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Open Access Publications from the University of California

Scholarly Works (124 results)

  • Thesis
  • Peer Reviewed
UC San Francisco Electronic Theses and Dissertations (1998)

    Cover page: Growing old in Tzintzuntzan
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2023)
    Social behaviours are typically modelled using neighbour-modulated fitness, which focuses on individuals having their fitness altered by neighbours. However, these models are either interpreted using inclusive fitness, which focuses on individuals altering the fitness of neighbours, or not interpreted at all. This disconnect leads to interpretational mistakes and obscures the adaptive significance of behaviour. We bridge this gap by presenting a systematic methodology for constructing inclusive-fitness models. We find a behaviours inclusive-fitness effect by summing primary and secondary deviations in reproductive value. Primary deviations are the immediate result of a social interaction; for example, the cost and benefit of an altruistic act. Secondary deviations are compensatory effects that arise because the total reproductive value of the population is fixed; for example, the increased competition that follows an altruistic act. Compared to neighbour-modulated fitness methodologies, our approach is often simpler and reveals the models inclusive-fitness narrative clearly. We implement our methodology first in a homogeneous population, with supplementary examples of help under synergy, help in a viscous population and Creels paradox. We then implement our methodology in a class-structured population, where the advantages of our approach are most evident, with supplementary examples of altruism between age classes, and sex-ratio evolution.
      Cover page: How to make an inclusive-fitness model.
      • Thesis
      • Peer Reviewed
      UC Berkeley Electronic Theses and Dissertations (2020)

      Abstract

      The Application of Peircean Semiotics to the Elder Futhark Tradition:

      Establishing Parameters of Magical Communication

      by

      Scott T. Shell

      Doctor of Philosophy in German

      University of California, Berkeley

      Professor Irmengard Rauch, Chair

      This dissertation addresses the issue of magical communication found in the Elder Futhark runic inscriptions. The study examines the Kragehul Spear Shaft (DR 196), Björketorp runestone (DR 360), the Horn(s) of Gallehus (DR 12), Gummarp runestone (DR 358), Lindholm amulet (DR 261), Straum whetstone (KJ 50), Ribe skull fragment (DR EM85; 151B), the Noleby runestone (KJ 67), and the Eggja runestone (N KJ 101). It seeks magical communication which may putatively be encompassed by my proposed law of magical semiosis, which reads:

      While operating within an Umwelt where we assume magic is a phaneron in the Weltanschauung of the Runemaster, he or she intentionally manipulates signs and sign-relations within a sign-network by the use of icons (like produces like), indices (contagious properties) and/or symbols (learned conceptual properties). While there will be more than one sign within the sign-network, it is the magical sign which is the most salient when working with such an object. This includes—but is not limited to—phonetic iconicity, semantic iconicity, indexical curses, iconic theophany formulas whereby the Runemaster becomes a god (degrees of iconicity), mythic reenactments, Begriffsrunen

      (symbolic indexical icons), and certain word-formulae especially alu ‘ecstatic state’ (disputed).

      I argue that, by setting objective parameters for measuring this law of magical communication, we can then determine whether or not a particular inscription should be understood as magical or non-magical specific to the Umwelt and Weltanschauung of the Runemaster. Essentially, this dissertation is meant to challenge runologists in postulating falsifiable criteria so we may, in an academic setting, discuss magical communication in the world of the Runemaster.

      This study begins by discussing how Charles Sanders Peirce can help provide us with a basic framework regarding the sign. His phenomenological framework is applied to the world of the Runemaster. The next section then addresses the problem with the word “magic,” which goes far beyond the concept of “if it does not make sense, it must be magical.” It then leads to a discussion of runes and numinous qualities and finally to a corpus chapter which applies the theories and methods I have adopted.

        Cover page: The Application of Peircean Semiotics to the Elder Futhark Tradition: Establishing Parameters of Magical Communication
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2019)
        Fields such as behavioural and evolutionary ecology are built on the assumption that natural selection leads to organisms that behave as if they are trying to maximise their fitness. However, there is considerable evidence for selfish genetic elements that change the behaviour of individuals to increase their own transmission. How can we reconcile this contradiction? Here we show that: (1) when selfish genetic elements have a greater impact at the individual level, they are more likely to be suppressed, and suppression spreads more quickly; (2) selection on selfish genetic elements leads them towards a greater impact at the individual level, making them more likely to be suppressed; (3) the majority interest within the genome generally prevails over 'cabals' of a few genes, irrespective of genome size, mutation rate and the sophistication of trait distorters. Overall, our results suggest that even when there is the potential for considerable genetic conflict, this will often have negligible impact at the individual level.
          Cover page: Adaptation is maintained by the parliament of genesCreative Commons 'BY' version 4.0 license
          • Thesis
          • Peer Reviewed
          UC Riverside Electronic Theses and Dissertations (2009)

          Soil temperature plays an important role in physical, biological and microbiological processes occurring in the soil. It can be used as indicative of regional climate change. A long-term soil temperature database was collected at 75 locations in the Mojave Desert region by the Pallmann method from 1982-2000. This long-term database of soil temperature is invaluable and was used to analyze the spatiotemporal change pattern of soil temperature, and to examine the relationship between regional climate change and soil temperature over an extended period of time.

          The main conclusions of this research are: 1) the accuracy and consistency of the Pallmann method was good in comparison with two other temperature measurement methods: thermistor sensor and diffusion-cell method. The Pallmann method is an ideal method for studying the spatial variation in soil temperature and long-term climate changes. 2) Elevation is the dominated factor governing the spatial variation of soil temperature in the Mojave Desert region and can be used to estimate the spatial distribution of soil temperature. In the Mojave Desert region, hyperthermic soil is the most extensive one, which accounts for around 55% of the whole region. Thermic soil accounts for 38.7%. Frigid and mesic soils only occur at high elevation mountains. 3) Seasonal soil temperatures vary greatly in the Mojave Desert region and decrease linearly with elevation. The differences of the summer and winter soil temperature are around 20 °C under the same elevation. The effect of elevation on soil temperature is more pronounced in summer season than in winter season. 4) Soil and air temperature are highly correlated in the Mojave Desert region. Both of the soil and air temperature were found to be highly correlated with elevation and their spatiotemporal variations are highly positively correlated. 5) The Mojave Desert is experiencing a warming trend. Based on continued measurements across the region, the air and soil temperatures have risen at the rates of 0.79 and 0.63°C per 10 year from 1982 to 2000. The anomalies of annual precipitation were inversely correlated with those of soil temperature. The soil temperature of the Mojave Desert would be cooler than normal under El Niño conditions. 6) The climatic variables of air temperature, precipitation and evaporation had significant correlation with soil temperature. The spatial-temporal variation of soil temperature can be predicted based on the linear regression equation with air temperature and precipitation as independent variables.

            Cover page: Distribution of Soil Temperature Regimes and Climate Change in the Mojave Desert Region
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2023)
            Croziers paradox suggests that genetic kin recognition will not be evolutionarily stable. The problem is that more common tags (markers) are more likely to be recognized and helped. This causes common tags to increase in frequency, eliminating the genetic variability that is required for genetic kin recognition. Two potential solutions to this problem have been suggested: host-parasite coevolution and multiple social encounters. We show that the host-parasite coevolution hypothesis does not work as commonly assumed. Host-parasite coevolution only stabilizes kin recognition at a parasite resistance locus if parasites adapt rapidly to hosts and cause intermediate or high levels of damage (virulence). Additionally, when kin recognition is stabilized at a parasite resistance locus, this can have an additional cost of making hosts more susceptible to parasites. However, we show that if the genetic architecture is allowed to evolve, meaning natural selection can choose the recognition locus, genetic kin recognition is more likely to be stable. The reason for this is that host-parasite coevolution can maintain tag diversity at another (neutral) locus by genetic hitchhiking, allowing that other locus to be used for genetic kin recognition. These results suggest a way that host-parasite coevolution can resolve Croziers paradox, without making hosts more susceptible to parasites. However, the opportunity for multiple social encounters may provide a more robust resolution of Croziers paradox.
              Cover page: Host-parasite coevolution and the stability of genetic kin recognition.
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2022)
              Crozier's paradox suggests that genetic kin recognition will not be evolutionarily stable. The problem is that more common tags (markers) are more likely to be recognised and helped. This causes common tags to increase in frequency, and hence eliminates the genetic variability that is required for genetic kin recognition. It has therefore been assumed that genetic kin recognition can only be stable if there is some other factor maintaining tag diversity, such as the advantage of rare alleles in host-parasite interactions. We show that allowing for multiple social encounters before each social interaction can eliminate Crozier's paradox, because it allows individuals with rare tags to find others with the same tag. We also show that rare tags are better indicators of relatedness, and hence better at helping individuals avoid interactions with non-cooperative cheats. Consequently, genetic kin recognition provides an advantage to rare tags that maintains tag diversity, and stabilises itself.
                Cover page: Multiple social encounters can eliminate Crozier’s paradox and stabilise genetic kin recognition
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2024)
                Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis is that genes which are more likely to be transferred, such as those on plasmids, should be more likely to code for cooperative traits. Testing this prediction requires identifying all genes for cooperation in bacterial genomes. However, previous studies used a method which likely misses some of these genes for cooperation. To solve this, we used a new genomics tool, SOCfinder, which uses three distinct modules to identify all kinds of genes for cooperation. We compared where these genes were located across 4648 genomes from 146 bacterial species. In contrast to the prediction of the hypothesis, we found no evidence that plasmid genes are more likely to code for cooperative traits. Instead, we found the opposite-that genes for cooperation were more likely to be carried on chromosomes. Overall, the vast majority of genes for cooperation are not located on plasmids, suggesting that the more general mechanism of kin selection is sufficient to explain the prevalence of cooperation across bacteria.
                  Cover page: Genes for cooperation are not more likely to be carried by plasmids.
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2010)
                    Cover page: Reframing Critical Needs in Vector Biology and Management of Vector-Borne DiseaseCreative Commons 'BY' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2023)
                    It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.
                      Cover page: Is cooperation favored by horizontal gene transfer?
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