Biological Notion Research Articles

Rethinking Organismic Unity: Object-Oriented Ontology and the Human Microbiome

Abstract In recent years, a vast array of thinkers have been invested in challenging the long-standing binary division between the human and nonhuman. The notion of the human microbiome especially attests to the truth of such a complication, since current research in biology strongly suggests that we are at the very least as much microbe as we are human and that the number of microorganisms in the human body outnumber distinctly human cells considerably. In this article, we aim to bring the biological notion of the human microbiome in dialogue with Object-Oriented Ontology (OOO) so as to ultimately show that there can be a fruitful exchange of ideas between the two currents of microbiome research and OOO more specifically, and that Graham Harman’s top-down account of objective emergence can be fruitfully a bottom-up approach according to which the parts of an object also impact and constrain the whole.

An Enigmatic Soft-Tissue Creeping Phenomenon: The Spontaneous Peri-Implant Mucosa Margin and Papilla Growth, Part Two-A Scientifically Supported Hypothesis Article.

In our previous article, we observed and measured a spontaneous growth in the coronal direction of the keratinized tissues present around implants. This growth involved both free margins and interdental papillae, and we indicated our hypothesis on the probable cause of this still-unexplained phenomenon. The growth of oral soft tissues involves several other structures, such as the linea alba and tongue indentation. Our idea holds that growth of these tissues is generated by the negative intraoral pressure created in the oral phase of swallowing and the subsequent resting position, which through the resulting suction causes a shift of these soft structures in the gaps around the dental crowns. Other hypotheses have been suggested in the past to understand this phenomenon of soft tissue growth, which still lacks data supporting etiological evidence. The purpose of this article is to thoroughly analyze and verify our model by comparing the clinical observations with citations and examples from the literature, combined with notions of physiology, biology, and physics that help in clarifying these events. To better explain the mechanisms of oral soft tissue growth, photographs of clinical cases paradigmatic of the phenomenon are shown.

An epistemic argument for evolutionary dispositions

The use of dispositions has been put into question many times in the philosophical literature, especially with regards to how dispositional attributions can be justified. Yet, dispositions are an important part not only of our everyday talk but also of our scientific practices. In this paper, we develop an argument that infers the epistemic justification of dispositional talk from itsindispensability for carrying out basic epistemological projects, and we apply it to the use of dispositions in evolutionary biology. For doing this, we first advocate for a function-based strategy for the epistemic justification of dispositional attributions. We next review the functional role of some key dispositional notions in evolutionary biology, such as fitness and evolvability. Then, we show that alternative non-dispositional substitutes of these dispositions fail to fulfill their roles to the same degree. We conclude that the use of dispositions is justified in evolutionary biology.

Political animality

AbstractThis essay contributes to contemporary discussions concerning so‐called animal politics by drawing from the history of the notion of political animal. Two different historical meanings of the notion are identified: (1) normative political animality that is intrinsically linked with rationality, language, and justice; (2) biological political animality that focuses on collaboration for the sake of a common aim. The former is applicable only to human beings, while the latter can also be used in relation to other animals. After briefly discussing the Aristotelian background of the notion, the essay argues that in medieval Aristotelian tradition, the normative meaning prevailed and the biological one was set aside. However, it is precisely the biological notion that appears useful today. The essay suggests several ways in which it might benefit contemporary theoretical discussions concerning animals, thus laying ground for further developments in animal politics.

Trans* Lives of Jadzia Dax: A Queer Ecology Reading of Symbiosis in Star Trek: Deep Space Nine

Abstract: This article explores the symbiotic relationship of the Trill species in Star Trek from nonbinary, trans*, and queer ecological perspectives. The Trill’s unique physiology allows them to enter into a symbiotic relationship with a symbiont, leading to nonheterosexual, nonbinary, and androgynous features. By examining the trans metaphor represented by Jadzia Dax, a Trill character in Star Trek: Deep Space Nine , the article highlights the ways in which the Trill challenge traditional notions of gender, biology, and symbiosis by introducing queerness. Furthermore, the article argues that symbiosis, when viewed through the lens of queer ecology, posthumanism, and more-than-humanisms, reveals that all living beings engage in queering, emphasizing the interconnectedness of life and the absence of living without symbiosis.

EVALUATING NANDINI RIVER WATER QUALITY: A SYSTEMATIC REVIEW OF PHYSICOCHEMICAL STUDIES

The quality of water is described to be the condition of the water, which includes the three basic forms of physical, chemical, and biological notions. Salinity, turbidity, the amount of dissolved oxygen and carbon dioxide, and microorganisms, herbicides, and pesticides along with the presence of heavy metals edit reminds to have a direct effect on the water quality. Because the universal solvent is a major factor affecting the lives of the humongous population of people, recognition of the quality of water is significantly important. Due to the fact that the presence of contaminants in water can directly lead to health issues such as reproductive problems, different kinds of neurological disorders, and gastrointestinal diseases, it is of vehement importance to understand the water quality. Nandini River flows through the Nashik city of Maharashtraand it is the tributary of the river Godavari which is is a vital source of water for the people of the Nashik region.Travelling from the heart of Nashik the river Nandini is faced with several issues related to its degrading water quality. Hence, the study sheds light onto the quality of water of the Nandini river, in terms of Physicochemical Studies.

Lay Misperceptions of Culture as “Biological” and Suggestions for Reducing Them

Culture is typically studied as socialized and learned. Yet lay intuitions may hold that culture is associated with biology via perceptions of race, presenting a problem for those who study culture: There may be a mismatch between how psychologists study culture and how their research is interpreted by lay audiences. This article is a call to researchers to recognize this mismatch as a problem and to critically evaluate the way we study culture. We first describe evidence that laypeople tend to associate culture with notions of folk biology. Next, we propose three suggestions for researchers: explicitly address whether biological processes are, or are not, relevant for studying culture in their work; consider using multiple methods because different methods for studying culture may come with assumptions about culture as more tied to socialization or biology; and represent all people as cultural by studying multiple forms of culture and by contextualizing all psychological research. Last, we provide an example for how researchers can implement these suggestions to encourage more accurate interpretations of findings.

Heritability of morphological and behavioural traits in evolving robots

AbstractIn the field of evolutionary robotics, choosing the correct genetic representation is a complicated and delicate matter, especially when robots evolve behaviour and morphology at the same time. One principal problem is the lack of methods or tools to investigate and compare representations. In this paper we introduce and evaluate such a tool based on the biological notion of heritability. Heritability captures the proportion of phenotypic variation caused by genotypic variation and is often used to better understand the transmissibility of traits in real biological systems. As a proof of concept, we compare the heritability of various robot traits in two systems, one using a direct (tree based) representation and one using an indirect (grammar based) representation. We measure changes in heritability during the course of evolution and investigate how direct and indirect representation can be biased towards more exploration or exploitation throughout the course of evolution. The empirical study shows that heritability can be a useful tool to analyze different representations without running complete evolutionary processes using them.

Genetic heritage of the Baphuthi highlights an over-ethnicized notion of “Bushman” in the Maloti-Drakensberg, southern Africa

Using contemporary people as proxies for ancient communities is a contentious but necessary practice in anthropology. In southern Africa, the distinction between the Cape KhoeSan and eastern KhoeSan remains unclear, as ethnicity labels have been changed through time and most communities were decimated if not extirpated. The eastern KhoeSan may have had genetic distinctions from neighboring communities who speak Bantu languages and KhoeSan further away; alternatively, the identity may not have been tied to any notion of biology, instead denoting communities with a nomadic "lifeway" distinct from African agro-pastoralism. The Baphuthi of the 1800s in the Maloti-Drakensberg, southern Africa had a substantial KhoeSan constituency and a lifeway of nomadism, cattle raiding, and horticulture. Baphuthi heritage could provide insights into the history of the eastern KhoeSan. We examine genetic affinities of 23 Baphuthi to discern whether the narrative of KhoeSan descent reflects distinct genetic ancestry. Genome-wide SNP data (Illumina GSA) were merged with 52 global populations, for 160,000 SNPs. Genetic analyses show no support for a unique eastern KhoeSan ancestry distinct from other KhoeSan or southern Bantu speakers. The Baphuthi have strong affinities with early-arriving southern Bantu-speaking (Nguni) communities, as the later-arriving non-Nguni show strong evidence of recent African admixture possibly related to late-Iron Age migrations. The references to communities as "San" and "Bushman" in historic literature has often been misconstrued as notions of ethnic/biological distinctions. The terms may have reflected ambiguous references to non-sedentary polities instead, as seems to be the case for the eastern "Bushman" heritage of the Baphuthi.

Chrysippus’ Theory of Cosmic Pneuma: Some Remarks in Light of Medical and Biological Doctrines on Respiration, Digestion and Pulse

Abstract The aim of this paper is to explore how the cosmic soul works and how it accomplishes its providential and demiurgic tasks in Chrysippus’ system. Drawing on (i) the analogy Chrysippus establishes between the individuum and the cosmos and (ii) biological and medical theories of respiration, digestion, and pulse, I will show that the movements of Chrysippus’ cosmic soul reproduce the processes of digestion, pulse, and respiration at a cosmic level. My claim is that Chrysippus, in addition to adopting Praxagoras’ notion that inhaled air nourishes pneuma—well established in the scholarship—appropriated Aristotle’s complex mechanism of respiration and digestion based on the teleological role of cold air, crucial for preserving vital heat. So understood, Chrysippus’ application of biological notions to cosmology allows him to endow the active principle with effective causation throughout the cosmos.

Delusions and beliefs: a knowledge-first approach

In Delusions and Beliefs (2019), Kengo Miyazono proposes an extended and convincing argument for the thesis that delusions are malfunctional beliefs. One of the key assumptions for this argument is that belief is a biological notion, and that the function of beliefs is a product of evolution. I challenge the thesis that evolutionary accounts can furnish an epistemologically satisfying account of beliefs because evolutionary success does not necessarily track epistemic success. Consequently, also delusions as beliefs cannot be explained in a satisfactory manner by looking at beliefs’ evolutionary function. How can we then salvage the notion of delusions as epistemologically relevant malfunctioning beliefs? I propose that knowledge-first epistemology gives us a way out. Knowledge-first accounts argue that knowledge is more primitive than belief. That is, knowledge is not a kind of successful beliefs (true, justified, etc.); instead, beliefs are failed attempts at knowledge. Being a belief derives from the norms of knowledge. Explaining the epistemology of beliefs through the primitive norms of knowledge, we can also explain why delusions are malfunctional beliefs: The cognitive and psychological defects that produce delusions block the beliefs from becoming knowledge. Consequently, delusions are attempts at knowledge that have failed particularly badly.

The GRN concept as a guide for evolutionary developmental biology.

Organismal phenotypes result largely from inherited developmental programs, usually executed during embryonic and juvenile life stages. These programs are not blank slates onto which natural selection can draw arbitrary forms. Rather, the mechanisms of development play an integral role in shaping phenotypic diversity and help determine the evolutionary trajectories of species. Modern evolutionary biology must, therefore, account for these mechanisms in both theory and in practice. The gene regulatory network (GRN) concept represents a potent tool for achieving this goal whose utility has grown in tandem with advances in "omic" technologies and experimental techniques. However, while the GRN concept is widely utilized, it is often less clear what practical implications it has for conducting research in evolutionary developmental biology. In this Perspective, we attempt to provide clarity by discussing how experiments and projects can be designed in light of the GRN concept. We first map familiar biological notions onto the more abstract components of GRN models. We then review how diverse functional genomic approaches can be directed toward the goal of constructing such models and discuss current methods for functionally testing evolutionary hypotheses that arise from them. Finally, we show how the major steps of GRN model construction and experimental validation suggest generalizable workflows that can serve as a scaffold for project design. Taken together, the practical implications that we draw from the GRN concept provide a set of guideposts for studies aiming at unraveling the molecular basis of phenotypic diversity.

“El Viudo De Pescado”

“El Viudo De Pescado”

The The Teleological Program. Ernst Mayr’s Teleonomy from Philosophy to Cybernetics (or Kant’s Revenge)

Teleology is still a source of embarrassment for the natural sciences and in particular for biology that seems unable to describe and explain the genesis and structure of life without it. How is it possible for something not yet existing to determine the occurrence of what is temporally prior to it? How can the future cause the present and the past? In what follows we intend to examine the elaboration of the biological notion of «teleonomy» through the writings of Ernst Mayr, in order to verify its rigor and strenght with respect to the criteria of scientificity adopted by Mayr himself, in particular with respect to the adoption of the cybernetic model. On the one hand, to show the consistency of the debt that the so-called scientific discourse owes to the philosophical tradition, where it elaborates notions that claim to be emancipated. On the other hand, to detect, within the scientific discourse itself, the limits that a certain position that claims to be scientifically founded can impose on research, becoming a dogmatic assumption.

Forensic Analytical Chemistry: Connecting Science and Justice

Currently, analytical chemistry is more than simply its division into classical and instrumental. It is an interdisciplinary area that involves notions of biology, toxicology, statistics, computer science, and physics, among others. There are several areas of knowledge applied in the development of a chemical analysis, which is configured as all the processes necessary for the identification and quantification of the different components of a sample. When this sample is a trace material from a crime scene, analytical chemistry assumes a central role in the conversion of this sample into material evidence with legal value through consolidated and validated procedures, obtained by exhaustive investigative and methodological studies. The responsibility assumed is in the confidence of the result obtained, which will only be possible with the validation of the method. Although not all methods are perfect, a quantitative determination requires a precise and accurate methodology. Therefore, analytical chemistry is very important to forensic chemistry. Material evidence has a great influence on a trial because it is clothed in technical characteristics, and the expectation is that it will help to unequivocally clarify the truth of the facts. It is this expectation that makes the work of the analytical chemist so important in conducting an analytical procedure for forensic purposes. The result obtained may or may not incriminate someone. Another analytical challenge in forensic analysis is the collection and preparation of a sample that has a criminal trace profile. Such procedures should preserve as much of the criminal evidence as possible. At a crime scene, several samples can be considered evidence: soils, fibers, glass, gunshot residues, explosives, among others. Locard's principle of exchange states that whenever two objects come into contact, an exchange of materials occurs between them and, thus, a connection is established between the suspect and the crime scene or between the suspect and the victim based on the transfer of fragments of the materials. Once again, analytical rigor will play a relevant role in the preservation and experimental conduct of the traces. A failure in the analytical procedure may make it impossible to use a trace as material evidence in a court of law, jeopardizing its use in the conviction of the judge or jury. It is up to the forensic analysts to provide a result with credibility and legal security, i.e., to rigorously follow the analytical protocols. Forensic research is dynamic. One example is the demand for analytical methods that encompass the wide variety of newly emerging psychoactive substances (NPS), formerly known as "designer drugs", which must continually be detected and catalogued. In the Interview in this volume, Dr. Barry Logan tells us about this challenge in his career. I want to register my special thanks to Prof. Dr. Bruno Martinis from the Department of Chemistry of the Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo (DQ-FFCLRP-USP) of -, who mediated and made possible the interview for BrJAC of one of the most prominent scientists in the area. In his Point of View, Federal Criminal Expert Marcus Andrade tells us about the complexity of forensic chemical analysis of works of art. The analysis of the surface of a painting requires, besides the historical study of the piece, the physical-chemical characterization of its components through an interesting combination of non-destructive analytical techniques such as microscopy, X-ray fluorescence, infrared spectroscopy, among others, which are powerful tools in the process of authenticating a work of art. Nevertheless, the art market, due to the high added value, has attracted organized crime in money laundering in cases of active and passive corruption. Prof. Dr. Jesus Antônio Velho, Federal Criminal Expert and lecturer at the DQ-FFCLRP-USP, addresses the new trends in analytical chemistry for the examination and interpretation of traces of crimes: the determination of the origin of seized drugs (chemical profile), the investigation of document fraud, and the analysis of the evaluation of works of art. Professor Jesus' letter is the result of his long experience in the field and his exceptional insight into the forensic sciences. The author of several books in the field, his text is a gift to us all. We hope readers will enjoy this special edition of BrJAC. Forensic professionals, students, professors, and researchers seek to contribute to criminal justice more broadly through tireless dedication. When we apply forensic analytical chemistry to a crime scene, more than an expert report, we give voice to the victims, who, through their traces, reveal to us the truth of the facts.

Morphogenesis – “The Riddles of Form” in Twenty-First Century Science

Morphogenesis – “The Riddles of Form” in Twenty-First Century Science

Through A Xenophobic Lens

At the turn of the twentieth century, social theories developed in both the U.S. and Europe suggested that those at the top, or those most well endowed with good genetics, would stay that way, while those with poor genetics had little hope of changing their circumstances. Degeneration theory, as this concept was called when it took root in the United States from the late 1890s, before it had evolved to formally become eugenics in the 1910s, and beyond. While eugenics offices opened in Berlin in 1905, in England in 1907-08, and in the United States in 1910, there were many forms of it, including degeneration theory. What bound all the theories together was the notion of biology and heredity.
 Westerns like Martyrs of the Alamo became a vehicle to explore these concerns because they inundated everyday Americans with illustrations of national identity. Films like these often mixed fantasy with ideology. This is clearly evident in W. Christy Cabanne’s anti-Mexican sentiment in Martyrs of the Alamo. Examining Cabanne’s film through the lens of degeneracy theory provides a greater understanding of American social concerns in the 1910s. These concerns, characterized by xenophobic depictions of immigrants, particularly Mexicans, culminated in the linking of immigrant bodies and disease with heredity and genetics, namely through theories of degeneration . Cabanne’s Martyrs of the Alamo suggests, through the reproduction of the conflict surrounding the Alamo Mission, that the alternative to “race suicide” is a fantasy of American heroism, collectivism, and cultural exclusion. (SS and TZCS)

"[This] system was not made for [you]:" A case for decolonial Scientia.

Sylvia Wynter's "recoded" form of science called decolonial Scientia (DS) is grounded in an understanding of humans as simultaneously biological and cultural. DS includes narrative interventions that destabilize Western scientific authority, and address limitations that empirical data collection and analysis place on capturing simultaneous realities. Therefore, Wynter's narrative "languaging" is both scientific critique and grounded in a tradition of Black radical imagining. In this article, I use languaging to destabilize the canonical narrative tied to W. M. Cobb's production of the article "Race and Runners." The standard telling focuses on Cobb's examination of Owens' lower extremities to expose the fallacy of racial differences in athletic ability. Destabilization of the narrative allows for identifying relational complexities between actors involved in the canonical story - and identifying ideologies embedded within it that guide our deconstructions of biological race. My alter(ed)native subjectivity informs my use of languaging to argue that the relationship between narrative and research practices belie Western scientific/unscientific binaries. Audiovisual and documentary sources of the public-facing "Race and Runners" story were subject to comparative analysis to verify the content and order of events in the canonical narrative. Letters focused on race and athletic ability obtained from the W. Montague Cobb Manuscript Collection at Howard University serve as "apocryphal" sources of information. Correspondence between Cobb and a representative member of the public named Howard Duncan took place within a period immediately before, during and after Cobb publishes "Race and Runners" in the Journal of Health and Physical Education. Contents were subject to a systematic analysis that involved reviewing documents to identify statements reflecting scientific practices, human interactions and relationships between race and athletic ability reflected in the canonical narrative. Contents were also examined for statements relevant to the narrative that departed from or added to the canonical story in the same three areas. Details regarding departures and additions were recorded along with the specific part of the narrative to which they corresponded. Narrative departures and additions were articulated with the canonical narrative in the interest of destabilizing it to identify "knots of ideas, histories and narratives that, contrary to Western science, can only be legible in relation to one another" (McKittrick, 2015b p. 2). Letters exchanged between Cobb and Duncan reveal dynamics that are obscured in the canonical storyline. For instance, Duncan's ability as a white male to assert himself as Cobb's peer demonstrates how racialized power is enacted through science. This is also reflected in Owens' position in the narrative as a voiceless object of knowledge. Letters also present Cobb's identity beyond being a "pioneer," rendering how he is studying and experiencing racism. This includes how he refuses to engage Duncan as a peer. More than mere stories, narratives are motivating and instructive forces that shape how we study human biology and use our research to oppose biological notions of race. Correspondence between Cobb and Duncan reveals how Western scientific ideologies that reinforce prescribed roles and boundaries are embedded in narratives. These ideologies can limit the transformative potential of our approaches to contesting biological notions of race.

Why the Debate about the Metaphysics of Biological Species Should Not Be Deflated

Abstract Some philosophers of biology state that the metaphysical status of biological species is context determined by the use different branches of biology make of their corresponding proper names, so that one and the same biological species can be both an individual and a natural kind. In this paper, I aim to undermine the idea, often associated with the present thesis, according to which the debate about the metaphysical status of biological species should be deflated, since it would be possible to translate every sentence from natural-kind talk to individual-talk and vice versa. I offer a charitable interpretation of the principle grounding such an idea and show how it is in tension with independent theoretical biological notions.

Nature Unnested

In Hans Christian Andersen’s iconic fairy tale, Den grimme ælling (The Ugly Duckling, 1843), we learn that “it does not matter that one has been born in the henyard as long as one has lain in a swan’s egg.” Claims to supremacy, worth, and belonging are nested in a children’s story about “nature” and bolstered by biological notions of kin and kind – some eggs are naturally better than others. Since Andersen’s nineteenth-century tale, the lost/found/switched egg narrative has become a trope in children’s literature, particularly in stories that explore themes of family and belonging, and yet little scholarly attention has been given to the egg in this regard. Drawing on queer, feminist, and posthumanist frameworks inspired by Donna Haraway’s natureculture thinking, this article examines the deployment of the egg-switch trope in Andersen’s The Ugly Duckling, in relation to two contemporary picturebooks, And Tango Makes Three (Parnell and Richardson, 2005), and The Odd Egg (Gravett, 2008). I treat the material-symbolic presence of the egg in these texts as a generative site for interrogating the construction and perpetuation of dominant notions of kin and kind, considering the complex and slippery ways that nature is called upon to uphold ideas of exceptionalism and normativity through discourses of origin and species. At the same time, acknowledging the concurrent conservative and radical potentialities of literature for children (Jaques), and guided by Rosi Braidotti’s affirmative ethics and Eve Sedgwick’s queer reparative approaches to criticism, I also read these texts as imaginative sites for noticing and theorizing alternative queer models of relationality that elevate chosen, non-biological, and cross-species kin.