Simulation as experiment: a philosophical reassessment for biological modeling

Some scientific modelers suggest that complex simulation models that mimic biological processes should have a limited place in ecological and evolutionary studies. However, complex simulation models can have a role that is different from that of simpler models that are designed to be fit to data. Simulation can be viewed as another kind of experimental system and should be analyzed as such. Here, I argue that current discussions in the philosophy of science and in the physical sciences fields about the use of simulation as an experimental system have important implications for biology, especially complex sciences such as evolution and ecology. Simulation models can be used to mimic complex systems, but unlike nature, can be manipulated in ways that would be impossible, too costly or unethical to do in natural systems. Simulation can add to theory development and testing, can offer hypotheses about the way the world works and can give guidance as to which data are most important to gather experimentally.     

The use of biomarkers in surveillance, medical screening, and intervention

Building on mechanistic information, much of molecular epidemiologic research has focused on validating biomarkers, that is, assessing their ability to accurately indicate exposure, effect, disease, or susceptibility. To be of use in surveillance, medical screening, or interventions, biomarkers must already be validated so that they can be used as outcomes or indicators that can serve a particular function. In surveillance, biomarkers can be used as indicators of hazard, exposure, disease, and population risk. However, to obtain rates for these measures, the population at risk will need to be assessed. In medical screening, biomarkers can serve as early indicators of disease in asymptomatic people. This allows for the identification of those who should receive diagnostic confirmation and early treatment. In intervention (which includes risk assessment and communication, risk management, and various prevention efforts), biomarkers can be used to assess the effectiveness of a prevention or control strategy as well as help determine whether the appropriate individuals are assigned to the correct intervention category. Biomarkers can be used to provide group and individual risk assessments that can be the basis for marshalling resources. Critical for using biomarkers in surveillance, medical screening, and intervention is the justification that the biomarkers can provide information not otherwise accessible by a less expensive and easier-to-obtain source of information, such as medical records, surveys, or vital statistics. The ability to use validated biomarkers in surveillance, medical screening, and intervention will depend on the extent to which a strategy for evidence-based procedures for biomarker knowledge transfer can be developed and implemented. This will require the interaction of researchers and decision-makers to collaborate on public health and medical issues.     

THE NATURE OF CLADISTIC DATA

Abstract— Cladistic data are the characters of organisms. Character is defined as a feature that can be evaluated as a variable with two or more mutually exclusive and ordered states. Cladistic characters must be treated as multistate variables, and coded as sequential numbers or in additive binary fashion. Any other interpretation and handling of cladistic data will introduce error into analysis. Character states cannot be treated independently as present or absent, i.e., as nominal variables, because redundancy is introduced into the data and information content is sacrificed. Non-additive binary coding demonstrates that treating cladistic variables as nominal data will lead to multiple, equally parsimonious solutions. Defining characters found universally in a group of organisms, but unknown outside those organisms have no alternative state that can be designated as absent. Absence, however, is valid as a character state if it can be shown to be apomorphic. When two or more character states occur within a taxon, that taxon must be coded as having an unknown state for that character, or the taxon must be split in two or more taxa. Continuously varying quantitative data are not suitable for cladistic analysis because there is no justifiable basis for recognizing discrete states among them. Quantitative data are questionable even when they exhibit mutually exclusive states because the states can be interpreted only in reference to an archetype, i.e., as implied homologies not subject to test.     

Induced humoral immunity and vaccination against major human fungal pathogens

Protection against fungal pathogens can theoretically be elicited by vaccines that stimulate humoral or cellular immunity, or both. There is conclusive evidence that humoral immunity can modify the course of infection against certain pathogenic fungi such as Candida albicans and Cryptococcus neoformans. However, for other fungi, such as Aspergillus fumigatus, the notion that humoral immunity contributes to host defence is unproven. Attempts to evaluate the potential efficacy of humoral immunity using immune sera are often inconclusive, whereas consistent results can be obtained with monoclonal antibodies. Protective monoclonal antibodies can be used to identify antigens that induce useful humoral responses.     

Fluorescence in situ hybridization on vibratome sections of plant tissues

This protocol describes the application of fluorescence in situ hybridization (FISH) to three-dimensionally (3D) preserved tissue sections derived from intact plant structures such as roots or florets. The method is based on the combination of vibratome sectioning with confocal microscopy. The protocol provides an excellent tool to investigate chromosome organization in plant nuclei in all cell types and has been used on tissues of both monocot and dicot plant species. The visualization of 3D well-preserved tissues means that cell types can be confidently identified. For example, meiocytes can be clearly identified at all stages of meiosis and can be imaged in the context of their surrounding maternal tissue. FISH can be used to localize centromeres, telomeres, repetitive regions as well as unique regions, and total genomic DNAs can be used as probes to visualize chromosomes or chromosome segments. The method can be adapted to RNA FISH and can be combined with immunofluorescence labeling. Once the desired plant material is sectioned, which depends on the number of samples, the protocol that we present here can be carried out within 3 d.     

A unifying theory for methods of systematic analysis

A unifying theory for systematic analysis states that a number of methods should be used jointly to cope with various kinds of data; also that groups should be as consistent as possible, be made with least information loss, and where needed, be polythetic. A test of relationship, homogeneity, can use various kinds of data. It can take account of the internal variation of aggregate items such as genera. It can give due emphasis to smaller clusters that have likely important contexts of external items. It helps in analysing trends, cores and hazes in dendrograms. A proposed detector for formal groups can be based on measures of isolation, identifiability and inclusiveness. Non-mathematical, inter-item reaction tests such as hybridization and serology can also be used in grouping. All relationship data are used polythetically to reveal natural groups. This leads to a unified informational concept for taxa. This is more useful than the biological species concept that is restricted to inter-breeding data. All the methods appear to be analogues of the powerful human grouping instinct. The resulting compatibility is important as precise methods are needed mainly when the data are too complex for the mind to use reliably. Cladograms can be made by self-graded deweighting of homogeneity and agglomerative clustering. Unlike classical cladistics this can reveal any polythetic group. Finding the derived states for making cladograms is often much too hypothetical for a fully cladistic approach to be properly precise. Instead, where the evidence is weak, a milder strength of graded deweighting is used for the cladistic properties, which help to show relationships along with the others. Axiomatic failures of other classes of grouping methods are discussed. Unavoidable remnants of instinctive processing lower the precision of all the methods. The Uniter computer program, based on the theory, is tested with finely graded values of artificially ‘evolved’ items and with coarsely coded cladistic data. The results show that with natural data, the program should act as a fairly sensitive probe of past evolutionary branching. Another test shows how specimens from species complexes can be grouped and how distinctions between groups are analysed.     

BYPASS1 negatively regulates a root-derived signal that controls plant architecture

Plant architecture is regulated by endogenous developmental programs, but it can also be strongly influenced by cues derived from the environment. For example, rhizosphere conditions such as water and nutrient availability affect shoot and root architecture; this implicates the root as a source of signals that can override endogenous developmental programs. Cytokinin, abscisic acid, and carotenoid derivatives have all been implicated as long-distance signals that can be derived from the root. However, little is known about how root-derived signaling pathways are regulated. Here, we show that BYPASS1 (BPS1), an Arabidopsis gene of unknown function, is required to prevent constitutive production of a root-derived graft-transmissible signal that is sufficient to inhibit leaf initiation, leaf expansion, and shoot apical meristem activity. We show that this root-derived signal is likely to be a novel carotenoid-derived molecule that can modulate both root and shoot architecture.     

Maximal power tests for detecting defects in meiotic recombination

We have determined the marker separations (genetic distances) that maximize the probability, or power, of detecting meiotic recombination deficiency when only a limited number of meiotic progeny can be assayed. We find that the optimal marker separation is as large as 30-100 cM in many cases. Provided the appropriate marker separation is used, small reductions in recombination potential (as little as 50%) can be detected by assaying a single interval in as few as 100 progeny. If recombination is uniformly altered across the genomic region of interest, the same sensitivity can be obtained by assaying multiple independent intervals in correspondingly fewer progeny. A reduction or abolition of crossover interference, with or without a reduction of recombination proficiency, can be detected with similar sensitivity. We present a set of graphs that display the optimal marker separation and the number of meiotic progeny that must be assayed to detect a given recombination deficiency in the presence of various levels of crossover interference. These results will aid the optimal design of experiments to detect meiotic recombination deficiency in any organism.     

EEG and implanted sources in the brain

Localisation procedures are based on models of the EEG that are relatively simple. The models are based on assumptions and choices of parameters that can be mistaken. Thus, it is crucial to validate the localisation procedures used in EEG. One of the options is to use the data obtained with electrodes that are implanted within the brain of an epileptic patient as part of the pre-surgical evaluation. When one of two neighbouring electrodes is used as a current source and the other as a current sink this can be regarded as a current dipole. The current injected has to be below the threshold for activation of cells. The position of this dipole can be deduced from magnetic resonance or X-ray images. The current dipole gives rise to a potential distribution at the scalp that can be measured by EEG. The measurements can be compared with the potential distribution that is calculated in a forward computation. Another method is to use the measured potential at the scalp to localize the source and to compare the result with the actual position of the dipole. In this paper the measured potential distributions at the scalp due to implanted dipoles were used to evaluate different volume conductor models. Since intracerebral and subdural electrodes were introduced through trephine holes over the fronto-central areas, and the diameter of the holes was rather large, approximately 23 mm, special effort was put into modelling the skull. Two important assumptions could be validated in this study: the electric currents within the head are Ohmic and a dipole can be used to model the induced electric activity of pairs of contacts on subdural electrodes or intra cerebral electrodes.     

A kinetic model for the quantitative analysis of complement

A simple model has been developed which accurately predicts the time course of complement mediated lysis of sensitized red cells. The model assumes that the one hit theory of immune hemolysis is applicable and that the rate of lysis is directly proportional to the concentration of a complement component present in rate limiting amounts. It also assumes that the rate of lysis is dependent on the fraction of cells lysed. The model can be related to the classical von Krogh equation for end point complement analyses and can be used to estimate the rate constant for the critical step in hemolysis, as well as the efficiency of the critical complement component in the rate limiting step. Parameters derived from the model can be quantitatively related to complement concentration and can be used as the basis for a quantitative assay of complement activity. The model can also be used to calculate, for a particular sample, the concentration at which complement activity becomes undectable, the complement activity of the pure, undiluted sample, and the time required for the sample to produce complete lysis of the available cells.     

Theory of electrostatic effects in soft biological interfaces using atomic force microscopy.

We calculated the electrostatic force between a planar interface, such as a planar-supported lipid bilayer membrane, and the tip of a stylus on which another lipid bilayer or some other biomacromolecular system might be deposited. We considered styli with rounded tips as well as conical tips. To take into account the effect of dynamical hydrogen-bonded structures in the aqueous phase, we used a theory of nonlocal electrostatics. We used the Derjaguin approximation and identified the systems for which its use is valid. We pointed out where our approach differs from previous calculations and to what extent the latter are inadequate. We found that 1) the nonlocal interactions have significant effects over distances of 10-15 A from the polar zone and that, at the surface of this zone, the effect on the calculated force can be some orders of magnitude; 2) the lipid dipoles and charges are located a distance L from the hydrophobic layer in the aqueous medium and this can have consequences that may not be appreciated if it is ignored; 3) dipoles, located in the aqueous region, can give rise to forces even though the polar layer is unchanged, and if this is ignored the interpretation of force data can be erroneous if an attempt is made to rationalize an observed force with a knowledge of an uncharged surface; 4) the shape of the stylus tip can be very important, and a failure to take this into account can result in incorrect conclusions, a point made by other workers; and 5) when L is nonzero, the presence of charges and dipoles can yield a force that can be nonmonotonic as a function of ionic concentration.     

Symmetries of S-systems.

An S-system is a set of first-order nonlinear differential equations that all have the same structure: The derivative of a variable is equal to the difference of two products of power-law functions. S-systems have been used as models for a variety of problems, primarily in biology. In addition, S-systems possess the interesting property that large classes of differential equations can be recast exactly as S-systems, a feature that has been proven useful in statistics and numerical analysis. Here, simple criteria are introduced that determine whether an S-system possesses certain types of symmetries and how the underlying transformation groups can be constructed. If a transformation group exists, families of solutions can be characterized, the number of S-system equations necessary for solution can be reduced, and some boundary value problems can be reduced to initial value problems.     

Nonparametric tests of association between survival time and continuously measured covariates: the logit-rank and associated procedures

O'Brien's logit-rank procedure (1978, Biometrics 34, 243-250) is shown to arise as a score test based on the partial likelihood for a proportional hazards model provided the covariate structure is suitably defined. Within this framework the asymptotic properties claimed by O'Brien can be readily deduced and can be seen to be valid under a more general model of censoring than that considered in his paper. More important, perhaps, it is now possible to make a more natural and interpretable generalization to the multiple regression problem than that suggested by O'Brien as a means of accounting for the effects of nuisance covariates. This can be achieved either by modelling or stratification. The proportional hazards framework is also helpful in that it enables us to recognize the logit-rank procedure as being one member of a class of contending procedures. One consequence of this is that the relative efficiencies of any two procedures can be readily evaluated using the results of Lagakos (1988, Biometrika 75, 156-160). Our own evaluations suggest that, for non-time-dependent covariates, a simplification of the logit-rank procedure, leading to considerable reduction in computational complexity, is to be preferred to the procedure originally outlined by O'Brien.     

Ecological developmental biology: environmental signals for normal animal development

The environment plays instructive roles in development and selective roles in evolution. This essay reviews several of the instructive roles whereby the organism has evolved to receive cues from the environment in order to modulate its developmental trajectory. The environmental cues can be abiotic (such as temperature or photoperiod) or biotic (such as those emanating from predators, conspecifics, or food), and the “alteration” produces a normal, not a pathological, phenotype, that is appropriate for the environment. In addition, symbiotic organisms can produce important signals during normal development. Environmental cues can be obligatory, such that the organism cannot develop without the environmental cue. These cues often permit and instruct the organism to proceed from one developmental stage to another, as when larvae receive cues to settle and undergo metamorphosis from substrates. Such obligatory cues can also be given by symbionts, as when Wolbachia bacteria prevent apoptosis in developing ovaries of some wasps. Other environmental cues can be used facultatively, allowing organisms to follow different developmental trajectories depending on whether the cue is present or not. This can be seen in the temperature‐dependent determination of sex in many reptiles and in the determination of thermotolerance in aphids by their symbiotic bacteria. Signaling from the environment is essential in development, and co‐development appears to be normative between symbionts and their hosts. Here, one sees the reciprocal induction of gene expression, just as within the embryonic organism. The ability of organisms to respond to environmental cues by producing different phenotypes may be critically important in evolution, and it may be an essential feature that can facilitate or limit evolution.     

THE INTERNAL ORGANIZATION OF MITOCHONDRIA

Sections of mitochondria in Paramecium and Euplotes present a consistent pattern. The mitochondrion in these cells can be conceived of as a twisted mass of closely compacted tubules. Two general kinds of substances can be recognized: the electron-dense that borders the lumen of the tubule, and the less dense that forms the continuum. In sections of mitochondria in rat kidney and snail oviduct, tubular internal organization can be recognized. In the same organs, mitochondria with lamellar internal structure can be demonstrated. The thesis is developed that the mitochondrion is a structure capable of differentiation and change, and that developmental continuity among the different kinds may exist. Mitochondria that appear to be different may be quite similar basically; mitochondria that appear to be similar in structure may be different in other ways. The tubule is proposed as the most basic of the presently recognized mitochondrial structures.     

A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering

A mixed-integer linear program (MILP) is described that can enumerate all the ways fluxes can distribute in a metabolic network while still satisfying the same constraints and objective function. The multiple solutions can be used to (1) generate alternative flux scenarios that can account for limited experimental observations, (2) forecast the potential responses to mutation (e.g., new reaction pathways may be used), and (3) (as illustrated) design (13)C NMR experiments such that different potential flux patterns in a mutant can be distinguished. The experimental design is enabled by using the MILP results as an input to an isotopomer mapping matrices (IMM)-based program, which accounts for the network circulation of (13)C from a precursor such as glucose. The IMM-based program can interface to common plotting programs with the result that the user is provided with predicted NMR spectra that are complete with splittings and Lorentzian line-shape features. The example considered is the trafficking of carbon in an Escherichia coli mutant, which has pyruvate kinase activity deleted for the purpose of eliminating acetate production. Similar yields and extracellular measurements would be manifested by the flux alternatives. The MILP-IMM results suggest how NMR experiments can be designed such that the spectra of glutamate for two flux distribution scenarios differ significantly.     

Modeling cell concentration in complex media

A model that continuously predicts the concentration of microorganisms in complex medium fermentations is suggested. The model uses carbon dioxide evolution as its primary input and assumes that respiration activity can be differentiated into growth-related and maintenance-related functions. This model can be programmed on computer-coupled vessels and used to standardize on a physiological fermentation inoculum transfer time. The cell concentration estimate can also be used to calculate specific growth rate and can be combined with additional monitored information to calculate other important fermentation parameters such as specific oxygen uptake.     

Crenation and cupping of the red cell: A new theoretical approach. Part I. Crenation

Crenation can be thought of as a surface instability caused by intrinsic precurvature of the membrane. Mathematical modeling, on the presupposition that the red blood cell is a thin shell consisting of a connected (coupled) bilayer having uniformly distributed elastic properties shows that crenation can be initiated by negative precurvature, that is, intrinsic curvature having its concavity directed towards the outside of the cell. This is contrary to the currently accepted view which attributes the effect to positive precurvature of an unconnected bilayer. Crenation and the biconcave shape can coexist in the red cell. This suggests that the bilayer must be connected even when the cell is crenated because the biconcave shape could not otherwise be maintained. The progressive development of crenation to more advanced stages, such as the echinocyte type III and the spheroechinocyte can be accounted for if the outer layer of the membrane is stressed beyond the range where strain is proportional to stress. This is consistent with the extremely small radius of curvature at the tips of the crenations.Certain small variations in the uncrenated biconcave shape of the red cell can be interpreted mathematically as due either to negative intrinsic curvature or to shear resistance. Since, however, a small amount of negative precurvature has been shown to be capable of inducing crenation, it is unlikely to be the cause of the variations in the biconcave shape. These must therefore be due to shear resistance.In the light of this new approach, membrane molecular models based on the assumption that crenation is due to positive precurvature need reconsideration.     

Functional salutogenic mechanisms of the brain

Neuroscientists are typically interested in the brain in relation to disease, but much could also be learned by studying the brain in relation to health. The brain has processes, functional salutogenic mechanisms, that contribute to health by enabling one's outlook on life to benefit one's health. For example, the belief that things will work out as well as can reasonably be expected is a key aspect of the outlook of people who tend to stay well even when in potentially stressful situations. Believing in God, feeling happy, being mutually in love, and expecting things to change for the better are also outlooks that can be salutogenic. Beliefs need not even be rational or realistic in order for them to be salutogenic, as shown by phenomena such as faith healing and the placebo effect. Thus, the brain responds to stimuli and interprets them, mainly without one's awareness, in ways that can enhance one's well-being. Although little is presently known concerning neuropathways of functional salutogenic mechanisms, further research on relations between salutogenesis and brain function can be expected to provide new strategies for improving health worldwide.