AUTOPHAGY 2016, VOL. 12, NO. 2, 223–224 http://dx.doi.org/10.1080/15548627.2016.1139264
EDITOR’S CORNER
Stepping back from the guidelines: Where do we stand? Daniel J. Klionsky Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
ABSTRACT
ARTICLE HISTORY
The third edition of the autophagy guidelines is now published. This turned out to be a major undertaking in part because of the tremendous increase in the number of researchers participating in autophagy studies, and hence in revising the guidelines. First, I cannot emphasize enough that this paper represents a true community effort—it would simply not be possible for one person to generate such an in-depth and up-to-date manuscript covering this diverse range of topics in the autophagy field. Second, it is of critical importance that this paper indeed does not represent the opinions of a single individual, but rather seeks to obtain a consensus opinion regarding the best methods to monitor autophagy and interpret the results of the corresponding experiments. So, thank you to all who have contributed to the latest version.
Received 23 December 2015 Revised 4 January 2016 Accepted 4 January 2016
I want to point out that the significance of the guidelines has now extended even beyond the autophagy community. The American Society for Cell Biology Data Reproducibility Task Force carried out a study to address the question of “How can scientists enhance rigor in conducting basic research and reporting research results?” This study resulted in a “White Paper”1 that made 13 specific recommendations. One of these was the following: “Educate the community about examples of
KEYWORDS
autophagy; lysosome; stress; vacuole; yeast
community-based standards. For example, highlight in ASCB publications the experience of Daniel Klionsky (U. Michigan) on his successful community engagement to reach consensus on accepted assays within the autophagy community.” Note the key point of “community engagement.” Following this recommendation, a paper is now in revision for publication in Molecular Biology of the Cell that describes the generation of the most recent set of guidelines from a very practical point of
Figure 1. Geographical locations of the guidelines authors. Countries shown in yellow correspond to those of current authors of the guidelines. Map used by permission of VectorTemplates.com.
CONTACT Daniel J. Klionsky [email protected] Color versions of one or more of the figures in the article can be found online at www.tandfonline.com/kaup. © 2016 Taylor & Francis Group, LLC
224
D. J. KLIONSKY
Figure 2. Changes in the number of issues and pages per year published in Autophagy.
view, with the goal of assisting others who might wish to undertake a similar task. Finally, the white paper states, “The Task Force finds this model of community-driven standards appealing because it is driven by the input and consensus of the scientists doing the work.” I note this last point to once again emphasize that the guidelines are a community effort that has been written by all of us—practicing scientists from undergraduates to full professors. Furthermore, the conclusions of the ASCB report were picked up by other news sites: “One of the task force’s strongest recommendations was to promote scientific community-based standards for assessing data from a given field…Concerned about differing standards of proof among autophagy labs, Klionsky spearheaded a community effort to draw up specific standards for proof, which are now widely accepted by researchers and journal editors in the field. The ASCB task force thought that other scientific societies and journals should encourage researchers in the fields they serve to cooperate in similar standard-setting efforts.”2,3 In other words, our guidelines should serve as a model for other fields of research. I want to conclude with a brief look at where the journal stands at the start of our 12th year. As with the previous versions, the 3rd edition of the guidelines includes authors from around the world (Fig. 1). The expansion of the “human autophagy network”4 has been mirrored by an increase in the number of issues of Autophagy published each year, and correspondingly by the number of pages (Fig. 2), and although this is very pleasing in many ways, it does increase the workload of all of the people involved in producing the journal, including the associate and assistant editors, the reviewers and the publishing staff. The graph that shows the page increase since we started publishing
Figure 3. What do the changes in content really mean in terms of how much you would have to read? A scaled representation of the entire contents of Autophagy for volume 1, 2005 (left) and volume 11, 2015 (right).
Autophagy (Fig. 2) is informative, but it is just a graph. A different way to consider this change is to imagine sitting down to read the entire volume of Autophagy from 2005— our first year of production—compared to the entire contents from last year (Fig. 3). Clearly autophagy research is still on the rise, and all I can say is that you had better find a comfortable place to sit, and be prepared for a lengthy read.
Disclosure of potential conflicts of interest No potential conflicts of interest were disclosed.
Funding This work was supported by NIH grant GM053396 to DJK.
References 1. http://www.ascb.org/reproducibility 2. http://phys.org/news/2015-07-ascb-task-scientific-action-reform.html 3. http://www.ascb.org/ascb-task-force-on-scientific-reproducibility-callsfor-action-and-reform/ 4. Klionsky DJ. A human autophagy interaction network. Autophagy 2012; 8:439-41; PMID:22781101; http://dx.doi.org/10.4161/auto.19926
EDITOR’S CORNER
Stepping back from the guidelines: Where do we stand? Daniel J. Klionsky Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
ABSTRACT
ARTICLE HISTORY
The third edition of the autophagy guidelines is now published. This turned out to be a major undertaking in part because of the tremendous increase in the number of researchers participating in autophagy studies, and hence in revising the guidelines. First, I cannot emphasize enough that this paper represents a true community effort—it would simply not be possible for one person to generate such an in-depth and up-to-date manuscript covering this diverse range of topics in the autophagy field. Second, it is of critical importance that this paper indeed does not represent the opinions of a single individual, but rather seeks to obtain a consensus opinion regarding the best methods to monitor autophagy and interpret the results of the corresponding experiments. So, thank you to all who have contributed to the latest version.
Received 23 December 2015 Revised 4 January 2016 Accepted 4 January 2016
I want to point out that the significance of the guidelines has now extended even beyond the autophagy community. The American Society for Cell Biology Data Reproducibility Task Force carried out a study to address the question of “How can scientists enhance rigor in conducting basic research and reporting research results?” This study resulted in a “White Paper”1 that made 13 specific recommendations. One of these was the following: “Educate the community about examples of
KEYWORDS
autophagy; lysosome; stress; vacuole; yeast
community-based standards. For example, highlight in ASCB publications the experience of Daniel Klionsky (U. Michigan) on his successful community engagement to reach consensus on accepted assays within the autophagy community.” Note the key point of “community engagement.” Following this recommendation, a paper is now in revision for publication in Molecular Biology of the Cell that describes the generation of the most recent set of guidelines from a very practical point of
Figure 1. Geographical locations of the guidelines authors. Countries shown in yellow correspond to those of current authors of the guidelines. Map used by permission of VectorTemplates.com.
CONTACT Daniel J. Klionsky [email protected] Color versions of one or more of the figures in the article can be found online at www.tandfonline.com/kaup. © 2016 Taylor & Francis Group, LLC
224
D. J. KLIONSKY
Figure 2. Changes in the number of issues and pages per year published in Autophagy.
view, with the goal of assisting others who might wish to undertake a similar task. Finally, the white paper states, “The Task Force finds this model of community-driven standards appealing because it is driven by the input and consensus of the scientists doing the work.” I note this last point to once again emphasize that the guidelines are a community effort that has been written by all of us—practicing scientists from undergraduates to full professors. Furthermore, the conclusions of the ASCB report were picked up by other news sites: “One of the task force’s strongest recommendations was to promote scientific community-based standards for assessing data from a given field…Concerned about differing standards of proof among autophagy labs, Klionsky spearheaded a community effort to draw up specific standards for proof, which are now widely accepted by researchers and journal editors in the field. The ASCB task force thought that other scientific societies and journals should encourage researchers in the fields they serve to cooperate in similar standard-setting efforts.”2,3 In other words, our guidelines should serve as a model for other fields of research. I want to conclude with a brief look at where the journal stands at the start of our 12th year. As with the previous versions, the 3rd edition of the guidelines includes authors from around the world (Fig. 1). The expansion of the “human autophagy network”4 has been mirrored by an increase in the number of issues of Autophagy published each year, and correspondingly by the number of pages (Fig. 2), and although this is very pleasing in many ways, it does increase the workload of all of the people involved in producing the journal, including the associate and assistant editors, the reviewers and the publishing staff. The graph that shows the page increase since we started publishing
Figure 3. What do the changes in content really mean in terms of how much you would have to read? A scaled representation of the entire contents of Autophagy for volume 1, 2005 (left) and volume 11, 2015 (right).
Autophagy (Fig. 2) is informative, but it is just a graph. A different way to consider this change is to imagine sitting down to read the entire volume of Autophagy from 2005— our first year of production—compared to the entire contents from last year (Fig. 3). Clearly autophagy research is still on the rise, and all I can say is that you had better find a comfortable place to sit, and be prepared for a lengthy read.
Disclosure of potential conflicts of interest No potential conflicts of interest were disclosed.
Funding This work was supported by NIH grant GM053396 to DJK.
References 1. http://www.ascb.org/reproducibility 2. http://phys.org/news/2015-07-ascb-task-scientific-action-reform.html 3. http://www.ascb.org/ascb-task-force-on-scientific-reproducibility-callsfor-action-and-reform/ 4. Klionsky DJ. A human autophagy interaction network. Autophagy 2012; 8:439-41; PMID:22781101; http://dx.doi.org/10.4161/auto.19926
