Rhodri Lewis

Multigene phylogeny resolves deep branching of Amoebozoa.

Amoebozoa is a key phylum for eukaryote phylogeny and evolutionary history, but its phylogenetic validity has been questioned since included species are very diverse: amoebo-flagellate slime-moulds, naked and testate amoebae, and some flagellates. 18S rRNA gene trees have not firmly established its internal topology. To rectify this we sequenced cDNA libraries for seven diverse Amoebozoa and conducted phylogenetic analyses for 109 eukaryotes (17-18 Amoebozoa) using 60-188 genes. We conducted Bayesian inferences with the evolutionarily most realistic site-heterogeneous CAT-GTR-Γ model and maximum likelihood analyses. These unequivocally establish the monophyly of Amoebozoa, showing a primary dichotomy between the previously contested subphyla Lobosa and Conosa. Lobosa, the entirely non-flagellate lobose amoebae, are robustly partitioned into the monophyletic classes Tubulinea, with predominantly tube-shaped pseudopodia, and Discosea with flattened cells and different locomotion. Within Conosa 60/70-gene trees with very little missing data show a primary dichotomy between the aerobic infraphylum Semiconosia (Mycetozoa and Variosea) and secondarily anaerobic Archamoebae. These phylogenetic features are entirely congruent with the most recent major amoebozoan classification emphasising locomotion modes, pseudopodial morphology, and ultrastructure. However, 188-gene trees where proportionally more taxa have sparser gene-representation weakly place Archamoebae as sister to Macromycetozoa instead, possibly a tree reconstruction artefact of differentially missing data.

Helkesimastix marina n. sp. (Cercozoa: Sainouroidea superfam. n.) a gliding zooflagellate of novel ultrastructure and unusual ciliary behaviour.

Unlike Helkesimastix faecicola and H. major, Helkesimastix marina is marine, ingests bacteria, is probably also a cannibal, and differs in cell cycle ciliary behaviour. Daughter kinetids have mirror symmetry; pre-division cilia beat asymmetrically. We sequenced its 18S rDNA and studied its ultrastructure to clarify its taxonomy. Helkesimastix (Helkesimastigidae fam. n.) differs unexpectedly radically from cercomonads, lacking their complex microtubular ciliary roots, grouping not with them but with Sainouridae within Pansomonadida. Longitudinal cortical microtubules emanate from a dense apical centrosomal plate, where a striated rhizoplast attaches the nucleus, and two very short subparallel centrioles attach by dense fibres. The marginally more posterior centriole, attached to the centrosomal plate by a dense forked fibre, bears the long 9+2 gliding posterior cilium and a microtubular root; the left-side, nucleus-attached, left centriole bears an immotile ciliary stump with abnormal axoneme of nine disorganized mainly singlet microtubules, unlike the sainourid anterior papilla. Both transitional regions have a proximal lattice, the posterior centriole with slender hub. Sainouroidea superfam. n. (Sainouridae; Helkesimastigidae) have homologous cytoskeletal geometry. Dorsal Golgi dictyosome and posterior microbody are attached to the nuclear envelope, which has slender micro-invaginations and probably a cortical lattice. Bacteria are digested posteriorly in association with numerous mitochondria with flat cristae.

Morphology and phylogeny of Sainouron acronematica sp. n. and the ultrastructural unity of Cercozoa.

Sainouron are soil zooflagellates of obscure taxonomy. We studied the ultrastructure of S. acronematica sp. n. and sequenced its extremely divergent 18S rDNA and that of Cholamonas cyrtodiopsidis (here grouped as new family Sainouridae) to clarify their phylogeny. Ultrastructurally similar, they weakly group together, deeply within Monadofilosa. Sainouron has three cytoplasmic microtubules; all organelles specifically link to them or the nucleus. Mature centrioles have fibrous rhizoplasts. The posterior centriole bearing the motile cilium (with cortical filaments) has a transitional hub-lattice; a dense spiral fibre links its thicker rhizoplast and triplets; its ciliary root has two microtubules: mt1, underlying the plasma membrane, initiates at the spiral fibre; mt2, laterally attached to mt1 and nucleus, initiates in the amorphous centrosomal region. The anterior younger cilium, an immotile stub with submembrane skeleton as in Cholamonas, lacks axoneme, microtubular root, rhizoplasts and spiral fibre, but becomes the posterior one every cell cycle. The nuclear envelope donates coated vesicles directly to the Golgi, which makes kinetocyst-type extrusomes, concentrated at the cell anterior for extrusion into phagosomes. Ciliary transition region proximal hub-lattices (postulated to contain centrin) and distal nonagonal fibres are cercozoan synapomorphies, found with slight structural variation in all flagellate Cercozoa, but not in outgroups.

Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista.

Heliozoan protists have radiating cell projections (axopodia) supported by microtubular axonemes nucleated by the centrosome and bearing granule-like extrusomes for catching prey. To clarify previously confused heliozoan phylogeny we sequenced partial transcriptomes of two tiny naked heliozoa, the endohelean Microheliella maris and centrohelid Oxnerella marina, and the cercozoan pseudoheliozoan Minimassisteria diva. Phylogenetic analysis of 187 genes confirms that all are chromists; but centrohelids (microtubules arranged as hexagons and triangles) are not sisters to Endohelea having axonemes in transnuclear cytoplasmic channels (triangular or square microtubular arrays). Centrohelids are strongly sister to haptophytes (together phylum Haptista); we explain the common origins of their axopodia and haptonema. Microheliella is sister to new superclass Corbistoma (zooflagellate Telonemea and Picomonadea, with asymmetric microfilamentous pharyngeal basket), showing that these axopodial protists evolved independently from zooflagellate ancestors. We group Corbistoma and Endohelea as new cryptist subphylum Corbihelia with dense fibrillar interorganellar connections; endohelean axopodia and Telonema cortex are ultrastructurally related. Differently sampled trees clarify why corticate multigene eukaryote phylogeny is problematic: long-branch artefacts probably distort deep multigene phylogeny of corticates (Plantae, Chromista); basal radiations may be contradictorily reconstructed because of their extreme closeness and the Bayesian star-tree paradox. Haptista and Hacrobia are holophyletic, and Chromista probably are.

A Kind of Sagacity: Francis Bacon, the Ars Memoriae and the Pursuit of Natural Knowledge

Within the emergent field of memory studies, many scholars have turned their attention to the reception of the ars memoriae, and have viewed a diverse range of intellectual and cultural practices through the prism it provides.1 These studies have much to recommend them: they have proposed valuable new ways of reading literary, artistic, scientific, social and educational history, to say nothing of the history of the book. Yet on other levels, these accounts have helped to foster confusion as to what exactly the ‘art of memory’ was in itself, and of what its proponents thought that it equipped one to achieve. The problem is particularly acute in early modern studies: despite the path-breaking work of Frances Yates, Paolo Rossi and Lina Bolzoni, the sixteenthand seventeenth-century ars memoriae has not been subject to the detailed reconstruction and analysis that Herwig Blum and Mary Carruthers have brought to bear on the ancient and medieval periods.2 In a preliminary attempt to come to better terms with the early modern ars memoriae and its contexts, this essay reconsiders a figure well-known from the extant literature on the subject: the English natural philosopher, lawyer, historian and statesman, Francis Bacon. I begin with a consideration of Bacon’s earliest writings on the subject, and identify some apparent tensions within them. These are, in some measure, resolved through a consideration of classical and early modern ideas about the psychology of memory; within these, the Aristotelian distinction between memory and recollection is shown to be crucial. After sketching the history of the ars memoriae in the long sixteenth

Francis Bacon and Ingenuity

This essay discusses the Latin term ingenium within the writings of Francis Bacon (1561–1626). It proposes that although ingenium does not easily translate into English, Bacon uses the term in a clearly defined range of senses. For the most part, he echoes the discourse of ingenuity and inventiveness common to many sixteenth-century humanists, but differs from them in sharply delimiting the scope and status of ingenious thinking. In particular, he excludes ingenuity from the logical portion of his reformed art of discovery: as the goal of this was demonstrative knowledge, Bacon (like the Aristotelian logicians he aimed to supplant) believed that it had to be the province of the intellect, not of ingenium. A fuller understanding of the ways in which Bacon uses ingenium casts his methodological thought into illuminating new relief, and draws attention to the manner in which Bacon’s ideas were appropriated, criticized, and misunderstood in the half century after his death — not least by the self-styled Bacon...

The publication of John Wilkins's Essay (1668): some contextual considerations

John Wilkinss Essay towards a Real Character and a Philosophical Language was published in 1668. It was an attempt to institute an artificial language based on the order of things, and was expected to contribute to improved scientific practice, to facilitate inter–linguistic communication and to ameliorate religious controversy. Wilkins was a founding member of The Royal Society, and the Essay was published under its imprimatur. The printer to The Royal Society was John Martyn, and this article traces the occasionally damaging impact Martyn had upon the publishing practice of the early Royal Society, before considering the steps Wilkins took to ensure the best possible reception for his work. Prominent amongst these was the fact that although Martyns name appeared on the title page of the Essay, Wilkins was principally dependent on Samuel Gellibrand—another, more creditable, printer with whom he had a long–standing relationship—for its publication. Wilkinss approach to the production of a book of the Essays size and typographic complexity is also considered.

On Looking Again into Champagnolla’s Homer

Abstract This article discusses a new source with which to reconstruct a lost artificial language scheme of the mid-seventeenth century, the author of which was said to have translated parts of Homer into his artificial character. Other than that he was an émigré (and presumably Francophone) scholar named Champagnolla, little has been known about this author or what his scheme involved. A much fuller account of it is provided by a manuscript in the National Library of Wales, Aberystwyth; it records the thoughts of those who had, at the instigation of King James I, been set to assess the value and practicability of proposals for an artificial language put forward by an anonymous French scholar. They provide a clear picture both of what Champagnolla had intended, and the political contours of intellectual life at the end of the Jacobean period.

Robert Hooke at 371

Writing in his manuscript treatise “An Idea of Education”, John Aubrey struck the Baconian attitude that to study with the greatest proatability a “few books, but well chosen, thoroughly digested with practice and observation, does the business”. Of those with whom Aubrey had discussed this, Thomas Hobbes and William Petty conaded in him their belief “that had they read as much as other men, they should have known no more than other men”. Further, Aubrey held that “neither are Sir Ch. Wren or Mr. R. Hooke great readers” (Aubrey 1972, 86). We recognize such claims as being of a piece with the Royal Society’s motto, nullius in verba—or, roughly, “take no-one’s word for it”; real knowledge came from the experimental study of nature, not through reliance on established authorities. But that the Royal Society only made bold to proclaim this on the authority of Horace is one clue that its modern students should not take these disavowals of conventional learning at face value. As historians have come to realize, the natural philosophers assembled within the Royal Society’s orbit were every bit as concerned with what they might learn from books as they were with investigating the book of nature. A case in point (indeed, an instance of the angerpost) is Robert Hooke, whose broad ranging scholarly, scientiac and philosophical interests are everywhere attested in Aubrey’s “Idea”, and whose personal library was both sizeable and diverse. To give a by no means systematic (or exhaustive) survey of the areas in which he was active, Hooke was a physicist, engineer, microscopist, meteorologist, horologist, chronologer, geologist, astronomer, psychologist, surveyor, architect, alchemist, mathematician, musicologist, logician, grammarian and bibliophile. When praising him, Aubrey knew whereof he spoke: Hooke was one of his closest friends and, during Aubrey’s increasingly frequent spells of impecuniosity, Hooke lent him support.