Learning how scientists work: experiential research projects to promote cell biology learning and scientific process skills

Facilitating not only the mastery of sophisticated subject matter, but also the development of process skills is an ongoing challenge in teaching any introductory undergraduate course. To accomplish this goal in a sophomore-level introductory cell biology course, I require students to work in groups and complete several mock experiential research projects that imitate the professional activities of the scientific community. I designed these projects as a way to promote process skill development within content-rich pedagogy and to connect text-based and laboratory-based learning with the world of contemporary research. First, students become familiar with one primary article from a leading peer-reviewed journal, which they discuss by means of PowerPoint-based journal clubs and journalism reports highlighting public relevance. Second, relying mostly on primary articles, they investigate the molecular basis of a disease, compose reviews for an in-house journal, and present seminars in a public symposium. Last, students author primary articles detailing investigative experiments conducted in the lab. This curriculum has been successful in both quarter-based and semester-based institutions. Student attitudes toward their learning were assessed quantitatively with course surveys. Students consistently reported that these projects significantly lowered barriers to primary literature, improved research-associated skills, strengthened traditional pedagogy, and helped accomplish course objectives. Such approaches are widely suited for instructors seeking to integrate process with content in their courses.     

A note on the responses of chimpanzees (Pan troglodytes) to live self-images on television monitors

The majority of studies on self-recognition in animals have been conducted using a mirror as the test device; little is known, however, about the responses of non-human primates toward their own images in media other than mirrors. This study provides preliminary data on the reactions of 10 chimpanzees to live self-images projected on two television monitors, each connected to a different video camera. Chimpanzees could see live images of their own faces, which were approximately life-sized, on one monitor. On the other monitor, they could see live images of their whole body, which were approximately one-fifth life-size, viewed diagonally from behind. In addition, several objects were introduced into the test situation. Out of 10 chimpanzees tested, 2 individuals performed self-exploratory behaviors while watching their own images on the monitors. One of these two chimpanzees successively picked up two of the provided objects in front of a monitor, and watched the images of these objects on the monitor. The results indicate that these chimpanzees were able to immediately recognize live images of themselves or objects on the monitors, even though several features of these images differed from those of their previous experience with mirrors.     

Gender-Heterogeneous Working Groups Produce Higher Quality Science

Here we present the first empirical evidence to support the hypothesis that a gender-heterogeneous problem-solving team generally produced journal articles perceived to be higher quality by peers than a team comprised of highly-performing individuals of the same gender. Although women were historically underrepresented as principal investigators of working groups, their frequency as PIs at the National Center for Ecological Analysis and Synthesis is now comparable to the national frequencies in biology and they are now equally qualified, in terms of their impact on the accumulation of ecological knowledge (as measured by the h-index). While women continue to be underrepresented as working group participants, peer-reviewed publications with gender-heterogeneous authorship teams received 34% more citations than publications produced by gender-uniform authorship teams. This suggests that peers citing these publications perceive publications that also happen to have gender-heterogeneous authorship teams as higher quality than publications with gender uniform authorship teams. Promoting diversity not only promotes representation and fairness but may lead to higher quality science.     

The simulation approach in synthetic biology

Synthetic biology and systems biology are often highlighted as antagonistic strategies for dealing with the overwhelming complexity of biology (engineering versus understanding; tinkering in the lab versus modelling in the computer). However, a closer view of contemporary engineering methods (inextricably interwoven with mathematical modelling and simulation) and of the situation in biology (inextricably confronted with the intrinsic complexity of biomolecular environments) demonstrates that tinkering in the lab is increasingly supported by rational design methods. In other words: Synthetic biology and systems biology are merged by the use of computational techniques. These computational techniques are needed because the intrinsic complexity of biomolecular environments (stochasticity, non-linearities, system-level organization, evolution, independence, etc.) require advanced concepts of bio bricks and devices. A philosophical investigation of the history and nature of bio parts and devices reveals that these objects are imitating generic objects of engineering (switches, gates, oscillators, sensors, etc.), but the well-known design principles of generic objects are not sufficient for complex environments like cells. Therefore, the rational design methods have to be used to create more advanced generic objects, which are not only generic in their use, but also adaptive in their behavior. Case studies will show how simulation-based rational design methods are used to identify adequate parameters for synthesized designs (stability analyses), to improve lab experiments by ‘looking through noise’ (estimation of hidden variables and parameters), and to replace laborious and time-consuming post hoc tweaking in the lab by in-silico guidance (in-silico variation of bio brick properties). The overall aim of these developments, as will be argued in the discussion, is to achieve adaptive-generic instrumentality for bio parts and devices and thus increasingly merging systems and synthetic biology.     

Acceptance tests of diagnostic displays in a PACS system according to AAPM TG18

In a filmless environment it is necessary to execute acceptance and constancy tests on monitors used for interpretation of medical images. Performances of Barco CRT MGD521 MKII, Barco LCD L685EX monitors have been evaluated. Acceptancepress were executed following AAPM Task Group 18 guidelines. Visual and instrumental evaluations of geometric distortions, reflections, luminances response, contrast, uniformity, resolution, angular response and veiling glare were made. Barco monitors showed optimal performances, while EIZO monitors were accepted with some reserve on their quality level.Finally a comparative evaluation between monitors and film (the actual gold standard) was performed by an interview of ten radiologists: the monitors showed a quality at least equal to film. These monitors are currently in use for routine medical interpretation.     

An introductory biology lab that uses enzyme histochemistry to teach students about skeletal muscle fiber types

One important goal of introductory biology laboratory experiences is to engage students directly in all steps in the process of scientific discovery. Even when laboratory experiences are built on principles discussed in the classroom, students often do not adequately apply this background to interpretation of results they obtain in lab. This disconnect has been described at the level of medical education (4), so it should not be surprising that educators have struggled with this same phenomenon at the undergraduate level. We describe a new introductory biology lab that challenges students to make these connections. The lab utilizes enzyme histochemistry and morphological observations to draw conclusions about the composition of functionally different types of muscle fibers present in skeletal muscle. We report that students were not only successful at making these observations on a specific skeletal muscle, the gastrocnemius of the frog Rana pipiens, but that they were able to connect their results to the principles of fiber type differences that exist in skeletal muscles in all vertebrates.     

Using a module-based laboratory to incorporate inquiry into a large cell biology course

Because cell biology has rapidly increased in breadth and depth, instructors are challenged not only to provide undergraduate science students with a strong, up-to-date foundation of knowledge, but also to engage them in the scientific process. To these ends, revision of the Cell Biology Lab course at the University of Wisconsin-La Crosse was undertaken to allow student involvement in experimental design, emphasize data collection and analysis, make connections to the "big picture," and increase student interest in the field. Multiweek laboratory modules were developed as a method to establish an inquiry-based learning environment. Each module utilizes relevant techniques to investigate one or more questions within the context of a fictional story, and there is a progression during the semester from more instructor-guided to more open-ended student investigation. An assessment tool was developed to evaluate student attitudes regarding their lab experience. Analysis of five semesters of data strongly supports the module format as a successful model for inquiry education by increasing student interest and improving attitude toward learning. In addition, student performance on inquiry-based assignments improved over the course of each semester, suggesting an improvement in inquiry-related skills.     

Enhancing Bioinformatics and Genomics Courses: Building Capacity and Skills via Lab Meeting Activities

Reading, writing, publishing, and publicly presenting scientific works are vital for a young researcher's profile building and career development. Generally, the traditional educational curricula do not offer training possibilities to learn and practice how to prepare, write, and present scientific works. These are rather a part of lab meeting activities in research groups. The lack of such training is more critical in some developing countries because this adds to the rare opportunities to discuss and become involved in the exchanges on state of the art scientific literature. Here the authors relate their experience in introducing a weekly 1-day lab meeting in the framework of two previously organized 3-month courses on “Bioinformatics and Genome Analyses”. The main activities which are developed during these lab meetings include scientific literature follow up as well as preparing and presenting oral and written scientific reviews. These activities prove to be useful for a student's self-confidence building, for enhancing their active participation during the lectures and practical sessions, as well as for the positive impact on running the whole course program. Incorporation of such lab meeting activities in the course program significantly improves the capacity building of the participants, their analytical and critical reading of scientific literature, as well as communication skills. In this work it is shown how to proceed with the different steps involved in the implementation of lab meeting activities, and to recommend their regular institution in similar courses.     

Little intervention,big results: intentional integration of information literacy into an introductory-level biology lab course

Abstract

Information literacy refers to a set of skills that allow its user to find appropriate resources and use them to develop, define and defend arguments. In many undergraduate programms, including biology and STEM related fields, students are expected to utilise these skills in writing lab reports, paper analyses, and in developing testable hypotheses. Here, we describe the development of a formalised information literacy module for an introductory biology laboratory course and a rubric to measure the effectiveness of this module, including suggestions for implementation. Our data show that while short-term gains were not made using previously published IL tests, application of a tailored rubric to writing assignments did show significant improvement in the students’ ability to find relevant sources, define the purpose of their work and explore that focus. The results of our evaluation demonstrate that even modest additions of formal instruction in information literacy to a course can significantly improve student gains in this area.     

Teachers' journal club: bridging between the dynamics of biological discoveries and biology teachers

Since biology is one of the most dynamic research fields within the natural sciences, the gap between the accumulated knowledge in biology and the knowledge that is taught in schools, increases rapidly with time. Our long-term objective is to develop means to bridge between the dynamics of biological discoveries and the biology teachers and students. Here we report on our recent initiative towards this objective in which we established a journal club forum as a means towards the professional development of biology teachers. We used the journal club format, which is common within the scientific community, in order to engage biology teachers in a constructivist type of learning in which they acquire new skills and at the same time are continuously updated as to biological discoveries, and can then develop updated activities for their biology students. We suggest using the journal club format for the long-term professional development of biology teachers.     

How are humans related to other primates? A guided inquiry laboratory for undergraduate students

Understanding that phylogenies depict the evolutionary history of species is a critical concept for undergraduate biology students. We present an inquiry-based laboratory exercise exploring this concept in the context of the human phylogeny. This activity reinforces several important biological concepts and skills. Bolstered concepts include that evolution is descent with modification, that evolution is a genetic process, and that humans are closely related to apes. In terms of thinking skills, the lab gives students practice with hypothetical-deductive thinking, quantifying patterns from complex data, and evaluating evidence.     

Virtual labs: a substitute for traditional labs?

Current technologies give us the ability to enhance and replace developmental biology classes with computer-based resources, often called virtual labs. In the process of using these resources, teachers may be tempted to neglect the simpler technologies and lab bench activities, which can be labor intensive. In this paper, I take a critical look at the role of computer-based materials for the teaching of developmental biology in order to aid teachers in assessing their value. I conclude that while digital tools have value, they should not replace all of the traditional laboratory activities. Clearly, both computer-enhanced activities and traditional labs must be included in laboratory exercises. Reliance on only one or the other is inappropriate. In order to determine when it is appropriate to use a particular educational tool, the goals of the course and the needs of biology students for an education that gives them a realistic and engaged view of biology must be understood. In this paper, I dispel some of the myths of computer tools and give specific guidelines for assessing their usage, taking into account the special needs of a developmental biology class and the difficulties of observing all the developmental stages of subject organisms in the timescale of class meetings.     

Digital image analysis of Zostera marina leaf injury

Current methods for assessing leaf injury in Zostera marina (eelgrass) utilize subjective indexes for desiccation injury and wasting disease. Because of the subjective nature of these measures, they are inherently imprecise making them difficult to use in quantifying complex leaf injuries from multiple sources. We have developed a method using color digital photography of eelgrass leaves which are then manipulated using image processing programs and analyzed using geographic digital image analysis. The resulting false color images are then assigned by the user into uninjured and injured groupings which may then be reported as a percentage of leaf area affected. If images are rectified, leaf area (cm²) of injured and uninjured leaf segments may be determined. Although this method is time consuming and still requires some subjective judgments, it does allow for precise analysis of highly complex leaf injuries and has the potential to be a substantial improvement over existing leaf injury indexes.     

Modern and simple construction of plasmid: Saving time and cost

Construction of plasmids has been occupying a significant fraction of laboratory work in most fields of experimental biology. Tremendous effort was made to improve the traditional method for constructing plasmids, in which DNA fragments digested with restriction enzymes were ligated. However, the traditional method remained to be a standard protocol more than 40 years. At last, several recent inventions are rapidly and completely replacing the traditional method, because they are far quicker with less cost, and requiring less material. We here introduce three such methods that cover up most of the cases. Moreover, they are complementary with each other. Our lab protocols are provided for “no strain, no pain” construction of plasmids.     

An unconventional route to becoming a cell biologist

I am honored to be the E. B. Wilson Award recipient for 2015. As we know, it was E. B. Wilson who popularized the concept of a “stem cell” in his book The Cell in Development and Inheritance (1896, London: Macmillan & Co.). Given that stem cell research is my field and that E. B. Wilson is so revered within the cell biology community, I am a bit humbled by how long it took me to truly grasp his vision and imaginative thinking. I appreciate it deeply now, and on this meaningful occasion, I will sketch my rather circuitous road to cell biology.I grew up in a suburb of Chicago. My father was a geochemist, and for everyone whose parents worked at Argonne National Laboratories, Downers Grove was the place to live. My father’s sister was a radiobiologist and my uncle was a nuclear chemist, both at Argonne; they lived in the house next door. Across the street from their house was the Schmidtke’s Popcorn Farm—a great door to knock on at Halloween. The cornfields were also super for playing hide-and-seek, particularly when you happened to be shorter than those Illinois cornstalks.Open in a separate windowElaine FuchsI remember when the first road in the area was paved. It made biking and roller-skating an absolute delight. Fields of butterflies were everywhere, and with development came swamps and ponds filled with pollywogs and local creeks with crayfish. It was natural to become a biologist. When coupled with a family of scientists and a mother active in the Girl Scouts, all the resources were there to make it a perfect path to becoming a scientist.I could hardly wait until I was in junior high school, when I could enter science fairs. You would think that my science-minded family might help me choose and develop a research project. True to their mentoring ethos, they left these decisions to me. My first project was on crayfish behavior. I recorded the response of the crayfish I had caught to “various external stimuli.” At the end of this assault, I dissected the crayfish and, using “comparative anatomy,” attempted to identify all the parts. The second project was no gentler. I focused on tadpole metamorphosis and the effects of thyroid hormone in accelerating development at low concentrations and death at elevated concentrations. Somehow, I ended up going all the way to the state fair, where it became clear that I had serious competition. That experience, however, whetted my appetite to gain more lab experience and to learn to read the literature more carefully.My experience with high school biology prompted me to gravitate toward chemistry, physics, and math. When it came to college, my father told me that if there was a $2000/year (translated in 2015 to be $30,000/year) reason why I should go anywhere besides the University of Chicago (where Argonne scientists received a 50% tuition cut for their children) or the University of Illinois (then $200/year tuition), we could “discuss” it further. Having a sister, father, aunt, and uncle who went to the University of Chicago, I chose the University of Illinois and saved my Dad a bundle of money. At Illinois, I thought I might revisit biology, but my choices for a major were “biology for teachers” or “honors biology.” The first did not interest me; the second seemed intimidating.I enrolled as a chemistry major. Four years went by, during which time I never took a biology class. I enjoyed quantum mechanics, physics, and differential equations, and problem solving became one of my strengths. In the midst of the Vietnam War era, however, Illinois was a hotbed of activity. I was inspired to apply to the Peace Corps, with a backup plan to pursue science that would be more biomedically relevant than quantum mechanics. I was accepted to go to Uganda with the Peace Corps, but with Idi Amin in office, my path to science was clear. Fortunately, the schools I applied to accepted me, even though, in lieu of GRE scores, I had submitted a three-page essay on why I did not think another exam was going to prove anything. I chose Princeton’s biochemistry program. This turned out to be a great, if naïve choice, as only after accepting their offer did I take a biochemistry class to find out what I was getting into. I chose to carry out my PhD with a terrific teacher of intermediary metabolism, Charles Gilvarg, who worked on bacterial cell walls. My thesis project was to tackle how spores break down one cell wall and build another as they transition from quiescence to vegetative growth.By my fourth year of graduate school, I was trained as a chemist and biochemist and was becoming increasingly hooked on biomedical science. I listened to a seminar given by Howard Green, who had developed a method to culture cells from healthy human skin under conditions in which they could be maintained and propagated for hundreds of generations without losing their ability to make tissue. At the time, Howard referred to them as epidermal keratinocytes, but in retrospect, these were the first stem cells ever to be successfully cultured. I was profoundly taken by the system, and Howard’s strength in cell biology inspired me. It was the perfect match for pursuing my postdoctoral research. The time happened to be at the cusp of DNA recombinant technology.At MIT, I learned how to culture these cells. I wanted to determine their program of gene expression and how this changed when epidermal progenitors embark on their terminal differentiation program. While the problem in essence was not so different from that of my graduate work at Princeton, I had miraculously managed to receive my PhD without ever having isolated protein, RNA, or DNA. Working in a quintessential cell biology lab and tackling a molecular biology question necessitated venturing outside the confines of the Green lab and beyond the boundaries of my expertise. Fortunately, this was easy at MIT. Richard Hynes, Bob Horvitz, Bob Weinberg, and Graham Walker were all assistant professors, and their labs were very helpful, as were those of David Baltimore and Phil Sharp, a mere walk across the street. On the floor of my building, Steve Farmer, Avri Ben Ze’ev, Gideon Dreyfuss, and Ihor Lemischka were in Sheldon Penman’s lab just down the hall, and they were equally interested in mRNA biology, providing daily fuel for discussions. Uttam Rhajbandary’s and Gobind Khorana’s labs were also on the same floor, making it easy to learn how to make oligo(dT)-Sepharose to purify my mRNAs. Vernon Ingram’s lab was also on the same floor, so learning to make rabbit reticulocyte lysates to translate my mRNAs was also possible. Howard bought a cryostat, so I could section human skin and separate the layers. And as he was already working with clinicians at Harvard to apply his ability to create sheets of epidermal cells for the treatment of burn patients, I had access to the leftover scraps of human tissue that were also being used in these operations.The three years of my postdoc were accompanied by three Fuchs and Green papers. The first showed that epidermal keratinocytes spend most of their time expressing a group of keratin proteins with distinct sequences. The second showed that these keratins were each encoded by distinct mRNAs. The third showed that, as epidermal keratinocytes commit to terminally differentiate, they switch off expression of basal keratins (K5 and K14) and switch on the expression of suprabasal keratins (K1 and K10). That paper also revealed that different stratified tissues express the same basal keratins but distinct sets of suprabasal keratins. I am still very proud of these accomplishments, and my MIT experience made me thirst to discover more about the epidermis and its stem cells.My first and only real job interview came during my second year of postdoc, at a time when I was not looking for a job. I viewed the opportunity, initiated by my graduate advisor, as a free trip home to visit my parents and my trial run to prepare me for future searching. I was thrilled when this interview materialized into an offer to join the faculty, for which the University of Chicago extended my start time to allow me to complete my three years with Howard.Times have clearly changed, and it is painful to see talented young scientists struggle so much more today. That said, I have never looked ahead very far, and having a lack of expectations or worry is likely to be as helpful today as it was then. I am sure it is easier said than done, but this has also been the same for my science. I have always enjoyed the experiments and the joy of discovery. There was no means to an end other than to contemplate what the data meant in a broader scope.I arrived at the University of Chicago with a well-charted route. My aim was to make a cDNA library and clone and characterize the sequences and genes for the differentially expressed keratins I had identified when I was at MIT. It was three months into my being at Chicago when my chair lined up some interviews for me to hire a technician. I was so immersed in my science that I did not want to take time to hire anyone. I hired the first technician I interviewed. Fortunately, it worked out. However, I turned graduate students away the first year, preferring to carry out the experiments with my technician and get results. After publishing two more papers—one on the existence of two types of keratins that were differentially expressed as pairs and the other on signals that impacted the differential expression of these keratin pairs, I decided to accept a student, who analyzed the human keratin genes. My first postdoc was a fellow grad student with me at Princeton; she studied signaling and keratin gene expression. My second postdoc was initiated by my father, who chatted with him at the elevator when I was moving into my apartment. He set up DNA sequencing and secondary-structure prediction methods, and the lab stayed small, focused, and productive.I was fascinated by keratins, how they assembled into a network of intermediate filaments (Ifs). When thalassemias and sickle cell anemia turned out to be due to defects in globin genes, I began to wonder whether there might be human skin disorders with defective keratin genes. I had no formal training in genetics, and there were no hints of what diseases to focus on. Thus, rather than using positional cloning to identify a gene mutation associated with a particular disease, we took a reverse approach: we first identified the key residues for keratin filament assembly. After discovering that mutations at these sites acted dominant negatively, we engineered transgenic mice harboring our mutant keratin genes and then diagnosed the mouse pathology. Our diagnoses, first for our K14 mutations and then for our K10 mutations, turned out to be correct: on sequencing the keratins from humans with epidermolysis bullosa simplex (EBS), we found K14 or K5 mutations; similarly, we found K1 or K10 mutations in affected, but not in unaffected, members of families with epidermolytic hyperkeratosis (EH). Both are autosomal-dominant disorders in which patients have skin blistering or degeneration upon mechanical stress. Without a proper keratin network, the basal (EBS) or suprabasal (EH) cells could not withstand pressure. Ironically, family sizes of all but the mildest forms of these disorders were small, meaning that the disorders were not amenable to positional cloning. But the beauty of this approach is that once we had made the connection to the diseases, we understood their underlying biology. In addition, the IF genes are a superfamily of more than 100 genes differentially expressed in nearly all tissues of the body. Once we had established EBS as the first IF gene disorder, the pathology and biology set a paradigm for a number of diseases of other tissues that turned out to be due to defects in other IF genes.Fortunately, I had students, Bob Vassar (professor, Northwestern University) and Tony Letai (associate professor, Harvard Medical School), and a postdoc, Pierre Coulombe (chair, Biochemistry and Molecular Biology, Johns Hopkins University), who jumped into this fearless venture with me. We had to go off campus to learn transgenic technology. I had never worked with mice before. When Bob returned to campus with transgenic expertise, we hired and trained Linda Degenstein, whose love for animal science was unparalleled. Pierre’s prior training in electron microscopy was instrumental in multiple ways. Additionally, I was not a dermatologist and had no access to human patients. Fortunately Amy Paller, MD, at Northwestern volunteered to work with us.The success of this project attests to an important recipe: 1) Pursue a question you are passionate about. 2) In carrying out rigorous, well-controlled experiments, each new finding should build upon the previous ones. 3) If you have learned to be comfortable with being uncomfortable, then you will not be afraid to chart new territory when the questions you are excited to answer take an unanticipated turn. 4) Science does not operate in a vacuum. Interact well with your lab mates and take an interest in their science as well as your own. And wherever you embark upon a pathway in which the lab’s expertise is limited, do not hesitate to reach out broadly to other labs and universities.I have followed this recipe now for more than three decades, and it seems to work pretty well. A lab works only when its students and postdocs are interactive, naturally inquisitive, and freely share their ideas and findings. I have been blessed to have a number of such individuals in my lab over the years. When push comes to shove, I am always inclined first to shave from the “brilliant” category and settle for smart, nice people who are passionate and interactive about science and original and unconventional in their thinking.So what questions have I been most passionate about? I have always been fascinated with how tissues form during development, how they are maintained in the adult, and how tissue biology goes awry in human disorders, particularly cancers. I first began to think about this problem during my days at Princeton. I also developed a dogma back then that I still hold: to understand malignancies, one must understand what is normal before one can appreciate what is abnormal. I think this is why I have spent so much of my life focusing on normal tissue morphogenesis, despite my passion for being at the interface with medicine. And because skin has so many amazingly interesting complexities, and because it is a great system to transition seamlessly between a culture dish and an animal, I have never found a reason to choose any other tissue over the one I chose many years back.I will not dwell on the various facets of skin biology we have tackled over the years. Our initial work on keratins was to obtain markers for progenitors and their differentiating lineages. This interest broadened to understanding how proliferative progenitors form cytoskeletal networks and how the cytoskeleton makes dynamic rearrangements during tissue morphogenesis.From the beginning, the lab has also been fascinated by how tissue remodeling occurs in response to environmental signals. Indeed, signals from the microenvironment trigger changes in chromatin dynamics and gene expression within tissue stem cells. Ultimately, this leads to changes in proteins and factors that impact on cell polarity, spindle orientation, asymmetric versus symmetric fate specifications, and ultimately, the balance between proliferation and differentiation.The overarching theme of my lab over these decades is clear, namely, to understand the signals that unspecified progenitors receive that instruct them to generate a stratified epidermis, make hair follicles, or make sweat and sebaceous glands. And if we can understand how this happens, then how are stem cells born, and how do they replace dying cells or regenerate tissue after injury? And, finally, how does this process change during malignant progression or in other aberrant skin conditions?In tackling tissue morphogenesis, I have had to forgo knowing the details of each tree and instead focus on the forest. There are many times when I stand back and can only admire those who are able to dissect beautiful cellular mechanisms with remarkable precision. But I crossed that bridge some years ago in tackling a problem that mandates an appreciation of nearly all the topics covered in Bruce Alberts’ textbook Molecular Biology of the Cell. I am now settled comfortably with the uncomfortable, and the problem of tissue morphogenesis in normal biology and disease continues to keep me more excited about each year’s research than I was the previous year. Perhaps the difference between my days as a student, postdoc, and assistant professor and now is that my joy and excitement is as strong for those I mentor and have mentored as it is for myself.     

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.     

Hypothesis testing as a laboratory exercise: a simple analysis of human walking,with a physiological surprise

This paper describes a laboratory exercise designed to provide students with experience testing a hypothesis by systematically isolating and controlling determinant variables. The study involves an analysis of walking and is performed by the students on a subject from within their lab group. The study requires use of a motorized treadmill, tape measure, stop watch, metronome, personal cassette player, and calculator. The exercise is designed to include factors that the students are familiar with, so they can focus on the isolation of variables without being confused about the process they are investigating. However, the exercise will not turn out as the students anticipate, meaning they will be forced to reevaluate the assumptions that formed the basis of their original hypothesis. This exercise is designed for a college-level course in exercise science, physiology, or biology but could easily be managed by a high school honors class with appropriate guidance.     

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.