Topic: Publication Ethics
February 19, 2016 | Posted By John Kaplan, PhD

Each day when I start work checking my email is among the first things I do. This is really a three step process. First I go to my quarantined email to see whether I need to salvage anything or if I can just press the “delete all” function.  This is the spam quarantine set up by my employer which uses some kind of rubric to prescreen my email for spam and save me from it. Usually I can just click that “delete all” button but occasionally there is a real email in there so I always look through it. For some reason this rubric often identifies email from my adult children as spam, especially if they send it from their workplace. Of course sometimes, in its wisdom, it does not quarantine such email so I cannot really figure out how it selects.

After viewing the quarantined email I scan through my non-quarantined email. Here I find a lot more spam which seems to me to be just like what was quarantined but was not. This further confuses me about how the spam filter works. But all is good now as I have reduced the remaining email to a reasonable and manageable amount. I need to make an aside here that I do not really like the term spam for junk email because I remember eating it as a kid and rather liking it.

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website.

September 25, 2015 | Posted By Zubin Master, PhD

The newest science journal on the block with several unique twists is Research Ideas and Outcomes (RIO). RIO aims to publish a variety of outputs in the research cycle, not only the results of research. The journal will publish papers on ideas, proposals, methods, research results, and software. They also publish review articles, opinion pieces, data papers, software descriptions, workflows, data management plans, conference abstracts, single figure publications, project reports and much more. Their aim is to better use the efforts scientists spend on writing and evaluating research proposals and other products within the research cycle. RIO does have limits; they will not accept teaching lectures or materials, clinical trials, patient or other data that may be considered unethical, homeopathy, nuclear or bioweapons research, creationist or religiously motivated research, cryptozoology, and pseudoscience. The journal also has many other interesting aspects. While they are an open access journal, unlike others, they do not charge the typical high costs of thousands of dollars. The journal charges between 50 to a few hundred euros for most types of publications. Peer review is also optional and RIO relies on public scrutiny to promote transparent and public peer review. Expert driven peer review, typically done in most medical and science journals, however, can be done upon the author’s request. The typical review process for papers submitted to RIO includes several technical checks and an external pre-submission review from a colleague.

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website.

August 25, 2015 | Posted By John Kaplan, PhD

One of the great things about scientific knowledge is that it is subject to confirmation or refutation by subsequent research. Science can be confirmed by other laboratories repeating the same studies and finding the same results. However this rarely occurs in the actual course of normally conducted science. In the course of doing science most scientists choose not to simply try to simply replicate the previous study. Rather they consider the findings in the previous study develop the next hypothesis and do a study to extend the findings. Now this seems to be changing.

In 2011 authors from Target Research, a component of Bayer Healthcare, published correspondence in Nature reported that surveys of their internal scientists found “that only in ~20–25% of the projects were the relevant published data completely in line with our in-house findings”. This figure has been widely quoted in the literature but has been transformed into only 20-25% of these research findings were reproducible. There are many problems with this statement and this argument. First it is predicated on the presumption that an appropriate standard for reproducibility is data being entirely “in line” with the work done by internal scientists at Bayer Healthcare. Moreover the studies at Bayer Healthcare, unlike the studies they sought to replicate, were not submitted to the scrutiny of external peer review. There is every reason to consider the possibilities that the fault lies with the replicating studies at Bayer or possibly they did not exactly replicate the studies. We are left to simply accept the word of Bayer without the normal standard of quality that derives from peer review.

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website.

July 21, 2015 | Posted By Zubin Master, PhD

More and more journals are moving to an open access (OA) platform. OA journals are great because they defer the costs of publication and editorial management onto the researcher and not on readers of journals. There are many advantages to the OA movement. For starters, individual or institutional subscription to expensive journals is not required and OA articles are readily sought, downloaded and cited. There are also advantages to the researchers (authors) of publications, including the potential for greater access, higher citation, and wider circulation. For these and other reasons, many journals are jumping on the OA bandwagon. However, OA is not for everyone because it relies on authors to pay anywhere from several hundred to several thousand dollars. This can be limiting to certain individuals or even fields of researchers. Take bioethics for instance. Bioethicists use conceptual research methods making normative arguments, and they also use various empirical, social science research methods. Most bioethicists do not obtain large research grants that can cover the high costs to publish in OA journals. Bioethicists can perform research without external grant support although having funds certainly helps with empirical research. Moreover, younger investigators who likely have little to no money from grants are at a disadvantage. Usually in biomedical science, there is a culture of grant writing, intra-institutional collaboration for junior scholars to team up with senior investigators who have funds, and support for junior scholars including start-up funds or seed money. Yet start-up and seed money are less common for bioethics researchers beginning their own research programs. The argument I wish to make is that OA and its movement are more geared towards the biomedical sciences where there is a culture and requirement to obtain external grant support and funding, and where research. Obtaining funds for research is certainly not commonplace for bioethics. I am not trying to say that all biomedical scientists have it easier to publish in OA journals; but I just think bioethics, and likely other humanities fields are at a bit of a disadvantage. Without some form of financial support, either from the bioethics department, institution, or external grant funding, bioethicists are at a disadvantage and publish cannot publish in OA journals. And transferring copyright to an OA journal is generally not an option because the philosophy of OA journals is to make articles free for readers and not retain copyright.

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website.

June 15, 2015 | Posted By John Kaplan, PhD

Advancement of Science and John Bohannon is a scientist. It does not seem unreasonable that they should aspire to operate under practices contextual to those expected of scientists.

I raise this point now because John Bohannon has again engaged in a sting operation. In this operation the goal was to see if he could get flawed science not only accepted into scientific journals but could he also have it distributed by the press thereby having it read by millions. So, to make a long story short, he created a fake research institute (Institute of Diet and Health) for which he created a fake website. He engaged in these activities under the name Johannes Bohannon. He had two collaborators, Peter Onmeken and Diane Lobl who were preparing a television documentary on junk-science in the diet industry. They were ready as he wrote to “recruit research subjects, a German doctor to run the study, and a statistician friend to massage the data.” So they recruited subjects without ethical review and approval by an Institutional Review Board or Research Ethics Committee. They recruited these unwitting subjects by deception, exposed them to at least some discomfort and risk as there were blood sample taken. They completed their study with the “real” result of increased weight loss in subjects who ate bitter chocolate. At least it was a real study with inadequate number of subjects, massaged statistics and apparent failure to do any sort of correction for the large number of comparisons they made.

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website.

January 12, 2015 | Posted By John Kaplan, PhD

Late in 2013 I posted an entry to this blog which described PubPeer, the newly implemented system for post publication peer review. In that blog I raised the question whether this is a good idea compared to other opportunities for post publication commentary such as letters to the editor or even new publications which would either support or challenge previously published research. The system has been going for a bit over a year now and I thought it would be appropriate to revisit the question of promise or chaos.

One of my principal concerns related to the ability of anyone who met the qualifications to comment to jump in and comment. The necessary qualifications are quite easy to meet and quite arbitrary. Anyone who has been funded to do research by the National Institutes of Health (US) or the Wellcome Trust (UK) is considered qualified. I have no idea why someone funded by the National Science Foundation (US) or the National Research Council (Canada) is not qualified.  

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website. 

November 26, 2014 | Posted By John Kaplan, PhD

When I was a young scientist (quite some time ago) there was a joke that seemed to be circulating about how our older established colleagues conducted science. This was a somewhat cynical exercise motivated, at least in part, by professional jealousy. The joke went on to say that one could establish a fact by writing two papers. In the first paper the author speculates that something might be true. In the second paper the author says that the previously speculated thing is true, and references the paper containing the original speculation. In fact I have rarely seen this actually done. But as I write blog I have an example sitting in front of me on my desk. It is especially intriguing that this paper was written by an individual who maintains that “most published research findings are false”.

The paper in question was published just last month with the rather presumptuous title: “How to make more published research true”.  This, of course, is a statement predicated on the presumption that much published research is false. Indeed the author says in the first paragraph, referring to scientific research, that “Many new proposed associations and/or effects are false or grossly exaggerated” and refers to two previously published papers both single author papers by him.

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website.

July 7, 2014 | Posted By John Kaplan, PhD

Imagine that you had just completed a component of an important task that you had worked on for years. Imagine you were a scientist, something that is easy for me because I am. Imagine that you had had an original idea about how something in nature worked. You mustered the available resources and performed some preliminary studies that were supportive that your idea was in fact correct. You spend weeks or months organizing your ideas, your vision, and your preliminary data into a grant proposal and submitted this to a federal agency or private foundation for funding. Imagine further that your grant proposal was viewed favorably by your peers who supported your idea so your grant application was funded. You would be able to support a laboratory and a staff allowing further studies. You and your coworkers execute these experiments over a period of time that is likely to be measured in years.  These studies provide strong support that meets the standards for scientific proof that your idea was in fact correct.

Now you are able to begin the process of writing the scientific paper so that you can tell the world your great idea and studies you have done which provide support that your idea is correct. You and your coworkers, now coauthors, carefully construct the introduction where you explain to the world why you thought what you thought and did what you did. You carefully and in excruciating detail describe exactly how you did the experiments which yielded the data, and how you analyzed the data. You are now able to show the results of those experiments illustrated by carefully generated tables and graphs. You have now reached the point of offering discussion of the significance and importance of this new contribution to the world’s knowledge. Throughout this process you have dutifully acknowledged all of those whose previous work set the stage for your own contribution.

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website.

January 27, 2014 | Posted By Michael McNichol and Zubin Master, PhD

Since the discovery of human embryonic stem cells in 1998, many promises have been made by individuals and groups about the potential of stem cell research to revolutionize the practice of regenerative medicine. Yet to date, very little has been seen in terms of novel therapies in the clinic. Because of the substantive economic investments made in stem cell research in order to realize the promise they can offer, greater efforts to translate stem cell research into medicines has ensued. However, many factors might impede the clinical translation of stem cell research. In this blog, we briefly highlight the ethical and scientific issues surrounding the successful translation and commercialization of stem cell research.

The process of clinical translation begins with preclinical research using in vitro systems and animal models to show proof-of-principle and demonstrate safety and efficacy of a potential therapeutic. For example, if a stem cell is to be transplanted into a patient to treat a degenerative disease, then the type of stem cell that is being used must show that it can successfully treat a similar disease in animals prior to testing the product in humans. There are many reasons for using appropriate animal models that mimic human diseases: low cost, reproductive cycle, number of offspring, genetic similarity, similarity in the manifestation of the disease in humans, and ease of handling. However, there are many limitations to animal models that do not result in direct translation in humans, meaning what may work in animals may not at the end of the day be effective in people. While we choose animals as models to mimic human disease, the biology of animals is still significantly different than humans and thus may simply not translate 100%. This issue is difficult to get around. 

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website.

January 2, 2014 | Posted By John Kaplan, PhD

In the good old days when I spent most of my time as a practicing biomedical research scientist it was pretty clear to me what qualified as a scholarly communication. Such communications consisted of submissions of presentations to meetings of scholarly academic societies; submissions and presentations of original research to journals; presenting seminars; and writing the occasional review articles, book chapters, or even books. Now that I spend much of my time as a bioethicist it is no longer so clear to me. It is probably important to note that the uncertainty I feel about this is probably only partly attributable to the difference in discipline and may indeed be primarily due to the emergence of our modern-day online communications including the blogging and social media culture.

The communication you are reading now is a blog, only a blog, not a scholarly communication. Al least I am pretty sure that is the case. I cite no evidence. I reference lightly if at all. I write what I want. I am merely expressing my opinions. I am not really accountable to anyone for what I say here. I can write it in minutes or hours, not weeks or months. This all sounds to me that this is not a scholarly publication. Yet I have read in both blogs and on social media such as facebook and twitter people raising questions about the distinction. (Please note that I did not reference my statement, further evidence that this is not a scholarly publication.) I have seen questions which ask how are blogs and scholarly writings different if indeed they are different. I have seen writers ask if blogs should be included in one’s Curriculum Vita as a publication. Please note that this will not be posted in my Curriculum Vita because it is, again, only a blog.

The Alden March Bioethics Institute offers a Master of Science in Bioethics, a Doctorate of Professional Studies in Bioethics, and Graduate Certificates in Clinical Ethics and Clinical Ethics Consultation. For more information on AMBI's online graduate programs, please visit our website.

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BIOETHICS TODAY is the blog of the Alden March Bioethics Institute, presenting topical and timely commentary on issues, trends, and breaking news in the broad arena of bioethics. BIOETHICS TODAY presents interviews, opinion pieces, and ongoing articles on health care policy, end-of-life decision making, emerging issues in genetics and genomics, procreative liberty and reproductive health, ethics in clinical trials, medicine and the media, distributive justice and health care delivery in developing nations, and the intersection of environmental conservation and bioethics.
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