We construct a new class of 1 categorical structures, disproving Zilber's conjecture, and study some of their properties.

Species’ adaptation to their environments occurs via a range of mechanisms of adaptation. These include genetic adaptations as well as non-traditional inheritance mechanisms such as learned behaviors, niche construction, epigenetics, horizontal gene transfer, and alteration of the composition of a host’s associated microbiome. We propose to supplement these with another modality of eco-evolutionary dynamics: cases in which adaptation to the environment occurs via what may be called a “distributed adaptation,” in which the adaptation is not conferred via something carried by (...) an individual of the adapted species (as with genes, behavior, or associated microbes), but by some structural or compositional aspect of the population. Put differently, the adaptively relevant information cannot be reduced to information possessed by a single individual, whether genetic or otherwise. Rather, the adaptively relevant information is distributed, and is found strictly at the population level. While human culture is presumably such a case, as may be cases found in social insects, we want to suggest that there are other cases that belong to this category and to explore its evolutionary implications. In particular, we discuss the factors that affect whether adaptive information is stored in a distributed way, to what degree, and what kinds of adaptive information are most likely to be found in this modality of adaptation. (shrink)

A first order theory T of power λ is called unidimensional if any twoλ+-saturated models of T of the same cardinality are isomorphic. We prove here that such theories are superstable, solving a problem of Shelah. The proof involves an existence theorem and a definability theorem for definable groups in stable theories, and an analysis of their relation to regular types.

Since the ENCODE project published its final results in a series of articles in 2012, there is no consensus on what its implications are. ENCODE’s central and most controversial claim was that there is essentially no junk DNA: most sections of the human genome believed to be «junk» are functional. This claim was met with many reservations. If researchers disagree about whether there is junk DNA, they have first to agree on a concept of function and how function, given a (...) particular definition, can be discovered. The ENCODE debate centered on a notion of function that assumes a strong dichotomy between evolutionary and non-evolutionary function and causes, prevalent in the Modern Evolutionary Synthesis. In contrast to how the debate is typically portrayed, both sides share a commitment to this distinction. This distinction is, however, much debated in alternative approaches to evolutionary theory, such as the EES. We show that because the ENCODE debate is grounded in a particular notion of function, it is unclear how it connects to broader debates about what is the correct evolutionary frame- work. Furthermore, we show how arguments brought forward in the controversy, particularly arguments from mathematical population genetics, are deeply embedded in their particular disciplinary contexts, and reflect substantive assumptions about the evolution of genomes. With this article, we aim to provide an anatomy of the ENCODE debate that offers a new perspective on the notions of function both sides employed, as well as to situate the ENCODE debate within wider debates regarding the forces operating in evolution. (shrink)

Organisms inherit various kinds of developmental information and cues from their parents. The study of inheritance systems is aimed at identifying and classifying the various mechanisms and processes of heredity, the types of hereditary information that is passed on by each, the functional interaction between the different systems, and the evolutionary consequences of these properties. We present the discussion of inheritance systems in the context of several debates. First, between proponents of monism about heredity (gene-centric views), holism about heredity (Developmental (...) Systems Theory), and those stressing the role of multiple systems of inheritance. Second, between those analyzing inheritance solely in terms of replication and transmission, and views that stress the multi-generation reproduction of phenotypic traits. A third debate is concerned with different criteria that have been proposed for identifying and delimiting inheritance systems. A fourth controversy revolves around the significance of the “Lamarckian” aspects of some of the inheritance systems that have been identified, such as epigenetic inheritance and behavioral inheritance, that allow the transmission of environmentally induced characters (i.e., “soft inheritance”). (shrink)

This paper applies the conceptual toolkit of Evolutionary Developmental Biology (evo‐devo) to the evolution of the genome and the role of the genome in organism development. This challenges both the Modern Evolutionary Synthesis, the dominant view in evolutionary theory for much of the 20th century, and the typically unreflective analysis of heredity by evo‐devo. First, the history of the marginalization of applying system‐thinking to the genome is described. Next, the suggested framework is presented. Finally, its application to the evolution of (...) genome modularity, the evolution of induced mutations, the junk DNA versus ENCODE debate, the role of drift in genome evolution, and the relationship between genome dynamics and symbiosis with microorganisms are briefly discussed. (shrink)

The dichotomy between Nature and Nurture, which has been dismantled within the framework of development, remains embodied in the notions of plasticity and evolvability. We argue that plasticity and evolvability, like development and heredity, are neither dichotomous nor distinct: the very same mechanisms may be involved in both, and the research perspective chosen depends to a large extent on the type of problem being explored and the kinds of questions being asked. Epigenetic inheritance leads to transgenerationally extended plasticity, and developmentally-induced (...) heritable epigenetic variations provide additional foci for selection that can lead to evolutionary change. Moreover, hereditary innovations may result from developmentally induced large-scale genomic repatterning events, which are akin to Goldschmidtian “systemic mutations”. The epigenetic mechanisms involved in repatterning can be activated by both environmental and genomic stress, and lead to phylogenetic as well as ontogenetic changes. Hence, the effects and the mechanisms of plasticity directly contribute to evolvability. (shrink)

Introduction The purpose of this study is to characterize a conception of prayer that plays an important role in the religious thought of the medieval ...

A likelihood order is defined over linear subspaces of a finite dimensional Hilbert space. It is shown that such an order that satisfies some plausible axioms can be represented by a quantum probability in two cases: pure state and uniform measure.

This article describes how empirical discoveries in the 1930s–1950s regarding population variation for chromosomal inversions affected Theodosius Dobzhansky and Richard Goldschmidt. A significant fraction of the empirical work I discuss was done by Dobzhansky and his coworkers; Goldschmidt was an astute interpreter, with strong and unusual commitments. I argue that both belong to a mechanistic tradition in genetics, concerned with the effects of chromosomal organization and systems on the inheritance patterns of species. Their different trajectories illustrate how scientists’ commitments affect (...) how they interpret new evidence and adjust to it. Dobzhansky was moved to revised views about selection, while Goldschmidt moved his attention to different genetic phenomena. However different, there are significant connections between the two that enrich our understanding of their views. I focus on two: the role of developmental considerations in Dobzhansky’s thought and the role of neutrality and drift in Goldschmidt’s evolutionary account. Dobzhansky’s struggle with chromosomal variation is not solely about competing schools of thought within the selectionist camp, as insightfully articulated by John Beatty, but also a story of competition between selectionist thinking and developmental perspectives. In contraposition, Goldschmidt emphasized the role of low penetrance mutations that spread neutrally and pointed out that drift could result from developmental canalization. This account adds to the dominant story about Goldschmidt’s resistance to the splitting of development from genetics, as told by Garland Allen and Michael Dietrich. The story I tell illustrates how developmental thinking and genetic thinking conflicted and influenced researchers with different convictions about the significance of chromosomal organization. (shrink)

Robert Brandom’s notion of historical rationality seeks to supplement his inferentialism thesis by providing an account for the validity of conceptual contents. This account, in the shape of a historical process, involves the same self-integration of Brandom’s earlier inferentialism and is similarly restricted by reciprocal recognition of others. This article argues that in applying the synchronic social model of normative discourse to the diachronic axis of engaging the past, Brandom premises a false analogy between present community and past tradition, which (...) obscures the important differences between the two axes. This is explored by looking closely at how Brandom’s own engagements with the past exemplify his historical rationality. Taking its cue from Brandom’s critics, the article shows that Brandom’s own discourse with tradition is not, and cannot be, dialogical and, in accordance, that historical rationality is not, and cannot be, governed by the same social structure of inferentialism. The article concludes with the implications of such a claim on Brandom’s thesis as a whole and on the role of tradition in the process of normative change, in light of it. (shrink)

Recent and not so recent advances in our molecular understanding of the genome make the once prevalent view of the genome as a passive container of genetic information (i.e., genes) untenable, and emphasize the importance of the internal organization and re-organization dynamics of the genome for both development and evolution. While this conclusion is by now well accepted, the construction of a comprehensive conceptual framework for studying the genome as a dynamic system, capable of self-organization and adaptive behavior is still (...) underway. This work deals with the effect of such a conceptual shift on evolutionary thought. Specifically, I try to articulate the conceptual commitments and obligations of views that privilege explanatorily or causally the genome, its dynamics and mechanisms, over genes. I refer to this class of views as belonging to ‘the genome perspective’. (shrink)

This article suggests a change of perspective on philosophy’s engagement with its past. It argues that rather than the putative purport of giving life to the past philosopher’s work, philosophical engagement with the past gives life to one’s own. Drawing on the neo-pragmatist thesis of Robert Brandom, it suggests looking to what philosophers do when they attribute meaning to concepts and considering their engagement with the past as appropriation in consequence. By scrutinizing Robert Pippin’s opposing thesis of philosophical engagement with (...) the past as dialogue, and carefully examining Brandom’s, the article suggests an account for appropriation that shows it to be non-dialogical, and hence unable to yield the fruits associated with this conception, but also insightful and rich with other philosophical values. Brandom and John McDowell’s dispute over the interpretation of Wilfrid Sellars provides an illustration of the proposed perspective and of those values. (shrink)

Persistent activity can be the product of mechanisms other than attractor reverberations. The single-unit data presented by Amit cannot discriminate between the different mechanisms. In fact, single-unit data do not appear to be adequate for testing neural network models.

[1]: meha-haḳdamah ṿe-ʻad pereḳ 19 --.

We use a new construction of an o-minimal structure, due to Lipshitz and Robinson, to answer a question of van den Dries regarding the relationship between arbitrary o-minimal expansions of real closed fields and structures over the real numbers. We write a first order sentence which is true in the Lipshitz-Robinson structure but fails in any possible interpretation over the field of real numbers.

Segmentation of post-operative glioblastoma multiforme (GBM) is essential for the planning of Tumor Treating Fields (TTFields) treatment and other clinical applications. Recent methods developed for pre-operative GBM segmentation perform poorly on post-operative GBM MRI scans. In this paper we present a method for the segmentation of GBM in post-operative patients. Our method incorporates an ensemble of segmentation networks and the Kullback–Leibler divergence agreement score in the objective function to estimate the prediction label uncertainty and cope with noisy labels and inter-observer (...) variability. Moreover, our method integrates the surgery type and computes non-tumorous tissue delineation to automatically segment the tumor. We trained and validated our method on a dataset of 340 enhanced T1 MRI scans of patients that were treated with TTFields (270 scans for train and 70 scans for test). For validation, we developed a tool that uses the uncertainty map along with the segmentation result. Our tool allows visualization and fast editing of the tissues to improve the results dependent on user preference. Three physicians reviewed and graded our segmentation and editing tool on 12 different MRI scans. The validation set average (SD) Dice scores were 0.81 (0.11), 0.71 (0.24), 0.64 (0.25), and 0.68 (0.19) for whole-tumor, resection, necrotic-core, and enhancing-tissue, respectively. The physicians rated 72% of the segmented GBMs acceptable for treatment planning or better. Another 22% can be edited manually in a reasonable time to achieve a clinically acceptable result. According to these results, the proposed method for GBM segmentation can be integrated into TTFields treatment planning software in order to shorten the planning process. To conclude, we have extended a state-of-the-art pre-operative GBM segmentation method with surgery-type, anatomical information, and uncertainty visualization to facilitate a clinically viable segmentation of post-operative GBM for TTFields treatment planning. (shrink)

This study compares the argumentative writing characteristics of students from different sociocultural backgrounds. We focused on Jewish ultra-Orthodox (Haredi) students, educated in a segregated religious school for boys (yeshiva), who are now attempting to integrate in secular higher education in Israel. To better understand the unique characteristics of this population, we reviewed 92 essays written by Haredi students, and compared them with 76 essays by public education (PE) graduates. Our analysis was based on the cognitive and sociocultural perspectives of argumentation. (...) Both bottom-up and top-down criteria were used to elicit the argumentative writing characteristics either emerging from the data or based on existing theories. Our primary findings indicate that Haredi students have distinct argumentative characteristics, including the use of more complex and dialectic arguments and unique persuasive tactics. These findings are discussed in light of previous research on yeshiva learning methods and recommendations are provided for adjusting the existing higher education curricula to suit both PE and Haredi students. (shrink)

A biographical sketch of the Hologenome Theory.

Using methods of geometric stability , we determine the structure of Abelian groups definable in ACFA, the model companion of fields with an automorphism. We also give general bounds on sets definable in ACFA. We show that these tools can be used to study torsion points on Abelian varieties; among other results, we deduce a fairly general case of a conjecture of Tate and Voloch on p-adic distances of torsion points from subvarieties.

Language and norms are both fundamental to human society. A social account of language evolution must take into account the normative context in which language acquisition, use, and change occur. However, at the same time, norms in human society are directly affected by language and the linguistic skills of individuals. My aim in this chapter is to explore the evolutionary consequences of this bi-directional interaction. I discuss how it can help explain central linguistic notions including imperatives, questions, possessives, modal vocabulary, (...) categorization, and performatives, and how it helps explain unique features of human normativity. (shrink)

A stable theory is finitely based if every set of indiscernibles is based on a finite subset. This is a common generalization of superstability and 1-basedness. We show that if such theories have more than one model they must have infinitely many, and prove some other conjectures.

Both von Neumann and Wiener were outsiders to biology. Both were inspired by biology and both proposed models and generalizations that proved inspirational for biologists. Around the same time in the 1940s von Neumann developed the notion of self reproducing automata and Wiener suggested an explication of teleology using the notion of negative feedback. These efforts were similar in spirit. Both von Neumann and Wiener used mathematical ideas to attack foundational issues in biology, and the concepts they articulated had lasting (...) effect. But there were significant differences as well. Von Neumann presented a how-possibly model, which sparked interest by mathematicians and computer scientists, while Wiener collaborated more directly with biologists, and his proposal influenced the philosophy of biology. The two cases illustrate different strategies by which mathematicians, the “professional outsiders” of science, can choose to guide their engagement with biological questions and with the biological community, and illustrate different kinds of generalizations that mathematization can contribute to biology. The different strategies employed by von Neumann and Wiener and the types of models they constructed may have affected the fate of von Neumann’s and Wiener’s ideas – as well as the reputation, in biology, of von Neumann and Wiener themselves. (shrink)

Many natural and biological phenomena can be depicted as networks. Theoretical and empirical analyses of networks have become prevalent. I discuss theoretical biases involved in the delineation of biological networks. The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between “program” and “data”. The evolutionary significance of the dynamics of trans-generational and inter-organism regulatory networks is explored and implications are presented for understanding the evolution of (...) the biological categories development-heredity; plasticity-evolvability; and epigenetic-genetic. (shrink)

Among his many contributions to philosophy, Carnap’s work also influenced the historiography of philosophy. In his Aufbau of 1928, he introduced the term ‘rational reconstruction’ (‘rationale Nachkonstruction’), which is now known as a central approach to the history of philosophy. Carnap’s own conception, though, had nothing to do with our engagement with the Mighty Dead. It was only later, when subsequent philosophers appropriated the term, that it entered the historiographical debate. In this chapter we sketch the development of the notion (...) of rational reconstruction, ending with a brief reflection on our sketch. (shrink)

In this Article we examine Israel’s ongoing process of bank privatization to explore the link between privatization programs and the ownership structure of public companies. Our thesis is that concentrated ownership provides regulators with a platform for exerting informal influence over corporate decision-making. This platform serves regulators as a safety valve when all else fails, especially when they would like firms to terminate senior executives or board members. Communicating with controlling shareholders increases the likelihood that both the regulatory intervention and (...) the reasons underlying it will remain confidential. Moreover, controlling shareholders can make swift decisions and implement them quickly, with no need for formal group deliberation. When informal influence is important — as in the case of banks — the government may prefer firms with controlling shareholders to widely held firms. It may therefore prefer to sell a control block in the firm undergoing privatization rather than distribute its shares through the stock market. (shrink)

We prove (Proposition 2.1) that if $\mu$ is a generically stable measure in an NIP (no independence property) theory, and $\mu(\phi(x,b))=0$ for all $b$ , then for some $n$ , $\mu^{(n)}(\exists y(\phi(x_{1},y)\wedge \cdots \wedge\phi(x_{n},y)))=0$ . As a consequence we show (Proposition 3.2) that if $G$ is a definable group with fsg (finitely satisfiable generics) in an NIP theory, and $X$ is a definable subset of $G$ , then $X$ is generic if and only if every translate of $X$ does not (...) fork over $\emptyset$ , precisely as in stable groups, answering positively an earlier problem posed by the first two authors. (shrink)

We attempt to formulate issues around modularity and Zilber’s trichotomy in a setting that intersects additive combinatorics. In particular, we update the open problems on quasi-finite structures from [9].

Distributed adaptations are cases in which adaptation is dependent on the population as a whole: the adaptation is conferred by a structural or compositional aspect of the population; the adaptively relevant information cannot be reduced to information possessed by a single individual. Possible examples of human-distributed adaptations are song lines, traditions, trail systems, game drive lanes and systems of water collection and irrigation. Here we discuss the possible role of distributed adaptations in human cultural macro-evolution. Several kinds of human-distributed adaptations (...) are presented, and their evolutionary implications are highlighted. In particular, we discuss the implications of population size, density and bottlenecks on the distributed adaptations that a population may possess and how they in turn would affect the population's resilience to ecological change. We discuss the implications that distributed adaptations may have for human collective action and the possibility that they played a role in colonization of new areas and niches, in seasonal migration, and in setting constraints for minimal inter-population connectivity. (shrink)

Kueker's conjecture is proved for stable theories, for theories that interpret a linear ordering, and for theories with Skolem functions. The proof of the stable case involves certain results on coordinatization that are of independent interest.

The notion of structure of evolution is proposed to capture what it means to say that two situations exhibit the same or similar constellations of factors affecting evolution. The key features of holobiont evolution and the hologenome theory are used to define a holobiont structure of evolution. Finally, Cultural Group Selection, a set of hypotheses regarding the evolution of human cognition, is shown to match the holobiont structure closely though not perfectly.

An argument is presented according to which exposing pseudo-scientific medical claims may be ethically wrong. It is then suggested that this argument gives an interesting explanation why the successful outing of pseudo-science may lead to an increase in medical pseudo-science overall.