The role of computation in modeling evolution

Artificial life uses computers and formal systems to model and explore the dynamics of evolution. A fundamental question for A-Life concerns the role of computation in these models, and how we are to interpret computer implementations that do not have actual contact with physical systems. In this paper I will discuss how models are seen to explain and predict in philosophy of science and how these ideas apply to A-Life. I will also explore how the notion of an epistemic cut, as defined by H. Pattee, can be realized in a computational model with an artificial physical world.     

Spatiotemporal population distributions and their implications for species coexistence in a variable environment

A population experiences environmental variation both directly, through effects on life history parameters such as fecundity, and indirectly, through effects on the population distributions of competitors and thus on the distribution of competition. Which spatial and temporal scales of environmental variation most influence the coexistence of two species thus depends in part on the degree to which the resident population responds to different scales of variation. In this paper, I calculate an approximation for a spatiotemporal population distribution as the result of a filter function convolved with the environmental variation. I find that there is no straightforward connection between spatial or temporal scales inherent to an organism's life history, such as mean lifetime or dispersal distance, and the population's sensitivity to variation at different scales. Rather, life history traits interact sensitively with the way environmental variation affects the organism. I comment on the implications for variation-mediated coexistence.     

Some Intellectual Genealogies for the Concept of Everyday Resistance

Concerns with how cultural factors influenced agrarian social change remained an abiding interest in the work of James Scott. I begin by sketching out the context of debates in Marxist theory, development studies, and social and political anthropology that, during the 1980s, turned to relations between ideas, power, and processes of conflict and change in a world of new postcolonial nations and rapid agrarian development. In the article, then, I carefully examine the ideas Scott developed about resistance and hegemony in conversation with the work of E. P. Thompson. Tracing the genealogy of Scott's ideas about hegemony and rural social protest, I comment in some detail on the literature on resistance that arose in anthropology during the 1980s and the role of Scott's Weapons of the Weak (1985) in shaping that literature while interacting with Subaltern Studies (Guha 1982–87), studies of social movements, and examinations of power in interpersonal relations.     

Balancing teaching and research experiences in doctoral training programs: lessons for the future educator

While a variety of alternative careers has emerged for Ph.D. life scientists in industry, business, law, and education in the past two decades, the structure of doctoral training programs in many cases does not provide the flexibility necessary to pursue career experiences not directly related to a research emphasis. Here I describe my efforts to supplement my traditional doctoral research training with independent teaching experiences that have allowed me to prepare myself for a career that combines both into a combined educational program. I describe the issues I have come across in finding and taking part in these endeavors, how these issues have affected my work in pursuing my Ph.D., and how my experiences translate into my hopes for a future education-based career in molecular and cell biology.     

How the genome got a life span

In the space of little more than a decade, ideas of the human genome have shifted significantly, with the emergence of the notion that the genome of an individual changes with development, age, disease, environmental inputs, and time. This paper examines the emergence of the genome with a life span, one that experiences drift, instability, and mutability, and a host of other temporal changes. We argue that developments in chromatin biology have provided the basis for this genomic embodiment of experience and exposure. We analyze how time has come to matter for the genome through chromatin, providing analysis of examples in which the human life course is being explored as a set of material changes to chromatin. A genome with a life span aligns the molecular and the experiential in new ways, shifting ideas of life stages, their interrelation, and the temporality of health and disease.     

The legitimacy of elite gatekeeping

Natasha Warikoo’s study of how students at Harvard, Brown, and Oxford Universities view race and fairness highlights the vast differences between the U.S. and Britain with respect to perceptions of meritocracy by these winners in the competition for places in elite institutions. The strict enforcement of uniform standards for admission is seen as critical and legitimate at Oxford, whereas a more holistic approach in the U.S. – one that sees racial diversity as an important and desirable part of the institution’s culture and identity – is seen as critical to a “diversity bargain”. I question the sources of students’ ideas about race and the diversity bargain, suggesting that they may be rooted more in their pre-college experiences than in their life at university. I also raise questions about whether and how an admissions lottery would work to address some of Warikoo’s concerns.     

Hare on potentiality: a rejoinder

Richard Hare's comment on an article by Lockwood in Bioethics (article and comment appeared in 1988 Jul; 2(3): 187-213, 214-226) pinpoints their crucial disagreement over the extent to which one is entitled to sacrifice the potential for worthwhile life of individuals whose actuality is already an established fact. Lockwood argues that, even though we can all feel gratitude toward our parents for our existence, the obligation one has towards an actual individual not to prevent his or her own potentiality for human life from being realized is far stronger than any obligation one has to bring into existence, or not to prevent from coming into existence, an otherwise merely possible individual with a similar potentiality.     

A Sorrow Shared is a Sorrow Halved: The Search for Empathetic Understanding of Family Members of a Person with Early-Onset Dementia

In this article, I explore how family members of a person with early-onset dementia in the Netherlands attempt to achieve empathetic understanding from significant others, and the barriers they encounter in the process. Based on qualitative interviews, I show that the type of relationship shapes the choices people have to communicate their suffering and their expectations regarding the reactions of others. This article builds on theoretical work on empathy and problematises the notion of shared experiences. It focuses on empathy between family members and significant others, arguing that empathetic understanding between these people is a field of study thus far insufficiently explored.     

Inflective and reflective whiteness in the sociology of race and ethnicity: a comment on an integrative framework for the field

Zulema Valdez and Tanya Golash-Boza offer an integrative framework for the sociology of race and ethnicity to bridge a divide undergirding different, yet related perspectives in the field. Their work provides an initial roadmap for linking the cultural perspectives often taken in the study of ethnicity to the structural perspectives utilized in the study of race. The authors put these perspectives in dialogue with one another to elucidate the strength of integrating commonly used approaches in each area, while avoiding the pitfalls of relying only on one paradigm. Behind much of sociology’s theoretical developments to understand racial and ethnic groups’ experiences in US society, and in relation to global discussions of race and ethnicity as well, are influences of identity and ideological processes inflected and reflected by whiteness. This comment reflects on how these processes can shape future conversations considering the intertwined cultural and structural processes framing group experiences and life chances.     

Economics of coronary artery bypass grafting.

To decide whether the number of operations for coronary artery bypass grafting should be increased, maintained at the present levels, or decreased we need to know how cost effective they are relative to other claimants on the resources of the National Health Service. For this purpose effectiveness is taken to be the effect on life expectancy adjusted for the quality of life. In an assessment of the cost per quality adjusted life year gained coronary artery bypass grafting rates well for cases of severe angina and extensive coronary artery disease. The cost, however, rises sharply for less severe cases. Bypass grafting seems to compare favourably with valve replacement for aortic stenosis and implantation of pacemakers for heart block; it is distinctly better than heart transplantation and the treatment of end stage renal failure but is probably less cost effective than hip replacement. If the number of operations for coronary artery bypass grafting were to increase it would be a fairly strong claimant only if restricted to the most severe cases. The data on which these judgments are based are crude and in need of refinement. The methodology is powerful, far reaching, and open to comment.     

Debates: Challenging a Recent Challenge to the Aggressive Spillover Hypothesis

Kralj‐Fiser et al. recently reviewed the lack of evidence in favor of the aggressive spillover hypothesis, an animal personality/behavioral syndrome explanation for pre‐copulatory sexual cannibalism. In doing so, they evaluated past tests of the hypothesis, set forth their ideas for criteria that need to be met to accept the spillover hypothesis, and conclude that the hypothesis is not generally supported. Here, I comment on several aspects of their position. In doing so, I identify areas in which we differ and point out several strengths of past tests of the spillover hypothesis. In particular, I suggest that researchers testing the spillover hypothesis have done an excellent job of studying sexual cannibalism in the broader context of a movement within behavioral ecology to understand where an animal's behavior falls along a continuum of plasticity.     

Sick Again,Well Again: Sorcery,Christianity and Kinship in Northern Aboriginal Australia

This article concerns the ways in which Yolngu people of the Galiwin'ku settlement in northern Australia employ contemporary constructions of sorcery doctrines and Christian practices to rearticulate their kinship relations. In particular, I discuss the adaptation of sorcery ideas and accusations to present-day circumstances and the Christian healing processes that have emerged alongside traditional healing behaviours and biomedicine. Sorcery and Christianity at Galiwin'ku, I argue, are intertwined ethical models that enable the person and community to heal over and over again in accordance with the vicissitudes of postcolonial life. They continue the moral imperative of ‘looking after’ kin even as the net of ‘looking after’ has expanded to encompass new experiences, behaviours, and persons.     

Designing for emotion (among other things)

Using computational approaches to emotion in design appears problematic for a range of technical, cultural and aesthetic reasons. After introducing some of the reasons as to why I am sceptical of such approaches, I describe a prototype we built that tried to address some of these problems, using sensor-based inferencing to comment upon domestic ‘well-being’ in ways that encouraged users to take authority over the emotional judgements offered by the system. Unfortunately, over two iterations we concluded that the prototype we built was a failure. I discuss the possible reasons for this and conclude that many of the problems we found are relevant more generally for designs based on computational approaches to emotion. As an alternative, I advocate a broader view of interaction design in which open-ended designs serve as resources for individual appropriation, and suggest that emotional experiences become one of several outcomes of engaging with them.     

Some speculations concerning the evolution of photosynthetic function

Following a brief review of the light-driven reactions in photosynthetic membranes, two questions are addressed. (1) Why is the first charge separation reaction in photosynthetic reaction centers so fast; and (2) given what we know about the contemporary structure and function of reaction centers, can we develop a simple model for a much more primitive reaction center? It is proposed that the primary charge separation step in reaction centers is optimized to be ultra-fast principally in order to compete with detrapping into the antenna complex, rather than to compete with radiative and non-radiative losses in the special pair. This leads to a notion of kinetic perfection analogous to that developed for enzymes which operate under diffusion-limited conditions, but elaborated to permit even more ‘perfect’ function. This hypothesis is testable by changing components in photosynthetic membranes and subjecting them to selective pressures. We speculate that the reaction center is far too complex to have served as an early functional unit, and consider possible roles for the iron-quinone part of the reaction center as a very primitive photosynthetic unit. It is suggested that this working end later became associated with primitive antenna complexes, which then evolved into the elaborate structure we find today. The role of photosynthesis in the origin of life has been a topic of speculation for many years. It is evident that photosynthetic function is ancient and central. As a person who does not work in the field of evolution. I am not very familiar with much of the speculation that precedes this paper. Proposals and speculation by others are likely based on much firmer ground, and therefore I apologize in advance if some of these ideas have already been suggested by others. In this chapter I take the liberty to speculate on how a structure as complex as the contemporary photosynthetic reaction center (RC) could have evolved from more primitive units, and why it retains some of its remarkable properties and seemingly unnecessary components. Both subjects lead to specific predictions and testable hypotheses.     

The place of genetics in ageing research

Rapidly increasing numbers of older people present many countries with growing social and economic challenges. Yet despite the far-reaching implications of ageing, its biological basis remains a topic of much debate. Recent advances in genomics have spurred research on ageing and lifespan in human populations, adding to extensive genetic studies being carried out in model organisms. But how far is ageing controlled by our genes? In this Viewpoint, six experts present their opinions and comment on future directions in ageing research.     

A career pathway in protein folding: from model peptides to postreductionist protein science

This review discusses the inherent challenge of linking "reductionist" approaches to decipher the information encoded in protein sequences with burgeoning efforts to explore protein folding in native environments-"postreductionist" approaches. Because the invitation to write this article came as a result of my selection to receive the 2010 Dorothy Hodgkin Award of the Protein Society, I use examples from my own work to illustrate the evolution from the reductionist to the postreductionist perspective. I am incredibly honored to receive the Hodgkin Award, but I want to emphasize that it is the combined effort, creativity, and talent of many students, postdoctoral fellows, and collaborators over several years that has led to any accomplishments on which this selection is based. Moreover, I do not claim to have unique insight into the topics discussed here; but this writing opportunity allows me to illustrate some threads in the evolution of protein folding research with my own experiences and to point out to those embarking on careers how the twists and turns in anyone's scientific path are influenced and enriched by the scientific context of our research. The path my own career has taken thus far has been shaped by the timing of discoveries in the field of protein science; together with our contemporaries, we become part of a knowledge evolution. In my own case, this has been an epoch of great discovery in protein folding and I feel very fortunate to have participated in it.     

Bodies and borders: a new cultural history of medicine

Both medicine and the history of medicine have seen many changes in the last four decades. The way we tell the story of medical developments no longer concentrates on the important doctors and their ideas. The influences of social history in the 1960s and 1970s and cultural history in the 1980s and 1990s have broadened and enriched the interpretations of our medical past. The social historians have helped us to include politics, economics, and the leading ideas of any period we wanted to study; the cultural approach has added ethnography as well as an emphasis on language or discourse.Today there is a new history of medicine, one far more willing to cross disciplinary boundaries to ask questions about how we know what we know and why we do what we do.This article highlights some of the work in the adjoining fields of medical anthropology and of literature and medicine to demonstrate new interests, new questions, and new methods of inquiry. However, although we have cast our nets far more widely in the process of professionalizing the history of medicine, there is a question about whether we have lost the appeal to one of our core constituencies: medical students and physicians. We need to welcome some of the new changes in medical history as in medicine itself; the common goal is to achieve a better understanding of what we have done and what we are doing.     

From illness narratives to social commentary: a Pirandellian approach to "nerves"

The concept of "nerves" is an integral component of the language of distress found in a number of societies. Individuals, however, often extend its meaning well beyond the realm of suffering. In this article, I examine some Sicilian-Canadian uses of "nerves" from a Pirandellian perspective. This, I believe, gives us an insight into how people (1) make use of illness narratives to give meaning to their life experiences, and (2) attempt to influence the thought and behavior of significant others. In the process, I address the question how do we move away from anthropological definitions and explanations that tend to simplify or mask some of the rich complexities surrounding the meaning(s) of "folk" concepts?     

Aliens at home?

If we ponder how alien life might look like on other planets, we don''t have to go far, Simon Conway Morris argues, since life forms on Earth have already pushed life to the limits.When in 1609 Galileo first saw the moons of Jupiter, he must have been spellbound. I was certainly so enrapt when I saw Europa and her three companions strung like a line of jewels. Galileo may have appreciated the irony that my guide was a Jesuit priest, and the somewhat antiquated telescope we used was but a few yards from the Papal summer residence in Castel Gandolfo. Galileo prized open the door and before long, scientific imagination was fired by the prospect of innumerable inhabited worlds. As the centuries progressed, imagination raced ahead of facts, with the Moon optimistically colonized by Selenites, and Mars transformed by immense canals to supply the parched regions of a planet plunging into desertification. From this dying planet H.G. Wells propelled his aliens to terrorize southern England with immense tripods housing sinister octopoids.Now we might be closer to knowing if Wells was in any sense on the right track. The spectacular success in detecting extrasolar planets has produced a roster in excess of 450, and this technology potentially allows us to detect Earth-like planets. Even if many of the known planets are too large to be habitable and lie, for the most part, beyond the inferred ‘habitable zones'', before long we will get some clues as to how densely our galaxy is inhabited. The consensus points in two directions. First, life is a universal. Second, our biosphere will be of almost no use when it comes to comparisons. Let me draw your attention to a remarkably unappreciated fact: if you want to understand aliens, stay at home.Am I serious? After all it is already clear that extrasolar planetary systems are vastly different to our Solar System. Immense planets orbit their suns every few days, their surfaces far more torrid than that of Venus. Other planets most likely possess giant oceans, hundreds of kilometres deep. The diversity of moons and planets in our Solar System is a reminder of what may await us light years from Earth. Even among our neighbours, a case can be made for possible life in the clouds of Venus and Jupiter, the oceans of Europa and hydrocarbon lakes of Titan, and—with perennial optimism—in the permafrost of Mars. We might assume, therefore, that the range of environments available to life, its ‘habitation box'', is gigantic, and that Earth''s biosphere just nestles in one tiny corner. Oddly enough the evidence is exactly the opposite. Life on Earth has reached the limits of what is possible—anywhere.Temperature? The current limit on Earth is 122 °C. Plunging in the opposite direction the evidence is just as remarkable. At temperatures well below freezing, life carries on cheerfully. Even far beyond the eutectic, in which free water cannot form, organisms remain in a state of suspended animation with rates of damage and repair almost precisely matched. What of extreme desiccation? Evidently life has reached the limits of water activity. Entertainingly some of the hardiest forms are fungi that inhabit the weird alien world of Blue Stilton cheese. So, too, the bright colouration of salt pans is a familiar sight, and these osmotic extremes not only host rich microbial faunas but life that can flourish in the most bitter of brines. What of the extremes of pH—bleach versus battery acid? Once again, alkaliphiles and acidophiles disport themselves in ponds and streams that would have the Health and Safety officers in a state of panic. Pressure, either crushingly high or extremely attenuated? Life, of course, exists in the deepest oceanic trenches, but how much deeper might be viable? The weakest link seems to be the pressure sensitivity of the phospholipid membranes, suggesting that even on planets with titanic oceans life won''t survive much deeper than in the Mariana Trench. The same argument applies to the deep crust: at about 5 km the crushingly high pressures also coincide with the thermal limits imposed by the geothermal gradient. Shall we look to the skies? Clouds carry bacteria, but even at quite modest heights it seems to be accidental freight rather than a nebulous ecosystem.Terrestrial life has conquered nearly all of the ‘habitation box'' and its evolution begs so many questions. Are some forms, such as the hyperthermophiles, survivors from the Earth''s apocalyptic beginnings? Maybe, but most have clearly been reinvented several times. Getting to the limits of life isn''t that difficult, but how do extremophiles not only survive but flourish in these environments? Often the adaptations seem minor, which merely means they are more subtle than we might realize. What of the future? So far as the Earth is concerned it must cope with ever increasing solar luminosity: the last men will long predecease the last microbe. Possibly long before, we will engage in the first great galactic diaspora; but wherever our biologists journey they may find that life ‘out there'' got no further than the blue jewel that is Earth.     

‘It's not my story to tell’: ownership and the politics of history in Mocímboa da Praia,Mozambique

The recent history of the northernmost districts of Mozambique has been one of movement and conflict leading people far from their areas of origin and into places where they have to rebuild networks and establish relationships. The Makonde moved from their original area in the Mueda Plateau to neighbouring districts and have to negotiate questions of legitimacy and belonging with the autochthonous population, the Mwani, seen as the ‘owners of the land’ and also the rightful bearers of the histories of the area. Recounting history – owning it – is loaded with references to identity, and weaves in memories and competing experiences of the past. Drawing on literature on history and legitimacy and local understandings of ownership, I discuss the importance of memory and storytelling in the maintenance and reshaping of past events and the different narratives that people create. I investigate how the past is appropriated by different groups and defines belonging by claiming or refusing ownership of local histories.