Putting the systems back into systems biology

In recent years the term "systems biology" has become widespread in the biological literature, but most of the papers in which these words appear have surprisingly little to do with older notions of biological systems: they often seem to imply little more than reductionist biology applied on a large scale, with a little attention to interactions between some of the components, but with minimal attention to the kinetic properties of enzymes, which supplied much of the reductionist foundation of biochemistry. A systemic approach to biology ought to put the emphasis on the entire system; insofar as it is concerned with components at all, it is to explain their roles in meeting the needs of the system as a whole. Genuinely systemic thinking allows us to understand how biochemical systems are regulated, and why clumsy attempts to manipulate them for biotechnological purposes may fail. At a more abstract level, it is necessary for understanding the nature of life, because as long as an organism is treated as no more than a collection of components, one cannot ask the right questions, and certainly cannot answer them.     

Science and nonsense

This article is a review of literature in developmental psychology concerned with children's thinking about their own bodies. There is an emphasis on ways in which children explain things that they know about their bodies. Very young children (younger than about 7 years of age) may have intuitive understanding of the distinction between the biological nature of the body and ways in which the mind controls and influences the body, but they sometimes explain processes that adults think of as biological in psychological ways. Older children acquire knowledge of internal organs and processes in the body, particularly ones concerned with the transformation of substances. However, they may understand these processes in ways different from that of a basic biological framework. The possibility that children have ideas about vital energies or forces is considered. Some implications for biology education are discussed.     

Resolving the Anti-Antievolutionism Dilemma: A Brief for Relational Evolutionary Thinking in Anthropology

ABSTRACT   Anthropologists often disagree about whether, or in what ways, anthropology is "evolutionary." Anthropologists defending accounts of primate or human biological development and evolution that conflict with mainstream "neo-Darwinian" thinking have sometimes been called "creationists" or have been accused of being "antiscience." As a result, many cultural anthropologists struggle with an "anti-antievolutionism" dilemma: they are more comfortable opposing the critics of evolutionary biology, broadly conceived, than they are defending mainstream evolutionary views with which they disagree. Evolutionary theory, however, comes in many forms. Relational evolutionary approaches such as Developmental Systems Theory, niche construction, and autopoiesis–natural drift augment mainstream evolutionary thinking in ways that should prove attractive to many anthropologists who wish to affirm evolution but are dissatisfied with current "neo-Darwinian" hegemony. Relational evolutionary thinking moves evolutionary discussion away from reductionism and sterile nature–nurture debates and promises to enable fresh approaches to a range of problems across the subfields of anthropology. [Keywords: evolutionary anthropology, Developmental Systems Theory, niche construction, autopoeisis, natural drift]     

Using models to enhance the intellectual content of learning in developmental biology

Models have been particularly useful in developmental biology over the last 30 years. At first, underlying control mechanisms were poorly understood, but over time a wealth of detailed information became available to provide an increasingly detailed knowledge of underlying mechanisms, at levels from genes through cells to organs, organisms and populations. Models are also of great value in teaching developmental biology, as they allow students to explore phenomena hard to perceive directly because of their scale, accessibility, expense or other considerations. A model may allow students to "experiment" in ways which would be impractical in real life, as well as give them a deep understanding of competing hypotheses of development. Lastly, students can be challenged to produce models of their own, whereas only rarely are they able to carry out original experiments. I discuss two main kinds of models and their uses in generating, testing and expounding hypotheses and point out dangers in the use of models in education. Models may draw upon and reflect the consensus paradigm in the field: a researcher may be able to appreciate that models are interim conditional statements of probability and use them to generate new knowledge. A student may be less able to do so and may fail to appreciate where new knowledge will come from. And unlike physics, biology is stochastic and contingent and can never be entirely deduced from first principles, implying that models can never be as perfect in any biological field as they can be in some other fields.     

Evolutionary thinking among biology students in a third world country

Background

Evolutionary thinking is traditionally directly related to education and inversely to religiosity. Accordingly, biology students are naturally expected to be more prone to naturalist evolution due to their close contact with this theory and high scientific literacy. To test this, we performed a cross-national study surveying biology students’ evolutionary opinions in Brazil, contrasting the proportions of creationism (Cr), divinely guided evolution (DGE) and naturalist evolution (NaE).

Results

We found that NaE comprised 44.4%, DGE 43.3%, and Cr 12.3% of students’ opinions. NaE was higher among postgraduate than undergraduate students. There were marked geographic differences, with NaE peaking in the most socioeconomically developed regions and Cr in the less. Opinions related to divine influence as a whole (Cr + DGE) became more likely as the score of students’ institutions decreased (i.e. institutions with lower-quality standards).

Conclusions

Most biology students paradoxically do not have NaE as an explanation (55.6%), a high proportion given their presumed contact with the theory. We demonstrate that socioeconomic and institution quality factors are apparently important in determining the evolutionary thinking patterns. NaE paucity among biology students may also be influenced by low scientific literacy and the extreme religiosity of the population, which incorporates divine influence in students’ opinions long before they have any contact with evolutionary theory.

     

Tree thinking cannot taken for granted: challenges for teaching phylogenetics

Tree thinking is an integral part of modern evolutionary biology, and a necessary precondition for phylogenetics and comparative analyses. Tree thinking has during the 20th century largely replaced group thinking, developmental thinking and anthropocentricism in biology. Unfortunately, however, this does not imply that tree thinking can be taken for granted. The findings reported here indicate that tree thinking is very much an acquired ability which needs extensive training. I tested a sample of undergraduate and graduate students of biology by means of questionnaires. Not a single student was able to correctly interpret a simple tree drawing. Several other findings demonstrate that tree thinking is virtually absent in students unless they are explicitly taught how to read evolutionary trees. Possible causes and implications of this mental bias are discussed. It seems that biological textbooks can be an important source of confusion for students. While group and developmental thinking have disappeared from most textual representations of evolution, they have survived in the evolutionary tree drawings of many textbooks. It is quite common for students to encounter anthropocentric trees and even trees containing stem groups and paraphyla. While these biases originate from the unconscious philosophical assumptions made by authors, the findings suggest that presenting unbiased evolutionary trees in biological publications is not merely a philosophical virtue but has also clear practical implications.

Genome,Evolution, Drosophila and Beyond: The New Dimensions

A century ago, a little fly with red eyes was first used for genetic studies. That insignificant fly called at that time, Drosophila ampelophila, was going to revolutionize biology while becoming the model we know today as Drosophila melanogaster. Since then, its study has never ceased, but the field of interest has somewhat changed over the century. Drosophila meetings are exceptional opportunities to gather biologists of diverse backgrounds to not only learn about the latest improvements in our field of interest, but also to appreciate learning another bit of biology. From this biological melting pot a culture very specific to the fly community has emerged. Thus, besides neurobiology, cell biology and development a diversity of other fields of research exist, and they all have their own place in the cultural and historical dimension of the "Drosophila" model. Several communications from these diverse fields of research were presented at the 8th Japanese Drosophila Research Conference (JDRC8) and they are briefly reported here.     

B chromosomes in plants: escapees from the A chromosome genome?

B chromosomes are dispensable elements that do not recombine with the A chromosomes of the regular complement and that follow their own evolutionary track. In some cases, they are known to be nuclear parasites with autonomous modes of inheritance, exploiting "drive" to ensure their survival in populations. Their "selfishness" brings them into conflict with their host nuclear genome and generates a host-parasite relationship, with anti-B-chromosome genes working to ameliorate the worst of their excesses in depriving their hosts of genetic resources. Molecular studies are homing in on their sequence organization to give us an insight into the origin and evolution of these enigmatic chromosomes, which are, with rare exceptions, without active genes.     

Using research projects and qualitative conceptual modeling to increase novice scientists’ understanding of ecological complexity

A new program, Teaching Ecological Complexity, is working to develop a heightened capacity for systems thinking among high school biology and environmental sciences teachers. During a 2-week field-based course, the teachers use qualitative conceptual modeling, participate in all stages of field experimentation, and formulate plans to teach field research with their own classes. Qualitative conceptual modeling was found to be useful in revealing the underlying perceptions of ecosystem functioning for these novice scientists. Preliminary results showed improvement in their ability to recognize and apply some of the attributes of complex ecosystem: non-linear feedback loops, hierarchical organization, patterns illustrating the spatial arrangements of species diversity. In addition to using models, teachers used peer-learning techniques. Collegial discussions about what they understood at particular points in time were useful in improving their understanding of ecosystem phenomenon.     

The essence of student visual-spatial literacy and higher order thinking skills in undergraduate biology

Science, engineering and mathematics-related disciplines have relied heavily on a researcher's ability to visualize phenomena under study and being able to link and superimpose various abstract and concrete representations including visual, spatial, and temporal. The spatial representations are especially important in all branches of biology (in developmental biology time becomes an important dimension), where 3D and often 4D representations are crucial for understanding the phenomena. By the time biology students get to undergraduate education, they are supposed to have acquired visual-spatial thinking skills, yet it has been documented that very few undergraduates and a small percentage of graduate students have had a chance to develop these skills to a sufficient degree. The current paper discusses the literature that highlights the essence of visual-spatial thinking and the development of visual-spatial literacy, considers the application of the visual-spatial thinking to biology education, and proposes how modern technology can help to promote visual-spatial literacy and higher order thinking among undergraduate students of biology.     

Dispersal Behaviour and Transmission Strategies of the Entomopathogenic Nematodes Heterorhabditis and Steinernema

Entomopathogenic nematodes of the Heterorhabditidae and Steinernematidae appear to be capable of long-distance dispersal and local migration. Their transmission strategies include both highly active seek-and-destroy behaviours and ambusher strategies, and they may be sensitive to sex-related factors in their own populations. Their host-finding abilities are poorly understood, despite the fact that these abilities are fundamental to their success as biocontrol agents in soil. Like the vast numbers of exotic hymenopterans and other natural enemies that have been released for biological control over the past century, they may be used in their ecologically competent wild-type form. On the other hand, because they are applied inundatively, they may be tailored, by breeding or transformation, to their intended purpose and to ecological incompetence, improving both their efficacy and their ecological safety.     

Video laboratories for the teaching and learning of professional ethics in exercise physiology curricula

Student researchers in physiology courses often interact with human subjects in classroom research but may be unfamiliar with the professional ethics of experimenter-subject interactions. This communication describes experiences related to an interactive video used in exercise science and general biology courses to help students become aware of, sensitive to, and comfortable with implementing professional ethics into their own thinking and behavior as researchers before entering the laboratory. The activity consisted of a filmed exercise physiology experiment complemented with interactive question sheets followed by small- and large-group discussion and culminating with individual student reflections. Student written responses from multiple courses indicated that students were able to 1) identify and consider the ethics of experimenter-subject interactions from the movie, 2) generalize broader ideas of professional ethics from those observations, and 3) consider their observations in terms of future experiments they would be conducting personally and how they should interact with human subjects. A majority of students indicated a positive reaction to the video and identified specific aspects they appreciated. It is hoped that this report will encourage other instructors to consider the use of interactive videos in the teaching and learning of professional ethics related to their courses.     

Teaching cell biology to nonscience majors through forensics, or how to design a killer course

Nonscience majors often do not respond to traditional lecture-only biology courses. However, these students still need exposure to basic biological concepts. To accomplish this goal, forensic science was paired with compatible cell biology subjects. Several topics such as human development and molecular biology were found to fulfill this purpose. Another goal was to maximize the hands-on experience of the nonscience major students. This objective was fulfilled by specific activities such as fingerprinting and DNA typing. One particularly effective teaching tool was a mock murder mystery complete with a Grand Jury trial. Another objective was to improve students' attitudes toward science. This was successful in that students felt more confident in their own scientific abilities after taking the course. In pre/post tests, students answered four questions about their ability to conduct science. All four statements showed a positive shift after the course (p values ranging from.001 to.036, df = 23; n = 24). The emphasis on experiential pedagogy was also shown to increase critical thinking skills. In pre/post testing, students in this course significantly increased their performance on critical thinking assessment tests from 33.3% correct to 45.3% (p =.008, df = 4; n = 24).     

Honoring Our Own: Rethinking Indigenous Languages and Literacy

Today Indigenous peoples worldwide are deconstructing Western paradigms, including the classic constructs of literacy connected to alphabet systems, and articulating and constructing their own distinct paradigms based on Indigenous epistemologies and rooted in self-determination and social justice. A vital aspect of these efforts is the "rethinking of our thinking" and a reexamination of our priorities as a means for reconstituting, reproducing, and validating our own intellectual traditions and cultural knowledge and processes.     

Population thinking and tree thinking in systematics

Two new modes of thinking have spread through systematics in the twentieth century. Both have deep historical roots, but they have been widely accepted only during this century. Population thinking overtook the field in the early part of the century, culminating in the full development of population systematics in the 1930s and 1940s, and the subsequent growth of the entire field of population biology. Population thinking rejects the idea that each species has a natural type (as the earlier essentialist view had assumed), and instead sees every species as a varying population of interbreeding individuals. Tree thinking has spread through the field since the 1960s with the development of phylogenetic systematics. Tree thinking recognizes that species are not independent replicates within a class (as earlier group thinkers had tended to see them), but are instead inter-connected parts of an evolutionary tree. It lays emphasis on the explanation of evolutionary events in the context of a tree, rather than on the states exhibited by collections of species, and it sees evolutionary history as a story of divergence rather than a story of development. Just as population thinking gave rise to the new field of population biology, so tree thinking is giving rise to the new field of phylogenetic biology.     

Why respiratory biology? The meaning and significance of respiration and its integrative study

Traditionally the process of respiration is divided into threephases: (1) cellular respiration, (2) transport of respiratorygases and (3) ventilation of the gas exchange organs (breathing).Thereby organisms assimilate chemical energy from the environment,and within their cells transfer it from molecule to moleculein a stepwise fashion. Although studied separately, these phasesrepresent a continuum and cellular respiration in all life formshas much in common. Ironically, these respiratory foci havebeen artificially delineated by their own practitioners, whotend to publish in their own journals, and attend their ownconferences. The goal of modern respiratory biology should beto understand biological connectivity and complexity by viewingan organism as a series of interconnecting systems from moleculeto ecosystem. The future of science in general, and biologyin particular, lies in disciplinary networking: combining theresults of traditional disciplines to better understand thewhole. Because of its universality, Respiratory Biology canbest provide this bridge and improve interdisciplinary studiesin biology generally. To this end, the First International Congressof Respiratory Biology was held from August 14 to 16, 2006,at Bonn, Germany. As evident from the success of this inauguralmeeting, these are exciting times for Respiratory Biology. Theexplosion of "X-omics" and systems biology, the powerful geneticapproaches to disease treatment, and the long-standing and newlyemerging questions in evolutionary biology and ecology; allportend a continuing role of respiratory biology as a key integrativediscipline.     

Peritoneovenous shunt - modification with the use of long saphenous vein

The authors describe their own initial experience with saphenoperitoneal modification of the peritoneovenous shunt in intractable ascites solution. Their findings with this easy type of permanent ascites drainage using the "patient's own resources" are puzzling.     

在"导、探"中培养学生的创新意识

以“减数分裂”一课为例,从“导、探”的准备阶段、操作阶段和巩固练习三个方面来说明在生物课堂教学中运用“导、探”模式进行教学,能激发学生思维空间,培养学生求异、求新、求变的创新意识.     

Mechanisms of bacterial morphogenesis: Evolutionary cell biology approaches provide new insights

How Darwin's “endless forms most beautiful” have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating “evolutionary thinking” into bacterial cell biology in the genomic era.     

An update on antigenic variation in African trypanosomes.

African trypanosomes can spend a long time in the blood of their mammalian host, where they are exposed to the immune system and are thought to take advantage of it to modulate their own numbers. Their major immunogenic protein is the variant surface glycoprotein (VSG), the gene for which must be in one of the 20--40 specialized telomeric expression sites in order to be transcribed. Trypanosomes escape antibody-mediated destruction through periodic changes of the expressed VSG gene from a repertoire of approximately 1000. How do trypanosomes exclusively express only one VSG and how do they switch between them?