Topological explanations in biology have been largely assumed to be free of mechanisms. However, by examining two classic topological explanations in the philosophical literature, this article has identified mechanisms in the corrected and complete formulations of both explanations. This constitutes the major work of this article. The minor work of this article is to address a follow-up question: given

In this paper, we understand the emergence of life as a pure individuation process. Individuation already occurs in open thermodynamics systems near equilibrium. We understand such open systems, as already recursively characterized (R1) by the relation between their internal properties, and their boundary conditions. Second, global properties emerge in such physical systems. We interpret this change

A core property of robust systems is given by the invariance of their function against the removal of some of their structural components. This intuition has been formalised in the context of input–output maps, thereby introducing the notion of exclusion independence. We review work on how this formalisation allows us to derive characterisation theorems that provide a basis for the design of robust

To what extent do simultaneous innovations occur and are independently from each other? In this paper we use a novel persistent keyword framework to systematically identify innovations in a large corpus containing academic papers in evolutionary medicine between 2007 and 2011. We examine whether innovative papers occurring simultaneously are independent from each other by evaluating the citation and

Many small nucleolar RNAs and many of the hairpin precursors of miRNAs are processed from long non-protein-coding host genes. In contrast to their highly conserved and heavily structured payload, the host genes feature poorly conserved sequences. Nevertheless, there is mounting evidence that the host genes have biological functions beyond their primary task of carrying a ncRNA as payload. So far, no

The relations, rather than the elements, constitute the structure of networks. We therefore develop a systematic approach to the analysis of networks, modelled as graphs or hypergraphs, that is based on structural properties of (hyper)edges, instead of vertices. For that purpose, we utilize so-called network curvatures. These curvatures quantify the local structural properties of (hyper)edges, that

In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology. Nevertheless, I argue that Shannon’s concept of information is useful in biology, although its application is not as straightforward as many people think. In fact, the recently developed theory of information

In 1835, the meaning of the cleavage furrows in the division of frog eggs was the cause of a heated argument between the Italian naturalist Mauro Rusconi and Karl Ernst von Baer. These furrows were first described by Prévost and Dumas (Ann Sci Nat 2:100–121, 129–149, 1824b) who did not realize they cut the egg into separate masses. Rusconi (Développement de la grenouille comune depuis le moment de

A generalized model of intra-host CHIKV infection with two routes of infection has been proposed. In a first step, the basic reproduction number \(\mathscr {R}_0\) was calculated using the next-generation matrix method and the local and global stability analyses of the steady states are carried out using the Lyapunov method. It is proven that the CHIKV-free steady state \(\bar{E}\) is globally asymptotically

The generation of a phenotypic diversity that is coherent across a bacterial population is a fundamental problem. We propose here that the DNA strand-specific segregation of certain nucleoid-associated proteins or NAPs results in these proteins being asymmetrically distributed to the daughter cells. We invoke a variety of mechanisms as responsible for this asymmetrical segregation including those based

The fate of “clade,” both as concept and word, is reconstructed here beginning with its first appearance in 1866 as “Cladus,” in Haeckel’s Generelle Morphologie, continuing up to the present. Although central to phylogenetics, the concept of clade is paradoxical since it has been ambiguously understood or even misunderstood by its own promoters. Writings by Ernst Haeckel, Lucien Cuénot, and Julian

The Anatomai, a lost work written by Aristotle, must have contained a collection of various drawings and figures of species as well as their organs. In his texts (mainly the Historia animalium), Aristotle is often referring to the drawings after the description of species. Our study applies the method of the comparative view (‘Vergleichendes Sehen’) to provide an access to and reconstruction of Aristotle’s

We propose and analyze a stochastic competing two-species population dynamics model subject to jump and continuous correlated noises. Competing benthic algae population dynamics in river environment, which is an important engineering problem, motivates this new model. The model is a system of stochastic differential equations having a characteristic that the two populations are competing with each

Most mathematical modeling in biology relies either implicitly or explicitly on the epistemology of physics. The underlying conception is that the historicity of biological objects would not matter to understand a situation here and now, or, at least, historicity would not impact the method of modeling. We analyze that it is not the case with concrete examples. Historicity forces a conceptual reconfiguration

Microbial symbioses based on nutrient exchange and interdependence are ubiquitous in nature and biotechnologically promising; however, an in-depth mathematical description of their exact underlying dynamics from first principles is still missing. Hence, in this paper a novel mechanistic mathematical model of such a relationship in a continuous chemostat culture is derived. In contrast to preceding

Diversity in metacommunities is traditionally viewed to consist of the diversity within communities (\(\alpha\)) that is complemented by the differences between communities (\(\beta\)) so as to result in the total diversity (\(\gamma\)) of the metacommunity. This perception of the partitioning of diversity, where \(\beta\) is a function of \(\gamma\) and \(\alpha\) (usually \(\beta =\gamma /\alpha\)

Swimming of spermatozoa through couple stress fluid in an asymmetric human cervical canal is investigated in the present theoretical analysis. A couple of fourth-order partial differential equations arising from the mathematical modelling of the proposed model is solved analytically. Flow variables like pressure gradient, propulsive velocity, mucus velocity and time mean flow rate are analysed for

Embryonic development, which inspired the first theories of biological form, was eventually excluded from the conceptual framework of the Modern Synthesis as irrelevant. A major question during the last decades has centred on understanding whether new advances in developmental biology are compatible with the standard view or whether they compel a new theory. Here, I argue that the answer to this question

In the present article, the dynamics of a novel combination of ratio-dependent incidence rate and saturated treatment rate in susceptible-infected-recovered disease compartmental model has been presented. The ratio-dependent incidence rate has been incorporated into the model to monitor the situation when ratio of the number of infectives to that of the susceptibles is getting higher. The saturated

Despite the near universal assumption of individuality in biology, there is little agreement about what individuals are and few rigorous quantitative methods for their identification. Here, we propose that individuals are aggregates that preserve a measure of temporal integrity, i.e., “propagate” information from their past into their futures. We formalize this idea using information theory and graphical

The aim of the paper is to identify psychosomatic evolutionary adaptations of hominids, which direct them at maximizing their reproductive success, and on the basis of which their various social structures are built. Selected features of the hominid last common ancestor were extracted; by reducing the influence of the social structure, they were defined as the hominid “sexual nature”; these considerations

Extending the previous 2-gender dioecious diploid gene-mating evolution model, we attempt to answer “whether the Hardy–Weinberg global stability and the exact analytic dynamical solutions can be found in the generalized N-gender N-polyploid gene-mating system with arbitrary number of alleles?” For a 2-gender gene-mating evolution model, a pair of male and female determines the trait of their offspring

Unfortunately, part of the article title was updated as subtitle which in turn resulted with complete title not appearing on website and in the bibliographic data. The complete version of title is updated here.

Fundamental properties of macroscopic gene-mating dynamic evolutionary systems are investigated. A model is studied to describe a large class of systems within population genetics. We focus on a single locus, any number of alleles in a two-gender dioecious population. Our governing equations are time-dependent continuous differential equations labeled by a set of parameters, where each parameter stands

The idea that selection works in different ways during free population growth and at the equilibrium population size has been present in theoretical biology for a long time. It was first expressed as an r and K selection concept and later clarified in the debate on fitness measures in life history theory. The latest discussion related to this topic is focused on the nest site lottery mechanism and

The original version of this article unfortunately contained a mistake.

Topological features evolved from genetic operators in the recombination space play a crucial role in the course of evolution. Different crossover models generated in a recombination space can be structured by pretopological space. This paper deals with several types of connectedness properties of recombination space in three different cases of unequal crossover of recombination space structured as

We formulate and analyze a within-host hepatitis B viral mathematical model for hepatitis B in the acute phase of infection. The model incorporates hepatocytes, hepatitis B virus, immune system cells and cytokine dynamics using a system of ordinary differential equations. We use the model to demonstrate the trends of the hepatitis B infection qualitatively without the effects of immune cells and cytokines

Unlike other organs, the thymus and gonads generate nonuniform cell populations, many members of which perish, and a few survive. While it is recognized that thymic cells are “audited” to optimize an organism’s immune repertoire, whether gametogenesis could be orchestrated similarly to favor high-quality gametes is uncertain. Ideally, such quality would be affirmed at early stages before the commitment

We determined the identity elements of each tRNA isoacceptor for the three domains of life: Eubacteria, Archaea, and Eukarya. Our analyses encompass the most updated and curated available databases using an information theory approach. We obtained a collection of identity clusters for each of the isoacceptors of the 20 canonical amino acids for the three major domains of life. The identity clusters

In this paper, a deterministic model for transmission of an epidemic has been proposed by dividing the total population into three subclasses, namely susceptible, infectious and recovered. The incidence rate of infection is taken as a nonlinear functional along with time delay, and treatment rate of infected is considered as Holling type III functional. We have structured a deterministic transmission

A non-smooth epidemic model with piecewise incidence rate dependent on the derivative of the case number is proposed for the transmission dynamics of an infectious disease with media coverage, enhanced vaccination and treatment policy. This is an implicitly defined system, which is converted into an explicit system with three thresholds by employing the properties of the Lambert W function. We first

The observed spatiotemporal ciliary beat patterns leading to proper mucociliary clearance on multiciliated epithelia are suspected to be the result of self-organizing processes on various levels. Here, we present a simplified pluricellular epithelium model, which intends to make the self-organization of ciliary beating patterns as well as of the associated fluid transport across the airway epithelium

In this paper, a delayed differential model based on the intravenous glucose tolerance test is considered. The conditions to determine stability or instability of the model’s steady state are obtained. We obtain the necessary conditions for the appearance of a bifurcation, and we investigate the direction and stability of the local bifurcation. For this purpose, the normal form theory is used. In addition

The average fitness difference between adjacent sites in a fitness landscape is an important descriptor that impacts in particular the dynamics of selection/mutation processes on the landscape. Of particular interest is its connection to the error threshold phenomenon. We show here that this parameter is intimately tied to the ruggedness through the landscape’s amplitude spectrum. For the NK model

Organisms must maintain proper regulation including defense and healing. Life-threatening problems may be caused by pathogens or by a multicellular organism’s own cells through cancer or autoimmune disorders. Life evolved solutions to these problems that can be conceptualized through the lens of information security, which is a well-developed field in computer science. Here I argue that taking an information

With a few exceptions, the literature on evolutionary transitions in individuality (ETIs) has mostly focused on the relationships between lower-level (particle-level) and higher-level (collective-level) selection, leaving aside the question of the relationship between particle-level and collective-level inheritance. Yet, without an account of this relationship, our hope to fully understand the evolutionary

A stochastic differential game model for animal migration between two habitats under uncertain environment, a new population dynamics model, is formulated. Its novelty is the use of an impulse control formalism to naturally describe migrations with different timings and magnitudes that the conventional models could not handle. Uncertainty of the environment that the population faces with is formulated

Whether or not cooperation is favored in evolutionary games on graphs depends on the population structure and spatial properties of the interaction network. The population structure can be expressed as configurations. Such configurations extend scenarios with a single cooperator among defectors to any number of cooperators and any arrangement of cooperators and defectors on the network. For interaction

In this paper, a fractional-order predator–prey mathematical model has been developed considering Holling type II functional response. Here, we have investigated the interaction dynamics of prey, middle predator and top predator. We assume that the middle predator consumes only the prey, and the top predator consumes only the middle predator. Here, the logistic growth of prey has been considered. Then

The illustrations of the late nineteenth-/twentieth-century scientist/artist Ernst Haeckel, as depicted in his book Art Forms in Nature (originally in German as Kunstformen der Natur, 1898–1904), have been at the intersection of art, biology, and mathematics for over a century. Haeckel’s images of radiolaria (microscopic protozoans described as amoeba in glass houses) have influenced various artists

Ernst Haeckel and Emil du Bois-Reymond were the most prominent champions of Darwin in Germany. This essay compares their contributions to popularizing the theory of evolution, drawing special attention to the neglected figure of du Bois-Reymond as a spokesman for a world devoid of natural purpose. It suggests that the historiography of the German reception of Darwin’s theory needs to be reassessed

As Blackwell (Am Biol Teach 69:135–136, 2007) pointed out, multiple authors have attempted to discredit Haeckel, stating that modern embryological studies have shown that Haeckel’s drawings are stylized or embellished. More importantly, though, it has been shown that the discussion within the scientific community concerning Haeckel’s drawings and the question of whether embryonic similarities are convergent

The vast scientific heritage of Ernst Haeckel, evolutionist and thinker, comprises ecology as well. It is well known that it was he in 1866 introduced the term “ecology” for the science on interaction of the organisms and the environment. Haeckel built his system of the biological science (to be more precise, of the zoological science), including ecology, on the basis of Charles Darwin’s evolutionary

The article aims to clarify the dynamics of the publication of E. Haeckel’s works in Russia, and the evolution of their perception by the authorities, various social groups and scientists in a rapidly changing sociocultural context and in relation to the various stages of the evolutionary synthesis. It is shown that his works were reprinted nearly 50 times. Until the beginning of twentieth century

Nearly 150 years ago, Ernst Haeckel published a three volume monograph on the calcareous sponges. These volumes contained the results of his extensive investigation of the anatomy, reproduction, and development of these marine invertebrate organisms. This paper discusses how Haeckel’s contribution to spongiology was so distinct from that of earlier writers on the natural history of sponges, by focusing

In the course of the second half of the nineteenth century, following the publication of Darwin’s On the Origin of Species (1859) and Haeckel’s Generelle Morphologie der Organismen (1866) (General Morphology of Organisms), the two men interacted like comrades in arms, leading the theory of evolution to victory in the international arena. This relationship broke up during the early decades of the twentieth

This paper offers the first ever published discussion of the ethical treatise Harmonie: Versuch einer monistischen Ethik [Harmony: an attempt at a monistic ethics] by Heinrich Schmidt (1874–1935), one of the leading figures in the circle of Ernst Haeckel. Published near the end of Schmidt’s life (1931), it constituted a kind of summation of decades of intense involvement in the “project” of German

The “German Darwin” Ernst Haeckel was influential not only in Germany, but in non-German-speaking countries as well. Due to the widespread use of German as a language of science in the Russian Empire along with growing Russian–German links in various scientific fields, Haeckel directly and indirectly influenced Russian intellectual landscape. The objective of the present paper is to investigate Haeckel’s

Biological individuality was a hotly debated concept in nineteenth-century German biology, both in botany and in zoology. Much discussion centered on a comparison of higher plants with colonial organisms that are subject to polymorphism and exhibit division of labor among their parts. Building on the work of Matthias Jakob Schleiden, Johannes Müller, Rudolf Leuckart, and especially the botanist Alexander

Detailed analyses into the life cycle of the soil-dwelling microbe Dictyostelium discoideum led to the conclusion that this “social amoeba” practices some form of “non-monoculture farming” via the transfer of bacteria to novel environments. Herein, we show that in myxomycetes (plasmodial slime molds or myxogastrids) a similar “farming symbiosis” has evolved. Based on laboratory studies of two representative

In our era of computers and computer models, the importance of physical or graphical models for both research and education in developmental biology (embryology) is often forgotten or at least underappreciated. Still, one important aspect of embryology is the (evolutionary) developmental anatomy of both human and animal embryos. Here, we present a short history of the visualization of Ernst Haeckel’s

The Haeckel reception in different European countries has received some attention from historians of biology, but the reception in Scandinavia remains relatively unknown. We have found letters to and from Haeckel to Swedish scientists and students in the Ernst Haeckel House in Jena and in the archives of the Royal Swedish Academy of Sciences (RSAS) in Stockholm. Here we present correspondence with

The year 2019 marks the 100th anniversary of the death of Ernst Haeckel, a German zoologist, artist, and philosopher of science, who defended and supplemented Charles Darwin’s system of theories regarding the mechanisms of biological evolution. We briefly recapitulate Haeckel’s remarkable career and reproduce the Laudatio read by the President of the Linnean Society of London (1 July 1908), when Haeckel

Ageing is the leading risk factor for the emergence of cancer in humans. Accumulation of pro-carcinogenic events throughout life is believed to explain this observation; however, the lack of direct correlation between the number of cells in an organism and cancer incidence, known as Peto’s Paradox, is at odds with this assumption. Finding the events responsible for this discrepancy can unveil mechanisms

Dengue is, in terms of death and economic cost, one of the most important infectious diseases in the world. So, its mathematical modeling can be a valuable tool to help us to understand the dynamics of the disease and to infer about its spreading by the proposition of control methods. In this paper, control strategies, which aim to eliminate the Aedes aegypti mosquito, as well as proposals for the

Clonal plants grow horizontally by producing multiple physiological individuals (ramets). We studied clonal growth in a homogeneous environment using a dynamic spatial model based on a stochastic cellular automaton. We investigated different growth forms from the aspect of ramet mortality. Non-steady-state and quasi-steady-state cases were defined, and we determined the number of steps suitable for