BIO403_Lecture3_data_documentation_shf_2025.pdf

# Scientific conduct and data documentation This section outlines the fundamental principles of scientific conduct, emphasizing the critical role of data recording, documentation, and ownership in ensuring research integrity and reproducibility. ### 1.1 The necessity of data documentation Data documentation is presented as a crucial requirement in scientific research, serving as the foundation for understanding and verifying scientific work [18](#page=18) [19](#page=19). ### 1.2 Principles of data recording and documentation Proper recording and documentation of data are essential components of scientific conduct [20](#page=20) [21](#page=21). #### 1.2.1 The lab book: a historical and practical tool The lab book, particularly following a "ZEN approach," is highlighted as a vital tool for recording scientific activities. It is not merely a record of what was done, but a comprehensive account that facilitates scientific rigor and integrity [22](#page=22). ##### 1.2.1.1 Content of a useful lab book A useful lab book should explain: * What you did [23](#page=23). * Why you did it [23](#page=23). * How you did it [23](#page=23). * When you did it [23](#page=23). * Where materials are located [23](#page=23). * What happened, including what did not happen [23](#page=23). * Your interpretations of the results [23](#page=23). * Contributions of others involved [23](#page=23). * What the next steps are [23](#page=23). ##### 1.2.1.2 Characteristics of good lab books Good lab books possess several key characteristics: * **Legibility:** They are legible and ideally written in ballpoint pen ink [24](#page=24) [25](#page=25). * **Organization and Up-to-dateness:** They are well-organized and kept current [24](#page=24). * **Accuracy and Completeness:** They are accurate and complete, including page numbers [24](#page=24) [25](#page=25). * **Inclusion of Data:** Data, such as photos, should be affixed to the pages [24](#page=24) [25](#page=25). * **Reproducibility:** They must allow for the repetition of experiments [24](#page=24) [25](#page=25). * **Compliance:** They should be compliant with funding agency and institutional requirements [24](#page=24) [25](#page=25). * **Accessibility:** They must be accessible to authorized persons [24](#page=24) [25](#page=25). * **Storage and Backup:** They need to be stored properly and appropriately backed up [24](#page=24) [25](#page=25). * **Witnessing:** They should be properly witnessed when necessary [24](#page=24) [25](#page=25). * **Ownership Recognition:** They must be properly recognized as the property of the institution [24](#page=24) [25](#page=25). * **Record of Contributions:** They serve as the ultimate record of scientific contributions [24](#page=24) [25](#page=25). > **Tip:** Lab books are not intended to be "neat books" but rather accurate and thorough records of experimental work [25](#page=25). ##### 1.2.1.3 Other considerations for lab books Further considerations for lab books include: * **Patents:** Patent applications require detailed records extending over significant periods [25](#page=25). * **Writing Tools:** Pens are preferred over pencils [25](#page=25). * **Error Correction:** Mistakes should be crossed out rather than erased or covered with correction fluid [25](#page=25). * **Format:** The choice between bound, spiral, or electronic lab books should be considered [25](#page=25). #### 1.2.2 Types of lab books and their trade-offs Different types of lab books offer distinct advantages and disadvantages: * **Bound/Stitched Books:** * **Advantages:** No lost pages; legally more convincing; difficult to alter [26](#page=26). * **Disadvantages:** Not logically organized; requires cross-referencing [26](#page=26). * **Spiral Bound/Loose Leaf Books:** * **Advantages:** Organized by experiment; data stored together [26](#page=26). * **Disadvantages:** Pages may get lost; difficult to authenticate [26](#page=26). * **Electronic Books:** * **Advantages:** Easy to search, read, and store; can offer security features [26](#page=26). * **Disadvantages:** Risk of corrupted files; potential software compatibility issues [26](#page=26). #### 1.2.3 The level of detail required in documentation The level of detail in documenting experiments is paramount. Specific information required includes: * **Reagents:** Source, product/order number, lot number, expiration date, and storage conditions [28](#page=28). * **Solutions:** How they were made and stored [28](#page=28). * **Cells:** Type, source, passage number, and growth medium used [28](#page=28). * **Instruments:** Type, name, location, and serial number of the equipment [28](#page=28). * **Settings and Procedures:** Detailed recording of instrument settings and experimental procedures is also critical [28](#page=28). > **Tip:** "Details – details – details" is the mantra for effective lab book entries [27](#page=27) [28](#page=28). ### 1.3 Data ownership Lab books are explicitly recognized as the property of the institution where the research is conducted. This underscores the importance of adhering to institutional policies regarding data management and intellectual property [24](#page=24) [25](#page=25). --- # Lab book examples and best practices This section explores exemplary lab books from historical scientists, outlines what constitutes useful and good lab book content, and discusses the pros and cons of different lab book formats [22](#page=22) [3](#page=3). ### 2.1 Exemplary historical lab books Classical examples of scientific inquiry documented in lab books include those by renowned figures such as Leonardo da Vinci, Isaac Newton, Charles Darwin, Thomas Edison, Marie Curie, and Albert Einstein. These historical records, while varying in style and detail, underscore the fundamental importance of meticulous documentation in scientific advancement [10](#page=10) [12](#page=12) [14](#page=14) [16](#page=16) [4](#page=4) [6](#page=6) [8](#page=8). ### 2.2 What useful lab books explain Useful lab books serve as comprehensive records of scientific activity, explaining key aspects of research. They should detail [22](#page=22) [23](#page=23): * **What you did:** A clear account of the procedures undertaken [23](#page=23). * **Why you did it:** The rationale and objectives behind the experiment [23](#page=23). * **How you did it:** The methodology and specific techniques employed [23](#page=23). * **When you did it:** The timeline of the research activities [23](#page=23). * **Where materials are:** Location and identification of all reagents, samples, and equipment used [23](#page=23). * **What happened (and what did not):** Comprehensive recording of all outcomes, including unexpected or negative results [23](#page=23). * **Your interpretations:** Personal analyses and conclusions drawn from the data [23](#page=23). * **Contributions of others:** Acknowledgment of any assistance or input from colleagues [23](#page=23). * **What’s next:** Future directions, follow-up experiments, or unanswered questions [23](#page=23). > **Tip:** Including what *did not* happen is as crucial as recording what did, as negative results can also be scientifically significant [23](#page=23). ### 2.3 Characteristics of good lab books Beyond simply recording what was done, good lab books possess several key characteristics that enhance their utility and integrity [24](#page=24) [25](#page=25): * **Legibility:** Entries must be clear and readable, ideally written in permanent ink like ballpoint pen, not pencil [24](#page=24) [25](#page=25). * **Organization:** The book should be well-structured and kept up-to-date to facilitate easy retrieval of information [24](#page=24) [25](#page=25). * **Accuracy and Completeness:** All entries must be factually correct and thoroughly detailed, including page numbering [24](#page=24) [25](#page=25). * **Inclusion of Data:** Direct incorporation of raw data, such as photographs or printouts, affixed to pages [24](#page=24) [25](#page=25). * **Reproducibility:** The documentation should be sufficient to allow for the repetition of experiments by oneself or others [24](#page=24) [25](#page=25). * **Compliance:** Adherence to requirements set by funding agencies and institutional policies [24](#page=24) [25](#page=25). * **Accessibility:** Records should be available to authorized individuals [24](#page=24) [25](#page=25). * **Proper Storage and Backup:** Secure storage practices and appropriate backup procedures for digital records [24](#page=24) [25](#page=25). * **Witnessing:** Proper witnessing of entries when required, particularly for patent or intellectual property purposes [24](#page=24) [25](#page=25). * **Property Acknowledgment:** Recognition that the lab book is the property of the institution [24](#page=24) [25](#page=25). * **Ultimate Record:** The lab book represents the definitive account of scientific contributions [24](#page=24) [25](#page=25). > **Tip:** A lab book is a record of research, not necessarily a polished narrative; focus on clear, accurate data over aesthetic perfection. Mistakes should be crossed out, not erased or whitened out [25](#page=25). ### 2.4 Types of lab books: advantages and disadvantages Different formats of lab books offer distinct benefits and drawbacks: #### 2.4.1 Bound or stitched books * **Advantages:** * Minimizes the risk of lost pages [26](#page=26). * Considered more legally convincing due to tamper-resistance [26](#page=26). * Difficult for pages to be surreptitiously altered or removed [26](#page=26). * **Disadvantages:** * May not be logically organized by experiment, requiring significant cross-referencing [26](#page=26). * Difficult to integrate supplementary materials like printouts without disorganization [26](#page=26). #### 2.4.2 Spiral-bound or loose-leaf books * **Advantages:** * Can be organized by experiment, keeping related data together [26](#page=26). * Easier to integrate supplementary data by inserting pages [26](#page=26). * **Disadvantages:** * Pages are more susceptible to getting lost or detached [26](#page=26). * May be more difficult to authenticate as a complete and unaltered record [26](#page=26). #### 2.4.3 Electronic lab books * **Advantages:** * Facilitates easy searching and retrieval of information [26](#page=26). * Generally easy to read and view [26](#page=26). * Offers efficient storage capabilities [26](#page=26). * Can incorporate robust security features [26](#page=26). * **Disadvantages:** * Vulnerable to corrupted files and data loss [26](#page=26). * Requires attention to software compatibility issues over time [26](#page=26). * Authentication can be complex if not managed properly [26](#page=26). > **Tip:** Regardless of the format chosen, ensure your lab book allows for the repetition of experiments and is compliant with all relevant institutional and funding requirements. Patents, for instance, may require records that can be defended for up to 23 years after filing [24](#page=24) [25](#page=25). --- # Data ownership and ethical considerations This topic explores the multifaceted issues surrounding data ownership and ethical conduct in scientific research through detailed case studies. ### 3.1 Data ownership Data ownership refers to who has the ultimate right to control, use, and disseminate the data generated during research. In a laboratory setting, the principal investigator (PI) typically holds institutional responsibility for the research and its associated data, even if generated by students or staff [29](#page=29). #### 3.1.1 Case study 1: Ownership This case involves a laboratory using new gel electrophoresis technology. Students provided photographs of their results to a company representative in exchange for a dinner. The PI, Prof. Ak, was unaware of this arrangement and did not benefit from it. * **Implications for data ownership and record keeping:** The scenario highlights that data generated within a lab usually belongs to the institution or the PI, not the individual students who collected it. Sharing data or images without the PI's knowledge or consent can lead to ethical breaches and potential conflicts. Proper laboratory record-keeping should include clear protocols for data sharing and external requests. * **Potential actions for Prof. Ak:** Prof. Ak could address the breach of protocol with his students, reiterating the lab's policies on data sharing and external engagement. He might also consider establishing clearer guidelines for such interactions in the future. ### 3.2 Primary data preservation Primary data refers to the original, raw data collected during an experiment. Its accurate preservation and documentation are crucial for scientific integrity. #### 3.2.1 Case study 2: Primary data Zehra Zehir, a graduate student, stored stained and dried polyacrylamide gels in plastic bags taped to her lab book pages, considering them primary data. Her mentor, Prof. Ak, ordered her to stop, citing the neurotoxic nature of polyacrylamide and instructing her to photograph the gels instead, considering the photographs as primary data. Zehra disagreed, believing the gels were more accurate and manipulation-proof than photographs, and that sealing them posed no danger. * **Advice for Zehra:** * **Safety first:** Prof. Ak's concern about the neurotoxic nature of polyacrylamide is valid and aligns with proper laboratory safety protocols. The gels should be disposed of as toxic waste [31](#page=31). * **Appropriate data recording:** Photographs, when taken with appropriate resolution and documentation, can serve as effective primary data records. However, Zehra's concern about manipulation is also valid. * **Documentation of process:** The key is meticulous documentation. This includes photographing the gels with proper scale and labeling, keeping high-resolution digital images, and recording all relevant experimental details in the lab notebook. The lab notebook should clearly reference these images and their location. * **Professional communication:** Zehra should engage in a constructive dialogue with Prof. Ak, acknowledging his safety concerns while articulating her own well-founded concerns about data integrity and proposing robust documentation methods that satisfy both safety and scientific rigor. ### 3.3 Authorship disputes Authorship in scientific publications signifies intellectual contribution and responsibility. Disputes can arise over who qualifies for authorship and the order of authors. #### 3.3.1 Case study 3: Authorship Didem Dirençli, a PhD student, obtained exciting results on ion channel function. A manuscript was submitted. While under review, Prof. Ak received another manuscript suggesting a key finding in Didem's work was incorrect. He questioned Didem, whose lab book records were incomplete. Prof. Ak suggested further experiments, which Didem refused due to her imminent graduation. The manuscript was accepted. Prof. Ak then insisted Didem withdraw the paper, but she refused. Their argument led to Prof. Ak requesting his name and grant reference be removed, and the paper was published with Didem as sole author. Subsequently, Prof. Ak's lab repeated the experiments, found Didem's findings incorrect, and published this correction. * **Prof. Ak’s handling of the situation:** Prof. Ak's initial handling was problematic. His questioning of Didem without revealing his source could be seen as confrontational. His insistence on removing his name after submission and acceptance, while perhaps stemming from a desire for accuracy, created a difficult situation for Didem and potentially damaged her career progression. His subsequent publication of contradictory results, while scientifically necessary, further complicated the relationship and the perception of the original publication. * **Alternative actions:** * Prof. Ak could have immediately and transparently discussed the concerns raised by the reviewed manuscript with Didem, explaining the source of the concern and the potential implications. * He could have collaboratively planned a rapid set of validation experiments to be conducted before the paper's publication, if time permitted. * If Didem was unwilling or unable to perform further experiments, a more collaborative discussion about the paper's future might have been beneficial, exploring options like revision or a joint correction. * The removal of his name and grant was a drastic step that ultimately left Didem solely responsible for potentially flawed data. * **Scientific misconduct:** The scenario raises questions about potential scientific misconduct, specifically regarding: * **Data Integrity:** The "incomplete and sloppy" lab records by Didem could suggest a lack of rigor in data recording. * **Falsification/Fabrication:** While not explicitly stated, the later findings by Prof. Ak's lab suggest that Didem's original results might have been incorrect, raising questions about whether she knowingly or unknowingly presented flawed data. * **Authorship Issues:** While Didem was removed as an author, the initial submission with potential inaccuracies and the subsequent dispute over authorship can be ethically complex. The decision to remove his name as a co-author after acceptance and while the paper was under review, citing concerns about accuracy, might be scrutinized, as authors are responsible for the content of their publications. ### 3.4 Data selectivity and manipulation The ethical presentation of scientific data requires transparency and honesty. Selectively presenting or manipulating data to achieve desired outcomes is a form of scientific misconduct. #### 3.4.1 Case study 4: Selectivity Asst. Prof. Serhat Saklamak admitted to manipulating a DNA gel image in his manuscript draft to "underexpose" smaller, unexpected DNA fragments. He did this to protect his hypothesis from being "scooped" while he conducted further work. He planned to include a note in the legend about "minor signals of unexplained origin." Prof. Ak cautioned him that this was data falsification and suggested electronically cropping the image to exclude the unexpected fragments, arguing no explanation would then be necessary. * **Comment on Serhat’s actions and Prof. Ak’s alternative solution:** * **Serhat's actions:** Serhat's attempt to hide or obscure data is a clear instance of data manipulation and falsification, which undermines scientific integrity. His rationalization of protecting his work from competition is a common, but ethically unacceptable, justification for such actions. The proposed figure legend, while acknowledging the presence of signals, still attempts to downplay their significance and is not a substitute for transparent data presentation. * **Prof. Ak’s alternative solution:** Prof. Ak’s suggestion to "electronically crop" the image is also ethically problematic. While it avoids the direct manipulation of the original image (like underexposing), it still amounts to selective presentation of data by omitting relevant bands. This is akin to a form of data suppression and misrepresentation, as it presents a partial truth. It might be less egregious than direct alteration, but it still fails to be fully transparent. * **Advice if they sought opinion:** * **For Serhat:** You would advise Serhat that his actions constitute data falsification. The ethical obligation is to present all relevant data transparently, even if it complicates the narrative or requires further research. He should aim to include the unexpected fragments and discuss their implications and the planned future work in the manuscript. * **For Prof. Ak:** You would advise Prof. Ak that his suggested "cropping" is also an unethical practice. True scientific transparency means presenting all pertinent findings. Instead of suggesting methods to hide data, he should guide Serhat towards ethically sound practices, such as including all data and clearly explaining its significance and the planned follow-up studies. The focus should be on robust scientific reporting, not on avoiding potential competition through data manipulation. ### 3.5 Recording of errors and corrections Maintaining an accurate record of research activities includes documenting any errors, unexpected events, and subsequent corrections made. #### 3.5.1 Case study 5: Confusion PhD student Samra Şaşkin collected blood samples from 100 patients, documenting clinical histories and meticulously labeling tubes. After assaying five racks, she discovered that labels had fallen off two racks in the freezer due to using inappropriate tape for cold temperatures. She re-numbered the tubes by rack location and repeated assays, finding the new results matched her original measurements. She then re-labeled the tubes with the assumed patient IDs. * **Advice on actions and lab book recording:** * **Document the event comprehensively:** Samra must immediately and thoroughly record the incident in her lab book. This includes: * The date the error was discovered. * The specific racks affected (racks 1 and 2). * The cause of the error (inappropriate tape for –70°C storage). * The steps taken to rectify the situation (re-numbering by rack location, repeating assays). * The validation process (comparing new results with original measurements). * The conclusion that the re-assigned patient IDs were likely correct based on the matching data. * The corrective action taken regarding the labeling (using appropriate tape). * **Ethical considerations:** While Samra's verification step is commendable and suggests her assumption about the IDs is likely correct, the initial loss of labeling and subsequent re-assignment, even with validation, introduces a layer of uncertainty. * **Transparency is key:** The lab book entry should be unambiguous. It should clearly state that the original labels were lost and that the patient IDs were re-established based on repeated assays and comparison. It should also note that while the data appears to match, there is an inherent assumption in the re-assignment. * **Witnessing:** It is good practice for such critical events to be witnessed and signed off in the lab book, as Samra requested from you. This adds an independent verification of the recorded events. * **Data integrity:** The goal is to ensure that the final dataset is as accurate and traceable as possible. The documentation should reflect the process, including the error and its correction, to maintain a transparent and auditable record. > **Tip:** Always use lab-appropriate materials for sample storage, especially at extreme temperatures. Thoroughly test new materials before committing large batches of samples. Proper labeling and tracking are foundational to reliable scientific data. > > **Example:** In Samra's case, the discovery of mismatched labels after assaying only three out of five racks means she could have potentially lost the identities of samples from racks 3, 4, and 5 if she hadn't discovered the issue before assaying them. This underscores the importance of regular checks of sample integrity. --- ## Common mistakes to avoid - Review all topics thoroughly before exams - Pay attention to formulas and key definitions - Practice with examples provided in each section - Don't memorize without understanding the underlying concepts

| Term | Definition | |------|------------| | Scientific Conduct | The adherence to ethical principles and best practices in the planning, execution, and reporting of scientific research. It encompasses integrity, honesty, and responsibility in all research activities. | | Data Recording | The systematic process of capturing observations, measurements, and experimental results in a structured and organized manner. This is a critical step in scientific research to ensure data is preserved for future analysis and verification. | | Data Documentation | The act of creating comprehensive records and explanations that accompany raw data. This includes details about the methods used, experimental conditions, and any observations made during data collection, ensuring transparency and reproducibility. | | Data Ownership | The legal and ethical rights and responsibilities associated with the data generated through research. This can involve who has the right to use, distribute, and control the data, often determined by institutional policies, funding agreements, and intellectual property laws. | | Lab Book | A detailed, chronological record of scientific experiments and observations maintained by a researcher. It serves as an essential tool for documenting procedures, results, hypotheses, and interpretations, ensuring a complete history of the research process. | | Primary Data | The original raw data collected directly from experiments or observations. This data is considered the most direct evidence of findings and is crucial for validating conclusions. | | Scientific Misconduct | Any action that violates widely accepted standards in the scientific community for proposing, performing, or reporting research. This includes fabrication, falsification, and plagiarism. | | Authorship | The designation of individuals who have made significant intellectual contributions to a published scientific work. Authorship criteria typically involve substantial contributions to conception or design, data acquisition, analysis, or interpretation, and drafting or revising the work. | | Fabrication | Making up data or results and recording or reporting them. This is a severe form of scientific misconduct. | | Falsification | Manipulating research materials, equipment, or processes, or changing or omitting data or results such that the research is not accurately represented in the research record. | | Plagiarism | The appropriation of another person's ideas, processes, results, or words without giving appropriate credit. | | Gel Electrophoresis | A laboratory technique used to separate DNA, RNA, or protein molecules based on their size and electrical charge. It involves applying an electric field to a gel matrix, causing charged molecules to migrate. | | PCR (Polymerase Chain Reaction) | A laboratory technique used to amplify specific segments of DNA. It allows for the creation of millions of copies of a particular DNA sequence from a small sample. | | Figure Legend | A descriptive text that accompanies a figure, table, or other illustration in a scientific publication. It provides necessary context and explanation for the visual content. | | Witnessing | In the context of lab books, this is the process where an authorized individual signs and dates specific entries to attest to their authenticity and accuracy at a particular time. |