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1. Place cells may simply be memory cells: Memory compression leads to spatial tuning and history dependence

   https://doi.org/10.1073/pnas.2018422118  

   Benna, Marcus K.; Fusi, Stefano (December 2021, Proceedings of the National Academy of Sciences)

   The observation of place cells has suggested that the hippocampus plays a special role in encoding spatial information. However, place cell responses are modulated by several nonspatial variables and reported to be rather unstable. Here, we propose a memory model of the hippocampus that provides an interpretation of place cells consistent with these observations. We hypothesize that the hippocampus is a memory device that takes advantage of the correlations between sensory experiences to generate compressed representations of the episodes that are stored in memory. A simple neural network model that can efficiently compress information naturally produces place cells that are similar to those observed in experiments. It predicts that the activity of these cells is variable and that the fluctuations of the place fields encode information about the recent history of sensory experiences. Place cells may simply be a consequence of a memory compression process implemented in the hippocampus. 

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2. The Case for Studying New Viruses of New Hosts

   https://doi.org/10.1146/annurev-virology-100220-112915  

   Stenglein, Mark D. (September 2022, Annual Review of Virology)

   Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways. 

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3. 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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4. Re-Interpreting Sedimentary Carbon Isotope Mass Balances

   Derry, Louis A (December 2024, American Geophysical Union)

   Plain-Language Summary: The use of carbon isotopes to constrain the relative rates of carbonate and organic carbon cycling has a long history. Most workers have assumed that the inputs of C to the ocean atmosphere system have isotopic compositions close to that of mantle, but that leads to substantial lower estimate of organic carbon burial and potential oxygen generation than sediment inventory approaches have found. A re-evaluation of carbon input shows that oxidation of old organic carbon and methane result in a signibcantly lower value for the isotopic composition of inputs, implying larger rates of carbon burial that agree much more closely with the inventory approaches. The new results also show that the sedimentary reservoirs of carbonate and organic carbon are experiencing net growth over the last 35 million years and that should increase the oxidation state of the Earth surface environment. Consideration of carbon isotope cycling under low oxygen conditions that were characteristic of the Precambrian shows that the standard assumptions may be lead to substantial mass balance errors under such conditions 

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5. An Anti-Anti-Turbulence Conjecture

   Dewar, W; Deremble, B (January 2021, Ocean and Coastal Research)

   null (Ed.)

   Sandstrom's theorem suggested that buoyancy fluxes can not drive the overturning circulation, an idea that physical oceanographers continue to debate. This paper attempts to provide the most fundamental examination of Sandstrom's theorem that is possible. We conclude that the fundamental role of buoyant forcing in the modern ocean is to damp the circulation, that buoyance fluxes drive significant levels of turbulence, that buoyant turbulent generation is not solely proportional to molecular diffusivity and that some of the main pathways to turbulence are non-Boussineq. We conjecture that the ocean might not be constrained by the `Anti-Turbulence' theorem. 

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