Introduction

Viruses enter the brain by many routes. Rabies virus enters via a bite from a rabid bat or animal, replicates locally, crosses the neuromuscular synapse, and travels retrograde to the central nervous system (CNS). Mosquitoes infected with West Nile virus (WNV) sting a bird or mammal; WNV replicates locally and then travels hematogenously, infecting the brain endothelium. Human immunodeficiency virus (HIV), whether the virus entered by injection or semen, enters lymph nodes, replicates, and then is carried to the brain by infected monocytes that traverse the microvascular endothelium and enter the perivascular space, ultimately transmitting HIV to microglia. Other viruses, such as reovirus, replicate in peripheral tissues, circulate as free infectious virions, and can infect the vascular endothelium of the CNS. Viruses can be inhaled and replicate in the olfactory neuroepithelium and spread caudally across the cribriforme plate along the olfactory nerve. Herpes simplex virus (HSV) can infect the eye (keratitis) or the oral or vaginal mucosa, enter the local nerve, and then be transmitted by retrograde passage to a ganglion and sometimes to the CNS, causing encephalitis. Once within the brain, viruses replicate in a variety of cell types and induce local innate immune responses.

Every cell type (endothelial cells, ependymal cells, perivascular macrophages and pericytes, astrocytes, microglia, oligodendrocyes, Schwann cells, and neurons) in the CNS can be infected by different viruses. Viral infections of the CNS challenge the host with a different set of problems than do peripheral viral infections.

Psychobiological propensities stem from the constraints of the human mind/brain and its computational abilities. We are born with diverse forms of cognitive abilities; there should be no mythology about this. The question is, “To what degree?” and here there are legitimate disputes. Our hypothesis-generating abilities exist in the specific culture in which we are immersed, and that shapes our thinking (Mill, 1843/1873; Peirce, 1899/1992); however, some of the categories reflect the cognitive machinations of the mind/brain and how it operates in problem solving with nature and other sentient creatures.

Common categories into which we can organize our responses are those that we inherit and those that we acquire (e.g., Carey & Smith, 1993; Gelman, 2003; Levinson, 1996, 2006; Medin & Atran, 1999). The process of evolution selected for a self-corrective capacity in our ability to get anchored to the world around us (Darwin, 1859/1958; Dewey, 1910/1965). Dewey, for example, understood that science, in part, is an extension of local adaptation or local problem solving.

This chapter focuses on the logic of inquiry from a pragmatist perspective, which, along with a cognitive and/or functional predilection toward kinds of objects, underlies the organization of action (see Johnson, 2007; Schulkin, 2004). Cognition functions in the context of adaptation and action. Cognitive systems are endemic to the organization of action, a common theme for pragmatists (e.g., Dewey, 1896).

Ours is the age of biological knowledge. In the scope of its objectives and in its potential for transforming how we think about our place in the world, the Human Genome Project is the direct descendant of the Manhattan Project. This seemingly incongruous analogy has at its center the common theme of an assembly of scientists working together toward a common end and with great potential power. For the Human Genome Project, that end is deciphering the molecular composition of our genetic heritage.

Experiment lies at the heart of modern science (Dear, 1995; see also Bernard, 1865/1957). The idea of reconstructing who we are, of illuminating a moment in our evolutionary journey, and of knowing in full detail the underlying blueprint and structure of our biological material is the ultimate legacy of Charles Darwin and Gregor Mendel, arguably the progenitors of the modern biological sciences. The depiction of our entire genetic structure is as revolutionary as was Albert Einstein's reconstruction of the world of physics once inhabited by Isaac Newton.

We can only comprehend the radical nature of the Human Genome Project's import because we come prepared to understand the world in terms of agents and action, direction. We come prepared to share and exploit experiences, to form meaningful connections – to be connected to others (Jaspers, 1913/1997).

Humans in the modern world still dwell in a world of contingency and abject uncertainty. Amid this uncertainty is the use of instrumental reason – reason devoted to coping with the lack of certainty in the search for the stable and somewhat secure. Although this state may create great grief and angst (e.g., Heidegger, 1927/1962), it also prompts action and inquiry. Pragmatists such as Dewey emphasized the plasticity of the modern world, the many diverse forms of adaptation and human expression (Margolis, 2002). Dewey (1925/1989) also noted, perhaps somewhat hopefully, that “the natural and original bias of man is all toward the life objective” (p. 14).

Problem solving is rooted in the existential condition of coping with our surroundings. Knowing occurs in interactions with others and with the world, which is a core pragmatist perspective. The knowing process takes place in the life world that we are adapting to, coping with, and trying to make sense of (Dewey, 1925/1989; Godfrey-Smith, 2002).

This chapter begins with an evolutionary account of the cognitive/behavioral adaptations that underlie our sense of agency and inquiry. Coping with and adapting to change are fundamental to a pragmatist perspective (e.g., Johnson, 2007; Schulkin, 1992; Smith, 1970).

To accept and, ultimately, understand evolving conceptions of ourselves and our human past, present, and uncertain future, we need to be educated. No one blueprint should or need be proposed, except that, at the heart, there should be some sense of being experimental, self-corrective, and kind to others. Reason needs to be demythologized and placed in instrumental and incremental units (e.g., Simon, 1962, 1982).

Underlying all forms of learning are cognitive events that set the proper conditions for learning, along with a propensity for self-correction. An experimental spirit is a humbling affair; we are wrong a fair amount of the time, and we should be aware of that. Also, hypotheses are shared – they are tentative.

Our brains are prepared to understand and consider the experiences of others through prosocial dispositions, which set the stage for appreciating others (Darwin 1859/1958, 1871/1874, 1872/1965) and facilitate social skills. We are drawn to tell our autobiographies and give away what we have learned, what we know; the human narrative is a fundamental way in which we learn from and about one another. Narrative tales convey a sense of other people's experience. When this consideration is linked to self-corrective learning and inquiry, our horizons can be broadened; after all, that is why open-mindedness is a virtue.

The human condition is determined on the one hand by our evolutionary history and on the other by pervading historical and social factors. We are thrust out in the world. The process of evolution engendered in humans a desire to compete and to cooperate, to form bonds of intimacy – and to deceive.

To placate the uncertainty and insecurity of existence, science has in some ways replaced the traditional theologies that attempted to satisfy our quest for certainty (Dewey, 1929/1960). Human desire for certain knowledge and boundless security is infinite in scope. Our aspirations rise higher than any barometer we can construct. Whatever science is, it is not about certainty but knowledge. And it does represent one of the glorious treasures of humankind.

A sense of history matters, not because all theories are equally as real but because history, our conception of ourselves, continues to change (Fuller, 1998; Kuhn, 2000). Science, like everything else human, is historically contingent (Dear, 1995, 2006; Hull, 1988; Shapin, 1995, 1996; Todes, 1989, 1997) and always needs to be linked to what matters to the human condition (Polanyi, 1946/1964). Perhaps a phrase from Kuhn is applicable: “post Darwinian/Kantianism” (Kuhn, 2000, p. 164), enriched by lexical entries in the common vocabulary of understanding (Levinson & Jaisson, 2006).

We are historical animals. We pass time, and codify it for endless use. Humans not only use the innate clocks endogenous to our biological system but also expand them to the ontological condition of being part of the larger world. The background for historical sensibility is grounded in our evolutionary past, with the problem-solving toolboxes that underlie both our evolutionary and our cultural pasts. Consider the psychological and neurological mechanisms of memory that underlie our historical sensibility.

William James (1890/1917) understood that memory, like consciousness, is not a thing but a set of adaptive functions. However, one of the more dubious distinctions is that between cognitive and noncognitive systems in memory; procedural or episodic memory is no less cognitive than declarative or semantic memory. It may be less complex, have fewer inferences, and so on, but one side is not noncognitive and the other cognitive. These are all information systems carried by the brain. Making this point does not discount the important differences in these systems, some of which reach an awareness level and are more transparent (declarative memory versus procedural systems: knowing how to do something versus knowing that I know how I know to do something; Mishkin, 1984; Ryle, 1949; Squire, 1987).

Introduction. Spiritual quests are not an aberration or a pathological state. They are, rather, a fundamental need. Moreover, conversions to “seeing” events in a certain way are at the basis of scientific and other forms of experience, as are spiritual quests (Heelan, 1994).

Importantly, as John Dewey (1934/1970) noted in his book A Common Faith, “any activity pursued in behalf of an ideal end against obstacles and in spite of threats of personal loss because of conviction of its general and enduring value is religious in quality” (p. 27). What is important is to provide sustenance for what is valuable and alive (see also Kitcher, 2007). Particularly in an age of theological fundamentalism, self-corrective inquiry, a commitment to nonviolence, and humility serve as useful adjuncts to any investigation of religious belief.

Religious quests are vital human activities and cut across both the sciences and the humanities. Religious sensibility is one thing; religious tyranny is quite another. Religious sensibility, at its normative best, is humble and pluralistic. The approach that I suggest avoids dismissive positivism and dogmatic theological fundamentalism to favor a pious naturalism.

My argument is that religious sensibility – a basic human predilection – needs to be knotted to self-corrective inquiry and humility to avoid religious tyranny, which is no easy chore.

This book emphasizes capturing the worth of human experience, the cognitive base of diverse forms of human activity, and the importance of dissolving the boundaries that decrease the pursuit of knowledge. The line between nature and culture and science and the humanities is and should be quite permeable, and the two are fairly continuous with each other. My hope is to demonstrate this permeability in my investigative approach.

The goal is a union of sorts through a regulative norm of self-corrective inquiry and an appreciation of the hypothetical nature of knowledge production and the embodied cognitive systems that reveal our diverse forms of interpretations and adaptation to circumstances.

Two concepts figure importantly with regard to human action: agency and animacy. The first is the recognition of another person as having beliefs, desires, a sense of experience. The second is the recognition of an object as alive, a piece of biology. Both reflect a predilection in our cognitive architecture and are fundamental to an evolving but fragile sense of humanity.

We need to be rooted to a sense of our evolution, our sense of living things. We need to develop sensibilities that highlight the importance of animate objects and recognize the beliefs and desires of others. Additionally, we need to further develop an educational sense rooted in history (a sense of agency), while still being mindful of the uncertain prospects and diverse threats.

My perspective is rooted in psychobiology, contemporary behavioral and cognitive neuroscience, and classical pragmatism.