Chapter10-Scientific Record Keeping.pdf

Scientific Record Keeping Chapter 10  Discussion Questions If an NIH-funded principal investigator takes a new position, does he have the right to take all of his data and data books with him to his new institution? If not, what policies or ethical issues apply to such a situat...

Scientific Record Keeping Chapter 10  Discussion Questions If an NIH-funded principal investigator takes a new position, does he have the right to take all of his data and data books with him to his new institution? If not, what policies or ethical issues apply to such a situation?  Data Ownership, Data Storage and Retention The Public Health Service recognizes the grantee institution as the owner of the data generated by the NIH-funded research. Neither the principal investigator nor any member of the laboratory research team owns the data generated under an NIH research grant. The NIH requires that data obtained under the aegis of an NIH grant be retained for 3 years beyond the date of the final financial expenditure report. Requirements for the amount of time research data must be retained may vary for various public and private funding agencies. Furthermore, investigators need to be aware of relevant state laws regarding the retention of data, because they usually override federal ones. For example, the Commonwealth of Virginia mandates that data gathered by state agencies be retained for 5 years, thus extending the NIH requirement for scientists at state-supported universities.  Discussion Questions Could sloppy and incomplete record- keeping ever qualify as scientific misconduct? Explain.  Data book zen Useful data books explain: What you did? Why you did it? How you did it? When you did it? Where materials are? What happened (and what did not)? Your interpretations Contributions of others What’s next?  Good Data Books Are legible and written in ballpoint pen ink? Are well organized and up-to-date? Are accurate and complete? Include data output affixed to pages (e.g., photos) Allow repetition of your experiments Are compliant with relevant funding agency and institutional requirements? Are accessible to authorized persons, stored properly, and appropriately backed up? Are properly witnessed when necessary? Are properly recognized as the property of your institution? Are the ultimate record of your scientific contributions?  Investigation of allegations of research misconduct Scientific records play a role in the investigation of allegations of research misconduct. In conducting investigations into allegations of research misconduct, the National Science Foundation Office of Inspector General considers the following in assessing laboratory data books and records. Completeness. The record should describe all the activities of the researcher, not just the “successful” ones. Linkage. A written laboratory notebook should reference electronic records by name and location in detail sufficient to locate the electronic records. Review. A regular (weekly or monthly) documented review of laboratory notebooks by a supervisor or a faculty advisor can help ensure the quality of laboratory records. Accuracy. Records should be a contemporaneous chronology of all pertinent laboratory activity and results, whether successful or not, and be sufficient to support the reconstruction of activities by another competent researcher. Safekeeping. All laboratory records should be maintained in a secure manner and backed up with copies stored in an alternate location.  Discussion Questions Do you think that electronic record-keeping will either increase or decrease our ability to detect scientific misconduct? Why or why not?  Electronic Record Keeping As its ultimate step, computer-assisted record keeping should involve printing all electronic files and affixing them to the pages of a traditional data book. An official procedure for the lab’s electronic record-keeping process should be developed and communicated to all users. The storage location and organization of electronic records should be clearly defined. Ideally, storage should be on servers that are password- protected. Electronic files should be write-protected, using read-only permission for anyone accessing research data files. To ensure authenticity, all electronic files should be time stamped.  Case 11 Ming Shu, biochemistry graduate student from China, can speak and write in English, but her speed at each task is relatively slow. Every few weeks Dr. Andrekia Keys, Ming’s graduate mentor, meets with her to discuss research and to generally inquire as to how her transition into academic life in the United States is progressing. This week Dr. Keys asks Ming to leave her research notebooks out so that she can stop by the lab and inspect them. When Dr. Keys arrives at the lab, Ming has left for the day, but she finds the notebooks lying on her desk. Upon inspection, she finds that several of the notebooks are written in Chinese. Upon further investigation, she discovers that Ming is recording her initial observations in Chinese in one notebook and then translating them into English at a later time. Furthermore, when Dr. Keys examines both sets of notebooks, she observes that the current English notebook is approximately 3 weeks behind the Chinese counterpart. Dr. Keys comes to you for advice. Is Ming guilty of improper notebook-keeping practices? Can the notebooks written in English be considered valid records of her research thus far? What advice on how to handle this situation do you have for Dr. Keys?  Why Do We Keep Records? A bound collection of serially numbered pages used to record the progress of scientific investigations. Platform for analysis and interpretation of results obtained in the field or the laboratory. They are the basis for scholarly writings, including reports, grant and patent applications, journal articles, and theses and dissertations. Good record-keeping fosters the scientific norms of accuracy, replication, and reliability.  Why Do We Keep Records? A scientist or scientist-trainee may take over a project, and it will be necessary for him or her to understand precisely the laboratory data book contents in order to continue the work. Funding agencies like the National Institutes of Health (NIH) may audit and examine records that are relevant to any research grant award. Providing primary research data is often a component of the approval process for new drugs or medical applications (e.g., data submitted to the U.S. Food and Drug Administration [FDA]). As one seeks the protection of intellectual property by applying for a patent, it may become necessary to disclose data book contents to the patent examiner.  Case 12 The research laboratory of a faculty investigator has begun using a new electrophoresis technique. The technique works well in the hands of the laboratory investigators. A field service representative from the company that manufactures the apparatus asks several of the workers in the laboratory if she may borrow some of the photographs of their results to show them to potential clients. In return, she offers to take the whole lab to dinner at an expensive restaurant. The lab members comply, and the whole group goes to dinner. You, as laboratory director, are told of these events after the fact. Comment on the implications of this scenario for data ownership and laboratory record keeping. What action, if any, will you take?  Case 13 Joshua Hanani is preparing his first major paper as an independent investigator. His faculty colleague Dr. Ellen Fang reviews the manuscript and they meet over coffee to discuss her critique. She has some questions about the image of a DNA gel analysis in the paper. She says part of the gel image appears deliberately altered. Joshua admits this to be true and offers the following explanation. The gel contains the products of PCR-amplified whole-cell DNA. The amplified DNA fragments are arrayed linearly from largest to smallest on the gel. The experiment produced the expected results but also contained some unexpected, exciting findings. Specifically, two small DNA fragments suggest an exciting hypothesis that will likely take 6 to 8 months to test. Worried that readers would recognize this and “scoop” him, Joshua used an image editor to “underexpose” those fragments so they were no longer visible. He mentions to Ellen that he included an explanation of this in the figure legend, writing: “Minor signals of unexplained origin were present in the lower molecular size range in this experiment, but they are not visible in the photograph.” This, he claims, will protect him from the competition of major labs working in the field. Ellen cautions him that his reasoning is flawed and he is deliberately falsifying data. She offers an alternative solution, saying he should just electronically crop the image so that it includes just the expected DNA fragments and not the unexpected ones. She says this can be easily done since the unexpected fragments are at the edge of the image. Then, she argues, no explanation about the image will be needed. Comment on Joshua’s actions and Ellen’s alternative solution. If they came to you for your opinion and advice, what would you tell them?,  Defining Data Data books may contain hand script or affixed typescript that records and reports measurements, observations, calculations, interpretations, and conclusions. Data are said to have authenticity and integrity. Authentic data represent the true results of work and observations. Integrity of data is dependent on results being collected using well-chosen methods carried out in the proper manner. Tangible data is used to describe materials such as cells, tissues or tissue sections, biological specimens, gels, photographs and micrographs, and other physical manifestations of research. Raw Data, Original Data, Primary Data  The Hardware of Note keeping Paper composition is printed on the bound data book cover. The longevity of laboratory data books is facilitated by proper storage. Never use pencil. Do not use pens with aqueous-based inks. Graphite smudges over time, and even a little water can obliterate the inks in many popular pens (e.g., felt-tip, fountain, rollerball [gel-based inks]). Ballpoint pen with black ink is best for scientific note keeping. Colored inks are not desirable, because their decomposition promoted by light is significant compared with black ink. However, varying the color of inks when drawing diagrams, for example, may be essential in some types of work. Bound, page-numbered data books: The use of a bound data book with chronological ordering of experimental protocols and results, with each page dated, serves the purpose of most academic research laboratories. Intentional page deletion or insertion becomes immediately obvious. Any other type of binding—plastic comb, wire spiral, or ring binder—is considered unacceptable because pages can be intentionally inserted, removed, or accidentally ripped out or lost. This could damage the integrity of the records, compromising, for example, the ability to gain patent protection.  Record-Keeping Practices The first several pages of an individual’s data book should be reserved for a table of contents. Experiments listed in the table of contents should have concise but descriptive titles. The numbering of experiments chronologically facilitates cross-referencing experiments. A glossary of abbreviations, symbols, or common designations may be included after the table of contents or, alternatively, can be listed at the end of the data book. Experimental methods should be described in sufficient detail to be useful even to the novice investigator. Do not skip pages. Many suggest writing each page in such a way that minimal margin space is left available for after- the-fact note-taking. Unused portions of any data book pages should be marked through with a pen stroke or a large “X.” Names of individuals who have played any role in your research need to be entered in the data book along with a description of their contributions.  Tangible Data Tangible forms of data such as photographs, negatives, autoradiograms, and printouts should be included in the data book when this is physically possible. Materials that cannot be glued or taped directly into the book should be inserted into plastic sleeves, which are then fixed in the data book. A record of the name and location of the digital file should also be described in your data book. Certain materials that contain or represent data cannot be practically included in the laboratory data book. When using remote-site storage, it is important that a description of the data storage system, the storage location, and the coding scheme be described in your laboratory data book. As a rule, an individual who inspects the data book should be able to locate all forms of data relevant to the experiments presented simply by reading its pages.  Format If an observation requires an explanation that is complex and must be described at extraordinary length, then this should be done without reservation. The same is true for interpretations and for thoughts on plans for additional work. Presentation and detail must be complete and comprehensible. Purpose. Each experiment should begin with a brief but instructive statement of the purpose of the experiment. This is done no matter how routine the experiment.  Format Materials and methods. A description of any methods not found in the laboratory central methods manual should be included in the data book. The appropriate literature from which methods are derived should be cited. If there are deviations from referenced procedure, such changes must be precisely indicated. To eliminate any confusion, it may be necessary to write the modified method in the data book. The grade, sources, and lot numbers of specialized chemicals, reagents, and enzymes should all be recorded. If there is any question about the name recognition of the supplier (e.g., the supplier of a rare chemical or unusual enzyme), the name, address, and phone number of the supplier should be included. In the case of biological materials such as cell lines, bacterial strains, or animals, specific information on properties (e.g., genotypes and phenotypes) and source should be recorded. Each repeat of an experiment should be written up separately in the data book. In the case of materials and methods, it is acceptable to record this section with appropriate detail and completeness the first time the experiment is performed. Assuming no changes in methodology are implemented in future runs, it is acceptable to refer back to the materials and methods section recorded in the first experiment of the series.  Format Observations and Results. Data should be recorded directly into the data book as soon as they become available. Original data recorded in hand script are always entered directly into the data book. Data should never be written on loose sheets of paper and then transcribed later into the data book. Should contain all renderings of the data, including calculations and organized presentations such as tables and graphs created using the data. Calculations should be explained. Tables and graphs should be clearly labeled. Photographic materials should be affixed to the page using archival-quality glue or tape. Any related materials not included in the data book should be catalogued and their storage location identified.  Format Discussion. Each experiment should be discussed following the recording of observations and calculations. It may be necessary to enter discussion comments at various places in the experimental write-up. The discussion for a single experiment need not be organized to appear at the conclusion of the write-up. It is appropriate to include comments that capture impressions and present interpretations at various places in the written experiment. Never make comments that could be subject to misinterpretation by others. Specifically, investigators are cautioned against using phrases like “the experiment failed” or describing a yield of some biological material as “no good.” Conclusion. The last entry in the completed write-up of the experiment should state the conclusions of the work. This should be done even if it repeats comments previously written into the data book. Conclusions logically belong at the end of the experiment.  Discussion Questions What are some conflicts of conscience that might be faced by scientists? For any examples, consider that the scientist in question has come to you for advice. Describe the advice you would provide, along with your rationale. Describe a conflict of effort that might be faced by a predoctoral or a postdoctoral trainee. Propose a mechanism for managing the conflict. A journal that publishes basic and applied biomedical research findings plans to change its peer review policy, eliminating the inclusion of editorial board members and reviewers who work for corporate entities. Defend or critique this proposal. What are the differences in equity ownership of common stock and a mutual fund? Do mutual funds and common stocks create the same level of financial conflict of interest?  Case 14 Andre Cesar is completing his degree at Research University. He has conducted some successful and exciting research in the laboratory of Dr. Ellen Zinderoff. Dr. Zinderoff’s project was supported in part by a research contract with Innovations, Inc. Dr. Zinderoff and the members of her laboratory developed new, rapid, accurate assays that can be adapted to kits for direct sale to the public. Innovations, Inc., is considering developing and marketing these kits but has not made a definite decision. Leaper Enterprises offers Andre a position in a new unit of the company to apply his training to develop kits based on the technology that he learned and helped develop in Dr. Zinderoff’s laboratory. Discuss any conflict that Andre may have in accepting a position in a company that competes with Dr. Zinderoff’s sponsor.  Case 15 Dr. Cecilia Jonas is on the editorial board of the leading chemical engineering journal. Dr. Jonas receives a manuscript for review reporting results similar to those in her draft manuscript. Dr. Jonas is awaiting replication of one experiment involving a novel method of polymer separation in order to prepare a new figure with better-defined graphical data. Although Dr. Jonas’s manuscript has content distinctly different from the one received for review, she believes it is likely that the impact of her publication will be greatly reduced by publication of the competing manuscript. Dr. Jonas redirects her effort toward completion and submission of her manuscript, setting aside the manuscript to be reviewed. Within 2 weeks, her well-prepared manuscript is submitted to another quality journal in the field of chemical engineering. Dr. Jonas then, over the next several days, critically reviews the manuscript that she received; makes a number of insightful suggestions, as she usually does; and returns the manuscript to the editor with the recommendation that the paper be accepted after major revision. She also requests that the revised article be sent to her for a final consideration on publication. What are the real or perceived conflicts of interest confronting Dr. Jonas as a member of an editorial board? Has she acted ethically and responsibly? If not, what do you think she should she have done in this situation?  Case 16 Dr. Rudee Prasad is an independent consultant in drug-related toxicology. Dr. Prasad also holds an adjunct faculty position at the local university, where he lectures to pharmacology graduate students and medical students. He also serves occasionally on state and federal advisory panels on product safety. Dr. Prasad invests a portion of his income in stocks of biomedical companies. A candidate drug being developed by a company for which he is consulting has impressed Dr. Prasad, and he has made sizable investments in the company. The company contracts with Dr. Prasad for a final toxicological assessment before submitting a request to initiate a clinical phase 2 study to determine the efficacy of the candidate drug. Dr. Prasad is astonished and alarmed to discover during his review of materials from the animal studies and the phase 1 study that the use of the drug is associated with serious and extensive nuclear aberrations in bone marrow and gonadal tissue. Dr. Prasad realizes that these findings will result in a delay or cancellation of the proposed phase 2 study. As he prepares his detailed report for the company, he notifies his investment counselor to sell all of his stock in the company over the next several weeks. What are Dr. Prasad’s obligations to avoid using confidential information for personal gain? What are Dr. Prasad’s real or perceived conflicts of interest? What third parties may be harmed by Dr. Prasad’s actions?