Darwinian Explanation Research Articles

Towards a More General Theory of Evolution by Natural Selection: A Manifesto

In this manifesto for a more comprehensive account of evolution by natural selection (ENS), we draw on Hull’s framework to expand the reach of Darwinian explanations. His approach is centered on the notions of interactor and replicator. He (and many others following him) defines the interactor in terms of cohesiveness. Often, such cohesiveness is cashed out by the vertical transmission to the next generation of the replicators that constitute the interactors. While we maintain the importance of the reciprocal influence of interactors and replicators (the differential extinction and proliferation of interactors leads to the differential extinction and proliferation of the replicators that produce them) central to Hull’s framework, we downplay the importance of the cohesiveness of interactors and eliminate any need for lineage formation among them. This suggested revision of the interactor synthesizes various recent contributions in the field, and it allows the interactor/replicator framework to tackle more complex entities. Our approach, however, stands in stark opposition to the classical approach to ENS centered on lineage formation. In this paper, we present our view and argue that it should replace the classical approach in structuring future work in evolutionary biology.

Running Mice and Successful Theories: The Limitations of a Classical Analogy

AbstractBas van Fraassen’s Darwinian explanation for the success of science has sparked four decades of discussion, with scientific realists and antirealists alike using biologically inspired reasoning to support their points of view. Based on critical engagement with van Fraassen’s proposal itself and later contributions by Stathis Psillos and K. Brad Wray, we claim that central arguments on both sides of this controversy suffer from an insufficient understanding of Darwinism and its underlying biological concepts. Adding the necessary biological background turns out to subvert the argumentative force of viewing the success of scientific theories as analogous to the behaviour of biotic entities. In conclusion, we sketch more productive ways of viewing the relationship between biology and scientific realism.

Fertility Impairment after Trekking at High Altitude: A Proof of Mechanisms on Redox and Metabolic Seminal Changes.

Many authors described negative but reversible effects of high-altitude hypoxic exposure on animal and human fertility in terms of sperm concentration, function, and biochemical alterations. The aim of this study was to evaluate the acute and chronic effects of high-altitude exposure on classical sperm parameters, redox status, and membrane composition in a group of travellers. Five healthy Italian males, all lowlanders not accustomed to the altitude, were evaluated after 19 days-trekking through low, moderate, and high altitudes in the Himalayas. Sperm samples were collected before (Pre), 10 days after (Post), and 70 days after the end of the expedition (Follow-up). Sperm concentration, cholesterol and oxysterol membrane content, and redox status were measured. Hypoxic trek led to a significant reduction in sperm concentration (p < 0.001, η2p = 0.91), with a reduction from Pre to Post (71.33 ± 38.81 to 60.65 ± 34.63 × 106/mL) and a further reduction at Follow-up (to 37.13 ± 39.17 × 106/mL). The seminal volume was significantly affected by the hypoxic trek (p = 0.001, η2p = 0.75) with a significant reduction from Pre to Post (2.86 ± 0.75 to 1.68 ± 0.49 mL) and with partial recovery at Follow-up (to 2.46 ± 0.45 mL). Moreover, subjects had an increase in ROS production (+86%), and a decrease in antioxidant capacity (−37%) in the Post period with partial recovery at Follow-up. These results integrated the hormonal response on thyroid function, hypothalamus–pituitary–gonadal axis, and the prolactin/cortisol pathways previously reported. An uncontrolled ROS production, rather than a compromised antioxidant activity, was likely the cause of impaired sperm quality. The reduction in fertility status observed in this study may lie in an evolutionary Darwinian explanation, i.e., limiting reproduction due to the “adaptive disadvantage” offered by the combined stressors of high-altitude hypoxia and daily physical exercise.

Scaffolding Natural Selection

Darwin provided us with a powerful theoretical framework to explain the evolution of living systems. Natural selection alone, however, has sometimes been seen as insufficient to explain the emergence of new levels of selection. The problem is one of “circularity” for evolutionary explanations: how to explain the origins of Darwinian properties without already invoking their presence at the level they emerge. That is, how does evolution by natural selection commence in the first place? Recent results in experimental evolution suggest a way forward: Paul Rainey and his collaborators have shown that Darwinian properties could be exogenously imposed via what they call “ecological scaffolding.” This could solve the “black box” dilemma faced by Darwinian explanations of new levels of organization. Yet, despite “scaffolding” recently becoming a popular term in the study of cognition, culture, and evolution, the concept has suffered from vagueness and ambiguity. This article aims to show that scaffolding can be turned into a proper scientific concept able to do explanatory work within the context of the major evolutionary transitions. Doing so will allow us to once again extend the scope of the Darwinian model of evolution by natural selection.

Science and the Good: The Tragic Quest for the Foundations of Morality

Science and the Good: The Tragic Quest for the Foundations of Morality

THE INEVITABILITY OF A GENERALIZED DARWINIAN THEORY OF BEHAVIOR, SOCIETY, AND CULTURE

AbstractThe paper argues that the evident features of all human affairs of interest to the social scientist demand Darwinian explanations. It must however be recognized that the range of regularities, models, theories that a successful Darwinian research program will inspire must be heterogeneous, operate at very different scales, identify a diversity of distinct and often unrepeated processes operating through multifarious instances of blind variation and environmental selection. There will be no canonical statement of a Darwinian theory of cultural and/or social affairs.

'Awareness' in metamorphosing pupae (Lepidoptera: Pieridae)

Neurobiological studies of model insect species have established that the nervous system retains some larval innervations, remodels others, and develops other new adult innervations during metamorphosis. Using a simple behavioral response – the ability to ‘kick’ by pupae of the pierid, Catopsilia pomona (Fabricius, 1775) - it was possible to assay for the retention of environmental awareness during ontogenetic reorganization. All pupae kicked 24h after ecdysis, 48% of pupae kicked at the pharate adult stage, and 28% of pupae kicked every day of their development (6.52 d ± 0.10). Both the mode and temporal expression of the response indicate that this retained awareness has larval origins. Variability in the response supports the inference that this response is mediated, to some extent, by prior experience rather than purely ‘reflex’. This is consistent with a Darwinian explanation of the behavior (and retained environmental awareness itself) as serving a protective function in pupae.

The behavioural ecology of irrational behaviours.

Natural selection is often envisaged as the ultimate cause of the apparent rationality exhibited by organisms in their specific habitat. Given the equivalence between selection and rationality as maximizing processes, one would indeed expect organisms to implement rational decision-makers. Yet, many violations of the clauses of rationality have been witnessed in various species such as starlings, hummingbirds, amoebas and honeybees. This paper attempts to interpret such discrepancies between economic rationality (defined by the main axioms of rational choice theory) and biological rationality (defined by natural selection). After having distinguished two kinds of rationality we introduce irrationality as a negation of economic rationality by biologically rational decision-makers. Focusing mainly on those instances of irrationalities that can be understood as exhibiting inconsistency in making choices, i.e. as non-conformity of a given behaviour to axioms such as transitivity or independence of irrelevant alternatives, we propose two possible families of Darwinian explanations that may account for these apparent irrationalities. First, we consider cases where natural selection may have been an indirect cause of irrationality. Second, we consider putative cases where violations of rationality axioms may have been directly favored by natural selection. Though the latter cases (prima facie) seem to clearly contradict our intuitive representation of natural selection as a process that maximizes fitness, we argue that they are actually unproblematic; for often, they can be redescribed as cases where no rationality axiom is violated, or as situations where no adaptive solution exists in the first place.

The Luria-Delbrück Fluctuation Test as a Classroom Investigation in Darwinian Evolution

Microbial cultures swiftly adapt to lethal agents such as antibiotics or viruses by acquiring resistance mutations. Does this remarkable adaptability require a Lamarckian explanation, whereby the agent specifically directs resistance mutations? Soon after the question arose, Luria and Delbrück devised a clever experiment, the fluctuation test, that answered this question in the negative: microbial adaptation, they showed, is entirely consistent with a Darwinian explanation. Their 1943 article is a classic of biology literature, with practical and theoretical implications that continue to expand today. Implementing an updated fluctuation test in a college teaching lab provides a simple experimental setting in which beginning students learn to apply basic principles of evolutionary biology and scientific reasoning, while gaining hands-on experience in core technical advances of contemporary life science.

Explanatory unification and conceptualization

There are several important criticisms against the unificationist model of scientific explanation: (1) Unification is a broad and heterogeneous notion and it is hard to see how a model of explanation based exclusively on unification can make a distinction between genuine explanatory unification from cases of ordering or classification. (2) Unification alone cannot solve the asymmetry and irrelevance problems. (3) Unification and explanation pull in different directions and should be decoupled, because for good scientific explanation extra ad explanandum information is often required. I am presenting a possible solution to those problems, by focusing on an often overlooked but important element of how theoretic unification is achieved—the conceptual frameworks of theories. The core conceptual assumptions behind theories are decisive for discriminating between explanatory and non-explanatory unification. The conceptual framework is also flexible enough to balance the tension between informativeness and maximum systematization in constructing explanatory inferences. A short case study of orthogenetic and Darwinian explanations in paleontology is presented as an illustration of how my addition to the unificationist model is applicable to a historical debate between rival explanations.

The imbalance of nature: revisiting a Darwinian framework for invasion biology

AbstractAimA major implication of natural selection is that species from different parts of the world will vary in their efficiency in converting resources into offspring for a given type of environment. This insight, articulated by Darwin, is usually overlooked in more recent studies of invasion biology that are often based on the more modern Eltonian perspective of imbalanced ecosystems. We formulate a renewed Darwinian framework for invasion biology, the evolutionary imbalance hypothesis (EIH), based only on the action of natural selection in historically isolated populations operating within a global network of repeated environments. This framework predicts that successful invaders are more likely to come from biotic regions of high genetic potential (with independent lineages of large population size), experiencing a given environment for many generations and under strong competition from other lineages.LocationGlobal.MethodsWe test the predictive power of this framework by examining disparities in recent species exchanges between global biotic regions, including patterns of plant invasions across temperate regions and exchanges of aquatic fauna as a result of modern canal building.ResultsOur framework successfully predicts global invasion patterns using phylogenetic diversity of the world's biotic regions as a proxy that reflects their genetic potential, historical stability and competitive intensity, in line with the Darwinian expectation. Floristic regions of higher phylogenetic diversity are more likely to be source areas of invasive plants, and regions of lower phylogenetic diversity are more likely to be invaded. Similar patterns are evident for formerly isolated marine or freshwater assemblages that have been connected via canals.Main conclusionsWe advocate an approach to understanding modern species invasions that recognizes the potential significance of both the original Darwinian explanation and the more modern view that emphasizes novel ecological or evolutionary mechanisms arising in the introduced range. Moreover, if biological invasions are a natural outcome of Darwinian evolution in an increasingly connected world, then invasive species should continue to displace native species and drive widespread shifts in the functioning of ecosystems.

A mechanistic framework for Darwinism or why Fodor’s objection fails

Fodor (Mind Lang 23:1–24, Mind Lang 2008a, 23:50–57, 2008b and Fodor and Piattelli-Palmarini (What Darwin go wrong, Picador, New York, 2011) argue that Darwinism cannot be true on the grounds that there are no laws of selection to support counterfactuals about why traits are selected-for. Darwinian explanations, according to this objection, amount to mere ‘plausible historical narratives’. I argue that the objection is predicated on two problematic assumptions: A nomic-subsumption account of causation and causal explanation, and a fine-grained view of the individuation of selected-for effects. Against the former, I argue that Darwinian explanations are a historical species of mechanistic explanation and that mechanisms are causally productive and counterfactual supporting in the absence of appropriate laws. Once this mechanistic framework is in place, the demand for laws of selection vanishes and the historical cum causal coherence of Darwinism is restored. As for the second assumption, I argue that it is an artefact of the teleosemantic program with no basis in evolutionary biology and that properly understood, Darwinian evolutionary biology shows just why teleosemantics cannot succeed.

The logical structure of evolutionary explanation and prediction: Darwinism’s fundamental schema

We present a logically detailed case-study of Darwinian evolutionary explanation. Special features of Darwin’s explanatory schema made it an unusual theoretical breakthrough, from the point of view of the philosophy of science. The schema employs no theoretical terms, and puts forward no theoretical hypotheses. Instead, it uses three observational generalizations—Variability, Heritability and Differential Reproduction—along with an innocuous assumption of Causal Efficacy, to derive Adaptive Evolution as a necessary consequence. Adaptive Evolution in turn, with one assumption of scale (‘Deep Time’), implies the observational generalization of Adaptation. It is a fascinating methodological task to regiment the premises and make the reasoning both rigorous and clear. Doing so reveals how surprisingly small an amount of mathematics is needed in order to carry out the argument. The investigation also reveals the crucial role played by heritability, and how heritability itself admits of Darwinian explanation.

Institutionalizing Ethical Innovation in Organizations: An Integrated Causal Model of Moral Innovation Decision Processes

This article answers several calls—coming as well from corporate governance practitioners as from corporate governance researchers—concerning the possibility of complying simultaneously with requirements of innovation and ethics. Revealing the long-term orientation as the variable which permits us to link the principal goal of organization, being “survival,” with innovation and ethic, the article devises a framework for incorporating ethics into a company’s processes and strategies for innovation. With the principal goal of organizations being “survival” in the long-term, it is assumed that innovation is necessary in order to realize a going concern. Firms that do not innovate and adapt to rapidly changing business environments are less likely to be sustainable. Thus, it is in a business’ best interests to adopt an innovation process for long-term success. We posit that there are two simultaneous sources of innovation and change that are unavoidable and embedded in the corporate landscape. First, we argue for genetically embedded, Darwinian explanations for adaptations that enable an entity’s survival. This view is combined with more conventional, social science explanations for change. Our new, comprehensive model of the governance of innovation processes hinges on the one hand on an organization’s long-term orientation, which we argue, is not possible without a consideration of an ethical dimension. On the other hand, the model employs, for the first time, the concept of duality, in order to make the positive coexistence of innovation and ethic analytically visible. Guided by this concept the roots of the ethic within innovation are traced from both natural science forces for change, and cultural pressures operating on members of an organization. We present our Integrated Causal Model of Innovation and propose theoretical relationships that will generate numerous avenues for future research in the field, and help managers to reorient their governance strategies.

Underqualified—maximal generality in Darwinian explanation: a response to Matt Gers

Gers (Biol Philos, 2011) provides a positive and constructive view of the project to generalise Darwinian principles in Geoffrey Hodgson and Thorbjorn Knudsen’s Darwin’s Conjecture. We note considerable overlap with his work and ours, and also with important recent work of Godfrey-Smith (2009), which Gers cites extensively. But we also note that there are differences in research objectives between Gers and Godfrey-Smith, on the one hand, and ourselves, on the other. Gers and Godfrey-Smith focus on the elucidation of the most general principles possible. Our aim is to derive principles that are sufficiently abstract to span the natural and human social worlds, and then add additional principles to help understand the Darwinian evolution of human society. Furthermore, Gers and Godfrey-Smith critique a replicator concept that is different from ours. Once these points are made apparent, the criticisms are essentially disabled, and we end up in a position with different but complementary and overlapping research projects.

The 3-Base Periodicity and Codon Usage of Coding Sequences Are Correlated with Gene Expression at the Level of Transcription Elongation

BackgroundGene transcription is regulated by DNA transcriptional regulatory elements, promoters and enhancers that are located outside the coding regions. Here, we examine the characteristic 3-base periodicity of the coding sequences and analyse its correlation with the genome-wide transcriptional profile of yeast.Principal FindingsThe analysis of coding sequences by a new class of indices proposed here identified two different sources of 3-base periodicity: the codon frequency and the codon sequence. In exponentially growing yeast cells, the codon-frequency component of periodicity accounts for 71.9% of the variability of the cellular mRNA by a strong association with the density of elongating mRNA polymerase II complexes. The mRNA abundance explains most of the correlation between the codon-frequency component of periodicity and protein levels. Furthermore, pyrimidine-ending codons of the four-fold degenerate small amino acids alanine, glycine and valine are associated with genes with double the transcription rate of those associated with purine-ending codons.ConclusionsWe demonstrate that the 3-base periodicity of coding sequences is higher than expected by the codon usage frequency (CUF) and that its components, associated with codon bias and amino acid composition, are correlated with gene expression, principally at the level of transcription elongation. This indicates a role of codon sequences in maximising the transcription efficiency in exponentially growing yeast cells. Moreover, the results contrast with the common Darwinian explanation that attributes the codon bias to translational selection by an adjustment of synonymous codon frequencies to the most abundant isoaccepting tRNA. Here, we show that selection on codon bias likely acts at both the transcriptional and translational level and that codon usage and the relative abundance of tRNA could drive each other in order to synergistically optimize the efficiency of gene expression.

Overqualified: generative replicators as Darwinian reproducers

Darwin’s Conjecture is a bold attempt to bring evolutionary explanation to the social sciences, particularly economics. The book outlines the history of Darwinian explanation in social science then puts forward a generalized replicator account of social evolution by natural selection. The authors identify habits and routines as examples of the generative replicators necessary in order that social evolution is Darwinian. This reviewer notes that the replicator approach limits the generality of this account and suggests that habits and routines might better be seen as members of a Darwinian population in the tradition of Godfrey-Smith’s (2009) generalized account of natural selection instead. Furthermore, the existence of levels of social evolution will constrain what evolution can occur low in the hierarchy.

The question of ethnic variability and the Darwinian significance of physiological neonatal jaundice in East Asian populations

Recent work in Darwinian medicine has suggested that physiological neonatal jaundice (PNJ) might serve an adaptive function in scavenging reactive oxygen species that in later life are removed by the mature antioxidant enzyme system in the liver. This treatise examines this hypothesis in light of novel epidemiological and genetic findings which suggest that the incidence of PNJ is significantly increased in East Asian populations. Though found across all ethnic groups, it has been established that neonates of East Asian origin are at a significantly greater risk of developing PNJ, with more than one studying finding the incidence to be near double. For any Darwinian explanation of physiological neonatal jaundice to be considered in clinical circles, it is essential that the elevated incidence of PNJ in this population be explained both mechanistically and in terms of adaptation. Recent work has linked PNJ to a specific enzyme polymorphism, a variation of the UGT1A1 gene, in the glucoronidation pathway which is essential for bilirubin metabolism and is strongly correlated with ethnic origin. In this paper it is hypothesized that the elevated incidence of PNJ in East Asian populations is not random or due to a flaw in the system but rather due to an evolved mechanism. Two potential pressures which might have selected for an elevated neonatal bilirubin in East Asian populations versus other ethnic groups are a diminished ability to reduce harmful oxidant radicals due to variations the P450 liver metabolic pathway and the endemic nature of Hepatitis B in the Asia-Pacific region. This is the first work to attempt to explain PNJ through a Darwinian yet clinically relevant lens while suggesting a specific proximate mechanism that is correlated with a pre-existing evolutionary environment and can be associated with differential reproductive success.

The predictability of evolution: glimpses into a post-Darwinian world

The very success of the Darwinian explanation, in not only demonstrating evolution from multiple lines of evidence but also in providing some plausible explanations, paradoxically seems to have served to have stifled explorations into other areas of investigation. The fact of evolution is now almost universally yoked to the assumption that its outcomes are random, trends are little more than drunkard's walks, and most evolutionary products are masterpieces of improvisation and far from perfect. But is this correct? Let us consider some alternatives. Is there evidence that evolution could in anyway be predictable? Can we identify alternative forms of biological organizations and if so how viable are they? Why are some molecules so extraordinarily versatile, while others can be spoken of as "molecules of choice"? How fortuitous are the major transitions in the history of life? What implications might this have for the Tree of Life? To what extent is evolutionary diversification constrained or facilitated by prior states? Are evolutionary outcomes merely sufficient or alternatively are they highly efficient, even superb? Here I argue that in sharp contradistinction to an orthodox Darwinian view, not only is evolution much more predictable than generally assumed but also investigation of its organizational substrates, including those of sensory systems, which indicates that it is possible to identify a predictability to the process and outcomes of evolution. If correct, the implications may be of some significance, not least in separating the unexceptional Darwinian mechanisms from underlying organizational principles, which may indicate evolutionary inevitabilities.

Having a Jolly Good Time—Together!

What's in a word? "Hybridization" is easy to say (for professors) but carries surprisingly deep meaning from an evolutionary viewpoint. Cliff Jolly's research contributions have included important work and thought on the nature of baboon diversity and interactions. Hybridization among baboon subspecies reflects compatible genes for many different physical and behavioral traits, essentially all traits, each of them complex. Modern developmental genetics has shown that a few general principles characterize the phenogenetic logic by which genes assemble embryos and maintain the complex traits and abilities of organisms, including behavior. How cooperative viability is maintained while complex adaptive traits evolve and populations diverge is a question we can begin to answer more definitively than has been possible before. A careful look leads us to challenge the nature of the Darwinian explanations that have been the standard for more than a century.