My paper draws on examples from molecular biology, the details of which I have developed elsewhere (Rheinberger 1992, 1993, 1995, 1997). Here, I can give only a brief outline of my argument. Reduction of complexity is a prerequisite for experimental research. To make sense of the universe of living beings, the modern biologist is bound to divide his world into fragments in which parameters can be defined, quantities measured, qualities identified. Such is the nature of any "experimental system." (...) Ontic complexity has to be reduced in order to make experimental research possible. The complexity of the research object, however, is epistemically retained in the rich context of an experimental landscape, where the eruption of "volcanic systems" can change the scenery dramatically as the result of particular, unprecedented findings. (shrink)

Even though complexity is a concept that is ubiquitously used by biologists and philosophers of biology, it is rarely made precise. I argue that a clarification of the concept is neither trivial nor unachievable, and I propose a unifying framework based on the technical notion of “effective complexity” that allows me to do justice to conflicting intuitions about biological complexity, while taking into account several distinctions in the usage of the concept that are often overlooked. In (...) particular, I propose a distinction between two kinds of complexity, “mechanical” and “emergent”, which can be understood as different ways of relating the effective complexity of mechanisms and of behaviors in biological explanations. I illustrate the adequacy of this framework by discussing different attempts to understand intracellular organization in terms of pathways and networks. My framework provides a different way of thinking about recent philosophical debates, for example, on the difference between mechanistic and topological explanations and about the concept of emergence. Moreover, it can contribute to a proper assessment of metascientific arguments that invoke biological complexity. (shrink)

Self-organized complexity in the physical, biological, and social sciences Donald L Turcotte*f and John B. Rundle* *Department of Earth and Atmospheric ...

In this paper we develop a new mathematical approach to the pattern formation problem in biology. This problem was first posed mathematically by A.M. Turing, however some principal questions were left open . Here we consider the pattern formation ability of some class of genetic circuits. First, we show that the genetic circuits are capable of generating arbitrary spatio-temporal patterns. Second, we give upper and lower bounds on the number of genes in a circuit generating a given pattern. A (...) connection between the complexity of gene interaction and the pattern complexity is found. We investigate the stochastic stability of patterning algorithms. Results are consistent with experimental data. (shrink)

In business administration or in economics it is absolutely relevant not to consider indexes like profit growth rate or gross domestic product as exhaustive indexes for economic wealth. Likewise, in biology it is important not to confuse the representation of life with life itself. The most important concepts in biology are information, memory, structure, plasticity, and robustness. Information is the difference that makes the difference. Memories are information registered in an organism. Plasticity is the capacity of a living (...) organism to change its own structure/sets of behaviors for having a competitive advantage. Robustness is the ability of a living organism to resist environmental changes without changing its own structure/sets of behavior, and fragility is when a living organism undergoes changes in its own structure without being able to resist non-adaptive changes. (shrink)

Living systems employ several mechanisms and behaviors to achieve robustness and maintain themselves under changing internal and external conditions. Regulation stands out from them as a specific form of higher-order control, exerted over the basic regime responsible for the production and maintenance of the organism, and provides the system with the capacity to act on its own constitutive dynamics. It consists in the capability to selectively shift between different available regimes of self-production and self-maintenance in response to specific signals and (...) perturbations, due to the action of a dedicated subsystem which is operationally distinct from the regulated ones. The role of regulation, however, is not exhausted by its contribution to maintain a living system’s viability. While enhancing robustness, regulatory mechanisms play a fundamental role in the realization of an autonomous biological organization. Specifically, they are at the basis of the remarkable integration of biological systems, insofar as they coordinate and modulate the activity of distinct functional subsystems. Moreover, by implementing complex and hierarchically organized control architectures, they allow for an increase in structural and organizational complexity while minimizing fragility. Finally, they endow living systems, from their most basic unicellular instances, with the capability to control their own internal dynamics to adaptively respond to specific features of their interaction with the environment, thus providing the basis for the emergence of minimal forms of cognition. (shrink)

Biology deals, notoriously, with complex systems. In discussing biological methodology, all three papers in this symposium honor the complexity of biological subject matter by preferring models and theories built to reflect the details of complex systems to models based on broad general principles or laws. Rheinberger's paper, the most programmatic of the three, provides a framework for the epistemology of discovery in complex systems. A fundamental problem is raised for Rheinberger's epistemology, namely, how to understand the referential continuity (...) of the theoretical terms and concepts employed in typical case studies involving complex systems. (shrink)

The use of biological samples in research raises a number of ethical issues in relation to consent, storage, export, benefit sharing and re-use of samples. Participant perspectives have been explored in North America and Europe, with only a few studies reported in Africa. The amount of research being conducted in Africa is growing exponentially with volumes of biological samples being exported from the African continent. In order to investigate the perspectives of African research participants, we conducted a study at research (...) sites in the Western Cape and Gauteng, South Africa. (shrink)

Complex Systems Biology approaches are here considered from the viewpoint of Robert Rosen’s (M,R)-systems, Relational Biology and Quantum theory, as well as from the standpoint of computer modeling. Realizability and Entailment of (M,R)-systems are two key aspects that relate the abstract, mathematical world of organizational structure introduced by Rosen to the various physicochemical structures of complex biological systems. Their importance for understanding biological function and life itself, as well as for designing new strategies for treating diseases such as (...) cancers, is pointed out. The roles played by multiple metastable states in the “continuous uphill flow of Life” supported through internal bioenergetic processes that are coupled to essential inflows are also discussed in relation to dynamic realizations of (M,R)-systems. Furthermore, the roles played by the underlying, many-valued, quantum logics and symbolic computations for ultra-complex biological systems are also briefly discussed. (shrink)

The comparison between biological and social macroevolution is a very important (though insufficiently studied) subject whose analysis renders new significant possibilities to comprehend the processes, trends, mechanisms, and peculiarities of each of the two types of macroevolution. Of course, there are a few rather important (and very understandable) differences between them; however, it appears possible to identify a number of fundamental similarities. One may single out at least three fundamental sets of factors determining those similarities. First of all, those similarities (...) stem from the fact that in both cases we are dealing with very complex non-equilibrium (but rather stable) systems whose principles of functioning and evolution are described by the General Systems' Theory, as well as by a number of cybernetic principles and laws. -/- Secondly, in both cases we do not deal with isolated systems; in both cases we deal with a complex interaction between systems of organic systems and external environment, whereas the reaction of systems to external challenges can be described in terms of certain general principles (that, however, express themselves rather differently within the biological reality, on the one hand, and within the social reality, on the other). -/- Thirdly, it is necessary to mention a direct ‘genetic’ link between the two types of macroevolution and their mutual influence. -/- It is important to emphasize that the very similarity of the principles and regularities of the two types of macroevolution does not imply their identity. Rather significant similarities are frequently accompanied by enormous differences. For example, genomes of the chimpanzees and the humans are very similar – with differences constituting just a few per cent; however, there are enormous differences with respect to intellectual and social differences of the chimpanzees and the humans hidden behind the apparently ‘insignificant’ difference between the two genomes. Thus, in certain respects it appears reasonable to consider the biological and social macroevolution as a single macroevolutionary process. This implies the necessity to comprehend the general laws and regularities that describe this process, though their manifestations may display significant variations depending on properties of a concrete evolving entity (biological, or social one). An important notion that may contribute to the improvement of the operationalization level as regards the comparison between the two types of macroevolution is the one that we suggested some time ago – the social aromorphosis (that was developed as a counterpart to the notion of biological aromorphosis well established within Russian evolutionary biology). We regard social aromorphosis as a rare qualitative macrochange that increases in a very significant way complexity, adaptability, and mutual influence of the social systems, that opens new possibilities for social macrodevelopment. In our paper we discuss a number of regularities that describe biological and social macroevolution and that employ the notions of social and biological aromorphosis such as ones of the module evolution (or the evolutionary ‘block assemblage’), ‘payment for arogenic progress’ etc. (shrink)

Early 20th century philosopher Henri Bergson posited an initial push that propelled the diversity of life forward into a varied, novel future: The élan vital, a necessary force or impulse that animated life’s progress and development. His idea had largely been abandoned by mid-century. Even so, much of the conceptual and explanatory work this impulse targeted is yet in want of an explanation. In particular, Bergson’s derelict ideas on evolution addressed three areas that have once again become relevant in the (...) effort to unite evolutionary genetics, biological development, and ecological context : the purposeful nature of individual organisms and their parts; the integrative, holistic, non-linear emergent dynamics seen in evolutionary processes; and how genuine novelty emerges into the universe :422, 2016; Simondon et al. in On the mode of existence of technical objects. Univocal series, Univocal Publishing LLC, Minneapolis, 2017; Bang, in: Winther-Lindqvist, Bang, Valsiner Nothingness: philosophical insights into psychology, Transaction Publishers, Somerset, 2016; Moreno and Mossio in Biological autonomy: a philosophical and theoretical enquiry. History, philosophy and theory of the life sciences, Springer, Dordrecht, 2015). In this paper I argue that Bergson’s ideas may yet be relevant to these questions, and his work warrants a reexamination in light of current problems in evolutionary biology. This is not a call to ‘return’ to Bergson, nevertheless his notions about complexity suggest ways of looking at current biological problems in ways that offer a heuristic insight worth entertaining. Bergson’s Nobel Prize-winning book, Creative Evolution, provided a strikingly prescient early 20th century framework for understanding how Darwinian evolution acts as an engine for generating new forms, University Press of America, Lanham, Bergson 1911). (shrink)

In this paper I shall discuss the concept of reduction—ontological, methodological, and epistemological or theoretical—in the biological sciences, with special emphasis on genetics and evolutionary biology. I suggest that perhaps, because the biological world has a form different from the non-biological world, it is appropriate to think of terms or metaphors different from those we would use when trying to understand the inorganic world. As such, the attempt to show that the biological is simply a deductive consequence of the (...) physicochemical is doomed to failure. The philosophical complexity of reductionism on the one hand and its potential for advancing the study of biology on the other thus requires continuing the ongoing dialogue between philosophers and biologists. (shrink)

Systems thinking is an increasingly recognized paradigm in education in both natural and social sciences, a particular focus being, naturally, in biology. This article argues that plant biology, and in particular, plant hormonal signaling, provides highly illustrative models for learning and teaching in a systems paradigm, because it offers examples of highly complex networks, ranging from the molecular‐ to ecosystem‐scale, and in addition lends itself to the use of real‐life biological objects.

Living organisms are currently most often seen as complex dynamical systems that develop and evolve in relation to complex environments. Reflections on the meaning of the complex dynamical nature of living systems show an overwhelming multiplicity in approaches, descriptions, definitions and methodologies. Instead of sustaining an epistemic pluralism, which often functions as a philosophical armistice in which tolerance and so-called neutrality discharge proponents of the burden to clarify the sources and conditions of agreement and disagreement, this paper aims at analysing: (...) (i) what has been Kant's original conceptualisation of living organisms as natural purposes; (ii) how the current perspectives are to be related to Kant's viewpoint; (iii) what are the main trends in current complexity thinking. One of the basic ideas is that the attention for structure and its epistemological consequences witness to a great extent of Kant's viewpoint, and that the idea of organisational stratification today constitutes a different breeding ground within which complexity issues are raised. The various approaches of complexity in biological systems are captured in terms of two different styles, universalism and (weak and strong) constructivism, between which hybrid forms exist. (shrink)

Ecologist Richard Levins argues population biologists must trade‐off the generality, realism, and precision of their models since biological systems are complex and our limitations are severe. Steven Orzack and Elliott Sober argue that there are cases where these model properties cannot be varied independently of one another. If this is correct, then Levins's thesis that there is a necessary trade‐off between generality, precision, and realism in mathematical models in biology is false. I argue that Orzack and Sober's arguments fail (...) since Levins's thesis concerns the pragmatic features of model building not just the formal properties of models. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations (...) that appeal to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

The major challenge in complex disease genetics is to understand the fundamental features of this complexity and why functional alterations at multiple independent genes conspire to lead to an abnormal phenotype. We hypothesize that the various genes involved are all functionally united through gene regulatory networks (GRN), and that mutant phenotypes arise from the consequent perturbation of one or more rate‐limiting steps that affect the function of the entire GRN. Understanding a complex phenotype thus entails unraveling the details of (...) each GRN, namely, the transcription factors that bind to cis regulatory elements affected by sequence variants altering transcription of specific genes, and their mutual feedback relationships. These GRNs can be identified through their rate‐limiting steps and are best uncovered by genomic analyses of rare, extreme phenotype families, thus providing a coherent molecular basis to complex traits and disorders. (shrink)

Pleiotropy, in which one mutation causes multiple phenotypes, has traditionally been seen as a deviation from the conventional observation in which one gene affects one phenotype. Epistasis, or gene–gene interaction, has also been treated as an exception to the Mendelian one gene–one phenotype paradigm. This simplified perspective belies the pervasive complexity of biology and hinders progress toward a deeper understanding of biological systems. We assert that epistasis and pleiotropy are not isolated occurrences, but ubiquitous and inherent properties of (...) biomolecular networks. These phenomena should not be treated as exceptions, but rather as fundamental components of genetic analyses. A systems level understanding of epistasis and pleiotropy is, therefore, critical to furthering our understanding of human genetics and its contribution to common human disease. Finally, graph theory offers an intuitive and powerful set of tools with which to study the network bases of these important genetic phenomena. (shrink)

Emergence is much discussed by both philosophers and scientists. But, as noted by Mitchell (2012), there is a significant gulf; philosophers and scientists talk past each other. We contend that this is because philosophers and scientists typically mean different things by emergence, leading us to distinguish being emergence and pattern emergence. While related to distinctions offered by others between, for example, strong/weak emergence or epistemic/ontological emergence (Clayton, 2004, pp. 9–11), we argue that the being vs. pattern distinction better captures what (...) the two groups are addressing. In identifying pattern emergence as the central concern of scientists, however, we do not mean that pattern emergence is of no interest to philosophers. Rather, we argue that philosophers should attend to, and even contribute to, discussions of pattern emergence. But it is important that this discussion be distinguished, not conflated, with discussions of being emergence. In the following section we explicate the notion of being emergence and show how it has been the focus of many philosophical discussions, historical and contemporary. In section 3 we turn to pattern emergence, briefly presenting a few of the ways it figures in the discussions of scientists (and philosophers of science who contribute to these discussions in science). Finally, in sections 4 and 5, we consider the relevance of pattern emergence to several central topics in philosophy of biology: the emergence of complexity, of control, and of goal-directedness in biological systems. (shrink)

The functional complexity, or the number of functions, of organisms hasfigured prominently in certain theoretical and empirical work inevolutionary biology. Large-scale trends in functional complexity andcorrelations between functional complexity and other variables, such assize, have been proposed. However, the notion of number of functions hasalso been operationally intractable, in that no method has been developedfor counting functions in an organism in a systematic and reliable way.Thus, studies have had to rely on the largely unsupported assumption thatnumber (...) of functions can be measured indirectly, by using number ofmorphological, physiological, and behavioral parts as a proxy. Here, amodel is developed that supports this assumption. Specifically, the modelpredicts that few parts will have many functions overlapping in them, andtherefore the variance in number of functions per part will be low. If so,then number of parts is expected to be well correlated with number offunctions, and we can use part counts as proxies for function counts incomparative studies of organisms, even when part counts are low. Alsodiscussed briefly is a strategy for identifying certain kinds of parts inorganisms in a systematic way. (shrink)

To study how expertise impacts the understanding of a complex system like the vineyard, three measures were used with 259 participants (190 non-experts, 34 winemakers and/or winegrowers, and 35 biologists): a questionnaire to check for expertise (the Plant Biology Questionnaire), a task about the Structure, Behaviour and Function model, and a measure of the content of the participants? discourse with the ALCESTE software. Results showed that biologists mentioned functions significantly more often than behaviours, whereas it was the opposite for (...) winegrowers. Non-experts mentioned functions and behaviours significantly less frequently than experts did. The content analysis confirmed the differential expression of each kind of expertise: scientific wording for biologists, technical wording for winegrowers, and words focused on perceptible structures for the non-experts. Results from all tasks were highly correlated and allowed for an interpretation of expertise in terms of mental models of the vineyard. (shrink)

Development and Evolution surveys and illuminates the key themes of rapidly changing fields and areas of controversy that the redefining the theory and philosophy of biology. It continues Stanley Salthe's investigation of evolutionary theory, begun in his influential book Evolving Hierarchical Systems, while negating the implicit philosophical mechanisms of much of that work. Here Salthe attempts to reinitiate a theory of biology from the perspective of development rather than from that of evolution, recognizing the applicability of general systems (...) thinking to biological and social phenomena and pointing towards a non-Darwinian and even a postmodern biology. (shrink)

This book is based on the outcome of the ""2012 Interdisciplinary Symposium on Complex Systems"" held at the island of Kos. The book consists of 12 selected papers of the symposium starting with a comprehensive overview and classification of complexity problems, continuing by chapters about complexity, its observation, modeling and its applications to solving various problems including real-life applications. More exactly, readers will have an encounter with the structural complexity of vortex flows, the use of chaotic dynamics (...) within evolutionary algorithms, complexity in synthetic biology. (shrink)

Does biology have general laws that apply to all levels of biological organisation, across all evolutionary time? In their book “Biology’s first law: the tendency for diversity and complexity to increase in evolutionary systems” (2010), Daniel McShea and Robert Brandon propose that the most fundamental law of biology is that all levels of biological organisation have an underlying tendency to become more complex and diverse over time. A range of processes, most notably selection, can prevent the (...) expression of this tendency, but they predict that, on average, we should see that lineages tend toward greater diversity and complexity, driven by fundamentally neutral processes. Their hypothesis can be summarised as “diversity is easy, stasis is hard”. Here, I consider evidence for this “zero force evolutionary law”. It provides a fair description of evolutionary change at the genomic level, but the predictions of the proposed law are not met for broad scale patterns in the evolution of the animal kingdom. (shrink)

This essay analyzes Theodosius Dobzhansky’s famous article, “Nothing in Biology Makes Sense Except in the Light of Evolution,” in which he presents some of his best arguments for evolution. I contend that all of Dobzhansky’s arguments hinge upon sectarian claims about God’s nature, actions, purposes, or duties. Moreover, Dobzhansky’s theology manifests several tensions, both in the epistemic justification of his theological claims and in their collective coherence. I note that other prominent biologists—such as Mayr, Dawkins, Eldredge, Ayala, de Beer, (...) Futuyma, and Gould—also use theology-laden arguments. I recommend increased analysis of the justification, complexity, and coherence of this theology. (shrink)

Autophagy and YAP1‐WWTR1/TAZ signalling are tightly linked in a complex control system of forward and feedback pathways which determine different cellular outcomes in differing cell types at different time‐points after perturbations. Here we extend our previous experimental and modelling approaches to consider two possibilities. First, we have performed additional mathematical modelling to explore how the autophagy‐YAP1 crosstalk may be controlled by posttranslational modifications of components of the pathways. Second, since analogous contrasting results have also been reported for autophagy as a (...) regulator of other transduction pathways engaged in tumorigenesis (Wnt/β‐catenin, TGF‐β/Smads, NF‐kB or XIAP/cIAPs), we have considered if such discrepancies may be explicable through situations involving competing pathways and feedback loops in different cell types, analogous to the autophagy‐YAP/TAZ situation. Since distinct posttranslational modifications dominate those pathways in distinct cells, these need to be understood to enable appropriate cell type‐specific therapeutic strategies for cancers and other diseases. (shrink)

The concept of information has acquired a strikingly prominent role in contemporary biology. This trend is especially marked within genetics, but it has also become important in other areas, such as evolutionary theory and developmental biology, particularly where these fields border on genetics. The most distinctive biological role for informational concepts, and the one that has generated the most discussion, is in the description of the relations between genes and the various structures and processes that genes play a (...) role in causing. For many biologists, the causal role of genes should be understood in terms of their carrying information about their various products. That information might require the cooperation of various environmental factors before it can be "expressed," but the same can be said of other kinds of message. An initial response might be to think that this mode of description is entirely anchored in a set of well-established facts about the role of DNA and RNA within protein synthesis, summarized in the familiar chart representing the "genetic code," mapping DNA base triplets to amino acids. However, informational enthusiasm in biology predates even a rudimentary understanding of these mechanisms (Schrodinger 1944). And more importantly, current applications of informational concepts extend far beyond anything that can receive an obvious justification in terms of the familiar facts about the specification of protein molecules by DNA. This includes: 1 (i) The description of whole-organism phenotypic traits (including complex behavioral traits) as specified or coded for by information contained in the genes, (ii) The treatment of many causal processes within cells, and perhaps of the wholeorganism developmental sequence, in terms of the execution of a program stored in the genes, (iii) The idea that genes themselves, for the purpose of evolutionary theorizing, should be seen as, in some sense, "made" of information.. (shrink)

1 The Zero-Force Evolutionary Law 2 Randomness, Hierarchy, and Constraint 3 Diversity 4 Complexity 5 Evidence, Predictions, and Tests 6 Philosophical Foundations 7 Implications.

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

In the present article, a depiction of complexity versus time will be used for the construction of a novel form of a tree of life, called The Pattern of Life, comprising the biological, cultural, and scientific forms of the evolutionary process. This diagram accentuates the implication of the successive modifications of developmental programs, in the cultural and scientific realms coupled to a feedback mechanism that is decisive for the accelerating pace of complexity growth, also suggested to be of (...) support of a cautious prediction of future evolution. (shrink)

In previous work, I have looked in detail at the capacity and the limits of the linguistics model as applied to gene expression. The recent use of a primitive applied linguistic model in Apple's SIRI system allows further analysis. In particular, the failings of this system resemble those of the HGP; the model used also helps point out the shortcomings of the concept of the "gene". This is particularly urgent as we are entering an era of applied biology in (...) the absence of theory, and indeed an era with a near-epidemic of retracted papers. There are a few workarounds proposed. One is to add to the nascent field of biosemiotics a more explicit concern with syntax. At the time of writing, Apple is being sued for false advertising of its iphone 4s, with the associated claim that apple had solved many of the problems of natural language processing by computer . The system was bought by Apple from a company called SIRI, and in turn was based on the notion, trumpeted by the prior art in a company called Dejima, that nlpbc could be done by keywords alone. Yet the hype resembles nothing so much as the misrepresentation of the Human Genome Project fed to the media in the glory days at the beginning of this millennium, and it says a lot for the status of scientists in society that they have avoided Apple's fate. In this paper, a short review of several current themes in theoretical and applied biology is first proposed. Then the tensions implicit in the notion that the "gene" is simultaneously to be identified as a unit of inheritance and spatially located over spatially well-defined nucleotides is explored and the notion is found to be incoherent. An expanded notion of inheritance is proposed in the context of a focus on inheritance as necessarily involving species, population and organism over time. While it is premature to talk about a paradigm shift, it is certainly arguable that biology urgently needs a sophisticated theory of how symbols work substantially more sophisticated than that implicit in the HGP; Biosemiotics affords a framework in which this might be tried. Indeed, as this paper concludes, there may yet be room for a "Bionoetics", a perspective in which biological explanation can be extended to include cognition in all its forms. Finally, a working sketch of a modeling environment written in LISP, one that shows promise in reflecting the complexities discussed in the paper, is included. Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}. (shrink)

Complex, multigenic biological traits are shaped by the emergent interaction of proteins being the main functional units at the molecular scale. Based on a phenomenological approach, algorithms for quantifying two different aspects of emergence were introduced (Wegner and Hao in Progr Biophys Mol Biol 161:54–61, 2021) describing: (i) pairwise reciprocal interactions of proteins mutually modifying their contribution to a complex trait (denoted as weak emergence), and (ii) formation of a new, complex trait by a set of n ‘constitutive’ proteins at (...) concentrations exceeding individual threshold values (strong emergence). The latter algorithm is modified here to take account of protein redundancy with respect to a complex trait (‘full redundancy’). Irreducibility is considered a necessary and sufficient criterion for strong biological emergence; if one constitutive protein is missing, or its concentration drops below the threshold the trait is lost. A definition based on ‘unpredictability’ is dismissed, because this criterion is irrelevant for the evolution of a complex trait, and apparent unpredictability may rather reflect our basic deficits in understanding unless we can provide an unequivocal proof for it. The phenomenological approach advocated here allows to identify hidden rules according to which strongly emergent traits may be organized. This is of high value for understanding the evolution of complex traits which seems to require the saltational advent of all constitutive proteins ‘in one turn’ to arrive at a functional trait providing for an improved fitness of the organism. Rather than being a purely random process, it may be guided by fundamental structural principles. (shrink)

This chapter analyzes the revolutionary impact of genomic science on the study of evolution, and addresses the issues that modern evolutionary biology has either learned or needs to grapple with in the age of genomics. It suggests that transposable elements are genomic constituents which can result in novel genes or gene functions. The chapter proposes that although epigenetic changes remain compatible with the Modern Synthesis, dissecting the details could possibly result in new insights into the dynamics of the evolutionary (...) process which are not currently considered. It shows that the nature of epistasis is increasingly gaining prominence, and offers new avenues of research into the genetic architecture of evolutionary change. (shrink)

This article is about the power of critical thinking through embryos and embryology in bioart. In this instance, critical thinking does not promise revolution or a takedown of bioengineering, but basic empowerment through scientific knowledge. I argue that the use of embryos in Jill Scott’s Somabook (2011) and Adam Zaretsky’s DIY Embryology (2015) constitutes an instance of what Philip Galanter identifies as complexism. In turn, the complexism of embryology reveals two modes of critical thinking. First, embryology distils the awe and (...) wonder that come with basic scientific literacy. In turn, scientific literacy provides agency for individuals through a trifecta of feeling, belief and pragmatism: based on the frisson of curiosity and wonder that comes with recognizing biological complexity, it frees individuals from the bounds of superstition and metaphysics while building a path to fact-based problem solving. Second, as works of art bearing embryos they are part of the politics and history of embryology that emerged in contrast to genetics almost a century ago. Distinct from the coding of genetics as nucleus-centric, separate, homogeneous, a matter of being, and male, embryology was coded as cytoplasmic, interactive, heterogeneous, a matter of becoming, and feminist. (shrink)

Drug development regularly has to deal with complex circumstances on two levels: the local level of pharmacological intervention on specific target proteins, and the systems level of the effects of pharmacological intervention on the organism. Different development strategies in the recent history of early drug development can be understood as competing attempts at coming to grips with these multi-level complexities. Both rational drug design and high-throughput screening concentrate on the local level, while traditional empirical search strategies as well as recent (...) systems biology approaches focus on the systems level. The analysis of these strategies reveals serious obstacles to integrating the study of interventive and systems complexity in a systematic, methodical way. Due to some fairly general properties of biological networks and the available options for pharmaceutical intervention, drug development is captured in an obstinate methodological dilemma. It is argued that at least in typical cases, drug development therefore remains dependent on coincidence, serendipity or plain luck to bridge the gap between development methodology and actual therapeutic success. (shrink)

The model provided by the organismic point of view is quite different. Without having recourse to any transcendent vital force or immanent teleology, it nevertheless rejects the basic ideas of mechanism. More specifically, it replaces the analytical- summative conception by the idea of biological organisms as wholes or systems which have unique system-properties and obey irreducible system-laws. The machine-theoretical conception is replaced by a dynamic interpretation of living things, wherein organic structures are due to a continuous flow of processes combining (...) to produce patterns of immense intricacy. The reaction-theoretical conception is jettisoned in favour of the view that the organism is primarily a center of activity which is autonomous and not a mere response to external stimuli. Finally, the organismic model considers that biological systems are stratified, so that, e.g., viruses, genes, chromosomes, cells, multicellular individuals, supra-individual aggregates, etc., form a hierarchy of "levels" exhibiting an increasing degree of complexity. The whole of nature, indeed, contains "a tremendous architecture, in which subordinate systems are united at successive levels into ever higher and larger systems.". (shrink)

Concepts of an organism’s biological environment and of niche construction as how organisms alter their environment and that of other organisms now play prominent roles in multiple sub-fields of biology, including ecology, evolution, and development. Some philosophers now use these concepts to understand the dynamics of scientific research. Others note divergences among the concepts of niche and niche construction employed in these biological fields, with implications for their possible conceptual integration. My (Rouse, 2015) account of scientific research as niche (...) constructive and of laws and lawful invariance in scientific practice illuminates these conceptual differences and their implications for integrating those domains of biological research in two ways. First, it accounts for the partial autonomy of these domains and their concepts as characteristic of scientific conceptual development. Second, it provides a more complex understanding of how research domains can be integrated, which shows how those different conceptions of niches and niche construction do not block their appropriate integration. The conclusion situates my account and its application to niche concepts both amid other philosophical uses of niche concepts to understand research environments and as exemplifying my revisionist conception of philosophical naturalism. (shrink)

We used agent-based modelling to highlight the advantages and disadvantages of several management styles in biology, ranging from centralized to egalitarian ones. In egalitarian groups, all team members are connected with each other, while in centralized ones, they are only connected with the principal investigator. Our model incorporated time constraints, which negatively influenced weakly connected groups such as centralized ones. Moreover, our results show that egalitarian groups outperform others if the questions addressed are relatively simple or when the communication (...) among agents is limited. Complex epistemic spaces are explored best by centralized groups. They outperform other team structures because the individual members can develop their own ideas with less interference of the opinions of others. The optimal ratio between time spent on experimentation and dissemination varies between different organizational structures. Furthermore, if the evidence is shared only after a relevant degree of certainty is reached, all investigated groups epistemically profit. We discovered that the introduction of seminars to the model changes the epistemic performance in favour of weakly connected teams. Finally, the abilities of the principal investigator do not seem to outperform cognitive diversity, as group performances were not strongly influenced by the increase of her abilities. (shrink)