Many Possible Worlds: Expanding the Ecological Scenarios in Experimental Evolution

Experimental microbial evolution has focused on the particular ecological scenario where a population is placed suddenly in an environment where its fitness is low, and then adapts while the environment remains stable. In line with this, most microbial evolution studies use fitness measures that report how evolved genotypes fare when competed directly against their own distant ancestor while other studies compare life history traits (such as growth rates) of ancestral and evolved genotypes. This standard way of measuring and reporting changes in fitness has resulted in a consistent body of literature that explains adaptation when populations evolve in this “standard ecological scenario.” Here, I suggest that for experimental evolution to investigate adaptation in other ecological scenarios, such as fluctuating or persistently changing environments, measures of fitness must be expanded such that they not only continue to be comparable between experiments, but also account for evolution and demographic effects in all environments that an evolving lineage experiences. I examine two non-standard measures of fitness—fitness flux and the total number of reproductive events—as potential ways to quantify adaptation by integrating historical information about selection over many environments. This approach could allow us to make quantitative and biologically-meaningful comparisons of adaptation across diverse ecological scenarios. I use the case study of understanding how phytoplankton communities may respond to global change, where environmental variables change continuously, to explore concrete ways of using non-standard fitness measures that consider both demographic effects and selection in changing, rather than in changed, environments.     

Interpreting co-variation in species richness and productivity in terrestrial vegetation: Making sense of causations and correlations at multiple scales

This commentary examines conventional and recent ideas regarding the interpretation of species richness-productivity relationships (SRPR) in terrestrial vegetation. A new conceptual modelling approach — cascading graph diagrams — is used to search for maximum parsimony by distilling and clarifying synthetic linkages between several potential causes of variation and co-variation in these two vegetation attributes at three distinctly different spatial scales: global/continental scale (variation between climatic/geographic regions within a continent, or across latitudes); regional scale (variation between local communities representing different habitat (soil) fertility types or different habitat disturbance levels within a climatic/geographic region); and local community scale (variation between neighbourhood plots within a particular plant community/habitat). In contrast with a number of interpretations in recent literature, the approach developed here emphases that SRPR at each scale in terrestrial vegetation involve a “cascade” of several intermediary causational variables that have not been generally accounted for in previous studies of SRPR. Accordingly, SRPR are expected usually to be correlational, sometimes indirectly causational, but never directly causational, at any scale. Rather than suggesting that causational mechanisms “scale up”, the analysis here illustrates that several mechanistic features may be shared across scales and that in some cases, mechanisms may “scale down”. This has crucial implications for identifying testable and un-confounded hypotheses for future research and for selecting effective experimental designs and appropriate methods of data analyses for the interpretation of SRPR in natural vegetation.     

Two Approaches to the Study of the Origin of Life

This paper compares two approaches that attempt to explain the origin of life, or biogenesis. The more established approach is one based on chemical principles, whereas a new, yet not widely known approach begins from a physical perspective. According to the first approach, life would have begun with—often organic—compounds. After having developed to a certain level of complexity and mutual dependence within a non-compartmentalised organic soup, they would have assembled into a functioning cell. In contrast, the second, physical type of approach has life developing within tiny compartments from the beginning. It emphasises the importance of redox reactions between inorganic elements and compounds found on two sides of a compartmental boundary. Without this boundary, “life” would not have begun, nor have been maintained; this boundary—and the complex cell membrane that evolved from it—forms the essence of life.     

Genomic medicine and neurological disease

“Genomic medicine” refers to the diagnosis, optimized management, and treatment of disease—as well as screening, counseling, and disease gene identification—in the context of information provided by an individual patient’s personal genome. Genomic medicine, to some extent synonymous with “personalized medicine,” has been made possible by recent advances in genome technologies. Genomic medicine represents a new approach to health care and disease management that attempts to optimize the care of a patient based upon information gleaned from his or her personal genome sequence. In this review, we describe recent progress in genomic medicine as it relates to neurological disease. Many neurological disorders either segregate as Mendelian phenotypes or occur sporadically in association with a new mutation in a single gene. Heritability also contributes to other neurological conditions that appear to exhibit more complex genetics. In addition to discussing current knowledge in this field, we offer suggestions for maximizing the utility of genomic information in clinical practice as the field of genomic medicine unfolds.     

A “Nonsterile” Method for Selecting and Growing <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> Transformants (T<Subscript>2</Subscript> Transgenic Lines) Resistant to Kanamycin

A breakthrough in transgenic Arabidopsis thaliana research was the development of the floral dip transformation protocol, a simple and reliable method of obtaining transformants, T₁ transgenic lines, at high efficiency while avoiding the use of tissue culture. However, the traditional protocol (a “sterile” method) of obtaining T₂ transgenic lines has not evolved along with improvements in transformation technology as it continues to be laborious and time-consuming. In this study, we report on the development of an improved protocol (a “nonsterile” method) for selecting and growing A. thaliana transformants (T₂ transgenic lines) resistant to kanamycin under nonsterile conditions. This protocol involves the use of a simple yet specialized device that will aid in solium selection of T₂ transgenic lines that can be rapidly grown in a hydroponic system. The “nonsterile” method reduces labor and time involved as compared to the “sterile” method; moreover, it is easy to set up and maintain. This method may also be applicable to other selecting agents, and perhaps to other plants.     

Structural feature of sorghum chloroplast psbA gene and regulation effects of its 5'-noncoding region*

Comparative analysis reveals remarkahle homology between the sequences of bothpsbA gene nucleotides and the inferred amino acids of sorghum, a C₄ plant, and those of rice, a C₃ plant. The 5′-noncoding region of sorghumpsbA gene contains the conservative promoter elements, “—35” element and “—10” element, like the prokaryote and the promoter element, TATA box, like the eukaryote. As compared with that of the rice, an extra sequence of 7 bp is found in the leader sequence of the mRNA in the former. Using anin vitro system, it has been demonstrated that protein factor exists in sorghum chloroplast protein extract which specifically hinds to the 5′-noncoding region ofpsbA gene. Measurement of the expression of luciferase shows a 2–5 time greater reaction of the expression plasmids pALqs which contain leader region of sorghumpsbA gene than that of the expression plasmids pALqr which contain leader region of ricepsbA gene inE. coli. Project supported by the Chinese National “863” and “973” Projects     

Analysis of the exponential decay model of the neuron showing frequency threshold effects

The exponential decay model of a neuron has been analyzed using the “random walk” approach of stochastic processes and an “absorbing barrier” solution is obtained forg ^T (s)—the Laplace transform of the output pulse interval density function. An expression for the mean output frequency is derived from this and a variety of input-output curves plotted which show frequency threshold effects in single neurons. Our results are compared with those of other authors obtained by computer simulation techniques, and the significance of these results discussed with reference to the possible behavior of networks constructed of such neuron units.     

Conditional genomic rearrangement by designed meiotic recombination using VDE (PI-SceI) in yeast

Meiotic recombination plays critical roles in the acquisition of genetic diversity and has been utilized for conventional breeding of livestock and crops. The frequency of meiotic recombination is normally low, and is extremely low in regions called “recombination cold domains”. Here, we describe a new and highly efficient method to modulate yeast meiotic gene rearrangements using VDE (PI-SceI), an intein-encoded endonuclease that causes an efficient unidirectional meiotic gene conversion at its recognition sequence (VRS). We designed universal targeting vectors, by use of which the strain that inserts the VRS at a desired site is acquired. Meiotic induction of the strains provided unidirectional gene conversions and frequent genetic rearrangements of flanking genes with little impact on cell viability. This system thus opens the way for the designed modulation of meiotic gene rearrangements, regardless of recombinational activity of chromosomal domains. Finally, the VDE–VRS system enabled us to conduct meiosis-specific conditional knockout of genes where VDE-initiated gene conversion disrupts the target gene during meiosis, serving as a novel approach to examine the functions of genes during germination of resultant spores.     

Contemporary evolution meets conservation biology II: impediments to integration and application

Conservation biology needs to be concerned not just with exogenous threats to populations, but also with the changing nature of populations themselves. In a previous review paper, we highlighted evolution in contemporary time (years to decades) as a largely overlooked aspect of population responses to environmental perturbations. We argued that these responses might affect the fate of natural, managed and exotic populations. In the present review, we discuss issues that may limit the integration of contemporary evolution into conservation biology—with the intent that recognition of these limitations may foster research, discussion and resolution. In particular, we consider (1) alternative perceptions of “evolutionary” and “ecological” time, (2) the role of contemporary evolution as an ecological process, (3) fitness as a bridge between evolution and conservation, and (4) challenges faced by conservation strategies based on gene flow estimation or manipulation. We close by highlighting some situations in which current conservation approaches and contemporary evolution may require reconciliation.     

I/We Narratives Among African American Families Raising Children with Special Needs

This paper examines a statistics debate among African American caregivers raising children with disabilities for insights into the work of “African American mothering.” Using ethnographic, narrative and discourse analyses, we delineate the work that African American mothers do—in and beyond this conversation—to cross ideological and epistemological boundaries around race and disability. Their work entails choosing to be an “I” and, in some cases, actively resisting being seen as a “they” and/or part of a collective “we” in order to chart alternative futures for themselves and their children.     

“Green water” microalgae: the leading sector in world aquaculture

Freshwater fish culture is generally considered the largest sector in world aquaculture. Several of the leading species consume “green water” plankton. This plankton—mostly microalgae (phytoplankton) and also bacteria, protozoa and zooplankton—grows in man-made fertilized water impoundments. The quantity of “green water” microalgae consumed by fish and shrimp is estimated here at a quarter billion ton fresh weight a year, about three and a half times as much as the entire recognized aquaculture. This estimate is based on the quantities of the microalgae consumed and the efficiencies of their use for growth by the main species in aquaculture. The cost of producing “green water” microalgae by the aquaculturists—mostly in SE Asia—is low. The populations in “green water” are biologically managed by the cultured fish themselves. The fish with their different feeding habits help “manage” the composition of the plankton and the overall water quality as they grow. The aquaculturists further manage “green water” through simple means, including water exchange and fertilization. Cost is remunerated partially by the income from sales of the fish and partially by bio mitigation services that “green water” polyculture ponds provide the aquaculturists in treating farm and household waste. A comprehension of the scale and importance of the microalgae sector to world aquaculture should lead to more research to improve understanding of algal population dynamics, growth factors, and efficiency of food chains. The consequent improved control of the plankton’s interaction with fish and shrimp production in “green water” will undoubtedly contribute much to the expansion in production of seafood.     

SSCP-SNP-based conserved ortholog set (COS) markers for comparative genomics in cassava (Manihot esculenta crantz)

The ever increasing body of information on genomics and functional genomics from model plants, and new tools of comparative genomics, provide an opportunity to accelerate the development of molecular markers for increasing the efficiency of breeding of lesser studied crops, so-called “orphan crops.” Conserved ortholog set (COS) markers represent orthologous genes in widely divergent plant species, and are currently the principal tool of choice for comparative genomics. EST sequences of 3 drought tolerance related genes—chalcone synthase (CHS), dihydroflavonol-4-reductase (DHRF) and drought responsive element binding factor 1 (DREB-1) fromMusa sp—were used to identify cassava EST homologs that were then scanned against the Arabidopsis genome database to identify them as COS markers. The CHS and DHRF ESTs were demonstrated to be COS markers, while the DREB EST was shown to belong to a gene family. The three genes were evaluated as single strand conformation polymorphism—single nucleotide polymorphism (SSCP-SNP) markers in the parents of an F1 mapping population and subsequently in the progenies. The DHRF COS marker mapped to linkage group R of the female-derived map while the DREB-1 EST mapped at an end of the male-derived linkage group K. The CHS COS marker could not be mapped because it was not polymorphic in the parents of the mapping population. These new marker tools should accelerate the development of markers associated with genes controlling traits of agronomic interest via the candidate gene loci (CGL) QTL-mapping approach.     

The Futility of Futility: Death Causation is the ��Elephant in the Room�� in Discussions about Limitation of Medical Treatment

The term “futility” has been widely used in medical ethics and clinical medicine for more than twenty years now. At first glance it appears to offer a clear-cut categorical characterisation of medical treatments at the end of life, and an apparently objective way of making decisions that are seen to be emotionally painful for those close to the patient, and ethically, and also potentially legally hazardous for clinicians. It also appears to deal with causation, because omission of a futile treatment cannot surely be a cause of death. The problem is that futility can be argued to be a “false friend”, in that it gives an appearance of representing a reliable conceptual basis, in ethics, for limitation of medical treatment—usually in the context of dying—without actually doing so. In fact, the concept of futility is a conflation of clinical judgement about outcomes of treatment and the quality or even value of life, and has really failed to contribute much to the advancement of decision-making and hence care at the end-of-life. It also has the capacity to medicalise the personal space. Deliberations about the likely outcomes of medical treatment are necessary, and medical expertise is pivotal. However, futility is argued to have a better future in partnership with a broad social action agenda about the process of dying, such as that articulated in health promoting palliative care, as a basis for better “death-ways” in the 21st century (Kellehear 2005). Medicine needs to more honest and upfront about its limits, as death is, after all, the elephant in everybody's room.     

Impacts of Foraging Facilitation Among Predators on Predator-prey Dynamics

Whereas impacts of predator interference on predator-prey dynamics have received considerable attention, the “inverse” process—foraging facilitation among predators—have not been explored yet. Here we show, via mathematical models, that impacts of foraging facilitation on predator-prey dynamics depend on the way this process is modeled. In particular, foraging facilitation destabilizes predator-prey dynamics when it affects the encounter rate between predators and prey. By contrast, it might have a stabilizing effect if the predator handling time of prey is affected. Foraging facilitation is an Allee effect mechanism among predators and we show that for many parameters, it gives rise to a demographic Allee effect or a critical predator density in need to be crossed for predators to persist. We explore also the effects of predator interference, to make the picture “symmetric” and complete. Predator interference is shown to stabilize predator-prey dynamics once its strength is not too high, and thus corroborates results of others. On the other hand, there is a wide range of model parameters for which predator interference gives rise to three co-occurring co-existence equilibria. Such a multi-equilibrial regime is rather robust as we observe it for all the functional response types we explore. This is a previously unreported phenomenon which we show cannot occur for the Beddington–DeAngelis functional response. An interesting topic for future research thus might be to seek for general conditions on predator functional responses that would produce multiple co-existence equilibria in a predator-prey model.     

Intragenomic bet-hedging

The notion of intragenomic bet-hedging is introduced by modeling a system where one locus is seen as setting the “environment” for selection in a two-locus genetic system. Using a spatially structured simulation model I show that bet-hedging alleles with a lower mean fitness and lower variance of fitness across genotypes at a different locus can go to fixation, potentially providing a mechanism for the reduction of severe heterozygote advantage.     

Don’t Call it “Darwinism”

Evolutionary biology owes much to Charles Darwin, whose discussions of common descent and natural selection provide the foundations of the discipline. But evolutionary biology has expanded well beyond its foundations to encompass many theories and concepts unknown in the 19th century. The term “Darwinism” is, therefore, ambiguous and misleading. Compounding the problem of “Darwinism” is the hijacking of the term by creationists to portray evolution as a dangerous ideology—an “ism”—that has no place in the science classroom. When scientists and teachers use “Darwinism” as synonymous with evolutionary biology, it reinforces such a misleading portrayal and hinders efforts to present the scientific standing of evolution accurately. Accordingly, the term “Darwinism” should be abandoned as a synonym for evolutionary biology.