The Evolutionary Hierarchies

Author(s):  
Niles Eldredge

Real-world hierarchies are usually treated as patently evident manifestations of nature, a fact that has somehow rendered them trivial. Familiarity breeds contempt. Everyone knows that atoms are the building blocks of molecules, small molecules combine to form the huge molecules of living Systems, organelles and other structures composed of such molecules make up cells, cells link up to form tissues, tissues do likewise to form organs, thence organ Systems, and finally we arrive at the integrated soma of the organism. And organisms are associated to make populations, or demes, or species. The very names of the subdisciplines of biology (especially as conceived fifty years ago) reflect this organisation. Though molecular biology is a recent arrival, physiological genetics, cytology (and cytogenetics), histology, and physiology nicely recognized the components of the somatic or organismic hierarchy. Thus, the somatic hierarchy retains a heuristic value still reflected in general biology texts. The molecules-to-organism hierarchy offers a handy way of organizing biological knowledge, information about living Systems. That nature itself is organized in such a fashion seems to have slipped to secondary significance. It is, though, common to view the sequences of codons that compose functional genes, as well as other organizational features of DNA molecules, as constituting the retention of information. One major biological hierarchy, the genealogical hierarchy, is evidently a hierarchy of information. It is as if the pragmatic, heuristic, epistemological aspects of biological hierarchies, providing us with a handy way of organizing, summarizing, and communicating what we think we know about biological Systems, serve to obscure the significance of hierarchical organization to the very workings of biological nature. All of this does not deny that there is an extensive literature on hierarchies, a multidisciplinary literature that includes a long, if episodic, history within the realm of biology. The analysis I develop here surely does not arise from a vacuum. Yet the current resurgence of hierarchical outlook on evolution reflects more, I think, a return to an alternative way of looking at nature, a way dictated by a pattern of organization of nature that is there for all to see, than it does the thickening of a continuous Intellectual strand that connects us with earlier interests in hierarchy both within biology and without.

Author(s):  
Paul F. M. J. Verschure

This chapter introduces the “Capabilities” section of the Handbook of Living Machines. Where the previous section considered building blocks, we recognize that components or modules do not automatically make systems. Hence, in the remainder of this handbook, the emphasis is toward the capabilities of living systems and their emulation in artifacts. Capabilities often arise from the integration of multiple components and thus sensitize us to the need to develop a system-level perspective on living machines. Here we summarize and consider the 14 contributions in this section which cover perception, action, cognition, communication, and emotion, and the integration of these through cognitive architectures into systems that can emulate the full gamut of integrated behaviors seen in animals including, potentially, our own capacity for consciousness.


2021 ◽  
Vol 11 (14) ◽  
pp. 6300
Author(s):  
Igor Smolyar ◽  
Daniel Smolyar

Patterns found among both living systems, such as fish scales, bones, and tree rings, and non-living systems, such as terrestrial and extraterrestrial dunes, microstructures of alloys, and geological seismic profiles, are comprised of anisotropic layers of different thicknesses and lengths. These layered patterns form a record of internal and external factors that regulate pattern formation in their various systems, making it potentially possible to recognize events in the formation history of these systems. In our previous work, we developed an empirical model (EM) of anisotropic layered patterns using an N-partite graph, denoted as G(N), and a Boolean function to formalize the layer structure. The concept of isotropic and anisotropic layers was presented and described in terms of the G(N) and Boolean function. The central element of the present work is the justification that arbitrary binary patterns are made up of such layers. It has been shown that within the frame of the proposed model, it is the isotropic and anisotropic layers themselves that are the building blocks of binary layered and arbitrary patterns; pixels play no role. This is why the EM can be used to describe the morphological characteristics of such patterns. We present the parameters disorder of layer structure, disorder of layer size, and pattern complexity to describe the degree of deviation of the structure and size of an arbitrary anisotropic pattern being studied from the structure and size of a layered isotropic analog. Experiments with arbitrary patterns, such as regular geometric figures, convex and concave polygons, contour maps, the shape of island coastlines, river meanders, historic texts, and artistic drawings are presented to illustrate the spectrum of problems that it may be possible to solve by applying the EM. The differences and similarities between the proposed and existing morphological characteristics of patterns has been discussed, as well as the pros and cons of the suggested method.


2020 ◽  
Vol 318 ◽  
pp. 01041
Author(s):  
Athena Baronos ◽  
Odysseas Manoliadis ◽  
Aristeidis Pavlidis

In today’s world the design of multiple mailboxes comes to cover the evolution of logistics in delivering mail where the postman is not required to visit every user. In this research the 3D visualization is used for the design of multiple mailboxes for domestic use. It concerns the design of mailboxes in ergonomic building blocks and apartment complexes in 3D design so that they can be easily manufactured. Between the advantages of this design will be rapid production of ready-made products production of prototypes that enables testing at the design stage and reduces the time and the cost of production. The design when done with 3D CAD can be manufactured with modern machine tooling methods. In this paper after an extensive Literature Review the postal multiple mailboxes is used as a case study in the use of 3D CAD for 3D printing. A methodology is proposed that enables the examination of prototypes at the design stage according to specifications and allows the manufacturing department of a company to prepare the right tools and begin installing production lines. Conclusively this method gives the advantage of designing the product and supporting the production of scaffolds that can be functionally and ergonomically tested before finalizing the production.


N. C. Wickramasinghe ( Department of Applied Mathematics and Astronomy, University College, Cardiff, U. K. ). The question of the origin of life is, of course, one of the most important scientific questions and it is also one of the most difficult. One is inevitably faced here with a situation where there are very few empirical facts of direct relevance and perhaps no facts relating to the actual transition from organic material to material that can even remotely be described as living. The time perspective of events that relate to this problem has already been presented by Dr Chang. Uncertainty still persists as to the actual first moment of the origin or the emergence of life on the Earth. At some time between 3800 and 3300 Ma BP the first microscopic living systems seem to have emerged. There is a definite moment in time corresponding to a sudden appearance of cellular-type living systems. Now, traditionally the evolution of carbonaceous compounds which led to the emergence of life on Earth could be divided into three principal steps and I shall just remind you what those steps are. The first step is the production of chemical building blocks that lead to the origin of the organic molecules necessary as a prerequisite for the evolution of life. Step two can be described in general terms as prebiotic evolution, the arrangement of these chemical units into some kind of sequence of precursor systems that come almost up to life but not quite; and then stage three is the early biological evolution which actually effects the transition from proto-cellular organic-type forms into truly cellular living systems. The transition is from organic chemistry, prebiotic chemistry to biochemistry. Those are the three principal stages that have been defined by traditional workers in the field, the people who, as Dr Chang said, have had the courage to make these queries and attempt to answer them. Ever since the classic experiments where organic materials were synthesized in the laboratory a few decades back, it was thought that the first step, the production of organic chemical units, is important for the origin of life on the Earth, and that this had to take place in some location on the Earth itself.


1994 ◽  
Vol 367 ◽  
Author(s):  
Eshel Ben-Jacob ◽  
Ofer Shochet ◽  
Inon Cohen ◽  
Adam Tenenbaum ◽  
Andras CzirÓk ◽  
...  

AbstractWe present a study of interfacial pattern formation during growth of bacterial colonies. Growth of bacterial colonies bears similarities but presents an inherent additional level of complexity in comparison with non-living systems. In the former case, the building blocks themselves are living systems, each with its own autonomous self-interest and internal degrees of freedom. The bacteria have developed sophisticated communication channels, which they utilize when growth conditions are tough. Here we present a non-local communicating walkers model to study the effect of local bacterium-bacterium interaction and communication via chemotaxis signaling. We demonstrate how communication enables the colony to develop complex patterns in response to adverse growth conditions. This self-organization of the colony, which can be achieved only via cooperative behavior of the bacteria, may be viewed as the outcome of an interplay between the micro-level (the individual bacterium) and the macro-level (the colony). Some qualitative features of the complex morphologies can be accounted for by invoking ideas from pattern formation in non-living systems together with a simplified model of chemotactic “feedback”.


MRS Bulletin ◽  
1998 ◽  
Vol 23 (10) ◽  
pp. 39-43 ◽  
Author(s):  
Alfons van Blaaderen

Because of their size and ability to selforganize, colloidal particles are ideal building blocks for the creation of three-dimensional (3D) structures that can have feature sizes of the order of the wavelength of electrons, photons, or both. This article is too short to provide an extensive literature survey but instead will give some illustrative examples, based on work of the author and co-workers, of how specially developed core-shell particles might be organized on a 3D lattice. These examples are only intended to give an impression of how colloidal-particle systems can be used in the design of new materials with interesting photonic properties.Generally particles are considered colloidal if their size is between several nm and several μm. This range is more or less defined by the importance of Brownian motion—that is, the irregular, overdamped, random displacements the particles make as a result of the not completely averaged-out bombardment of solvent (or gas) molecules. Consequently the lower size range is determined by the size of the solvent molecules. Compared to the particle size, the solvent molecules need to be so small that the time scales of the solvent molecules and particles are so far apart that the solvent molecules can be “integrated out” in a description of the particles. If such a description holds, the solvent can be approximated well by a continuum. The upper size limit is determined by the size at which external fields, like gravity, start to overshadow the effects of Brownian motion.


2021 ◽  
Vol 10 (9) ◽  
pp. e14310917607
Author(s):  
Adriana Amaral Carvalho ◽  
Daniella Reis Barbosa Martelli ◽  
Maria Fernanda Amaral Carvalho ◽  
Mário Sérgio Oliveira Swerts ◽  
Hercílio Martelli Júnior

Several studies describe the frequent association of cafe-au-lait spots with neurofibromatosis. However, many other genetic diseases might be associated with the presence of café-au-lait spots. Several genetic diseases are rare. In most cases, syndromes present themselves as a set of signs and symptoms that may present varied penetrance, therefore largely reducing the percentage of final diagnosis. Exploration of clinical symptomatology is essential for the understanding and diagnosis of syndromes. In this review, we conduct an extensive literature search looking for research that investigated diseases that may be present simultaneously with the cafe-au-lait spots. A total of 60 genetic diseases were found, all of them rare. These syndromes were evaluated based on their most relevant features and described in a summary of the typical, general, and head and neck findings. The available OMIM number, mode of inheritance, chromosome, mutated genes, and affected proteins were also listed. The considerable variety of diseases associated with the presence of cafe-au-lait spots and the fact that many of these conditions affect various organ systems with diverse phenotypic presentations is a diagnostic and therapeutic challenge. The objective of this study was to provide health professionals with an instrument containing a broad spectrum of genetic diseases coincident with the presence of cafe-au-lait spots in order to facilitate the differential and final diagnosis of these syndromes.


2021 ◽  
Vol 18 (4) ◽  
pp. 644-656
Author(s):  
İbrahim İhsan Arıkan ◽  
Summani Ekici ◽  
Varol Tutal

Reasearch problem/aim: In this study, it was aimed to evaluate them under the titles of the sports sector (media,   consumption, marketing) by mentioning primarily popular culture and sports issues.  Method: In this study, a descriptive research model, which is used to investigate the events as they are, trying to determine the situation that happened, investigating the events and situations discussed in detail and examining their relationship. Findings: The notion that sports is one of the building blocks of popular culture, and as a result of its action, the media sheds considerable light on consumption and marketing. The popular culture field, which started to develop as a field of study on its own, has become important by societies in the world and scientific studies on this subject have increased rapidly. Especially the innovations brought by popular culture in the world and the rapidly increasing interest in sports, media, marketing and consumer products have made this issue more up-to-date. Today, most of the sources explain that popular culture is under the influence of the media and that sports, marketing and consumption provide access to more people. Especially, social media, which enters our homes and becomes the most important part of our daily life, is extremely important in creating and conveying these topics (sports, marketing, consumption). In this context, the relationship between popular culture, media, consumption and marketing in sports and their roles among each other was discussed as a result of the extensive literature review. Conclusion: it is seen that sports have an effect on popular culture products on media, marketing and consumption.


Author(s):  
Vasundra Touré ◽  
Åsmund Flobak ◽  
Anna Niarakis ◽  
Steven Vercruysse ◽  
Martin Kuiper

Abstract Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. Logical regulatory networks can be used to predict biological and cellular behaviors by system perturbations and in silico simulations. Today, broad sets of causal interactions are available in a variety of biological knowledge resources. However, different visions, based on distinct biological interests, have led to the development of multiple ways to describe and annotate causal molecular interactions. It can therefore be challenging to efficiently explore various resources of causal interaction and maintain an overview of recorded contextual information that ensures valid use of the data. This review lists the different types of public resources with causal interactions, the different views on biological processes that they represent, the various data formats they use for data representation and storage, and the data exchange and conversion procedures that are available to extract and download these interactions. This may further raise awareness among the targeted audience, i.e. logical modelers and other scientists interested in molecular causal interactions, but also database managers and curators, about the abundance and variety of causal molecular interaction data, and the variety of tools and approaches to convert them into one interoperable resource.


2021 ◽  
Vol 14 (11) ◽  
pp. 1922-1935
Author(s):  
Maciej Besta ◽  
Zur Vonarburg-Shmaria ◽  
Yannick Schaffner ◽  
Leonardo Schwarz ◽  
Grzegorz Kwasniewski ◽  
...  

We propose GraphMineSuite (GMS): the first benchmarking suite for graph mining that facilitates evaluating and constructing high-performance graph mining algorithms. First, GMS comes with a benchmark specification based on extensive literature review, prescribing representative problems, algorithms, and datasets. Second, GMS offers a carefully designed software platform for seamless testing of different fine-grained elements of graph mining algorithms, such as graph representations or algorithm subroutines. The platform includes parallel implementations of more than 40 considered baselines, and it facilitates developing complex and fast mining algorithms. High modularity is possible by harnessing set algebra operations such as set intersection and difference, which enables breaking complex graph mining algorithms into simple building blocks that can be separately experimented with. GMS is supported with a broad concurrency analysis for portability in performance insights, and a novel performance metric to assess the throughput of graph mining algorithms, enabling more insightful evaluation. As use cases, we harness GMS to rapidly redesign and accelerate state-of-the-art baselines of core graph mining problems: degeneracy reordering (by >2X), maximal clique listing (by >9×), k -clique listing (by up to 1.1×), and subgraph isomorphism (by 2.5×), also obtaining better theoretical performance bounds.


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