The water-tower analogy of the cardiovascular system

The cardiovascular system is a complex arrangement of hydraulic, yet living, components. The complexity of this system may make it difficult for students to see the "forest" instead of the "trees." To better explain the dynamics of cardiovascular function and control, an analogy has been drawn to the operation of a city water supply. In cities that use a water tower, fresh water is pumped up into the tower from a river or other source. The tower serves as a pressure reservoir for providing water to homes through a largely parallel arrangement of distribution pipes. Local homeowners control their own water usage through faucets, whereas the city maintains water pressure by monitoring the level in the tower. Key analogous points with the cardiovascular system are the heart as the city pump, the aorta as the water tower, arteries as parallel distribution pipes, and arterioles as faucets. Baroreceptor reflex control is discussed as well as such features as the capacitance role of veins, the skeletal muscle pump, and the competition between locally mediated vasodilation and sympathetically mediated vasoconstriction. Subjective student and peer evaluations have indicated that this analogy is effective in improving student comprehension of the cardiovascular system.     

Australopithecine diet based on a baboon analogy

Recent analyses suggest that both gracile and robust australopithecines could have been “small object feeders” in the sense suggested by Jolly (1970). Data are presented on the diet of Theropithecus gelada, a grassland baboon which has been put forward as a possible analogy for this stage in hominid evolution. The relevance of these data for a reconstruction of australopithecine diet is assessed and the implications of a “small object” diet for the evolution of hunting are discussed.     

Conformational analogy between substance P and physalaemin

The three-dimensional structure of physalaemin, pGlu-Ala-Asp-Pro-Asn-Lys-Phe-Tyr-Gly-Leu-Met-NH2, has been studied by one- and two-dimensional 500 MHz NMR spectroscopies in two solvents: methanol and dimethyl sulfoxide. As previously observed for substance P in methanol, the core of physalaemin 4----8 is folded into an helical conformation. This structure is stabilized by the presence of a salt bridge between Asp-3 and Lys-6 in both solvents. The only differences observed reside in the N-terminal sequences; the N-terminal tripeptide of substance is flexible whereas that of physalaemin is in an extended conformation.     

Mechanistic analogy: how microcosms explain nature

Microcosm studies of ecological processes have been criticized for being unrealistic. However, since lack of realism is inherent to all experimental science, if lack of realism invalidates microcosm models of ecological processes, then such lack of realism must either also invalidate much of the rest of experimental ecology or its force with respect to microcosm studies must derive from some other limitation of microcosm apparatus. We believe that the logic of the microcosm program for ecological research has been misunderstood. Here, we respond to the criticism that microcosm studies play at most a heuristic role in ecology with a new account of scientific experimentation developed specifically with ecology and other environmental sciences in mind. Central to our account are the concepts of model-based reasoning and analogical inference. We find that microcosm studies are sound when they serve as models for nature and when certain properties, referred to as the essential properties, are in positive analogy. By extension, our account also justifies numerous other kinds of ecological experimentation. These results are important because reliable causal accounts of ecological processes are necessary for sound application of ecological theory to conservation and environmental science. A severe sensitivity to reliable representation of causes is the chief virtue of the microcosm approach.     

Arguing by analogy in the fetal tissue debate

In the debate over fetal tissue use, an analogy is often drawn between removing organs from the body of a person who has been murdered to use for transplantation, and collecting tissue from an aborted fetus to use for the same purpose. The murder victim analogy is taken by its proponents to show that even if abortion is the moral equivalent of murder, there is still no good reason to refrain from using the fetal tissue, since as a society we do not see any problem about using organs from murder victims. However, I argue that the analogy between murder victims and aborted fetuses does not hold — the two situations are not the same in all morally relevant respects. Thus the murder victim analogy does not provide an argument in favour of fetal tissue transplant. In conclusion, I point to some of the potential pitfalls of using analogies in ethical argument.     

Formal Darwinism,the individual-as-maximizing-agent analogy and bet-hedging

The central argument of The origin of species was that mechanical processes (inheritance of features and the differential reproduction they cause) can give rise to the appearance of design. The ''mechanical processes'' are now mathematically represented by the dynamic systems of population genetics, and the appearance of design by optimization and game theory in which the individual plays the part of the maximizing agent. Establishing a precise individual-as-maximizing-agent (IMA) analogy for a population-genetics system justifies optimization approaches, and so provides a modern formal representation of the core of Darwinism. It is a hitherto unnoticed implication of recent population-genetics models that, contrary to a decades-long consensus, an IMA analogy can be found in models with stochastic environments (subject to a convexity assumption), in which individuals maximize expected reproductive value. The key is that the total reproductive value of a species must be considered as constant, so therefore reproductive value should always be calculated in relative terms. This result removes a major obstacle from the theoretical challenge to find a unifying framework which establishes the IMA analogy for all of Darwinian biology, including as special cases inclusive fitness, evolutionarily stable strategies, evolutionary life-history theory, age-structured models and sex ratio theory. This would provide a formal, mathematical justification of fruitful and widespread but ''intentional'' terms in evolutionary biology, such as ''selfish'', ''altruism'' and ''conflict''.     

Accurate quantification of functional analogy among close homologs

Correctly evaluating functional similarities among homologous proteins is necessary for accurate transfer of experimental knowledge from one organism to another, and is of particular importance for the development of animal models of human disease. While the fact that sequence similarity implies functional similarity is a fundamental paradigm of molecular biology, sequence comparison does not directly assess the extent to which two proteins participate in the same biological processes, and has limited utility for analyzing families with several parologous members. Nevertheless, we show that it is possible to provide a cross-organism functional similarity measure in an unbiased way through the exclusive use of high-throughput gene-expression data. Our methodology is based on probabilistic cross-species mapping of functionally analogous proteins based on Bayesian integrative analysis of gene expression compendia. We demonstrate that even among closely related genes, our method is able to predict functionally analogous homolog pairs better than relying on sequence comparison alone. We also demonstrate that the landscape of functional similarity is often complex and that definitive "functional orthologs" do not always exist. Even in these cases, our method and the online interface we provide are designed to allow detailed exploration of sources of inferred functional similarity that can be evaluated by the user.     

On the analogy between forskolin and D-glucose.

2-O-Acetyl-D-glucose was synthesized in order to evaluate the influence of an acyl group on the binding with the glucose carrier protein (GluT); as its affinity neighbours that of glucose itself, the glucose-forskolin analogy appears to be coincidental and several explanations are proposed.     

A physical analogy of the genetic toggle switch.

We show that there is a physical analogy between a stochastic model of a genetic toggle switch system and a thermostated particle moving in a potential field, derived from the probability distribution of the toggle switch. This result suggests that one can actually simulate the dynamics of a more complex gene network by considering an ensemble of thermostated particles moving in a potential field, derived from the stationary distribution of the chemical stochastic model describing the gene network.     

Evolution, language and analogy in functional genomics.

Almost a century ago, Wittgenstein pointed out that theory in science is intricately connected to language. This connection is not a frequent topic in the genomics literature. But a case can be made that functional genomics is today hindered by the paradoxes that Wittgenstein identified. If this is true, until these paradoxes are recognized and addressed, functional genomics will continue to be limited in its ability to extrapolate information from genomic sequences.     

Computerized planning for multiprobe cryosurgery using a force-field analogy

Cryosurgery is the destruction of undesired biological tissues by freezing. For internal organs, multiple cryoprobes are inserted into the tissue with the goal of maximizing cryoinjury within a predefined target region, while minimizing cryoinjury to the surrounding tissues. The objective of this study is to develop a computerized planning tool to determine the best locations to insert the cryoprobes, based on bioheat transfer simulations. This tool is general and suitable for all available cooling techniques and hardware. The planning procedure employs a novel iterative optimization technique based on a force-field analogy. In each iteration, a single transient bioheat transfer simulation of the cryoprocedure is computed. At the end of the simulation, regions of tissue that would have undesired temperatures apply "forces" to the cryoprobes directly moving them to better locations. This method is more efficient than traditional numerical optimization techniques, because it requires significantly fewer bioheat transfer simulations for each iteration of planning. For demonstration purposes, 2D examples on cross sections typical of prostate cryosurgery are given.     

A thermal analogy for modelling drug elution from cardiovascular stents

Restriction of blood flow by the narrowing or occlusion of arteries is one of the most common presentations of cardiovascular disease. One treatment involves the introduction of a metal scaffold, or stent, designed to prevent recoil and to provide structural stability to the vessel. On the occasions that this treatment is ineffective, failure is usually associated with re-invasion of tissue. This can be prevented by local delivery of drugs which inhibit tissue growth. The drug might be delivered locally in a polymer coating on the stent. This paper develops and explores the use of a thermal analogue of the drug delivery process and the associated three-dimensional convection-diffusion equation to model the spatial and temporal distribution of drug concentration within the vessel wall. This allows the routine use of commercial finite element analysis software to investigate the dynamics of drug distribution, assist in the understanding of the treatment process and develop improved delivery systems. Two applications illustrate how the model might be used to investigate the effects of controllable or measurable parameters on the progression of the process. It is demonstrated that the geometric characteristics of the stent can have significant impact on the homogeneity of the dosing in the vessel wall.     

Planctomycetes and eukaryotes: a case of analogy not homology

Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.     

Darwin's use of the analogy between artificial and natural selection

Conclusion The central role played by Darwin's analogy between selection under domestication and that under nature has been adequately appreciated, but I have indicated how important the domesticated organisms also were to other elements of Darwin's theory of evolution-his recognition of the constant principle of change, for instance, of the imperfection of adaptation, and of the extent of variation in nature. The further development of his theory and its presentation to the public likewise hinged on frequent reference to domesticates.We have seen that Darwin's reliance on the analogy between domesticated varieties and wild species was a bold and original step, in light of contemporary views on the nature of domesticates. However, as Darwin undoubtedly foresaw, his reliance on the analogy created difficulties as well as solving problems, and these began with his Malthusian codiscoverer of the principle of natural selection, Alfred Russel Wallace. Wallace's paper On the Tendency of Varieties to Depart Indefinitely from the Original Type, presented to the Linnean Scoiety along with the first public unveiling of Darwin's theory, states: We see, then, that no inferences as to varieties in a state of nature can be deduced from the observation of those occurring among domestic animals. The two are so much opposed to each other in every circumstance of their existence, that what applies to the one is almost sure not to apply to the other. Domestic animals are abnormal, irregular, artificial; they are subject to varieties which never occur and never can occur in a state of nature.⁶² Much has been made of the similarity of views of Darwin and Wallace, but this quotation surely reveals how utterly different their views were on what to Darwin was an important matter. Several critics of the Origin saw Darwin's reliance on the domesticates as his Achilles heel. As Young has pointed out, Samuel Wilberforce included the following passage in his attack on the Origin: Nor must we pass over unnoticed the transference of the argument from the domesticated to the untamed animals. Assuming that man as the selector can do much in a limited time, Mr. Darwin argues that Nature, a more powerful, a more continuous power, working over vastly extended ranges of time, can do more. But why should Nature, so uniform and persistent in all her operations, tend in this instance to change? Why should she become a selector of varieties?⁶³ Another critic, Fleeming Jenkin, found the analogy a weakness in Darwin's theory because of the limited extent of variation in any one direction in domestic animals and plants.⁶⁴ We have already seen that Darwin had confided a similar view to his notebook thirty years earlier, but changed his mind as a result of his profound study of domesticates. De Beer's reference to an English country gentleman's knowledge of domestic plants and animals and their breeding⁶⁵ fails totally to recognize the originality and depth of Darwin's knowledge of domesticates.Why did Darwin, against the currents of his time, rely so heavily on mankind's experience with domesticated organisms to shape his theory about species in nature? On reason is that only with domesticates was an approach that came close to experimental verification possible. Darwin fully realized the inadequacies of the experiment, as is emphasized by his repeated contrasting of selection under nature and selection by man. Yet the extensive experience and data of plant and animal breeders offered the only reliable base against which Darwin could continually challenge his views. As he wrote in the introduction to Variation, with domestication, man ... may be said to have been trying an experiment on a gigantic scale.⁶⁶ Given Darwin's high opinion of the quantitative work of Malthus and Quetelet (as emphasized by Schweber),⁶⁷ and his unremitting efforts to secure data by which to test his theories, it was inevitable that he should attach high significance to domesticated varieties. John Tyndall, in his Belfast address of 1874, said: The strength of the doctrine of Evolution consists, not in experimental demonstration (for the subject is hardly accessible to this mode of proof), but in its general harmony with scientific thought.⁶⁸ Darwin would have agreed with the latter thought, but I think he would have challenged the preceding one on the grounds that long experience with domesticated varieties did provide an element of experimental demonstration. It gave him confidence in his theory, and he used his vast knowledge of artificial selection boldly and creatively.