Steven Burgess

My dissertation has two main parts. In the first half, I draw out an underlying presupposition of Descartes' philosophy: what I term "atomism of thought." Descartes employs a radical procedure of doubt in order to show that the first principle of his philosophy, the cogito, is an unshakeable foundation of knowledge. In the dialogue that follows his dissemination of the Meditations, Descartes reveals that a whole set of concepts and rational principles innate in our minds are never doubted. These fundamental units of thought are indivisible, distinct, and isolated, and enable the possibility of any rational demonstration. Atoms of thought are perfectly individuated because God has created them as such. Likewise, our minds have been fashioned such that we necessarily have a clear and distinct perception every time we alight upon these simple notions. In the second part of the dissertation, I take up critiques of Descartes' view given by Nietzsche and Heidegger. In the chapter on Nietzsche, I attempt to fill a lacuna in scholarship about Nietzsche's commentary on Descartes. More specifically, I argue that once the foundation of God is displaced, the basis for accepting atomism of thought dissolves. In the final chapter, I analyze Heidegger's critique of Cartesian atomism. I first look at Heidegger's critique of classical truth as correspondence from Being and Time, and show how it is relevant to a critique of atomism. Then I show how the early Heidegger's holistic philosophical framework can provide an alternative that avoids the pitfalls of atomism. While I limit the scope of my analysis to Descartes' particular formulation, atomism of thought was an influential doctrine throughout modern philosophy. This aspect of Cartesianism has persisted and continues to be a significant theoretical underpinning of many contemporary views. It is my contention that Nietzsche and Heidegger have important contributions to make to this area of thought, and the relative neglect of their work in recent scholarship is a detrimental oversight.

This paper is a phenomenological case study analysis of the hormone testosterone as narrated in medical education textbooks. This analysis demonstrates that these accounts of testosterone depend on three elements of what Judith Butler terms the “heterosexual matrix,” binary sex, naturalized masculinity, and heteronormativity. Those whose sex-assigned-at-birth is inaccurate will mostly receive care on the male/female model of medical practice; likewise, the sexual health of trans, queer, and non-binary populations is poorly represented in medical education, leaving individual practitioners to rely solely on their heteronormative training. In both cases, there is a strong likelihood that patients will receive inadequate care.

BackgroundPreprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the reader’s ability to independently interpret data and reproduce findings.MethodsIn this observational study, we initially compared independent samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. After that, we performed paired comparisons between preprints from bioRxiv to their own peer-reviewed versions in journals.ResultsPeer-reviewed articles had, on average, higher quality of reporting than preprints, although the difference was small, with absolute differences of 5.0% [95% CI 1.4, 8.6] and 4.7% [95% CI 2.4, 7.0] of reported items in the independent samples and paired sample comparison, respectively. There were larger differences favoring peer-reviewed articles in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Changes in reporting from preprints to peer-reviewed versions did not correlate with the impact factor of the publication venue or with the time lag from bioRxiv to journal publication.ConclusionsOur results suggest that, on average, publication in a peer-reviewed journal is associated with improvement in quality of reporting. They also show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions.

BackgroundReproducibility remains a major concern in scientific research, particularly in complex methods such as quantitative polymerase chain reaction (qPCR). Stringent reporting standards are essential to ensure reproducibility, validity of data, and trustworthiness of conclusions. The MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines, introduced in 2009, aimed to improve reporting practices. However, a 2013 study highlighted persistent deficiencies. To further assess the transparency and completeness of qPCR reporting, we conducted a systematic evaluation of recently published research.MethodsWe systematically reviewed research articles employing qPCR that were published in the top 20 journals in genetics and heredity (n = 186) and plant sciences (n = 246). Articles were assessed for completeness of methodological reporting with respect to RNA quality control, reference gene reporting, and details of RNA extraction, RNA-to-cDNA conversion, and qPCR procedures. Frequencies of reporting deficiencies were recorded and descriptively analyzed.ResultsOur analysis identified frequent omissions and insufficient detail in reporting key information required to evaluate and replicate qPCR experiments. RNA integrity was reported in only 7—10% of studies, and assessment methods or instruments used for integrity evaluation were specified in just 14—16%. While primer sequences were often disclosed (88—93%), the traceability of housekeeping/reference genes was limited: accession numbers were provided in only 11% of genetics/heredity papers and 32% of plant science papers. Critical methodological details—including kit names, catalog numbers, and reagent specifications for RNA extraction, RNA-to-cDNA conversion, and qPCR—were also frequently missing, appearing in only 7—14% of reports.ConclusionsThis study underscores the urgent need for improved reporting practices in qPCR experiments. Greater emphasis should be placed on quality controls, detailed descriptions of reagents and materials, and increased analytical transparency. Addressing these deficiencies is vital to enhance reproducibility and to strengthen the trustworthiness of qPCR-based research. Potential solutions include encouraging the citation of protocols in online repositories, providing structured reporting templates, and developing automated tools to support compliance with MIQE standards.Trial registrationNot applicable (not a clinical trial). The study was preregistered on the Open Science Framework (OSF): https://doi.org/10.17605/osf.io/9zp5m.Graphical Abstract.

My dissertation has two main parts. In the first half, I draw out an underlying presupposition of Descartes' philosophy: what I term "atomism of thought." Descartes employs a radical procedure of doubt in order to show that the first principle of his philosophy, the cogito, is an unshakeable foundation of knowledge. In the dialogue that follows his dissemination of the Meditations, Descartes reveals that a whole set of concepts and rational principles innate in our minds are never doubted. These fundamental units of thought are indivisible, distinct, and isolated, and enable the possibility of any rational demonstration. Atoms of thought are perfectly individuated because God has created them as such. Likewise, our minds have been fashioned such that we necessarily have a clear and distinct perception every time we alight upon these simple notions. In the second part of the dissertation, I take up critiques of Descartes' view given by Nietzsche and Heidegger. In the chapter on Nietzsche, I attempt to fill a lacuna in scholarship about Nietzsche's commentary on Descartes. More specifically, I argue that once the foundation of God is displaced, the basis for accepting atomism of thought dissolves. In the final chapter, I analyze Heidegger's critique of Cartesian atomism. I first look at Heidegger's critique of classical truth as correspondence from Being and Time, and show how it is relevant to a critique of atomism. Then I show how the early Heidegger's holistic philosophical framework can provide an alternative that avoids the pitfalls of atomism. While I limit the scope of my analysis to Descartes' particular formulation, atomism of thought was an influential doctrine throughout modern philosophy. This aspect of Cartesianism has persisted and continues to be a significant theoretical underpinning of many contemporary views. It is my contention that Nietzsche and Heidegger have important contributions to make to this area of thought, and the relative neglect of their work in recent scholarship is a detrimental oversight.

The question of what Descartes did and did not doubt in the Meditations has received a significant amount of scholarly attention in recent years. The process of doubt in Meditation I gives one the impression of a rather extreme form of skepticism, while the responses Descartes offers in the Objections and Replies make it clear that there is in fact a whole background of presuppositions that are never doubted, including many that are never even entertained as possible candidates of doubt. This paper resolves the question of this undoubted background of rationality by taking seriously Descartes’ claim that he is carrying out demonstrations modeled after the great geometers. The rational order of geometrical demonstration demands that we first clear away previous demonstrations not proven with the certainty necessary for genuine science. This is accomplished by the method of doubt, which is only applied to the results of possible demonstrations. What cannot be doubted are the very concepts and principles employed in carrying out geometrical demonstration, which enable it to take place. It would be senseless to ask whether we can doubt the essential components of the structure through which questioning, doubting, and demonstration are made possible.

Recent commentators on Nietzsche’s philosophy have paid careful attention to his reflections on truth. While this issue has generated significant dispute, one prominent school of thought is in tacit agreement about the view of language that underlies Nietzschean truth. This view holds that certain linguistic entities can capture precise, distinct units of propositional content and static, rigidly designated conceptual meanings. A closer look at Nietzsche’s various analyses of language and logic reveals not only that he does not subscribe to such a position, but that he offers a sustained critique against the possibility of any form of atomism of language. It was only in the 1880s, after Nietzsche overcame his dualistic commitments to Kant and Schopenhauer and embraced a philosophy of becoming, that the full power of his critique is made manifest.

Central to Descartes’ philosophy is a view about immutable essences and eternal truths. After mentioning a Platonist account of recollection in Meditation V, Descartes declares that the ideas we have of mathematical notions “are not my invention but have their own true and immutable natures” (AT VII, 64/CSM II, 44).Descartes claims that other important philosophical notions, such as God, mind, body, and human free will (AT VII, 68; AT VIII-2, 348; AT III, 383; AT VII, 433, respectively), also have immutable natures or essences. Although Descartes says a good many things about this view, nowhere does he offer definitive doctrine on the matter, and in fact frequently confuses his reader with apparently inconsistent pronouncements about immutable natures and eternal truths. In this essay, I focus on the immutable natures and propose a solution to two of the main problems associated with Descartes’ position, the metaphysical status of immutable natures and the purported indivisibility of their existence as ideas in the mind.