Teaching critical thinking in a developmental biology course at an American liberal arts college

We all expect our students to learn facts and concepts, but more importantly, we want them to learn how to evaluate new information from an educated and skeptical perspective; that is, we want them to become critical thinkers. For many of us who are scientists and teachers, critical thought is either intuitive or we learned it so long ago that it is not at all obvious how to pass on the skills to our students. Explicitly discussing the logic that underlies the experimental basis of developmental biology is an easy and very successful way to teach critical thinking skills. Here, I describe some simple changes to a lecture course that turn the practice of critical thinking into the centerpiece of the learning process. My starting point is the "Evidence and Antibodies" sidelight in Gilbert's Developmental Biology (2000), which I use as an introduction to the ideas of correlation, necessity and sufficiency, and to the kinds of experiments required to gather each type of evidence: observation ("show it"), loss of function ("block it") and gain of function ("move it"). Thereafter, every experiment can be understood quickly by the class and discussed intelligently with a common vocabulary. Both verbal and written reinforcement of these ideas dramatically improve the students' ability to evaluate new information. In particular, they are able to evaluate claims about cause and effect; they become experts at distinguishing between correlation and causation. Because the intellectual techniques are so powerful and the logic so satisfying, the students come to view the critical assessment of knowledge as a fun puzzle and the rigorous thinking behind formulating a question as an exciting challenge.     

Acetyl Phosphate as a Primordial Energy Currency at the Origin of Life

Metabolism is primed through the formation of thioesters via acetyl CoA and the phosphorylation of substrates by ATP. Prebiotic equivalents such as methyl thioacetate and acetyl phosphate have been proposed to catalyse analogous reactions at the origin of life, but their propensity to hydrolyse challenges this view. Here we show that acetyl phosphate (AcP) can be synthesised in water within minutes from thioacetate (but not methyl thioacetate) under ambient conditions. AcP is stable over hours, depending on temperature, pH and cation content, giving it an ideal poise between stability and reactivity. We show that AcP can phosphorylate nucleotide precursors such as ribose to ribose-5-phosphate and adenosine to adenosine monophosphate, at modest (~2%) yield in water, and at a range of pH. AcP can also phosphorylate ADP to ATP in water over several hours at 50 °C. But AcP did not promote polymerization of either glycine or AMP. The amino group of glycine was preferentially acetylated by AcP, especially at alkaline pH, hindering the formation of polypeptides. AMP formed small stacks of up to 7 monomers, but these did not polymerise in the presence of AcP in aqueous solution. We conclude that AcP can phosphorylate biologically meaningful substrates in a manner analogous to ATP, promoting the origins of metabolism, but is unlikely to have driven polymerization of macromolecules such as polypeptides or RNA in free solution. This is consistent with the idea that a period of monomer (cofactor) catalysis preceded the emergence of polymeric enzymes or ribozymes at the origin of life.     

Life as a planetary phenomenon

The success of recent spacecraft from the U.S.A. and the U.S.S.R. has given us a wealth of new data about the planets in our solar system. We can now develop a much better rationale for the reasons that abundant life is only found on our planet. Mars, smaller and more distant from the Sun, may nevertheless hold clues to the early development of Earth's atmosphere. The origin of life on Mars early in that planet's history cannot be ruled out. Titan offers a contemporary example of extremely primitive conditions, where chemical reactions resembling those that preceded the development of life on Earth may be occurring today. Venus and Jupiter illustrate the need for a planet to be the right size and the right distance from the sun if chemical evolution leading to the origin of life is to occur.     

Prior consent as a liberal theory of health care rationing: commments of Savulescu's constructive critique

[In his review essay in this issue of Bioethics,] Julian Savulescu lucidly summarizes and assesses each essay in Strong Medicine. I would like to clarify a few important general points about prior consent as a conceptual framework for the ethical rationing of health care, correct several specific misreadings, and defend my basic claim despite some acknowledged problems.     

Life on high: the diversity of small mammals at high altitude in South Africa

The Great Escarpment is the major mountain system in South Africa, yet very few biological surveys have been conducted outside of the well-known Drakensberg section. This is surprising given the important role that mountains play in local and global biodiversity patterns. In this study, small mammal diversity and community composition were estimated at three high altitude (>1,700?m) sites within the Sneeuberg Mountain Complex (SMC) of the Great Escarpment, South Africa from June 2009 to May 2010. The influences of selected environmental variables on diversity were also tested. Of 423 live-captures, a total of 292 unique individuals of 12 small mammal species (one shrew, one elephant shrew and 10 rodents) were identified during 5,280 trap nights. No single environmental variable could account for the variation observed in diversity measurements but vegetation height appeared to be the most important factor to influence the number of individuals captured. It is hypothesised that the high species richness and diversity of small mammals observed in the SMC compared to other parts of the Great Escarpment is due to the SMC being located in a transition zone of the Grassland and Nama-Karoo biomes. Our results suggest that the SMC could be important in conserving small mammal species from western and eastern assemblages across South Africa.     

RNA as a small molecule druggable target

Small molecule drugs have readily been developed against many proteins in the human proteome, but RNA has remained an elusive target for drug discovery. Increasingly, we see that RNA, and to a lesser extent DNA elements, show a persistent tertiary structure responsible for many diverse and complex cellular functions. In this digest, we have summarized recent advances in screening approaches for RNA targets and outlined the discovery of novel, drug-like small molecules against RNA targets from various classes and therapeutic areas. The link of structure, function, and small-molecule Druggability validates now for the first time that RNA can be the targets of therapeutic agents.     

Emergy as a Life Cycle Impact Assessment Indicator

Founded in thermodynamics and systems ecology, emergy evaluation is a method to associate a product with its dependencies on all upstream environmental and resource flows using a common unit of energy. Emergy is thus proposed as an indicator of aggregate resource use for life cycle assessment (LCA). An LCA of gold mining, based on an original life cycle inventory of a large gold mine in Peru, is used to demonstrate how emergy can be incorporated as an impact indicator into a process‐based LCA model. The results demonstrate the usefulness of emergy in the LCA context. The adaptation of emergy evaluation, traditionally performed outside of the LCA framework, requires changes to the conventional accounting rules and the incorporation of uncertainty estimations of the emergy conversion factors, or unit emergy values. At the same time, traditional LCA boundaries are extended to incorporate the environmental processes that provide for raw resources, including ores. The total environmental contribution to the product, doré, is dominated by mining and metallurgical processes and not the geological processes forming the gold ore. The measure of environmental contribution to 1 gram (g) of doré is 6.8E + 12 solar‐equivalent Joules (sej) and can be considered accurate within a factor of 2. These results are useful in assessing a process in light of available resources, which is essential to measuring long‐term sustainability. Comparisons are made between emergy and other measures of resource use, and recommendations are made for future incorporation of emergy into LCA that will result in greater consistency with existing life cycle inventory (LCI) databases and other LCA indicators.     

Life cycle ofPseudodiamesa branickii (Chironomidae) in a small upland stream

The generation time ofP. branickii was studied using larval samples in conjunction with rearing experiments and continuous collection of egg masses across one year. This species produced three generations per year in a central German stream (280 m a.s.l., 50° 40 N). Its generation time was variable and obviously influenced by the photoperiod to which eggs and larvulae were subjected. It is thus concluded that two strains ofP. branickii were present in a single population, one bivoltine and the other trivoltine.     

Life at the edge

Extremophiles: Microbial Life in Extreme Environments (1998). Koki Horikoshi and William D. Grant (Eds). Wiley-Liss, 311 pp. hardback; ISBN 0 471 02618 2 ($134.50)     

Bacterial Life and Dinitrogen Fixation at a Gypsum Rock

The organisms of a bluish-green layer beneath the shards of a gypsum rock were characterized by molecular techniques. The cyanobacterial consortium consisted almost exclusively of Chroococcidiopsis spp. The organisms of the shards expressed nitrogenase activity (C₂H₂ reduction) aerobically and in light. After a prolonged period of drought at the rock, the cells were inactive, but they resumed nitrogenase activity 2 to 3 days after the addition of water. In a suspension culture of Chroococcidiopsis sp. strain PCC7203, C₂H₂ reduction required microaerobic conditions and was strictly dependent on low light intensities. Sequencing of a segment of the nitrogenase reductase gene (nifH) indicated that Chroococcidiopsis possesses the alternative molybdenum nitrogenase 2, expressed in Anabaena variabilis only under reduced O₂ tensions, rather than the widespread, common molybdenum nitrogenase. The shards apparently provide microsites with reduced light intensities and reduced O₂ tension that allow N₂ fixation to proceed in the unicellular Chroococcidiopsis at the gypsum rock, unless the activity is due to minute amounts of other, very active cyanobacteria. Phylogenetic analysis of nifH sequences tends to suggest that molybdenum nitrogenase 2 is characteristic of those unicellular or filamentous, nonheterocystous cyanobacteria fixing N₂ under microaerobic conditions only.