Identification of differentially expressed genes in the developing antler of red deer Cervus elaphus

Understanding the molecular mechanisms underlying bone development is a fundamental and fascinating problem in developmental biology, with significant medical implications. Here, we have identified the expression patterns for 36 genes that were characteristic or dominant in the consecutive cell differentiation zones (mesenchyme, precartilage, cartilage) of the tip section of the developing velvet antler of red deer Cervus elaphus. Two major functional groups of these genes clearly outlined: six genes linked to high metabolic demand and other five to tumor biology. Our study demonstrates the advantages of the antler as a source of mesenchymal markers, for distinguishing precartilage and cartilage by different gene expression patterns and for identifying genes involved in the robust bone development, a striking feature of the growing antler. Putative roles for “antler” genes that encode α-tropomyosine (tpm1), transgelin (tagln), annexin 2 (anxa2), phosphatidylethanolamine-binding protein (pebp) and apolipoprotein D (apoD) in intense but still controlled tissue proliferation are discussed.     

Variation in stigma morphology – How does it contribute¶to pollination adaptation in Pedicularis (Orobanchaceae)?

 Stigma morphology in Pedicularis and its role in pollination have not been evaluated. This paper reports for the first time the relationship between stigma morphology and other aspects of floral design. 17 species of Pedicularis representing all the different types of corolla structure in the genus were studied in the field and in the laboratory. Results indicate that the stigmatic surface morphology of Pedicularis species is related to the type of corolla structure occurring in the species. Pollination studies in eight Pedicularis species demonstrated adaptation between stigmatic surface morphology and other aspects of floral biology. Species with larger, more corrugated stigmatic surfaces always possess a subsidiary construction (“tooth” or “beak”) on the galea. In addition, they have relatively longer flower tubes, higher stigmatic pollen loads, bigger pollen size and a shorter blooming period for individual flowers. Finally, the authors discuss the evolutionary significance of floral design in genus Pedicularis. Received April 8, 2002; accepted June 11, 2002 Published online: December 11, 2002     

“Force-Talk” in Evolutionary Explanation: Metaphors and Misconceptions

The notion of “pressure” as an evolutionary “force” that “causes” evolution is a pervasive linguistic feature of biology textbooks, journal articles, and student explanatory discourse. We investigated the consequences of using a textbook and curriculum that incorporate so-called force-talk. We examined the frequency with which biology majors spontaneously used notions of evolutionary “pressures” in their explanations, students’ definitions and explanations of what they meant when they used pressures, and the structure of explanatory models that incorporated evolutionary pressures and forces. We found that 12–20 percent of undergraduates spontaneously used “pressures” and/or “forces” as explanatory factors but significantly more often in trait gain scenarios than in trait loss scenarios. The majority of explanations using “force-talk” were characterized by faulty evolutionary reasoning. We discuss the conceptual similarity between faulty notions of evolutionary pressures and linguists’ force-dynamic models of everyday reasoning and ultimately question the appropriateness of force-talk in evolution education.     

Effects of glutamine supplementation on kidney of diabetic rat

Glutamine is the most important donor of NH₃ in kidney playing an important role in acid–base buffering system. Besides this effect, glutamine presents many other relevant functions in the whole body, such as a precursor of arginine in adult and neonates. In addition to these effects, some studies have shown that glutamine can potentiate renal disease. In the present study, the effect of short-term treatment (15 days) with glutamine on control and diabetic rats was investigated. Using biochemical, histological and molecular biology analysis from control and diabetic rats we verified that glutamine supplementation increase in pro-inflammatory interleukins (IL)-1β and IL-6 content in renal cortex and induce alteration in glomerular characteristics. This study showed that short-term treatment with glutamine in association with increased glucose levels could cause important alterations in glomerular morphology that may result in fast progression of kidney failure.     

Evolutionary Morphology in Belgium

In historical literature, Edouard van Beneden (1846–1910) is mostly remembered for his cytological discoveries. Less well known, however, is that he also introduced evolutionary morphology – and indeed evolutionary theory as such – in the Belgian academic world. The introduction of this research programme cannot be understood without taking both the international and the national context into account. It was clearly the German example of the Jena University that inspired van Beneden in his research interests. The actual launch of evolutionary morphology at his University of Liège was, however, also connected with the dynamic of Belgian university reforms and the local rationale of creating a research “school.” Thanks to his networks, his mastering of the rhetoric of the “new” biology, his low ideological profile and his capitalising on the new academic élan in late-19th century Belgium, van Beneden managed to turn his programme into a local success from the 1870s onwards. Two decades later, however, the conceptual underpinnings of evolutionary morphology came under attack and the “Van Beneden School” lost much of its vitality. Despite this, van Beneden’s evolutionary morphology was prototypical for the research that was to come. He was one of the first scientific heavyweights in Belgium to turn the university laboratory into a centre of scientific practice and the hub of a research school.     

Misconceptions About the Evolution of Complexity

Despite data and theory from comparative anatomy, embryology, molecular biology, genomics, and evolutionary developmental biology, antievolutionists continue to present the eye as an example of a structure too complex to have evolved. They stress what we have yet to explain about the development and evolution of eyes and present incomplete information as evidence that evolution is a “theory in crisis.” An examination of the evidence, however, particularly evidence that has accumulated in the twentieth and twenty-first centuries, refutes antievolutionists’ claims. The distribution of eyes in extant organisms, combined with what we now know about the control of eye development across diverse groups of organisms, provides significant evidence for the evolution of all major components of the eye, from molecular to morphological, and provides an excellent test of predictions based on common ancestry.     

Response to commentaries on “The Transmission Sense of Information”

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a shallow notion of correlation, the so-called “causal sense” of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a “semantic sense,” whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence.     

Post-Haeckelian comparative biology — Adolf Naef’s idealistic morphology

Summary The present study describes the conceptual framework of Adolf Naef’s idealistic morphology as presented at the onset of the 20^th century. According to Naef, Haeckel’s and Gegenbaur’s approaches towards a phylogenetic biology were insufficient. He made it clear that Haeckel’s ideas were based on typological morphology. Thus, Haeckel’s views on comparative biology pointed back to pre-Darwinian concepts. Naef’s consequence was not to work out his own evolutionary morphology but to systematize the earlier typological concept. Consequently, he separated comparative morphology from phylogenetic studies. This idea was adopted by Hennig and was even imported into modern cladism.     

Recent changes in allometric relationships among morphological traits in the dipper (Cinclus cinclus)

Organisms are responding to recent climate warming by changing different aspects of their biology, including morphology. The present work examines the way in which dipper (Cinclus cinclus) morphology has varied over the past 20 years (1985–2005) in Sierra Nevada (south-eastern Spain). Tarsus length has decreased, but wing and tail length have increased in the same period. These opposite trends have provoked changes in the allometric relationships among the different parts of the body in the dipper. A decrease in body size is predicted by Bergmann’s rule, and similar results have been found in other birds. However, although this study found a decrease in tarsus length, no change was found for body mass. The increase in wing and tail length may be related to a variation in the trophic niche in response to the decrease in water volume of rivers that occurred during the study period. Other studies show that the dipper’s diet varies with water flow, and water flow has decreased in the study area as a consequence of climatic warming.     

Biomedical and Environmental Ethics Alliance: Common Causes and Grounds

In the late 1960s Van Rensselaer Potter, a biochemist and cancer researcher, thought that our survival was threatened by the domination of military policy makers and producers of material goods ignorant of biology. He called for a new field of Bioethics—“a science of survival.” Bioethics did develop, but with a narrower focus on medical ethics. Recently there have been attempts to broaden that focus to bring biomedical ethics together with environmental ethics. Though the two have many differences—in habits of thought, scope of concern, and value commitments—in this paper we argue that they often share common cause and we identify common ground through an examination of two case studies, one addressing drug development, the other food production.     

Will systems biology offer new holistic paradigms to life sciences?

A biological system, like any complex system, blends stochastic and deterministic features, displaying properties of both. In a certain sense, this blend is exactly what we perceive as the “essence of complexity” given we tend to consider as non-complex both an ideal gas (fully stochastic and understandable at the statistical level in the thermodynamic limit of a huge number of particles) and a frictionless pendulum (fully deterministic relative to its motion). In this commentary we make the statement that systems biology will have a relevant impact on nowadays biology if (and only if) will be able to capture the essential character of this blend that in our opinion is the generation of globally ordered collective modes supported by locally stochastic atomisms.     

San Marco and evolutionary biology

Gould and Lewontin use San Marco, Venice, to criticise the adaptationist program in biology. Following their lead, the architectural term “spandrel” is now widely used in biology to denote a feature that is a necessary byproduct of other aspects of the organism. I review the debate over San Marco and argue that the spandrels are not necessary in the sense originally used by Gould and Lewontin. I conclude that almost all the claims that Gould makes about San Marco are wrong and that it is reasonable to view the architectural spandrel as an adaptation. The spandrels example has not provided a good illustration of why adaptive explanations should be avoided. In fact, it can be used as an example of how adaptive explanations can be dismissed even when there is evidence in their favour. I also discuss the use of the concept of a spandrel in biology.     

Parts and Theories in Compositional Biology

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict.     

Simple models for excitable and oscillatory neural networks

 Chains of coupled oscillators of simple “rotator” type have been used to model the central pattern generator (CPG) for locomotion in lamprey, among numerous applications in biology and elsewhere. In this paper, motivated by experiments on lamprey CPG with brainstem attached, we investigate a simple oscillator model with internal structure which captures both excitable and bursting dynamics. This model, and that for the coupling functions, is inspired by the Hodgkin–Huxley equations and two-variable simplifications thereof. We analyse pairs of coupled oscillators with both excitatory and inhibitory coupling. We also study traveling wave patterns arising from chains of oscillators, including simulations of “body shapes” generated by a double chain of oscillators providing input to a kinematic musculature model of lamprey.. Received: 25 November 1996 / Revised version: 9 December 1997     

Reproductive biology and pollination of Utricularia reniformis A.St.‐Hil. (Lentibulariaceae)

Utricularia reniformis is an endemic Brazilian carnivorous plant, most common in high‐altitude grasslands. Knowledge of the reproductive biology of U. reniformis is essential for planning conservation strategies, but it is currently poorly understood. Thus, we studied the floral morphology, floral biology, breeding system and pollination of this species. U. reniformis produces and stores nectar in the flower spur, a classic feature of bee‐pollinated flowers, and we recorded Xylocopa sp. and Bombus sp. as pollinators. Moreover, although it is self‐compatible it is an obligate animal‐pollinated species, as the sensitive stigma avoids self‐pollination. However, in natural conditions reproductive success is low due to the rarity of visits from pollinators. We suggest that the low reproductive success caused by a deficit of pollinators may affect gene flow, causing loss of genetic diversity in U. reniformis.     

Again,What the Philosophy of Biology is not

There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the “new” philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European philosophers of biology could do to improve the situation of their discipline locally, regionally, and internationally, paying particular attention to the lessons to be learned from the “Science Wars.” This paper grew out of my contribution to the symposium Philosophy of Biology in the Netherlands and Flanders organized by Thomas Reydon and Sabina Leonelli in Amsterdam in February 2004. It is a rather personal reaction to many of the opinions voiced in the quite heated atmosphere of the Symposium. My main concern is to convey an idea of what, according to me, is required to turn “our” philosophy of biology into a more successful enterprise than it currently is. This is motivated by a disconcerting discovery I made at the Symposium: Contrary to my expectations, a sensitivity for the sorts of things that make possible philosophy of biology of the best kind available today seems to be largely lacking in our part of the world. I wish to stress from the outset that although I will be quite polemical at times, this is always intended in the spirit of constructive dialogue.     

Evolutionary biology and feminism

Evolutionary biology and feminism share a variety of philosophical and practical concerns. I have tried to describe how a perspective from both evolutionary biology and feminism can accelerate the achievement of goals for both feminists and evolutionary biologists. In an early section of this paper I discuss the importance of variation to the disciplines of evolutionary biology and feminism. In the section entitled “Control of Female Reproduction” I demonstrate how insight provided by participation in life as woman and also as a feminist suggests testable hypotheses about the evolution of social behavior—hypotheses that are applicable to our investigations of the evolution of social behavior in nonhuman animals. In the section on “Deceit, Self-deception, and Patriarchal Reversals” I have overtly conceded that evolutionary biology, a scientific discipline, also represents a human cultural practice that, like other human cultural practices, may in parts and at times be characterized by deceit and self-deception. In the section on “Femininity” I have indicated how questions cast and answered and hypotheses tested from an evolutionary perspective can serve women and men struggling with sexist oppression. Patricia Adair Gowaty studies the evolution of social behavior, particularly mating systems and sex allocation, primarily in birds. She is most well-known for her long-term studies of eastern bluebirds, which began in 1977 and are on-going. She was an undergraduate at H. Sophie Newcomb College of Tulane University (1963–1967). In the late sixties and early seventies, while employed at the Bronx Zoo (New York Zoological Society), she belonged to a feminist “consciousness-raising” group. She started graduate school in 1974 at the University of Georgia and received her Ph.D. from Clemson University (1980). She had a postdoctoral position at the University of Oklahoma (1982–1983) and a visiting faculty position at Cornell University through the Visiting Professorships for Women NSF program (1983–1984) before returning to her bluebird study sites at Clemson in 1985. She has supported herself and her research efforts throughout her academic career on a series of awards and grants. She is currently (1990–1995) supported by a Research Scientist Development Award from The National Institute of Mental Health.     

Problems with the current deinococcal hypothesis: an alternative theory

All theories related to the evolution of Deinococcus radiodurans have a common denominator: the strong positive correlation between ionizing-radiation resistance and desiccation tolerance. Currently, the widespread hypothesis is that D. radiodurans’ ionizing-radiation resistance is a consequence of this organism’s adaptation to desiccation (desiccation adaptation hypothesis). Here, we draw attention to major discrepancy that has emerged between the “desiccation adaptation hypothesis” and recent findings in computational biology, experimental research, and terrestrial subsurface surveys. We explain why the alternative hypothesis, suggesting that D. radiodurans’ desiccation tolerance could be a consequence of this organism’s adaptation to ionizing radiation (radiation adaptation hypothesis), should be considered on equal basis with the “desiccation adaptation hypothesis”.     

Reproductive biology and morphology of eggs and larvae of Stiphodon percnopterygionus (Gobiidae: Sicydiinae) collected from Okinawa Island

Reproductive biology and morphology of eggs and early larvae of the sicydiine goby Stiphodon percnopterygionus were investigated on Okinawa Island, southern Japan. Spawning season was estimated as being from May to December. Standard length at maturity was approximately 20 mm in both sexes, and batch fecundity was approximately 1000–10 000 per female. The egg masses, guarded by the male, were laid on the undersurface of stones in freshwater. The pyriform eggs had long- and short-axis diameters of 0.54–0.58 mm and 0.49–0.50 mm, respectively. Newly hatched larvae (1.20–1.32 mm notochord length: NL) were poorly developed, with large yolk sacs and unopened mouths. Three days after hatching (1.87–2.05 mm NL), eyes were fully pigmented and mouths were opened. An erratum to this article is available at .     

Texas Biology and Biological Anthropology Faculty Express Their Views on Teaching Evolution

Unsurprisingly, survey results indicate that Texas biology and biological anthropology faculty with expertise in an evolutionary area strongly support teaching “just evolution” (100%; N = 54) and not creationism/intelligent design. Importantly, they do not think that religious faith is incompatible with acceptance of evolutionary biology (91%; N = 55), even though 50% (N = 52) describe themselves as “not at all religious.” As school boards nationwide debate science standards, it is important that faculty with relevant expertise have a voice. Biological anthropologists should not be overlooked as a public resource in these debates.