Brackets and tables, circles and maps, 1554-1872 -- Early botanical networks and trees, 1766-1815 -- The first evolutionary tree, 1786-1820 -- Diverse and unusual trees of the early nineteenth century, 1817-1834 -- The rule of five, 1819-1854 -- Pre-Darwinian branching diagrams, 1828-1858 -- Evolution and the trees of Charles Darwin, 1837-1868 -- The trees of Ernst Haeckel, 1866-1905 -- Post-Darwinian nonconformists, 1868-1896 -- More late-nineteenth-century trees, 1874-1897 -- Trees of the early twentieth century, 1901-1930 -- The trees of Alfred (...) Sherwood Romer, 1933-1966 -- Additional trees of the mid-twentieth century, 1931-1943 -- The trees of William King Gregory, 1938-1951 -- Hints of new approaches, 1954-1969 -- Phenograms and cladograms, 1958-1966 -- Early molecular trees, 1962-1987 -- Notable trees of the past four decades, 1970-2010 -- Primeval branches and universal trees of life, 1997-2010. (shrink)

The canonical view of a 3‐domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2‐domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment‐dependent approaches, which often fail to satisfactorily address the problem of ‘‘gaps.’’ In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods. Alignment‐free methodologies lift most difficulties (...) but require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open. Also see the video abstract here: https://youtu.be/-6TBN0bubI8. (shrink)

Abstract: Biology continues to use the Tree of Life image to show the temporal continuity and discontinuity of the living beings. Moreover, the development of genetic, molecular biology and paleontology has originated phylogenetics. This discipline studies evolutionary relatedness among various groups of organisms through molecular sequencing data and morphological data matrices. The Tree offers interesting points for semiotic perspectives and for theological approaches too. The symbolic reading of the Tree of Life, on the one hand, (...) and the analogies with the Biblical genealogies and some Christian images, on the other hand, will be explored. -/- . (shrink)

The ‘Tree of Life’ is intended to represent the pattern of evolutionary processes that result in bifurcating species lineages. Often justified in reference to Darwin’s discussions of trees, the Tree of Life has run up against numerous challenges especially in regard to prokaryote evolution. This special issue examines scientific, historical and philosophical aspects of debates about the Tree of Life, with the aim of turning these criticisms towards a reconstruction of prokaryote phylogeny and even (...) some aspects of the standard evolutionary understanding of eukaryotes. These discussions have arisen out of a multidisciplinary collaboration of people with an interest in the Tree of Life, and we suggest that this sort of focused engagement enables a practical understanding of the relationships between biology, philosophy and history. (shrink)

As a way forward in assessing how the Old Testament wisdom tradition might speak to decisions in a modern medical context, in this paper, I propose exploring the iconographic function of the “tree of life” in the Old Testament, which is consistently associated with both wisdom as well as life and health, in order to tease out two-related issues that can help in providing a Christian theological framework for thinking about the problem of the medicalization of risk: (...) first, how should the natural and good human desire for health and long life be framed in terms of the pursuit of wisdom? And, second, how might a sapientially formed character approach risk and uncertainty in making medical decisions? The answers to these questions help establish a framework in which more specific questions related to the medicalization of risk can be assessed. As such, this paper is deliberately programmatic and perspectival rather than prescriptive. (shrink)

Viewing education through the prism of the Torah, Tree of Life, Tree of Knowledge takes the reader through the stages of learning, growth, and self-development that characterize human lives. The journey begins with education as it happens in the home, moves on to the institutions of society, especially schools, and then on to the questions of identity and commitment which constitute the hidden agenda of “informal educational networks.” The self-education of the individual is explored: When does one (...) “grow up”? What is really worth knowing? How does one cope with memories, illness, and anticipations of what lies ahead? This book examines some of the millennial conversation in an attempt to discover an educational philosophy in the Torah that can be relevant to life in the contemporary world. (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.

This paper discusses a krater recently discovered in a cultic building at Tel Burna in the Shephelah. Of special interest is the krater’s relatively well-preserved decoration containing multiple nature scenes related to the so-called tree of life or sacred tree motif. The krater’s physical description and archaeological context and the decoration’s relationship to relevant comparanda are explored in order to elucidate the significance of its iconography. In light of this discussion, we conclude that the decoration includes an (...) abstract representation of a Canaanite goddess as a “pubis of life” variation of the “tree of life” motif on the krater as a votive vessel in the Late Bronze Age cult. (shrink)

In a recent paper,(1) palaeontologist Mike Benton claimed that our ability to reconstruct accurately the tree of Life may not have improved significantly over the last 100 years. This implies that the cladistic and molecular revolutions may have promulgated as much bad “black box” science as rigorous investigation. Benton's assessment was based on the extent to which cladograms (typically constructed with reference only to distributions of character states) convey the same narrative as the geochronological ages of fossil taxa (...) (an independent data set). Fossil record quality varies greatly between major clades, and the palaeontological dating “yardstick” may be more appropriate for some groups than others. BioEssays 24:203–207, 2002. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/bies.10065. (shrink)

This study of the Jewish legal system (the Halakhah) demonstrates that the law embraces every corner of life.

Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology, it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. In this paper, I draw from the species concept debate to argue for a set of desiderata for the (...) concept of “biodiversity” that is both principled and coheres with the concept’s use. Given these desiderata, this concept should be understood as referring to difference quantified in terms of the phylogenetic structure of lineages, also known as the ‘tree of life’. (shrink)

Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more (...) class='Hi'>tree-like history because successful lateral events tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes. (shrink)

A common view is that species occupy a unique position on the Tree of Life. Evaluating this claim requires an understanding of what the Tree of Life represents. The Tree represents history, but there are at least three biological levels that are often said to have genealogies: species, organisms, and genes. Here I focus on defending the plausibility of a gene-based account of the Tree. This leads to an account of species that are determined (...) by gene genealogies. On this view, an exclusive group is a group of organisms that forms a clade for a higher proportion of the genome than any conflicting clade. Taxa occupy a unique position in what can be called the ‘primary concordance tree’. But each gene has its own historical ‘Tree of Life’. I conclude by arguing that both organismal pedigrees with their corresponding Tree as well as gene genealogies and their trees are objectively real and play important, but different, roles in biological practice. (shrink)

This article examines a proverbial saying "Wisdom is a tree of life" (Prov. 3:18) through the lens of conceptual metaphor. Such a metaphor works by mapping two conceptual domains. The direction goes from the SOURCE domain (an ancient myth of a miraculous tree that whets human’s appetite for eternal youth) to the TARGET domain (a concept of wisdom in life). Conceptual metaphor helps us to understand that the tree metaphor in Prov. 3:18 instills in the (...) readers’ mind a kind of reward powerful enough to motivate them to pursue wisdomand to persevere in that quest. The boon will arouse their desire so that they will do anything. This article also suggests that the tree metaphor in Proverbs receives its fuller sense through Prov. 11:30; 13:12; 15:4. Conceptual metaphor, thus, enables the reader to notice a holistic presentation of the book of Proverbs, which has been all too often considered as a compilation of various self-contained sayings. Abstrak Artikel ini menganalisis ungkapan "Hikmat adalah pohon kehidupan" (Ams. 3:18) dengan perspektif metafora konseptual. Metafora konseptual adalah sebuah pendekatan linguistik yang menitikberatkan pemetaan relasi yang terjadi antara dua domain yang berbeda. Pada ayat tersebut, akan dicermati arah pergerakan dari domain SUMBER (yakni, sebuah mitos kuno tentang pohon mujarab yang berkhasiat menghidupkan) menuju domain TARGET (yakni, konsep kebijaksanaan dalam hidup). Tidak seperti metafora stilistika yang berfokus pada aspek keindahan bahasa metaforis itu sendiri, metafora konseptual lebih berfokus pada proses pemahaman kognitif yang ada dalam benak si pembaca. Melalui kajian konseptual ini, akan ditunjukkan bagaimana metafora pohon kehidupan (Ams. 3:18) beserta aspek mitologisnya menstimulasi imajinasi para pembaca tentang adanya ganjaran yang amat menggiurkan ketika seseorang mengejar hikmat. Ia akan tergerak untuk melakukan segala daya upaya dalam meraih hikmat demi memperoleh ganjaran tersebut. Artikel ini juga bertujuan menunjukkan bahwa ketiga pemunculan lain dari metafora pohon ini (pada Ams. 11:30; 13:12; 15:4) rupanya berperan menyajikan gambaran yang lebih utuh mengenai pohon mujarab ini. Apabila dilihat lebih luas lagi, keempat ayat secara bersama-sama mengikat seluruh isi kitab Amsal. Metafora konseptual tentang pohon kehidupan ini menawarkan sebuah gagasan holistik terhadap pembacaan kitab Amsal. Kata-kata Kunci: metafora stilistika, metafora konseptual, hikmat, pohon kehidupan, ganjaran. (shrink)

argue that natural selection does not explain the genotypic arid phenotypic properties of individuals. On this view, natural selection explains the adaptedness of individuals, not by explaining why the individuals that exist have the adaptations they do, but rather by explaining why the individuals that exist are the ones with those adaptations. This paper argues that this ‘Negative’ view of natural selection ignores the fact that natural selection is a cumulative selection process. So understood, it explains how the genetic sequences (...) that individuals inherit and that are responsible for their complex (and co-adapted) adaptations first arose in the gene-pool. (shrink)

Do trees of life have roots? What do these roots look like? In this contribution, I argue that research on the origins of life might offer glimpses on the topology of these very roots. More specifically, I argue (1) that the roots of the tree of life go well below the level of the commonly mentioned ‘ancestral organisms’ down into the level of much simpler, minimally living entities that might be referred to as ‘protoliving systems’, and (...) (2) that further below, a system of roots gradually dissolves into non-living matter along several functional dimensions. In between non-living and living matter, one finds physico-chemical systems that I propose to characterize by a ‘lifeness signature’. In turn, this ‘lifeness signature’ might also account for a diverse range of biochemical entities that are found to be ‘less-than-living’ yet ‘more-than-non-living’. (shrink)

The article reviews about esoteric symbolism of the tree of life in shamanic cultures and oriental traditions including classical Hindu and Buddhist systems, together with various esoteric and indigenous traditions. The very idea of the tree of life, in indigenous cultures, which is often called the ‘world tree’ or ‘shamanic tree’, is connected with human illumination process in the form of mystical or ecstatic experience gained through the process of the self-realization. These various forms (...) of mystico-religious experiences could be found in many religious traditions, considered to be cross-cultural phenomena. The author made an attempt to make a classification of chakras and energetic structure of the human body according to cross-cultural analysis of various cultures. (shrink)

Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable (...) TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL. (shrink)

Venerable tradition allies the Torah with Wisdom, a “tree of life.”2 The tree of life is an ancient mythic symbol of the earth mother. This essay demonstrates the capacity of the Torah to facilitate a reintegrative return to the mother when, as now, the religious narratives falter that once seemed to ensure the unity of man made in the image of God conceived only as the Father. Participating in the process of this return one discovers beneath (...) the Torah's fractured narrative surface a reduplicative pattern based on the logic of the unconscious, which is founded on the repressed prelinguistic bond with all life formed at the maternal breast. This pattern reflects the recombinant properties that the unconscious shares with the earth, which breaks down and regenerates dead matter as the unconscious breaks down and regenerates the meaning of words. Folded into rhetorical tropes as into a single letter, the Torah's regenerative pattern repeatedly recalls to man what it means to be human, unique among but also one with all the diverse life of the earth. (shrink)

The "tree of life" iconography, representing the history of life, dates from at least the latter half of the 18th century, but evolution as the mechanism providing this bifurcating history of life did not appear until the early 19th century. There was also a shift from the straight line, scala naturae view of change in nature to a more bifurcating or tree-like view. Throughout the 19th century authors presented tree-like diagrams, some regarding the Deity (...) as the mechanism of change while others argued for evolution. Straight-line or anagenetic evolution and bifurcating or cladogenetic evolution are known in biology today, but are often misrepresented in popular culture, especially with anagenesis being confounded with scala naturae. Although well known in the mid 19th century, the geologist Edward Hitchcock has been forgotten as an early, if not the first author to publish a paleontologically based "tree of life" beginning in 1840 in the first edition of his popular general geology text Elementary Geology. At least 31 editions were published and those between 1840 and 1859 had this "paleontological chart" showing two trees, one for fossil and living plants and another for animals set within a context of geological time. Although the chart did not vary in later editions, the text explaining the chart did change to reflect newer ideas in paleontology and geology. Whereas Lamarck, Chambers, Bronn, Darwin, and Haeckel saw some form of transmutation as the mechanism that created their "trees of life," Hitchcock, like his contemporaries Agassiz and Miller, who also produced "trees of life," saw a deity as the agent of change. Through each edition of his book Hitchcock denounced the newer transmutationist hypotheses of Lamarck, then Chambers, and finally Darwin in an 1860 edition that no longer presented his tree-like "paleontological chart.". (shrink)

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: (...) Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life? A schematic of the process of building a unified tree of life. Inputs are published phylogenetic estimates and a unified taxonomy. These inputs are combined into a summary supertree containing ≈2 million taxa. The relationships among any subset of taxa may easily be accessed and used in downstream analyses. (shrink)

Considering the properties of mirror neurons (MNs) in terms of development and phylogeny, we offer a novel, unifying, and testable account of their evolution according to the available data and try to unify apparently discordant research, including the plasticity of MNs during development, their adaptive value and their phylogenetic relationships and continuity. We hypothesize that the MN system reflects a set of interrelated traits, each with an independent natural history due to unique selective pressures, and propose that there are at (...) least three evolutionarily significant trends that gave raise to three subtypes: hand visuomotor, mouth visuomotor, and audio–vocal. Specifically, we put forward a mosaic evolution hypothesis, which posits that different types of MNs may have evolved at different rates within and among species. This evolutionary hypothesis represents an alternative to both adaptationist and associative models. Finally, the review offers a strong heuristic potential in predicting the circumstances under which specific variations and properties of MNs are expected. Such predictive value is critical to test new hypotheses about MN activity and its plastic changes, depending on the species, the neuroanatomical substrates, and the ecological niche. (shrink)

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...) prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history. Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a ‘meta-heuristic’ in the normative commitments guiding scientific practice. (shrink)

Andrey Bely's autobiographical novel Kotik Letaev and Terrence Malick's film The Tree of Life do not share a common subtext. Nevertheless, they have strikingly similar themes. They each deal with an adult's confrontation of his past through memory, a memory that extends back before birth. Coming to terms with the past prepares the adult protagonist of each work for his destiny. The essay discusses Malick's use of William Blake's mysticism and Bely's dependence on the religious-philosophical ideas of Rudolf (...) Steiner. Memory plays an important role in both works as it touches on the recapitulation of cosmic origins in the development of the individual human being. What the quester discovers through memory enables him to find the way back to Eternity from which he has descended. Both artists invoke the World Tree uniting heaven and earth and its association with the Cross of Christ. In both the novel and the film the world is seen first through a child's eyes, then through growing understanding of the adult. Malick illustrates with cinematography what Bely describes in words. Malick uses music in a way that fleshes out what Bely attempted to create through using musical tropes in language. (shrink)

Lateral gene transfer, the exchange of genetic information between lineages, not only makes construction of a universal Tree of Life difficult to achieve, but calls into question the utility and meaning of any result. Here I review the science of prokaryotic LGT, the philosophy of the TOL as it figured in Darwin’s formulation of the Theory of Evolution, and the politics of the current debate within the discipline over how threats to the TOL should be represented outside it. (...) We could encourage a more realistic and supportive public understanding of evolution by admitting that what we believe in is not a unified meta-theory but a versatile and well-stocked explanatory toolkit. (shrink)

The "tree of life" iconography, representing the history of life, dates from at least the latter half of the 18th century, but evolution as the mechanism providing this bifurcating history of life did not appear until the early 19th century. There was also a shift from the straight line, scala naturae view of change in nature to a more bifurcating or tree-like view. Throughout the 19th century authors presented tree-like diagrams, some regarding the Deity (...) as the mechanism of change while others argued for evolution. Straight-line or anagenetic evolution and bifurcating or cladogenetic evolution are known in biology today, but are often misrepresented in popular culture, especially with anagenesis being confounded with scala naturae. Although well known in the mid 19th century, the geologist Edward Hitchcock has been forgotten as an early, if not the first author to publish a paleontologically based "tree of life" beginning in 1840 in the first edition of his popular general geology text Elementary Geology. At least 31 editions were published and those between 1840 and 1859 had this "paleontological chart" showing two trees, one for fossil and living plants and another for animals set within a context of geological time. Although the chart did not vary in later editions, the text explaining the chart did change to reflect newer ideas in paleontology and geology. Whereas Lamarck, Chambers, Bronn, Darwin, and Haeckel saw some form of transmutation as the mechanism that created their "trees of life," Hitchcock, like his contemporaries Agassiz and Miller, who also produced "trees of life," saw a deity as the agent of change. Through each edition of his book Hitchcock denounced the newer transmutationist hypotheses of Lamarck, then Chambers, and finally Darwin in an 1860 edition that no longer presented his tree-like "paleontological chart.". (shrink)

Andrey Bely's autobiographical novel Kotik Letaev and Terrence Malick's film The Tree of Life do not share a common subtext. Nevertheless, they have strikingly similar themes. They each deal with an adult's confrontation of his past through memory, a memory that extends back before birth. Coming to terms with the past prepares the adult protagonist of each work for his destiny. The essay discusses Malick's use of William Blake's mysticism and Bely's dependence on the religious-philosophical ideas of Rudolf (...) Steiner. Memory plays an important role in both works as it touches on the recapitulation of cosmic origins in the development of the individual human being. What the quester discovers through memory enables him to find the way back to Eternity from which he has descended. Both artists invoke the World Tree uniting heaven and earth and its association with the Cross of Christ. In both the novel and the film the world is seen first through a child's eyes, then through growing understanding of the adult. Malick illustrates with cinematography what Bely describes in words. Malick uses music in a way that fleshes out what Bely attempted to create through using musical tropes in language. (shrink)

It is often said that there is just one “objective” tree of life: a single accurate branching hierarchy of species reflecting order of descent. For any two species, there is a single correct answer as to whether one is a “daughter” of the other, whether the two are “sister species” by virtue of their descent from a common parental species, whether they belong to a family line that excludes any given third species, and so on. The idea is (...) intrinsically interesting. It has consequences for what we should think about the evolutionary origins of Homo sapiens as well as other species.The idea also has important connections to the scientific discipline of systematics, which classifies organisms into related groups. The connection to systematics is what has made objectivity a topic of discussion for biologists and philosophers of biology. Cladism, now the dominant school of systematics, places organisms into groups depending just on their place in the tree of life. That is supposed to render classifica- tion objective. In section i, I recite claims to objectivity. In sections ii–v, I argue that the apparent objectivity is not what it seems to be. In section vi, I briefly revisit systematics. (shrink)

In this essay, I explore the relationship between the kabbalistic Tree of Life and that of Logic. I begin defining my terms, then analyze the question posed through that of science; philosophy; art and the concept of knowledge in general. I conclude that while a unified and complete account of knowledge cannot be gained, one can get a semblance of this knowledge. This I call a tending towards infinity or more precisely – a calculus of infinity. I conjecture (...) that this may lead to world-bettering, a wise kind of knowledge if you like that is neither of the Tree of Life nor that of the Tree of Knowledge as such, but the light itself which remains unnamable, that is to say beyond the realm of human knowledge. (shrink)