Causal Explanation of Indonesian Forest Fires: Concepts, Applications, and Research Priorities

Problems with studies, claims, and assumptions that have been made about the causes of fires in Indonesia's tropical moist forests are identified, and the kinds of concepts, methods, prioritizing, and data needed to resolve the problems are discussed. Separate sections are devoted to studying ignitions, studying fire susceptibility and fire behavior, and using the goal of causal explanation to guide interdisciplinary research.

Creationist Teaching in School Science: A UK Perspective

The creation/evolution controversy in UK schools made headlines in the national press, on TV, and radio in 2002. Claims were made that creationism was being taught in schools. This article looks at the impact this controversy had on the UK government and how creationism is trying to gain ground in UK state schools by introducing students to Intelligent Design through promotional DVDs. Student attitude surveys eliciting views toward science and religion are examined. Concern is also expressed at how the teaching of evolution through standard textbooks may not deliver a persuasive case for evolutionary theory. The article concludes with a number of implications for researchers, teachers, and schools.

Individual variability of behavioural responses by Wandering Albatrosses (Diomedea exulans) to human disturbance

Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.

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Negotiating Values: Narrative and Exposition

In this paper I focus on the limits of narrative by asking what kinds of things narratives do, and what kinds of texts do related things in other ways. In particular I focus on how narrative genres organise time in relation to value, drawing on functional linguistic models of temporality and evaluation. From a linguistic perspective, the various narrative genres negotiate different kinds of solidarity with listeners, and so the limits of narrative materialise various possibilities for communing in a culture, alongside the potentialities for construing community through related and other genres of discourse—since in general, the limits/possibilities of our language (and attendant modalities of communication) are the limits/possibilities of our social world.

Hennigian Phylogenetic Systematics and the ‘Groundplan’ vs. ‘Post-Groundplan’ Approaches: A Reply to Kukalová-Peck

The recent contribution by Jarmila Kukalová-Peck on Hennigian phylogenetics and hexapod limb evolution is critically evaluated.

Leitlinien zur molekulargenetischen Diagnostik: Fragiles-X und Fragiles-X assoziiertes Tremor/Ataxie Syndrom

Ohne Zusammenfassung

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Marine invertebrates,model organisms,and the modern synthesis: epistemic values,evo-devo,and exclusion

A central reason that undergirds the significance of evo-devo is the claim that development was left out of the Modern synthesis. This claim turns out to be quite complicated, both in terms of whether development was genuinely excluded and how to understand the different kinds of embryological research that might have contributed. The present paper reevaluates this central claim by focusing on the practice of model organism choice. Through a survey of examples utilized in the literature of the Modern synthesis, I identify a previously overlooked feature: exclusion of research on marine invertebrates. Understanding the import of this pattern requires interpreting it in terms of two epistemic values operating in biological research: theoretical generality and explanatory completeness. In tandem, these values clarify and enhance the significance of this exclusion. The absence of marine invertebrates implied both a lack of generality in the resulting theory and a lack of completeness with respect to particular evolutionary problems, such as evolvability and the origin of novelty. These problems were salient to embryological researchers aware of the variation and diversity of larval forms in marine invertebrates. In closing, I apply this analysis to model organism choice in evo-devo and discuss its relevance for an extended evolutionary synthesis.

The connectionist framework for gene regulation

I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability that can be learned by examining the generic features of connectionist networks.

A single operon-encoded form of the acetyl-CoA decarbonylase/synthase multienzyme complex responsible for synthesis and cleavage of acetyl-CoA in <Emphasis Type="Italic">Methanosarcina thermophila</Emphasis>

Methanogens growing on C-1 substrates synthesize 2-carbon acetyl groups in the form of acetyl-CoA for carbon assimilation using the multienzyme complex acetyl-CoA decarbonylase/synthase (ACDS) which contains five different subunits encoded within an operon. In species growing on acetate ACDS also functions to cleave the acetate C-C bond for energy production by methanogenesis. A number of species of Methanosarcina that are capable of growth on either C-1 compounds or acetate contain two separate ACDS operons, and questions have been raised about whether or not these operons play separate roles in acetate synthesis and cleavage. Methanosarcina thermophila genomic DNA was analyzed for the presence of two ACDS operons by PCR amplifications with different primer pairs, restriction enzyme analyses, DNA sequencing and Southern blot analyses. A single ACDS operon was identified and characterized, with no evidence for more than one. MALDI mass spectrometric analyses were carried out on ACDS preparations from methanol- and acetate-grown cells. Peptide fragmentation patterns showed that the same ACDS subunits were present regardless of growth conditions. The evidence indicates that a single form of ACDS is used both for acetate cleavage during growth on acetate and for acetate synthesis during growth on C-1 substrates. Electronic Supplementary Material  Supplementary material is available for this article at

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Rethinking of risk communication: lessons from the decision sciences

Risk communication involves three primary elements: process, content and intent. Much has been written about the first two. Much is known, for example, about the guiding principles that should be considered during the design of a risk communication. Likewise, many studies have been conducted about how best to establish the technical and informational content of a risk communication. Very little attention, by contrast, has been devoted to the intent of risk communication, which is to inform decision making for risk management. While appropriate information upon which to base risk management decisions is important, so to is an understanding of how people instinctively approach decision making under conditions of risk. Work in the decision sciences provides this often-missing perspective for many risk communication efforts and is, therefore, the focus of this paper.

Hierarchical analysis of piecewise affine models of gene regulatory networks

A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions. In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns out to be quite relevant because of the strong discrete structure underlying these equations. Its biological relevance is shown on a 7-dimensional PWA system modeling the gene network responsible for the carbon starvation response in Escherichia coli.

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The strategy of “The strategy of model building in population biology”

In this essay, I argue for four related claims. First, Richard Levins’ classic “The Strategy of Model Building in Population Biology” was a statement and defense of theoretical population biology growing out of collaborations between Robert MacArthur, Richard Lewontin, E. O. Wilson, and others. Second, I argue that the essay served as a response to the rise of systems ecology especially as pioneered by Kenneth Watt. Third, the arguments offered by Levins against systems ecology and in favor of his own methodological program are best construed as “pragmatic”. Fourth, I consider limitations of Levins’ arguments given contemporary population biology.

Politics or metaphysics? On attributing psychological properties to animals

Following recent arguments that there is no logical problem with attributing mental or agential states to animals, I address the epistemological problem of how to go about making accurate attributions. I suggest that there is a two-part general method for determining whether a psychological property can be accurately attributed to a member of another species: folk expert opinion and functionality. This method is based on well-known assessments used to attribute mental states to humans who are unable to self-ascribe due to an early stage of development or impairment, and can be used to describe social and emotional development as well as personality. I describe how instruments such as the Child Behavior Checklist, which relies on intersubjective expert opinion, could be modified to assess other species subjects. The measures are validated via the accuracy of the predictions that are derived, which is an example of the functionality of attribution. I respond to theoretical criticisms against use of this method, and argue that if the method counts as good science for infant cognition research, then it should count as good science for animal cognition research as well. Correspondingly, if the method doesn’t count as good science for animal cognition research, then we must be very skeptical of its use with nonverbal humans.

Defining vision: what homology thinking contributes

The specialization of visual function within biological function is reason for introducing “homology thinking” into explanations of the visual system. It is argued that such specialization arises when organisms evolve by differentiation from their predecessors. Thus, it is essentially historical, and visual function should be regarded as a lineage property. The colour vision of birds and mammals do not function the same way as one another, on this account, because each is an adaptation to special needs of the visual functions of predecessors—very different kinds of predecessors in each case. Thus, history underlies function. We also see how homology thinking figures in the hierarchical classification of visual systems, and how it supports the explanation of visual function by functional role analysis.

Is it a revolution?

Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence properties is also discussed.

Corpus Interruptus: Biotech Drugs, Insurance Providers and the Treatment of Breast Cancer

In researching the biomedically-engineered drug Neulasta (filgrastim), a breast cancer patient becomes aware of the extent to which knowledge about the development and marketing of drugs influences her decisions with regard to treatment. Time spent on understanding the commercial interests of insurers and pharmaceutical companies initially thwarts but ultimately aids the healing process. This first-person narrative calls for physicians to recognize that the alignment of commercial interests transgresses the patient’s humanity.

Salal Harvester Local Ecological Knowledge, Harvest Practices and Understory Management on the Olympic Peninsula, Washington

Despite growing interest in traditional and local ecological knowledge for conservation and resource management, the role of migrant resource users is largely unexplored. Challenging many assumptions about what constitutes “local knowledge,” migrant and immigrant harvesters of non-timber forest products on the Olympic Peninsula, Washington possess useful ecological knowledge of overstory–understory relationships and how forestry practices affect understory biological and commercial production. Harvesters of salal (Gaultheria shallon), a shrub used in the multi-million dollar floral greens industry, were interviewed in Mason County, Washington in 2001–2003. Interviews revealed that harvesters possess different kinds of resource management knowledge depending on whether they are experienced harvesters or more recent newcomers to the area. These differences may also correlate with differences in their harvesting practices. Understanding how resource management knowledge differs between experienced and newcomer harvesters can inform forest managers in their efforts to develop effective management and permitting policies for floral greens and other non-timber forest resources in the Pacific Northwest of the United States.