Archive for the Open Access Category

New Publication at the Open Journal of Astrophysics

Posted in Open Access, The Universe and Stuff on May 14, 2022 by telescoper

The last couple of days have been very busy but at last I’ve got time to announce a new publication in the Open Journal of Astrophysics! This one is the 5th paper in Volume 5 (2022) and the 53rd in all. It was published on Thursday in fact but I’ve only just found time to mention it here.

The latest publication is entitled “Statistical Uncertainties of the NDW=1 QCD Axion Mass Window from Topological Defects” and is written by Sebastian Hoof & Jana Riess of the Georg-August-Universität Göttingen in Germany and David Marsh of King’s College London.

This paper is in the Cosmology and Nongalactic Astrophysics folder (cross-listed on arXiv from High-Energy Physics).

Here is a screen grab of the overlay which includes the abstract:

 

You can click on the image to make it larger should you wish to do so. You can find the arXiv version of the paper here.

P.S. We have quite a number of papers out there waiting for revised versions to be submitted. I get the feeling that everyone is very busy these days. Hopefully as we emerge from the pandemic things will improve.

A Road to Living Documents?

Posted in The Universe and Stuff, Open Access with tags on May 4, 2022 by telescoper

A few weeks ago I posted an item arguing that the scientific paper is an outdated concept and the whole business of research publishing should change to reflect more accurately how science is actually done. I’d argued previously that

the future for many fields will be defined not in terms of “papers” which purport to represent “final” research outcomes, but by living documents continuously updated in response to open scrutiny by the community of researchers. I’ve long argued that the modern academic publishing industry is not facilitating but hindering the communication of research. The arXiv has already made academic journals virtually redundant in many of branches of  physics and astronomy; other disciplines will inevitably follow.

I thought I would explain how the Open Journal of Astrophysics represents a small move in the direction of the “living document” idea.

Recently the author of a paper we published in 2019 contacted me to explain that readers had pointed some errors in that publication and he wished to amend it to correct the mistakes, which were typographical in nature but did propagate through a number of equations though they did not affect the main results. We had dealt with one post-publication amendment in the past and we handled this one in the same way:

  1. The author sent us a new version containing the proposed revisions;
  2. The Editor checked that they were reasonable (i.e. minor and without any significant changes to the scientific content);
  3. After getting the green light the author placed a revised version on arXiv with a comment explanation the revisions (in this case v3);
  4. We changed our overlay to point at the new version.

Here is the new overlay updated this morning.

You will see that there is a note on the overlay after the abstract. There is also a comment alongside the arXiv submission and another in the acknowledgements section of the revised paper. Owing to the separation between the overlay and the arXiv it is not necessary to change the Digital Object Identifier (DOI) or any of the article metadata.

This is a lot easier than the old-fashioned method of publishing an erratum. It may not represent the idea of a living document exactly, but it does demonstrate a way of feeding back to the publication after the “open scrutiny by the community of researchers” I referred to in my quote above.

It also demonstrates that peer review, however thorough, is never perfect and having wider scrutiny can find errors a referee might not.

Why we don’t need scientific papers

Posted in Open Access, Science Politics with tags , , on April 21, 2022 by telescoper

There’s a recent piece by Stuart Ritchie in The Grauniad that argues that the concept of the “scientific paper” has outlived its usefulness and should be scrapped. I think there’s a lot in the arguments presented and the article is well worth reading. Indeed, I have made similar points myself a number of times on this blog relating both to individual papers and to the journals in which they are published.

In this post from a couple of years ago, for example, I asked the question: what are scientific papers for? Here is an extract:

I can think of two main purposes (which aren’t entirely mutually exclusive): one is to disseminate knowledge and ideas; the other is to confer status on the author(s) .

The academic journal began hundreds of years ago with the aim of achieving the former through distribution of articles in print form. Nowadays the distribution of research results is achieved much less expensively largely through online means. Nevertheless, journals still exist (largely, as I see it, to provide editorial input and organize peer review) .

Alongside this there is the practice of using articles as a measure of the ‘quality’ of an author. Papers in certain ‘prestigious’ ‘high impact’ journals are deemed important because they are indicators of status, like epaulettes on a uniform, and bibliometric data, especially citation counts, often seem to be more important than the articles themselves.

By the way, I put up a poll in that piece, which is still open. You can vote here:

The point – also made by Stuart Ritchie – is that the traditional scientific journal is a 17th Century invention and, as such, does not reflect the way modern scientific is performed and disseminated.

In fields like astrophysics and particle physics this anachronistic approach leads to absurdities such as papers with thousands of authors, many of whom won’t have even read, let alone contributed any writing to, the article. Reflecting on the publication of a paper with 5000 authors back in 2015, I wrote this:

It seems quite clear to me that the academic journal is an anachronism. Digital technology enables us to communicate ideas far more rapidly than in the past and allows much greater levels of interaction between researchers. I agree with Daniel Shanahan that the future for many fields will be defined not in terms of “papers” which purport to represent “final” research outcomes, but by living documents continuously updated in response to open scrutiny by the community of researchers. I’ve long argued that the modern academic publishing industry is not facilitating but hindering the communication of research. The arXiv has already made academic journals virtually redundant in many of branches of  physics and astronomy; other disciplines will inevitably follow. The age of the academic journal is drawing to a close. Now to rethink the concept of “the paper”…

This is the closing paragraph of Ritchie’s piece, which says much the same thing:

We’ve made astonishing progress in so many areas of science, and yet we’re still stuck with the old, flawed model of publishing research. Indeed, even the name “paper” harkens back to a bygone age. Some fields of science are already moving in the direction I’ve described here, using online notebooks instead of journals – living documents instead of living fossils. It’s time for the rest of science to follow suit.

It seems to me that the barrier to opening up the processes of scientific publication to these is that the more accurately publications reflect how science is actually done in the digital age, the more difficult it is for the bean counters to assess research quality or productivity. The academic publishing industry has cornered the market on bibliometric indicators so it rather than the scientific community gets to dictate how scientific quality will be measured. The tail is wagging the dog. Until that ends – and it will only end when we fairer ways of evaluating research – we will be saddled with the broken system we have now.

Overlay journals: a study of the current landscape

Posted in Open Access with tags , , on April 11, 2022 by telescoper

There’s a recent paper on the arXiv by Rousi & Laakso (both based in Finland) with the above title and the following abstract:

Overlay journals are characterised by their articles being archived on public open access repositories, often already starting in their initial preprint form as a prerequisite for submission to the journal prior to initiating the peer-review process. In this study we aimed to identify currently active overlay journals and examine their characteristics. We utilised an explorative web search and contacted key service providers for additional information. The final sample consisted of 35 active overlay journals. While the results show an increase in the number of overlay journals in recent years, the current presence of overlay journals is diminutive compared to the overall number of open access journals. The majority of overlay journals publish articles in the natural sciences, mathematics or computer sciences. Overlay journals are commonly published by groups of scientists rather than formal organisations and overlay journals may also rank highly within the traditional journal citation metrics. Nearly none of the investigated journals charge fees from authors, which is likely related to the cost-effectiveness of the overlay publishing model. Both the growth in adoption of open access preprint repositories, and researchers willingness to publish in overlay journals will determine the models wider impact on scholarly publishing.

You can find a discussion of overlay journals in general here, where I learnt that the term “overlay journal” was coined back in 1996 but it obviously took quite a long time to implement the idea in functioning platforms. The paper is well worth reading. It contains some analysis of journal citation metrics but because most of the journals are young this information is very sparse. The Open Journal of Astrophysics of course gets a mention. It doesn’t yet have a Journal Impact Factor. Some of the journals in the Rousi-Laakso paper have a JIF but this dates from a time before the journal flipped to overlay state. For your information, the JIF for year n is based on citations received in that year for papers published in years n-1 and n-2. The Open Journal of Astrophysics should qualify for a JIF for 2021 based on papers published in 2019 and 2020 but Clarivate (who control such things) doesn’t seem to be in a hurry to issue one.

I think Journal Impact Factors are a waste of time. Why use journal level metrics when there is plenty of information at the article level? On the other hand the bean-counters in charge of science funding in several countries (including Italy) insist that papers resulting from this funding should be published in papers with a high JIF so I’m aware that not having a JIF is a limiting factor for some.

Of course many fields do not use the arXiv, but there is no reason why the principle of the overlay journal could not be applied to other forms of repository. There has been a culture in physics and astronomy of circulating preprints for a very long time now, and it may take a while for this to permeate into other disciplines.

New Publication at the Open Journal of Astrophysics

Posted in Open Access, The Universe and Stuff on March 30, 2022 by telescoper

It’s time yet again to announce a new publication in the Open Journal of Astrophysics! This one is the 4th paper in Volume 5 (2022) and the 52nd in all.

The latest publication is entitled A SiPM photon-counting readout system for Ultra-Fast Astronomy and is written by Albert Wai Kit Lau & Yan Yan Chan (of the Hong Kong University of Science and Technology), Mehdi Shafiee (Nazarbayev University, Kazakhstan) and George F. Smoot & Bruce Grossan (Lawrence Berkeley Laboratory).

This paper is in the Instrumentation and Methods for Astrophysics section, and is also the first paper we have published with a Nobel Laureate in the author list!

Here is a screen grab of the overlay which includes the abstract:

 

You can click on the image to make it larger should you wish to do so. You can find the arXiv version of the paper here.

 

The Flexibility of Overlay Journals

Posted in Open Access on March 11, 2022 by telescoper

In the summer of 2021 we published a paper in the Open Journal of Astrophysics entitled A Differentiable Model of the Assembly of Individual and Populations of Dark Matter Halos. The authors are Andrew P. Hearin,  Jonás Chaves-Montero, Matthew R. Becker and Alex Alarcon, all of the Argonne National Laboratory.

Here is a screen grab of the overlay which includes the abstract:

One of the authors contacted me recently to ask if it would be possible to make some minor textual modifications to the version we already published. After discussing this with the Editorial Board we agreed on the following steps:

  1. The author sent us a new version containing the proposed revisions;
  2. The Editor checked that they were reasonable (i.e. minor and without any significant changes to the scientific content);
  3. After getting the green light the author placed a revised version on arXiv with a comment explanation the revisions (in this case v3);
  4. We changed our overlay to point at the new version.

The way we are set up no further action was necessary. I think this is a nice demonstration of the flexibility of an overlay journal!

New Publication at the Open Journal of Astrophysics

Posted in Open Access, The Universe and Stuff with tags , , , on February 21, 2022 by telescoper

It’s time yet again to announce a new publication in the Open Journal of Astrophysics! This one is the 3rd paper in Volume 5 (2022) and the 51st in all. We actually published this on Friday, byt I’ve only just got around to announcing it here now.

The latest publication is entitled Differentiable Predictions for Large Scale Structure with SHAMNet and is written by Andrew Hearin, Nesar Ramachandra and Matthew R. Becker of the Argonne National Laboratory and Joseph DeRose of the Lawrence Berkeley Laboratory (both institutions being in the USA).

Here is a screen grab of the overlay which includes the abstract:

You can click on the image to make it larger should you wish to do so. You can find the arXiv version of the paper here. This paper is in our popular Cosmology and Non-galactic Astrophysics section.

P. S. Here’s a bit of feedback from the author of this paper about the referees:

They reviewed the paper in conscientious detail, and every comment was thoughtful. We feel that our paper has materially improved in clarity as a result of their critique.”

Say hello to ar5iv!

Posted in Open Access with tags , , , on February 16, 2022 by telescoper

Yesterday I stumbled across a new thing which I think is very cool.

Usually if you want to read a paper posted on arXiv you have to view, e.g. a PDF file. Now someone has set up a facility to view every article as a modern HTML5 page. To use this function you just need to change the “X” in the link to an arXiv paper to a “5” and you can view the whole paper, equations and all, in your browser as a web page.

You can check this out using a recent paper from the Open Journal of Astrophysics:

Here is the standard arXiv link to the paper:

https://arxiv.org/abs/2107.05639v2

Now try looking at

https://ar5iv.org/abs/2107.05639v2

I have found a few conversion errors using this facility but I assume these can be ironed out in due course. Now I have to persuade Scholastica to let us link to the ar5iv versions of OJAp papers (although I think the plan is to integrate ar5iv with arXiv at some point).

A Peer Review Poll

Posted in Open Access on February 14, 2022 by telescoper

A long time ago I posted a poll to see what people think about the issue of peer review. Now seems a good time to circulate it again.

In previous posts (e.g. this one) I had advanced the view that, at least in the subject I work in (astrophysics), while in its usual form peer review does achieve some degree of quality control, it is by no means perfect. Some good papers get rejected and some poor papers get accepted. Moreover, the refereeing is usually done for free by members of the academic community while journal publishers use peer review as a justification for levying publication charges in that it provides added value to the publication process – a view I disputed here.

Any system operated by humans is bound to be flawed to some extent, but the question is whether there might be a way to improve the system so that it is fairer and more transparent.

I suggested that it could be replaced by a kind of crowd-sourcing, in which papers are put on an open-access archive or repository of some sort, and can then be commented upon by the community and from which they can be cited by other researchers. This would, if you like, be a sort of “arXiv plus” – good papers would attract attention and poor ones would disappear.

We did consider having open peer review of the sort mentioned above for the Open Journal of Astrophysics but this option was not available for the no-frills off-the-shelf Scholastica platform we went for so we now operate a version of the traditional peer review system. This achieves some level of gate-keeping but also (and much more importantly, in my view) makes constructive criticism to allow authors to improve their papers. We also discussed publishing referee reports alongside the papers, but that is also beyond the scope of our current system (and would of course require the consent of referees).

I have no idea really how strongly others rate the current system of peer review. The following poll is not very scientific, but ‘ve tried to include a reasonably representative range of views from “everything’s OK – let’s keep the current system” to the radical suggestion I make above.

Is the Hubble crisis connected with the extinction of dinosaurs?

Posted in Open Access with tags , , on February 7, 2022 by telescoper

There is a paper on the arXiv (in the astro-ph section) with the title Is the Hubble crisis connected with the extinction of dinosaurs?

The abstract is here:

You can read the paper and make your own mind up, but I’m going to stick my neck out and go for “no” as the answer to the question posed…

And while I’m here I’ll give anyone who is yet to do so the chance to vote on whether there really is a Hubble constant crisis in the first place: