Organismal Biology Research Papers - Academia.edu (original) (raw)

- by
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- Philosophy of Biology, Affordance Theory, Niche Construction Theory, Organismal Biology

In my talk, I will present key ideas of my four-year research project "Bio-Agency and Natural Freedom" which aims to defeat free will scepticism on a fresh metaphysical basis informed by biology. I will proceed from the diagnosis that a convincing naturalist account of both human free will and human agency is prevented from the outset by the mechanistic-physicalist view of nature espoused by the majority of metaphysicians. More specifically, I will show that mechanistic physicalism, being part of a broadly substance or thing ontological orientation, makes it impossible to explain how human agency fits into the natural world and that, as a consequence of this, we are at a loss with respect to human free will too. In other words, we need to solve the problem of agency first before we can hope to solve the problem of free will, and to this end we need to radically revise our most fundamental ontological commitments. On this basis, I will then propose a therapy that reflects and brings together two recent developments in the philosophy of biology: the increasing interest in, and appreciation of, bio-agency, i.e., the capability of organisms to interact with the environment in an adaptive manner, and the emerging turn towards an understanding of organisms as processes rather than as substances or things. Human as well as non-human agents, I will argue, are biological beings and, i.e., a particular type of process. They are dynamical from tip to toe and endowed with agential capacities as a function of their dynamical organisation. Metaphysically speaking, this means to endorse a process ontology of both biological agents and their actions. I will explain how the resulting bio-process account of agency solves the metaphysical problem of agency, and I conclude by indicating how this may also help us with tackling the problem of free will.

- by Anne Sophie Meincke (Spann)
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- Philosophy, Metaphysics, Ontology, Philosophy of Agency

BACKGROUND:
In spite of its indusrial usefulness and varied daily uses, lead (Pb) pollution is a widespread ecological problem that faces the humans in the 21th century. Pb was found to produces a wide range of toxic effects including neurotoxicity especially to the developing and young offspring. Recently, the utilization of herbal plants has received a significant attention where there has been rising awareness in their therapeutic use; among these is the garlic.
AIM OF THE WORK:
In light of the above, the current study is designed experimentally in female pregnant rats in order to investigate the beneficial role of garlic extract in the protection from the maternal and fetal cerebellar damage that produced by administration of different doses of Pb during pregnancy.
MATERIALS AND METHODS:
Positively pregnant female rats were divided into five groups; one control group, two Pb-treated groups (exposed to 160 and 320 mg/kg b.wt. of Pb, respectively) and two groups treated with both Pb and garlic (exposed to Pb as previous groups together with 250 mg/ kg b.wt. /day of garlic extract). Treatments started from day 1 till day 20 of pregnancy, where the mother rats of different experimental groups were sacrified to obtain the fetuses. Pb level in the maternal nd fetal blood and cerebellum was estimated by spectrophotometry. Specimens of the cerebellum of different mother and fetal groups were processed to histological and immunohistochemical staining for microscopic examination.
RESULTS:
The results showed that administration of Pb to pregnant rats resulted in a dose-dependent toxicity for both mothers and fetuses in the form of decrease of maternal weight gain, placental and fetal weights, brain weight and diminished fetal growth parameters, which were prominent in rat's group treated with larger dose of Pb. In Pb-treated rats, Pb level in blood and cerebellum was high when compared to the control. The histopathological examination of the cerebellum of treated dams and fetuses showed marked alterations mainly in the form of Purkinje cell degeneration and lack of deveopmet of fetal cerebellum. Co-treatment of garlic extract along with Pb resulted in a significant decrease in Pb levels as compared with those treated with Pb alone with improvement of the histopathological changes.
CONCLUSIONS:
This study was useful in evaluating the hazardous effects of uncontrolled use of Pb in general and in assessing the developmental and neurotoxicity of fetuses due to exposure during pregnancy in particular. Co-administration of garlic has beneficial effects in amelioration of Pb-induced neurotoxicity and reversing the histopathological changes of the cerebellum of mother rats and fetuses.
KEYWORDS:
garlic; glial fibrillary acidic protein; lead; purkinje cells

- by Felipe Johnson
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- Martin Heidegger, Organismal Biology, Animality, Zoologia

Die Entwicklung des Phänotypus eines Organismus beziehungsweise dessen Embryogenese galt als die zentrale Problematik des biologischen Denkens bis zur Entwicklung der Evolutionstheorie Charles Darwins und wurde in verschiedenen Epochen sehr unterschiedlich erklärt. Mit dem Aufkommen der mechanistischen Philosophie und Naturwissenschaft im 17. Jahrhundert begann der Siegeszug der Vorstellung, dass die Embryogenese auf materielle deterministische Vorgänge zu reduzieren ist. Im 20. Jahrhundert wurde diese Idee von der Vorstellung des Gens verkörpert. Das sogenannte "Zentraldogma der Molekularbiologie", das 1970 von Francis Crick seine endgültige Formulierung bekam, besagt, dass die Information für den Aufbau des Phänotypus immer von den Genen zu den Proteinen weitergegeben wird, so dass sie niemals von einem Protein zum anderen oder von den Proteinen zu den Genen übertragen werden kann. Die Vorstellung der einseitigen Richtung des Informationsflusses führte zur Reduktion der Entwicklung eines Organismus auf den Ablauf eines sogenannten "genetischen Programms", in dem die phänotypische Form des Organismus kodiert sei. In den letzten Jahrzehnten wurde die Vorstellung, dass die Gene den Organismus formen, stark kritisiert. Zudem hat die Integration systemtheoretischer Denkweisen der Selbstorganisations- und Komplexitätstheorie in die Biologie zusätzlich die Idee des genetischen Programms untergraben. Bedeutende theoretische Biologen und Philosophen der Gegenwart betrachten Organismen als besonders komplexe dynamische physikochemische Systeme, die sich aus Interaktionen zwischen Genen und Proteinen selbstorganisieren.
Die Philosophie der Biologie sollte diese Entwicklungen ernst nehmen und ihre Grenzen kritisch beleuchten, um mögliche negative Folgen zu antizipieren und ihnen entgegen zu wirken. So befürchte ich, dass viele Kritiker der neodarwinistischen genzentrierten Biologie unbewusst dabei sind, das biologische Denken des 21. Jahrhunderts auf eine physikalistische Grundlage zu stellen.

Behavior analysis relies on the idea of a science dealing with specific interactions between the organism and its environment. Yet it is not always clearly defined what does an “organism” mean. I will contend that disagreements arise from the roles the organism is said to have in behavioral settings. I will also argue for the organismal level as appropriate for explaining behavior in an attempt to reconcile physiology with behavior analysis thus considering organismal variables as either bodily conditions or physiological mechanisms without neglecting the selective pressures of the environment for guiding behavior.

- by Daniel J Nicholson and +1
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- Metaphysics, Philosophy of Science, Philosophy of Biology, Individuality

Die erste und zweite Sektion dieser Studie sind der Darstellung der Visionen des Transhumanismus gewidmet. Sie stellen diese futuristische Richtung und einige wichtige Gegenargumente ihrer Kritiker dar. Alle darauf folgenden Sektionen dienen dem Aufbau eines neuen Argumentes, das auf einer kürzlich vom Autor eingeführten Philosophie des Lebendigen und insbesondere des biologischen Organismus beruht, die als "prozessontologische Biophilosophie" bezeichnet werden kann (S.Koutroufinis, "Organismus als Prozess", Freiburg/München: Karl Alber, 2019). In der dritten Sektion wird gezeigt, dass der Transhumanismus verschiedene Dimensionen der menschlichen Freiheit berührt und fest an der Frage des menschlichen Wesens gebunden ist, das unlösbar mit der Freiheit des Menschen verflochten ist. Die Verwirklichung der transhumanistischen Visionen setzt sowohl den umfassenden Einbau komplexer Maschinen in den menschlichen Körper voraus als auch den massiven Einsatz naturwissenschaftlicher Formalismen bei der Planung der Transformation des Körpers mittels unterschiedlicher Eingriffe. Aus diesem Grund wird in der vierten Sektion gezeigt, dass jeder Organismus, somit auch der Organismus des Menschen, eine bestimmte Logik verkörpert, die der Logik aller Maschinen und Formalismen der modernen Naturwissenschaften diametral entgegensteht. Davon ausgehend wird in der fünften und letzten Sektion inferiert, dass der Transhumanismus der Logik der organismischen Seinsweise und somit der Natur des Menschen widerspricht. Dieses Resultat wird auf die Besonderheit des Wesens jedes Menschen und seines zur Freiheit bestimmten individuellen Bewusstseins zugespitzt, um dadurch die eigentliche Bedeutung dieses futuristischen Diskurses und die Herausforderung, die er an die Menschheit stellt, aus einer biophilosophischen Perspektive zu betrachten.

- by Spyridon A . Koutroufinis
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- Theory Of Mechanisms, Biophilosophy, Transhumanism, Organismal Biology

The creation of a process ontology for biology is one of the most ambitious and important projects of current philosophy of biology. Process ontology is usually seen as opposing mechanistic ontology which currently dominates biology. However, the terms 'process' and 'mechanistic' are not always clearly defined in current debates. In this paper I provide a new definition of 'mechanism' and 'mechanistic ontology' based on the most abstract definition of 'machine'—von Foerster's 'non-trivial machine' that is related to Turing machine. I argue that the main methods of modeling used in systems biology rest upon the implicit assumption that organisms abide by the non-trivial or Turing machine logic. By showing that organisms and machines obey two incompatible logics of causality I demonstrate the limits of this assumption. The paper concludes by introducing an organism centered concept of process and arguing that Whitehead's process metaphysics offers a way of understanding organisms as exemplifications of a specific category of process.

After the discovery of the DNA in the 1950´s, 20th century biology focused on the concept of the gene. In the 21st century, however,
the concept of organism is regaining its primary role in biological
thought. At present there is a rapidly growing literature verifying that
living beings are able not only to deeply reorganize themselves but also
to modify their genomes. The emergence of a theory of organism requires, however, first the elaboration of a logic of organismic causality that proceeds from organismic phenomenality. In the following I will attempt to outline what I label "logic of organisms." In order to achieve this aim I will first try to articulate a "logic of mechanisms" because it constitutes a sharp contrast to the "logic of organisms."

- by Spyridon A . Koutroufinis
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- Theory Of Mechanisms, The Self, Immanuel Kant, Jakob von Uexküll

Mathematical models applied in contemporary theoretical and systems biology are based on some implicit ontological assumptions about the nature of organisms. This article aims to show that real organisms reveal a logic of internal causality transcending the tacit logic of biological modeling. Systems biology has focused on models consisting of static systems of differential equations operating with fixed control parameters that are measured or fitted to experimental data. However, the structure of real organisms is a highly dynamic process, the internal causality of which can only be captured by continuously changing systems of equations. In addition, in real physiological settings kinetic
parameters can vary by orders of magnitude, i.e., organisms vary the value of internal quantities that in models are represented by fixed control parameters. Both the plasticity of organisms and the state
dependence of kinetic parameters adds indeterminacy to the picture and asks for a new statistical perspective. This requirement could be met by the arising Biological Statistical Mechanics project, which promises to do more justice to the nature of real organisms than contemporary modeling. This article concludes that Biological Statistical Mechanics allows for a wider range of organismic ontologies than does the tacitly followed ontology of contemporary theoretical and systems biology,
which are implicitly and explicitly based on systems theory.

Darwin introduced the concept that random variation generates new living forms. In this paper, we elaborate on Darwin's notion of random variation to propose that biological variation should be given the status of a fundamental theoretical principle in biology. We state that biological objects such as organisms are specific objects. Specific objects are special in that they are qualitatively different from each other. They can undergo unpredictable qualitative changes, some of which are not defined before they happen. We express the principle of variation in terms of symmetry changes, where symmetries underlie the theoretical determination of the object. We contrast the biological situation with the physical situation, where objects are generic (that is, different objects can be assumed to be identical) and evolve in well-defined state spaces. We derive several implications of the principle of variation, in particular, biological objects show randomness, historicity and contextuality. We elaborate on the articulation between this principle and the two other principles proposed in this special issue: the principle of default state and the principle of organization.

- by Maël Montévil and +3
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- Evolutionary Biology, Biophysics, Organizational Change, Plasticity

The present study was written with the intent of opening up new
ontological dimensions to the debate concerning the nature of the
organism, which broaden the horizons of contemporary biological
science. Various traditions from the natural sciences and Naturphilosophie
are further developed and synthesized into a novel theory of
the organism. Organismic genesis is contemplated in light of the process
of individual ontogenesis and its most dramatic phase, embryogenesis.
The ontogenetic theme also gives rise to the problem of organismic
self-maintenance, which exists both for multicellular and
unicellular life. In the synthesis here proposed, foundational principles
of Alfred North Whitehead’s and Henri Bergson’s process ontologies
find new integration in the concept of the organism. From the
unicellular to the most highly-developed of organisms, subjective interiority
is awarded in degrees to all life forms, wherein experience is
granted a central role in the ontogeny and self-maintenance of the
organism. Finally, a vision for a future process metaphysics is
sketched in which essential elements of the ontologies of both thinkers
are brought together.
Die vorliegende Untersuchung wurde verfasst, um der Diskussion
zum Wesen des Organismus neue ontologische Dimensionen zu eröffnen,
die den weltanschaulichen Horizont der gegenwärtigen Biowissenschaften
erweitert. Unterschiedliche naturwissenschaftliche
und naturphilosophische Traditionen werden weitergedacht und zu
einer neuen Theorie des Organismus synthetisiert. Organismisches
Werden wird in Bezug auf die Ontogenese des Individuums und vor
allem ihre dramatischste Phase, die Embryogenese, betrachtet. Zur
ontogenetischen Thematik gehört zwangsläufig auch die Problematik
der Selbsterhaltung des Organismus, die auch für einzellige Lebewesen
besteht. In der hier vorgeschlagenen Synthese werden Grundgedanken
der Prozessontologien von Alfred North Whitehead und
Henri Bergson auf eine neue Weise in die Idee des Organismus integriert.
Von den Einzellern bis zu höchst entwickelten Organismen
wird jedem Lebewesen in abgestufter Form subjektive Innerlichkeit
zugesprochen, wobei dem Erleben eine zentrale Rolle für die Ontogenese
und Selbsterhaltung des Organismus zukommt. Überdies wird
eine zukünftige Prozessmetaphysik skizziert, in der essentielle Elemente
der Ontologien beider Denker miteinander integriert werden.

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization , are not " just " processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions.

- by Giuseppe Longo and +1
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- Evolutionary Biology, Physiology, Physics, Theoretical Physics

In recent years, an increasing number of theoretical biologists and philosophers of biology have been opposing reductionist research agendas by appealing to the concept of biological autonomy which draws on the older concept of autopoiesis. In my paper, I
investigate some of the ontological implications of this approach. The emphasis on autonomy and autopoiesis, together with the associated idea of organisational closure, might evoke the impression that organisms are to be categorised ontologically as substances: ontologically independent, well-individuated, discrete particulars. However, I argue that this is mistaken. Autopoiesis and biological autonomy, properly understood, require a rigorous commitment to a process ontological view of life.

- by Anne Sophie Meincke (Spann)
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- Metaphysics, Philosophy of Biology, Systems Biology, Autopoiesis

Virus mencakup kelompok yang luar biasa dari berbagai macam mikroorganisme penyebab penyakit infeksi. Studi ilmiah baru-baru ini melaporkan keberhasilan agen antivirus baru, yang umumnya menghambat siklus replikasi virus dengan mempengaruhi faktor sel inang penting (s) untuk replikasi virus dan / atau elemen virus (Lou, Z. et al., 2004). Meskipun terjadi perkembangan yang ditandai dengan adanya obat-obatan antivirus selama beberapa dekade terakhir, pasien yang terinfeksi virus sangat menderita dengan adanya kegagalan pengobatan karena banyak munculnya virus rekombinan, resistensi obat, dan toksisitas sel (Tantillo, C., et al., 1994; Morfin, F., et al., 2003; Gilbert, C., et al., 2005) .

- by Cici Hermayanti
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- Organismal Biology, Virus, Antivirus Technology, Microorganisms

In this introduction of the volume "Life and Process. Towards a New Biophilosophy," first I will explain why I believe it is necessary to differentiate between biophilosophy and the philosophy of biology. Second, I will review some of the shortcomings of today's biology and philosophy of biology and demonstrate how a biophilosophy grounded in a process-oriented metaphysics can overcome them. Third, I will provide a summary of Whitehead's process ontology, emphasizing those fundamental ideas from this paradigm that play essential roles in the present book. Finally, I will briefly describe the main ideas presented in subsequent chapters.

Topics include levels of biological organization, biological diversity, plant and animal structure and function, and comparative study of structure-function relationships in living organisms. BI 115 is one of the introductory courses required of biology majors and all pre-health students regardless of academic major.
Laboratory exercises will emphasize the scientific process. Students will apply the scientific method to experiments in organismal biology. As a part of this process, students will conduct experiments to test hypotheses, collect and analyze data, and prepare a scientific paper or complete assignments on the experiments. Some experiments will require students to work in lab at times other than the designated laboratory period.

- by Jason Heaton
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- Biology, Evolution, Organismal Biology, Introductory Biology

Contemporary biology is affected with a controversy between the developmentalist viewpoint and the adaptationist viewpoint proper to the neo-darwinian Modern Synthesis (MS), partly triggered by the rise of Evo-Devo. Some called for a new synthesis, some advocate going on with the basic MS program as likely to integrate Evo-Devo novelties, but some even doubt the possibility of a Synthesis. On the other hand, Kant's views on organisms have often been seen as the philosophical matrix of developmental theory (Gilbert and Sarkar 2000), or as ancestor of current theories of autopoiesis or autonomy (Weber and Varela 2002). Both research programs can be contrasted with the biological viewpoint defended by the MS, which privileges natural selection explanations over developmental or self-organization explanation (the latter being potentially an instance of the former). In this paper, I argue that this diagnostic is partly true, but that Kant's concept of organism is more complex than what those genealogies assume. Kant defends a regulative notion of purposiveness, in which this unique concept is refracted into two criteria in order to capture organisms as natural purposes, namely a design criterion and an epigeneticity criterion. After having reconstructed this concept, I turn to a contemporary interpretation of those two criteria, showing that the first one is indeed still fulfilled by organisms within MS, and the second one is satisfied in the viewpoint of cell and developmental theory by developing organisms. I conclude by showing that Kant's notion of organisms provides a matrix for a synthesis between a developmentalist and an adaptationist viewpoints, and I consider in this light some possible empirical obstacles to this synthesis.

- by John Dupre
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- Philosophy, Metaphysics, Philosophy of Science, Philosophy of Biology

This paper argues that Cassirer's thinking about the relationship between the different symbolic forms is best elucidated via the paradigm of "organic harmony." Although Cassirer did not use the term himself, the harmonious cooperation between the parts found in the organic world provided him with a welcome alternative to traditional accounts of order (i.e. identity or hierarchy). This paper will give three examples of "organic harmony": Goethe and his idealistic morphology, Wilhelm von Humboldt's account of language, Herder's account of history. The thought of all three example key characteristics of "organic harmony": holism, particularism/perspectivism, and subjective judgment. This paper will show that Cassirer's own "organic harmony" is indebted to these thinkers. From the perspective of "organic harmony" we can make better sense of the pluralistic spirit of Cassirer's PSF as well as providing it with greater theoretical articulation. This paper also shows how the motif of organic harmony is the normative moment in his own challenge to 20 th c. fascism. Finally, this paper argues that the Cassirerian emphasis on finding a coherence which does justice to the uniqueness of particulars-i.e. harmony-is an ethical injunction relevant for our times.

- by Shuchen Xiang (项舒晨)
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- Multiculturalism, Cosmopolitan Studies, Cosmopolitanism, Biology

Open Access Download: http://fdslive.oup.com/www.oup.com/academic/pdf/openaccess/9780198779636.pdf This collection of essays explores the metaphysical thesis that the living world is not made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organised as an interdependent hierarchy of processes, which are stabilised and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be found in the empirical findings of science. Biology provides compelling reasons for thinking tha...

- by John Dupre
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- Philosophy, Metaphysics, Philosophy of Science, Philosophy of Biology

This paper investigates Hegel's account of the animal organism as it is presented in the Philosophy of Nature, with a special focus on its normative implications. I argue that the notion of "organisation" is fundamental to Hegel's theory of animal normativity. The paper starts by showing how a Hegelian approach takes up the scientific image of organism and assigns a basic explanatory role to the notion of "organisation" in its understanding living beings. Moving from this premise, the paper turns to the group of accounts in contemporary theoretical biology known as "organisational accounts" (OA), which offer a widely debated strategy for naturalizing teleology and normativity in organisms. As recent scholarship recognizes, these accounts explicitly rely on insights from Kant and Post-Kantianism. I make the historical and conceptual argument that Hegel's view of the organism shares several basic commitments with OAs, especially regarding the notion of "organisational closure". I assess the account of normativity that such accounts advance and its implications for how we approach Hegel. Finally, I argue that the notion of "organisation" is more fundamental to Hegel's theory of animal normativity than the Aristotelian notion of "Gattung" or "species", which by contrast appears derivative-at least in the Philosophy of Nature and the Lectures-and does not play the central role in his account maintained by some scholars.

- by Luca Corti
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- History and Philosophy of Biology, Hegel, Normativity, History of Biology

Das Ziel dieses Beitrags ist es, die Eignung der Whiteheadschen Prozeßphilosophie für eine zeitgemäße teleologische Auffassung der organismischen Ontogenese zu demonstrieren. Zu diesem Zweck wird eine Möglichkeit der Verbindung der Whiteheadschen Prozeßphilosophie mit der aktuellen Form systemischen Denkens, das in der Theoretischen Biologie gegenwärtig maßgebend ist, vorgestellt. Die Gründe der Beschäftigung mit alternativen Ontologien, wie der Whiteheadschen, hängen mit den Problemen des systemischen Denkens zusammen, die aufgrund der enormen Komplexität schon der einfachsten Organismen auftreten. Die Erläuterung dieser Thematik setzt eine kurze Vorstellung des biosystemischen Ansatzes und seiner Grenzen voraus. Das verlangt seinerseits nach gewissen physikalisch-systemtheoretischen Vorkenntnissen, die für jede formale Reduktion von Organismen unerläßlich sind. Daher bietet ein vorsichtiges Studium des ersten Teils, das eine Einführung in grundsätzliche Begriffe und Arbeitsweisen der modernen Theorie dynamischer Systeme leistet, eine gute Vorbereitung für die Beschäftigung mit dem biophilosophischen Teil dieses Beitrags.

- by Spyridon A . Koutroufinis
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- Self-Organization, Complex Systems, Complexity, Alfred North Whitehead

Sia per Aristotele sia per Tommaso d'Aquino la vita è, anzitutto, un modo di essere, anzi, il modo più eccellente di essere, tanto che si può attribuire all'essere più perfetto, Dio. Infatti, nel libro XII della Metafisica Aristotele lo dice esplicitamente (cfr. Metaph., XII 7, 1072b 13-30). La vita [concretamente la zoé], dunque, appartiene a Dio, è uno dei suoi attributi, e le appartiene in un modo ottimo, eminente. Dio è il vivente [zoon] per eccellenza. Dal punto di vista metafisico, si può stabilire una differenza fondamentale tra il vivente e il non vivente: il vivente è più perfetto del non vivente, cioè è più atto. L'essere del non vivente è ristretto e chiuso in se stesso; la sua attività, al contrario, è puramente transitiva. Invece l'essere del vivente è l'opposto: esso è aperto, cioè è capace d'interagire con l'ambiente circostante e con gli altri viventi, mentre la sua attività, invece, è immanente, di auto-perfezionamento o, come oggi dicono alcuni, di 'auto-poiesi'.

- by Rafael Pascual
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- Philosophy of Biology, Biology, Philosophy of Nature, Organismal Biology

Organisms, be they uni- or multi-cellular, are agents capable of creating their own norms; they are continuously harmonizing their ability to create novelty and stability, that is, they combine plasticity with robustness. Here we articulate the three principles for a theory of organisms proposed in this issue, namely: the default state of proliferation with variation and motility, the principle of variation and the principle of organization. These principles profoundly change both biological observables and their determination with respect to the theoretical framework of physical theories. This radical change opens up the possibility of anchoring mathematical modeling in biologically proper principles.

- by Giuseppe Longo and +6
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- Evolutionary Biology, Physiology, Developmental Biology, Cellular Biology

Apesar de aparecer no título da obra primeira de B. F. Skinner, O comportamento dos organismos, está ausente, nessa e em outras obras do autor, uma definição explícita de “organismo”, de modo que uma análise do termo em seus escritos se faz necessária para eluci- dar regularidades contextuais de sua ocorrência. Partindo do Procedimento de Interpretação Conceitual de Texto (PICT), analisamos o contexto de ocorrência do termo “organismo” em uma amostra de 8 obras de Skinner, abrangendo um período de 60 anos. Notamos que o termo ocorre em pelo menos 15 diferentes contextos, cada um deles consistindo em um nexo onde confluem diferentes discussões na literatura da analítico-comportamental. Ressaltamos algumas ambiguidades relativas ao critério de demarcação entre organismo e ambiente, ao papel da história filogenética no desenvolvimento do organismo, e à extensão metafórica referente ao uso do termo para tratar da dimensão grupal ou social.

- by Diego Zilio
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- The Self, Personal Identity, Radical Behaviorism, Organismal Biology

Individuality is an important concept in biology, yet there are many non-equivalent criteria of individuality expressed in different kinds of biological individuals. This paper evaluates these different kinds in terms of their capacity to support explanatory generalizations over the systems they individuate. Viewing the problem of individuality from this perspective promotes a splitting strategy in which different kinds make different epistemic trade-offs which suit them for different explanatory roles. I argue that evolutionary individuals, interpreted as forming a functional kind, face difficulties of individuation and explanatory power that are mitigated by relying on more structurally based properties and non-evolutionary kinds.

- by James DiFrisco
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- Natural Kinds, Organismal Biology, Multiple realization, Biological Individuality

Due to its long development since classical antiquity, biophilosophy is able to exhibit different naturalistic understandings of life in general and of the organism in particular which transcend the physicalistic metaphysics of most biologists. One central problem for the biosciences, namely, whether or not the concept of teleology has any legitimacy in biological explanation — a notion which has been discussed extensively since antiquity — exemplifies the central philosophical differences between the major representatives of the philosophy of biology and the more metaphysically open-minded considerations of the nature of life carried out by the biophilosophers. Yet, even inside current philosophy of biology, there are widely varying understandings of teleology. In this paper, I will show how a recently suggested model of pre-cellular organization introduces a new form of teleology that has important consequences for our understanding of biological naturalism.

- by Spyridon A . Koutroufinis
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- Self-Organization, Teleology, Organismal Biology, Teleodynamics

In the last few decades, several biologists and philosophers of biology have claimed that organisms may be considered teleological entities, spurring on a movement that is often celebrated as the renaissance of teleological thinking and that I describe as ‘neo-teleologism’. Neo-teleological approaches have been provided by cyberneticists, neo-Darwinists, theorists of self-organization, and some philosophers of biology. In Aristotle’s work Physics the term ‘telos’ has a double meaning: final state on the one hand and purpose, aim, or goal on the other. In all neo-teleological approaches the concept of ‘telos’ is understood as final-state-directedness, but here the final state of a material process is considered to be achieved by blind, deterministic, non-mental factors alone. Philosophy of biology gives to all neo-teleological approaches great credit for providing interpretations of ‘purpose’ and ‘aim’ without any reference to mental or psychical factors. According to Aristotle, in contrast, organismic final-state-directedness is the result of striving factors. This does not, however, mean that Aristotle ascribes a human-like conscious mentality to biological processes. Aristotle’s concept of striving may be interpreted in terms of non-conscious proto-experiential agency, as it was introduced by Alfred North Whitehead. I will claim that his metaphysics offers to biophilosophy a modern basis for a re-conception of genuine Aristotelian insights concerning ‘telos’ and biological organism.

- by Spyridon A . Koutroufinis
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- Aristotle, Self-Organization, Cybernetics, Biophilosophy

The Cartesian metaphysical background of most contemporary
bioscientists limits their ability to understand the uniqueness of biological processes. This book aims to contribute to the foundation of a new direction in biophilosophy which goes beyond many of the core metaphysical assumptions of contemporary mainstream biology. All of the co-authors of this volume treat central metaphysical questions about the nature of life from the perspective of Whitehead's process philosophy. These questions are crucial for the biosciences, but cannot be addressed by them since they touch on metaphysical issues. The authors of this volume explore the viability of process ontology for increasing our understanding of core concepts of biology such as organism, evolution, and teleology. The book presents a new philosophical approach to several dimensions of the phenomenon of life.

This paper questions the “arguments from design” that inferred from the functions of organism, their structure or their fit to their environnemental, the fact that they have been designed by an intelligent architect. These arguments are very old, and have been pervasive in philosophy and natural history since Antiquity. Each version connects in some way functions, structure, complexity, with randomness and low probability. Darwin claimed to have solved this argument, because natural selection eliminate the need to appeal to a designer. After having distinguished several types of arguments, regarding whether they consider mostly adaptation and contrivances, or mostly complexity, I analyze the rational core of these arguments in terms of computational notions of complexity and randomness. In the last section, I show the reason why natural selection indeed solves the design argument ; I finally focus on the link between complex adaptation and cumulative selection, and draws some conclusions regarding the relation between chance and selection in current evolutionary biology.

- by Sebastjan Vörös
- •
- Life Sciences, History of Biology, Theoretical biology, Umwelt

Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what I consider as the two main theses of the book, namely: i) genes are better conceived as tools; ii) genes become causes only in a context. I situate these two theses in the wider perspective of developmental systems theory (DST). This leads me to emphasize that Griffiths and Stotz reflect very well an on going process in genetics, which I call the “epigenetization” of genetics, i.e., the growing interest in the complex processes by which gene activation is regulated. I then make a factual objection, which is that Griffiths and Stotz have almost entirely neglected the perspective of ecological developmental biology, and more precisely recent work on developmental symbioses, and I suggest that this omission is unfortunate in so far as an examination of developmental symbioses would have considerably strengthened Griffiths and Stotz’s own conclusions.

- by Thomas Pradeu
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- Genetics, Microbiology, Environmental Science, Information Science

Expert peer review at Medicine® Journal Hesham N. Mustafa Presented April 8, 2018 (Wolters Kluwer)

Contemporary biology is affected by a controversy between the adaptationist viewpoint , central to the neo-Darwinian Modern Synthesis (MS), and the developmentalist viewpoint, central in Evo-Devo. The possibility of a synthesis between those viewpoints , as granting unity between the laws of form and the laws of function in biology, is therefore currently hotly debated. Kant's concept of organism is often seen as the philosophical precursor of developmentalism. Yet this view is incomplete, and Kant's unique regulative notion of purposiveness relies on two criteria in order to capture organisms as natural purposes: a design criterion and an epigenesis criterion. While the former is fulfilled within MS, the latter is satisfied by organisms from the developmen-talist viewpoint. Under some conditions, Kant's notion of organism can thus allow for a synthesis of developmentalism and adaptationism.

- by philippe huneman
- •
- Evolutionary Biology, Philosophy of Biology, Immanuel Kant, Organismal Biology

The physical singularity of life phenomena is analyzed by means of comparison with the driving concepts of theories of the inert. We outline conceptual analogies, transferals of methodologies and theoretical instruments between physics and biology, in addition to indicating significant differences and sometimes logical dualities. In order to make biological phenomenalities intelligible, we introduce theoretical extensions to certain physical theories. In this synthetic paper, we summarize and propose a unified conceptual framework for the main conclusions drawn from work spanning a book and several articles, quoted throughout.

- by Maël Montévil and +1
- •
- Evolutionary Biology, Physiology, Theoretical Physics, Complex Systems Science

Der Panprotopsychismus ist eine besondere Form des Panpsychismus und kann in Abhängigkeit von der Interpretation der Termini „Psychismus“, „pan“ und „proto“ sehr unterschiedliche Bedeutungen haben. Es gibt mindestens zwei Versionen des biologischen Panprotopsychismus: Die schwache und die starke. Letztere weist psychische Aktivität und Teleologie allen Organismen zu und besteht auf die ungebrochene Einheit von Leben und der inneren Seite der Erfahrung. Ich plädiere für die starke Version des Panprotopsychismus wegen des prinzipiellen Unvermögens naturwissenschaftlicher Systemtheorien, überzeugende Modelle selbst von den einfachsten Organismen zu liefern. Emergentismus und Panprotopsychismus können in der Philosophie des Lebendigen eine fruchtbare Synthese eingehen. Ersterer kann sich auf den modalen und letzterer auf den aktualen Aspekt des Organismus beziehen. Das protopsychische Subjekt, das die innere Seite des Organismus ausmacht, trifft permanent Entscheidungen zwischen physikochemisch gleichwertigen Möglichkeiten und verwirklicht einige von ihnen, die biologisch sinnvoll sind.

- by Spyridon A . Koutroufinis
- •
- Process Philosophy, Panpsychism, Teleology, Darwin

More realistic approaches are needed to understand the complexity of ecological systems. Emergent properties of real systems can be used as a basis for a new, neither reductionist nor holistic, approach. Three systems, termed here BUBBLEs, WAVEs and CRYSTALs, have been identified as exhibiting emergent properties. They are non-hierarchical assemblages of individual components, with amplification and connectedness being two main principles that govern their build-up, maintenance and mutual relationships. Examples from various fields of biological and ecological science are referred to, ranging from individual organisms to landscapes.

- by Jean-François Ponge
- •
- Landscape Ecology, Epistemology, Philosophy of Science, Self-Organization

The first diverse and morphologically complex macroscopic communities appear in the late Ediacaran period, 575 to
541 million years ago (Ma). The enigmatic organisms that make up these communities are thought to have formed
simple ecosystems characterized by a narrow range of feeding modes, with most restricted to the passive absorption
of organic particles (osmotrophy). We test between competing feeding models for the iconic Ediacaran organism
Tribrachidium heraldicum using computational fluid dynamics. We show that the external morphology of
Tribrachidium passively directs water flow toward the apex of the organism and generates low-velocity eddies
above apical “pits.” These patterns of fluid flow are inconsistent with osmotrophy and instead support the interpretation
of Tribrachidium as a passive suspension feeder. This finding provides the oldest empirical evidence for
suspension feeding at 555 to 550 Ma, ~10 million years before the Cambrian explosion, and demonstrates that
Ediacaran organisms formed more complex ecosystems in the latest Precambrian, involving a larger number of
ecological guilds, than currently appreciated.

- by Simon Darroch and +2
- •
- Evolutionary Biology, Paleobiology, Geobiology, Organismal Biology

Biological thinking is structured by the notion of level of organization. We will show that this notion acquires a precise meaning in critical phenomena: they disrupt, by the appearance of infinite quantities, the mathematical (possibly equational) determination at a given level, when moving at an “higher” one. As a result, their analysis cannot be called genuinely bottom-up, even though it remains upward in a restricted sense. At the same time, criticality and related phenomena are very common in biology. Because of this, we claim that bottom-up approaches are not sufficient, in principle, to capture biological phenomena. In the second part of this paper, following (Bailly, 1991b), we discuss a strong criterium of level transition. The core idea of the criterium is to start from the breaking of the symmetries and determination at a “first” level in order to “move” at the others. If biological phenomena have multiple, sustained levels of organization in this sense, then they should be interpreted as extended critical transitions.

- by Arnaud Pocheville and +2
- •
- Fractals, Reductionism, Organismal Biology, Bottom-up strategies

Spyridon Koutroufinis (ed.), Process and Life — Towards a Whiteheadian View of Living Beings, 2014 (310 pp. ; 978-3-11-035259-7 ; 109,95 €)
Alfred North Whitehead is arguably the most original 20th-century philosopher of nature and metaphysics. In recent decades a number of physicists have produced ground-breaking new theories in fundamental physics influenced by his process philosophy. In contrast, few biologists are even aware that Whitehead’s radical rethinking of the Cartesian assumptions implicit in 19th-century sciences might be relevant to their enterprise. This book seeks to fill this gap by exploring how Whitehead’s process ontology might provide a new philosophical foundation for the biosciences of the 21st century. The central premise shared by all of the volume’s authors is the idea that all living processes are irreducible processes. Each chapter focuses on assumptions implicit in some of the core concepts of biology—such as organism, evolution, information, and teleology—that play crucial explanatory roles in the biosciences, but as metaphysical concepts fall outside its purview. The authors each identify important shortcomings implicit in contemporary biological paradigms and show how an approach grounded in a process-oriented metaphysics can avoid them.

- by Michel Weber
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- Philosophy, Metaphysics, Philosophy of Biology, Alfred North Whitehead

Immunology — though deeply experimental in everyday practice — is also a theoretical discipline. Recent advances in the understanding of innate immunity, how it is triggered and how it shares features that have previously been uniquely ascribed to the adaptive immune system, can contribute to the refinement of the theoretical framework of immunology. In particular, natural killer cells and macrophages are activated by transient modifications, but adapt to long-lasting modifications that occur in the surrounding tissue environment. This process facilitates the maintenance of self-tolerance while permitting efficient immune responses. In this Essay we extend this idea to other components of the immune system and we propose some general principles that lay the foundations for a unifying theory of immunity — the discontinuity theory. According to this theoretical framework, effector immune responses (namely, activated responses that lead to the potential elimination of the target antigen) are induced by an antigenic discontinuity; that is, by the sudden modification of molecular motifs with which immune cells interact.

- by Thomas Pradeu
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- Immunology, Cancer, Autoimmunity, Innate immunity