The Extended Synthesis: Something Old, Something New

The eclipse of Darwinism began to end in the 1980s and hangs in the balance today. We need an Extended Synthesis, using “extension” metaphorically. We must extend back in time to recover important aspects of Darwinism that were set aside, and then lost during neo-Darwinism, then move forward beyond neo-Darwinism to encompass new data and concepts. The most comprehensive framework for the Extended Synthesis is the Major Transitions in Evolution. The Extended Synthesis rests comfortably within a philosophical perspective in which biology does not need to be connected with other areas of science in order to justify itself. I am attracted to an older concept in which biology needs a covering law to connect it with the rest of the natural sciences. Darwin implicated a “higher law,” but did not specify it. If we can elucidate that law, the Extended Synthesis will become the Unified Theory of Biology called for by Brooks and Wiley 25 years ago.     

Neo-rationalism versus neo-Darwinism: Integrating development and evolution

An increasing number of biologists are expressing discontent with the prevailing theory of neo-Darwinism. In particular, the tendency of neo-Darwinians to adopt genetic determinism and atomistic notions of both genes and organisms is seen as grossly unfair to the body of developmental theory. One faction of dissenteers, the Process Structuralists, take their inspiration from the rational morphologists who preceded Darwin. These neo-rationalists argue that a mature biology must possess universal laws and that these generative laws should be sought within organismal development. Such a rational biology will only be possible once the neo-Darwinian paradigm, with its reliance on inherently stochastic processes, is overthrown.To facilitate this revolution, process structuralism launches a broad attack on the theoritical adequacy of its opponent. It is charged that neo-Darwinism is untestable and therefore its hypotheses are nothing more than adaptive stories. Further, the lamentable tendencies toward genetic determinism and atomism by modern biologists is seen as the inescapable consequences of adopting the neo-Darwinian outlook.I allow that neo-Darwinism is untestable but argue that this does not pose a major difficulty for the theory. Further, it is not clear to what extent genetic determinism and atomism result from sloppy methodology as opposed to fundamental theoritical commitments. But the process structuralist critique does reveal some deep-seated problems with orthodox evolutionary theory and some of its suggestions may be employed to good effect.     

Naturalising purpose: From comparative anatomy to the ‘adventure of reason’

Kant’s analysis of the concept of natural purpose in the Critique of judgment captured several features of organisms that he argued warranted making them the objects of a special field of study, in need of a special regulative teleological principle. By showing that organisms have to be conceived as self-organizing wholes, epigenetically built according to the idea of a whole that we must presuppose, Kant accounted for three features of organisms conflated in the biological sciences of the period: adaptation, functionality and conservation of forms. Kant’s unitary concept of natural purpose was subsequently split in two directions: first by Cuvier’s comparative anatomy, that would draw on the idea of adaptative functions as a regulative principle for understanding in reconstituting and classifying organisms; and then by Goethe’s and Geoffroy’s morphology, a science of the general transformations of living forms. However, such general transformations in nature, objects of an alleged ‘archaeology of nature’, were thought impossible by Kant in §80 of the Critique of judgment. Goethe made this ‘adventure of reason’ possible by changing the sense of ‘explanation’: scientific explanation was shifted from the investigation of the mechanical processes of generation of individual organisms to the unveiling of some ideal transformations of types instantiated by those organisms.     

The effect of the reproductive system on mutation load

J. B. S. Haldane (Amer. Nat. 71, 337–349, 1937) argued that, in equilibrium populations, the effect of deleterious mutation on average fitness depends primarily on the mutation rate and is independent of the severity of the mutations. Specifically, the equilibrium population fitness is e^−μH, where μ_H is the haploid genomic mutation rate. Here we extend Haldane's result to a variety of reproductive systems. Using an analysis based on the frequency of classes of individuals with a specified number of mutations, we show that Haldane's principle holds exactly for haploid sex, haploid apomixis, and facultative haploid sex. In the cases of diploid automixis with terminal fusion, diploid automixis with central fusion, and diploid selfing, Haldane's principle holds exactly for recessive mutations and approximately for mutations with some heterozygous effect. In the cases of K-ploid apomixis, diploid endomitosis, and haplodiploidy, we show that Haldane's principle holds exactly for recessive lethal mutations. In addition we extend Haldane's result to various mixtures of the above-mentioned reproductive systems. In the case of diploid out-crossing sexuals, we do not obtain an exact analytic result, but present arguments and computer simulations which show that Haldane's result extends to this case as well in the limit as the number of loci becomes large. Although diverse reproductive systems are equally fit at equilibrium, different reproductive systems harbor vastly different numbers of recessive genes at equilibrium and we provide estimates of these numbers. These different numbers of mutations may create transient selective pressures on individuals with reproductive systems different from that of the equilibrium population.     

The uncertain foundation of neo-Darwinism: metaphysical and epistemological pluralism in the evolutionary synthesis

The Evolutionary Synthesis is often seen as a unification process in evolutionary biology, one which provided this research area with a solid common theoretical foundation. As such, neo-Darwinism is believed to constitute from this time onward a single, coherent, and unified movement offering research guidelines for investigations. While this may be true if evolutionary biology is solely understood as centred around evolutionary mechanisms, an entirely different picture emerges once other aspects of the founding neo-Darwinists’ views are taken into consideration, aspects potentially relevant to the elaboration of an evolutionary worldview: the tree of life, the ontological distinctions of the main cosmic entities (inert matter, biological organisms, mind), the inherent properties of self-organizing matter, evolutionary ethics, and so on. Profound tensions and inconsistencies are immediately revealed in the neo-Darwinian movement once this broader perspective is adopted. This pluralism is such that it is possible to identify at least three distinct and quasi-incommensurable epistemological/metaphysical frameworks as providing a proper foundation for neo-Darwinism. The analysis of the views of Theodosius Dobzhansky, Bernhard Rensch, and Ernst Mayr will illustrate this untenable pluralism, one which requires us to conceive of the neo-Darwinian research agenda as being conducted in more than one research programme or research tradition at the same time.     

Candida albicans‐associated sepsis in a pre‐term neonatal rhesus macaque (Macaca mulatta)

Invasive Candida infections (ICI) have been associated with neurodevelopmental impairment or death in human pre‐term neonates. Candidiasis in nonhuman primates is seen mostly in immunosuppressed animals, and ICI is not commonly reported. Here, we report a case of Candida albicans‐associated ICI in a pre‐term neonatal rhesus macaque.     

Celebrating a life by recognizing realities

This special issue on nonhuman primate behavior and welfare, the proceedings of a special Animal Behavior Society session, celebrates the life of Dr. Sylvia Taylor (1963-2005). Sylvia's premature death reminded her friends to recognize the reality that life is short, but one can make the most of it. Many individuals and organizations have also recognized the reality that an educational venture such as this one requires adequate funding and support. Their generosity has made this undertaking a success. The idea behind the session was to recognize the reality that one cannot ensure nonhuman animal welfare without understanding animal behavior, and to explore the ways in which this principle applies to primates. One must also recognize the reality that nonhuman primate welfare depends on understanding the behavior of the human primate as well as the nonhuman primate. Ensuring the welfare of the nonhuman primate sometimes requires educating and motivating the human primate. This special issue will hopefully provide helpful information to increase the reader's knowledge of primate behavior and welfare and to help the reader educate others on these important topics.     

State-dependent decisions cause apparent violations of rationality in animal choice

Normative models of choice in economics and biology usually expect preferences to be consistent across contexts, or “rational” in economic language. Following a large body of literature reporting economically irrational behaviour in humans, breaches of rationality by animals have also been recently described. If proven systematic, these findings would challenge long-standing biological approaches to behavioural theorising, and suggest that cognitive processes similar to those claimed to cause irrationality in humans can also hinder optimality approaches to modelling animal preferences. Critical differences between human and animal experiments have not, however, been sufficiently acknowledged. While humans can be instructed conceptually about the choice problem, animals need to be trained by repeated exposure to all contingencies. This exposure often leads to differences in state between treatments, hence changing choices while preserving rationality. We report experiments with European starlings demonstrating that apparent breaches of rationality can result from state-dependence. We show that adding an inferior alternative to a choice set (a “decoy”) affects choices, an effect previously interpreted as indicating irrationality. However, these effects appear and disappear depending on whether state differences between choice contexts are present or not. These results open the possibility that some expressions of maladaptive behaviour are due to oversights in the migration of ideas between economics and biology, and suggest that key differences between human and nonhuman research must be recognised if ideas are to safely travel between these fields.     

Rank atmospheres: The more‐than‐human scentspace and aesthetic of a pigdogging hunt

Pigdogging is a popular pastime in Australia, a form of recreational hunting whereby people collaborate with dogs to chase and catch wild pigs. This paper analyses the hunt as an interspecies event that unfolds through the sensual and sensory entanglements of human and nonhuman, with a particular focus on the perspectives of the hunters. The concept of ‘atmosphere’ will be employed to frame an ethnographic analysis of two facets of pigdogging. First, by hunting with a dog, humans augment their capacity to identify the presence of pigs through the canine's extraordinary sense of scent. Through this relationship, the world of scent is revealed as having atmospheric properties: an enveloping phenomenon which is known through the dog, yet also escapes the hunter's perceptual apprehension. Second, this paper will illustrate examples of how atmosphere develops through the sensual relations between human and nonhuman bodies during the hunt. An affectively charged interspecies encounter is composed and participated in by the hunter through this recreational practice, and affords the enactment of subjectivities central to an aesthetics of pigdogging. Hunting atmospheres in this paper emerge at the juncture of human and more‐than‐human bodies, perspectives and worlds.     

The rebirth of rational morphology

This paper examines a new challenge to neo-Darwinism, a movement known as process structuralism. The process structuralist critique of neo-Darwinism holds 1) that there are general laws in biology and that biologists should search for these laws; 2) that there are general forms of morphology and development and that biologists should attempt to uncover these forms; 3) that organisms are unified wholes that cannot be understood without adopting a holistic perspective; and 4) that no special, causal primacy should be given to the genes in development and morphology. This paper places process structuralism in its historical context, examines the philosophical underpinnings of the movement, and discusses some of the evidence used to support its claims.     

Micro-economics based resource allocation in Grid-Federation environment

A Grid-Federation environment is composed of a collection of autonomous and selfish distributed cluster resource managers. These selfish managers participate in Grid-Federation to share their resources. Market models could be used to motivate the self-interested participants to share their resources. In this paper, firstly, a market for resource exchange in grid federation environment is established. Then, in order that the market reaches a Walrasian equilibrium, a computationally tractable mechanism is proposed. A Walrasian equilibrium problem consists of finding a set of prices and allocations of resources in such a way that the cluster resource managers could maximize their utilities and the market clears. Market clears when the resource supply equals to the demand. We show that in a Walrasian equilibrium, the Grid Federation market reaches an efficient resource allocation.     

Silencing of the tobacco pollen pectin methylesterase NtPPME1 results in retarded in vivo pollen tube growth

Sperm delivery in flowering plants requires extensive pollen tube growth through the female sporophytic tissues of the pistil. The apical cell wall emerges as a central player in the control of pollen tube growth, since it provides strength to withstand the internal turgor pressure, while imparting sufficient plasticity to allow cell wall extension through the incorporation of new membrane and wall material. Within this scenario, pectin methylesterases (PMEs; EC 3.1.1.11) emerge as crucial regulators in determining the mechanical properties of pectins, the major component of the apical pollen tube wall. We previously identified NtPPME1, a pollen specific PME from Nicotiana tabacum. Here we show that silencing of NtPPME1 results in a mild but significant decrease of in vivo pollen tube growth while the overall PME activity in pollen is not significantly affected. Although the precise mechanisms responsible for the observed phenotype are not known, it seems likely that the cell must maintain a closely regulated level of PME activity in order to maintain the equilibrium between strength and plasticity in the apical cell wall. A relatively minor disturbance of this equilibrium, as caused by NtPPME1 silencing, compromises pollen tube growth.     

Acoustic structure of male loud-calls support molecular phylogeny of Sumatran and Javanese leaf monkeys (genus <Emphasis Type="Italic">Presbytis</Emphasis>)

Background  

The degree to which loud-calls in nonhuman primates can be used as a reliable taxonomic tool is the subject of ongoing debate. A recent study on crested gibbons showed that these species can be well distinguished by their songs; even at the population level the authors found reliable differences. Although there are some further studies on geographic and phylogenetic differences in loud-calls of nonhuman primate species, it is unclear to what extent loud-calls of other species have a similar close relation between acoustic structure, phylogenetic relatedness and geographic distance. We therefore conducted a field survey in 19 locations on Sumatra, Java and the Mentawai islands to record male loud-calls of wild surilis (Presbytis), a genus of Asian leaf monkeys (Colobinae) with disputed taxanomy, and compared the structure of their loud-calls with a molecular genetic analysis.     

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”.     

Evaluation of "unique" aspects of human vertebral bodies and pedicles with a consideration of Australopithecus africanus

Recent functional studies of human vertebrae have revealed that loads borne by the axial skeleton during bipedal postures and locomotion pass through the pedicles and posterior elements as well as through the bodies and discs. Accordingly, particular morphological attributes of these vertebral elements have been linked exclusively with bipedalism. In order to test the validity of current form-function associations in human vertebral anatomy, this study considers the morphology of human thoracolumbar vertebral bodies and pedicles in the context of a wide comparative primate sample. The last lumbar vertebra of STS 14 (Australopithecus africanus) is also included in the analysis. Results indicate that certain features of human vertebrae previously thought to reflect bipedalism are characteristic of several nonhuman primates, including those whose posture is habitually pronograde. These features include the decrease in vertebral body surface area and the increase in cross-sectional area of the pedicle between the penultimate and last lumbar vertebra. In addition, although humans have relatively large and wide last lumbar pedicles, the enlargement and widening of the pedicle between the penultimate and last lumbar vertebra is not unique to humans. On the other hand, human vertebrae do exhibit several unique adaptations to bipedal posture and locomotion: (1) the vertebral body surface areas of the lower lumbar vertebrae and the cross-sectional areas of the last lumbar pedicles are large relative to body size, and (2) the last lumbar pedicles are wider relative to length and to body size than are those of nonhuman primates. The last lumbar vertebra of STS 14 does not exhibit any of these human-like vertebral features—its pedicles and body surface areas are relatively small, and its pedicles are not relatively wide, but relatively short.     

Higher Gene Duplicabilities for Metabolic Proteins Than for Nonmetabolic Proteins in Yeast and <Emphasis Type="Italic">E. coli</Emphasis>

Although the evolutionary significance of gene duplication has long been appreciated, it remains unclear what factors determine gene duplicability. In this study we investigated whether metabolism is an important determinant of gene duplicability because cellular metabolism is crucial for the survival and reproduction of an organism. Using genomic data and metabolic pathway data from the yeast (Saccharomyces cerevisiae) and Escherichia coli, we found that metabolic proteins indeed tend to have higher gene duplicability than nonmetabolic proteins. Moreover, a detailed analysis of metabolic pathways in these two organisms revealed that genes in the central metabolic pathways and the catabolic pathways have, on average, higher gene duplicability than do other genes and that most genes in anabolic pathways are single-copy genes.Reviewing Editor: Dr. Rüdiger Cerff     

Genetic analysis of the human infective trypanosome <Emphasis Type="Italic">Trypanosoma brucei gambiense</Emphasis>: chromosomal segregation,crossing over,and the construction of a genetic map

Background  

Trypanosoma brucei is the causative agent of human sleeping sickness and animal trypanosomiasis in sub-Saharan Africa, and it has been subdivided into three subspecies: Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, which cause sleeping sickness in humans, and the nonhuman infective Trypanosoma brucei brucei. T. b. gambiense is the most clinically relevant subspecies, being responsible for more than 90% of all trypanosomal disease in humans. The genome sequence is now available, and a Mendelian genetic system has been demonstrated in T. brucei, facilitating genetic analysis in this diploid protozoan parasite. As an essential step toward identifying loci that determine important traits in the human-infective subspecies, we report the construction of a high-resolution genetic map of the STIB 386 strain of T. b. gambiense.     

Two organizing principles of vocal production: Implications for nonhuman and human primates

Vocal communication in nonhuman primates receives considerable research attention, with many investigators arguing for similarities between this calling and speech in humans. Data from development and neural organization show a central role of affect in monkey and ape sounds, however, suggesting that their calls are homologous to spontaneous human emotional vocalizations while having little relation to spoken language. Based on this evidence, we propose two principles that can be useful in evaluating the many and disparate empirical findings that bear on the nature of vocal production in nonhuman and human primates. One principle distinguishes production-first from reception-first vocal development, referring to the markedly different role of auditory-motor experience in each case. The second highlights a phenomenon dubbed dual neural pathways, specifically that when a species with an existing vocal system evolves a new functionally distinct vocalization capability, it occurs through emergence of a second parallel neural pathway rather than through expansion of the extant circuitry. With these principles as a backdrop, we review evidence of acoustic modification of calling associated with background noise, conditioning effects, audience composition, and vocal convergence and divergence in nonhuman primates. Although each kind of evidence has been interpreted to show flexible cognitively mediated control over vocal production, we suggest that most are more consistent with affectively grounded mechanisms. The lone exception is production of simple, novel sounds in great apes, which is argued to reveal at least some degree of volitional vocal control. If also present in early hominins, the cortically based circuitry surmised to be associated with these rudimentary capabilities likely also provided the substrate for later emergence of the neural pathway allowing volitional production in modern humans.     

Observed octameric assembly of a Plasmodium yoelii peroxiredoxin can be explained by the replacement of native “ball‐and‐socket” interacting residues by an affinity tag

Peroxiredoxins (Prxs) are ubiquitous and efficient antioxidant enzymes crucial for redox homeostasis in most organisms, and are of special importance for disease‐causing parasites that must protect themselves against the oxidative weapons of the human immune system. Here, we describe reanalyses of crystal structures of two Prxs from malaria parasites. In addition to producing improved structures, we provide normalizing explanations for features that had been noted as unusual in the original report of these structures (Qiu et al., BMC Struct Biol 2012;12:2). Most importantly, we provide evidence that the unusual octameric assembly seen for Plasmodium yoelii Prx1a is not physiologically relevant, but arises because the structure is not of authentic P. yoelii Prx1a, but a variant we designate PyPrx1a^N* that has seven native N‐terminal residues replaced by an affinity tag. This N‐terminal modification disrupts a previously unrecognized, hydrophobic “ball‐and‐socket” interaction conserved at the B‐type dimer interface of Prx1 subfamily enzymes, and is accommodated by a fascinating two‐residue “β‐slip” type register shift in the β‐strand association at a dimer interface. The resulting change in the geometry of the dimer provides a simple explanation for octamer formation. This study illustrates how substantive impacts can occur in protein variants in which native residues have been altered.