The expanded evolutionary synthesis—a response to Godfrey-Smith,Haig, and West-Eberhard

In responding to three reviews of Evolution in Four Dimensions (Jablonka and Lamb, 2005, MIT Press), we briefly consider the historical background to the present genecentred view of evolution, especially the way in which Weismann’s theories have influenced it, and discuss the origins of the notion of epigenetic inheritance. We reaffirm our belief that all types of hereditary information—genetic, epigenetic, behavioural and cultural—have contributed to evolutionary change, and outline recent evidence, mainly from epigenetic studies, that suggests that non-DNA heritable variations are not rare and can be quite stable. We describe ways in which such variations may have influenced evolution. The approach we take leads to broader definitions of terms such as ‘units of heredity’, ‘units of evolution’, and ‘units of selection’, and we maintain that ‘information’ can be a useful concept if it is defined in terms of its effects on the receiver. Although we agree that evolutionary theory is not undergoing a Kuhnian revolution, the incorporation of new data and ideas about hereditary variation, and about the role of development in generating it, is leading to a version of Darwinism that is very different from the gene-centred one that dominated evolutionary thinking in the second half of the twentieth century.     

Structural and Narrative Reconstruction of Rural Residents’ Representations of ‘Nature’, ‘Wildlife’, and ‘Landscape’

The objective of this paper is the structural and narrative reconstruction of representations of ‘nature’, ‘wildlife’ and ‘landscape’, held by rural residents of the Dadia Forest Reserve. Data collection involved in-depth interviews. Employing a social representations’ approach, we recovered representational elements that are expected in the case of rural belief systems, such as negative dispositions towards wolves and foxes, as well as elements of an urban adherence, such as nature’s independence. Representational elements refer to visual aspects of the countryside, which seem compatible with the figurative nucleus of the rural idyll. Concerning ‘wildlife’, residents focused on vultures, which comprise the main tourist attraction of the reserve. Scientific knowledge adds to the complexity of the narrative schema, which corresponds to the representation of ‘wildlife’. Interviewees perceived the rural landscape as an interface between the natural and the human-conditioned environment. Our study shows that interviewees make no reference to environmental conservation or quality of life issues, as it could be expected according to relatively wide definitions of the term ‘environmentalism’. Environmental messages reinforced by ecotourism development seem to be recalled primarily in terms of their compatibility with the perceived economic benefit of local people. Despite ecotourism development, representational elements that diverge from a tourist version of ‘nature’, ‘wildlife’ and ‘landscape’ were not pronounced within rural belief-systems. Further interventions within the study area are needed, in order to address a variety of topics under the environmental conservation discourse and raise the environmental awareness of rural residents.     

Expression of a unique plastid-localized heat-shock protein is genetically linked to acquired thermotolerance in wheat

 We have used a combination of molecular and classical genetic approaches to delineate the relationship between a specific HSP member and cell viability under heat stress. Using recombinant inbred lines (RILs) of wheat, derived from a cross of the thermotolerant cultivar ‘Mustang’ and the thermosusceptible cultivar ‘Sturdy,’ we have identified a unique HSP and a differentially expressed cDNA sequence, both related to the plastid-localized HSP26 gene family, that are closely associated with acquired thermotolerance in wheat. An isoform of HSP26 was synthesized under heat stress in all examined thermotolerant RILs and ‘Mustang’, and was absent in all examined thermosusceptible RILs and ‘Sturdy.’ Using a modified differential-display method, we have also identified a gene-specific cDNA sequence that is similar to other known members of the wheat HSP26 gene family and is selectively expressed in ‘Mustang’ and most of the examined thermotolerant RILs, but not expressed in ‘Sturdy’ and all the thermosusceptible RILs. These results suggest a genetic linkage between the acquired thermotolerance trait and the differential expression of a unique member of the HSP26 gene family. Received: 21 April 1997 / Accepted: 2 May 1997     

Technological biology? Things and kinds in synthetic biology

Social scientific and humanistic research on synthetic biology has focused quite narrowly on questions of epistemology and ELSI. I suggest that to understand this discipline in its full scope, researchers must turn to the objects of the field—synthetic biological artifacts—and study them as the objects in the making of a science yet to be made. I consider one fundamentally important question: how should we understand the material products of synthetic biology? Practitioners in the field, employing a consistent technological optic in the study and construction of biological systems, routinely employ the mantra ‘biology is technology’. I explore this categorization. By employing an established definition of technological artifects drawn from the philosophy of technology, I explore the appropriateness of attributing to synthetic biological artifacts the four criteria of materiality, intentional design, functionality, and normativity. I then explore a variety of accounts of natural kinds. I demonstrate that synthetic biological artifacts fit each kind imperfectly, and display a concomitant ontological ‘messiness’. I argue that this classificatory ambivalence is a product of the field’s own nascence, and posit that further work on kinds might help synthetic biology evaluate its existing commitments and practices.     

Microbiology and the species problem

This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes and eukaryotes). Prokaryote biology also undermines recent attempts to save the species category, such as the suggestion that species are metapopulation lineages and the idea that ‘species’ is a family resemblance concept.     

Genetic control theory of developmental events

An earlier theory of cell differentiation and morphogenesis (Wassermann, 1972, 1973, 1978) is combined with the genetic control model of Davidson and Britten (e.g. 1979). The resulting new theory suggests how, bysystematic process algorithms, specifically enumerated combinations of batteries of structural genes can become switched on in particularly enumerated cells, via battery-specific enumerable regulator genes. The systematization is idealized. Up to a certain stage of development in each mitotically arising cell a unique cell-specific combination of structural genes called ‘marker genes’ is active. Marker genes are assumed to code for cell-specifying marker proteins (CSMPs) which permit cells carrying related markers to recognize each other, thus permitting specific cell sorting.Batteries of marker genes could ensure great developmental precision and can safeguard—via redundancies of CSMP types—against accidental loss or detrimental mutational modification of CSMPs or marker genes, respectively. This paper is much concerned with cell lineage in relation to ‘microdifferentiation’, where ‘microdifferentiation’ of a cell refers to a cell's active marker genes and its syntheses of CSMPs. A drastic distinction is made between ‘microdifferentiation’ and ‘gross’ differentiation of a cell, where the same ‘gross’ differentiation may be shared by a large number of cells that could each be uniquely ‘microdifferentiated’. Typical ‘gross’ differentiation could manifest itself in tissue specificity, whereas, up to certain stages of development, all cells of the same gross differentiation type (say tissue specificity) could each be uniquely ‘microdifferentiated’. The theory also assumes that at certain stages of the developmental process some (or in some organisms all) of the previously uniquely specified cells could give rise to small (or occasionally large) clones of equispecified cells, some of which might form clusters that represent complete ‘morphogenetic fields’ Tentative implementation mechanisms are proposed which suggest how the theory could operate in molecular biological terms. In particular, CSMPs could endow cell surface membranes with a highly specific protein network, and an associated equally specific cell surface coat. It is suggested how these highly specified cell surface coats and other systems could provide an ‘extracellular guidance network’ which could help to direct cells to attain energetically optimal locations relative to each other based on the matching of their surface specificities. In numerous experimental situations, where normally present optimal matching of cells is excluded, ‘alternative matching’ based on experiment-specific suboptimal matching could explain many data, notably in experimental development neurobiology (Wassermann, 1978).     

What do the basal ganglia do? A modeling perspective

Basal ganglia (BG) constitute a network of seven deep brain nuclei involved in a variety of crucial brain functions including: action selection, action gating, reward based learning, motor preparation, timing, etc. In spite of the immense amount of data available today, researchers continue to wonder how a single deep brain circuit performs such a bewildering range of functions. Computational models of BG have focused on individual functions and fail to give an integrative picture of BG function. A major breakthrough in our understanding of BG function is perhaps the insight that activities of mesencephalic dopaminergic cells represent some form of ‘reward’ to the organism. This insight enabled application of tools from ‘reinforcement learning,’ a branch of machine learning, in the study of BG function. Nevertheless, in spite of these bright spots, we are far from the goal of arriving at a comprehensive understanding of these ‘mysterious nuclei.’ A comprehensive knowledge of BG function has the potential to radically alter treatment and management of a variety of BG-related neurological disorders (Parkinson’s disease, Huntington’s chorea, etc.) and neuropsychiatric disorders (schizophrenia, obsessive compulsive disorder, etc.) also. In this article, we review the existing modeling literature on BG and hypothesize an integrative picture of the function of these nuclei.     

Necessity,Futility and the Possibility of Defining Life are all Embedded in its Origin as a Punctuated-gradualism

The criteria used for defining life are influenced by various philosophical visions about life, ranging from holism to reductionism and from mechanistic-reductionism to vitalism. Using different scenarios about the origin and evolution of life as well as properties of energy-dissipative systems, artificial life simulations and basic tenets of xenobiology, guidelines can be established for formulating a definition of life. A definition of life is proposed that is parametric, non-Earth-centric, quantitative and capable of discriminating ‘living entities’ from ‘life’. Living entities are defined as self-maintained systems, capable of adaptive evolution individually, collectively or as a line of descend. Life is a broader concept indicating that the capacity to express these attributes is either virtual or actual. At least four major phase transitions can be recognized during the origin of life (reflexive activity; self-regulated homeostasis; the advent of informatons and the origin of adaptive evolution); these make the origin and evolution of early life an example of ‘punctuated gradualism’. Such phase transitions can be used to identify a boundary in early evolution where life began. This contribution identifies the step in the evolution of a dynamic system when digital control of the system’s state becomes dominant over analogical control, and genetic information is irreversibly used for adaptive evolution, as the boundary between non-living and living systems.     

Characterization,Ecological Status and Type-specific Reference Conditions of Surface Water Bodies in Wallonia (Belgium) using Biocenotic Metrics based on Benthic Invertebrate Communities

The river types in Wallonia (Belgium) were defined according to the system B of the European Water Framework Directive (WFD) taking into account obligatory and optional factors synthesized in three criteria: ‘size’, ‘slope’ and ‘natural region’. Under the hypothesis that benthic invertebrate assemblages would be specialized according to river type, a set of 627 faunal samples originating from an 11-year sampling period was tested to characterize river types with faunal assemblages. A multivariate approach led to gather 23 river types into seven groups exhibiting similar faunal assemblages. Using biocenotic metrics based on benthic invertebrate assemblages (e.g., the French standard IBGN), type-specific reference conditions and ecological status class limits were defined for each ‘natural’ river type group. Ecological potential was defined for heavily modified and for artificial (i.e., man-made canals) types. An ‘ecological status’ evaluation strategy was therefore developed and applied in the southern – and more natural – part of Wallonia, where many reference sites were available. In the northern part of Wallonia (i.e., the ‘Loess region’) where no high quality site was available, the expert judgement took a larger part in the definition of the reference conditions and of the ecological status class limits, in addition to the calculations. Two independent distribution gradients of taxa assemblages resulted from multivariate ordination: a first ‘saprobity axis’, as the taxa-sensitivity to organic contamination was increasing from ‘very resistant’ taxa (mainly located in the ‘Loess region’) to ‘sensitive’ and ‘very sensitive’ taxa (from the river types belonging to the Condroz, the Famenne, the Arden and the Jurassic regions) and a second axis characterizing the Meuse-specific faunal assemblage, gathering exotic species and typical limnophilous taxa of large heavily modified rivers. The ecological status monitoring management system developed in this study – i.e., the definition of faunal river type groups, related reference conditions and ecological status class limits – represents a proposal to be integrated in the ecological status assessment of biological elements for the implementation of the WFD and was tested in Wallonia. For the period 2000–2002 involving 349 different sites, the element ‘benthic invertebrate fauna’ was in that way classified ‘high status’ for 31.5% of sites, ‘good status’ for 31.5% and below ‘good status’ for 37% of sites. The best ecological status (i.e., 100% ‘high’ and ‘good’ status) was found in river type ‘Arden’s xenotrophic brooks with strong slope’ and in river types 8large rivers with medium slope’. The worst status was found in river types ‘Loess brooks and rivers with medium slope’.     

Defining Life or Bringing Biology to Life

In the present, post-genomic times, systemic or holistic approaches to living phenomena are compulsory to overcome the limits of traditional strategies, such as the methodological reductionism of molecular biology. In this paper, we propose that theoretical and philosophical efforts to define life also contribute to those integrative approaches, providing a global theoretical framework that may help to deal with or interpret the huge amount of data being collected by current high-throughput technologies, in this so-called ‘omics’ revolution. We claim that two fundamental notions can capture the core of the living, (basic) autonomy and open-ended evolution, and that only the complementary combination of these two theoretical constructs offers an adequate solution to the problem of defining the nature of life in specific enough—but also encompassing enough—terms. This tentative solution should also illuminate, in its most elementary version, the leading steps towards living beings on Earth.     

A consistent terminology for quantifying species diversity? Yes, it does exist

The prevailing terminological confusion around the concept ‘diversity’ has hampered accurate communication and caused diversity issues to appear unnecessarily complicated. In fact, a consistent terminology for phenomena related to (species) diversity is already available. When this terminology is adhered to, diversity emerges as an easily understood concept. It is important to differentiate between diversity itself and a diversity index: an index of something is just a surrogate for the thing itself. The conceptual problem of defining diversity also has to be separated from the practical problem of deciding how to adequately quantify diversity for a community of interest. In practice, diversity can be quantified for any dataset where units of observation (such as individuals) have been classified into types (such as species). All that needs to be known is what proportion of the observed units belong to a type of mean abundance. Diversity equals the inverse of this mean, and it quantifies the effective number of the types of interest. In ecology, interest often (but not always) focuses on species diversity. If the dataset consists of (or gets divided into) subunits, then the total effective number of species (gamma diversity) can be partitioned into the effective number of compositionally distinct subunits (beta diversity) and the mean effective number of species per such subunit (alpha diversity). Species richness is related to species diversity, but they are not the same thing; richness does not take the proportional abundances into account and is therefore the actual—rather than the effective—number of types. Most of the phenomena that have been called ‘beta diversity’ in the past do not quantify an effective number of types, so they should be referred to by names other than ‘diversity’ (for example, species turnover or differentiation).     

An Overview of the Introns-First Theory

We review the introns-first hypothesis a decade after it was first proposed. It is that exons emerged from non-coding regions interspersed between RNA genes in an early RNA world, and is a subcomponent of a more general ‘RNA-continuity’ hypothesis. The latter is that some RNA-based systems, especially in RNA processing, are ‘relics’ that can be traced back either to the RNA world that preceded both DNA and encoded protein synthesis or to the later ribonucleoprotein (RNP) world (before DNA took over the main coding role). RNA-continuity is based on independent evidence—in particular, the relative inefficiency of RNA catalysis compared with protein catalysis—and leads to a wide range of predictions, ranging from the origin of the ribosome, the spliceosome, small nucleolar RNAs, RNases P and MRP, and mRNA, and it is consistent with the wide involvement of RNA-processing and regulation of RNA in modern eukaryotes. While there may still be cause to withhold judgement on intron origins, there is strong evidence against introns being uncommon in the last eukaryotic common ancestor (LECA), and expanding only within extant eukaryotic groups—the ‘very-late’ intron invasion model. Similarly, it is clear that there are selective forces on numbers and positions of introns; their existence may not always be neutral. There is still a range of viable alternatives, including introns first, early, and ‘latish’ (i.e. well established in LECA), and regardless of which is ultimately correct, it pays to separate out various questions and to focus on testing the predictions of sub-theories.     

Aggressive and Docile Colony Defence Patterns in Apis mellifera. A Retreater–Releaser Concept

Colony defence in Apis mellifera involves a variety of traits ranging from ‘aggressive’ (e.g. entrance guarding, recruitment of flying guards) to ‘docile’ (e.g. retreating into the nest) expression. We tested 11 colonies of three subspecies (capensis, scutellata, carnica) regarding their defensiveness. Each colony was selected as reportedly ‘aggressive’, ‘intermediate’ or ‘docile’ and consisted of about 10,000 bees. We applied three stimulation regimes (mechanical disturbance, exposure to alarm pheromones, and the combination of both) and measured their behaviours by tracking the rates of outflying bees at the entrance sites of the test hives. We provided evidence that for mechanical disturbances the test colonies resolved into two response types, if the ‘immediate’ defence response, assessed in the first minute of stimulation, was taken as a function of foraging: ‘releaser’ colonies allocated flying guards, ‘retreater’ colonies reduced the outside-hive activities. This division was observed irrespective of the subspecies membership and maintained in even roughly changing environmental conditions. However, if pheromone and mechanical stimulation were combined, the variety of colony defensiveness restricted to two further types irrespective of the subspecies membership: six of nine colonies degraded their rate of flying defenders with increasing foraging level, three of the colonies extended their ‘aggressiveness’ by increasing the defender rate with the foraging level. Such ‘super-aggressive’ colonies obviously are able to allocate two separate recruitment pools for foragers and flying defenders.     

Fluid and particle passage in three duiker species

Ruminants are characterised by two different types of reticulorumen (RR) physiology. ‘Cattle-type’ ruminants have, amongst other features such as RR contents stratification and a heterogenous intraruminal papillation, a distinct difference between the mean retention time (MRT) of small particles and fluids (the ratio is called the selectivity factor, SF). ‘Moose-type’ ruminants have RR contents that are less stratified, a more homogenous intraruminal papillation and low SFs, indicating less difference in the MRT of small particles and fluids. To date, physiological data indicating a ‘moose-type’ physiology have only been measured in giraffids and Odocoilean cervids, raising the question whether it is limited to these taxonomic groups only. Here, we measured MRTs of fluids and particles in five duikers (Bovidae, Cephalophinae) from three species (Sylvicapra grimmia, Cephalophus monticola and Cephalophus sylvicultor) and found SFs in the RR of 1.27 ± 0.18—well within the range of these other browsers. These results are the first physiological indication that a ‘moose-type’ physiology may also occur in bovid species and thus might represent a true convergent adaptation.     

Energy aspects in LCA of forest products

Intention and Background.  

This paper outlines guidelines for the treatment of energy in LCAs of forest products. The paper is a result of the Cost Action E 9 ‘Life cycle assessment of forestry and forest products’ and reflects the experience of Cost E9 delegates, contributing to Working Group ‘End of life — recycling, disposal and energy generation’.     

Screening of a broad range of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) germplasm for <Emphasis Type="Italic">in vitro</Emphasis> rapid plant regeneration and development of an early prediction system

Rice has emerged as a model monocot for studies in agriculture and biotechnology due to its relatively small genome and a ready accessibility to plant material. Tissue culture is one of the tools required for genetic transformation and some breeding programs, and the selection of high-frequency regenerator types is essential for success in these technologies. Thirty-three rice entries with agricultural and biotechnological characteristics of interest were screened with the aim to identify the best regenerators. Entries that exhibited between 50% and 90% regeneration frequencies include ‘Taipei-309,’ ‘Super Dwarf,’ ‘Norin’ (japonica types), PI 312777, ‘Ali Combo’ (indica types), ‘STG-S,’ and ‘LA3’ (red rice types). One third of the entries tested were at least two times better at regeneration than the often-cited regenerator ‘Nipponbare.’ Those entries showing at least 85% frequency of greening or somatic embryo formation at 15 or 30 d on regeneration medium ultimately produced whole plants after 45 d on regeneration medium at high frequency (at least 40%); those entries not reaching the 85% threshold of greening by Days 15 or 30 exhibited moderate (15–40%) to low (less than 10%) frequency of whole plant regeneration. This greening response suggests the means for an early prediction system for identification of useful rice regenerator lines, which would be beneficial for high-throughput screening of germplasm as well as for decreasing the time and cost of in vitro culture.