Developmental Systems Theory as a Process Theory

Griffiths and Russell D. Gray (1994, 1997, 2001) have argued that the fundamental unit of analysis in developmental systems theory should be a process – the life cycle – and not a set of developmental resources and interactions between those resources. The key concepts of developmental systems theory, epigenesis and developmental dynamics, both also suggest a process view of the units of development. This chapter explores in more depth the features of developmental systems theory that favour treating processes as fundamental in biology and examines the continuity between developmental systems theory and ideas about process in the work of several major figures in early 20th century biology, most notable C.H Waddington

A Developmental Systems Account of Human Nature

It is now widely accepted that a scientifically credible conception of human nature must reject the folkbiological idea of a fixed, inner essence that makes us human. We argue here that to understand human nature is to understand the plastic process of human development and the diversity it produces. Drawing on the framework of developmental systems theory and the idea of developmental niche construction we argue that human nature is not embodied in only one input to development, such as the genome, and that it should not be confined to universal or typical human characteristics. Both similarities and certain classes of differences are explained by a human developmental system that reaches well out into the 'environment'. We point to a significant overlap between our account and the ‘Life History Trait Cluster’ account of Grant Ramsey, and defend the developmental systems account against the accusation that trying to encompass developmental plasticity and human diversity leads to an unmanageably complex account of human nature

Genetic, epigenetic and exogenetic information

We describe an approach to measuring biological information where ‘information’ is understood in the sense found in Francis Crick’s foundational contributions to molecular biology. Genes contain information in this sense, but so do epigenetic factors, as many biologists have recognized. The term ‘epigenetic’ is ambiguous, and we introduce a distinction between epigenetic and exogenetic inheritance to clarify one aspect of this ambiguity. These three heredity systems play complementary roles in supplying information for development. We then consider the evolutionary significance of the three inheritance systems. Whilst the genetic inheritance system was the key innovation in the evolution of heredity, in modern organisms the three systems each play important and complementary roles in heredity and evolution. Our focus in the earlier part of the paper is on ‘proximate biology’, where information is a substantial causal factor that causes organisms to develop and causes offspring to resemble their parents. But much philosophical work has focused on information in ‘ultimate biology’. Ultimate information is a way of talking about the evolutionary design of the mechanisms of development and inheritance. We conclude by clarifying the relationship between the two. Ultimate information is not a causal factor that acts in development or heredity, but it can help to explain the evolution of proximate information, which is

Emotion & evolution

In my introductory chapter I briefly outline the present state of philosophical emotion theory. I state my position on the status and future of "folk psychology", and the future of traditional propositional attitude psychology. The next three chapters of the thesis expound and criticise some current theories of emotion. In chapter two I outline the prevalent "cognitivist" orthodoxy. I present a series of problems for this theory, and show how successive refinements to the theory have attempted to meet them. In the last section of the chapter I discuss the relationship between a cognitive taxonomy of emotions and the folk taxonomy. In chapter three I give an account of the philosophically neglected psychoevolutionary theory of emotions. I describe Darwin's remarkable work in this field, and compare it to the present state of play. In sections four and five of the chapter I outline an "affect-program" model of emotions, and connect it with current work in other areas of the philosophy of mind. In chapter four I discuss the constructionist theories of emotion which have been taken up in recent years by certain philosophers. I criticise many of the current accounts of constructionism, and produce my own, substantially revised version, which I claim has been purged of many muddles, conflations, and controversial commitments. Chapter five defends the core contentions of the thesis. I argue that none of the three theories discussed are adequate accounts of the whole domain, and that each should only properly apply to certain subdomains of emotional phenomena. I call this a "multi-vocal" theory of emotion, in contrast to the traditional insistence on univocal theories. Univocal theories, I argue, are merely Procrustean. In chapter six I provide a cognate account of emotion attribution, stressing the diversity of modes of attribution that corresponds to the diversity of "emotional" phenomena. Chapter seven provides a theory of mood and trait phenomena. Although independently motivated, the theory turns out to dovetail neatly with my account of affect -program states. The appendices deal with matters referred to in the thesis, but which would interrupt the flow of my argument if included in the main body of the text. Appendix I gives details of experiments referred to in chapter three. Appendix II defends the uses of sociobiology suggested in chapter five. Appendix three gives a theory of sensations referred to in chapter six and elsewhere. Format of the Thesis I have used three levels of headings. First, the thesis is divided into chapters, numbered with Arabic numerals 1-7. Next, each chapter is divided into subsections numbered decimally, 1.1, 1.2, 1.3, etc. Finally, simple underlined heads, such as that used to introduce this paragraph, are inserted at various points to aid the exposition. These are not listed in the table of contents, or used for cross referencing. Appendices to the thesis are numbered with Roman numerals, I-ill. They are divided into decimally numbered subsections, I.I. I.II, etc, in a manner analogous to the chapters. Each appendix is linked to the particular chapter where the questions it deals with are most frequently referred to Figures and tables are also numbered decimally. Figures in chapters are labeled Figure 3.1, Figure 3.2, etc. Tables in Appendix I are labeled Table I.I, Table I.II, etc

The idea of mismatch in evolutionary medicine

Mismatch is a prominent concept in evolutionary medicine and a number of philosophers have published analyses of this concept. The word ‘mismatch’ has been used in a diversity of ways across a range of sciences, leading these authors to regard it as a vague concept in need of philosophical clarification. Here, in contrast, we concentrate on the use of mismatch in modelling and experimentation in evolutionary medicine. This reveals a rigorous theory of mismatch within which the term ‘mismatch’ is indeed used in several ways, not because it is ill-defined but because different forms of mismatch are.distinguished within the theory. Contemporary evolutionary medicine has unified the idea of ‘evolutionary mismatch’, derived from the older idea of ‘adaptive lag’ in evolution, with ideas about mismatch in development and physiology derived from the Developmental Origins of Health and Disease (DOHaD) paradigm. A number of publications in evolutionary medicine have tried to make this theoretical framework explicit. We build on these to present the theory in as simple and general a form as possible. We introduce terminology, largely drawn from the existing literature, to distinguish the different forms of mismatch. This integrative theory of mismatch captures how organisms track environments across space and time on multiple scales in order to maintain an adaptive match to the environment, and how failures of adaptive tracking lead to disease. Mismatch is a productive organising concept within this theory which helps researchers articulate how physiology, development and evolution interact with one another and with environmental change to explain health outcomes

Are biological traits explained by their 'selected effect' functions?

The selected effects or ‘etiological’ theory of Proper function is a naturalistic and realist account of biological teleology. It is used to analyse normativity in philosophy of language, philosophy of mind, philosophy of medicine and elsewhere. The theory has been developed with a simple and intuitive view of natural selection. Traits are selected because of their positive effects on the fitness of the organisms that have them. These ‘selected effects’ are the Proper functions of the traits. Proponents argue that this analysis of biological teleology has the unique advantage that the selected effect function of a trait is also a causal explanation of the trait: the trait exists because it performs this function. We show, however, that selected effect functions as currently defined explain the existence of traits only under highly restrictive assumptions about evolutionary dynamics. In many common scenarios in which traits evolve by natural selection, selected effect functions do not explain those traits. This is because definitions of selected effect function extract from any evolutionary scenario only the information that would be explanatorily relevant in the simple evolutionary scenario implicit in those definitions. When applied to more complex scenarios selected effect functions omit the key information that is explanatorily relevant in those scenarios. The assumptions required for selected effect functions to be explanatory are particularly unlikely to hold in the domain that its proponents care most about - the evolution of representation. A more adequate selected effects theory of Proper functions may be possible, but will require much greater attention to the structure of actual evolutionary explanations

The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). The Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. Here we also highlight Duotang, a web platform that presents genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses

Enteral lactoferrin supplementation for very preterm infants : a randomised placebo-controlled trial

Background: Infections acquired in hospital are an important cause of morbidity and mortality in very preterm infants. Several small trials have suggested that supplementing the enteral diet of very preterm infants with lactoferrin, an antimicrobial protein processed from cow's milk, prevents infections and associated complications. Methods: In this randomised, placebo-controlled trial, very preterm infants (born before 32 weeks' gestation) in 37 UK hospitals were allocated randomly (1:1) within 72 hours after birth to receive enteral bovine lactoferrin (150 mg/kg/day; maximum 300 mg/day) versus sucrose (same dose) once daily until 34 weeks' postmenstrual age. Web-based randomisation minimised for recruitment site, gestation (completed weeks), sex, and single versus multifetal pregnancy. Parents, caregivers and outcomes assessors were unaware of group assignment. The primary outcome was microbiologically-confirmed or clinically-suspected lateonset infection (occurring >72 hours after birth). The trial was registered with the International Standard Randomised Controlled Trial Number 88261002. Findings: We recruited 2203 participants between May 2014 and September 2017. Four infants had consent withdrawn or unconfirmed leaving 1098 infants in the lactoferrin group and 1101 in the sucrose group. Primary outcome data for 2182 infants were available for inclusion in the intention-to-treat analyses. In the intervention group, 316/1093 (28.9%) infants acquired a late-onset infection versus 334/1089 (30.7%) in the control group: risk ratio (RR) adjusted for minimisation factors 0.95 (95% confidence interval [CI] 0.86, 1.04). Pre-specified subgroup analyses did not show statistically significant interactions for gestation at birth (completed weeks') or type of enteral milk received (human, formula, or both). Interpretation: Enteral supplementation with bovine lactoferrin does not reduce the incidence of late-onset infection in very preterm infants. Funding: UK National Institute for Health Research Health Technology Assessment programme (10/57/49)

Adjunctive rifampicin for Staphylococcus aureus bacteraemia (ARREST): a multicentre, randomised, double-blind, placebo-controlled trial.

BACKGROUND: Staphylococcus aureus bacteraemia is a common cause of severe community-acquired and hospital-acquired infection worldwide. We tested the hypothesis that adjunctive rifampicin would reduce bacteriologically confirmed treatment failure or disease recurrence, or death, by enhancing early S aureus killing, sterilising infected foci and blood faster, and reducing risks of dissemination and metastatic infection. METHODS: In this multicentre, randomised, double-blind, placebo-controlled trial, adults (≥18 years) with S aureus bacteraemia who had received ≤96 h of active antibiotic therapy were recruited from 29 UK hospitals. Patients were randomly assigned (1:1) via a computer-generated sequential randomisation list to receive 2 weeks of adjunctive rifampicin (600 mg or 900 mg per day according to weight, oral or intravenous) versus identical placebo, together with standard antibiotic therapy. Randomisation was stratified by centre. Patients, investigators, and those caring for the patients were masked to group allocation. The primary outcome was time to bacteriologically confirmed treatment failure or disease recurrence, or death (all-cause), from randomisation to 12 weeks, adjudicated by an independent review committee masked to the treatment. Analysis was intention to treat. This trial was registered, number ISRCTN37666216, and is closed to new participants. FINDINGS: Between Dec 10, 2012, and Oct 25, 2016, 758 eligible participants were randomly assigned: 370 to rifampicin and 388 to placebo. 485 (64%) participants had community-acquired S aureus infections, and 132 (17%) had nosocomial S aureus infections. 47 (6%) had meticillin-resistant infections. 301 (40%) participants had an initial deep infection focus. Standard antibiotics were given for 29 (IQR 18-45) days; 619 (82%) participants received flucloxacillin. By week 12, 62 (17%) of participants who received rifampicin versus 71 (18%) who received placebo experienced treatment failure or disease recurrence, or died (absolute risk difference -1·4%, 95% CI -7·0 to 4·3; hazard ratio 0·96, 0·68-1·35, p=0·81). From randomisation to 12 weeks, no evidence of differences in serious (p=0·17) or grade 3-4 (p=0·36) adverse events were observed; however, 63 (17%) participants in the rifampicin group versus 39 (10%) in the placebo group had antibiotic or trial drug-modifying adverse events (p=0·004), and 24 (6%) versus six (2%) had drug interactions (p=0·0005). INTERPRETATION: Adjunctive rifampicin provided no overall benefit over standard antibiotic therapy in adults with S aureus bacteraemia. FUNDING: UK National Institute for Health Research Health Technology Assessment

Enteral lactoferrin supplementation for very preterm infants : a randomised placebo-controlled trial

Background: Infections acquired in hospital are an important cause of morbidity and mortality in very preterm infants. Several small trials have suggested that supplementing the enteral diet of very preterm infants with lactoferrin, an antimicrobial protein processed from cow's milk, prevents infections and associated complications. Methods: In this randomised, placebo-controlled trial, very preterm infants (born before 32 weeks' gestation) in 37 UK hospitals were allocated randomly (1:1) within 72 hours after birth to receive enteral bovine lactoferrin (150 mg/kg/day; maximum 300 mg/day) versus sucrose (same dose) once daily until 34 weeks' postmenstrual age. Web-based randomisation minimised for recruitment site, gestation (completed weeks), sex, and single versus multifetal pregnancy. Parents, caregivers and outcomes assessors were unaware of group assignment. The primary outcome was microbiologically-confirmed or clinically-suspected lateonset infection (occurring >72 hours after birth). The trial was registered with the International Standard Randomised Controlled Trial Number 88261002. Findings: We recruited 2203 participants between May 2014 and September 2017. Four infants had consent withdrawn or unconfirmed leaving 1098 infants in the lactoferrin group and 1101 in the sucrose group. Primary outcome data for 2182 infants were available for inclusion in the intention-to-treat analyses. In the intervention group, 316/1093 (28.9%) infants acquired a late-onset infection versus 334/1089 (30.7%) in the control group: risk ratio (RR) adjusted for minimisation factors 0.95 (95% confidence interval [CI] 0.86, 1.04). Pre-specified subgroup analyses did not show statistically significant interactions for gestation at birth (completed weeks') or type of enteral milk received (human, formula, or both). Interpretation: Enteral supplementation with bovine lactoferrin does not reduce the incidence of late-onset infection in very preterm infants. Funding: UK National Institute for Health Research Health Technology Assessment programme (10/57/49)