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1. Natural kinds

   https://doi.org/10.4324/9780415249126-N099-3  

   Kendig, Catherine (August 2023, Routledge)

   Natural kinds are widely understood to be the real classifications of things that actually exist in the world. Natural kinds are the categories we tend to aim for when we seek to understand the world, as it really is. Discovering what these real classifications are is often considered to be the project of scientific research in many fields from astronomy and agronomy to zoology and zymurgy. When we discover something unfamiliar to us and we want to know what sort of thing it is, we might ask: ‘what kind is that?’ For instance, in a physics class, we might ask: ‘what kind of quark is that?’, where the answer might be: ‘that is a charm quark’. In biology, we might ask: ‘what kind of plant is that?’, with the answer being: ‘it is a Venus flytrap (Dionaea muscipula)’. Or, in chemistry, we might ask: ‘what element is that?’, with the answer being: ‘lithium’. Knowing that the thing we asked about is a member of that particular kind tells us a lot about it if it is a natural kind. Membership in a natural kind tells us that the thing in question shares many important characteristics with other things that are in the same natural kind category. For example, consider the category of Venus flytraps. All plants that belong to that category share many important characteristics; among these include: perennial flowering, carnivorous eating habits, capable of thigmonastic responses (closing their ‘trap’ when prey alight on their trichomes), ability to photosynthesise, belonging to the family Droseraceae and the kingdom Plantae. Some of these important characteristics and properties have been referred to as ‘essential’ by philosophers because they are the properties that are thought to be necessary for the thing to be a member of that natural kind. That means that if the thing does not have those necessary properties, then it cannot be a member of that natural kind. When we ask the question: ‘what kind is that?’, we do not always discover natural kinds. Sometimes when we ask: ‘what kind of thing is that?’, we find out, for instance, that this thing that we are asking about is green. This means we find out that it belongs to the category of green things. The category of green things is a kind category, but it is not a natural kind. The category of all green things includes the Venus flytrap but also green traffic lights, green tea, guacamole, collards, and dark jade-painted 1978 Ford Mustang sportscars. What all of these things have in common is that they are all green. However, they do not share any other properties or characteristics apart from being green. Green kinds of things are not natural kinds like those mentioned earlier. The kinds that are picked out by the classifications of charm quark, Venus flytrap, and lithium are considered to be very different from the classification of green things. Whilst all charm quarks, all Venus flytraps, and all samples of lithium are each considered to be classifications of natural kinds, the category of green things is not. The philosophical question that arises is: ‘what makes classifications like that of the natural kind that includes all charm quarks natural and classifications like that of all green things not natural?’ Put a different way: ‘what makes something a natural kind and how can we tell the difference between natural kinds and what we might call “artificial kinds”, like the grouping of green things?’ A popular answer to this question is that natural kinds pick out natural groupings whose existence in the world is not dependent upon human interests or activities, whereas artificial kinds pick out groupings whose existence in the world is dependent upon human interests or activities. However, others have provided substantial evidence challenging this claim, arguing that there are at least some natural kinds that are dependent upon human activities and practices for their existence. In addition to questions concerning what qualifies as naturalness in natural kinds and what is the distinction between natural and artificial kinds, philosophical discussion also focuses on the metaphysics of natural kinds and the epistemic value of natural kinds. A perennial question widely debated is whether the classifications used in scientific disciplines – physics, chemistry, biology, neuroscience, geology, linguistics, anthropology, and more –really do map on to a natural classification that really exists in the world. That is, are the ways we partition elements in chemistry, organisms in biology, or quarks in physics, the same partitionings that naturally exist? A lot of the literature on natural kinds relies on using examples that are thought to be quintessential natural kinds, like biological species and chemical elements. But others argue that there is clear evidence that many, if not most, biological species and chemical elements are not natural kinds, especially if membership within a natural kind requires possession of an essential property. Within the discussion of natural kinds, there are also questions with regard to the conditions of membership that challenge the view that natural kinds membership is determined by the possession of a particular essence. Instead of the possession of a particular essence, some argue that membership in a natural kind may instead be determined by the possession of a cluster of properties, a relationship, or something else. In many of these discussions, Plato’s metaphor of carving nature at its joints is used to describe the mapping of natural classifications onto natural kinds by the implied comparison to the butchering of an animal along its natural divisions (knuckles, limbs, etc.) rather than partitioning it in a way that does not coincide with the animal’s body structure. Whilst the metaphor helps explain the nature of natural kinds, it does so by assuming nature is that which is pre-partitioned. 

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2. Sealing from iterability

   Sargsyan, Grigor; Trang, Nam (January 2021, Transactions of the American Mathematical Society)

   null (Ed.)

   We show that if V has a proper class ofWoodin cardinals, a strong cardinal, and a generically universally Baire iteration strategy (as defined in the paper) then Sealing holds after collapsing the successor of the least strong cardinal to be countable. This result is complementary to other work by the authors where it is shown that Sealing holds in a generic extension of a certain minimal universe. The current theorem is more general in that no minimality assumption is needed. A corollary of the main theorem is that Sealing is consistent relative to the existence of a Woodin cardinal which is a limit of Woodin cardinals. This improves significantly on the first consistency of Sealing obtained by W.H. Woodin. The Largest Suslin Axiom (LSA) is a determinacy axiom isolated byWoodin. It asserts that the largest Suslin cardinal is inaccessible for ordinal definable bijections. Let LSA-over-uB be the statement that in all (set) generic extensions there is a model of LSA whose Suslin, co-Suslin sets are the universally Baire sets. The other main result of the paper shows that assuming V has a proper class of inaccessible cardinals which are limit of Woodin cardinals, a strong cardinal, and a generically universally Baire iteration strategy, in the universe V [g], where g is V -generic for the collapse of the successor of the least strong cardinal to be countable, the theory LSA-over-UB fails; this implies that LSA-over-UB is not equivalent to Sealing (over the base theory of V [g]). This is interesting and somewhat unexpected, in light of other work by the authors. Compare this result with Steel’s well-known theorem that “AD in L(R) holds in all generic extensions” is equivalent to “the theory of L(R) is sealed” in the presence of a proper class of measurable cardinals. 

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3. Pseudodeterminism: promises and lowerbounds

   https://doi.org/10.1145/3519935.3520043  

   Dixon, Peter; Pavan, A.; Woude, Jason Vander; Vinodchandran, N. V. (July 2022, Symposium on Theory of Computing (STOC))

   Stefano Leonardi and Anupam Gupta (Ed.)

   A probabilistic algorithm A is pseudodeterministic if, on every input, there exists a canonical value that is output with high probability. If the algorithm outputs one of k canonical values with high probability, then it is called a k-pseudodeterministic algorithm. In the study of pseudodeterminism, the Acceptance Probability Estimation Problem (APEP), which is to additively approximate the acceptance probability of a Boolean circuit, is emerging as a central computational problem. This problem admits a 2-pseudodeterministic algorithm. Recently, it was shown that a pseudodeterministic algorithm for this problem would imply that any multi-valued function that admits a k-pseudodeterministic algorithm for a constant k (including approximation algorithms) also admits a pseudodeterministic algorithm (Dixon, Pavan, Vinodchandran; ITCS 2021). The contribution of the present work is two-fold. First, as our main conceptual contribution, we establish that the existence of a pseudodeterministic algorithm for APEP is fundamentally related to the gap between probabilistic promise classes and the corresponding standard complexity classes. In particular, we show the following equivalence: APEP has a pseudodeterministic approximation algorithm if and only if every promise problem in PromiseBPP has a solution in BPP. A conceptual interpretation of this equivalence is that the algorithmic gap between 2-pseudodeterminism and pseudodeterminism is equivalent to the gap between PromiseBPP and BPP. Based on this connection, we show that designing pseudodeterministic algorithms for APEP leads to the solution of some open problems in complexity theory, including new Boolean circuit lower bounds. This equivalence also explains how multi-pseudodeterminism is connected to problems in SearchBPP. In particular, we show that if APEP has a pseudodeterministic algorithm, then every problem that admits a k(n)-pseudodeterministic algorithm (for any polynomial k) is in SearchBPP and admits a pseudodeterministic algorithm. Motivated by this connection, we also explore its connection to probabilistic search problems and establish that APEP is complete for certain notions of search problems in the context of pseudodeterminism. Our second contribution is establishing query complexity lower bounds for multi-pseudodeterministic computations. We prove that for every k ≥ 1, there exists a problem whose (k+1)-pseudodeterministic query complexity, in the uniform query model, is O(1) but has a k-pseudodeterministic query complexity of Ω(n), even in the more general nonadaptive query model. A key contribution of this part of the work is the utilization of Sperner’s lemma in establishing query complexity lower bounds. 

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4. LuxT Is a Global Regulator of Low-Cell-Density Behaviors, Including Type III Secretion, Siderophore Production, and Aerolysin Production, in Vibrio harveyi

   https://doi.org/10.1128/mbio.03621-21  

   Eickhoff, Michaela J.; Fei, Chenyi; Cong, Jian-Ping; Bassler, Bonnie L. (February 2022, mBio)

   Storz, Gisela (Ed.)

   ABSTRACT Quorum sensing (QS) is a chemical communication process in which bacteria produce, release, and detect extracellular signaling molecules called autoinducers. Via combined transcriptional and posttranscriptional regulatory mechanisms, QS allows bacteria to collectively alter gene expression on a population-wide scale. Recently, the TetR family transcriptional regulator LuxT was shown to control Vibrio harveyi qrr 1, encoding the Qrr1 small RNA that functions at the core of the QS regulatory cascade. Here, we use RNA sequencing to reveal that, beyond the control of qrr 1, LuxT is a global regulator of 414 V. harveyi genes, including those involved in type III secretion, siderophore production, and aerolysin toxin biosynthesis. Importantly, LuxT directly represses swrZ , encoding a GntR family transcriptional regulator, and LuxT control of type III secretion, siderophore, and aerolysin genes occurs by two mechanisms, one that is SwrZ dependent and one that is SwrZ independent. All of these target genes specify QS-controlled behaviors that are enacted when V. harveyi is at low cell density. Thus, LuxT and SwrZ function in parallel with QS to drive particular low-cell-density behaviors. Phylogenetic analyses reveal that luxT is highly conserved among Vibrionaceae , but swrZ is less well conserved. In a test case, we find that in Aliivibrio fischeri , LuxT also represses swrZ . SwrZ is a repressor of A. fischeri siderophore production genes. Thus, LuxT repression of swrZ drives the activation of A. fischeri siderophore gene expression. Our results indicate that LuxT is a major regulator among Vibrionaceae , and in the species that also possess swrZ , LuxT functions with SwrZ to control gene expression. IMPORTANCE Bacteria precisely tune gene expression patterns to successfully react to changes that occur in the environment. Defining the mechanisms that enable bacteria to thrive in diverse and fluctuating habitats, including in host organisms, is crucial for a deep understanding of the microbial world and also for the development of effective applications to promote or combat particular bacteria. In this study, we show that a regulator called LuxT controls over 400 genes in the marine bacterium Vibrio harveyi and that LuxT is highly conserved among Vibrionaceae species, ubiquitous marine bacteria that often cause disease. We characterize the mechanisms by which LuxT controls genes involved in virulence and nutrient acquisition. We show that LuxT functions in parallel with a set of regulators of the bacterial cell-to-cell communication process called quorum sensing to promote V. harveyi behaviors at low cell density. 

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5. Comments on “horizontal gravity disturbance vector in atmospheric dynamics” by Peter C. Chu

   https://doi.org/10.1016/j.dynatmoce.2023.101382  

   Chang, Edmund KM; Wolfe, Christopher L_P; Stewart, Andrew L; McWilliams, James C (September 2023, Dynamics of Atmospheres and Oceans)

   In a recent paper [Chu (2023; Chu23)], the author formulated the equations governing atmospheric motion in a spheroidal coordinate system. Since the mass distribution of the Earth is not exactly spheroidal, the true gravity is not vertical in that coordinate system. Chu23 compared the magnitude of the static horizontal component of gravity in that system to those of the dynamically active forces and concluded that the horizontal components of gravity should not be neglected. In recent papers by the authors [Chang and Wolfe (2022; CW22) and Stewart and McWilliams (2022; CW22)], we explained that the actual interpretation of the approximation made in atmospheric and oceanic modeling is not neglecting the horizontal component of the true gravity, but is a geometrical approximation, approximating nearly spheroidal geopotential surfaces with bumps on which the true gravity is vertical by exactly spheroidal surfaces. We showed that under such an interpretation, the errors due to the geometrical approximation are small. Chu23 claimed that CW22 and SM22 erroneously neglected the gravity perturbations in their analyses. Here, we explain further the differences between these approaches, in the process showing that the criticisms of Chu23 on CW22 and SM22 are invalid, further supporting our conclusion that the horizontal component of the true gravity is not relevant in ocean and atmospheric dynamics. Physically, the reason why horizontal gravity is irrelevant in the coordinate system used by Chu23 is that it is balanced by a static horizontal pressure gradient force. 

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