Albany Medical Center
 Search
Home / Caring / Educating / Find a Doctor / News / Give Now / Careers / About / Calendar / Directions / Contact
Topic: Publication Ethics
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.

December 16, 2013 | Posted By John Kaplan, PhD

Open post-publication scientific peer review is here. Almost. Now we need to ask whether or not that is a good thing. Some are trumpeting this as a game-changing innovation which will improve the quality of scientific publication. Others are concerned that scientific publication will become more like Twitter and Facebook.

The site Pubmed Commons allows one to comment on any Pubmed indexed publication. Although the system now permits access in a limited way for testing, it will be open to essentially all who have Pubmed indexed papers in the relatively near future. Just as there are sites to review movies, restaurants, and contractors one will soon be able to include their insights and feelings about scientific papers. The advocates of this system believe that post-publication will open the peer review system to all qualified and can allow science to be communicated in a more transparent and less biased manner.

Advocates of post-publication peer review have been very critical of conventional pre-publication 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.

December 3, 2013 | Posted By Zubin Master, PhD

This is part 2 of a blog written last month. In Part 1, I explained how open access (OA) journals work and some of the shortcomings of peer review. This was done to provide a background on a recently published study by staff at the leading journal Science. In this part, I will cover the specific experiment reported by Science and explain some of the limits of its design followed by an interesting and novel model of the non-profit OA journal BioéthiqueOnline.

Part 2: Open Access Journals, Peer Review, and Conflicts of Interest

Do OA Journals Perform Rigorous Peer Review?

Recently, John Bohannon of the Science group conducted an investigation where he submitted scientifically flawed papers using fake names and provided the names of research or academic institutions that didn’t exist to 304 OA journals (Science 342: 60-65, 2013). The idea was to create a scientific paper with major errors, so that “[a]ny reviewer with more than a high-school knowledge of chemistry and the ability to understand a basic data plot should have spotted the paper’s shortcomings immediately.” Bohannon created a database of molecules, lichens and cancer cell lines and ran them through a computer program to generate unique papers, but with a standard structure: “molecule X from lichen species Y inhibits the growth of cancer cell Z.” He also created fake authors from fictitious African institutions with the hope that using developing world authors would lessen suspicion by journal editors. The main flawed graph showed a dose-dependent decrease in cell growth yet despite rising concentrations, the effects on cells were modest. In addition, the anti-proliferative molecule was dissolved in a large amount of ethanol and because the control group was not treated with the same solution buffer, the anti-proliferative effects seen could simply be due to the cytotoxic effects of ethanol. In a second experiment, Bohannon attempted to show an “interactive effect” by adding the molecule with radiation, but the control cells were not exposed to any radiation. As the experiments had a tragically flawed design, the idea was that any peer reviewer should pick them up and the article should be rejected.

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.

SEARCH BIOETHICS TODAY
SUBSCRIBE TO BIOETHICS TODAY
ABOUT BIOETHICS TODAY
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.
TOPICS