Systematic Biology, Misc

At its core this book is concerned with logic and computation with respect to the mathematical characterization of sentient biophysical structure and its behavior. -/- Three related theories are presented: The first of these provides an explanation of how sentient individuals come to be in the world. The second describes how these individuals operate. And the third proposes a method for reasoning about the behavior of individuals in groups. -/- These theories are based upon a new explanation of experience in (...) nature, the construction of senses, and motile behavior. This new approach is developed from first principles to enable a rigorous and systematic explanation of the variety of associated intelligent behaviors. -/- Alongside this development is a further account that focuses upon the nature of our work. It discusses the existential aspects of scientific inquiry, its epistemology and logic. It seeks to clarify the nature of the mathematical characterization and computation of natural behaviors, dealing with questions in the foundations of logic. It explores methodological issues related to reduction and the refinement of ideas from intuition to formal logical structure. -/- In support of this inquiry we work toward the development of a calculus for biophysical construction and its dynamics. If successful this mechanics mathematically characterizes sensory and motile behavior. -/- Upon this foundation we propose a model of apprehension and explore how its products are processed by the organism. Finally, we develop a probabilistic theory that enables us to reason about inaccessible factors in group behavior. -/- The mechanics we propose suggests the design and physical realization of a new model of computation; one in which structure and the concurrency of action are a first-order consideration. -/- We identify opportunities for experimental verification of the theory and we suggest a proof of our results in practice by the identification of this mechanism, allowing the construction of machines that experience. (shrink)

What should the best practices be for modeling zoonotic disease risks, e.g. to anticipate the next pandemic, when background assumptions are unsettled or evolving rapidly? This challenge runs deeper than one might expect, all the way into how we model the robustness of contemporary phylogenetic inference and taxonomic classifications. Different and legitimate taxonomic assumptions can destabilize the putative objectivity of zoonotic risk assessments, thus potentially supporting inconsistent and overconfident policy decisions.

This paper poses a problem for traditional phylogenetics: The identity of organisms that reproduce through fission can be understood in several different ways. This prompts questions about how to differentiate parent organisms from their offspring, making vertical gene transfer unclear. Differentiating between parents and offspring stems from what I call the identity problem. How the problem is resolved has implications for phylogenetic groupings. If the identity of a particular asexual organism persists through fission, the vertical lineage on a phylogenetic tree (...) will split differently than if the identity of an organism does not survive the fission process. (shrink)

Though biologists identify individuals as ‘male’ or ‘female’ across a broad range of animal species, the particular traits exhibited by males and females can vary tremendously. This diversity has led some to conclude that cross-animal sexes (males, or females, of whatever animal species) have “little or no explanatory power” (Dupré 1986: 447) and, thus, are not natural kinds in any traditional sense. This essay will explore considerations for and against this conclusion, ultimately arguing that the animal sexes, properly understood, are (...) “historical explanatory kinds”: groupings that can be scientifically significant even while their members differ radically in their current properties and particular histories. Whether this makes them full-fledged natural kinds is a question I take up at the very end. (shrink)

The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on (...) settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or “settled” science. (shrink)

Pluralisms of various sorts are popular in philosophy of science, including those that imply some scientific concept x should be eliminated from science in favour of a plurality of concepts x1, x2, … xn. This article focuses on influential and representative arguments for such eliminative pluralism about the concept species. The main conclusions are that these arguments fail, that all other extant arguments also fail, and that this reveals a quite general dilemma, one that poses a defeasible presumption against many (...) eliminative pluralisms about various scientific concepts. The article ends by outlining a novel integrative alternative in defence of species. 1) Introduction 2) The species Concept, the Category ‘Species’, and the ‘Species’ Category Problem 3) What Are Eliminative Pluralism about species, and the Arguments for It? 4) Evaluation of Arguments 4.1 Splitting? 4.2 Lumping? 4.3 The eliminative pluralist’s dilemma 5) More General Lessons6Species Cohesion: An Integrative Alternative7Conclusion. (shrink)

After decades of debates about species concepts, there is broad agreement that species are evolving lineages. However, species classification is still in a state of disorder: different methods of delimitation lead to competing outcomes for the same organisms, and the groups recognised as species are of widely different kinds. This paper considers whether this problem can be resolved by developing a unitary scale for evolutionary independence. Such a scale would show clearly when groups are comparable and allow taxonomists to choose (...) a conventional threshold of independence for species status. Existing measurement approaches to species delimitation are typically shot down by what I call the heterogeneity objection, according to which independently evolving groups are too heterogeneous to be captured by a single scale. I draw a parallel with the measurement of temperature to argue that this objection does not provide sufficient reasons to abandon the measurement approach, and that such an approach may even help to make the vague notion of evolutionary independence more precise. (shrink)

Lynch, Parke, and O’Malley highlight the need for better evaluative criteria for causal explanations in microbiome research. They propose new interventionist criteria, show that paradigmatic examples of microbiome explanations are flawed using those criteria, and suggest numerous ways microbiome explanations can be improved. While we endorse their primary criticisms and suggestions for improvements in microbiome research, we make several observations regarding the use of mooted causal models in microbiome research that have significant implications for their overall argument. In sum, we (...) contend that their critique is too modest and that even flawed causal inferences like those they criticize can be valuable for generating better causal models and evaluating explanatory outcomes in individual cases. (shrink)

Organisms leave a variety of traces in the fossil record. Among these traces, vertebrate and invertebrate paleontologists conventionally recognize a distinction between the remains of an organism’s phenotype and the remains of an organism’s life activities. The same convention recognizes body fossils as biological structures and trace fossils as geological objects. This convention explains some curious practices in the classification, as with the distinction between taxa for trace fossils and for tracemakers. I consider the distinction between “parallel taxonomies,” or parataxonomies, (...) which privileges some kinds of fossil taxa as “natural” and others as “artificial.” The motivations for and consequences of this practice are inconsistent. By comparison, I examine an alternative system of classification used by paleobotanists that regards all fossil taxa as “artificially” split. While this system has the potential to inflate the number of taxa with which paleontologists work, the system offers greater consistency than conventional practices. Weighing the strengths and weaknesses of each system, I recommend that paleontologists should adopt the paleobotanical system more broadly. (shrink)

Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, if (...) at all, does genealogical discordance challenge, modify, or revise how we conceive of species? (2) How has growing appreciation of genealogical discordance impacted scientific practice? Of systematics in particular? (3) How do lineages at different levels diverge and diversify? All told, genealogical discordance enriches and complicates our taxonomic ontology, as well as the practice of reconstructing phylogenies. This presents both challenges and opportunities for the study of divergence and diversification. (shrink)

Charles Darwin, in his species notebooks, engaged seriously with the quinarian system of William Sharp Macleay. Much of the attention given to this engagement has focused on Darwin’s attempt to explain, in a transmutationist framework, the intricate patterns that characterized the quinarian system. Here, I show that Darwin’s attempt to explain these quinarian patterns primarily occurred before he had read any work by Macleay. By the time Darwin began reading Macleay’s writings, he had already arrived at a skeptical view of (...) the reality of these patterns. What most interested Darwin, as he read Macleay, was not the quinarian system itself. Rather, Darwin’s notes on his reading primarily concerned certain background principles animating Macleay’s work, in particular: the non-existence of a saltus between human and animal minds, the difficulty of establishing boundaries between species and varieties, and Macleay’s method of variation. Darwin’s interest in the last of these left a mark on his discussion of taxonomic methodology in the Origin. (shrink)

In this article, I discuss and critique how metaphysicians of race have conceived of and defended racial realism according to how biologists use “race”. I start by defining “racial realism” in the broadest accepted way in the metaphysics of race. Next, I summarize a representative sample of recent attempts from metaphysicians of race and biologists to defend racial realism and the main criticisms against each attempt. I discuss how metaphysicians of race have defended racial realism according to how ordinary people (...) use “race” in Part II. (shrink)

It is time to escape the constraints of the Systematics Wars narrative and pursue new questions that are better positioned to establish the relevance of the field in this time period to broader issues in the history of biology and history of science. To date, the underlying assumptions of the Systematics Wars narrative have led historians to prioritize theory over practice and the conflicts of a few leading theorists over the less-polarized interactions of systematists at large. We show how shifting (...) to a practice-oriented view of methodology, centered on the trajectory of mathematization in systematics, demonstrates problems with the common view that one camp straightforwardly “won” over the other. In particular, we critique David Hull’s historical account in Science as a Process by demonstrating exactly the sort of intermediate level of positive sharing between phenetic and cladistic theories that undermines their mutually exclusive individuality as conceptual systems over time. It is misleading, or at least inadequate, to treat them simply as holistically opposed theories that can only interact by competition to the death. Looking to the future, we suggest that the concept of workflow provides an important new perspective on the history of mathematization and computerization in biology after World War II. (shrink)

Computational systems biologists create and manipulate computational models of biological systems, but they do not always have straightforward epistemic access to the content and behavioural profile of such models because of their length, coding idiosyncrasies, and formal complexity. This creates difficulties both for modellers in their research groups and for their bioscience collaborators who rely on these models. In this paper we introduce a new kind of visualization that was developed to address just this sort of epistemic opacity. The visualization (...) is unusual in that it depicts the dynamics and structure of a computer model instead of that model’s target system, and because it is generated algorithmically. Using considerations from epistemology and aesthetics, we explore how this new kind of visualization increases scientific understanding of the content and function of computer models in systems biology to reduce epistemic opacity. (shrink)

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)

In Objectivity, Daston and Galison argue that scientific objectivity has a history. Objectivity emerged as a distinct nineteenth-century “epistemic virtue,” flanked in time by other epistemic virtues. The authors trace the origins of scientific objectivity by identifying changes in images from scientific atlases from different periods, but they emphasize that the same history could be narrated using different sorts of scientific objects. One could, for example, focus on the changing uses of “type specimens” in biological taxonomy. Daston :153–182, 2004) indeed (...) provides a detailed account of the history of the type specimen which purports to show this. I argue that this attempt hinges on a conceptual confusion and therefore fails. I show that the actual history of the type specimen does not reinforce the account of epistemic virtues from Objectivity, but rather threatens to subvert it. (shrink)

This study analyzes shells of marine gastropods of a zoological museum and the Latin epithets expressing perceptual and connotative attributes that they have received in the standard, Linnaean nomenclature. Making use of the Osgood semantic differential, we presented the subjects with digital 3-D reproductions of the shell specimens to be subjectively evaluated according to 17 pairs of attributes. The results show that, overall, the subjective evaluations given by the subjects are consistent, which suggests that an intersubjective characterization of the shells (...) as wholes according to their qualitative and morphological traits is possible and scientifically explicable. This may apply to other biological items as well. The results also show that the epithets given to the shells by taxonomists do not always reflect the perceptual evaluation of the general population, being a product of the well-known ambiguity in taxonomic categorization and naming. (shrink)

It is proposed that the collective identification of objects is a necessary phase in the evolution of language. A procedure of identification based on the first-person perspective is assumed that is guided by object constancy, the naming insight, and other more obvious features of language production. The mental image is the basic element of this procedure. The comparison of mental images is used to define recognition, and the identification and naming of macroscopic objects by a group of persons is formulated. (...) This is shown to effect a binary relation of the order type on the set of objects that reduces to an equivalence relation in the case of observer independence. (shrink)

Early nineteenth century systematists sought to describe what they called the Natural System or the Natural Classification. In the nineteenth century, there was no agreement about the basis of observed patterns of similarity between organisms. What did these systematists think they were doing, when they named taxa, proposed relationships between taxa, and arranged taxa into representational schemes? In this paper I explicate Charles Frederic Girard’s (1822–1895) theory and method of systematics. A student of Louis Agassiz, and subsequently (1850–1858) a collaborator (...) with Spencer Baird, Girard claimed that natural classificatory methods do not presuppose either a special creationist or an evolutionary theory of the natural world. The natural system, in Girard’s view, comprises three distinct ways in which organisms can be related to each other. Girard analyzed these relationships, and justified his classificatory methodology, by appeal to his embryological and physiological work. Girard offers an explicit theoretical answer to the question, what characters are evidence for natural classificatory hypotheses? I show that the challenge of simultaneously depicting the three distinct types of relationship led Girard to add a third dimension to his classificatory diagrams. (shrink)

Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are pragmatic trade-offs between precision (...) and ambiguity that are key to designing effective solutions for generating big data about biodiversity. We focus on the importance of theory-dependence as a source of ambiguity in taxonomic nomenclature and hence a persistent challenge for implementing a single, long-term solution to storing and accessing meaningful sets of biological specimens. We argue that ambiguity does have a positive role to play in scientific progress as a tool for efficiently symbolizing multiple aspects of taxa and mediating between conflicting hypotheses about their nature. Pursuing a deeper understanding of the trade-offs and synthesis of precision and ambiguity as virtues of scientific language and communication systems then offers a productive next step for realizing sound, big biodiversity data services. (shrink)

One of the purposes of the research program referred to as “systematic biogeography” is the use of species distributions to identify regions and reconstruct biotic area relationships. The reverse, i.e. to group species according to the areas that they live in, leads to the recognition of chorological categories. Biogeographers, working under these two different approaches, have proposed several terms to refer to groups of species that have similar distributions, such as “element”, “chorotype” and “component”. A historical reconstruction, including semantic observations (...) and philosophical implications, shows that these terms have been used in a variety of senses. The word “component” should not be used in biogeography. The word “element” has been used to identify both a group of species defined according to the biogeographic areas they occupy and a group of species with an assumed shared biogeographic history. It is especially because of the influence of the dispersalist paradigm, which dominated evolutionary thought until the mid-twentieth century, that the second definition has been frequently adopted. The term “element” is therefore ambiguous and its use should always be associated with an explicit definition. The word “chorotype” should be used to define groups of species with similar ranges when no causal assumption is made. The concept of “chorotype,” finally, should not be confounded with other concepts such as distributional pattern, cenocron, horofauna, biota, endemic area, area of endemism, biotic element, and generalized track, which are also discussed in this paper. (shrink)

“To arrange in or analyse into classes according to shared qualities or characteristics; to make a formal or systematic classification” (OED). For many, classification provokes images of dull cataloging and arcane knowledge. However, in the eighteenth century it was neither dull nor arcane and had momentous import for natural philosophers and everyday individuals alike. Susannah Gibson has captured this expertly in her new book, and the subtitle accents the stakes: How Eighteenth-Century Science Disrupted the Natural Order. Although originating out of (...) a doctoral dissertation, this is not a dense monograph. Instead, Gibson targets a wider academic audience using compelling vignettes in digestible chapters with compact endnotes and helpful suggestions for further reading. On the whole, the book is a success, though more illuminating in some places than others. (shrink)

I respond to the bad lot argument in the context of biological systematics. The response relies on the historical nature of biological systematics and on the availability of pattern explanations. The basic assumption of common descent enables systematic methodology to naturally generate candidate explanatory hypotheses. However, systematists face a related challenge in the issue of character analysis. Character analysis is the central problem for contemporary systematics, yet the general problem of which it is a case—what counts as evidence?—has not been (...) adequately discussed by proponents of inference to the best explanation. Facing this problem is the price of adopting abductive methods. I sketch an account of how systematists approach the problem of evidence. (shrink)

When working with garden archaeology and garden archaeobotany, the plant material is of great importance. It is important to be able to identify which plants have grown in a particular garden and which have not, which of the plants you find in the garden today that are newly introduced or have established themselves on their own, and which plants that may be remnants of earlier cultivation. During the past two years, my colleagues and I have been involved in a project (...) that deals with the latter kind of plants, that is, plants that were once actively cultivated and that have survived in their original place of cultivation until the present time(Persson, Ansebo & Solberg, this volume). When we started the project we simply called the plants we worked with ‘relict plants’. This is also the term that has been used unofficially in this field of research for some time. It was in no way an official term, however, and as it turned out, the term already had a different meaning in botany that was both older and better established. We were therefore in need of a better name for the plants we worked with. To single out the plants we were working with, we used the following working definition: “Plants that were once, but are no longer cultivated in a certain area, and where a part of the population still exists even though it is no longer actively maintained”. Although we still think this is a decent approximation, we have realized that there are several complicating factors we have had to think more about. We thus needed both a better name and a better definition. Both these tasks became important parts of the project. (shrink)

We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought to (...) formalize the work of classification, but Mayr introduced a qualitative formalism based on human judgment for determining the taxonomic rank of populations, while the numerical taxonomists introduced a quantitative formalism based on automated procedures for computing classifications. The key contrast between Mayr and the numerical taxonomists is how they conceptualized the temporal structure of the workflow of classification, specifically where they allowed meta-level discourse about difficulties in producing the classification. (shrink)

Synthetic biology and systems biology are often highlighted as antagonistic strategies for dealing with the overwhelming complexity of biology (engineering versus understanding; tinkering in the lab versus modelling in the computer). However, a closer view of contemporary engineering methods (inextricably interwoven with mathematical modelling and simulation) and of the situation in biology (inextricably confronted with the intrinsic complexity of biomolecular environments) demonstrates that tinkering in the lab is increasingly supported by rational design methods. In other words: Synthetic biology and systems (...) biology are merged by the use of computational techniques. These computational techniques are needed because the intrinsic complexity of biomolecular environments (stochasticity, non-linearities, system-level organization, evolution, independence, etc.) require advanced concepts of bio bricks and devices. A philosophical investigation of the history and nature of bio parts and devices reveals that these objects are imitating generic objects of engineering (switches, gates, oscillators, sensors, etc.), but the well-known design principles of generic objects are not sufficient for complex environments like cells. Therefore, the rational design methods have to be used to create more advanced generic objects, which are not only generic in their use, but also adaptive in their behavior. Case studies will show how simulation-based rational design methods are used to identify adequate parameters for synthesized designs (stability analyses), to improve lab experiments by ‘looking through noise’ (estimation of hidden variables and parameters), and to replace laborious and time-consuming post hoc tweaking in the lab by in-silico guidance (in-silico variation of bio brick properties). The overall aim of these developments, as will be argued in the discussion, is to achieve adaptive-generic instrumentality for bio parts and devices and thus increasingly merging systems and synthetic biology. (shrink)

För att kunna känna igen liv när vi hittar det och för att veta hur vi skall leta behöver vi ha en uppfattning om vad liv är. Att försöka konstruera en definition av liv hjälper oss också att formulera våra tankar kring vad liv är. De flesta av oss har nog en intuitiv uppfattning av vad liv är, och kan i de flesta situationer utan problem skilja ut vad som är levande från vad som inte är det. Det finns dock (...) situationer när det inte är fullt så enkelt. Man är till exempel inte överens om huruvida virus är liv. Virus kan föröka sig och genomgår evolution men de har ingen egen metabolism vilket många hävdar är en nödvändig egenskap för att vara levande. Numera finns det också datorprogram som har vissa egenskaper gemensamma med sådant som vi normalt kallar liv. De kan till exempel föröka sig och genomgå en slags evolution. Däremot är de inte uppbyggda av DNA, och dessutom är de ju tillverkade av oss. Trots detta finns det de som vill hävda att datorprogram kan vara levande. Å andra sidan finns det desto fler som förnekar det. Många förnekar också att levande datorprogram alls är möjligt. De som gör det kan till exempel hävda att liv måste ha en viss form av kemisk bas eller vara ett resultat av naturligt urval i motsats till urval baserat på regler som vi människor har konstruerat. När man diskuterar utomjordiskt liv så blir det ofta ännu svårare att avgöra vad som är levande än när vi diskuterar liv här på jorden. Utomjordiskt liv kommer förmodligen att vara väldigt olikt det vi normalt kallar liv men någonting bör det ju ha gemensamt med livet på jorden för att det skall vara befogat att använda beteckningen liv om båda. När man letar efter liv i extrema miljöer här på jorden, och i ännu högre grad när man letar efter liv på andra himlakroppar, är det av avgörande betydelse att man har någon slags uppfattning om vad liv är. Det finns framför allt två skäl till det. Det ena är att man behöver kunna avgöra om det man hittar är liv. Det andra är att vi behöver bestämma oss för hur och var vi skall leta (resurserna för att leta efter liv är ju inte obegränsade). Man behöver till exempel välja rätt slags instrument som reagerar på rätt saker. För att kunna göra det behöver man veta vilka egenskaper man skall leta efter, det vill säga man behöver veta vad liv är. (shrink)

All the central assumptions of the Modern Synthesis (Neo-Darwinism) have been disproven. [1, 2] An article with the title, "Rocking the foundations of molecular genetics,” appearing in the prestigious Proceedings of the National Academy of Sciences at the end of 2012 [3] would have not been possible a decade ago. Groundbreaking experimental evidence of epigenetic maternal inheritance over several generations was published in the same journal, throwing the whole foundation of 21st century molecular genetics into question. Neo-Darwinism attributed genetic change (...) to random events, in which physiology was assumed to play little role. "The germ line was thought to be isolated from any influence by the rest of the organism and its response to the environment. [3] The fundamental concepts that constitute the foundations of contemporary systems biology include holism, emergentism, and robustness, compared to the concepts of reductionism, mechanism, and homeostasis, that form the foundations of molecular biology. [18] Holism is to be contrasted with reductionism which considers a system as merely composed of a sum of parts. Emergentism, the appearance of hierarchical levels of organization, is contrasted with mechanism of independent linear events. Robustness refers to the preservation of the functionality of a system to a certain degree despite external or internal changes, while homeostasis refers to maintaining the stability of the state of a system. The Vedantic view also proposes viewing life from the Organic Whole perspective, in which consciousness forms the supporting basis. The conscious agent is an important part of that view, but the absolute conception of a unifying center is not to be omitted if a proper conception is to be achieved. (shrink)

Book review of Richard A. Richards' The Species Problem: A Philosophical Analysis.

The Swedish naturalist Carl Linnaeus is famous for having turned botany into a systematic discipline, through his classification systems—most notably the sexual system—and his nomenclature. Throughout his life, Linnaeus experimented with various paper technologies designed to display information synoptically. The list took pride of place among these and is also the common element of more complex representations he produced, such as genera descriptions and his “natural system.” Taking clues from the anthropology of writing, this essay seeks to demonstrate that lists (...) can be considered as genuine research technologies. They possess a potential to generate research problems of their own but also pose limitations to inquiries that can be overcome only by the use of new media. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...) of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

Systematics based solely on structuralist principles is non-science because it is derived from first principles that are inconsistent in dealing with both synchronic and diachronic aspects of evolution, and its evolutionary models involve hidden causes, and unnameable and unobservable entities. Structuralist phylogenetics emulates axiomatic mathematics through emphasis on deduction, and “hypotheses” and “mapped trait changes” that are actually lemmas and theorems. Sister-group-only evolutionary trees have no caulistic element of scientific realism. This results in a degenerate systematics based on patterns of (...) fact or evidence being treated as so fundamental that all other data may be mapped to the cladogram, resulting in an apparently well-supported classification that is devoid of evolutionary theory. Structuralism in systematics is based on a non-ultrametric analysis of sister-group informative data that cannot detect or model a named taxon giving rise to a named taxon, resulting in classifications that do not reflect macroevolutionary changes unless they are sister lineages. Conservation efforts are negatively affected through epistemological extinction of scientific names. Evolutionary systematics is a viable alternative, involving both deduction and induction, hypothesis and theory, developing trees with both synchronic and diachronic dimensions often inferring nameable ancestral taxa, and resulting in classifications that advance evolutionary theory and explanations for particular groups. (shrink)

‘‘Adaptive radiation’’ is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making ‘‘adaptive radiation’’ so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny-based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts to shoehorn the (...) results of these techniques into categorical ‘‘adaptive radiation: yes/no’’ schemes lead to reification, in which arbitrary quantitative thresholds are regarded as real. Our account of the life cycle of metaphors in science suggests that it is time to exchange the spent metaphor for new concepts that better represent the full range of diversity, disparity, and speciation rate across all of life. (shrink)

I begin with a description of the benefits and limits of DNA barcoding as presented by its advocates not its critics. Next, I argue that due to the mutually dependent relationship between defining and delimiting species, all systems of classification are grounded in theory, even if only implicitly. I then proceed to evaluate DNA barcoding in that context. In particular, I focus on the barcoders’ use of a sharp boundary by which to delimit species, arguing that this boundary brings along (...) additional theoretical commitments inconsistent with the way taxonomists conceive of species, viz., as entities that have vague boundaries and that cannot be defined by any single attribute other than ancestry. Given these inconsistencies, I conclude that even if groupings based on DNA barcodes match those of an existing taxonomy, the two systems of classification are not necessarily tracking the same entities, i.e., species. (shrink)

There is a nested hierarchy of wholes that characterizes reality, and especially life. The most fundamental principle is that Reality in the Vedantic/Bhagavat conception is based on Personality, as mentioned in the very first aphorism of the Bhagavat Purana, “janmady asya yatho nvayat itaratas charteshu abhijnah svarat.” Here and in many other scriptures the foundation or origin of everything is centered upon the abhijna or cognizant (conscious) primordial Personality of Godhead. Modern science in the West has become centered on matter (...) as the foundation of everything, and this is called materialism. But matter is impersonal. The question is: how can a person come from what is impersonal? We consider such an approach to be backward. Person cannot come from an impersonal material substratum. It is very difficult to conceive how a rock can give rise to a concept of rock. But it is quite natural to understand that a rock exists as a concept for a conscious person. So too can the concept of objectivity, concreteness and perception arise from a personal substratum, and historically, this has been demonstrated by the detailed philosophical study of these ideas by numerous philosophers. (shrink)

I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.

The history of science often has difficulty connecting with science at the lab-bench level, raising questions about the value of history of science for science. This essay offers a case study from taxonomy in which lessons learned about particular failings of numerical taxonomy in the second half of the twentieth century bear on the new movement toward DNA barcoding. In particular, it argues that an unwillingness to deal with messy theoretical questions in both cases leads to important problems in the (...) theory and practice of identifying taxa. This argument makes use of scientific and historical considerations in a way that the authors hope leads to convincing conclusions about the history of taxonomy as well as about its present practice. (shrink)

This book is a state-of-the-art review on the Physics of Emergence. Foreword v Gregory J. Chaitin Preface vii Ignazio Licata Emergence and Computation at the Edge of Classical and Quantum Systems 1 Ignazio Licata Gauge Generalized Principle for Complex Systems 27 Germano Resconi Undoing Quantum Measurement: Novel Twists to the Physical Account of Time 61 Avshalom C. Elitzur and Shahar Dolev Process Physics: Quantum Theories as Models of Complexity 77 Kirsty Kitto A Cross-disciplinary Framework for the Description of Contextually Mediated (...) Change 109 Liane Gabora and Diederik Aerts Quantum-like Probabilistic Models Outside Physics 135 Andrei Khrennikov Phase Transitions in Biological Matter 165 Eliano Pessa Microcosm to Macrocosm via the Notion of a Sheaf (Observers in Terms of t-topos) 229 Goro Kato The Dissipative Quantum Model of Brain and Laboratory Observations 233 Walter J. Freeman and Giuseppe Vitiello Supersymmetric Methods in the Traveling Variable: Inside Neurons and at the Brain Scale 253 H.C. Rosu, O. Cornejo-Perez, and J.E. Perez-Terrazas Turing Systems: A General Model for Complex Patterns in Nature 267 R.A. Barrio Primordial Evolution in the Finitary Process Soup 297 Olof Gornerup and James P. Crutchfield Emergence of Universe from a Quantum Network 313 Paola A. Zizzi Occam's Razor Revisited: Simplicity vs. Complexity in Biology 327 Joseph P. Zbilut Order in the Nothing: Autopoiesis and the Organizational Characterization of the Living 339 Leonardo Bich and Luisa Damiano Anticipation in Biological and Cognitive Systems: The Need for a Physical Theory of Biological Organization 371 Graziano Terenzi How Uncertain is Uncertainty? 389 Tibor Vamos Archetypes, Causal Description and Creativity in Natural World 405 Leonardo Chiatti . (shrink)

Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different methods (...) of assigning prior probabilities to trees. I argue that priors need to be derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and about macroevolutionary processes more generally. (shrink)

In a series of articles, Rieppel (2005, Biol. Philos. 20:465–487; 2006a, Cladistics 22:186–197; 2006b, Systematist 26:5–9), Keller et al. (2003, Bot. Rev. 69:93–110), and Nixon and Carpenter (2000, Cladistics 16:298–318) criticize the philosophical foundations of the PhyloCode. They argue that species and higher taxa are not individuals, and they reject the view that taxon names are rigid designators. Furthermore, they charge supporters of the individuality thesis and rigid designator theory with assuming essentialism, committing logical inconsistencies, and offering proposals that render (...) taxonomy untestable. These charges are unsound. Such charges turn on confusions over rigid designator theory and the distinction between kinds and individuals. In addition, Rieppel’s, Keller et al.’s, and Nixon and Carpenter’s proposed alternatives are no better and have their own problems. The individuality thesis and rigid designator theory should not be quickly abandoned. [Individuals; kinds; PhyloCode; rigid designators; species; taxa; taxon names.]. (shrink)

The circumscription of taxa and classification of organisms are fundamental tasks in the systematization of biological diversity. Their success depends on a unified idea concerning the species concept, evolution, and taxonomy; paradoxically, however, it requires a complete distinction between taxa and evolutionary units. To justify this view, I discuss these three topics of systematics. Species concepts are examined, and I propose a redefinition for the Taxonomic Species Concept based on nomenclatural properties, in which species are classes conventionally represented by a (...) binomial. Speciation is subsequently discussed, to demonstrate that concepts on the evolutionary process are damaged when species are considered as evolutionary units. Speciation should be considered a transition among patterns of a population and, consequently, always a sympatric process. This view contrasts with the majority of speciation models, which analyze cladogeneses and classify speciation geographically, usually considering allopatry the essential condition for the differentiation process. Finally, taxonomy is considered, to show that the equivalence between evolutionary and taxonomic units may also damage the practice of biological systematization. Principles and rules of nomenclature and classification should offer freedom to accommodate divergent opinions about systematics and to incorporate the evolution of knowledge; therefore, they should remain independent of biological theories. (shrink)

In biosemiotics, life and living phenomena are described by means of originally anthropomorphic semiotic concepts. This can be justified if we can show that living systems as self-maintaining far from equilibrium systems create and update some kind of representation about the conditions of their self-maintenance. The point of view is the one of semiotic realism where signs and representations are considered as real and objective natural phenomena without any reference to the specifically human interpreter. It is argued that the most (...) basic concept of representation must be forward looking and that both C. Peirce’s and J. v. Uexküll’s concepts of sign assume an unnecessarily complex semiotic agent. The simplest representative systems do not have phenomenal objects or Umwelten at all. Instead, the minimal concept of representation and the source of normativity that is needed in its interpretation can be based on M. Bickhard’s interactivism. The initial normativity or natural self-interest is based on the ‘utility-concept’ of function: anything that contributes to the maintenance of a far from equilibrium system is functional to that system — every self-maintaining far from equilibrium system has a minimal natural self-interest to serve that function, it is its existential precondition. Minimal interactive representation emerges when such systems become able to switch appropriately between two or more means ofmaintaining themselves. At the level of such representations, a potentiality to detect an error may develop although no objects of representation for the system are provided. Phenomenal objects emerge in systems that are more complex. If a system creates a set of ongoingly updated ’situation images’ and can detect temporal invariances in the updating process, these invariances constitute objects for the system itself. Within them, a representative system gets an Umwelt and becomes capable of experiencing triadic signs. The relation between representation and its object is either iconic or indexical at this level. Correspondingly as in Peirce’s semeiotic, symbolic signs appear as more developed — for the symbolic signs, a more complex system is needed. (shrink)

Any attempt to develop biosemiotics either towards a new biological ground theory or towards a metaphysics of living nature necessitates some kind of naturalization of its semiotic concepts. Instead of standard physicalistic naturalism, a certain kind of semiotic naturalism is pursued here. The naturalized concepts are defined as referring only to the objects of our external experience. When the semiotic concepts are applied to natural phenomena in biosemiotics, there is a risk of falling into anthropomorphic errors if the semiotic concepts (...) remain mentalistic. It is suggested that there really is an anthropomorphic error or “hidden prototype fallacy” arising from Peirce’s prototype for semiosis: the research process of an experimental scientist. The fallacy lies in the concept of the object of representation — it is questionable whether there are any objects of representation for bacteria and whether the DNA-signs have any objects. The conclusion is that Peircean semiotic concepts are naturalizable but only if they are based on some more primitive concept of representation. The causal origins of representations are not relevant, only their anticipative consequences (i.e. meaning). (shrink)