model assumptions. Although these assumptions are reasonable as a modeling starting point, slight biologically-reasonable modifications of the assumptions lead to qualitatively different outcomes.
Behavioral and Brain Sciences
Baumard's perspective asserts that “opportunity is the mother of innovation,” in contrast to ... more Baumard's perspective asserts that “opportunity is the mother of innovation,” in contrast to the adage ascribing this role to necessity. Drawing on behavioral ecology and cognition, we propose that both extremes – affluence and scarcity – can drive innovation. We suggest that the types of innovations at these two extremes differ and that both rely on mechanisms operating on different time scales.
Nature Communications
Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to t... more Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated ‘pathogen packages’ could have generated feedback that allowed modern humans to overcome disease burden earlier than Neandert...
ABSTRACTIn the first longitudinal study of bat microbiomes, we find that unlike the pattern descr... more ABSTRACTIn the first longitudinal study of bat microbiomes, we find that unlike the pattern described in humans and other mammals, the prominent dynamics in Egyptian fruit bats’ fur microbiomes are those of change over time at the level of the colony as a whole. Thus, on average, a pair of fur microbiome samples from different individuals in the same colony collected on the same date are more similar to one another than a pair of samples from the same individual collected at different time points. This pattern suggests that the whole colony may be the appropriate biological unit for understanding some of the roles of the host microbiome in social bats’ ecology and evolution. This pattern of synchronized colony changes over time is also reflected in the profile of volatile compounds in the bats’ fur, but differs from the more individualized pattern found in the bats’ gut microbiome.
Quaternary Science Reviews
Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to m... more Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to modern humans’ spread into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. We propose that disease dynamics can explain the localization and persistence of the inter-species boundary; in this view, each species carried pathogens to which it was largely immune and tolerant, but that could spread to the other, vulnerable, species, inducing a significant disease burden. Epidemics and endemic diseases along the interspecies boundary would have mitigated against bands of one species migrating into regions dominated by the other species. Together with decreased population densities and limited inter-group interactions due to disease burden, this mechanism could have resulted in a fixed and narrow contact-zone. We further prop...
Behavioral and Brain Sciences
We propose that food-related uncertainty is but one of multiple cues that predicts harsh conditio... more We propose that food-related uncertainty is but one of multiple cues that predicts harsh conditions and may activate “incentive hope.” An evolutionarily adaptive response to these would have been to shift to a behavioral-metabolic phenotype geared toward facing hardship. In modernity, this phenotype may lead to pathologies such as obesity and hoarding. Our perspective suggests a novel therapeutic approach.
Theoretical Population Biology
This article consists of commentaries on a selected group of papers of Marc Feldman published in ... more This article consists of commentaries on a selected group of papers of Marc Feldman published in Theoretical Population Biology from 1970 to the present. The papers describe a diverse set of population-genetic models, covering topics such as cultural evolution, social evolution, and the evolution of recombination. The commentaries highlight Marc Feldman's role in providing mathematically rigorous formulations to explore qualitative hypotheses, in many cases generating surprising conclusions.
Nature Ecology & Evolution
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Apr 5, 2018
Language plays a pivotal role in the evolution of human culture, yet the evolution of the capacit... more Language plays a pivotal role in the evolution of human culture, yet the evolution of the capacity for language-uniquely within the hominin lineage-remains little understood. Bringing together insights from cognitive psychology, neuroscience, archaeology and behavioural ecology, we hypothesize that this singular occurrence was triggered by exaptation, or 'hijacking', of existing cognitive mechanisms related to sequential processing and motor execution. Observed coupling of the communication system with circuits related to complex action planning and control supports this proposition, but the prehistoric ecological contexts in which this coupling may have occurred and its adaptive value remain elusive. Evolutionary reasoning rules out most existing hypotheses regarding the ecological context of language evolution, which focus on ultimate explanations and ignore proximate mechanisms. Coupling of communication and motor systems, although possible in a short period on evolutiona...
Nature communications, Jan 31, 2017
Most hypotheses in the heated debate about the Neanderthals' replacement by modern humans hig... more Most hypotheses in the heated debate about the Neanderthals' replacement by modern humans highlight the role of environmental pressures or attribute the Neanderthals' demise to competition with modern humans, who occupied the same ecological niche. The latter assume that modern humans benefited from some selective advantage over Neanderthals, which led to the their extinction. Here we show that a scenario of migration and selectively neutral species drift predicts the Neanderthals' replacement. Our model offers a parsimonious alternative to those that invoke external factors or selective advantage, and represents a null hypothesis for assessing such alternatives. For a wide range of parameters, this hypothesis cannot be rejected. Moreover, we suggest that although selection and environmental factors may or may not have played a role in the inter-species dynamics of Neanderthals and modern humans, the eventual replacement of the Neanderthals was determined by the repeated...
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Apr 5, 2018
Culture evolves according to dynamics on multiple temporal scales, from individuals' minute-b... more Culture evolves according to dynamics on multiple temporal scales, from individuals' minute-by-minute behaviour to millennia of cultural accumulation that give rise to population-level differences. These dynamics act on a range of entities-including behavioural sequences, ideas and artefacts as well as individuals, populations and whole species-and involve mechanisms at multiple levels, from neurons in brains to inter-population interactions. Studying such complex phenomena requires an integration of perspectives from a diverse array of fields, as well as bridging gaps between traditionally disparate areas of study. In this article, which also serves as an introduction to the current special issue, we highlight some specific respects in which the study of cultural evolution has benefited and should continue to benefit from an integrative approach. We showcase a number of pioneering studies of cultural evolution that bring together numerous disciplines. These studies illustrate t...
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Jan 5, 2018
Creativity is a central phenomenon in human life. World-famous scientists and artists are praised... more Creativity is a central phenomenon in human life. World-famous scientists and artists are praised for their creative genius. Schools and universities seek to educate creativity in students and many employers want to hire creative personnel. However, the measurement of creativity is difficult up to the present day. Standard creativity tests typically require human expertise in the evaluation of test responses. This evaluation is often more time-intensive than taking the test itself. Moreover, creativity tests are still regularly conducted in a pen-and-paper format, rendering the data analysis all the more tedious. In this article, we propose a digital game for assessing creativity. It can be hosted online. The data analysis can be automated and conducted in real-time. The test is implemented as a tower defense game ("Immune Defense"). We submit that a video game constitutes a natural setting, as opposed to a formal testing scenario, and provides an opportunity to test real-...
One of the outstanding questions regarding the human gut microbiota is how interventions designed... more One of the outstanding questions regarding the human gut microbiota is how interventions designed to manipulate the microbiota may influence host phenotypic traits. Here, we employed a dietary intervention to probe this question in the context of lactose intolerance. To assess the effects of dairy elimination and reintroduction on the microbiota and host phenotype, we paired fecal 16S rRNA amplicon sequencing with a clinical assay for lactose intolerance, the hydrogen breath test. We studied 12 self-reported mildly lactose intolerant adults, each with tri-weekly collection of fecal samples over a 12-week study period (2 weeks baseline, 4 weeks of dairy elimination, 6 weeks of gradual milk reintroduction) and a hydrogen breath test before and after each phase. We found that although none of the subjects experienced a change in clinically defined status of lactose intolerant or tolerant, most subjects were qualitatively better able to tolerate dairy products with minimal symptoms at t...
Philosophical Transactions of the Royal Society B: Biological Sciences
In the last decade, we have witnessed a major paradigm shift in the life sciences: the recognitio... more In the last decade, we have witnessed a major paradigm shift in the life sciences: the recognition that the microbiome, i.e. the set of microorganisms associated with healthy animals (including humans) and plants, plays a crucial role in the sustained health and fitness of its host. Enabled by rapid advances in sequencing technologies and analytical methods, substantial advances have been achieved in both identifying the microbial taxa and understanding the relationship between microbiome composition and host phenotype. These breakthroughs are leading to novel strategies for improved human and animal health, enhanced crop yield and nutritional quality, and the control of various pests and disease agents. This article is part of the theme issue ‘The role of the microbiome in host evolution'.
Philosophical Transactions of the Royal Society B: Biological Sciences
Host-associated microbiomes influence their host's fitness in myriad ways and can be viewed a... more Host-associated microbiomes influence their host's fitness in myriad ways and can be viewed as a source of phenotypic plasticity. This plasticity may allow the host to accommodate novel environmental challenges and thus influence the host's evolutionary adaptation. As with other modalities of phenotypic plasticity in phenomena such as the Baldwin effect and genetic assimilation, the microbiome-mediated plasticity may influence host genetic adaptation by facilitating and accelerating it, by slowing it down, or even by preventing it. The dynamics involved are likely more complex than those of previously studied phenomena related to phenotypic plasticity, and involve different processes on each time scale, such as acquired recognition of newly associated microbes by the host's immune system on single- and multiple-generation time scales, or selection on transmission dynamics of microbes between hosts, acting on longer time scales. To date, it is unclear if and how any of th...
Open Biology
The course of infection by SARS-CoV-2 frequently includes a long asymptomatic period, followed in... more The course of infection by SARS-CoV-2 frequently includes a long asymptomatic period, followed in some individuals by an immune dysregulation period that may lead to complications and immunopathology-induced death. This course of disease suggests that the virus often evades detection by the innate immune system. We suggest a novel therapeutic approach to mitigate the infection's severity, probability of complications and duration. We propose that priming an individual's innate immune system for viral attack shortly before it is expected to occur may allow pre-activation of the preferable trajectory of immune response, leading to early detection of the virus. Priming can be carried out, for example, by administering a standard vaccine or another reagent that elicits a broad anti-viral innate immune response. By the time that the expected SARS-CoV-2 infection occurs, activation cascades will have been put in motion and levels of immune factors needed to combat the infection wi...
Proceedings of the National Academy of Sciences
Van Vliet & Doebeli (1) (henceforth VVD) present a multi-level selection framework simulating hos... more Van Vliet & Doebeli (1) (henceforth VVD) present a multi-level selection framework simulating host-microbiome evolutionary dynamics. The model explores the conditions under which the association between hosts and their “helper” microbiome – microbes that developed a trait that provides a benefit to the host at a cost to themselves – is strong enough to allow for selection at the holobiont level. The model is an important contribution to the holobiont debate, making the notion quantifiable and highlighting the involved parameters.In the study, VVD conclude that the parameter space in which selection occurs at the level of the holobiont is extremely restricted (Fig 1). Here we show that this result stems from specific model assumptions. Although these assumptions are reasonable as a modeling starting point, slight biologically-reasonable modifications of the assumptions lead to qualitatively different outcomes.
Behavioral and Brain Sciences
Baumard's perspective asserts that “opportunity is the mother of innovation,” in contrast to ... more Baumard's perspective asserts that “opportunity is the mother of innovation,” in contrast to the adage ascribing this role to necessity. Drawing on behavioral ecology and cognition, we propose that both extremes – affluence and scarcity – can drive innovation. We suggest that the types of innovations at these two extremes differ and that both rely on mechanisms operating on different time scales.
Nature Communications
Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to t... more Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated ‘pathogen packages’ could have generated feedback that allowed modern humans to overcome disease burden earlier than Neandert...
ABSTRACTIn the first longitudinal study of bat microbiomes, we find that unlike the pattern descr... more ABSTRACTIn the first longitudinal study of bat microbiomes, we find that unlike the pattern described in humans and other mammals, the prominent dynamics in Egyptian fruit bats’ fur microbiomes are those of change over time at the level of the colony as a whole. Thus, on average, a pair of fur microbiome samples from different individuals in the same colony collected on the same date are more similar to one another than a pair of samples from the same individual collected at different time points. This pattern suggests that the whole colony may be the appropriate biological unit for understanding some of the roles of the host microbiome in social bats’ ecology and evolution. This pattern of synchronized colony changes over time is also reflected in the profile of volatile compounds in the bats’ fur, but differs from the more individualized pattern found in the bats’ gut microbiome.
Quaternary Science Reviews
Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to m... more Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to modern humans’ spread into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. We propose that disease dynamics can explain the localization and persistence of the inter-species boundary; in this view, each species carried pathogens to which it was largely immune and tolerant, but that could spread to the other, vulnerable, species, inducing a significant disease burden. Epidemics and endemic diseases along the interspecies boundary would have mitigated against bands of one species migrating into regions dominated by the other species. Together with decreased population densities and limited inter-group interactions due to disease burden, this mechanism could have resulted in a fixed and narrow contact-zone. We further prop...
Behavioral and Brain Sciences
We propose that food-related uncertainty is but one of multiple cues that predicts harsh conditio... more We propose that food-related uncertainty is but one of multiple cues that predicts harsh conditions and may activate “incentive hope.” An evolutionarily adaptive response to these would have been to shift to a behavioral-metabolic phenotype geared toward facing hardship. In modernity, this phenotype may lead to pathologies such as obesity and hoarding. Our perspective suggests a novel therapeutic approach.
Theoretical Population Biology
This article consists of commentaries on a selected group of papers of Marc Feldman published in ... more This article consists of commentaries on a selected group of papers of Marc Feldman published in Theoretical Population Biology from 1970 to the present. The papers describe a diverse set of population-genetic models, covering topics such as cultural evolution, social evolution, and the evolution of recombination. The commentaries highlight Marc Feldman's role in providing mathematically rigorous formulations to explore qualitative hypotheses, in many cases generating surprising conclusions.
Nature Ecology & Evolution
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Apr 5, 2018
Language plays a pivotal role in the evolution of human culture, yet the evolution of the capacit... more Language plays a pivotal role in the evolution of human culture, yet the evolution of the capacity for language-uniquely within the hominin lineage-remains little understood. Bringing together insights from cognitive psychology, neuroscience, archaeology and behavioural ecology, we hypothesize that this singular occurrence was triggered by exaptation, or 'hijacking', of existing cognitive mechanisms related to sequential processing and motor execution. Observed coupling of the communication system with circuits related to complex action planning and control supports this proposition, but the prehistoric ecological contexts in which this coupling may have occurred and its adaptive value remain elusive. Evolutionary reasoning rules out most existing hypotheses regarding the ecological context of language evolution, which focus on ultimate explanations and ignore proximate mechanisms. Coupling of communication and motor systems, although possible in a short period on evolutiona...
Nature communications, Jan 31, 2017
Most hypotheses in the heated debate about the Neanderthals' replacement by modern humans hig... more Most hypotheses in the heated debate about the Neanderthals' replacement by modern humans highlight the role of environmental pressures or attribute the Neanderthals' demise to competition with modern humans, who occupied the same ecological niche. The latter assume that modern humans benefited from some selective advantage over Neanderthals, which led to the their extinction. Here we show that a scenario of migration and selectively neutral species drift predicts the Neanderthals' replacement. Our model offers a parsimonious alternative to those that invoke external factors or selective advantage, and represents a null hypothesis for assessing such alternatives. For a wide range of parameters, this hypothesis cannot be rejected. Moreover, we suggest that although selection and environmental factors may or may not have played a role in the inter-species dynamics of Neanderthals and modern humans, the eventual replacement of the Neanderthals was determined by the repeated...
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Apr 5, 2018
Culture evolves according to dynamics on multiple temporal scales, from individuals' minute-b... more Culture evolves according to dynamics on multiple temporal scales, from individuals' minute-by-minute behaviour to millennia of cultural accumulation that give rise to population-level differences. These dynamics act on a range of entities-including behavioural sequences, ideas and artefacts as well as individuals, populations and whole species-and involve mechanisms at multiple levels, from neurons in brains to inter-population interactions. Studying such complex phenomena requires an integration of perspectives from a diverse array of fields, as well as bridging gaps between traditionally disparate areas of study. In this article, which also serves as an introduction to the current special issue, we highlight some specific respects in which the study of cultural evolution has benefited and should continue to benefit from an integrative approach. We showcase a number of pioneering studies of cultural evolution that bring together numerous disciplines. These studies illustrate t...
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Jan 5, 2018