When Experiments Fail: Troubleshooting Guide for Protein, Molecular, and Immunological Research
About this ebook
Divided into well-structured parts, the book begins with the philosophy of scientific failure, exploring how failed experiments often pave the way to breakthroughs. From there, it dives into the heart of wet lab work, offering deeply detailed troubleshooting strategies for each step of the experimental workflow:
Part I covers the foundations experimental design, common human errors, and how to avoid wasting weeks because of a mislabeled tube or contaminated reagent.
Part II focuses on molecular biology, with real-world solutions to PCR nightmares, cloning frustration, nucleic acid extraction disasters, and the elusive art of clean reverse transcription.
Part III unpacks protein biochemistry, from smudgy SDS-PAGE gels to vanishing Western blot signals and uncooperative enzyme assays.
Part IV explores cell culture and transfection pitfalls, highlighting contamination issues, low transfection efficiency, and media misadventures.
Part V dives into immunological techniques like ELISA, co-IP, and flow cytometry offering crisp, practical guidance on minimizing background noise and maximizing specific signal.
Part VI ties everything together by addressing higher-level concerns like reproducibility, data integrity, proper documentation, and how to interpret results without letting bias lead the way.
What makes When Experiments Fail stand out is its hybrid of scientific rigor and grounded lab realism. It doesn’t just list protocols it helps you diagnose problems like a lab detective, with flowcharts, reagent preparation guides, glossaries, and real anecdotes (like performing PCR of PCR to rescue an elusive band). Whether you’re a seasoned researcher troubleshooting an inexplicably dead western blot, a student panicking over an absent PCR product, or a curious reader wanting to understand the human side of scientific research, this book will feel like a trusted bench mate such that an honest, helpful, and maybe just a little bit sarcastic when things go really wrong. Because in science, failure isn’t the end. It’s just your experiment trying to teach you something.
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About the author
Mohammad Hafiz Ganie is a young biochemist, researcher, and science communicator hailing from Kashmir. With a Bachelor's degree in Biochemistry and Physiology from Cluster University Srinagar and a Master's in Biochemistry and Molecular Biology from the University of Kashmir (Class of 2025), Hafiz has combined academic rigor with hands-on lab experience. During his research, Hafiz has encountered and overcome many experimental dead ends, from PCR failures to elusive Western blots, from transformation inefficiencies to signal noise in ELISAs. His previous works include the autobiographical Carvaan: The Story of Time and the upcoming title p53: What Next? When he’s not in the lab or writing, Hafiz enjoys teaching, mentoring young scientists, and exploring the philosophical dimensions of science and failure. His passion lies in making science accessible, practical, and real for the next generation of researchers
Tanzeela Bashir is a budding cancer biologist with a strong academic and research background in biochemistry. She completed her Master’s degree in Biochemistry from the University of Kashmir and is currently pursuing her Ph.D. in the same field at the University of Kashmir.
Her doctoral research focuses on angiogenesis and cancer progression, with a specific emphasis on epigenetic regulation of the ANGPTL1 gene through methylation. With a keen interest in understanding the molecular pathways that control tumor suppression and vascular development, Tanzeela’s work aims to uncover potential therapeutic strategies for halting cancer metastasis.
Driven by curiosity, persistence, and a commitment to scientific rigor, she has presented her research at various academic forums and is passionate about translating lab findings into meaningful advances in cancer treatment. When not in the lab, she engages in scientific writing and mentoring young students entering the world of molecular biology.
Haadi Manzoor is a postgraduate researcher currently pursuing his Master’s degree in Biochemistry at the University of Kashmir. His academic journey is fueled by a strong interest in molecular oncology and cell signaling.
Haadi's current research focuses on the role of Rho GDP-dissociation inhibitors (Rho GDIs) in suppressing cancer progression. By investigating how these molecular regulators influence cellular dynamics and tumor development, his work aims to contribute to the understanding of novel therapeutic targets in cancer biology.
Dedicated to the pursuit of translational research, Haadi is passionate about bridging the gap between benchwork and clinical application. With a detail-oriented approach and growing expertise in molecular techniques, he represents the next generation of scientists striving to decode the complexities of cancer.
Showkat Ahmad Dar is a passionate molecular biologist with a Master’s degree in Biochemistry from the University of Kashmir. Currently, he is working at the Centre for Interdisciplinary Research, where his research bridges plant biology and protein biochemistry.
Showkat’s work focuses on a plant-derived AAA+ protein, a member of a functionally diverse and structurally conserved family of ATPases. He is actively involved in cloning and expressing this protein using a bacterial expression system, aiming to uncover its structural and functional properties for future applications in biotechnology and plant stress biology.
His research reflects a strong interdisciplinary approach, combining molecular cloning, protein expression, and functional analysis to study plant proteins with potential significance in agriculture and industry. With a sharp analytical mindset and hands-on technical skills, Showkat is steadily building a path in experimental science.
Dr. Mohammad Amin Hajam is a dedicated cancer epidemiologist and molecular biochemist with a strong academic and research foundation in clinical and molecular biology. He holds an M.Sc. in Clinical Biochemistry and earned his Ph.D. from the University of Kashmir, where his research focused on the interplay between 14-3-3 epsilon and Rho GDI proteins in the context of cancer progression and regulation.
Dr. Hajam has also completed a prestigious research internship at the Centre for Cellular and Molecular Biology (CCMB), where he gained advanced training in molecular biology and protein interaction techniques. His work lies at the intersection of molecular signaling and cancer biology, aiming to decipher how key regulatory proteins contribute to tumor development and metastasis.
Auqib Manzoor is a molecular biologist and science writer with a Master’s degree in Biochemistry from the University of Kashmir. Currently pursuing his Ph.D., his research focuses on the role of ubiquitination in cellular regulation and disease, with a particular interest in how this post-translational modification impacts cancer biology.
In addition to his lab work, Auqib is an accomplished academic writer. He has contributed book chapters on cutting-edge topics such as "Computational Tools and Approaches for CRISPR/Cas Technology" and "Mechanism of RNA Splicing Alternative Splicing and Cancer", showcasing his versatility in both wet-lab and computational biology.
Auqib’s work bridges molecular mechanisms and bioinformatics, aiming to develop a deeper understanding of cellular control systems and their implications in cancer progression. With a passion for teaching and scientific communication, he continues to inspire young researchers through both his experiments and his writing.
