Common ancestry is a central feature of the theory of evolution, yet it is not clear what “common ancestry” actually means; nor is it clear how it is related to other terms such as “the Tree of Life” and “the last universal common ancestor”. I argue these terms describe three distinct hypotheses ordered in a logical way: that there is a Tree of Life is a claim about the pattern of evolutionary history, that there is (...) a last universal common ancestor is an ontological claim about the existence of an entity of a specific kind, and that there is universal common ancestry is a claim about a causal pattern in the history of life. With these generalizations in mind, I argue that the existence of a Tree of Life entails a last universal common ancestor, which would entail universal common ancestry, but neither of the converse entailments hold. This allows us to make sense of the debates surrounding the Tree, as well as our lack of knowledge about the last universal common ancestor, while still maintaining the uncontroversial truth of universal common ancestry. (shrink)

We explore the evidential relationships that connect two standard claims of modern evolutionary biology. The hypothesis of common ancestry (which says that all organisms now on earth trace back to a single progenitor) and the hypothesis of natural selection (which says that natural selection has been an important influence on the traits exhibited by organisms) are logically independent; however, this leaves open whether testing one requires assumptions about the status of the other. Darwin noted that an extreme version (...) of adaptationism would undercut the possibility of making inferences about common ancestry. Here we develop a converse claim—hypotheses that assert that natural selection has been an important influence on trait values are untestable unless supplemented by suitable background assumptions. The fact of common ancestry and a claim about quantitative genetics together suffice to render such hypotheses testable. Furthermore, we see no plausible alternative to these assumptions; we hypothesize that they are necessary as well as sufficient for adaptive hypotheses to be tested. This point has important implications for biological practice, since biologists standardly assume that adaptive hypotheses predict trait associations among tip species. Another consequence is that adaptive hypotheses cannot be confirmed or disconfirmed by a trait value that is universal within a single species, if that trait value deviates even slightly from the optimum. 1 Two Darwinian hypotheses 2 Logical independence 3 How adaptive hypotheses bear on the tree of life hypothesis 4 How the tree of life hypothesis bears on adaptive hypotheses 5 What do adaptive hypotheses predict? 6 Common ancestry and quantitative genetics to the rescue 7 Conclusion. (shrink)

ABSTRACT Darwin claims in the Origin that similarity is evidence for common ancestry, but that adaptive similarities are ‘almost valueless’ as evidence. This second claim seems reasonable for some adaptive similarities but not for others. Here we clarify and evaluate these and related matters by using the law of likelihood as an analytic tool and by considering mathematical models of three evolutionary processes: directional selection, stabilizing selection, and drift. Our results apply both to Darwin’s theory of evolution and (...) to modern evolutionary biology. _1_ Introduction _2_ The Likelihood Framework _3_ A Sufficient Condition for a Similarity to Favour Common Ancestry over Separate Ancestry _4_ The 1/p Criterion and Its Limitations _5_ Directional Selection versus Drift _6_ Stabilizing Selection versus Drift _7_ Going beyond Two Taxa _8_ Conclusions Appendix. (shrink)

Darwin claims in the Origin that similarity is evidence for common ancestry, but that adaptive similarities are ‘almost valueless’ as evidence. This second claim seems reasonable for some adaptive similarities but not for others. Here we clarify and evaluate these and related matters by using the law of likelihood as an analytic tool and by considering mathematical models of three evolutionary processes: directional selection, stabilizing selection, and drift. Our results apply both to Darwin’s theory of evolution and to (...) modern evolutionary biology. 1 Introduction2 The Likelihood Framework3 A Sufficient Condition for a Similarity to Favour Common Ancestry over Separate Ancestry4 The 1/p Criterion and Its Limitations5 Directional Selection versus Drift6 Stabilizing Selection versus Drift7 Going beyond Two Taxa8 ConclusionsAppendix. (shrink)

I consider three theses that are friendly to anthropomorphism. Each makes a claim about what can be inferred about the mental life of chimpanzees from the fact that humans and chimpanzees both have behavioral trait B and humans produce this behavior by having mental trait M. The first thesis asserts that this fact makes it probable that chimpanzees have M. The second says that this fact provides strong evidence that chimpanzees have M. The third claims that the fact is evidence (...) that chimpanzees have M. The third thesis follows from a plausible Reichenbachian model of how a common ancestor is probabilistically related to its descendants. The first two theses do not, and they have no general evolutionary justification. (shrink)

This paper is an attempt to offer a concrete contribution to the study of indigenous African religions and in particular to the support of creating a set of traditions from whose perspective one could engage in the study of indigenous African religions as well as of African spirituality in general through the unifying theme of ecodomy. Defined in terms of a constructive process, ecodomy seeks to provide families and communities with a common element, that of ancestors, which is not (...) only specific to African spirituality but also potentially capable of strengthening and improving the life of African people. Thus, this methodology based on working with ancestry as economy is applied to four distinct scholars and their specific approaches to indigenous African religions: John S. Mbiti, who believes that ancestors have mainly social, not religious roles; Issiaka P. Laleye, for whom ancestors make a connection between the social and religious aspects of life; Jacob K. Olupona, who restricts ancestors to religion, and Israel Kamudzandu, in whose philosophy ancestors can provide African societies with the possibility of moving beyond their indigenous religions into accepting other religious beliefs, such as those provided by Christianity. (shrink)

This paper is an attempt to identify common factors which constitute the foundation of decolonization in indigenous African religions. Since such aspects need to be essentially constructive in order to effectively and positively replace Colonial ideas, this particular search for common ground concerning decolonization in indigenous African religions is going to be pursued through the concept of ecodomy, seen as constructive process. When applied to decolonization with this postulated positivity, ecodomy coagulates three distinct aspects of indigenous African religions (...) into a common reality. These three aspects are ancestry, goodness, and the relationship with Christianity; they can function therefore as common denominator for various attempts to provide indigenous African religions with specific methodology in dealing with decolonization. This article is going to investigate four such methodologies which can confer positivity as well as an ecodomic, constructive character to decolonization efforts throughout the spectrum of indigenous African religions as they are reflected in the writings of John Mbiti, Isiaka P. Lalèyê, Jakob K. Olupona, and Israel Kamudzandu, all intellectuals of different geographical origin, religious backgrounds, university training, and personal convictions. With Mbiti promoting the superiority of Christianity, Lalèyê accepting it as irrelevant, Olupona preferring to deal without it, and Kamudzandu seeing it as essential, decolonizing efforts in indigenous African religions have at least four different methodologies which all aim at providing African communities with positive and ecodomic, essentially constructive ways to move forward beyond Colonial intellectual paradigms by making sure that peace and goodness are secured for everybody, African or not. (shrink)

After clarifying how Darwin understood natural selection and common ancestry, I consider how the two concepts are related in his theory. I argue that common ancestry has an evidential priority. For Darwin, arguments about natural selection often make use of the assumption of common ancestry, whereas defending common ancestry does not require the assumption that natural selection has been at work. In fact, Darwin held that the key evidence for common (...) class='Hi'>ancestry comes from characters whose evolution is not caused by natural selection. This raises the question of why Darwin puts natural selection first and foremost in the Origin. (shrink)

The growth of consumer DNA ancestry testing has resulted in questions and critiques being raised in social and research contexts. This study examined individuals discussing their ancestry DNA testing results on YouTube by searching for the two most popular testing companies (23andMe; Ancestry) and the phrase “DNA results.” The finalized dataset consisted of 117 videos, on which directed content analysis was performed. In the videos, individuals used results to clarify, confirm, question, and re-evaluate their previously held conceptions (...) of racial/ethnic identities. Reactions were more positive than negative (88.1% vs. 8.1%), and results more commonly reaffirmed (77.8%) than re-conceptualized (40.0%) one’s racial/ethnic identity. Ancestry testing and personal social media accounts were commonly promoted, demonstrating biotechnological hype where promotion abounds and critiques are scarce. Questions persist around the impact of ancestry DNA testing in reifying a scientifically inaccurate conception of race and what impact YouTube videos might have on audiences. (shrink)

Reid’s rejection of the “theory of ideas” implies that sensations are not copies of external qualities such as extension and figure. Reid also says that not even the order of sensations is spatial. However, in his early manuscripts Reid did not deny that sensations are arranged spatially. He simply denied that our ideas of extension and figure are copied from any single atomic sensation. Only subsequently did Reid explicitly reject the view that sensations are arranged spatially. The question of the (...) spatiality of color sensation was a central concern of early interpreters of Reid, like Dugald Stewart, John Fearn, and William Hamilton. In particular, John Fearn thought that the denial of the spatiality of color sensations is the result of Reid’s commitment to the immateriality of the soul. Against Reid’s view, Fearn argued that the perception of visible figure necessarily implies the spatiality of color sensations. (shrink)

This book explores important topics in Darwin’s theory of evolution and in the twentieth- and twenty-first-century theories that grew out of it. These topics include fitness, adaptation, altruism, intragenomic conflict, units of selection, genetic drift, the randomness of mutation, gradualism, common ancestry, taxonomy, race, phylogenetic inference, and optimality models. The book brings these and other biological topics into contact with numerous philosophical ideas − operationalism, reductionism, conventionalism, null hypotheses and default reasoning, instrumentalism versus realism, likelihoods versus probabilities, model (...) selection, essentialism, falsifiability, parsimony, the principle of the common cause, comparisons of causal power, interpretations of probaiblity, indeterminism, sensitivity to initial conditions, and the knowability of the past. (shrink)

ABSTRACT:A wide range of research uses patterns of genetic variation to infer genetic similarity between individuals, typically referred to as genetic ancestry. This research includes inference of human demographic history, understanding the genetic architecture of traits, and predicting disease risk. Researchers are not just structuring an intellectual inquiry when using genetic ancestry, they are also creating analytical frameworks with broader societal ramifications. This essay presents an ethics framework in the spirit of virtue ethics for these researchers: rather than (...) focus on rule following, the framework is designed to build researchers’ capacities to react to the ethical dimensions of their work. The authors identify one overarching principle of intellectual freedom and responsibility, noting that freedom in all its guises comes with responsibility, and they identify and define four principles that collectively uphold researchers’ intellectual responsibility: truthfulness, justice and fairness, anti-racism, and public beneficence. Researchers should bring their practices into alignment with these principles, and to aid this, the authors name three common ways research practices infringe these principles, suggest a step-by-step process for aligning research choices with the principles, provide rules of thumb for achieving alignment, and give a worked case. The essay concludes by identifying support needed by researchers to act in accord with the proposed framework. (shrink)

In July 2000, the Seminole Nation of Oklahoma passed a resolution that would effectively expel a significant portion of its tribal members. The resolution amended the Nation's constitution by changing its membership criteria. Previously, potential members needed to show descent from an enrollee of the 1906 Dawes Rolls, the official American Indian tribal rolls established by the Dawes Commission to facilitate the allotment of reservation land. The amended constitution requires possession of one-eighth Seminole Indian blood, a requirement that a significant (...) portion of the tribe's membership cannot fulfill. The members of the Nation who fail to meet this new membership criterion all have one thing in common: they are black.Descendents of former slaves who came to live among the Seminole Indians of Florida in the seventeenth and eighteenth centuries, the black Seminoles have been officially recognized by the U.S. government as members of the Seminole Nation of Oklahoma since 1866. (shrink)

Common ancestry is one of the pillars of Darwin’s theory of evolution. Today, the Tree of Life, which represents how all life is genealogically related, is often thought of as an essential component in the foundations of biological systematics and so therefore of evolutionary theory – and perhaps all of biology itself. It is an iconic representation in biology and even penetrates into popular culture.

Why do creationists persist in rejecting the evidence for Darwin’s theory of evolution? This paper explores longstanding disagreements among Christians over the epistemic status of evolution. Like other studies that have tried to define the evidence for evolution, a recent analysis by Gijsbert van den Brink, Jeroen de Ridder, and René van Woudenberg does not adequately face up to antecedent commitments that play into any assessment of evolution. The scientific theory of evolution involves higher-level models that are associated with a (...) range of non-scientific factors, including theological judgments. In light of these realities, an emphasis on mutual dialogue and understanding offers promising opportunities for Christians trying to discover the truth about God’s creation. (shrink)

How should the concept of evidence be understood? And how does the concept of evidence apply to the controversy about creationism as well as to work in evolutionary biology about natural selection and common ancestry? In this rich and wide-ranging book, Elliott Sober investigates general questions about probability and evidence and shows how the answers he develops to those questions apply to the specifics of evolutionary biology. Drawing on a set of fascinating examples, he analyzes whether claims about (...) intelligent design are untestable; whether they are discredited by the fact that many adaptations are imperfect; how evidence bears on whether present species trace back to common ancestors; how hypotheses about natural selection can be tested, and many other issues. His book will interest all readers who want to understand philosophical questions about evidence and evolution, as they arise both in Darwin's work and in contemporary biological research. (shrink)

Alvin Plantinga claims that Christian believer can rationally disbelieve in some elements of the theory of evolution: the Common Ancestry Thesis; Darwinism, taken as explanation of origin of life by the mechanism of natural selection operating on random genetic mutation, and Naturalistic Origins Thesis - the view that present life itself developed from nonliving matter without special activity of God. After the justification of the possibility of conflicts between faith and science, Plantinga's arguments are examined and assessed as (...) successful, with a few exceptions. The main thesis of this paper is that Plantinga is right claiming that rational disbelieving in evolution is possible, but his arguments are not enough to justify special creationism as theistic knowledge, supposing that knowledge warrants the truth. (shrink)

A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of “the” Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with (...) species. Instead, species must meet the more restrictive criterion of being genealogically exclusive groups where the members are more closely related to each other than to anything outside the group. I carefully spell out different versions of what this might mean and arrive at a working definition of exclusivity that forms groups that can function within phylogenetic theory. I conclude by arguing that while a phylogenetic species concept must use exclusivity as a grouping criterion, a variety of ranking criteria are consistent with the requirement that species can be placed on phylogenetic trees. (shrink)

In the eukaryotic cell, DNA compaction is achieved through its interaction with histones, constituting a nucleoprotein complex called chromatin. During metazoan evolution, the different structural and functional constraints imposed on the somatic and germinal cell lines led to a unique process of specialization of the sperm nuclear basic proteins (SNBPs) associated with chromatin in male germ cells. SNBPs encompass a heterogeneous group of proteins which, since their discovery in the nineteenth century, have been studied extensively in different organisms. However, the (...) origin and controversial mechanisms driving the evolution of this group of proteins has only recently started to be understood. Here, we analyze in detail the histone hypothesis for the vertical parallel evolution of SNBPs, involving a “vertical” transition from a histone to a protamine‐like and finally protamine types (H → PL → P), the last one of which is present in the sperm of organisms at the uppermost tips of the phylogenetic tree. In particular, the common ancestry shared by the protamine‐like (PL)‐ and protamine (P)‐types with histone H1 is discussed within the context of the diverse structural and functional constraints acting upon these proteins during bilaterian evolution. (shrink)

Modus Darwin is the name given by Elliott Sober to a form of argument that Sober attributes to Darwin in the Origin of Species, and to subsequent evolutionary biologists who have reasoned in the same way. In short, the argument form goes: Similarity, ergo common ancestry. In the present paper I review and critique Sober's analysis of Darwin's reasoning. I argue that modus Darwin has serious limitations that make the argument form unsuited for supporting Darwin's conclusions, and that (...) Darwin did not reason in this way. (shrink)

New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage‐specific genes. It was recently reported that an excess of primate‐specific and human‐specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in (...) both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under‐characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination. (shrink)

"The Natural System" is the name given to the underlying arrangement present in the diversity of life. Unlike a classification, which is made up of classes and members, a system or arrangement is an integrated whole made up of connected parts. In the pre-evolutionary period a variety of forms were proposed for the Natural System, including maps, circles, stars, and abstract multidimensional objects. The trees sketched by Darwin in the 1830s should probably be considered the first genuine evolutionary diagrams of (...) the Natural System—the first genuine evolutionary trees. Darwin refined his image of the Natural System in the well-known evolutionary tree published in the Origin of Species, where he also carefully distinguished between arrangements and classifications. Following the publication of the Origin, there was a great burst of evolutionary tree building, but interest in trees declined substantially after 1900, only to be revived in recent years with the development of cladistic analysis. ¶ While evolutionary trees are modern diagrams of the Natural System, they are at the same time instances of another broad class of diagrams that may be called "trees of history": branching diagrams of genealogical descent and change. During the same years that Darwin was sketching his first evolutionary trees, the earliest examples of two other trees of history also appeared: the first trees of language evolution and of manuscript genealogy. Though these were apparently independent of evolutionary trees in their origin, the similarities among all these trees of history, and among the historical processes that underlie them, were soon recognized. Darwin compared biological evolution and language evolution several times in the Origin of Species, and both Ernst Haeckel and the linguist August Schleicher made similar comparisons. Both linguists and stemmaticists (students of manuscript descent) understood the principle of apomorphy—the principle that only shared innovations provide evidence of common ancestry—more clearly than did systematists, and if there had been more cross-fertilization among these fields the cladistic revolution in systematics might well have taken place in the nineteenth century. ¶ Although historical linguists and stemmaticists have in some respects had sounder theory than have systematists, at least until recently, they have also had the practical problem of very large amounts of data, a problem not often faced by systematists until the advent of molecular sequencing. The opportunity now exists for systematists to contribute to the theory and practice of linguistics and stemmatics, their sister disciplines in historical reconstruction, through application of our commonly used computer programs for tree estimation. Preliminary results from the application of numerical cladistic analysis to a large stemmatic data set have been very encouraging, and have already generated much discussion in the stemmatics community. (shrink)

Cowpea mosaic virus (CPMV) is the type member of the comovirus group, which contains 14 different plant viruses that have the same structural organization of genomic RNAs and virions and use the same mechanism for expression of the viral RNAs. The combined structure and organization of the two CPMV genomic RNAs is strikingly similar to that of the single genome of animal picornaviruses. This suggests a common ancestry and similar replication mechanisms. CPMV is by far the best‐studied comovirus (...) and we shall limit this review to some recent data on this virus. For additional general information the reader is referred to other recent reviews on CPMV and comoviruses1,2. (shrink)

The empirical evidence often justifies belief in scientific theories. For instance, the great wealth of chemical and other relevant data leaves us with no real alternative to believing that matter is made of atoms. Similarly, the natural history of past and present organisms makes it irrational to deny that life on earth has evolved from a common ancestry. Again, the character and epidemiology of infectious diseases effectively establishes that they are caused by microbes. Peter Lipton did much to (...) illuminate the logic of these and many similar inferences. Often the observed facts admit of only one good theoretical explanation. Rationality therefore dictates that we infer the truth of this explanation. (shrink)

This essay set the stage for the 2003 Star Island conversation on “Ecomorality” by remembering the cosmic, geological, and ecological context in which we live. It reflects on the immense journey that matter and life have traveled from the beginning and reminds us that, throughout that journey, all that was and is emerged from a fertile mix of individual well-being and reciprocity. But to sense the meaning of the story and to know our place in it takes more than hearing (...) its broad outline. We need to remember the individual actors who have gone before us; to read their stories in particular places, like the rocks and ecosystems of Star Island; and to listen carefully for the meaning to be found in those actors and those places. Those stories, actors, and places invite us to sense the sacredness of our time and place and to reconsecrate our selves and our energies to developing an ethic that honors our common ancestry. (shrink)

Human genetics has blossomed from an obscure biological science and explanation for rare disorders to a field that is profoundly altering health care for everyone. This thoroughly updated new edition of _Human Genetics: The Basics_ provides a concise background of gene structure and function through the lens of real examples, from families living with inherited diseases to population-wide efforts in which millions of average people are learning about their genetic selves. The book raises compelling issues concerning: • The role of (...) genes in maintaining health and explaining sickness • Genetic testing, gene therapy, and genome editing • The common ancestry of all humanity and how we are affecting our future. Written in an engaging, narrative manner, this concise introduction is an ideal starting point for anyone who wants to know more about genes, DNA, genomes, and the genetic ties that bind us all. (shrink)

Race was once thought to be a real biological kind. Today the dominant view is that objective biological races don't exist. I challenge the trend to reject the biological reality of race by arguing that cladism (a school of classification that individuates taxa by appeal to common ancestry) provides a new way to define race biologically. I also reconcile the proposed biological conception with constructivist theories about race. Most constructivists assume that biological realism and social constructivism are incompatible (...) views about race; I argue that the two conceptions can be compatible. (shrink)

How justified are those who think that the clamour for one-party politics in Africa was inspired by the character of African consensual democracy such as the one defended by Kwasi Wiredu? I show that though Wiredu’s consensual democracy may share some similarities with a one-party polity, it does not necessarily follow that it has inspired the emergence of one-party polities in Africa. Similarly, the absence of any discernible similarities between African consensual democracy and one-party polity may not also necessarily entail (...) that the former has not inspired the latter. When one considers the ontological nature of Wiredu’s consensual democracy and the one-party polity, it becomes contentious to claim that the latter emerges from the former. However, based on Wiredu’s idea of consensual democracy, one might argue that consensual democracy has a common ancestry with a one-party polity because they both seem to emerge from “party1”. (shrink)

For many species that reproduce sexually, how sex is expressed at different points across lifespan is highly contingent and dependent on various environmental factors. For example, in many species of fish, environmental cues can trigger a natural process of sex transition where a female transitions to male. For many species of turtle, incubation temperature influences the likelihood that turtle eggs will hatch males or females. What is the case for Homo sapiens? Is human sex expression influenced by contingent environmental factors (...) like we see in fish and turtles, with whom we share common ancestry and DNA? Our paper explores the current biological science of sex determination and how it applies to philosophical and theological accounts of the human person. We argue that while human sex determination is not susceptible to environmental cues to the same degree we see in other species, there is sufficient variability among the pathways of human sex development to complicate simplistic biological categories of male and female. (shrink)

Contemporary biomedical ethics and environmental ethics share a common ancestry in Aldo Leopold's and Van Rensselaer Potter's initial broad visions of a connected biosphere. Over the past five decades, the two fields have become strangers. Public health ethics, a new subfield of bioethics, emerged from the belly of contemporary biomedical ethics and has evolved over the past 25 years. It has moved from its traditional concern with the tension between individual autonomy and community health to a wider focus (...) on social justice and solidarity. Public health has a broad focus that includes individual, community, and environmental health. Public health ethics attends to these broad commitments reflected in the increasing concern with the connectedness of health of individuals to the health of populations, to the health of animals, to the health of the environment; it is well situated to reconnect all three “fields” of ethics to promote a healthier planet. (shrink)

Historical sciences like evolutionary biology reconstruct past events by using the traces that the past has bequeathed to the present. Markov chain theory entails that the passage of time reduces the amount of information that the present provides about the past. Here we use a Moran process framework to show that some evolutionary processes destroy information faster than others. Our results connect with Darwin’s principle that adaptive similarities provide scant evidence of common ancestry whereas neutral and deleterious similarities (...) do better. We also describe how the branching in phylogenetic trees affects the information that the present supplies about the past. (shrink)

"More than any thing else technology creates our world. It creates our wealth, our economy, our very way of being," says W. Brian Arthur. Yet, until now the major questions of technology have gone unanswered. Where do new technologies come from -- how exactly does invention work? What constitutes innovation, and how is it achieved? Why are certain regions -- Cambridge, England, in the 1920s and Silicon Valley today -- hotbeds of innovation, while others languish? Does technology, like biological life, (...) evolve? How do new industries, and the economy itself, emerge from technologies? In this groundbreaking work, pioneering technology thinker and economist W. Brian Arthur sets forth a boldly original way of thinking about technology that gives answers to these questions. The Nature of Technology is an elegant and powerful theory of technology's origins and evolution. It achieves for the progress of technology what Thomas Kuhn's The Structure of Scientific Revolutions did for scientific progress. Arthur explains how transformative new technologies arise and how innovation really works. Conventional thinking ascribes the invention of technologies to "thinking outside the box," or vaguely to genius or creativity, but Arthur shows that such explanations are inadequate. Rather, technologies are put together from pieces -- themselves technologies -- that already exist. Technologies therefore share common ancestries and combine, morph, and combine again to create further technologies. Technology evolves much as a coral reef builds itself from activities of small organisms -- it creates itself from itself; all technologies are descended from earlier technologies. Drawing on a wealth of examples, from historical inventions to the high-tech wonders of today, and writing in wonder fully engaging and clear prose, Arthur takes us on a mind-opening journey that will change the way we think about technology and how it structures our lives. (shrink)

“Absence of evidence isn’t evidence of absence” is a slogan that is popular among scientists and nonscientists alike. This article assesses its truth by using a probabilistic tool, the Law of Likelihood. Qualitative questions (“Is E evidence about H ?”) and quantitative questions (“How much evidence does E provide about H ?”) are both considered. The article discusses the example of fossil intermediates. If finding a fossil that is phenotypically intermediate between two extant species provides evidence that those species have (...) a common ancestor, does failing to find such a fossil constitute evidence that there was no common ancestor? Or should the failure merely be chalked up to the imperfection of the fossil record? The transitivity of the evidence relation in simple causal chains provides a broader context, which leads to discussion of the fine-tuning argument, the anthropic principle, and observation selection effects. (shrink)

The task of Philosophy in Science (PinS) is to use philosophical tools to help solve scientific problems. This article describes how I stumbled into this line of work and then addressed several topics in philosophy of biology—units of selection, cladistic parsimony, robustness and trade-offs in model building, adaptationism, and evidence for common ancestry—often in collaboration with scientists. I conclude by offering advice for would-be PinS practitioners.

Sijilmassi et al. argue that myths serve to gain coalitional support by detailing shared histories of ancestry and cooperation. They overlook the emotional influences of stories, which include myths of human origin. We suggest that influential myths do not promote cooperation principally by signaling common ancestry, but by prompting human emotions of interdependence and connection.

In a recent paper, Walter Gilbert's group has estimated the number of original exons from which all extant proteins might have been constructed. The approach used is subjected to a critical analysis here. It is shown that there are flawed assumptions about both the mechanism and generality of exon‐shuffling and in the sequence comparison procedures employed, the latter failing to distinguish chance similarity from similarity due to common ancestry. These methodological errors lead to the omission of many known (...) cases of exonshuffling and the inclusion of others which may not be genuine. In consequence, the analysis from the Gilbert group cannot give a reliable estimate of those modules that actually participated in exon‐shuffling and provides no information on the number of protein archetypes that did not participate in these processes. (shrink)

Is it accurate to label Darwin's theory "the theory of evolution by natural selection," given that the concept of common ancestry is at least as central to Darwin's theory? Did Darwin reject the idea that group selection causes characteristics to evolve that are good for the group though bad for the individual? How does Darwin's discussion of God in The Origin of Species square with the common view that he is the champion of methodological naturalism? These are (...) just some of the intriguing questions raised in this volume of interconnected philosophical essays on Darwin. The author's approach is informed by modern issues in evolutionary biology, but is sensitive to the ways in which Darwin's outlook differed from that of many biologists today. The main topics that are the focus of the book--common ancestry, group selection, sex ratio, and naturalism--have rarely been discussed in their connection with Darwin in such penetrating detail. (shrink)

Homology is the similarity between organisms due to common ancestry. Introduced by Richard Owen in 1843 in a paper entitled “Lectures on comparative anatomy and physiology of the invertebrate animals”, the concept of homology predates Darwin's “Origin of Species” and has been very influential throughout the history of evolutionary biology. Although homology is the central concept of all comparative biology and provides a logical basis for it, the definition of the term and the criteria of its application remain (...) controversial. Here, I will discuss homology in the context of the hierarchy of biological organization. I will provide insights gained from an exemplary case study in evolutionary developmental biology that indicates the uncoupling of homology at different levels of biological organization. I argue that continuity and hierarchy are separate but equally important issues of homology. BioEssays 30:653–658, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions (...) of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (shrink)

Homology is a central concept of comparative and evolutionary biology, referring to the presence of the same bodily parts (e.g., morphological structures) in different species. The existence of homologies is explained by common ancestry, and according to modern definitions of homology, two structures in different species are homologous if they are derived from the same structure in the common ancestor. Homology has traditionally been contrasted with analogy, the presence of similar traits in different species not necessarily due (...) to common ancestry but due to a similar function or convergent evolution resulting from similar selective pressure in different species. (A more recent contrastive notion is homoplasy, the presence of similar traits in different species without common ancestry, i.e., as an instance of parallel evolution.) This sounds straightforward, but in fact the homology concept has a rich history and currently is the subject of extensive theoretical reflection, resulting in different contemporary approaches to homology. (shrink)

Here I reply to Jean Gayon's, Tim Lewens's, and Samir Okasha's comments on Did Darwin write the Origin backwards? The topics addressed include: Darwin's thinking that common ancestry is "evidentially prior" to natural selection; how Darwin uses phylogenetic trees to test hypotheses concerning natural selection; how group and indivdiual selection should be defined, and how each is related to the concept of adaptation.

de Queiroz (1995), Griffiths (1999) and LaPorte (2004) offer a new version of essentialism called "historical essentialism". According to this version of essentialism, relations of common ancestry are essential features of biological taxa. The main type of argument for this essentialism proposed by Griffiths (1999) and LaPorte (2004) is that the dominant school of classification, cladism, defines biological taxa in terms of common ancestry. The goal of this paper is to show that this argument for historical (...) essentialism is unsatisfactory: cladism does not assume that relations of common ancestry are essential attributes of biological taxa. Therefore, historical essentialism is not justified by cladism. (shrink)

Taxa and homologues can in our view be construed both as kinds and as individuals. However, the conceptualization of taxa as natural kinds in the sense of homeostatic property cluster kinds has been criticized by some systematists, as it seems that even such kinds cannot evolve due to their being homeostatic. We reply by arguing that the treatment of transformational and taxic homologies, respectively, as dynamic and static aspects of the same homeostatic property cluster kind represents a good perspective for (...) supporting the conceptualization of taxa as kinds. The focus on a phenomenon of homology based on causal processes (e.g., connectivity, activity-function, genetics, inheritance, and modularity) and implying relationship with modification yields a notion of natural kinds conforming to the phylogenetic-evolutionary framework. Nevertheless, homeostatic property cluster kinds in taxonomic and evolutionary practice must be rooted in the primacy of epistemological classification (homology as observational properties) over metaphysical generalization (series of transformation and common ancestry as unobservational processes). The perspective of individuating characters exclusively by historical-transformational independence instead of their developmental, structural, and functional independence fails to yield a sufficient practical interplay between theory and observation. Purely ontological and ostensional perspectives in evolution and phylogeny (e.g., an ideographic character concept and PhyloCode’s ‘individualism’ of clades) may be pragmatically contested in the case of urgent issues in biodiversity research, conservation, and systematics. (shrink)

Is religion a positive reality in your life? If not, have you lost anything by forfeiting this dimension of your humanity? This book compares the theology of Tillich with the psychology of Jung, arguing that they were both concerned with the recovery of a valid religious sense for contemporary culture. _Paul Tillich, Carl Jung and the Recovery of Religion_ explores in detail the diminution of the human spirit through the loss of its contact with its native religious depths, a problem (...) on which both spent much of their working lives and energies. Both Tillich and Jung work with a naturalism that grounds all religion on processes native to the human being. Tillich does this in his efforts to recover that point at which divinity and humanity coincide and from which they differentiate. Jung does this by identifying the archetypal unconscious as the source of all religions now working toward a religious sentiment of more universal sympathy. This book identifies the dependence of both on German mysticism as a common ancestry and concludes with a reflection on how their joint perspective might affect religious education and the relation of religion to science and technology. Throughout the book, John Dourley looks back to the roots of both men's ideas about mediaeval theology and Christian mysticism making it ideal reading for analysts and academics in the fields of Jungian and religious studies. (shrink)

I propose a new account of homology, according to which homology is a correspondence of developmental mechanisms due to common ancestry, formally defined as an isomorphism of causal graphs over lineages. The semiformal definition highlights the role of homology as a higher-order principle unifying evolutionary models and also provides definite meanings to concepts like constraints, evolvability, and novelty. The novel interpretation of homology suggests a broad perspective that accommodates evolutionary developmental biology and traditional population genetics as distinct but (...) complementary approaches to understand evolution, prompting further empirical and theoretical research. (shrink)

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions (...) of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (shrink)

The minimalist concept of race represents the barest characterization of the ordinary concept race possible. Minimalist races are groups of human beings distinguished by patterns of visible physical features, groups whose members are linked by a common ancestry peculiar to members of the group, and which originate from a distinctive geographic location. Minimalist races exist because there are existing human groups that satisfy the minimalist concept of race. Their existence is not precluded by the findings of population genetics. (...) Appeal to contemporary studies in evolutionary biology and population genetics makes it possible to rebut the objection that minimalist races do not exist because they are not genetically distinct. (shrink)

It has recently been argued by both lay people, church leaders and academic philosophers that evolutionary theory – and especially the theory of common ancestry – rules out any adequate notion of human dignity (I). In this paper, this claim is examined and refuted. First of all, when spelled out in a conceptually unambiguous way, it turns out that the evolutionary argument against human dignity hinges on the belief that human uniqueness , as this was traditionally encapsulated in (...) the doctrine of the imago Dei , has been falsified (II). Secondly, therefore, a recent proposal to reinterpret this doctrine in a way which allows us to drop the notion of human uniqueness but to still uphold a robust notion of human dignity is discussed (III). It is concluded, however, that this proposal is problematic for several reasons. Thirdly, therefore, a more fruitful avenue is explored, namely the attempt to reinterpret the notions of human uniqueness and human dignity along theological rather than biological lines (IV). It will turn out that this attempt, which is inspired by both contemporary biblical scholarship and systematic theology, in fact enables us to adhere to notions of human uniqueness and human dignity (and to connect this to the doctrine of the imago Dei ) which are not at odds with evolutionary theory. Finally, some conclusions are drawn (V). (shrink)

While it is generally agreed that the concept of homology refers to individuated traits that have been inherited from common ancestry, we still lack an adequate account of trait individuation or inheritance. Here I propose that we utilize a counterfactual criterion of causation to link each trait with a developmental-causal (DC) gene. A DC gene is made up of the genetic information (which might or might not be physically contiguous in the genome) that is needed for the production (...) of the organismic attributes that comprise the trait. I argue that individuated traits—phenes—correspond to organismic features that are caused by DC genes. Using such an approach, we can define a DC map, which shows the relations between each pair of phenes and provides a succinct summary of genotype-phenotype relationships and phenotypic complexity. Phenes in parents and offspring are judged to be homologous if their DC genes are composed of orthologous genetic factors. When comparing more distantly related organisms, traits are homologous when linked by a chain of parent-offspring homologs along the path of ancestry that links the two organisms. There are three possible ways to deal with the potential for multiple equivalent DC genes: maximal, minimal, and consensus homology. Whereas maximal homology has limited utility, the other two approaches have value and can help to guide research at the intersection of evolution and development. (shrink)