What is Life? Defining Life in the Context of Emergent Complexity

Erwin Schrödinger defined life not only as a “self-reproducing” aperiodic crystal of DNA coding for proteins but within the context of living entities increasing their order by dissipating matter/energy gradients to maintain themselves away from equilibirium. Since then most definitions of life have focused on the former. But living cells do more than replicate their DNA. Cells also have membrane barriers across which metabolites must move, via which energy transduction as well as information processing occurs, and within which metabolic transformation occurs. An approach of complex systems dynamics, including nonequilibrium thermodynamics, may provide a more robust approach for defining life than a “naked replicator” at the origin of life. The crucial issue becomes the process of emergence of life from pre-biotic chemistry, concomitant with the emergence of function, information, and semiosis. Living entities can be viewed as bounded, informed autocatalytic cycles feeding off matter/energy gradients, exhibiting agency, capable of growth, reproduction, and evolution. Understanding how life might have emerged should sharpen our definition of what life is.     

TREEasy: An automated workflow to infer gene trees,species trees,and phylogenetic networks from multilocus data

Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user‐friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python—TREEasy—that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ‐Tree), species inference from concatenated data (with IQ‐Tree and RaxML‐NG), species tree inference from gene trees (with ASTRAL, MP‐EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the “WGD clade” of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology ( https://github.com/MaoYafei/TREEasy ).     

Life history focus on a malaria parasite: linked traits and variation among genetic clones

Life history theory has long been a major campaign in evolutionary ecology, but has typically focused only on animals and plants. Life history research on single-celled eukaryotic protists such as malaria parasites (Plasmodium) will offer new insights into the theory’s general utility as well as the parasite’s basic biology. For example, parasitologists have described the Plasmodium life cycle and cell types in exquisite detail, with little discussion of evolutionary issues such as developmental links between traits. We measured 10 life history traits of replicate single-genotype experimental Plasmodium mexicanum infections in its natural lizard host to identify groups of linked traits. These 10 traits formed 4 trait groups: “Rate/Peak” merges measures of growth rate and maximum parasitemia of infections; “Timing” combines time to patency and maximum parasitemia; “Growth Shape” describes the fit to an exponential growth curve; and “Sex Ratio” includes only the gametocyte sex ratio. Parasite genotype (clone) showed no effect on the life history trait groups, with the exception of gametocyte sex ratio. Therefore, variation in most life history traits among infections appears to be driven by environmental (individual host) effects. The findings support the model that life history traits are often linked by developmental constraints. Understanding why life history traits of Plasmodium are linked in this way would offer a new window into the evolution of the parasites, and also should inform public health efforts to control infection prevalence.     

Bemerkungen zur Evolution von., Sprachen bei Säugetieren1 Zur Variabilität innerartlicher Kommunikation bei Caniden

Remarks on the evolution of “languages” of mammals. The variability of the intraspecific communication of canids The canid species mainly considered in this study, the golden jackal (Canis aureus), the cojote (Canis latrans), and especially the wolf (Canis lupus) have an extremely variable species-specific intraspecific communication. Communities, but also differences between the species become evident; the wolf with its distinct social behavior has the greatest differentiation. These results make also clear, that forms of communication in mammals develop in evolutionary processes and events. A safe statement on the beginning of the forms of communication in canids cannot be given so far. This is also true for humans. The ideas of Lenneberg (1967) of the parallel and disjunct origin of the forms of communication in mammals has a high probability for higher systematic units, but on lower systematic level a gradual change can be observed. The forms of communication in mammals are highly differentiated structures, where specific pecularities of the brain are of a special importance. The observations on the variability of intraspecific communication of canids, representing nonhuman mammals, suggest to define “language” in a very general form. In this way, similarities, analogies, and differences between the species of mammals, inclusive man, can be seen more clearly. In only this way the material can be gained to answer the question, if the language of man has in principle exceptional position biologically. It is important for the valuation of forms of intraspecific communication, the “languages”, of mammals not to choose human theory of life and human thinking as a basis, but to start with the biological pecularities of the species. Also canids, as higher mammals, have the ability to abstract, a form of thinking. In their special, species-specific way also non-human mammals arrange their area of experience and thinking. They form for themselves a species-specific “theory of live”. This will of course be different from the human one, according to the systematic position and the biological environment of the species. It is generally accepted that man has special abilities of thinking, he possesses an extraordinary developed brain, compared to all other mammals. This must effect his communication, his language, and result in differences to other mammal species. Gipper (1977) pointed out especially these differences, but they should not be interpreted as differences in principle. Canids use different gestures and sounds for communication within the species; dialog relations can be observed. Different connections of gestures and sounds have different contents of information. It is remarkable that canids do not use their total abilities in using the means of communication in the same way. This is very striking in the change from the wolf, as the only ancestor, to the domestic dog. It is evident that the brain has a greater importance in developing intraspecific communication, than do the peculuarities of organs causing the understanding. A dependanc of intraspecific communication from the environment can be observed either in differences of wird species of canids as well as in the domestication. In the domestic dog, but also in other domestic animals, there is an increase in vocalisations. But the content of information of sounds and gestures decreases in domestication, expressions of arousal become more important. A remarkable plasticity of intraspecific communication becomes evident by domestication. The transformations can be evaluated in the sense of Kosswig (1963, 1965) as first stages of a regressive evolution. Experiments of cross-breeding canid species show exemplarily that forms of communication within these mammal species have a highly polygene regulation, and that processes of learning have an influence. Also from this point of view, no basic differences between nonhuman mammals and humans can be assured, especially when taking into account the facts and thoughts described by Lenneberg. The findings in the canids give useful hints for a better understanding of the human language and its relations to the forms of communication in other mammals. Altogether one can conclude that genetic variability, numerous recombinations, the synorganisation of the processes caused in this way, and natural selection plays definite role in the evolution of “languages”.     

The Cell and Protoplasm as Container,Object, and Substance, 1835–1861

This article revisits the development of the protoplasm concept as it originally arose from critiques of the cell theory, and examines how the term “protoplasm” transformed from a botanical term of art in the 1840s to the so-called “living substance” and “the physical basis of life” two decades later. I show that there were two major shifts in biological materialism that needed to occur before protoplasm theory could be elevated to have equal status with cell theory in the nineteenth century. First, I argue that biologists had to accept that life could inhere in matter alone, regardless of form. Second, I argue that in the 1840s, ideas of what formless, biological matter was capable of dramatically changed: going from a “coagulation paradigm” (Pickstone, 1973) that had existed since Theophrastus, to a more robust conception of matter that was itself capable of movement and self-maintenance. In addition to revisiting Schleiden and Schwann’s original writings on cell theory, this article looks especially closely at Hugo von Mohl’s definition of the protoplasm concept in 1846, how it differed from his primordial utricle theory of cell structure two years earlier. This article draws on Lakoff and Johnson’s theory of “ontological metaphors” to show that the cell, primordial utricle, and protoplasm can be understood as material container, object, and substance, and that these overlapping distinctions help explain the chaotic and confusing early history of cell theory.     

Relative efficiency of using summary versus individual data in random-effects meta-analysis

Meta-analysis is a statistical methodology for combining information from diverse sources so that a more reliable and efficient conclusion can be reached. It can be conducted by either synthesizing study-level summary statistics or drawing inference from an overarching model for individual participant data (IPD) if available. The latter is often viewed as the “gold standard.” For random-effects models, however, it remains not fully understood whether the use of IPD indeed gains efficiency over summary statistics. In this paper, we examine the relative efficiency of the two methods under a general likelihood inference setting. We show theoretically and numerically that summary-statistics-based analysis is at most as efficient as IPD analysis, provided that the random effects follow the Gaussian distribution, and maximum likelihood estimation is used to obtain summary statistics. More specifically, (i) the two methods are equivalent in an asymptotic sense; and (ii) summary-statistics-based inference can incur an appreciable loss of efficiency if the sample sizes are not sufficiently large. Our results are established under the assumption that the between-study heterogeneity parameter remains constant regardless of the sample sizes, which is different from a previous study. Our findings are confirmed by the analyses of simulated data sets and a real-world study of alcohol interventions.     

Mooring “super-diversity” to a brutal migration milieu

The migration milieu in which “super-diversity” locates is not a crisis of human mobility, but a crisis of political imagination to engage with mobility as integral to twenty-first-century citizenship. Western capitalism requires and refutes the migrant, making a volatile life-world of migration in public discourse, policy and everyday life and I engage with whether super-diversity has explanatory cogency for this brutal migration milieu. Vertovec's original outline of super-diversity points to accelerated migrations in which the elaboration of borders have become more multiple and stratified. While migration processes have discernible scale, breadth and pace, I focus on the formative conditions of history, atmosphere and ideology. My aim is to relate processes of diversity-making to the punitive effects of the European border complex. I expand on the politics of contradiction and the fear generated by the migration “crisis”, connected to the discriminatory sorting of migrants sustained by an historic ethos of subordination.     

THE ROLES OF LIFE‐HISTORY SELECTION AND SEXUAL SELECTION IN THE ADAPTIVE EVOLUTION OF MATING BEHAVIOR IN A BEETLE

Although there is continuing debate about whether sexual selection promotes or impedes adaptation to novel environments, the role of mating behavior in such adaptation remains largely unexplored. We investigated the evolution of mating behavior (latency to mating, mating probability and duration) in replicate populations of seed beetles Callosobruchus maculatus subjected to selection on life‐history (“Young” vs. “Old” reproduction) under contrasting regimes of sexual selection (“Monogamy” vs. “Polygamy”). Life‐history selection is predicted to favor delayed mating in “Old” females, but sexual conflict under polygamy can potentially retard adaptive life‐history evolution. We found that life‐history selection yielded the predicted changes in mating behavior, but sexual selection regime had no net effect. In within‐line crosses, populations selected for late reproduction showed equally reduced early‐life mating probability regardless of mating system. In between‐line crosses, however, the effect of life‐history selection on early‐life mating probability was stronger in polygamous lines than in monogamous ones. Thus, although mating system influenced male–female coevolution, removal of sexual selection did not affect the adaptive evolution of mating behavior. Importantly, our study shows that the interaction between sexual selection and life‐history selection can result in either increased or decreased reproductive divergence depending on the ecological context.     

Rethinking the Dismal River Aspect and the plains Athapaskans,A.D. 1692-1768

Abstract

Shortly before A.D. 1650, two major and separate cultural traditions of Plains Apache of mixed horticultural-hunting economies evolved in the central High Plains, both with different origins. The “northern” aspect is identical with the Nebraska Sand Hills Athapaskans, or the “Dismal River proper,” and the result of immigration by people of the Fremont culture. The “Southern Aspect of Plains Apache Tradition,” extending from south of the Platte to the middle Pecos, developed as a response to changes stimulated and introduced by Pueblo farming in western Kansas, the core area of this aspect, after 1639. The history of both traditions and their transformations are described from 1692 to 1768. Archaeological sites in the central High Plains of the first half of this period reflect but an episode in the continuing culture of Plains Athapaskans of both traditions. Archaeological and historical information is used to elucidate the dynamics characteristic of the time and the area. The prehistory and history of a given area is viewed as a changing functional entity over time.     

ON OPTIMAL LEARNING SCHEDULES AND THE MARGINAL VALUE OF CUMULATIVE CULTURAL EVOLUTION

The age‐dependent choice between expressing individual learning (IL) or social learning (SL) affects cumulative cultural evolution. A learning schedule in which SL precedes IL is supportive of cumulative culture because the amount of nongenetically encoded adaptive information acquired by previous generations can be absorbed by an individual and augmented. Devoting time and energy to learning, however, reduces the resources available for other life‐history components. Learning schedules and life history thus coevolve. Here, we analyze a model where individuals may have up to three distinct life stages: “infants” using IL or oblique SL, “juveniles” implementing IL or horizontal SL, and adults obtaining material resources with learned information. We study the dynamic allocation of IL and SL within life stages and how this coevolves with the length of the learning stages. Although no learning may be evolutionary stable, we find conditions where cumulative cultural evolution can be selected for. In that case, the evolutionary stable learning schedule causes individuals to use oblique SL during infancy and a mixture between IL and horizontal SL when juvenile. We also find that the selected pattern of oblique SL increases the amount of information in the population, but horizontal SL does not do so.     

The intracellular pathogen concept

The intracellular pathogen concept classifies pathogenic microbes on the basis of their site of replication and dependence on host cells. This concept played a fundamental role in establishing the field of cellular microbiology, founded in part by Dr. Pascale Cossart, whose seminal contributions are honored in this issue of Molecular Microbiology. The recognition that microbes can access and replicate in privileged compartments within host cells has led to many new and fruitful lines of investigation into the biology of the cell and mechanisms of cell-mediated immunity. However, like any scientific concept, the intracellular pathogen concept can become a dogma that constrains thinking and oversimplifies complex and dynamic host–pathogen interactions. Growing evidence has blurred the distinction between “intracellular” and “extracellular” pathogens and demonstrated that many pathogens can exist both within and outside of cells. Although the intracellular pathogen concept remains useful, it should not be viewed as a rigid classification of pathogenic microbes, which exhibit remarkable variation and complexity in their behavior in the host.     

And One Day There Was a Coup d’état: Notes and Insights from a Photographic Experience at the Paine Memorial

This article reflects upon the expectation, the encounter and redefinition of strategies, based on a concrete field experience: the photographic workshop named “Fotografías Vitales, Memorias Biográficas y Álbumes Familiares” (Life photographs, biographic memories and family albums), developed at the end of 2014 at the Memorial of the locality of Paine, Chile, with participation of members of that Memorial who are relatives of “disappeared” people. This work aims to think ethnographically about the particular ways photographic images can become relevant in life history and memories, as well as how sociopolitical events form part of an individual narration with varying strategies, divergences and convergences, with tensions or omissions.     

Validation of 走肖爲王: Can insects write letters on leaves?

The Annals of the Joseon Dynasty report that large‐scale reformations undertaken by Jungjong, 11th king of the Joseon dynasty, were stopped after Kwang‐Jo Cho was slandered and subsequently executed. Reportedly, a party opposing the reformations wrote a phrase “走肖爲王” on a leaf in the palace by using sugary water; subsequently, insects ingested the sugary parts of leaf and the phrase was left behind. The phrase “走肖爲王” means “Cho will become king” and Jungjong accepted the phrase as a warning sign from heaven that Cho was attempting a coup d'état. Although there are several historical records that report such insect writing, it has not been determined whether creating a phrase on a leaf by using insects is possible. In a field study conducted on Gwanak Mountain, Korea, we tested whether writing letters on leaves by insects is possible. The results showed no sign of selective insect ingestion creating the form of a letter on a leaf after sugary water was applied. There is a high possibility that 走肖爲王 incident was fictional; particularly when considering the complexity of the phrase and the life history and behavior of insects.     

Male–male relationships in chimpanzees and the evolution of human pair bonds

The evolution of monogamy has been a central question in biological anthropology. An important avenue of research has been comparisons across “socially monogamous” mammals, but such comparisons are inappropriate for understanding human behavior because humans are not “pair living” and are only sometimes “monogamous.” It is the “pair bond” between reproductive partners that is characteristic of humans and has been considered unique to our lineage. I argue that pair bonds have been overlooked in one of our closest living relatives, chimpanzees. These pair bonds are not between mates but between male “friends” who exhibit enduring and emotional social bonds. The presence of such bonds in male–male chimpanzees raises the possibility that pair bonds emerged earlier in our evolutionary history. I suggest pair bonds first arose as “friendships” and only later, in the human lineage, were present between mates. The mechanisms for these bonds were co-opted for male-female bonds in humans.     

WI-38 cell long-term quiescence model system: A valuable tool to study molecular events that regulate growth

A number of cell culture model systems have been used to study the regulation of cell cycle progression at the molecular level. In this paper we describe the WI-38 cell long-term quiescence model system. By modulating the length of time that WI-38 cells are density arrested, it is possible to proportionately alter the length of the prereplicative or G-1 phase which the cell traverses after growth factor stimulation in preparation for entry into DNA synthesis. Through studies aimed at understanding the cause and molecular nature of the prolongation of the prereplicative phase, we have determined that gene expression plays an important role in establishing growth factor “competence” and that once the cell becomes “competent” there is a defined order to the molecular events that follow during the remainder of G-1. More specifically, we have determined that the prolongation represents a delay in the ability of long term quiescent cells to become fully “competent” to respond to growth factors which regulate progression through G-1 into S. This prolongation appears to occur as a result of changes during long term quiescence in the ability of immediate early G-1 specific genes (such as c-myc) to activate the expression of early G-1 specific genes (such as ornithine decarboxylase). While ODC is the first and thus far only growth associated gene identified as a target of c-myc (and the Myc/Max protein complex), it is likely that further studies in this model system will reveal other early G-1 growth regulatory genes. We anticipate that future follow-up studies in this model system will provide additional valuable information abuot the function of growth-regulatory genes in controlling growth factor responsiveness and cell cycle progression.     

Developmental plasticity of limb bone microstructural organization in Apateon: histological evidence of paedomorphic conditions in branchiosaurs

SUMMARY Apateon, a key genus among Branchiosauridae from the Carboniferous—Permian of Europe, is often considered closely related to salamanders on the basis of developmental similarities, anatomical features, and life history. The current work deals with recognition of heterochronies among three “time‐averaged populations” of Apateon based on inference from histological features already studied in extant urodeles. Our study is performed on the long bones of 22 specimens of Apateon pedestris and Apateon caducus. Histological observations show that diaphyseal and epiphyseal ossification patterns of Apateon are similar to those of urodeles. From skeletochronological analysis, the identification of the age of sexual maturity allows us to discriminate juveniles from adults and to confirm the previous hypothesis of a paedomorphic condition based on anatomical data among these species. The current study also suggests a paedomorphic condition of each “population” at the histological level. This heterochrony may have been linked to peculiar ecological conditions such as hypoxic and fresh water environment. Functional reasons may also be invoked to explain differences of ossification between fore‐ and hindlimbs of the “populations” from Odernheim and Niederkirchen because paleoecological conditions are very different from one locality to another. This study illustrates the role that the acquisition of heterochronic features plays at the microevolutionary scale.     

Towards “A Natural History of Data”: Evolving Practices and Epistemologies of Data in Paleontology, 1800–2000

The fossil record is paleontology’s great resource, telling us virtually everything we know about the past history of life. This record, which has been accumulating since the beginning of paleontology as a professional discipline in the early nineteenth century, is a collection of objects. The fossil record exists literally, in the specimen drawers where fossils are kept, and figuratively, in the illustrations and records of fossils compiled in paleontological atlases and compendia. However, as has become increasingly clear since the later twentieth century, the fossil record is also a record of data. Paleontologists now routinely abstract information from the physical fossil record to construct databases that serve as the basis for quantitative analysis of patterns in the history of life. What is the significance of this distinction? While it is often assumed that the orientation towards treating the fossil record as a record of data is an innovation of the computer age, it turns out that nineteenth century paleontology was substantially “data driven.” This paper traces the evolution of data practices and analyses in paleontology, primarily through examination of the compendia in which the fossil record has been recorded over the past 200 years. I argue that the transition towards conceptualizing the fossil record as a record of data began long before the emergence of the technologies associated with modern databases (such as digital computers and modern statistical methods). I will also argue that this history reveals how new forms of visual representation were associated with the transition from seeing the fossil record as a record of objects to one of data or information, which allowed paleontologists to make new visual arguments about their data. While these practices and techniques have become increasingly sophisticated in recent decades, I will show that their basic methodology was in place over a century ago, and that, in a sense, paleontology has always been a “data driven” science.     

The Rise of Man's Best Friend: The Popularity of Dogs as Companion Animals in Late Eighteenth-Century London as Reflected by the Dog Tax of 1796

ABSTRACT

The history of the relationship between humans and their companion animals is long and more than a little complex. This is in large part due to the special status of these animals. Over the years these animals have evolved socially from that of an impersonal “object” to a “subject,” i.e. a sentient being with a recognized mental and emotional life. Histories of this change in relationship are rare. This is due mainly to a lack of source material; little is available and what there is is rarely reflective of a general population. Recently, records of a 1796 English dog tax have become available and they provide a fairly complete overview of the status of the dog as a companion animal in late eighteenth-century London.

The evidence indicates the dog was very popular as a companion animal in late eighteenth-century English urban society. While some of these creatures were former working-class canines others were what might be described as “professional companion animals” i.e. creatures who had no previous work history. The tax records further indicate that concern as to specific breed was still in the future. Dogs often received a generic title such as “yard dog” or “lapdog” or “housedog.” What is particularly interesting from these records is the number of mixed breed creatures—animals with the title of either “mongrel” or “curr.” (At least three Londoners kept foxes as pets.) There is also an almost total absence of kennels of hunting dogs in eighteenth-century London. Other historical records suggest this to be a recent phenomenon. Lastly, this outline appears to correlate strongly with the literary remarks, material accoutrements, and even religious practices of the late eighteenth-century urban dog population of England.