Discussion: Three Ways to Misunderstand Developmental Systems Theory

Developmental systems theory (DST) is a general theoretical perspective on development, heredity and evolution. It is intended to facilitate the study of interactions between the many factors that influence development without reviving `dichotomous' debates over nature or nurture, gene or environment, biology or culture. Several recent papers have addressed the relationship between DST and the thriving new discipline of evolutionary developmental biology (EDB). The contributions to this literature by evolutionary developmental biologists contain three important misunderstandings of DST.     

From Sea to Tree: Saga of a Land Crab

There are advantages to be gained when an animal abandons itsancestral home, the ocean, and advances across the littoralzone to the land. But along with the advantages come the inevitableproblems. How a land crab, Gecarcinus lateralis, has solvedits problems of life on land is the subject of this paper. Itsuse of dew as a source of moisture and of its burrow as a refugefrom predators and a hostile environment; its ability to collectmoisture from a damp substrate and conduct this moisture toits branchial chambers and its gills; its capacity to retainlarge amounts of water before ecdysis and to use this waterto stretch its new soft exoskeleton and attain its proper shapeafter ecdysis are only a few of the crab's special adaptationsfor terrestrial life. Its feeding and reproductive behaviorare equally adaptive, as is its propensity for tree-climbingwhen danger threatens–or at other times. During the pastseveral decades, much interesting and important research hasbeen done on G. lateralis, as well as on other land crabs–butmuch remains to be done. Land crabs are and will undoubtedlycontinue to be promising objects of scientific research.     

Fredrik Barth: From Fieldwork to Theory

Fredrik Barth: From Fieldwork to Theory. 1999. 56 minutes, color. video by Werner Sperschneider. Coproduced by the Institut für den Wissenschaftlichen Film (IWF) and the Danish Film Institute Workshop. For more information, contact the IWF-Knowledge and Media, Nonnenstieg 72, 37075, Göttingen, Germany; www.iwf.de .     

From Umwelt to Soundtope: An Epistemological Essay on Cognitive Ecology

Capturing information means for every organism acquiring knowledge about the living and not living objects that exist in its surroundings. In this way, the “historical” concept of Umwelt, as a subjective surrounding has been recently integrated in the theory of landscape ecology where a landscape is not only a geographical entity but also a cognitive medium. The landscape may be considered a semiotic context used by the organisms to locate resources heterogeneously distributed in space and time. In particular, inside a landscape there are different eco-fields defined as spatial arrangements of objects carrier of meaning that organisms utilize to track resources. Along this epistemic path the sonic component of the landscape is an important carrier of information commonly used by the majority of animal species to managing many vital functions. In particular birds, which are animals with a complex system of acoustic communication, seem to organize acoustic centers for public information. These sonic patterns (soundtopes) are characterized by a great variability in space and time and function like a special eco-field that allows species to share information about the status of resources and the dynamics of populations. The availability of such public information avoids a deeper and more expensive exploration of the environment to assess its quality.     

Ecological Equivalence: A Realistic Assumption for Niche Theory as a Testable Alternative to Neutral Theory

Background

Hubbell''s 2001 neutral theory unifies biodiversity and biogeography by modelling steady-state distributions of species richness and abundances across spatio-temporal scales. Accurate predictions have issued from its core premise that all species have identical vital rates. Yet no ecologist believes that species are identical in reality. Here I explain this paradox in terms of the ecological equivalence that species must achieve at their coexistence equilibrium, defined by zero net fitness for all regardless of intrinsic differences between them. I show that the distinction of realised from intrinsic vital rates is crucial to evaluating community resilience.

Principal Findings

An analysis of competitive interactions reveals how zero-sum patterns of abundance emerge for species with contrasting life-history traits as for identical species. I develop a stochastic model to simulate community assembly from a random drift of invasions sustaining the dynamics of recruitment following deaths and extinctions. Species are allocated identical intrinsic vital rates for neutral dynamics, or random intrinsic vital rates and competitive abilities for niche dynamics either on a continuous scale or between dominant-fugitive extremes. Resulting communities have steady-state distributions of the same type for more or less extremely differentiated species as for identical species. All produce negatively skewed log-normal distributions of species abundance, zero-sum relationships of total abundance to area, and Arrhenius relationships of species to area. Intrinsically identical species nevertheless support fewer total individuals, because their densities impact as strongly on each other as on themselves. Truly neutral communities have measurably lower abundance/area and higher species/abundance ratios.

Conclusions

Neutral scenarios can be parameterized as null hypotheses for testing competitive release, which is a sure signal of niche dynamics. Ignoring the true strength of interactions between and within species risks a substantial misrepresentation of community resilience to habitat loss.     

Alternative Functions of Arabidopsis YELLOW STRIPE-LIKE3: From Metal Translocation to Pathogen Defense

YELLOW STRIPE-LIKE1 (YSL1) and YSL3 are involved in iron (Fe) and copper (Cu) translocation. Previously, we reported that upregulation of YSL1 and YSL3 under excess Cu caused high accumulation of Cu in the siz1 mutant, impaired in small ubiquitin-like modifier (SUMO) E3 ligase. Interestingly, the siz1 mutant contains high levels of salicylic acid (SA), involved in plant defense against biotrophic pathogens. In this study, we found that YSL1 and YSL3 were upregulated by SA. SA-regulated YSL3 but not YSL1 depended on NONEXPRESSOR OF PR1 (NPR1). Susceptibility to the pathogen Pseudomonas syringe pv. tomato (Pst) DC3000 was greater for ysl3 than the wild type. Also, during Pst DC3000 infection, YSL3 was positively regulated by SA signaling through NPR1 and the upregulation was enhanced in the coi1 mutant that defective in the jasmonic acid (JA) receptor, CORONATINE INSENSITIVE1. This line of evidence indicates that the regulation of YSL3 is downstream of SA signaling and interplays with JA signaling for involvement in pathogen-induced defense. We provide new insights into the biological function of the metal transporter YSL3 in plant pathogen defense.     

Tree Diversity in Western Kenya: Using Profiles to Characterise Richness and Evenness

Species diversity is a function of the number of species and the evenness in the abundance of the component species. We calculated diversity and evenness profiles, which allowed comparing the diversity and evenness of communities. We applied the methodology to investigate differences in diversity among the main functions of trees on western Kenyan farms. Many use-groups (all trees and species that provide a specific use) could not be ranked in diversity or evenness. No use-group had perfectly even distributions. Evenness could especially be enhanced for construction materials, fruit, ornamental, firewood, timber and medicine, which included some of the most species-rich groups of the investigated landscape. When considering only the evenness in the distribution of the dominant species, timber, medicine, fruit and beverage ranked lowest (> 60% of trees belonged to the dominant species of these groups). These are also use-groups that are mainly grown by farmers to provide cash through sales. Since not all communities can be ranked in diversity, studies that attempt to order communities in diversity should not base the ordering on a single index, or even a combination of several indices, but use techniques developed for diversity ordering such as the Rényi diversity profile. The rarefaction of diversity profiles described in this article could be used in studies that compare results from surveys with different sample sizes.     

From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives

Modeling and visualization of the cellular mesoscale, bridging the nanometer scale of molecules to the micrometer scale of cells, is being studied by an integrative approach. Data from structural biology, proteomics, and microscopy are combined to simulate the molecular structure of living cells. These cellular landscapes are used as research tools for hypothesis generation and testing, and to present visual narratives of the cellular context of molecular biology for dissemination, education, and outreach.     

Using Marine Snails to Teach Biogeography and Macroevolution: The Role of Larvae and Dispersal Ability in the Evolution and Persistence of Species

While some marine animals are capable of traveling great distances, many have limited mobility as adults and spend the majority of their lifetimes in a small geographical area or may even be cemented to a single place. While it might be expected that species with limited mobility would have small geographic distributions, some nevertheless occur over very large areas. This is the case for some marine snails (gastropods). A key factor that impacts the geographic distribution of marine snails is the type of larvae they have during the phase of their life history that follows hatching from an egg. Because adult snails do not typically travel vast distances, the mobility of the larval stage determines the species?? ability to reach new territories. Some larvae are capable of long-distance travel, while others are not. An important component of the process of speciation involves geographic isolation, so the type of larvae a snail species possesses impacts the likelihood that it will become geographically isolated and give rise to a new species. Larval form also affects how long snail species will persist on geological timescales before going extinct, as well as rates of speciation. This paper briefly reviews the evolutionary consequences of different types of larval development in marine gastropods (especially cone snails, which are one of the most diverse groups of marine animals), particularly in determining the dispersal ability and geographic ranges of individual species, the amount of genetic exchange among populations within species, and the duration of species through time. The goal of this short review is to provide context and examples for classroom discussions of the connections between biogeography and macroevolution. Furthermore, a classroom activity is presented that involves students?? using information about snail life history and biogeography to develop research plans (and predicted results) that could be utilized to test (i.e., support or reject) several macroevolutionary hypotheses.     

Learning to Control Actions: Transfer Effects following a Procedural Cognitive Control Computerized Training

Few studies have addressed action control training. In the current study, participants were trained over 19 days in an adaptive training task that demanded constant switching, maintenance and updating of novel action rules. Participants completed an executive functions battery before and after training that estimated processing speed, working memory updating, set-shifting, response inhibition and fluid intelligence. Participants in the training group showed greater improvement than a no-contact control group in processing speed, indicated by reduced reaction times in speeded classification tasks. No other systematic group differences were found across the different pre-post measurements. Ex-Gaussian fitting of the reaction-time distribution revealed that the reaction time reduction observed among trained participants was restricted to the right tail of the distribution, previously shown to be related to working memory. Furthermore, training effects were only found in classification tasks that required participants to maintain novel stimulus-response rules in mind, supporting the notion that the training improved working memory abilities. Training benefits were maintained in a 10-month follow-up, indicating relatively long-lasting effects. The authors conclude that training improved action-related working memory abilities.     

A Novel Approach to Identify and Map Kitten Clusters Using Geographic Information Systems (GIS): A Case Study From Tompkins County,NY

A retrospective study using a geographic information system (GIS) was conducted to capture, map, and analyze intake data of caregiver (owner)-surrendered kittens (aged 0–6 months) to the Society for the Prevention of Cruelty to Animals (SPCA) of Tompkins County, NY, from 2009 to 2011. Addresses of caregiver-surrendered kittens during the study period were mapped (n = 1,017). Mapping and analysis of the resultant data set revealed that the distribution of kittens was nonrandom. Seventeen statistically significant (p = .001) clusters were identified, 1 of which was the SPCA of Tompkins County (due to anonymously surrendered nonhuman animals). The remaining 16 clusters were composed of 52 homes; 27.5% (280/1,017) of the kittens in the data set originated from these 52 homes. The majority of kittens within clusters were surrendered from high-density residential and manufactured residential home parks. Analyzing such clusters using GIS is a novel approach for targeting spay/neuter and educational programs to areas contributing disproportionately to shelter populations. This method may prove useful to help shelters more effectively allocate their limited resources, but further evaluation of this and other targeted approaches is needed to assess the long-term efficacy of such programs.     

Genetic Characterization of Human Populations: From ABO to a Genetic Map of the British People

From 1900, when Landsteiner first described the ABO blood groups, to the present, the methods used to characterize the genetics of human populations have undergone a remarkable development. Concomitantly, our understanding of the history and spread of human populations across the earth has become much more detailed. As has often been said, a better understanding of the genetic relationships among the peoples of the world is one of the best antidotes to racial prejudices. Such an understanding provides us with a fascinating, improved insight into our origins as well as with valuable information about population differences that are of medical relevance. The study of genetic polymorphisms has been essential to the analysis of the relationships between human populations. The evolution of methods used to study human polymorphisms and the resulting contributions to our understanding of human health and history is the subject of this Perspectives.THE A, B, and O blood types of the ABO blood group system were first described by Landsteiner in 1900, the year of the rediscovery of Mendel’s work. Landsteiner had set out to see whether the sorts of differences between species that had been detected by serological methods might also occur within species (see Owen, 2008). The experiment was very simple: mix the red blood cells of one person with the serum of another and do this pairwise for a number of people. To his surprise, he found that certain combinations of serum and red cells led to clumping or agglutination of the red cells. Based on the resulting patterns of agglutination of the red cells, three types of serum and red cells were identified: A (which agglutinates only B cells), B (which agglutinates only A cells), and O (which agglutinates both A and B cells). [Landsteiner did not at first observe AB serum (which agglutinates neither A or B cells) because of the small size of his sample.] These types seemed to be intrinsic to the individual and did not change with time or, for example, the presence of infections. They were, as we now know, the inherited characteristics of an individual’s red blood cells. Landsteiner’s work, together with many subsequent developments, meant that blood transfusions became possible and eventually much safer. In addition, this simple but fundamental analysis was the initial stimulus for all subsequent studies of the frequency of genetic variation in different human populations and the use of genetic variants for characterizing genetic differences among humans.     

From LOC to LIC: Using individual cells as experimentation platforms

There are many efforts today trying to mimic the properties of single cells in order to design chips that are as efficient as cells. However, cells are nature’s nanotechnology engineering at the scale of atoms and molecules. Therefore, it might be better to vision a microchip that utilizes a single cell as experimentation platform. A novel, so-called Lab-in-a-Cell (LIC) concept is described, where advantage is taken of micro/nanotechnological tools to enable precise control of the biochemical cellular environment and possibility to analyze the composition of single cells.     

Using Homolog Groups to Create a Whole-Genomic Tree of Free-Living Organisms: An Update

Genomic trees have been constructed based on the presence and absence of families of protein-encoding genes observed in 27 complete genomes, including genomes of 15 free-living organisms. This method does not rely on the identification of suspected orthologs in each genome, nor the specific alignment used to compare gene sequences because the protein-encoding gene families are formed by grouping any protein with a pairwise similarity score greater than a preset value. Because of this all inclusive grouping, this method is resilient to some effects of lateral gene transfer because transfers of genes are masked when the recipient genome already has a homolog (not necessarily an ortholog) of the incoming gene. Of 71 genes suspected to have been laterally transferred to the genome of Aeropyrum pernix, only approximately 7 to 15 represent genes where a lateral gene transfer appears to have generated homoplasy in our character dataset. The genomic tree of the 15 free-living taxa includes six different bacterial orders, six different archaeal orders, and two different eukaryotic kingdoms. The results are remarkably similar to results obtained by analysis of rRNA. Inclusion of the other 12 genomes resulted in a tree only broadly similar to that suggested by rRNA with at least some of the differences due to artifacts caused by the small genome size of many of these species. Very small genomes, such as those of the two Mycoplasma genomes included, fall to the base of the Bacterial domain, a result expected due to the substantial gene loss inherent to these lineages. Finally, artificial ``partial genomes' were generated by randomly selecting ORFs from the complete genomes in order to test our ability to recover the tree generated by the whole genome sequences when only partial data are available. The results indicated that partial genomic data, when sampled randomly, could robustly recover the tree generated by the whole genome sequences. Received: 30 May 2001 / Accepted: 10 October 2001     

Highly Sensitive Plasmonic Refractive Index Sensor Using Doped Silicon: an Alternative to MIM Structures

Plasmonics - Metal–Insulator-Metal (MIM) structures possess a number of shortcomings which include optical loss, tenability, nanofabrication challenges, chemical instability, incompatible...     

The Scaling of Blood Flow Resistance: From a Single Vessel to the Entire Distal Tree

Although the flow resistance of a single vessel segment is easy to compute, the equivalent resistance of a network of vessel segments or the entire vasculature of an organ is difficult to determine in an analytic form. Here, we propose what we believe is a novel resistance scaling law for a vascular tree (i.e., the resistance of a vessel segment scales with the equivalent resistance of the corresponding distal tree). The formulation can be written as (Rs/Rc)∝(Ls/Lc) (where Rs and Ls are the resistance and length of a vessel segment, respectively, and Rc and Lc are the equivalent resistance and total length of the corresponding distal tree, respectively), which was validated for the coronary vascular systems of the heart. The scaling law was also shown to apply to the vascular systems of the lung, mesentery, muscle, eye, and so on. The novel resistance scaling law, coupled with the 3/4-power scaling law for metabolic rates, can predict several structure-function relations of vascular trees, albeit with a different exponent. In particular, the self-similar nature of the scaling law may serve as a diagnostic tool with the help of noninvasive imaging modalities.     

From Rhetoric to Reality: Using Specific Environmental Concerns to Identify Critical Sustainability Issues

Natural resource managers, environmental interest groups, and public agencies are interested in appropriate, identifiable, and measurable indicators of sustainability. At the same time, public agencies, including natural resource management agencies, are attempting to identify research and management priorities that address major environmental concerns at local and broad scales. The Identify the Specifics approach, described here, uses local (ecodistrict or smaller) ecological/biological “experts' ” knowledge to identify and prioritize the local natural resources of concern (commonly species), associated management practices and ecosystems to form a concern matrix. Local ecological/biological concerns form the environmental base of a broader-scale (ecoregion/ecozone) concern matrix. This matrix identifies similarities and differences among local matrices and appropriate components for promotion to broader scales. Scale-specific matrices identify appropriate local, regional, and broader-scale indicators to monitor and assess, and provide public agencies with direction for documenting effects of management and identifying where research is needed. This approach can provide industries, public agencies, environmental interest groups, and governments with ecosystem-based, prioritized information for balancing social, economic, and ecological concerns on public and private lands. Received 22 July 1997; accepted 7 January 1998.