Ever since the advent of molecular biology in the 1970s, mechanical models have become the dogma in the field, where a "true" understanding of any subject is equated to a mechanistic description. This has been to the detriment of the biomedical sciences, where, barring some exceptions, notable new feats of understanding have arguably not been achieved in normal and disease biology, including neurodegenerative disease and cancer pathobiology. I argue for a "mechanism-plus-X" paradigm, where mainstay elements of mechanistic models such as (...) hierarchy and correlation are combined with nomological principles such as general operative rules and generative principles. Depending on the question at hand and the nature of the inquiry, X could range from proven physical laws to speculative biological generalizations, such as the notional principle of cellular synchrony. I argue that the "mechanism-plus-X" approach should ultimately aim to move biological inquiries out of the deadlock of oft-encountered mechanistic pitfalls and reposition biology to its former capacity of illuminating fundamental truths about the world. (shrink)

Following an analysis of the state of investigations and clinical outcomes in the Alzheimer's research field, I argue that the widely-accepted 'amyloid cascade' mechanistic explanation of Alzheimer's disease appears to be fundamentally incomplete. In this context, I propose that a framework termed 'principled mechanism' (PM) can help with remedying this problem. First, using a series of five 'tests', PM systematically compares different components of a given mechanistic explanation against a paradigmatic set of criteria, and hints at various ways of making (...) the mechanistic explanation more 'complete'. These steps will be demonstrated using the amyloid explanation, and its missing or problematic mechanistic elements will be highlighted. Second, PM makes an appeal for the discovery and application of 'biological principles' (BPs), which approximate ceteris paribus laws and are operative at the level of a biological cell. As such, although thermodynamic, evolutionary, ecological and other laws or principles from chemistry and the broader life sciences could inform them, BPs should be considered ontologically unique. BPs could augment different facets of the mechanistic explanation but also allow further independent nomological explanation of the phenomenon. Whilst this overall strategy can be complementary to certain 'New Mechanist' approaches, an important distinction of the PM framework is its equal attention to the explanatory utility of biological principles. Lastly, I detail two hypothetical BPs, and show how they could each inform and improve the potentially incomplete mechanistic aspects of the amyloid explanation and also how they could provide independent explanations of the cellular features associated with Alzheimer's disease. (shrink)

Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...) This could in part be explained by a relatively recent tendency in which a "data first", rather than a "theory first", approach is preferred. Moreover, generating hypotheses has at times become procedural rather than theoretical, therefore perhaps inadvertently leading some hypotheses to become perfunctory in nature. This situation leaves our understanding enmeshed in data, which should be disentangled from much noise. Given the many unresolved questions in biology and medicine, big and small, ranging from the problem of protein folding to unifying causative frameworks of complex non-Mendelian human diseases, it seems apt to revive the role of pure theory in the biological sciences. This paper, using the current biomedical literature and historical precedents, makes the case for a "philosophical biology" (philbiology), distinct from but quite complementary to philosophy of biology (philobiology), which would entail biological investigation through philosophical approaches. Philbiology would thus be a reincarnation of theoretical biology, adopting the true sense of the word "theory" and making use of a rich tradition of serious philosophical approaches in the natural sciences. A philbiological investigation, after clearly defining a given biological problem, would aim to propose a set of empirical questions, along with a class of possible solutions, about that problem. Importantly, whether or not the questions can be tested using current experimental paradigms would be secondary to whether the questions are inherently empirical or not. These issues will be illustrated using a range of specific examples. The final goal of a philbiological investigation would be to develop a theoretical framework that can lead observational and/or interventional experimental studies of the defined problem, a framework that is structured, generative and expandable, and, crucially, one that simplifies some aspect(s) of the said problem. (shrink)

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in (...) this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined. (shrink)

This paper is about interpreting the aim of Plato's Sophist in a linguistic framework and arguing that in its attempt at resolving the conundrum of what the true meaning and essence of the word "sophist" could be, it resembles a number of themes encountered in contemporary linguistics. I think it is important to put our findings from the Sophist in a broader Platonic context: in other words, I assume—I think not too unreasonably—that Plato pursued (or at least had in mind) (...) a number of overall projects ('OP' for short) throughout some or most of the dialogues, while each one of the dialogues would in addition have more specific projects ('SP') as part of its individual blueprint. To be sure, the OPs, if they actually existed, might have evolved from the earlier-written to later dialogues, but their foundational premises should have remained intact. In Section A, I provide evidence for reading the Sophist on a linguistic basis. In Section B, I focus on two OPs that I think are relevant to our discussion, one having to do with language and meaning acquisition, and the second concerning the "mind" or a "thought faculty". Ultimately, in Section C, I will use the OPs to contextualise two (related) SPs in the Sophist: (i) identifying cases of intentional referrals for names versus (ii) identifying internal references when searching for word meanings without particular referable instances. At the end of this section, I will draw close parallels between this interpretation of the dialogue and a congruous project of modern 'generative' linguistics. (shrink)

Recently, a few of scientific journals raise serious questions about scientific ethics and moral judgment of some of the Iranian government’s senior executives in their papers. Plagiarism, under any circumstances is not justified, and we do not intend to justify it in this note. However, we find it useful in understanding why otherwise respected, responsible individuals may engage in plagiarism by terse review of the history Iranian academia.

Conflict of interests is a situation when someone is in need of other people’s trust on one the hand and has personal or general interests on the other hand, resulting in conflict with the given responsibility. In this research work, an attempt was made to find the relation between declarations of conflict of interests and reporting positive outcomes in the dental journals in Iran. In this analytical/cross-sectional study, first Health and Biomedical Information was searched and all the Persian and English (...) dental journals published in Iran were collected. Then, all the papers published in the journals from December 2000 to December 2016 were collected and categorized in terms of the year of publication, author or authors’ affiliations, Persian and English journal, type of the substance or the drug used, declarations of conflict of interests and the positive or negative conclusion of the report. Data were analyzed with the Fisher’s exact test and Chi squared test, using the program SPSS 18. In numerical analysis, the significance was set at P < 0.05. Seventeen dental journals in Persian and English were analyzed: 10 in English and 7 in Persian. Reviewing these studies showed that of 1021 articles in Persian, in 128 cases there was no mention of a declaration of conflict of interests and in 11 cases, the COI had been stated. In addition, from 1220 articles in English, in 825 cases there was no mention of declarations of conflict of interests and in 45 cases, the declarations of COI had been mentioned. There was no significant relation between the COI and ‘no’ COI and the reporting of positive outcomes in papers in Iranian dental journals in terms of the journal type, year of publication and the journals’ guarantee form. A total of 83% of studies with declarations of COI had one positive outcome, with a significant relationship in this field; however, in 73% of studies with no COI, there was one positive outcome, too. In general, the society expects that doctors would not consider any incentives except the health of the patients in the efforts made by them. The severity of the consequences of COI is of higher value when the patients’ health is endangered due to it. In addition, COI might change the attitude and approach of other doctors and peers. (shrink)

Background: While advanced driver assistance technologies have the potential to increase safety, there is concern that driver inattention resulting from overreliance on these features may result in crashes. Driver monitoring technologies to assess a driver’s state may be one solution. The purpose of this study was to replicate and extend the research on physiological responses to common driving hazards and examine how these may differ based on driving experience.Methods: Learner and Licensed drivers viewed a Driving Hazard Perception Task while electrodermal (...) activity was measured. The task presented 30 Event and 30 Non-Event videos. A skin conductance response score was calculated for each participant based on the percentage of videos that elicited an SCR.Results: Analysis of the SCR score during Event videos revealed a medium effect of group differences, whereby Licensed drivers were more likely to have an SCR than Learner drivers. Interaction effects revealed Licensed drivers were more likely to have an SCR earlier in the Event videos compared to the end, and the Learner drivers were more likely to have an SCR earlier in the Non-Event videos compared to the end.Conclusion: Our results support the viability of using SCR during driving videos as a marker of hazard anticipation differing based on experience. The interaction effects may illustrate situational awareness in licensed drivers and deficiencies in sustained vigilance among learner drivers. The findings demand further examination if physiological measures are to be validated as a tool to inform driver potential performance in an increasingly automated driving environment. (shrink)

Patients' rights observance is one of the effective measures of patients' satisfaction of health care services. We performed this study at the aim of evaluation of nurses' awareness of patients' rights in a teaching hospital in Tehran.This cross-sectional study was conducted in 2010. In this study 156 nurses were randomly selected. Two-part questionnaire was used for data collection. The validity and reliability of questionnaire was determined and then it was distributed between subjects. The data were analyzed by SPSS version 15 (...) using descriptive and inferential statistics. Our results showed that %58.33, %39.10 and % 2.56 of nurses have good, medium, and poor levels of awareness respectively. We observed a significant relationship between nurses awareness and work experience and concurrent work in public and private hospitals. The most of the nurses were aware of "right to privacy protection and ensure confidentiality of information" and the least of them were aware of "right to receiving necessary information about the health care providers, the rate of tariff and insurance coverage".According to our survey it is concluded that implementation of Patients' Right Charter in this hospital is accompanied by some limitations which necessitates promotion of the nurses' awareness about patients' rights. Taken together in order to enhance nurses' awareness special measures and strategies should be considered. (shrink)

Today, the speed at which science and technology is progressing around the world is so fast that any lag in this race may result in irrevocable consequences for certain countries. For emerging scientific powers such as Iran, this issue is a matter of the country's reputation. This study seeks to investigate plagiarism in different fields of science in Iran. With the growing number of scientific publications in Iran, several reports about the increase of plagiarism in Iranian academia have been published. (...) Hence, the current study aims to investigate whether there is any difference between plagiarism volumes in different fields of study in Iran. If so, what about other countries? Specifically, we will examine if there is any significant difference in these statistics among five countries: Iran, United States, Turkey, Australia, and China.We analyzed one percent of the articles published by Iranian researchers in international journals in 2010 and 50 articles by authors from the United States, Turkey, Australia and China . Our tool was the premium version of a plagiarism checker software named Dustball. Using the software, we could detect the exact percentage of copy and pasted text from other sources.Our results show that there was no trace of plagiarism in 6 out of 27 fields under consideration for Iranian papers. Unfortunately, most cases of plagiarism were reported in three scientific fields, with medicine on top of the list. Generally, there were 8 fields with plagiarism of 30 percent or more. Our results for other countries illustrate that in medicine, the United States, Turkey, Australia and China had a plagiarism rate of 18 percent, 38 percent, 32 percent and 36 percent respectively and the rate in the field of engineering was 12 percent, 34 percent, 28 percent, 36 percent respectively. The paper suggests that more frequent instances of plagiarism in Iranian articles are due to the unawareness of the international standards of science writing and editing. According to our interesting results about other countries, we find that in the field of engineering, Iran with an 11 percent plagiarism rate has the best situation even relative to the United States with 12 percent but in medicine Iran has the higher rate .The main limitation is this study pertains to the validity of the plagiarism checker software. In Iran, access to strong and free plagiarism checker software is not provided. However, for covering this limitation, we purchased an account from Dustball that offers 3 times more powerful detection. Moreover, while the application of the above-mentioned software might be considered a limitation for this study, the software tends to under-report the plagiarism percentage in scientific papers. (shrink)

Breaking bad news is quite often not done in an effective manner in clinical settings due to the medical staff lacking the skills necessary for speaking to patients and their families. Bad news is faced with similar reactions on the part of the news receiver in all cultures and nations. The purpose of this study was to explore the perspectives of Iranian nurses on breaking bad news to patients and their families. In this research, a qualitative approach was adopted. In-depth (...) and semi-structured interviews were conducted with 19 nurses who had at least one year work experience in the ward, and content analysis was performed to analyze the data. Five major categories emerged from data analysis, including effective communication with patients and their families, preparing the ground for delivering bad news, minimizing the negativity associated with the disease, passing the duty to physicians, and helping patients and their families make logical treatment decisions. The results of this study show that according to the participants, it is the physicians' duty to give bad news, but nurses play an important role in delivering bad news to patients and their companions and should therefore be trained in clinical and communicative skills to be able to give bad news in an appropriate and effective manner. (shrink)

In Iran, as in many Asian and Middle Eastern countries, a significant proportion of cancer patients are never informed of their illness. One of the proposed solutions to tackle this challenge is to develop a localized protocol based on the culture and values of community members about cancer and the truth-telling phenomenon, and training of health care team members to disclose the bad news using this protocol. In the same vein, this study also introduced a localized protocol for disclosure of (...) bad news to cancer patients, resulting from a larger mixed study. The implementation of the present protocol demands a team work and its stages are as follows: assessment, planning, preparation, disclosure, support and conclusion. (shrink)