Morgan, G. J. 2006. Virus design, 1955–1962: Science meets art. Phytopathology 96:1287-1291. This... more Morgan, G. J. 2006. Virus design, 1955–1962: Science meets art. Phytopathology 96:1287-1291. This paper traces the beginnings of structural virology in the mid-20th century, focusing especially on the synergy between models of virus structure and models within art, notably Buckminster Fuller’s geodesic domes and Kenneth Snelson’s tensegrity structures. As Donald Caspar and Aaron Klug sought to extend the Crick-Watson theory of spherical virus structure, they explored analogies between biology and architecture, eventually publishing the classic Caspar-Klug theory of virus structure in 1962.
In this paper, I argue against John Beatty’s position in his paper “The Evolutionary Contingency ... more In this paper, I argue against John Beatty’s position in his paper “The Evolutionary Contingency Thesis” by counterexample. Beatty argues that there are no distinctly biological laws because the outcomes of the evolutionary processes are contingent. I argue that the heart of the Caspar–Klug theory of virus structure—that spherical virus capsids consist of 60T subunits (where T = k 2 + hk + h 2 and
The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed most... more The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), and their associated reticulated phylogenies, we need to rethink the notion of species as the natural unit, and we discover additional problems with phylogenetic notions of distance. These problems suggest that a phenetic approach based on morphospaces has just as much appeal, if not more, for microbes as they do for multi-cellular life. Facts about LGT, however, offer no new insight into the additional challenge of reconciling units and differences into a single measure of biodiversity.
Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, Dec 1, 2014
The Polish-American scientist Ludwik Gross made two important discoveries in the early 1950s. He ... more The Polish-American scientist Ludwik Gross made two important discoveries in the early 1950s. He showed that two virusesd murine leukemia virus and parotid tumor virusd could cause cancer when they were injected into susceptible animals. At first, Gross's discoveries were greeted with skepticism: it seemed implausible that viruses could cause a disease as complex as cancer. Inspired by Gross's initial experiments, similar results were obtained by Sarah Stewart and Bernice Eddy who later renamed the parotid tumor virus SE polyoma virus after finding it could cause many different types of tumors in mice, hamsters, and rats. Eventually the "SE" was dropped and virologists adopted the name "polyoma virus." After Gross's work was published, additional viruses capable of causing solid tumors or blood-borne tumors in mice were described by Arnold Graffi, Charlotte Friend, John Moloney and others. By 1961, sufficient data had been accumulated for Gross to confidently publish an extensive mono-graphdOncogenic Virusesdthe first history of tumor virology, which became a standard reference work and marked the emergence of tumor virology as a distinct, legitimate field of study.
In the mid 1950s, Francis Crick and James Watson attempted to explain the structure of spherical ... more In the mid 1950s, Francis Crick and James Watson attempted to explain the structure of spherical viruses. They hypothesized that spherical viruses consist of 60 identical equivalently situated subunits. Such an arrangement has icosahedral symmetry. Subsequent biophysical and electron micrographic data suggested that many viruses had > 60 subunits. Drawing inspiration from architecture, Donald Caspar and Aaron Klug discovered a solution to the problem-they proposed that spherical viruses were structured like miniature geodesic domes.
... In Science, Policy, and the Value-Free Ideal, Heather Douglas (2009) describes the value free... more ... In Science, Policy, and the Value-Free Ideal, Heather Douglas (2009) describes the value free ideal for science, ''that social, ethical, and political values should have no influence over the reasoning of scientists, and ... In B. Gruber & R. Millman (Eds.), Symmetries in science (pp. ...
In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical i... more In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical importance of microbes through an examination of their impact on ecosystems, evolution, biological classification, collaborative behavior, and multicellular organisms. She identifies many understudied conceptual issues in the study of microbes. If philosophers follow her lead, the philosophy of biology will be expanded and enriched.
We use theory and first-principles calculations to investigate how structural changes induced by ... more We use theory and first-principles calculations to investigate how structural changes induced by ultrafast optical excitation of infrared-active phonons change with hydrostatic pressure in LaAlO3. Our calculations show that the observed structural changes are sensitive to pressure, with the largest changes occurring at pressures near the boundary between the cubic perovskite and rhombohedral phases. We rationalize our findings by defining a figure of merit that depends only on intrinsic materials quantities, and show that the peak response near the phase boundary is dictated by different microscopic materials properties depending on the particular phonon mode being excited. Our work demonstrates how it is possible to systematically identify materials that may exhibit particularly large changes in structure and properties due to optical excitation of infrared-active phonons.
ABSTRACT In his Particles and Waves, Peter Achinstein gives a precise probabilistic version of th... more ABSTRACT In his Particles and Waves, Peter Achinstein gives a precise probabilistic version of theoretical coherence inspired by William Whewell's somewhat vague notion of coherence. Whewell believed that as theoretical science proceeds, it becomes more coherent and rejects false incoherent theories. Achinstein offers a challenge: try to make Whewell's idea more precise while maintaining the properties that Whewell claimed coherence to have. This chapter argues (1) that Achinstein's probabilistic rendition of coherence fails to capture Whewell's notion since the probabilistic rendition of coherence is not an a priori sign of truth and (2) that Achinstein's approach is better seen as a critique of Whewell's central methodological claims than as an interpretation of Whewell's ideas.
Morgan, G. J. 2006. Virus design, 1955–1962: Science meets art. Phytopathology 96:1287-1291. This... more Morgan, G. J. 2006. Virus design, 1955–1962: Science meets art. Phytopathology 96:1287-1291. This paper traces the beginnings of structural virology in the mid-20th century, focusing especially on the synergy between models of virus structure and models within art, notably Buckminster Fuller’s geodesic domes and Kenneth Snelson’s tensegrity structures. As Donald Caspar and Aaron Klug sought to extend the Crick-Watson theory of spherical virus structure, they explored analogies between biology and architecture, eventually publishing the classic Caspar-Klug theory of virus structure in 1962.
In this paper, I argue against John Beatty’s position in his paper “The Evolutionary Contingency ... more In this paper, I argue against John Beatty’s position in his paper “The Evolutionary Contingency Thesis” by counterexample. Beatty argues that there are no distinctly biological laws because the outcomes of the evolutionary processes are contingent. I argue that the heart of the Caspar–Klug theory of virus structure—that spherical virus capsids consist of 60T subunits (where T = k 2 + hk + h 2 and
The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed most... more The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), and their associated reticulated phylogenies, we need to rethink the notion of species as the natural unit, and we discover additional problems with phylogenetic notions of distance. These problems suggest that a phenetic approach based on morphospaces has just as much appeal, if not more, for microbes as they do for multi-cellular life. Facts about LGT, however, offer no new insight into the additional challenge of reconciling units and differences into a single measure of biodiversity.
Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, Dec 1, 2014
The Polish-American scientist Ludwik Gross made two important discoveries in the early 1950s. He ... more The Polish-American scientist Ludwik Gross made two important discoveries in the early 1950s. He showed that two virusesd murine leukemia virus and parotid tumor virusd could cause cancer when they were injected into susceptible animals. At first, Gross's discoveries were greeted with skepticism: it seemed implausible that viruses could cause a disease as complex as cancer. Inspired by Gross's initial experiments, similar results were obtained by Sarah Stewart and Bernice Eddy who later renamed the parotid tumor virus SE polyoma virus after finding it could cause many different types of tumors in mice, hamsters, and rats. Eventually the "SE" was dropped and virologists adopted the name "polyoma virus." After Gross's work was published, additional viruses capable of causing solid tumors or blood-borne tumors in mice were described by Arnold Graffi, Charlotte Friend, John Moloney and others. By 1961, sufficient data had been accumulated for Gross to confidently publish an extensive mono-graphdOncogenic Virusesdthe first history of tumor virology, which became a standard reference work and marked the emergence of tumor virology as a distinct, legitimate field of study.
In the mid 1950s, Francis Crick and James Watson attempted to explain the structure of spherical ... more In the mid 1950s, Francis Crick and James Watson attempted to explain the structure of spherical viruses. They hypothesized that spherical viruses consist of 60 identical equivalently situated subunits. Such an arrangement has icosahedral symmetry. Subsequent biophysical and electron micrographic data suggested that many viruses had > 60 subunits. Drawing inspiration from architecture, Donald Caspar and Aaron Klug discovered a solution to the problem-they proposed that spherical viruses were structured like miniature geodesic domes.
... In Science, Policy, and the Value-Free Ideal, Heather Douglas (2009) describes the value free... more ... In Science, Policy, and the Value-Free Ideal, Heather Douglas (2009) describes the value free ideal for science, ''that social, ethical, and political values should have no influence over the reasoning of scientists, and ... In B. Gruber & R. Millman (Eds.), Symmetries in science (pp. ...
In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical i... more In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical importance of microbes through an examination of their impact on ecosystems, evolution, biological classification, collaborative behavior, and multicellular organisms. She identifies many understudied conceptual issues in the study of microbes. If philosophers follow her lead, the philosophy of biology will be expanded and enriched.
We use theory and first-principles calculations to investigate how structural changes induced by ... more We use theory and first-principles calculations to investigate how structural changes induced by ultrafast optical excitation of infrared-active phonons change with hydrostatic pressure in LaAlO3. Our calculations show that the observed structural changes are sensitive to pressure, with the largest changes occurring at pressures near the boundary between the cubic perovskite and rhombohedral phases. We rationalize our findings by defining a figure of merit that depends only on intrinsic materials quantities, and show that the peak response near the phase boundary is dictated by different microscopic materials properties depending on the particular phonon mode being excited. Our work demonstrates how it is possible to systematically identify materials that may exhibit particularly large changes in structure and properties due to optical excitation of infrared-active phonons.
ABSTRACT In his Particles and Waves, Peter Achinstein gives a precise probabilistic version of th... more ABSTRACT In his Particles and Waves, Peter Achinstein gives a precise probabilistic version of theoretical coherence inspired by William Whewell's somewhat vague notion of coherence. Whewell believed that as theoretical science proceeds, it becomes more coherent and rejects false incoherent theories. Achinstein offers a challenge: try to make Whewell's idea more precise while maintaining the properties that Whewell claimed coherence to have. This chapter argues (1) that Achinstein's probabilistic rendition of coherence fails to capture Whewell's notion since the probabilistic rendition of coherence is not an a priori sign of truth and (2) that Achinstein's approach is better seen as a critique of Whewell's central methodological claims than as an interpretation of Whewell's ideas.
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