Hardwiring: innateness in the age of the brain

“Hardwired” is a term commonly used to describe the properties of certain behaviors or brain regions. As its usage has increased exponentially in the past 50 years, both in popular media and the scholarly literature, the concept appears to have gained a cloak of respectability in scientific discourse. However, its specific meaning is difficult to pinpoint. In this paper, I examine how “hardwired” has been used in the psychological and neuroscientific literature. The analysis reveals two major themes: one centers on certain purported characteristics of behaviors or brain regions, such as fixedness; the other places these and other characteristics within an evolutionary framework. Overall, the analysis reveals a degree of overlap between “hardwiring” and the folk biology concept of innateness. Various complications arise from such overlap, casting doubts on the usefulness and legitimacy of “hardwired” in scientific discourse.     

Plant phenological research enhances ecological restoration

While phenology data (the timing of recurring biological events) has been used to explain and predict patterns related to global change, and to address applied environmental issues, it has not been clearly identified as pertinent for restoration. This opinion article thus aims to raise awareness of the potential of phenology to enhance the quality of restoration projects and ecological restoration theory. We based our analysis on a systematic literature survey carried out in February 2014, searching the words “phenology” or “phenological” in books dealing with restoration, the term “phenolog*” in the journal Restoration Ecology, and the terms “restoration” and “phenolog*” in the database Web of Science until February 2014. We finally selected 149 studies relevant to our goals, and first classified them according to the context in which phenology was addressed. We then analyzed them within the framework of the five key steps of restoration projects: (1) the reference ecosystem; (2) biotic resources; (3) restoration methods; (4) monitoring; and (5) adaptive management. The literature survey showed that phenological information improved decision‐making in the few restoration projects in which it was incorporated. We thus advocate taking phenological data into account at all stages of restoration when appropriate: from the acquisition of baseline data on the reference ecosystem to treatment design, and from restoration action planning and timing to monitoring. Phenological data should at minimum be collected for sown, keystone, dominant, and/or rare species to improve restoration quality. Phenology studies and monitoring should be promoted in future restoration guidelines.     

How to Start a Wet Forest Ablaze: Perspectives on the Question of the Origins of Human Mindedness

This paper is a methodological and theoretical meditation on how some research has approached the question of the evolution of human cognitive traits. I discuss views that explicitly or implicitly endorse a view of human cognition as originating from a cause that can be singled out. Following Ross and Ladyman (2010), I suggest that this “singling-out” strategy correlates with a “container” metaphor that doesn’t fit with the interactive process-ontology of modern physics (Campbell 2009). Instead, Ross and Ladyman as well as Campbell recommend the metaphor of ‘emergence’. The logic and ontology of emergent systems finds resonance with developmental systems theory in biology. I suggest in agreement with Stotz (Phenomenology and the Cognitive Sciences 9(4), 2010) that we view the origins of human mindedness within such a framework.     

The role of fossils in phylogeny reconstruction: Why is it so difficult to integrate paleobiological and neontological evolutionary biology?

Why has it been so difficult to integrate paleontology and “mainstream” evolutionary biology? Two common answers are: (1) the two fields have fundamentally different aims, and (2) the tensions arise out of disciplinary squabbles for funding and prestige. This paper examines the role of fossil data in phylogeny reconstruction in order to assess these two explanations. I argue that while cladistics has provided a framework within which to integrate fossil character data, the stratigraphic (temporal) component of fossil data has been harder to integrate. A close examination of how fossil data have been used in phylogeny reconstruction suggests that neither explanation is adequate. While some of the tensions between the fields may be intellectual “turf wars,” the second explanation downplays the genuine difficulty of combining the distinctive data of the two fields. Furthermore, it is simply not the case that the two fields pursue completely distinct aims. Systematists do disagree about precisely how to represent phylogeny (e.g., minimalist cladograms or trees with varying levels of detail) but given that every tree presupposes a pattern of branching (a cladogram), these aims are not completely distinct. The central problem has been developing methods that allow scientists to incorporate the distinctive bodies of data generated by these two fields. Further case studies will be required to determine if this explanation holds for other areas of interaction between paleontology and neontology.     

Morgan’s Canon, meet Hume’s Dictum: avoiding anthropofabulation in cross-species comparisons

How should we determine the distribution of psychological traits—such as Theory of Mind, episodic memory, and metacognition—throughout the Animal kingdom? Researchers have long worried about the distorting effects of anthropomorphic bias on this comparative project. A purported corrective against this bias was offered as a cornerstone of comparative psychology by C. Lloyd Morgan in his famous “Canon”. Also dangerous, however, is a distinct bias that loads the deck against animal mentality: our tendency to tie the competence criteria for cognitive capacities to an exaggerated sense of typical human performance. I dub this error “anthropofabulation”, since it combines anthropocentrism with confabulation about our own prowess. Anthropofabulation has long distorted the debate about animal minds, but it is a bias that has been little discussed and against which the Canon provides no protection. Luckily, there is a venerable corrective against anthropofabulation: a principle offered long ago by David Hume, which I call “Hume’s Dictum”. In this paper, I argue that Hume’s Dictum deserves a privileged place next to Morgan’s Canon in the methodology of comparative psychology, illustrating my point through a discussion of the debate over Theory of Mind in nonhuman animals.     

A Comprehensive Energy and Economic Assessment of Biofuels: When “Green” Is Not Enough

Referee: Dr. Charles A. S. Hall, Department of Environmental Studies, State University of New York, College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210 Biofuel production systems are sometimes claimed to be able to fill in for future fossil fuel shortages as well as to decrease carbon dioxide emissions and global warming. As such, they are often promoted as a “green” alternative to fossil fuels. I present a comprehensive, system-based case study of biofuel production from maize or corn (Zea mays L.) and evaluate it critically in this review. The case study is taken as an example of the comprehensive approach that I suggest for any energy crop. I conclude that the biofuel option on a large scale is not a viable alternative based on economic, energy and eMergy (amount of available energy [exergy] of one form [usually solar] that is directly or indirectly required to provide a given flow or storage of exergy or matter) analyses of the case study data and estimated possible improvement of yield and efficiency. This is true for developed countries due to their huge energy demand compared with what biofuel options are able to supply as well as for developing countries due to the low yield of their agriculture and competition for land and water for food production. However, biofuels may contribute to optimizing the energy and resource balance of agricultural, livestock, or industrial production systems at an appropriate scale. I present a proposal to integrate ethanol production with industrial activities within a “zero emission framework” as a suggestion for optimization strategies capable of making the biofuel option more sustainable and profitable in those cases where it is appropriate.     

Aquaporin Water Channels

Thank you very much. I am humbled, I am delighted; I am honored. This is every scientist’s dream: to give the Nobel Lecture in Stockholm. But I would not be honest if I did not tell you that I am having a little anxiety being on this platform. I have lectured a number of times in Sweden, and I thought I would share with you some events preceding a special lecture that I gave here a few years ago. Arriving at Arlanda Airport, I waited in line at the Pass Control behind a group of businessmen in suits with briefcases. I heard the first in line asked by the control officer to state the purpose of his visit to Sweden. When the man replied “business,” the officer approved and stamped his passport. One at a time, each stepped forward and was asked the same thing; each answered “business” and was approved. Eventually it was my turn, and I was dressed in rumpled clothes after spending the night in the Economy Minus section of an SAS jetliner. The officer asked me the purpose of my visit, and I said “I am here to give the von Euler Lecture at Karolinska Institute.” The officer immediately looked up, stared at me, and asked, “Are you nervous?” At that point I became intensely nervous and said “Yes, I am a little nervous.” The officer looked up again and stated “Well, you should be!“ So if the lecturers look a little nervous, the problem is at Arlanda.     

Uncovering hidden phylogenetic consensus in large data sets

Many of the steps in phylogenetic reconstruction can be confounded by “rogue” taxa—taxa that cannot be placed with assurance anywhere within the tree, indeed, whose location within the tree varies with almost any choice of algorithm or parameters. Phylogenetic consensus methods, in particular, are known to suffer from this problem. In this paper, we provide a novel framework to define and identify rogue taxa. In this framework, we formulate a bicriterion optimization problem, the relative information criterion, that models the net increase in useful information present in the consensus tree when certain taxa are removed from the input data. We also provide an effective greedy heuristic to identify a subset of rogue taxa and use this heuristic in a series of experiments, with both pathological examples from the literature and a collection of large biological data sets. As the presence of rogue taxa in a set of bootstrap replicates can lead to deceivingly poor support values, we propose a procedure to recompute support values in light of the rogue taxa identified by our algorithm; applying this procedure to our biological data sets caused a large number of edges to move from “unsupported” to “supported” status, indicating that many existing phylogenies should be recomputed and reevaluated to reduce any inaccuracies introduced by rogue taxa. We also discuss the implementation issues encountered while integrating our algorithm into RAxML v7.2.7, particularly those dealing with scaling up the analyses. This integration enables practitioners to benefit from our algorithm in the analysis of very large data sets (up to 2,500 taxa and 10,000 trees, although we present the results of even larger analyses).     

Response to “Different measures of ‘genome-wide’ DNA methylation exhibit unique properties in placental and somatic tissues”

I found the research paper “Different measures of ‘genome-wide’ DNA methylation exhibit unique properties in placental and somatic tissues” by Price ME and colleagues in the June 2012 issue of Epigenetics to be an interesting read, but it contains errors in regards to the use of the MethylFlash Methylated DNA Quantification Kit. The text contained in the “Global DNA Methylation” paragraph under the “Methods” section of the paper claims that the kit was used by “following the manufacturer’s protocol.” I find that this is quite misleading to the reader as we have identified, based on the original electronic publication ahead of print, that the steps had not been correctly carried out.

The original text was the following: “DNA was hybridized to wells treated to have a high affinity for DNA. The wells were washed with a 5-mC-specific capture antibody followed by a detection antibody. The absorbance (or optical density) of each well was measured using a microplate spectrophotometer. Correlation of technical replicates was poor (r = 0.09, p = 0.72) using this kit.” However, the user guide of this kit clearly states that DNA is bound, not hybridized, to the strip wells and that the wells should be washed with the included Wash Buffer rather than a “5-mC-specific capture antibody.”

Therefore, it is not surprising that the result or correlation of replicates was poor and that the authors’ “results were variable” due to improper use of the kit. Based on our quality control tests and feedback from the vast amount of users of this popular kit, the variation between replicates should be less than 10% with R value > 0.9 (p < 0.01), assuming proper user performance according to the product manual.

I hope this helps to correct the misinformation presented in the paper as I feel that it is important to promote accuracy on behalf of the epigenetic research community. I also kindly encourage any users of an Epigentek product to work with our very knowledgeable technical support team should they have any difficulties.     

The death of dignity is greatly exaggerated: Reflections 15 years after the declaration of dignity as a useless concept

Fifteen years ago, Ruth Macklin shook the medical community with her claim in the BMJ that dignity is a useless concept. Her essay provoked a storm of reactions. What have we learned from the debate? In this article I analyse the responses to her essay and the following debate to investigate whether she was right that “[d]ignity is a useless concept in medical ethics and can be eliminated without any loss of content.” While some of the commentaries misconstrued her claim and argue against strawmen, others forcefully maintained that the concept of dignity has functions beyond “respect for persons and their autonomy.” One important point that came out of the debate is that dignity is a generic concept that covers more ground than “respect for persons or their autonomy.” In particular, dignity seems to have a wide range of protective functions as well as having reciprocal, relational, and social aspects. Dignity appears more attributional and norm-formative than respect for persons and autonomy. While the claim that dignity is unclear, vague, and can be used sloganistically seems highly relevant, it is argued that this vagueness fulfils important functions in ethics. Moreover, dismissing dignity because of its lack of clarity has implications for “respect for persons” and “autonomy,” which are also used vaguely and sloganistically. No doubt medical ethics should use as a clear concept as the context requires. Nonetheless, dignity still seems to be a widely used generic concept in ethical debates and doing as much ethical work as “respect for persons” or “respect for autonomy.” Therefore, the death of dignity seems to be greatly exaggerated.     

Marked Point Process: Using Correlation Functions to Explore a Spatial Data Set

The relationship between the locations of the clumps of sprouts, some morphological characteristics of the clumps and the local soil environment in an old sweet chestnut coppice are studied. The theory of marked point process, which has not yet been used extensively in forestry studies, is shown to be adequate for the analysis of this type of spatial data. The marks correspond to morphological characteristics of the clumps: “diameter”, “number of sprouts”, “height at one year”, and “height at three years”. Several covariance functions are described which give a method for exploring the spatial relationships within the stand. Some of these functions are introduced for the first time in an actual statistical analysis. By using these functions, it is shown that the clumps are regularly distributed. The variables “diameter” and “number of sprouts” are strongly spatially negatively correlated, whereas the heights are slightly or not correlated. By categorising the individuals according to the mark values, it is shown that the small clumps tended to be aggregated in the gaps between medium and large clumps. Values of heights in the ties of the distribution are related as well as their spatial correlation to the local soil environment.     

The MIDAS database system

The Molecular Interactive Display and Simulation (MIDAS) database system is a hierarchical database specifically designed for complex macromolecular models, such as proteins and nucleic acids. Each molecular model consists of one or more molecules made up of a linear sequence of smaller units that we refer to loosely as “residues.” Each of these residue units, in turn, is composed of one or more even smaller units called “atoms.” The complete model might consist of a single component molecule, as in the case of a water molecule, or it might be a long chain of more complex residue components, such as in the case of amino acid and nucleic acid sequences. Complex functional groups, such as heme and NADH, can also be specified as single subunit components, and the user can then incorporate these groups into a larger model to form a single complex.The various model component types are defined as arbitrary graphs of atoms with defined starting and ending points. The component type thus defines the connectivity of atoms for that component, as well as the linkage atoms to adjacent model components. Molecular “data” are stored in the “leaves” of the database hierarchy and are therefore directly associated with the atoms of a particular residue component, the component having been specified by type and position in the sequence of residues making up the chain. Individual atom data, however, are not restricted to a specific format or quantity, thereby allowing both flexibility and future extensions to easily be made to the database.     

Invasive species denialism: a reply to Ricciardi and Ryan

This paper offers a defense against ad hominem aspersions cast in this journal by Ricciardi and Ryan (Biol Invasions 20(3):549–553, 2018) who allege that several articles I wrote represent “invasive species denialism” and “science denialism.” I summarize the arguments found in those articles. They are (1) science cannot define ecological “harm” and thus cannot measure its risk; (2) invasion biologists rely on tautologies, i.e., definitions of concepts like “biodiversity” and “ecosystem intactness,” that exclude exotic species; (3) no empirical evidence shows that introduced plants have been significant causes of extinction; (4) biologists cannot tell by observing a species whether it is native or a naturalized alien; and (5) debates over the meanings and measurements of key concepts in invasion biology have passed the point of diminishing returns. These arguments may be wrong but none is “similar to the denialism that has affected climate science and medical science” as Ricciardi and Ryan aver.     

Outgroup sampling in phylogenetics: Severity of test and successive outgroup expansion

Outgroup sampling is a fundamental step in the design of phylogenetic analyses, independent of optimality criterion, taxonomic group, or source of evidence. Studies have demonstrated the efficient analysis of many thousands of terminals, all of which could be included in any empirical investigation, yet outgroup samples typically include only a small number of terminals. Most discussion of outgroup sampling centers on employing “correct” or “appropriate” outgroup terminals to increase “accuracy” or “reliability” by preventing “errors” such as long branch attraction and “incorrect” ingroup rooting. As an alternative, I develop a theory of outgroup sampling grounded in the logic of scientific discovery, whereby the objective is to test nested hypotheses of ingroup topology and character‐state transformation as severely as possible by incorporating outgroup terminals in unconstrained, simultaneous analysis, using background knowledge to select the terminals that have the greatest chance of refuting those hypotheses. This framework provides a logical basis for selecting outgroup taxa but does not provide grounds for limiting the outgroup sample, given that, ceteris paribus, testability and explanatory power increase with the inclusion of additional terminals. Therefore, I propose the ancillary procedure of successively expanding the outgroup sample until ingroup hypotheses become stable (insensitive) to increased sampling, with each expansion guided by the scientific objectives of outgroup sampling. This is a heuristic procedure that does not prevent more outgroup terminals from being sampled or guarantee that ingroup hypotheses will remain insensitive to further outgroup expansion, and it has no bearing on the objective support of a given hypothesis. Nevertheless, it provides an objective, empirical basis for limiting outgroup sampling in a given research cycle. I illustrate this procedure by examining the effect of successive outgroup expansion on the relationships among the poison frog genera Adelphobates, Dendrobates, and Oophaga.     

The cultural construction of gendered bodies: Biology and metaphors of production and destruction*

One way of conceiving of the anthropological task is that of countering the degradations and “dehumanizations” of the “other” to which the species is prone by promoting “transcendent humanization.” However efficiently and professionally anthropologists gather their materials and form them into their ethnographic and ethnologic analyses, may not this “ethical impulse” be postulated as the “final cause” of our efforts? But what could such a sonorous phrase mean ? And what is its relationship to the systematic study of the “differences that make or do not make a difference” in culture to which anthropology has long been devoted? I will argue that it involves a dynamic of categories and that this dynamic is itself an object of systematic study. Recently, for example, some anthropologists have been writing “against culture,” seeing the culture concept and associated theory more as barriers than as benefits to pan‐human understanding. I will argue that this is an instance of “transcendent humanization.” One cannot but be sympathetic to the thrust and merits of this argument. But at the same time one wants to ask what implications it holds for the systematic study and understanding of the other. This article, then, examines some elementary vectors in the “dynamic of the categorical” involved in these and related recent debates which also may be seen in terms of transcendence and humanization: the debate over relativism and the recently emergent debate over “enlightenment mythmaking” in anthropology.     

THE GENOMIC LOCATION OF SEXUALLY ANTAGONISTIC VARIATION: SOME CAUTIONARY COMMENTS

Sexually antagonistic polymorphisms are polymorphisms in which the allele that is advantageous in one sex is deleterious in the other sex. In an influential 1984 paper, W. Rice hypothesized that such polymorphisms should be relatively common on the X chromosome (or on the W in female‐heterogametic species) but relatively rare on the autosomes. Here, I show that there are plausible assumptions under which the reverse is expected to be true, and point out recent studies that give evidence for sexually antagonistic variation on the autosomes. Although more work is needed to resolve the issue, it is premature to conclude that the X chromosome is a “hot spot” for the accumulation of sexually antagonistic variation.     

“If we work in conservation, money will flow our way”: hegemony and duplicity on the Coast of Oaxaca, Mexico

Conservation is the “common discursive framework” through which any meaningful action takes place within a strip of land on the Coast of Oaxaca. What is meant by it is a contested process of class struggle given the strength of regional transformations since 1990. Spearheaded by the tourist industry, conservation is a hegemonic game of duplicity. This article discusses how this is a successful case of “neoliberal conservation” and provides an ideological analysis of such a consensus.     

Ecological theatre and the evolutionary game: how environmental and demographic factors determine payoffs in evolutionary games

In the standard approach to evolutionary games and replicator dynamics, differences in fitness can be interpreted as an excess from the mean Malthusian growth rate in the population. In the underlying reasoning, related to an analysis of “costs” and “benefits”, there is a silent assumption that fitness can be described in some type of units. However, in most cases these units of measure are not explicitly specified. Then the question arises: are these theories testable? How can we measure “benefit” or “cost”? A natural language, useful for describing and justifying comparisons of strategic “cost” versus “benefits”, is the terminology of demography, because the basic events that shape the outcome of natural selection are births and deaths. In this paper, we present the consequences of an explicit analysis of births and deaths in an evolutionary game theoretic framework. We will investigate different types of mortality pressures, their combinations and the possibility of trade-offs between mortality and fertility. We will show that within this new approach it is possible to model how strictly ecological factors such as density dependence and additive background fitness, which seem neutral in classical theory, can affect the outcomes of the game. We consider the example of the Hawk–Dove game, and show that when reformulated in terms of our new approach new details and new biological predictions are produced.