Reproducibility: Dissecting the impact of differentiation stage, replicative history, and cell type composition on epigenetic clocks
Richard J. Acton 
manuscript doi: 10.1016/j.stemcr.2024.07.009
Quick notes
Due to time constraints we don’t have a full breakdown of Gorelov et al. (2024) but instead have some quick notes on thoughts arising from this paper on reproducibility and open science questions. The biology was very interesting as we spent more time discussing that than reproducibility questions.
Openness and the choice of license by the journal
Stem Cell Reports (SCR) have chosen an interesting license under which to to publish papers in their journal, namely the CC-BY-NC-ND license. The longer name of this license is: The creative commons, attribution, non-commercial, no derivatives license. This means that whilst you can re-distribute this paper if you do so you must attribute it for example by citing it, you cannot do so for commercial purposes and cannot distribute modified versions of it.
In practice this means that we could host a copy of this paper on this blog, so that anyone could download it. However we would potentially be in violation of SCRs copyright on this paper if we hosted a copy marked up with our notes, or that was otherwise edited. As this might fall into distributing a derived work as is prohibited by the no derivatives clause. Similarly if we ran advertisements on this blog, or offered paid consulting services on figure design, it might be argued that we were commercially benefiting from re-distributing the paper and in violation of SCR’s copyright If for example we offered to sell access to copies of the paper marked up with our notes on the figure design and our re-designed versions this might be argued to violate both the non-commercial and no derivatives clauses.
So the no derivatives clause might in theory expose us to some liability for infringing on SCR’s copyright if we performed our usual figure re-work and data re-visualisation exercise on this paper. However there are fair-use / fair-dealing exemptions to the distribution of copyrighted works which would apply here so we would have every confidence in doing so. These exemptions however are not hard and fast rules, but rather criteria to inform a judgement to be made about a particular case. So in theory SCR could take legal action against us for doing so and we might have to comply with a takedown request from them, and/or pay damages, or counter-sue under the provisions which are intended protect parties being targeted by illegitimate takedown requests where the party should be aware that fair-use exemptions apply.
Whilst in practice unlikely to be an issue the possibility of this sort of legal mess that arises from the use of a license like the CC-BY-NC-ND in the context of an academic paper makes it unappealing.
Avoiding having additional encumbrances placed on your work by publishers underlines the importance of Author’s Rights Retention strategies, even when submitting to open access journals, if the license used may not be to the author’s liking. Checkout Network and Eglen (2023) for a primer on author’s rights retention. If you can ensure that you retain the rights to your submitted manuscript then you are free redistribute it under a more permissive license. For example if an author’s manuscript version of this paper existed and was under a CC-BY license we could use that and have no concerns about the terms under which SCR are distributing the work.
Something Stem Cell Reports did that is good
Something the SCR is doing right is including a section for a ‘Materials availability statement’ there was nothing in this section in the case of this paper but it is good to see effort in the direction of ensuring reproducibility of the benchtop experiments by encouraging authors to note any where any of the pre-requisite materials such as specific cell lines used are available.
Specific to this Manuscript
There was a lack of version information included for the software tools used in the methods section.
Also the level of detail about the data analysis had some room for ambiguity in how precisely previously developed methods where applied in this instance. This is in contrast to the bench methods where specifics about points of divergence from cited methods where noted in greater detail.
Administrative note
We Skipped data visualisation and figure design session on this manuscript and instead had a workshop on using git. (This doesn’t have anything to do with the copyright stuff we talked about above it’s just there weren’t any figures we felt inspired to re-design in this paper)
Slides
slides from the discussion session on this manuscript.