What We Do Not Know About Differentiation

The outstanding recent advances in the analysis of differentiationare in concept and method. In this paper examples are providedto demonstrate that formulation of the problem of differentiationin terms of biosynthesis and its control poses questions innew and more manageable ways. As examples, reference will bemade to: (1) the question of control of the sets of specializedproperties by which we define a cell type; (2) propagabilityof differentiated states; (3) developmental bias in relationto intracellular events; and (4) the mechanisms of extrinsiccontrol of differentiation. Particular attention, also, willbe focused on the relationship of morphogenetic to biosyntheticevents.     

Germination of Spores of Bacillus Species: What We Know and Do Not Know

Spores of Bacillus species can remain in their dormant and resistant states for years, but exposure to agents such as specific nutrients can cause spores'' return to life within minutes in the process of germination. This process requires a number of spore-specific proteins, most of which are in or associated with the inner spore membrane (IM). These proteins include the (i) germinant receptors (GRs) that respond to nutrient germinants, (ii) GerD protein, which is essential for GR-dependent germination, (iii) SpoVA proteins that form a channel in spores'' IM through which the spore core''s huge depot of dipicolinic acid is released during germination, and (iv) cortex-lytic enzymes (CLEs) that degrade the large peptidoglycan cortex layer, allowing the spore core to take up much water and swell, thus completing spore germination. While much has been learned about nutrient germination, major questions remain unanswered, including the following. (i) How do nutrient germinants penetrate through spores'' outer layers to access GRs in the IM? (ii) What happens during the highly variable and often long lag period between the exposure of spores to nutrient germinants and the commitment of spores to germinate? (iii) What do GRs and GerD do, and how do these proteins interact? (iv) What is the structure of the SpoVA channel in spores'' IM, and how is this channel gated? (v) What is the precise state of the spore IM, which has a number of novel properties even though its lipid composition is very similar to that of growing cells? (vi) How is CLE activity regulated such that these enzymes act only when germination has been initiated? (vii) And finally, how does the germination of spores of clostridia compare with that of spores of bacilli?     

Waste Not,Want Not: Why Rarefying Microbiome Data Is Inadmissible

Current practice in the normalization of microbiome count data is inefficient in the statistical sense. For apparently historical reasons, the common approach is either to use simple proportions (which does not address heteroscedasticity) or to use rarefying of counts, even though both of these approaches are inappropriate for detection of differentially abundant species. Well-established statistical theory is available that simultaneously accounts for library size differences and biological variability using an appropriate mixture model. Moreover, specific implementations for DNA sequencing read count data (based on a Negative Binomial model for instance) are already available in RNA-Seq focused R packages such as edgeR and DESeq. Here we summarize the supporting statistical theory and use simulations and empirical data to demonstrate substantial improvements provided by a relevant mixture model framework over simple proportions or rarefying. We show how both proportions and rarefied counts result in a high rate of false positives in tests for species that are differentially abundant across sample classes. Regarding microbiome sample-wise clustering, we also show that the rarefying procedure often discards samples that can be accurately clustered by alternative methods. We further compare different Negative Binomial methods with a recently-described zero-inflated Gaussian mixture, implemented in a package called metagenomeSeq. We find that metagenomeSeq performs well when there is an adequate number of biological replicates, but it nevertheless tends toward a higher false positive rate. Based on these results and well-established statistical theory, we advocate that investigators avoid rarefying altogether. We have provided microbiome-specific extensions to these tools in the R package, phyloseq.     

Fossils that Change Everything We Know About Human Evolution (...Or Not)

Dramatic headlines touting new fossil discoveries often proclaim that our view of human evolution has been revolutionized. While this is occasionally the case, it is more often true that new fossils enrich our understanding of our own ancestry or answer scientific questions that could not be resolved with previous data. Even spectacular new discoveries, such as the now famous “hobbit” skeleton (Homo floresiensis), can usually be included in the human family tree without any significant change in the inferences about the phylogenetic relationships or taxonomic status of the rest of its members. It is a testament to the power of evolutionary theory and the careful comparative study of human and other fossils that what we know about human evolution changes so little, even when spectacular new discoveries are announced.     

Prebiotic Chemistry: What We Know,What We Don't

How life on Earth began remains an unexplained scientific problem. This problem is nuanced in its practical details and the way attempted explanations feedback with questions and developments in other areas of science, including astronomy, biology, and planetary science. Prebiotic chemistry attempts to address this issue theoretically, experimentally, and observationally. The ease of formation of bioorganic compounds under plausible prebiotic conditions suggests that these molecules were present in the primitive terrestrial environment. In addition to synthesis in the Earth's primordial atmosphere and oceans, it is likely that the infall of comets, meteorites, and interplanetary dust particles, as well as submarine hydrothermal vent synthesis, may have contributed to prebiotic organic evolution. The primordial organic soup may have been quite complex, but it did not likely include all of the compounds found in modern organisms. Regardless of their origin, organic compounds would need to be concentrated and complexified by environmental mechanisms. While this review is by no means exhaustive, many of the issues central to the state of the art of prebiotic chemistry are reviewed here.     

Root Hair Development in the Grasses: What We Already Know and What We Still Need to Know

A priority in many crop improvement programs for a long time has been to enhance the tolerance level of plants to both abiotic and biotic stress. Recognition that the root system is the prime determinant of a plant’s ability to extract both water and minerals from the soil implies that its architecture is an important variable underlying a cultivar’s adaptation. The density and/or length of the root hairs (RHs) that are formed are thought to have a major bearing on the plant’s performance under stressful conditions. Any attempt to improve a crop’s root system will require a detailed understanding of the processes of RH differentiation. Recent progress in uncovering the molecular basis of root epidermis specialization has been recorded in the grasses. This review seeks to present the current view of RH differentiation in grass species. It combines what has been learned from molecular-based analyses, histological studies, and observation of the phenotypes of both laboratory- and field-grown plants.     

The Macroevolution of our Ancient Lineage: What We Know (or Think We Know) about Early Hominin Diversity

Quantitative, evolutionary models that incorporate within- and between-species variation are critical for interpreting the fossil record of human diversity, and for making taxonomic distinctions. However, small sample sizes, sexual dimorphism, temporal trends, geographic variation, and the limited number of relevant extant models have always made the consideration of variation difficult for paleoanthropologists. Here we provide a brief overview of current early hominin diversity. We then argue that for many species our limited understanding of within species variation hampers our ability to make taxonomic decisions with any level of statistical certainty. Perhaps more significantly, the underlying causes of between-species variation among early hominins are poorly studied. There have been few attempts to correlate aspects of the phenotype with meaningful evidence for niche differentiation, to demonstrate the selective advantage of traits, or to provide other evidence for macroevolutionary divergence. Moreover, current depictions of vast pattern (but not size) diversity are inconsistent with expectations derived from most other extant primate clades that have adaptively radiated. If indeed the early hominin record is highly speciose, the reasons for this remain unclear.     

Rana Pipiens: Health and Disease--How Little We Know

The potential impact of frog diseases on basic research is discussedin practical terms.     

Smoothness without Smoothing: Why Gaussian Naive Bayes Is Not Naive for Multi-Subject Searchlight Studies

Spatial smoothness is helpful when averaging fMRI signals across multiple subjects, as it allows different subjects'' corresponding brain areas to be pooled together even if they are slightly misaligned. However, smoothing is usually not applied when performing multivoxel pattern-based analyses (MVPA), as it runs the risk of blurring away the information that fine-grained spatial patterns contain. It would therefore be desirable, if possible, to carry out pattern-based analyses which take unsmoothed data as their input but which produce smooth images as output. We show here that the Gaussian Naive Bayes (GNB) classifier does precisely this, when it is used in “searchlight” pattern-based analyses. We explain why this occurs, and illustrate the effect in real fMRI data. Moreover, we show that analyses using GNBs produce results at the multi-subject level which are statistically robust, neurally plausible, and which replicate across two independent data sets. By contrast, SVM classifiers applied to the same data do not generate a replication, even if the SVM-derived searchlight maps have smoothing applied to them. An additional advantage of GNB classifiers for searchlight analyses is that they are orders of magnitude faster to compute than more complex alternatives such as SVMs. Collectively, these results suggest that Gaussian Naive Bayes classifiers may be a highly non-naive choice for multi-subject pattern-based fMRI studies.     

Creating and Maintaining the Gastrointestinal Ecosystem: What We Know and Need To Know from Gnotobiology

Studying the cross talk between nonpathogenic organisms and their mammalian hosts represents an experimental challenge because these interactions are typically subtle and the microbial societies that associate with mammalian hosts are very complex and dynamic. A large, functionally stable, climax community of microbes is maintained in the murine and human gastrointestinal tracts. This open ecosystem exhibits not only regional differences in the composition of its microbiota but also regional differences in the differentiation programs of its epithelial cells and in the spatial distribution of its component immune cells. A key experimental strategy for determining whether “nonpathogenic” microorganisms actively create their own regional habitats in this ecosystem is to define cellular function in germ-free animals and then evaluate the effects of adding single or several microbial species. This review focuses on how gnotobiotics—the study of germ-free animals—has been and needs to be used to examine how the gastrointestinal ecosystem is created and maintained. Areas discussed include the generation of simplified ecosystems by using genetically manipulatable microbes and hosts to determine whether components of the microbiota actively regulate epithelial differentiation to create niches for themselves and for other organisms; the ways in which gnotobiology can help reveal collaborative interactions among the microbiota, epithelium, and mucosal immune system; and the ways in which gnotobiology is and will be useful for identifying host and microbial factors that define the continuum between nonpathogenic and pathogenic. A series of tests of microbial contributions to several pathologic states, using germ-free and ex-germ-free mice, are proposed.     

What We Expect Is Not Always What We Get: Evidence for Both the Direction-of-Change and the Specific-Stimulus Hypotheses of Auditory Attentional Capture

Participants were requested to respond to a sequence of visual targets while listening to a well-known lullaby. One of the notes in the lullaby was occasionally exchanged with a pattern deviant. Experiment 1 found that deviants capture attention as a function of the pitch difference between the deviant and the replaced/expected tone. However, when the pitch difference between the expected tone and the deviant tone is held constant, a violation to the direction-of-pitch change across tones can also capture attention (Experiment 2). Moreover, in more complex auditory environments, wherein it is difficult to build a coherent neural model of the sound environment from which expectations are formed, deviations can capture attention but it appears to matter less whether this is a violation from a specific stimulus or a violation of the current direction-of-change (Experiment 3). The results support the expectation violation account of auditory distraction and suggest that there are at least two different expectations that can be violated: One appears to be bound to a specific stimulus and the other would seem to be bound to a more global cross-stimulus rule such as the direction-of-change based on a sequence of preceding sound events. Factors like base-rate probability of tones within the sound environment might become the driving mechanism of attentional capture—rather than violated expectations—in complex sound environments.     

We Know in Part: James McCosh on Evolution and Christian Faith

James McCosh (1811–1894), president of Princeton College from 1868 to 1888, played a significant role in the American reception of evolution in the late 1800s – he was one of the more prominent clergyman to assuage the public’s fears of evolution while incorporating evolution into a conservative Christian worldview. McCosh was a prolific writer, whose books document his intellectual journey from hostility to acceptance of evolution. Three things will stand out in this overview that have not been emphasized in detail in other works: (1) James McCosh’s perspective on evolution dramatically changed over time; (2) McCosh’s motivations for engaging in the evolution-religion debate serve to clear up confusion regarding McCosh’s final position on evolution; and (3) the theological and philosophical basis for McCosh’s acceptance of evolution was established while McCosh was still hostile to evolution. His theological background therefore ‘pre-adapted’ him for evolution, and he was able to preach theology and evolution without substantially altering his theology.     

What We Think We Know vs. What We Need to Know About Orchid Pollination and Conservation: <Emphasis Type="Italic">Cypripedium</Emphasis> L. as a Model Lineage

While Darwin (1862, 1877) showed that reproductive success in orchid populations depended on adaptive floral morphology coupled with pollinator visitation a more recent review of the literature (Tremblay et al., 2005) confirmed that many out-breeding species are pollinator-limited because most orchid species showing low fecundity also lack rewards. The absence of rewards depresses both pollinator fidelity and the frequency of pollinator visits to an orchid population even though orchid flowers that lack rewards retain the same interlocking floral structures for precise pollinia removal and deposition found in related species that offer rewards. Using the genus, Cypripedium, as a model lineage of non-rewarding flowers this study also shows that the correlation between low fruit set in a Cypripedium sp. and its specific pollinator(s) is insufficient to predict specific frequencies of low fecundity. Annual rates of fruit set often vary broadly between populations of the same species and within the same population over several seasons. We speculate that fruit-set rates also decline when orchid demography and additional biotic and abiotic factors interrupt rates of pollinator activity (pre-zygotic) and fertilization/fruit maturation (post-zygotic). We suggest that that traditional field studies on pollination ecology and breeding systems be combined with data sets recording genetic variation and orchid flower demography in relation to seasonal variation in climate. We also propose that the same information be collected in regard to genetic variation, demography and phenology of populations of known orchid pollinators and co-blooming angiosperm species native to orchid habitats.