Limitations on the Use of Impermeable Mesocosms for Ecological Experiments Involving Aurelia sp. (Scyphozoa: Semaeostomeae)

Microcosms permit controlled ecological experiments but theeffects of small enclosures on predators, prey, and their interactions,compromise their relevance to field populations. I examinedthe effects of Aurelia size on the utility of impermeable mesocosmsdeployed in highly stable water columns. Aurelia of all sizes(5-29 cm bell diameter) were observed adhered to walls. Individualslarger than 10 cm adhered to walls in disproportionately highnumbers, experienced a significant decline in mean size, andincurred physical damage at greater rates, than those less than10 cm. These results demonstrate that, at least for impermeablewalled mesocosms deployed in low turbulence environments, largerenclosures will not necessarily (i) ameliorate wall effectsfor animals of the size typically manipulated in microcosmsand (ii) make enclosures suitable for manipulating Aurelia largerthan those normally enclosed in microcosms. The mechanism proposedto explain adhesion suggests that enclosure walls alter thehydrodynamics of fluid flow around Aurelia, which may have implicationsfor estimating the predation impact of these animals since thehydrodynamics of feeding and swimming have co-evolved.     

Experiments

In this article, I have provided a brief history of my life. After tracing my family background and my early interest in physical sciences, I discuss how I entered biology under the influence of Robert Emerson. I have always enjoyed doing experiments and this led to new measurements and analyses of chlorophyll unit, efficiency of photosynthesis, excitation energy transfer, delayed light emission, thermoluminescence and electroluminescence in photosynthetic organisms. It is my view that discoveries are made because we follow our scientific curiosities.This article was written at the invitation of Govindjee.     

Limitations of entropy maximization in ecology

Applying ideas of statistical mechanics in ecology have recently received quite some attention. The entropy maximization (EM) formalism looks particularly attractive, as it provides a simple algorithm to infer detailed system variables from a limited number of constraints. However, we point out that a blind application of this formalism can easily lead to wrong conclusions. To illustrate this, we reanalyze an ecological data set that has been used to claim the good performance of EM in predicting species abundances from trait measurements. We show that these results are entirely due to the restrictive constraints, and do not provide any support for the applicability of EM in ecology. By comparing with a simple example from physics, we indicate which characteristic mechanism of EM, and of statistical mechanics in general, is missing for the ecological example. This analysis introduces a series of methods to evaluate future attempts to apply EM in ecology.     

Limitations of oviductal transfers in swine

Eighty-six crossbred gilts were used in a series of experiments 1) to determine if eight-cell embryos enter the uterus before four-cell embryos do, and 2) to investigate the effects of transferring older, more developed embryos, either with or without intact zona pellucidae, to the oviducts of swine. Results of these experiments suggested that both four-and eight-cell embryos randomly enter the uterus on Days 3.5 to 4 (Day 0 = onset of estrus). Though there were no differences in survival rates or subsequent morphology of recovered embryos when transferred to the oviduct or uterus on Day 4, the transfer. of Day-6 embryos to the oviduct resulted in lower (P < 0.01) survival rates, and the recovered embryos were smaller (P < 0.01) than those introduced into the uterus. Survival rates were lower (P < 0.06) for zonae-free embryos transferred to the oviduct than for zonae-intact embryos; however, these differences were not evident when zonae-free embryos were transferred into the uterus. These experiments demonstrate that oviductal transfer procedures in swine are limited to zonae-intact, preblastocyst stage embryos.     

On the Limitations of Biological Knowledge

Scientific knowledge is grounded in a particular epistemology and, owing to the requirements of that epistemology, possesses limitations. Some limitations are intrinsic, in the sense that they depend inherently on the nature of scientific knowledge; others are contingent, depending on the present state of knowledge, including technology. Understanding limitations facilitates scientific research because one can then recognize when one is confronted by a limitation, as opposed to simply being unable to solve a problem within the existing bounds of possibility. In the hope that the role of limiting factors can be brought more clearly into focus and discussed, we consider several sources of limitation as they apply to biological knowledge: mathematical complexity, experimental constraints, validation, knowledge discovery, and human intellectual capacity.     

Limitations of next-generation genome sequence assembly

High-throughput sequencing technologies promise to transform the fields of genetics and comparative biology by delivering tens of thousands of genomes in the near future. Although it is feasible to construct de novo genome assemblies in a few months, there has been relatively little attention to what is lost by sole application of short sequence reads. We compared the recent de novo assemblies using the short oligonucleotide analysis package (SOAP), generated from the genomes of a Han Chinese individual and a Yoruban individual, to experimentally validated genomic features. We found that de novo assemblies were 16.2% shorter than the reference genome and that 420.2 megabase pairs of common repeats and 99.1% of validated duplicated sequences were missing from the genome. Consequently, over 2,377 coding exons were completely missing. We conclude that high-quality sequencing approaches must be considered in conjunction with high-throughput sequencing for comparative genomics analyses and studies of genome evolution.     

Statistical Limitations on Molecular Evolution

Abstract

Complexity of functions evolving in an evolution process are expected to be limited by the time length of an evolution process among other factors. This paper outlines a general method of deriving function-complexity limitations based on mathematical statistics and independent from details of a biological or genetic mechanism of the evolution of the function. Limitations on the emergence of life are derived, these limitations indicate a possibility of a very fast evolution and are consistent with “RNA world” hypothesis. The discussed method is general and can be used to characterize evolution of more specific biological organism functions and relate functions to genetic structures. The derived general limitations indicate that a co-evolution of multiple functions and species could be a slow process, whereas an evolution of a specific function might proceed very fast, so that no trace of intermediate forms (species) is preserved in fossil records of phenotype or DNA structure; this is consistent with a picture of “punctuated equilibrium”.