Where to publish our next paper? Letter to a group member

This post was originally published in JUNQ, the Journal of Unsolved Questions.  I thank the editor David Huesmann for his feedback on an earlier version of the manuscript and for the authorization to reproduce it here.


Hi X

Thank you for sending your draft. Really nice work! I will give you more detailed feedback in the next couple of days, but I want to answer now your question about where we should submit our paper.

In the last couple of years, partly because of my involvement in the stripy controversy (more below), I have thought a lot about publishing… and concluded (along with many other people) that the system is absurd, worse, toxic. Public funds are paid to commercial publishers to put publicly-funded research behind paywalls. The (unpaid) hard work of reviewers (which may or may not have led to improvements in the article) remain confidential and does not benefit the community. Publicly-funded researchers waste their time reviewing articles which have already been reviewed several times by other researchers for other journals. Researchers are evaluated on the impact factor of the journals in which they publish even though this is not at all a measurement of the quality of an article. There is a serious reproducibility crisis but no incentive to reproduce or criticise published work. Those flaws and their consequences can be illustrated by briefly looking at two recent controversies.

It took us three years to publish “Stripy Nanoparticles Revisited”. The numerous (and still unfolding) events that followed this publication opened a window into our disfunctioning scientific system, highlighting the failure of journals and institutions to promote correction of the scientific record. The stripy controversy also shows the role that (open) post-publication peer review and social media can play in enabling those discussions which are almost impossible to get through the traditional journals. A positive example of these new dynamics is the case of Brian Pauw, who came across the controversy via Twitter, made interesting contributions on his blog and in the online discussion (PubPeer) of the arXiv pre-print of our follow-up paper, and eventually became an author of the revised version.

Announced as a major discovery with two publications in Nature and massive media coverage, the generation of stem cells through an acid bath (STAP) rapidly turned into a scientific and human disaster which culminated with the suicide of one author [see tribute]. It is hard to overestimate the impact that this disaster had on Japanese science and on stem cell science more generally. Yet, severe flaws in these articles had been identified before publication by reviewers at Science (where the work had been initially submitted) and by reviewers at Nature. All of this could have been avoided if Nature had decided to reject the article, or, if the work had been published alongside the reviews that cast serious doubts on its validity, leaving it to the readers to make up their mind or wait for replications (which never came in spite of attempts)

The system is so severely flawed that it threatens scientific progress and the fabric of science. Not all those problems are due to the publishing model, but it certainly plays a key role.

We need to change the ways we share scientific progress and we have the opportunity to do so: innovative publishing platforms can transform the way scientists share, discuss and evaluate their findings. I believe that this is the future and embracing this future will be beneficial to young researcher’s careers but I know that this is a gamble because many colleagues and institutions still evaluate researchers through the impact factor of where they publish. In our own institute, at a recent research strategy event, colleagues one after the other argued the excellence of their research groups on the basis of the number of articles published in high impact factor journals. I do not underestimate the gamble and this is one with your own career so it is not one I can make on your behalf. If you are happy to try one of these platforms, I’ll be delighted. If you prefer to go for a more traditional venue, I’ll help you as much as I can and we will pay the fees to make the article open access (all journals offer to make your articles open access though this hybrid model is further filling the pockets of publishers and does not seem to help the transition to full open access; see paragraph entitled Get value for money in this post by Stephen Curry).

The ideal system would be a high quality platform combining these three features: #1 not-for-profit, #2 open access (and reasonably priced), and, #3 with articles published immediately followed by open peer review. There are a lot of experiments in publishing at the moment and I list below just a few which are relevant to our area of research.

All the best,

Raphaël

Twitter @raphavisses 

Journal/Publication platform not-for-profit open access immediate publication followed by open peer review
ScienceOpen  

F1000 Research

Beilstein Journal of Nanotechnology

(and free!)

PloS One

Royal Society Open Science

Chemical Science

(free in 2015-16)

Update 1: For a more biology orientated manuscript, we could also consider Biology Open and eLife which fit criteria #1 and #2 (HT @clathrin, @christlet)

Update 2: The Winnover fits #2 and #3

Update 3: a useful tool to navigate the journal jungle here via @sharmanedit

Update from PloS One

The publication of Julian Stirling et al, submitted in December 2013 to PloS One, has been held for more than two months over copyright issues.

In a comment at Julian’s blog, PloS One editor Damian Pattinson explains why PloS One is inflexible with their use of the CCBY licence:

Hi Julian,
First of all, I’m sorry for how long this is taking, but I want to assure you that it is top priority for us.
We want to ensure that your paper is fully re-usable, mineable, machine-readable etc. That is central to our mission as open-access publishers.
To do this, we need the whole article to be fully CC-BY, not CC-BY-except-for-where-we-say-it’s-not. Adding exemptions like that will make the whole corpus unstable for things like data mining (and whatever else the future brings), and devalue your paper and the others we publish. That’s the reason we are trying to obtain permission.
We are *this* close to getting this sorted, so I ask that you just bear with us a little longer.
thanks,
Damian (from PLOS ONE)

Making the Most of Microscopy: First day of Centre for Cell Imaging Workshop

It is always like this in Liverpool.

But we went indoors anyway…

For what happened next, see here.

The workshop is sponsored by Zeiss Microscopy with a best talk prize offered by Andor.

Julian: When it comes to scientific publishers, I just don’t know who to trust anymore.

Julian:

This article is a direct follow up of my previous post: How can we trust scientific publishers with our work if they won’t play fair?

When I posted my last post I knew who the good guys were: PLoS ONE, a non-for-profit open-access journal who had agreed to publish a controversial article and were actively seeking for permission for us to reuse figures from other journals.

I also knew who the bad guys were: Wiley, a huge publishing house that makes large profits directly from our science and library budgets and who were refusing us permission to reuse images.

The story got a lot more attention than I had expected. Wiley and Nature Publishing Group both submitted comments on the blog, the Times Higher Education wrote an article about it, some other blogs picked it up, and quite a few people contacted me privately. However, it turns out things are a lot less simple than I had thought.

Continue reading at Julian’s blog.

Can of NanoWorms or NanoMuseum? (Nano What?? Part Two)

Nano What?? Part One documented NanoDisco Balls, NanoWimbles, NanoCabbages, Nano Sea Anemones, NanoFruits (Nano-cranberries, nano-strawberries, nano-rasberries & nano-pineapple), NanoPistons for a NanoCar and NanoSpanners to fix those!

Stephen Davey replied

The linked paper is Chanteau et al, Synthesis of Anthropomorphic Molecules:  The NanoPutians J. Org. Chem., 2003, 68 (23), pp 8750–8766 Abstract in full

Described here are the synthetic details en route to an array of 2-nm-tall anthropomorphic molecules in monomeric, dimeric, and polymeric form. These anthropomorphic figures are called, as a class, NanoPutians. Using tools of chemical synthesis, the ultimate in designed miniaturization can be attained while preparing the most widely recognized structures:  those that resemble humans.

{I have checked: Chanteau et al has not been published a first of April} TOC graphic:

NanoPutians

NanoPutians, TOC graphic of Chanteau et al

Figure 1

NanoPutians, reproduced from Fig 1 of Chanteau et al. The original Figure legend reads: "Figure 1 NanoKid (13) was treated with a series of 1,2- or 1,3-diols in the presence of catalytic acid and microwave oven-irradiation to effect acetal exchange and hence head conversion to afford a series of new NanoPutians, termed NanoProfessionals. See Table 1 for the specific diol used and the yield for each head conversion."

NanoPutians, reproduced from Fig 1 of Chanteau et al. The original Figure legend reads: “Figure 1 NanoKid (13) was treated with a series of 1,2- or 1,3-diols in the presence of catalytic acid and microwave oven-irradiation to effect acetal exchange and hence head conversion to afford a series of new NanoPutians, termed NanoProfessionals. See Table 1 for the specific diol used and the yield for each head conversion.”

However…

To which Stephen Davey replied

Unfortunately, this is well beyond my capabilities, so we will have to pursue our quest for a Nanocurator elsewhere… That quest is pressing though because the list of #NanoExhibit is growing fast and I am struggling to keep up. Indeed, as Brian R Pauw suggests, I have opened a can of…

nano-worms“, courtesy of Kandalkar et al, Synthesis of cobalt oxide interconnected flacks and nano-worms structures using low temperature chemical bath deposition, (2009) Journal of Alloys and Compounds, 478, 594–598

NanoWorms. Reproduced from Fig 4 of Kandalkar et al

NanoWorms. Reproduced from Fig 4 of Kandalkar et al

nanocherries [again!], nanomultipeds and nanospindlesZhang et al, Synthesis, optical and field emission properties of three different ZnO nanostructures, Materials Letters, 61, (2007), 3890–3892 (via Martin Hollaby)

Nanocherries, nanomultipeds and nanospindles. Reproduced from Zhang et al

Nanocherries, nanomultipeds and nanospindles. Reproduced from Zhang et al

nano-balloonsIkeda et al, Preparation of Arc Black and Carbon Nano Balloon by Arc Discharge and Their Application to a Fuel Cell, 2011 Jpn. J. Appl. Phys. 50 01AF13

NanoBalloon (??) Reproduced from Fig 1 of Ikeda et al.

NanoBalloon (??) Reproduced from Fig 1 of Ikeda et al.

nanocarrotsLiang et al, Asymmetric Silver “Nanocarrot” Structures: Solution Synthesis and Their Asymmetric Plasmonic Resonances, J. Am. Chem. Soc., 2013, 135, 9616–9619 

NanoCarrots (left) and Carrots (right). Left, reproduced from Liang et al; right, carrots (picture by the author of this blog, vegetable procured from Adams Apple - Greengrocer in Liverpool L18 2DG)

NanoCarrots (left) and Carrots (right). Left, reproduced from Liang et al; right, carrots (picture by the author of this blog, vegetable procured from Adams Apple – Greengrocer in Liverpool L18 2DG)

NanoTadpolesYu et al, Large-Scale Nonhydrolytic Sol–Gel Synthesis of Uniform-Sized Ceria Nanocrystals with Spherical, Wire, and Tadpole Shapes, Angewandte Chemie International Edition, 44, 7411–7414, 2005

NanoTadpoles. Reproduced from Fig 3 of Yu et al

NanoTadpoles. Reproduced from Fig 3 of Yu et al

NanoChopsticks” these, of course deserve a special place in the #NanoMuseum; maybe a wall of shame?

Withdrawn article

Chopsticks Nanorods, via Chemistry-Blog, picture from the now retracted article

: Chopstick Nanorods: Tuning the Angle between Pairs with High Yield, Anumolu et al, Nano Lett., 2013, 13 (9), pp 4580–4580

NanoBalloons, Carrots, Chopsticks and Tadpoles were via Brian R Pauw

Nano WHAT??

“NanoDisco balls”, Chhour et al, in ACS Nano, 2014, 8 (9), pp 9143–9153, DOI: 10.1021/nn502730q

nanodiscoball

…that’s right, Chhour et al did include a picture of a real disco ball (Fig 2d), just in case some readers were unfamiliar with the concept.

“Nanowimble”, Wang et al in Phys. Status Solidi A, 2007, 204: 4029–4032. doi: 10.1002/pssa.200777334 (via Martin Hollamby)

Nanowimble

Adapted from Fig 1b of Wang et al

I must admit I was unfamiliar with that concept… Merriam-Webster saysany of various instruments for boring holes”. The authors were not as helpful and did not provide any picture. Here is one from Wikipedia

Gimlet, probably a diminutive of the Anglo-French “wimble”; from the Gimlet Wikipedia page

Update (04/10/2014) via Philip Moriarty

“nano-cabbageNanoporous TiO2 nanoparticle assemblies with mesoscale morphologies: nano-cabbage versus sea-anemone, Darbandi et al, DOI: 10.1039/C3NR06154J (Communication) Nanoscale, 2014, 6, 5652-5656

Reproduced from Darbandi et al, Fig 1b. Figure legend says: "This nanostructure was characterized as having nano-cabbage morphology."

Reproduced from Darbandi et al, Fig 1b. Figure legend says: “This nanostructure was characterized as having nano-cabbage morphology.”

Cabbage (macro). Picture by 'psyberartist' (https://www.flickr.com/photos/psyberartist/) via Flickr. [I changed it to greyscale]

Cabbage whorls. Picture by ‘psyberartist’ (https://www.flickr.com/photos/psyberartist/) via Flickr. [I changed it to greyscale]

From the same paper,

“nano sea anemone”

Reproduced from fig 2a of Darbandi et al. Figure legend says: "This nanostructure was characterized as having sea-anemone morphology."

Reproduced from fig 2a of Darbandi et al. Figure legend says: “This nanostructure was characterized as having sea-anemone morphology.”

Sea anemone. Picture by 'beana_cheese' (https://www.flickr.com/photos/beana_cheese/) via Flickr. [I changed it to greyscale]

Sea anemone. Picture by ‘beana_cheese’ (https://www.flickr.com/photos/beana_cheese/) via Flickr. [I changed it to greyscale]

Update (06/10/2014) via Zoe Schnepp

Nano-cranberries, nano-strawberries, nano-rasberries & nano-pineapples

I had not included the titles in the articles citation, but I have now corrected this oversight for all articles which cite their nano-shoehorn in the title… Growing “Nanofruit” Textures on Photo-Crosslinked SU-8 Surfaces through Layer-by-Layer Grafting of Hyperbranched Poly(Ethyleneimine) from Ford et al, Chem. Mater., 2009, 21 (3), pp 476–483, DOI: 10.1021/cm801913q

From the TOC graphic of Chem. Mater., 2009, 21 (3), pp 476–483 DOI: 10.1021/cm801913q

From the TOC graphic of Chem. Mater., 2009, 21 (3), pp 476–483
DOI: 10.1021/cm801913q

One-step preparation of positively-charged gold nanoraspberry. Shiigi et al, Chem. Commun., 2006, 4288–4290, 

AFM image reproduced from Fig 1B of Shiigi et al

AFM image reproduced from Fig 1B Chem. Commun., 2006, 4288–4290, DOI: 10.1039/b610085f

Update (06/10/2014) via Martin Hollaby

“Nanopistons” Zhao et al, J. Am. Chem. Soc., 2010, 132 (37), pp 13016–13025, pH-Operated Nanopistons on the Surfaces of Mesoporous Silica Nanoparticles

Here we will have to settle for a scheme rather than a microscopy picture (unfortunately).

Scheme of Nanopiston. Reproduced from Scheme 1 of J. Am. Chem. Soc., 2010, 132 (37), pp 13016–13025

Scheme of Nanopiston. Reproduced from Scheme 1 of J. Am. Chem. Soc., 2010, 132 (37), pp 13016–13025

“Nanocar” Shirai et al Directional Control in Thermally Driven Single-Molecule Nanocars, Nano Lett., 2005, 5 (11), pp 2330–2334

Reproduced from Fig 3e of Shirai et al

Reproduced from Fig 3e of Shirai et al

“Nanospanners” Hu et al, Preparation and Surface Activity of Single-Crystalline NiO(111) Nanosheets with Hexagonal Holes: A Semiconductor Nanospanner. Adv. Mater., 2008, 20: 267–271.
Reproduced from 1c-d of Hu et al

Reproduced from 1c-d of Hu et al

Keep them coming! Tweet your favourites at #NanoExhibit and I’ll update the post…

How can we trust scientific publishers with our work if they won’t play fair?

Julian Stirling:

I am angry. Very, very angry. Personally I have never liked how scientific journals charge us to read the research that we produce, and that we review for them free of charge. But that is another debate for another day. What I really hate is how they abuse this power to stifle debate in the name of their business interests. This is now going to dramatically affect the quality of a paper into which I poured a huge amount of effort – a critique of the (lack of) evidence for striped nanoparticles. (More information can be found here and here.)

The oft-repeated mantra is that science is inherently self-correcting, as all science is up for debate. In theory this is true.

Read it all here.