Simple signaling games of sexual selection (Grafen’s revisited)

We investigate several versions of a simple game of sexual selection, to explore the role of secondary sexual characters (the “handicap paradox”) with the tools of signaling theory. Our models admit closed form solutions. They are very much inspired by Grafen’s (J Theor Biol 144:517–546, 1990a; J Theor Biol 144:473–516, 1990b) seminal companion papers. By merging and simplifying his two approaches, we identify a not so minor artifact in the seminal study. We propose an alternative model to start with Grafen’s sexual selection theory, with several similarities with Getty (Anim Behav 56:127–130, 1998).     

Inclusive fitness and the sociobiology of the genome

Inclusive fitness theory provides conditions for the evolutionary success of a gene. These conditions ensure that the gene is selfish in the sense of Dawkins (The selfish gene, Oxford University Press, Oxford, 1976): genes do not and cannot sacrifice their own fitness on behalf of the reproductive population. Therefore, while natural selection explains the appearance of design in the living world (Dawkins in The blind watchmaker: why the evidence of evolution reveals a universe without design, W. W. Norton, New York, 1996), inclusive fitness theory does not explain how. Indeed, Hamilton’s rule is equally compatible with the evolutionary success of prosocial altruistic genes and antisocial predatory genes, whereas only the former, which account for the appearance of design, predominate in successful organisms. Inclusive fitness theory, however, permits a formulation of the central problem of sociobiology in a particularly poignant form: how do interactions among loci induce utterly selfish genes to collaborate, or to predispose their carriers to collaborate, in promoting the fitness of their carriers? Inclusive fitness theory, because it abstracts from synergistic interactions among loci, does not answer this question. Fitness-enhancing collaboration among loci in the genome of a reproductive population requires suppressing alleles that decrease, and promoting alleles that increase the fitness of its carriers. Suppression and promotion are effected by regulatory networks of genes, each of which is itself utterly selfish. This implies that genes, and a fortiori individuals in a social species, do not maximize inclusive fitness but rather interact strategically in complex ways. It is the task of sociobiology to model these complex interactions.     

An analysis of a ‘community-driven’ reconstruction of the human metabolic network

Following a strategy similar to that used in baker’s yeast (Herrgård et al. Nat Biotechnol 26:1155–1160, 2008). A consensus yeast metabolic network obtained from a community approach to systems biology (Herrgård et al. 2008; Dobson et al. BMC Syst Biol 4:145, 2010). Further developments towards a genome-scale metabolic model of yeast (Dobson et al. 2010; Heavner et al. BMC Syst Biol 6:55, 2012). Yeast 5—an expanded reconstruction of the Saccharomyces cerevisiae metabolic network (Heavner et al. 2012) and in Salmonella typhimurium (Thiele et al. BMC Syst Biol 5:8, 2011). A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2 (Thiele et al. 2011), a recent paper (Thiele et al. Nat Biotechnol 31:419–425, 2013). A community-driven global reconstruction of human metabolism (Thiele et al. 2013) described a much improved ‘community consensus’ reconstruction of the human metabolic network, called Recon 2, and the authors (that include the present ones) have made it freely available via a database at http://humanmetabolism.org/ and in SBML format at Biomodels (http://identifiers.org/biomodels.db/MODEL1109130000). This short analysis summarises the main findings, and suggests some approaches that will be able to exploit the availability of this model to advantage.     

A commentary on “The Formal Darwinism Project”: there is no grandeur in this view of life

The Formal Darwinism Project is an attempt to use mathematical theory to prove the claim that fitness maximization is the outcome of evolution in nature. Grafen’s (2014, p. 12) conclusion from this project is that “….there is a very general expectation of something close to fitness maximisation, which will convert into fitness-maximisation unless there are particular kinds of circumstances—and further, that fitness is the same quantity for all genetic architectures.” Grafen’s claim appears to mean to him that natural populations are expected to contain individuals whose traits are optimal, i.e., any given trait outperforms all reasonable alternatives. I describe why Grafen’s attempt can never provide a meaningful expectation as to the ubiquity of optimal traits in nature. This is so because it is based upon a misconception of the relationship between theory and empirical analysis. Even if one could use theory in the way Grafen proposes, I describe how his theory is causally incomplete. Finally, I describe how Grafen’s conceptual framework is ambiguous. The Formal Darwinism Project has been inspired by “On The Origin of Species” by Darwin. The great lesson of this book was Darwin’s demonstration of the necessary dialog between theory and data, with each influencing and being influenced by the other. Grafen’s Formal Darwinism Project, an attempt to create understanding of nature by removing data from this dialog, reflects a failure to understand Darwin’s great lesson.     

On the ‘transmission sense of information’

In order to illuminate the role of information in biology, Bergstrom and Rosvall (Biol Philos 26:159–176, 2011a; Biol Philos 26:195–200, 2011b) propose a ‘transmission sense of information’ which builds on Shannon’s theory. At the core of the transmission sense is an appeal to the reduction in uncertainty in receivers and to etiological function. I explore several ways of cashing out uncertainty reduction as well as the consequences of appealing to function.     

Phenomenology of Psychoanalytic Data. A Biosemiotic Framework

In my continuing efforts to build a bridge between psychoanalytic findings and biosemiotics here, as in previous works, ‘biosemiotic’ refers to the hierarchy of meaning-forms (from biological to semiotic-organizations) underlying an updated psychoanalytic model of mind. Within this framework I present a broad range of bio-semiotic phenomena, processes, dynamics, defenses, and universal and unique internalized interpersonal patterns, that in psychoanalysis all commonly fall under the broad heading of the “Unconscious.” Reconceptualized as interpretive data within the purview of a psychoanalytic discourse-semantic this biosemiotic framework posits an epigenetic continuum of human meaning-organizations originating at basic organic levels, moving upward through biological, psycho-somatic and affective expression, proto-semiotic transmissions, represented forms, and finally to explicit linguistic signs and complex symbol systems. In addition to assuming an uninterrupted epigenetic continuum crystallizing in hierarchic organization, this framework accentuates the multilayered and increasingly condensed quality of higher more elaborate organizations of meaning in human communication, drawing attention to persisting biological undercurrents in implied sense, intent, and motivation, all of which impact on repressive/defensive mechanisms. Drawing from previous works (Aragno 1997, 2005, 2008a, b, Psychoanalytic Inquiry 29(1):30–47, 2009, Biosemiotics 3:57–77, 2010, 2011a, Signs 5:71–74, 2011b, Journal of the American Psychoanalytic Association, Centennial Paper, Special Centennial Issue 59(2):239–288, 2011b, Signs 5:29–70, 2011c) in which I labored to update and revise Freud’s first topographical theory of mind, this paper presents the phenomenology of unconscious ‘data’ for the purpose of introducing a diverse range of non-linguistic signifying forms from which psychoanalysts infer mental processes and ‘interpret’ meanings. An important underlying premise regarding psychoanalytic data and its relation to the basic biosemiotic ‘agenda’ is that until grounded in an updated developmental theory of mind inclusive of pre- and proto-semiotic-forms, that is evolutionarily plausible, epistemologically based, and correlates with contemporary neuroscience, the term “sign” is merely an abstract linguistic ‘label’ rather than a mental act with antecedent developmental stages manifesting meanings through different forms and modes of expression. Drawn from the yields of the psychoanalytic method and semantic this revised metatheoretical approach provides insights into the sensory-emotive, bodily origins of unconscious layers of non-linguistic signification thereby expanding our understanding of the formative stages of the ‘semiotic function’ in human evolution. This being the third in a series of papers integrating the yields of psychoanalytic methodology with the underlying premises of ‘Biosemiotics,’ some familiarity with the background knowledge provided in the previous two is strongly recommended.     

The (Paleo)Geography of Evolution: Making Sense of Changing Biology and Changing Continents

During the voyage of the H.M.S. Beagle, Charles Darwin quickly realized that geographic isolation led to significant changes in the adaptation of local flora and fauna (Darwin 1859). Genetic isolation is one of the well-known mechanisms by which adaptation (allopatric speciation) can occur (Palumbi, Annu Rev Ecol Syst 25:547?C72, 1994; Ricklefs, J Avian Biol 33:207?C11, 2002; Burns et al., Evolution 56:1240?C52, 2002; Hendry et al., Science 290:516?C8, 2009). Evolutionary changes can also occur when landmasses converge or are ??bridged.?? An important and relatively recent (Pliocene Epoch) example known as the ??Great American Biotic Interchange?? allowed for the migration of previously isolated species into new ecological niches between North and South America (Webb 1985, Ann Mo Bot Gard 93:245?C57, 2006; Kirby and MacFadden, Palaeogeogr Palaeoclimatol Palaeoecol 228:193?C202, 2005). Geographic isolation (vicariance) or geographic merging (geodispersal) can occur for a variety of reasons (sea level rise, splitting of continents, mountain building). In addition, the growth of a large supercontinent (or breakup) may change the climatic zonation on the globe and form a different type of barrier for species migration. This short review paper focuses on changing paleogeography throughout the Phanerozoic and the close ties between paleogeography and the evolutionary history of life on Earth.     

Formal Darwinism

Two questions are raised for Grafen’s formal darwinism project of aligning evolutionary dynamics under natural selection with the optimization of phenotypes for individuals of a population. The first question concerns mean fitness maximization during frequency-dependent selection; in such selection regimes, not only is mean fitness typically not maximized but it is implausible that any parameter closely related to fitness is being maximized. The second question concerns whether natural selection on inclusive fitness differences can be regarded as individual selection or whether it leads to a departure from the central motivation that led to the formal darwinism project, viz., to show that “Darwinian” evolution through individual selection leads to “good design” or phenotypic adaptation through trait optimization.     

Leges sine moribus vanae: does language make moral thinking possible?

Does language make moral cognition possible? Some authors like Andy Clark have argued for a positive answer whereby language and the ways people use it mark a fundamental divide between humans and all other animals with respect to moral thinking (Clark, Mind and morals: essays on cognitive science and ethics. MIT Press, Cambridge, MA, 1996; Moral Epistemol Nat Can J Philos Suppl XXVI, 2000a; Moral Epistemol Nat Can J Philos Suppl XXVI, 2000b; Philosophy of mental representation. Oxford University Press, Oxford, pp 37–43 and discussion, 44–61, 2002). I take issue with Clark’s view and argue that language is probably unnecessary for the emergence of moral cognition. I acknowledge, however, that humans unlike other animals seem to posses what Haugeland in Philosophy of mental representation. Oxford University Press, Oxford (2002) terms ‘norm-hungriness’: an idiosyncratic need or desire to create and abide by a multitude of norms. Our peculiar norm-hungriness, I suggest, depends on what can be called florid control rather than on language.     

Extending, changing, and explaining the brain

This paper addresses concerns raised recently by Datteri (Biol Philos 24:301–324, 2009) and Craver (Philos Sci 77(5):840–851, 2010) about the use of brain-extending prosthetics in experimental neuroscience. Since the operation of the implant induces plastic changes in neural circuits, it is reasonable to worry that operational knowledge of the hybrid system will not be an accurate basis for generalisation when modelling the unextended brain. I argue, however, that Datteri’s no-plasticity constraint unwittingly rules out numerous experimental paradigms in behavioural and systems neuroscience which also elicit neural plasticity. Furthermore, I propose that Datteri and Craver’s arguments concerning the limitations of prosthetic modelling in basic neuroscience, as opposed to neuroengineering, rests on too narrow a view of the ways models in neuroscience should be evaluated, and that a more pluralist approach is needed. I distinguish organisational validity of models from mechanistic validity. I argue that while prosthetic models may be deficient in the latter of these explanatory virtues because of neuroplasticity, they excel in the former since organisational validity tracks the extent to which a model captures coding principles that are invariant with plasticity. Changing the brain, I conclude, is one viable route towards explaining the brain.     

Typical Cyclical Behavioural Patterns: The Case of Routines,Rituals and Celebrations

The dynamics inherent to the life activity of all living systems presents itself in the form of regular patterns viewed by the observer as taking place in an extended timeline. Routines, rituals and celebrations, each in their own way, are defined by the typical cyclical behavioural patterns exhibited by individuals embedded in specific semiospheres. The particular nature of these semiospheres will determine the distinct patterns of behaviour to be adopted in different life contexts so that existential functions are fulfilled. The restricted and protected family circle normally provides the initial learning environment where the definition of the individual’s Umwelt (von Uexküll 1909, 1934; Ferreira, Biosemiotics 3(1):107–130, 2010, 2011) his/her meaningful world, starts to take shape. This learning process comprehends the progressive identification of distinct physical entities, the development of basic patterns of physical and social behaviour- the incorporation of basic routines and the assignment of meaning to particular events.     

Neural Crest and Olfactory System: New Prospective

Sensory neurons in vertebrates are derived from two embryonic transient cell sources: neural crest (NC) and ectodermal placodes. The placodes are thickenings of ectodermal tissue that are responsible for the formation of cranial ganglia as well as complex sensory organs that include the lens, inner ear, and olfactory epithelium. The NC cells have been indicated to arise at the edges of the neural plate/dorsal neural tube, from both the neural plate and the epidermis in response to reciprocal interactions Moury and Jacobson (Dev Biol 141:243?C253, 1990). NC cells migrate throughout the organism and give rise to a multitude of cell types that include melanocytes, cartilage and connective tissue of the head, components of the cranial nerves, the dorsal root ganglia, and Schwann cells. The embryonic definition of these two transient populations and their relative contribution to the formation of sensory organs has been investigated and debated for several decades (Basch and Bronner-Fraser, Adv Exp Med Biol 589:24?C31, 2006; Basch et al., Nature 441:218?C222, 2006) review (Baker and Bronner-Fraser, Dev Biol 232:1?C61, 2001). Historically, all placodes have been described as exclusively derived from non-neural ectodermal progenitors. Recent genetic fate-mapping studies suggested a NC contribution to the olfactory placodes (OP) as well as the otic (auditory) placodes in rodents (Murdoch and Roskams, J Neurosci Off J Soc Neurosci 28:4271?C4282, 2008; Murdoch et al., J Neurosci 30:9523?C9532, 2010; Forni et al., J Neurosci Off J Soc Neurosci 31:6915?C6927, 2011b; Freyer et al., Development 138:5403?C5414, 2011; Katoh et al., Mol Brain 4:34, 2011). This review analyzes and discusses some recent developmental studies on the OP, placodal derivatives, and olfactory system.     

Two ants (Insecta: Hymenoptera: Formicidae: Formicinae) from the Late Pliocene of Willershausen, Germany, with a nomenclatural note on the genus Camponotites

Two species of the genus Camponotites (Formicidae, Formicinae) are described from the Late Pliocene deposits of Willershausen, Lower Saxony, northern Germany: C. silvestris Steinbach, 1967, and C. steinbachi n. sp. The generic name Camponotites has been established for fossil (Tertiary) ants independently by Steinbach (Bericht der Naturhistorischen Gesellschaft zu Hannover 111:95–102, 1967) and by Dlussky (Trudy paleontologi?eskogo instituta, akademiâ nauk SSSR, 1981), each for materials of different stratigraphical and geographical origin. Though poorly described, Camponotites Steinbach, 1967, and the single included (type) species C. silvestris Steinbach, 1967 (a monotypic species from the Late Pliocene of Willershausen), were based upon indication in the sense of the ICZN. Therefore, both the generic and specific names are valid and available. Camponotites Dlussky, 1981 (and its type species C. macropterus Dlussky, 1981) were certainly introduced correctly and are therefore available, too; but due to its homonymy the generic name is not valid. The revision shows that in this rare case both generic names are not only homonyms but also synonyms.     

Early Humans’ Egalitarian Politics

This paper proposes a model of human uniqueness based on an unusual distinction between two contrasted kinds of political competition and political status: (1) antagonistic competition, in quest of dominance (antagonistic status), a zero-sum, self-limiting game whose stake—who takes what, when, how—summarizes a classical definition of politics (Lasswell 1936), and (2) synergistic competition, in quest of merit (synergistic status), a positive-sum, self-reinforcing game whose stake becomes “who brings what to a team’s common good.” In this view, Rawls’s (1971) famous virtual “veil of ignorance” mainly conceals politics’ antagonistic stakes so as to devise the principles of a just, egalitarian society, yet without providing any means to enforce these ideals (Sen 2009). Instead, this paper proposes that human uniqueness flourished under a real “adapted veil of ignorance” concealing the steady inflation of synergistic politics which resulted from early humans’ sturdy egalitarianism. This proposition divides into four parts: (1) early humans first stumbled on a purely cultural means to enforce a unique kind of within-team antagonistic equality—dyadic balanced deterrence thanks to handheld weapons (Chapais 2008); (2) this cultural innovation is thus closely tied to humans’ darkest side, but it also launched the cumulative evolution of humans’ brightest qualities—egalitarian team synergy and solidarity, together with the associated synergistic intelligence, culture, and communications; (3) runaway synergistic competition for differential merit among antagonistically equal obligate teammates is the single politically selective mechanism behind the cumulative evolution of all these brighter qualities, but numerous factors to be clarified here conceal this mighty evolutionary driver; (4) this veil of ignorance persists today, which explains why humans’ unique prosocial capacities are still not clearly understood by science. The purpose of this paper is to start lifting this now-ill-adapted veil of ignorance, thus uncovering the tight functional relations between egalitarian team solidarity and the evolution of human uniqueness.     

Stukalinia, a new substitute generic name for fossil crinoid Lobocrinus Stukalina non Wachsmuth and Springer 1897 (Echinodermata: Crinoidea)

A new generic name, Stukalinia nom. nov., is proposed for a fossil Ordoviacian crinoid that currently has the preoccupied fossil generic name Lobocrinus Stukalina 1982 non Wachsmuth and Springer (1897), along with a new family name, Stukaliniidae nom. nov., instead of the illegitimate family name Lobocrinidae Stukalina (1982).     

Bringing Homologies Into Focus

Anyone who has skimmed a high school biology textbook will be familiar with the iconic examples of homology that seem inseparable from any explanation of the term: the limb structure of four-legged animals, the human tailbone and the more elaborate tail of monkeys, and the remarkable similarities among the embryological development of fish, birds, and humans. These same examples make their way from edition to edition, along with the classic illustration of an analogous structure: the wings of butterflies, birds, and bats. But is that really all there is to say about homologies and analogies? Several articles in this issue discuss these concepts more deeply in the context of eye evolution (Gregory 2008; Oakley and Pankey 2008; Piatigorsky 2008). Homologies and analogies, it seems, are not a black and white issue—especially when it comes to vision.