What is speciation and how should we study it?

To understand speciation, we first need to know what species are. Yet debates over species concepts have seemed endless, with little obvious relevance to the study of speciation. Recently, there has been progress in resolving these debates, favoring a lineage-based, evolutionary species concept. This progress calls for reconsideration of the study of speciation. Traditional speciation research based on the biological species concept has led to great advances in understanding how nonallopatric speciation occurs and how species diverge and remain separate from each other. However, this research has neglected the question of how new species arise in the first place for the most common geographic mode (allopatric). A new and very different research program is needed to understand the ecological and evolutionary processes that split an ancestral species into new allopatric lineages. This research program will connect speciation to many other fundamental questions in evolutionary biology, ecology, biogeography, and conservation biology.     

The optimal strategy for brood-parasitism: how many eggs should be laid in the host's nest?

We consider the optimal strategy for intra-specific brood-parasitism, especially with respect to the number of eggs laid by the parasitic individual in the nest of non-parasitic individual, in particular, a host that does not reject the parasite's eggs. With a fundamental mathematical model, assuming that the survival probability of the parasite's offspring in the nest of the host is significantly smaller than that in parasite's own nest, we determine the optimal number of eggs laid in the nest of host that maximizes the expected reproductive fitness of the parasite. We show that the invasion success of brood-parasitism could significantly depend on the total number of eggs laid by the parasite in a breeding season, and that the successfully invading brood-parasitism could realize maximum fitness with a specific number of parasite's eggs laid in the nest of the host.     

The impact of the summer 2003 heat wave in Iberia: how should we measure it?

We present a new approach to improve the reliability of quantifying the impact of a heat wave on mortality rates. We show, for the recent European summer 2003 heat wave, that the use of absolute maximum temperature values, or number of days above a given threshold, can be misleading. Here, we have assessed the impact of the heat wave on Iberian mortality by applying a four step procedure: (1) calculating, for each observatory, the local maximum temperature (T _max) distributions, (2) calculating the corresponding 95th percentile values (T _threshold), (3) locally defining extremely hot days (EHD) as those days on which the local threshold of the 95th percentile of the series is exceeded, and (4) calculating the total degrees-days (DD) of exceedance, by calculating the difference T _max−T _threshold and summing these values for all days above T _threshold. We show that the relationship between summer mortality rates and the DD index is non-linear and can be described by a logarithmic function, with a correlation coefficient of 0.78, which explains 60.6% of the mortality variance (F value of 24.64, significant at P<0.0001). Using maximum temperatures, no significant relationship is found with mortality, whereas the EHD frequency shows a significant association with mortality, albeit weaker than that obtained with DD.     

Divide and conquer: when and how should competitors share?

When two individuals are unwilling to fight over a valuable resource, then they may obtain it with equal probability, or they may choose to divide the resource in some way. Although both strategies have been observed in nature, modelers have so far implicitly assumed that their long-term payoffs are the same. First we show that increasing returns to size in the value of a resource favor random allocation over sharing, whereas diminishing returns favor the reverse. Next we extend our approach to understand the conditions under which sharing will evolve when contestants vary in their resource-holding potential. We show that although closely matched individuals are more likely to share, it is by no means a prerequisite when contestants have limited information about one another’s abilities. Collectively, our models support recent observations of physical sharing as a solution to conflict resolution, and elucidate the conditions under which sharing will arise.     

DNA microarrays in the clinic: how soon,how extensively?

Although DNA microarrays are now widely used in research settings, they have been slow to penetrate clinical practice in spite of their apparent advantages. This is due to the very different requirements for a clinical test in contrast to a research tool, and to a strict necessity for demonstrated clinical utility. There is a clear differentiation between two types of DNA array tests: "genomic" diagnostics, developed to ascertain the presence or absence of mutations, deletions or duplications, and for which clinical evidence is already established, and tests using expression profiling for prognosis or predictive purposes, in which case the clinical correlate must be proven. Most array diagnostics currently used belong, understandably, to the "genomic" variety. It is to be expected that future improvements in tailored technology, as well as a logical trend towards measuring an ever-increasing number of parameters, will ensure an important diagnostic role for DNA arrays in the coming decade.     

Botanical literacy: What and how should students learn about plants?

Botanists benefit from a scientifically literate society and an interested and botanically literate student population, and we have opportunities to promote literacy in our classes. Unfortunately, scientific illiteracy exists, in part, because students are technologically advanced but lack intellectual curiosity and rigor. Botanical illiteracy results from several interacting factors, including a lack of interest in plants and infrequent exposure to plant science before students reach college. If scientific or botanical literacy is a goal, we must understand what literacy means and how we can help students reach that goal. A model of biological literacy recognizes four levels; students enter courses at the lowest level possessing misconceptions about concepts; however, misconceptions can be used to our advantage, especially by using concept inventories. Inquiry-based instruction is advocated for all science courses, and learning theory supports inquiry. Seven principles of learning inform recommendations about how botanists should teach, including using themes and "thinking botanically" to illustrate all biological concepts. Overall, consideration of the botanical content taught is less critical than the methods used to teach that content. If botanists emphasize thinking and process skills with an understanding of concepts, we will prepare scientifically literate students and citizens and benefit from our efforts.     

Begging and sibling competition: how should offspring respond to their rivals?

Godfray's influential model of competitive begging predicted that offspring should respond to each other's behavior, displaying more intensely when competing with needier rivals. Empirical tests of this prediction have, however, yielded equivocal results. Here, I develop a series of evolutionarily stable strategy models of begging as a signal of need, which show that this prediction holds only for competitive aspects of display that influence the division of food among the brood. No such response is expected for cooperative begging (which influences the total level of provisioning by the parent), and the models even predict the opposite trend under some circumstances (where the indirect costs of extracting additional resources from the parent are high). These contrasting sets of predictions may help to explain the varying empirical results obtained by studies of sibling interaction. Cooperative (as opposed to competitive) begging is likely to be of greater significance in cases where dominant young can gain direct control of allocation (or enjoy some competitive advantage). Dominants are then predicted to parasitize the efforts of their weaker rivals and reduce their own investment in cooperative signaling while continuing to claim a disproportionately large share of the resources provided by the parent.     

Antibody array analysis of labelled proteomes: how should we control specificity?

Researchers who use protein binders in multiplexed assays can be divided into two camps. One believes that arrays with proteome-wide coverage will become a reality once we have developed binders for all proteins. The sceptics claim that detection with immobilized protein binders and sample labelling will not provide the required specificity. In this article, we review the evidence showing that antibody array analysis of labelled samples can provide meaningful data and discuss the issues raised by the sceptics. We argue that direct the evidence for monospecificity has yet to be published. This will require assays designed to resolve the proteins captured by each binder. One option is to combine array measurement with protein separation. We have developed an assay where labelled sample proteins are separated by size exclusion chromatography (SEC) before contact with microsphere-based arrays (Size-MAP; size exclusion chromatography-resolved microsphere-based affinity proteomics). The effect is an 'antibody array Western blot' where reactivity of immobilized binders is resolved against the size of the proteins in the sample. We show that Size-MAP is useful to discriminate monospecific- and polyreactive antibodies and for automatic detection of reacting with the same target. The possibility to test specificity directly in array-based measurement should be useful to select the best binders and to determine whether the DNA microarray for the proteome is a realistic goal or not.     

Global elimination of trachoma: how frequently should we administer mass chemotherapy?

The World Health Organization has recommended repeat mass drug administration as part of their global initiative to eliminate blinding trachoma by the year 2020. The efficacy of repeat treatment will be tested empirically, but the results will not be available for many years, and recommendations for the necessary frequency of treatment are needed immediately. We have developed a mathematical model that uses available epidemiological data from a variety of countries. We recommend, based on our analysis, that in areas where trachoma is moderately prevalent (<35% in children), it should be treated annually, but hyperendemic areas (>50% in children), it should be treated biannually.     

After the ribosome structures: how are the subunits assembled?

The recent structures of the ribosome and the ribosomal subunits only heighten the intrigue of trying to understand how the ribosome is assembled. Biochemical and mechanistic studies have mapped out the basic series of protein binding events that occur, but we do not yet have a clear picture of the RNA conformational changes that must accompany the protein binding. Recent studies point to roles of protein folding chaperones and RNA helicases as facilitators of ribosome assembly, but the basic process of assembly seems to be encoded in the RNA sequences and can occur for the most part spontaneously in vitro, and quite possibly in vivo as well.     

Cancer of the lung: what should be the present approach?

The best opportunities at present for improving the results in the treatment of patients with cancer of the lung are by way of (a) utilizing the information obtained on routine x-ray examination of the chest, (b) decreasing the delay between the time of the first symptoms and the time the patient consults a physician, and (c) decreasing the delay between the time the patient first consults a physician and the time the cancer is surgically removed. The medical profession must increase its index of suspicion of cancer of the lung and persist in efforts to make a diagnosis when lung cancer is suspected. Exploratory thoracotomy should be used in suspicious cases when the diagnosis cannot be established by other methods.