Teaching critical thinking.

The ability to make decisions based on data, with its inherent uncertainties and variability, is a complex and vital skill in the modern world. The need for such quantitative critical thinking occurs in many different contexts, and although it is an important goal of education, that goal is seldom being achieved. We argue that the key element for developing this ability is repeated practice in making decisions based on data, with feedback on those decisions. We demonstrate a structure for providing suitable practice that can be applied in any instructional setting that involves the acquisition of data and relating that data to scientific models. This study reports the results of applying that structure in an introductory physics laboratory course. Students in an experimental condition were repeatedly instructed to make and act on quantitative comparisons between datasets, and between data and models, an approach that is common to all science disciplines. These instructions were slowly faded across the course. After the instructions had been removed, students in the experimental condition were 12 times more likely to spontaneously propose or make changes to improve their experimental methods than a control group, who performed traditional experimental activities. The students in the experimental condition were also four times more likely to identify and explain a limitation of a physical model using their data. Students in the experimental condition also showed much more sophisticated reasoning about their data. These differences between the groups were seen to persist into a subsequent course taken the following year.

What influences students' abilities to critically evaluate scientific investigations?

Critical thinking is the process by which people make decisions about what to trust and what to do. Many undergraduate courses, such as those in biology and physics, include critical thinking as an important learning goal. Assessing critical thinking, however, is non-trivial, with mixed recommendations for how to assess critical thinking as part of instruction. Here we evaluate the efficacy of assessment questions to probe students' critical thinking skills in the context of biology and physics. We use two research-based standardized critical thinking instruments known as the Biology Lab Inventory of Critical Thinking in Ecology (Eco-BLIC) and Physics Lab Inventory of Critical Thinking (PLIC). These instruments provide experimental scenarios and pose questions asking students to evaluate what to trust and what to do regarding the quality of experimental designs and data. Using more than 3000 student responses from over 20 institutions, we sought to understand what features of the assessment questions elicit student critical thinking. Specifically, we investigated (a) how students critically evaluate aspects of research studies in biology and physics when they are individually evaluating one study at a time versus comparing and contrasting two and (b) whether individual evaluation questions are needed to encourage students to engage in critical thinking when comparing and contrasting. We found that students are more critical when making comparisons between two studies than when evaluating each study individually. Also, compare-and-contrast questions are sufficient for eliciting critical thinking, with students providing similar answers regardless of if the individual evaluation questions are included. This research offers new insight on the types of assessment questions that elicit critical thinking at the introductory undergraduate level; specifically, we recommend instructors incorporate more compare-and-contrast questions related to experimental design in their courses and assessments.

Ready student one: Exploring the predictors of student learning in virtual reality.

Immersive virtual reality (VR) has enormous potential for education, but classroom resources are limited. Thus, it is important to identify whether and when VR provides sufficient advantages over other modes of learning to justify its deployment. In a between-subjects experiment, we compared three methods of teaching Moon phases (a hands-on activity, VR, and a desktop simulation) and measured student improvement on existing learning and attitudinal measures. While a substantial majority of students preferred the VR experience, we found no significant differences in learning between conditions. However, we found differences between conditions based on gender, which was highly correlated with experience with video games. These differences may indicate certain groups have an advantage in the VR setting.

Exploring bias in mechanical engineering students' perceptions of classmates.

Gender disparity in science, technology, engineering, and math (STEM) fields is an on-going challenge. Gender bias is one of the possible mechanisms leading to such disparities and has been extensively studied. Previous work showed that there was a gender bias in how students perceived the competence of their peers in undergraduate biology courses. We examined whether there was a similar gender bias in a mechanical engineering course. We conducted the study in two offerings of the course, which used different instructional practices. We found no gender bias in peer perceptions of competence in either of the offerings. However, we did see that the offerings' different instructional practices affected aspects of classroom climate, including: the number of peers who were perceived to be particularly knowledgeable, the richness of the associated network of connections between students, students' familiarity with each other, and their perceptions about the course environment. These results suggest that negative bias against female students in peer perception is not universal, either across institutions or across STEM fields, and that instructional methods may have an impact on classroom climate.

Tools for Change: Measuring Student Conceptual Understanding Across Undergraduate Biology Programs Using Bio-MAPS Assessments.

Assessing learning across a biology major can help departments monitor achievement of broader program-level goals and identify opportunities for curricular improvement. However, biology departments have lacked suitable tools to measure learning at the program scale. To address this need, we developed four freely available assessments-called Biology-Measuring Achievement and Progression in Science or Bio-MAPS-for general biology, molecular biology, ecology/evolution, and physiology programs. When administered at multiple time points in a curriculum, these instruments can provide departments with information on how student conceptual understanding changes across a major and help guide curricular modifications to enhance learning.

The carotenoid shift in Rhodopseudomonas sphaeroides. The flash induced change.

A mutant, Rhodopseudomonas sphaeroides GIC, having only one major carotenoid, neurosporene, is described. The spectrum of the carotenoid shift in this mutant is analysed and it is concluded that only 7-11% of the pigment is involved under conditions of steady-state illumination and that this pigment undergoes a shift of 7 nm. The spectrum of the carotenoid shift under conditions of multi-flash illumination is examined for changes in shape concordant with a progressive red shift of the pigment with increasing membrane potential; the spectra of the fast change after each of three flashes does not agree well with predictions from a model involving a progressive shift of the pigment, the slow change shows qualitative agreement with such a model but the small size of the signal and the presence of more than one phase makes analysis of this phase more difficult. No separate pool of carotenoid, that might correspond to that postulated to participate in the carotenoid shift, could be identified by fourth derivative analysis of, or curve fitting to, the spectrum of the neurosporene.

The carotenoid shift in Rhodopseudomonas sphaeroides. Change induced under continuous illumination.

The spectrum of the carotenoid shift generated under continuous illumination in the GIC mutant of Rhodopseudomonas sphaeroides, which has a single carotenoid, has been examined under a variety of conditions expected to alter the size of the membrane potential. If the difference spectrum observed was due to a species with the spectrum of the bulk pigment, it would correspond to a change of a variable proportion of the pigment to a form absorbing at a higher wavelength. The maximal change induced by light could be described as a shift of about 10% of the pigment by 7 nm to the red, assuming that the shifted species was spectrally identical to the bulk carotenoid. It is concluded that the changes seen are not easily compatible with a progressive red shift in the whole spectrum with increasing applied potential as would be expected from a simple linear electrochromic mechanism; alternative hypotheses are discussed.

Membranes of Rhodopseudomonas sphaeroides. VII. Photochemical properties of a fraction enriched in newly synthesized bacteriochlorophyll a-protein complexes.

Previous pulse-chase studies have shown that bacteriochlorophyll a-protein complexes destined eventually for the photosynthetic (chromatophore) membrane of Rhodopseudomonas sphaeroides appear first in a distinct pigmented fraction. This rapidly labeled material forms an upper band when extracts of phototrophically grown cells are subjected directly to rate-zone sedimentation. In the present investigation, flash-induced absorbance changes at 605 nm have demonstrated that the upper fraction is enriched two-fold in photochemical reaction center activity when compared to chromotophores; a similar enrichment in the reaction center-associated B-875 antenna bacteriochlorophyll complex was also observed. Although b- and c-type cytochromes were present in the upper pigmented band, no photoreduction of the b-type components could be demonstrated. The endogenous c-type cytochrome (Em = +345 mV) was photooxidized slowly upon flash illumination. The extent of the reaction was increased markedly with excess exogenous ferrocytochrome c but only slightly in chromatophores. Only a small light-induced carotenoid band shift was observed. These results indicate that the rapidly labeled fraction contains photochemically competent reaction centers associated loosely with c-type and unconnected to b-type cytochrome. It is suggested that this fraction arises from new sites of cytoplasmic membrane invagination which fragment to form leaky vesicles upon cell disruption.

The reconstitution of energy transfer in membranes from a bacteriochlorophyll-less mutant of Rhodopseudomonas sphaeroides by addition of light-harvesting and reaction centre pigment-protein complexes.

Antenna and reaction centre complexes purified from photosynthetically-grown cells of Rhodopseudomonas sphaeroides have been mixed with cytoplasmic membranes prepared from an aerobically-grown bacteriochlorophyll-less mutant of Rp. sphaeroides (designated 01) in the presence of 1% sodium cholate. After removal of the cholate by dislysis, the dislysate was subjected to isopycnic centrifugation. Reconstituted cytochrome c2 photooxidation and cytochrome b photoreduction was demonstrated in a pigmented fraction recovered from the sucrose gradient, suggesting that the pigment-proteins were incorporated into the 01 membrane. The fluorescence properties of the system were examined. The appearance of a variable component after the initial fast fluorescence rise indicated that energy transfer occurred between the antenna and reaction centre proteins in the presence of 01 membrane. The order in which the system was assembled was important. Reconstituted energy transfer with a pre-dialysed reaction centre-antenna complex was more effective than when all the components were mixed at once. Energy transfer was also reconstituted between added reaction centre protein and the endogenous antenna present in membranes from the pigmented, but aerobically-grown reaction centre-less mutant PM8dp of Rp. sphaeroides. Preparations of 01 membranes reconstituted with reaction centre exhibited a light intensity dependent cytochrome c2 photooxidation. At low exciting light intensities, preparations containing reconstituted antenna protein in addition to reaction centres showed greated membrane cytochrome c2 photooxidation than preparations with the antenna omitted; this improvement was maximal when a pre-dialysed antenna-reaction centre complex was used.

Bacteriochlorophyll fluorescence of purple bacteria at low redox potentials. The relationship between reaction center triplet yield and the emission yield.

This work describes fluorescence yield measurements in suspensions of strains of Rhodospirillum rubrum and Rhodopseudomonas sphaeroides in which the iron . quinone complex (X) was chemically reduced (state [PIX-]; P is the reaction center bacteriochlorophyll dimer, I is the long wavelength bacteriopheophytin), and compares these with the fluorescence observed when all the traps are open (state [PIX]) and with the fluorescence observed when all the traps are closed (state [P+IX]). At 77 K the amplitude and the shape of the fluorescence emission spectrum in [PIX-] are identical to those observed in [PIX]. This is a strong indication that all the extra fluorescence observed at room temperature in [PIX-] is, in fact, caused by an efficient back reaction [P+I-X-] leads to [P*IX-]. Using an equation similar to the original Vredenberg-Duysens relationship (Vredenburg, W.J. and Duysens, L.N.M. (1963) Nature 197, 355-357) but now assuming that a single reaction center has a probability pt of trapping an excitation and (1--pt) of re-emitting it to the surroundings, we are able to calculate pt as a function of the temperature by measuring the fluorescence in [PIX], [PIX-] and [P+IX] as a function of the temperature. The calculated pt values agree reasonably well with triplet yields measured in isolated reaction centers. Finally, we have measured the reaction center triplet yield (PTR) in intact systems and we have shown that the sum of the triplet yield and the remaining loss processes (PL) in the antenna bacteriochlorophyll including the bacteriochlorophyll dimer (such as fluorescence, internal conversion or direct triplet formation) is approximately constant; if we assume that at 77 K the only process which occurs in the reaction center is the formation of a reaction center triplet, than PTR + PL=1. The energy barrier between [P*IX-] and [P+I-X-] was estimated to be 0.11--0.15 eV for a set of preparations.

Flash-induced changes in the in vivo bacteriochlorophyll fluorescence yield at low temperatures and low redox potentials in carotenoid-containing strains of photosynthetic bacteria.

The changes in the in vivo bacteriochlorophyll fluorescence induced by a Xenon flash at low temperatures (77--200 K) with the "primary" acceptor X chemically prereduced have been examined in whole cells of several species of photosynthetic bacteria which contain carotenoids absorbing in the visible part of the absorption spectrum. Two groups of species with different behaviour could be distinguished. In both cases a flash-induced rise of the fluorescence yield was observed with X prereduced at 77 k; as the temperature was increased the ratio of the maximum fluorescence (FM) and the basal fluorescence (F0) decreased and the kinetics of the decay of the high fluorescent state, as observed during the tail of the flash, apparently accelerated. Of the species examined the flash-induced changes in fluorescence-yield kinetics appeared to occur at higher temperatures in the members of one group (Chromatium vinosum, Rhodopseudomonas gelatinosa and Rhodopseudomonas palustris) than in the members of the other (Rhodopseudomonas palustris) than in the members of the other (Rhodopseudomonas sphaeroides and Rhodospirillum rubrum). These effects are interpreted in terms of the light-induced generation of triplet states within the reaction centre. It is suggested that the species-dependent differences may reflect differences in the molecular organisation of the reaction centre. It was found that in all species the reaction centre carotenoid triplet does not act as a fluorescence quencher under these conditions.

Protein phosphorylation and control of excitation energy transfer in photosynthetic purple bacteria and cyanobacteria.

The function of phosphorylation of light-harvesting polypeptides is well characterised in chloroplasts of green plants, but the prokaryotic cyanobacteria and purple photosynthetic bacteria have quite different light-harvesting polypeptides whose structure and function cannot be controlled in precisely the same way. Nevertheless, cyanobacteria show light-dependent phosphorylation of membrane polypeptides associated with photosystem II and with the light-harvesting phycobilisome, and purple bacteria show light-dependent phosphorylation of low molecular-weight chromatophore membrane polypeptides. In both cases membrane protein phosphorylation is associated with functional changes observed by chlorophyll fluorescence spectroscopy or chlorophyll fluorescence induction kinetics. Here we report on our recent protein sequence and other data concerning the identities of these phosphoproteins. We also discuss the significance of these findings for regulation by protein phosphorylation of photosynthesis in prokaryotes.

Characterization of canine microsatellites.

Canine DNA was cloned in M13 and screened for the presence of (dC-dA)n.(dG-dT)n repeats. Oligonucleotide primers were synthesised to the microsatellite flanking sequences and used in the polymerase chain reaction to amplify those loci from genomic DNA. The polymorphism of each microsatellite was estimated in a set of unrelated dogs.

DNA marker C04107 for copper toxicosis in a population of Bedlington terriers in the United Kingdom.

The DNA microsatellite marker C04107, linked to the Bedlington terrier copper toxicosis locus, is used diagnostically in the USA to detect the disease allele. This marker has been typed in Bedlington terriers of known disease status in the United Kingdom, and it is concluded that it should be useful in eradicating the disease from the breed in the UK. The marker also identified a dog which had been diagnosed on the basis of a liver biopsy as having the disease, as being unaffected; a second liver biopsy confirmed that the dog did not have copper toxicosis.

Dog parentage testing using canine microsatellites.

Canine microsatellites, comprising one to four base pair repeated sequences, were identified as part of a project to generate a genetic linkage map of the dog. They have been used to assign parentage in a range of doubtful paternity cases, for example, all the pups in a litter from a bitch mated on different days to two different stud dogs were identified by DNA analysis to come from one dog only. DNA typing in another case was able to exclude a male dog as the father of a litter. DNA analysis can be of relevance by allowing pedigree dogs, which would have previously been excluded on the basis of unknown paternity, to be registered with the appropriate kennel club.

Von Wille-brand's disease in UK dobermanns: possible correlation of a polymorphic DNA marker with disease status.

Ninety-one dobermanns have been typed for a polymorphic microsatellite DNA marker situated within an intron of the von Willebrand factor gene and the alleles correlated with von Wille-brand's disease status. Two alleles were identified, one associated only with the normal gene and the other with both normal and disease genes.