Category Archives: Science Content

Using the Primary Literature in your Classroom

36233488When I think about the skills I want my students to leave college with the ability to think critically is prominently displayed at the top of the list. Thinking about my own development as a scholar I can see that reading, writing and learning to understand the primary scientific literature are some of the activities that helped me to develop those skills.

Handing an article from the primary literature to a brand new college student without giving them the skills to tackle it is bound to result in some students leaving the activity feeling frustrated and “stupid”. If you approach using the primary literature with a little creativity though I think you’ll find that your students gain in leaps and bounds.

For those of you who teach Physiology a resource by Teresa Alvarez1, located on the LifeSciTRC, is a fun way to get your students working in groups, communicating what they learn to others and reading and understanding the primary literature. Students work in groups and are expected to read an article from the primary literature pertaining to a certain topic in Physiology. The group that reads the article is expected to summarize the article addressing bullet points that are highlighted in the resource and then they present that article to the class.

The C.R.E.A.T.E. method2 has been used and thoroughly tested. Students get down and dirty with the primary literature. They read a series of papers from the same lab, following that lab groups progress through a particular initial question that may morph into other questions. After reading each paper students design a follow up study and then read the next article in that laboratories sequence. They end the activity by sending the authors of the papers a series of questions they generated through this process and discuss author responses at the end of the module. They learn more deeply about the scientific method and scientists in general. The C.R.E.A.T.E. website has a wealth of information that might help you implement this technique in your classes.

I have taken a variety of different approaches to incorporating the primary literature into my classes. I always enjoy the more traditional journal club, where students read an article and present it to the rest of the class. I have found good results with this method when my students are slightly more advanced in their understanding but I have colleagues that have used this technique in lower level classes to great effect.

More recently I’ve been using figures taken from the primary literature in my classes. Students see the figures and answer questions about the figures. I generally start with questions that help them to orient themselves to the graph. I might ask students to identify the dependent or independent variable in the graph. Then I move students toward questions that ask them to describe the results the figures, determine conclusions the authors might draw from the results and finally end with implications of the results.

It is exciting to see students discussing the primary literature in their groups. They often argue about what a figure means and become deeply invested in convincing those on their team that they are right. It is reassuring how often they come to the same conclusion as the authors in the paper.

These are just a few ways to expose your students to the primary literature. How do you do it in your classes? Have you used any of the methods highlighted above? What has been most effective for your classes?


  1. Alvarez, Teresa. 2008. Primary Literature Scavenger Hunt.
  2. CREATE (transform understanding of science). 2014.





Lynn Diener, PhD, is an Associate Professor, Sciences Department Chair and Biology Program Director at Mount Mary College. Lynn regularly teaches Human Physiology, Human Anatomy, and Ecology. She is also a LifeSciTRC Scholar, Fellow, and Advisory Board Member.


Biomarkers and Cancer: the Science and the Issues

What are Biomarkers? 

Glial cells with biomarkers

This image shows one way that biomarker proteins such as glial fibrillary acid protein can be labeled as a biomarker for normal development of human nerve cells.Photo courtesy of the National Institute of Neurological Disorders and Stroke (NINDS)





Imagine being told by your physician that you will likely have your first heart attack at 50 years with at least a 90% certainty.  It is not too surprising to hear that physicians provide health advice with patients based on a patient’s life style or family history.  However, there is a growing body of research that searches for molecular fingerprints that can accurately predict the occurrence of life-threatening disorders. These molecular fingerprints are called biomarkers.

Biomarker studies are not the same as the traditional DNA testing that identifies known alleles or mutations from the norm that are identified with genetic diseases. A variety of cellular and molecular parameters can be measures as biomarkers of cell and bodily activities. Biomarker research today is primarily targeted at predicting and treating diseases. However, biomarkers are also indicators of any physiological or environmental factor that elicits responses in specific cells, tissues, or organs. The journal Biomarker provides a good idea of the latitude of biomarker research.

Likely the fastest growing area of biomarker research is in cancer studies.  Cancer is a globally distributed disease that needs better treatment suited for targeting the cancer cells without causing needless harm to normal body cells.  The Biomarkers in Cancer journal is one of many biomarker journals that contain the latest findings on how biomarkers can predict the incidence of cancer and be used to find cancer treatments.

Official Definition of Biomarker
The National Cancer Institute at the United States National Institutes of Health defines biomarkers as “A biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease. A biomarker may be used to see how well the body responds to a treatment for a disease or condition. Also called molecular marker and signature molecule.”

How are Biomarkers used in Cancer Research?

The occurrence of melanoma, as shown above, can be better and more simply predicted using biomarkers produced by the cancer cells. Image courtesy of the National Cancer Institute (NCI)

The occurrence of melanoma, as shown above, can be better and more simply predicted using biomarkers produced by the cancer cells. Image courtesy of the National Cancer Institute (NCI)





Cancer is unlike most other diseases because of the variety of factors can predispose a person to cancer.  A combination of environmental factors acting on various genetic and epigenetic errors can induce cancerous cells. More and more studies are showing One area of cancer biomarker research is to improve the easy at which the cancers can be detected.  For example, simpler ways of detecting prostate cancer are being developed through finding biomarkers in seminal fluids. This is much less invasive than blood tests and prostate biopsies.  Breast cancer has many causes one of which is caused by mutations in the brca genes. However, identification of the BRCA mutation does not necessarily predict the chance of developing breast cancer. Researchers are seeking a variety of biomarkers that accurately predict the factors that contribute to onset of breast cancer.

There are many types of cancers cause by a multitude of factors.  Biomarkers seem to be the best way to understand the molecular biology of cancer detection and treatment. There is a growing interest by pharmaceutical companies for designing biomarkers for a variety of diagnostic purposes. There will likely never be one biomarker profile that identifies all cancers. However, it hoped that biomarkers for specific cancers can catch cancers long before they develop.

What are the Issues with using Cancer Biomarkers?

Biomarker identification research is causing quite a commotion in the medical and scientific communities. Epidemiologists and physicians are currently debating the accuracy and precision of biomarkers. It is often difficult to predict the success rate of biomarker predictions. It will take many more studies on large populations of people to find strong correlations between biomarkers and the cancer cell’s biological processes. Issues of accuracy particularly bring up concerns about determining the probabilities of false positive and false negative results that can result in grave diagnostic errors for various diseases and inappropriate policies based on inappropriate associations between biomarkers and causative factors of disease.

Bioethicists, psychologists, and public health officials have many other concerns about biomarkers.   Probably, the biggest issue is the confidential nature of biomarker information.  It is possible that biomarker information about a person can accidently become publically available. Certain conditions carry social stigmas that a patient may wish to keep private. Also, a person’s employability and insurability can be hindered by certain conditions.

A variety of cell products and cell structures can be used as biomarkers for disease and changes in metabolic processes due to environmental factors and pharmaceuticals. Biomarkers are effective only if they accurately identify the condition they designed to detect. Image courtesy National Institute of General Medical Sciences (NIGMS)

A variety of cell products and cell structures can be used as biomarkers for disease and changes in metabolic processes due to environmental factors and pharmaceuticals. Biomarkers are effective only if they accurately identify the condition they designed to detect. Image courtesy National Institute of General Medical Sciences (NIGMS)

Biomarker information must be collected in a way to protect patient confidentiality. It important to avoid any negative consequences from diagnosing disease. Image courtesy of National Eye Institute (NEI).

Biomarker information must be collected in a way to protect patient confidentiality. It important to avoid any negative consequences from diagnosing disease.Image courtesy of National Eye Institute (NEI).












How do you teach the importance of cancer biomarkers in the biology curriculum?

Scientifically accurate resources are essential for teaching reliable and contemporary information related to biomarkers in cancer research.  All of the teaching resources mentioned in section are available on the American Physiological Society’s Life Science Teaching Resource Community (LifeSciTRC) website. Resources on the LifeSciTRC are peer reviewed and rated by instructors who testing the resources in their teaching.

Cancer biology is a fundamental component of the biological sciences core content. It can be used to reinforce the principles of cell structure, cell differentiation, and cell division. Strategies for diagnosing and treating cancer are use skills that are needed for STEM careers in the biomedical sciences and biotechnology. Students can be introduced to cancer biology using the Northwest Association for Biomedical Research BRCA1 and Breast Cancer website. A variety of resources about cell structure and function related to cancer are available at the Cold Spring Harbor Laboratory and Dolan DNA Learning Center. Am article called “Inflammation and Stem Cells in Gastrointestinal Carcinogenesis” provides good information about how measuring inflammation can lead to the discovery of cancer indicators.

Biomarker research is still an emerging science that applies information about biochemistry, cell differentiation, cell structure, embryology, genetics, and molecular biology. Plus, the issues raised by biomarker research is important for understanding the principles of bioethics and public health. A general resource giving specific examples of biomarker uses is available in the article “Detailing Deadly Effects of Household Air Pollution From Biomass Fuels Leads to Call For Studies Into Biomarkers of Exposure and Predictors of Respiratory Disease Adolescents“.

Students can then be given the following resources to read and hypothesize what type of biomarkers can be developed to predict health problems from the measurements used in the research studies:

The Vision and Change in Undergraduate Biology Education project encourages undergraduate biology faculty to encourage critical thinking and career skills exploration in their teaching. Biomarkers are an interesting topic that be used integrate higher order thinking and science careers skill into the biology curriculum.  Students should be encourage do find cancer and biomarker websites that can be submitted to the LifeSciTRC website as content and teaching resources.

All images are from the National Institutes of Health Image Bank at





Brian Shmaefsky, PhD, is currently a professor of biology at Lone Star College – Kingwood, near Houston, TX. His research emphasis is in environmental physiology. He has served in leadership capacities for the American Institute of Biological Sciences, Biotechnology Institute, National Association of Biology Teachers, National Science Teachers Association, Society for College Science Teachers, and Academies of Science in Illinois, Oklahoma, and Texas. He has been a speaker at many local and international conferences on various topics including biotechnology, industrial hygiene, media relations, science education, sustainable development, workforce safety, and workforce training. Brian is LifeSciTRC Scholar, Fellow, and Advisory Board Member.