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.

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.

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.

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.

Canine RPGRIP1 mutation establishes cone-rod dystrophy in miniature longhaired dachshunds as a homologue of human Leber congenital amaurosis.

Cone-rod dystrophy 1 (cord1) is a recessive condition that occurs naturally in miniature longhaired dachshunds (MLHDs). We mapped the cord1 locus to a region of canine chromosome CFA15 that is syntenic with a region of human chromosome 14 (HSA14q11.2) containing the retinitis pigmentosa GTPase regulator-interacting protein 1 (RPGRIP1) gene. Mutations in RPGRIP1 have been shown to cause Leber congenital amaurosis, a group of retinal dystrophies that represent the most common genetic causes of congenital visual impairment in infants and children. Using the newly available canine genome sequence we sequenced RPGRIP1 in affected and carrier MLHDs and identified a 44-nucleotide insertion in exon 2 that alters the reading frame and introduces a premature stop codon. All affected and carrier dogs within an extended inbred pedigree were homozygous and heterozygous, respectively, for the mutation. We conclude the mutation is responsible for cord1 and demonstrate that this canine disease is a valuable model for exploring disease mechanisms and potential therapies for human Leber congenital amaurosis.

Characterization of the COMMD1 (MURR1) mutation causing copper toxicosis in Bedlington terriers.

Copper toxicosis is an autosomal recessive disorder affecting Bedlington terriers, characterized by elevated liver copper levels and early death of affected dogs. Genetic linkage mapping studies initially identified linkage between the disease and the microsatellite marker C04107. Subsequently, the deletion of exon 2 of the copper metabolism domain containing 1 (COMMD1) gene (formerly MURR1) was shown to be the major cause of copper toxicosis, although the deletion breakpoints were not defined. In this investigation, polymerase chain reaction (PCR)-based techniques and sequencing were used to isolate the deletion breakpoints, utilizing the newly available dog genome sequence. The breakpoints were positioned at 65.3091 and 65.3489 Mb of dog chromosome 10, in intron 1 and intron 2 of COMMD1 respectively, a deletion of 39.7 kb. The two breakpoints share sequence homology suggesting that homologous recombination may have been responsible for the deletion. Using this information, a genomic diagnostic test for the COMMD1 deletion was developed and compared with microsatellite C04107 genotypes of 40 Bedlington terriers. Results from the 40 samples showed allele 2 of C04107 to be in linkage disequilibrium with the COMMD1 deletion.

Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes.

We present here the first fully integrated, comprehensive map of the canine genome, incorporating detailed cytogenetic, radiation hybrid (RH), and meiotic information. We have mapped a collection of 266 chromosome-specific cosmid clones, each containing a microsatellite marker, to all 38 canine autosomes by fluorescence in situ hybridization (FISH). A 1500-marker RH map, comprising 1078 microsatellites, 320 dog gene markers, and 102 chromosome-specific markers, has been constructed using the RHDF5000-2 whole-genome radiation hybrid panel. Meiotic linkage analysis was performed, with at least one microsatellite marker from each dog autosome on a panel of reference families, allowing one meiotic linkage group to be anchored to all 38 dog autosomes. We present a karyotype in which each chromosome is identified by one meiotic linkage group and one or more RH groups. This updated integrated map, containing a total of 1800 markers, covers >90% of the dog genome. Positional selection of anchor clones enabled us, for the first time, to orientate nearly all of the integrated groups on each chromosome and to evaluate the extent of individual chromosome coverage in the integrated genome map. Finally, the inclusion of 320 dog genes into this integrated map enhances existing comparative mapping data between human and dog, and the 1000 mapped microsatellite markers constitute an invaluable tool with which to perform genome scanning studies on pedigrees of interest.

An integrated cytogenetic, radiation-hybrid, and comparative map of dog chromosome 5.

The development of a detailed genome map for the domestic dog (Canis familiaris, CFA) is a prerequisite for the continued use of this species as a model system for the study of inherited traits. We present an integrated cytogenetic, radiation-hybrid, and comparative map of dog Chromosome (Chr) 5 (CFA 5). The map comprises 14 gene markers, selected from loci previously mapped within the corresponding evolutionarily conserved chromosome segments (ECCS) of the human genome. Large-insert clones representing each marker were first isolated and mapped by fluorescence in situ hybridization (FISH) analysis to determine their subchromosomal localization on CFA 5. Thirteen gene markers were subsequently mapped by using a commercially available whole genome radiation hybrid (WG-RH) panel for the dog. Nine anonymous markers were also assigned to CFA 5 by both FISH and WG-RH analysis. The 22 markers formed six RH-linkage groups, spanning each of the four ECCS comprising this 99 megabase chromosome. All cytogenetic, WG-RH, and comparative mapping data were in agreement and were combined to determine both the most likely locus order within each linkage group, and also the gross relative orientation of the corresponding ECCS. This study provides a resource for the transfer of information from the human transcript map to that of the dog, and extends existing data regarding the structural relationships between CFA 5 and its evolutionary counterparts within the human genome.

Refined genetic and comparative physical mapping of the canine copper toxicosis locus.

Recently, the copper toxicosis (CT) locus in Bedlington terriers was assigned to canine chromosome region CFA10q26, which is homologous to human chromosome region HSA2p13-21. A comparative map between CFA10q21-26 and HSA2p13-21 was constructed by using genes already localized to HSA2p13-21. A high-resolution radiation map of CFA10q21-26 was constructed to facilitate positional cloning of the CT gene. For this map, seven Type I and eleven Type II markers were mapped. Using homozygosity mapping, the CT locus could be confined to a 42.3 cR(3000) region, between the FH2523 and C10.602 markers. On the basis of a partial BAC contig, it was estimated that 1-cR(3000) is equivalent to approximately 210 kb, implying that the CT candidate region is therefore estimated to be about 9 Mb.

Melanocortin 1 receptor variation in the domestic dog.

The melanocortin 1 receptor (Mc1r) is encoded by the Extension locus in many different mammals, where a loss-of-function causes exclusive production of red/yellow pheomelanin, and a constitutively activating mutation causes exclusive production of black/brown eumelanin. In the domestic dog, breeds with a wild-type E allele, e. g., the Doberman, can produce either pigment type, whereas breeds with the e allele, e.g., the Golden Retriever, produce exclusively yellow pigment. However, a black coat color in the Newfoundland and similar breeds is thought to be caused by an unusual allele of Agouti, which encodes the physiologic ligand for the Mc1r. Here we report that the predicted dog Mc1r is 317 residues in length and 96% identical to the fox Mc1r. Comparison of the Doberman, Newfoundland, Black Labrador, Yellow Labrador, Flat-coated Retriever, Irish Setter, and Golden Retriever revealed six sequence variants, of which two, S90G and R306ter, partially correlated with a black/brown coat and red/yellow coat, respectively. R306ter was found in the Yellow Labrador, Golden Retriever, and Irish Setter; the latter two had identical haplotypes but differed from the Yellow Labrador at three positions other than R306ter. In a larger survey of 194 dogs and 19 breeds, R306ter and a red/yellow coat were completely concordant except for the Red Chow. These results indicate that the e allele is caused by a common Mc1r loss-of-function mutation that either reoccurred or was subject to gene conversion during recent evolutionary history, and suggest that the allelic and locus relationships for dog coat color genes may be more analogous to those found in other mammals than previously thought.

Five new linkage groups in the canine linkage map.

Nineteen further polymorphic loci were typed on the DogMap reference panel. Five new linkage groups were identified. Additionally, five markers were added to earlier defined linkage groups. Three of the new linkage groups contain markers mapped earlier to specific dog chromosomes by physical mapping. These results make a further contribution to the canine genome map and provides more linkage groups physically assigned to known chromosomes.

Seven new linkage groups assigned to the DogMap reference families.

Twenty microsatellite markers have been typed on to the DogMap reference families, of which 18 were found to be polymorphic. One marker has been assigned to an existing linkage group and nine others have formed seven new linkage groups with previously typed markers. Only one of the new groups could be ordered.

FISH mapping and identification of canine chromosomes.

The karyotype of the domestic dog (Canis familiaris) is widely accepted as one of the most difficult mammalian karyotypes to work with. The dog has a total of 78 chromosomes; all 76 autosomes are acrocentric in morphology and show only a gradual decrease in length. Standardization of the canine karyotype has been performed in two stages. The first stage dealt only with chromosomes 1-21 which can be readily identified by conventional G-banding techniques. The remaining 17 autosomal pairs have proven to be very difficult to reliably identify by banding alone. To facilitate the identification of all canine chromosomes, chromosome-specific paint probes have been produced by DOP-PCR from flow-sorted dog chromosomes. Each paint probe has been used for FISH to identify the corresponding chromosome(s), allowing precise identification of all 78 canine chromosomes. The identification of the undesignated 17 autosomal pairs has been agreed upon by the standardization committee during the second stage of their role. Cosmid clones containing microsatellite markers may now be conclusively assigned to their chromosomal origin by simultaneous dual-color FISH with the corresponding paint probe. In this way a collection of chromosome-specific cosmid clones is being constructed, comprising at least one marker per chromosome, which will allow anchoring of existing and future linkage groups to the physical map.

Use of cosmid-derived and chromosome-specific canine microsatellites.

The majority of microsatellite markers being used to generate the emerging genetic linkage maps of the dog are derived from small-insert, random clones. While such markers are easy to generate, they have the disadvantage that they cannot easily be physically mapped by fluorescence in situ hybridization (FISH), making it difficult to assess the extent of genome coverage represented by such maps. In contrast, microsatellite markers from large-insert libraries enable the linkage groups within which they fall to be physically anchored to specific chromosomes. One aim of our work is to identify at least one microsatellite-containing cosmid clone for each canine chromosome, to ensure that linkage groups exist for all chromosomes. This is particularly important for a species with as complex a karyotype as the dog. Locating two cosmids on each chromosome would allow the orientation of the linkage groups to be established. Chromosomal locations of cosmid clones containing microsatellites have been determined by FISH and confirmed using canine chromosome-specific paints. Microsatellite sequences have been genotyped on the DogMap reference family. Microsatellites derived from flow-sorted, chromosome-specific libraries represent another source of useful markers. Initial studies have been carried out on the canine X chromosome, on which markers were underrepresented in our initial studies.

Genetic markers linked to neuronal ceroid lipofuscinosis in English setter dogs.

The neuronal ceroid lipofuscinoses (NCL) are a group of fatal autosomal recessive neurodegenerative diseases occurring in human and some domesticated animal species. A canine form of the disease (CNCL) has been extensively studied in a Norwegian colony of inbred English setters since 1960. A resource family developed for genetic mapping and comprising 170 individuals was typed for 103 genetic markers. Linkage analysis showed three genetic markers to be linked to the disease locus with the closest marker at a distance of about 3 CM. Two other loci were linked with these markers making a linkage group of five genetic markers. The linkage group spanned a distance of 54 CM. Two genes for human forms of the disease, CLN2 and CLN3, have been identified and mapped to human chromosome 11p15 and 16p12, respectively. The present study did not indicate any linkage between CNCL and the canine CLN3 homologue or to homologues of markers for genes that map close to human CLN2.

A comparative genetic analysis of the Irish greyhound population using multilocus DNA fingerprinting, canine single locus minisatellites and canine microsatellites.

Pairwise analysis of HinfI/33.6 DNA fingerprints from a total of one hundred and fifty-three Irish greyhounds of known pedigree were used to determine band-share estimates of unrelated, first-degree and second-degree relationships. Forty-eight unrelated Irish greyhounds were used to determine allele frequencies for three single-locus minisatellites, and following a preliminary screen, eight of the most polymorphic tetra-nucleotide microsatellites from a panel of 15. The results indicated that both band-share estimates by DNA fingerprinting and microsatellite allele frequencies are highly effective in resolving parentage in this greyhound population, while single-locus minisatellites showed limited polymorphism and could not be used alone for routine parentage testing in this breed. The present study also demonstrated that, to obtain optimal resolution of parentage, sample sets of known pedigree status are required to determine the band-share distribution and/or microsatellite allele frequencies.