How to start an Open Science revolution! An interview with patient advocate, Graham Steel.

November 7, 2016

Continuing our Open Science Stars interview series, today we’re happy to bring to you Graham Steel, a relentless campaigner for all things Open!

Hi Graham, and thanks for joining us here! Could you start off by letting us know a little bit about your background?

For 25 years, my background (as in day job) was dealing with insurance claims for various insurers, legal firms and service providers. In my spare time as of around 2001, I became involved in research/science outreach and as of now, I would class myself as an open science enthusiast. From Jan 2015 – August 2016, I acted as Community Manager (then Social Media Manager) for ContentMine.

When did you first hear about open access/data/science? What were your initial thoughts?

In order, I first heard about open access late 2006, open science the following year and then open data. My initial thoughts were that all these entities were much needed and refreshing alternatives to all that I had seen or read about such topics up until then, i.e., closed access, prohibitive paywalls, “data not shown” etc.

You’re what some people call a ‘Patient Advocate’ – what is that, and what’s the story there?

The terms Patient Advocate and Patient Advocacy broadly speaking can mean a number of things. By definition, “Patient advocacy is an area of lay specialization in health care concerned with advocacy for patients, survivors, and carers”. For myself personally, this began in 2001 and mainly concerned bereaved relatives and then patients and their family members. See here for further details.

You relentlessly campaign for various aspects of open science – what drives you in this?

My means of background, I would say with certainty that during the period of around 2008 – 2011, the (sadly now deceased) social media aggregator site Friendfeed was the space in which the foundations for a lot of my current thinking were set out. Prior to that, having already been primed with open access and open data, that’s pretty much where open science really took off in earnest. Science and indeed research in the open is without question the way forward for all.

Science and indeed research in the open is without question the way forward for all.

You’re not exactly silent in your angst against some publishers for their business practices. What are the major issues that you have here?

With regards to the “angst” you mention, I have been become a more mature/level headed individual these days in this respect compared to a few years ago. Looking through my blog posts over the years, these have mainly been about ‘pro open’ issues rather than ‘bashing certain publishers’. As a prolific tweeter though, I may have put out ‘a few’ ones where I have not exactly been ‘silent’ as you say.

How does social media play a role in your daily activities as an open advocate?

What is this thing called social media that you mention? Having joined Twitter in January 2008, initially I didn’t use it that much but that has certainly changed over time. “@McDawg posts an average of 53.51 tweets per day” according to one of many free online tools. Social media is pretty much essential for what I and many many others do pretty much everyday.

How does open access play into the bigger picture of open knowledge and open culture?

Great question! Firstly, I thought about a comment (in part) I made in an interview back in 2012. “OA itself however is just one cog (but a significant one) in the wheel of Open Science!!” In my mind, I don’t think it’s easy to ‘timeline’ as you were the onset and development of all things open. I’ve not studied free/open culture in vast detail myself. A good source in this area (not surprisingly) is Lawrence Lessig. See here for details. The history of open access dates back to around the 1950s. When ArXiv.org started in 1991 that was the precursor to what we know as open access today. In short, I would say that open access is a foundation stone to the grander scheme of things.

I would say that open access is a foundation stone to the grander scheme of things

You’re a major player in communities such as OpenCon – what position do you think these play in the development of open initiatives across the planet?

I think it’s important to have a number of open communities/initiatives across the planet and that there should be synergy between them wherever possible. Specifically, OpenCon “was convened in response to incredible desire from the next generation to advance these issues.” [Open Access, Open Data, and Open Education]. Other than the annual OpenCon event which has taken place every year since 2014, the community hold regular calls online (open to anyone with an internet connection) as well as many satellite events around the planet before, during and after the main event each year. I am extremely encouraged by such activities.

You once said at SpotOn London that getting younger students and researchers to practice open science was the real revolution – what did you mean by this?

What I meant by that is reflected by the answer to it. In context, that was a short comment I made when live-streaming a Panel Discussion, “What do you need to start a revolution?” in 2012 in London. VIDEO. Transcript of what I said:- “A question for Ethan (Ethan Perlstein) from an Open Science Enthusiast to an Open Scientist. What can we do to further encourage upcoming younger researchers to be open scientists? That’s the revolution!”

Ethan replied, “For sure. I mean to me, the first step was simply getting on Twitter and realizing there’s a community of solidarity out there ‘cause otherwise, you’re just stewing in your own thoughts. So that’s my definition of the first step. And then from there, people are going to have more specific interests and you’ll find a sub group within the larger community that you can then complement the social network activity with real face to face activity and then you can start to do important things. The only thing I can say is that you need to first find that community of solidarity and Twitter is the easiest way to find them.” 

How can younger students commit to open research practices without the fear of career or scooping risk hanging over them?

In reverse order, the issue of scooping. My advice would be to get your work/data/code out there on the internet as quickly as possible. This could be via an Open Notebook, on GitHub, or somewhere within the many platforms of Wikipedia etc. In terms of research papers, there are now many options to choose from in terms of uploading a preprint of your work. With regards to the fear of career risk, be bold! Take a ‘wear open on your sleeve’ attitude. I can highly recommend watching Erin McKeirnan’s talk My pledge to be Open from OpenCon 2015.

Also check out her project Why Open Research?. Also from that event, I would suggest watching Michael Eisen’s talk, Wear Open on Your Sleeve.

How have policies in the UK with regards to open science changed over the last few years? What do you think the most influential factors here have been? Do you think they are generally progressive policies?

This is a complex issue with so many players involved. When I first started to follow the UK’s position with regards to open access many years ago, most of the key research funders had a reasonably strong position on ‘encouraging’ open access. (The exception being Wellcome Trust who started mandating open access in 2005). That wasn’t largely effective (as elsewhere) which in part led to The Finch Group/Report around 2012. The outcome of Finch was a preference for Gold open access.

finch

Since then, there have been influential factors by funders such as Wellcome Trust, the world’s largest medical research charity funding research into human and animal health. Wellcome’s progressive policies/position on open access can be found on various pages on their website such as here, here, and here. This year, they announced their own unique open access publishing venture, Wellcome Open Research which will start publishing research as early as next month.

I am also mindful of some salient responses from Jan Velterop when I interviewed him in 2012. “What always surprises me in these discussions is their national focus, whereas science is one of the most global enterprises on earth. The most positive developments for OA have been the greater awareness of it, even in the general media. Little else is new. And even attention to open access by the Guardian isn’t, as this article from February 2005 shows”.

What do you think the biggest impediments to open research are? How can we collectively combat or overcome them

impact-factor-opium

First and foremost has to be Journal Impact Factor (JIF). This is despite an abundance of evidence which over the years has shown that this is a highly flawed metric. I would encourage academics to make enquiries within their Institutions to take a pledge and sign the San Francisco Declaration on Research Assessment, DORA. Secondly, as mentioned earlier, embrace the fact that it takes very little effort these days to get a preprint of your work archived on the web.

I would encourage academics to make enquiries within their Institutions to take a pledge and sign the San Francisco Declaration on Research Assessment, DORA

What tools or platforms would you recommend to researchers looking to get into open science?

There are so many these days, where does one start? The best resource out there at present (I am not alone in this view) is Innovations in Scholarly Communication (now available in seven languages) created by Bianca Kramer and Jeroen Bosman. Also see https://innoscholcomm.silk.co/ which is super awesome.

Where do you see the future of scholarly communication? What steps are needed to get there? Whose responsibility do you think it is to lead this change?

I don’t have the answers to those myself. As of the time of writing, I would highly recommend Open Science Framework. I am moving more and more in the direction of advocating preprints for any paper with optionally, publication in journals later.

give_a_scientist_a_tool_t_shirt-r4cf3a7eedf96422797ad5594e9eea10a_jg4de_512

SOURCE

Thanks for the great interview, Graham!

So how can we “Share It” exactly ?

October 28, 2016

paywall-behind

On a one year trial basis, in late 2014 Nature.com launched a potentially ‘interesting’ initiative which they called #scishare – Press Release

In December 2014, a 12-month content sharing trial was set up to enable subscribers to 49 journals on nature.com to legitimately and conveniently share the full text of articles of interest with colleagues without a subscription via a shareable web link on nature.com, enabled by publishing technology company, ReadCube. The trial was also extended to 100 media outlets and blogs around the world that report on the findings of articles published on nature.com, allowing them to provide their own readers with a link to a full text, read-only view of the original scientific paper.

Shortly after the launch, a number of people turned to social media/blogs to express their views.

On ReadCube, and Nature‘s give-away – Mike Taylor

Why Nature’s “SciShare” experiment is bad for altmetrics – Impactstory

– John Wilbanks

High-priced research publishers warily open up to the Web

Open access and the direction of travel in scholarly publishing – Stephen Curry

Macmillan may now offer ‘free access’, but is it really open?– Martin Eve


Some were of the view that Nature.com were making subscription based content Open Access which they were not.

Content sharing is *not* open access and why NPG is committed to both 

Nature.com content sharing: action and reaction – Timo Hannay

Clearing Up Misperceptions About Nature.com Content Sharing

There was a lot of discussion about all of this at the following Reddit thread.

Science AMA Series: I’m Timo Hannay, former director of nature.com, Nature Publishing Group recently announced a “free to view” program which has created some excitement and misunderstandings. Ask me anything about it.


The results of the trial were released in December 2015 – Press Release

Some of the ‘key’ findings (emphasis in bold mine):-

• The most popular method of sharing of scientific articles has been via the media and blogger referral programme, which gave readers of articles free, read-only access to the full text of scientific articles in news stories and posts. (77%)
• High-profile media reports of Nature journal articles from a plethora of international media outlets drove the most traffic of the trial. The most popular article of 2015 was, “A new antibiotic kills pathogens without detectable resistance” published in Nature in January 2015.
• In order, the most popular news outlets were: the BBC, the Guardian, the New York Times, Science Magazine and the Washington Post.
• Peer to peer sharing, where subscribers send or post shareable links to journal articles on nature.com tended to be mostly (67%) between subscribers and non-subscribers, with the remainder mainly accounted for by sharing between those who already had subscription access.
The trial had no adverse implications for subscription-based journals either in terms of institutional business or individual article sales.
• The free read-only links were shared all across the globe but the most active sharing was instigated by subscribers in: the USA, the UK, Japan, Germany, China, Canada, Spain, France, India and the Republic of Korea.

In March 2016, it was announced that Springer Nature were set to extend content sharing to the entire Springer Nature-owned journal portfolio – Press Release

springer-scishare

Springer Nature will provide authors with free, shareable links to view-only versions of their peer-reviewed research papers, starting with authors of Nature and the Nature research journals. This initiative will then be extended to authors of all other Springer Nature-owned primary research journals, and ultimately to all authors of Springer Nature published primary research journals. These links can be posted anywhere, including via social channels and on other highly-used sites, institutional repositories and authors’ own websites, as well as scholarly collaborative networks, which many researchers are using to collaborate and to share both publicly and privately. These sharing services are expected to be operational within the next two months for all Springer Nature-owned primary research titles, with sharing services for additional portfolio titles to follow once agreed with their owners in the following months.

The range of media partners enabled to use this sharing facility will also be extended. These media partners already represent over 100 other sites, many aimed at the public, including TheBBC, The Economist, Wired and The New York Times, as well as many leading science bloggers.

The tools that enable the content sharing initiative are provided by ReadCube, whose industry-leading functionality enables sharers to make available final published versions of research papers in the streaming Enhanced PDF format. In addition to the full text of the articles the Enhanced PDF provides hyperlinked in-line citations and figures, annotation capabilities, one-click access to supplemental content and figures and advanced article metrics.

Beyond these measures, Springer Nature plans additional steps to further extend sharing options which address the long-term needs of the research community.

I for one was having various technical issues getting this to work in practice.

At that time, it meant having to manually download a paper then manually uploading it to my library on ReadCube and then trying to find the sharable link which didn’t always work.

An example of when it did.

readcube4

From a DRM perspective though, here’s what these shortened URLs actually look like in full

readcube-link

Devils Advocate

On the above point, I have to mention the following post by Dr Ross Mounce, March 2015 who has strong views on ReadCube.

assimilate-readcube

How to Block Readcube and Why


On October 17th 2016, following on from the earlier announcement in March above, Springer Nature did indeed roll this out on a much larger scale – Press Release

Springer Nature is delighted to announce that it has rolled out its free content sharing initiative, now named SharedIt, to all of the Springer Nature-owned portfolio and over one thousand additional co-owned and partner-owned journals. This now encompasses over 2,300 journals and enables authors and subscribers to post links to free-to-read versions of primary research articles anywhere, including social media platforms, repositories, websites, scholarly collaborative networks and via emails. It follows a successful trial and roll out of the initiative for research articles in Nature-branded journals which has resulted in over 2.2 million additional article views since its launch in December 2014.

“As the first publisher to trial free sharing of subscription journal articles back in December 2014 via a new service now named SharedIt, we were confident that our initiative would be a useful service to our authors and subscribers, which was why we took the bold step to trial it. Uptake of the service and the positive feedback we have received since then clearly demonstrate that there is a need – and a real appetite – for a simple, quick and legitimate way to share research in the academic community. This led us to the decision to invest in extending SharedIt across the entire portfolio, in combination with our partners at ReadCube,” said Steven Inchcoombe, Chief Publishing Officer at Springer Nature. “We believe that SharedIt is particularly beneficial because, unlike when PDFs or paper versions of research are circulated, the SharedIt links ensure that the most up to date, online version of the article is accessed, as well as providing valuable information to librarians, our authors and the wider community about how content is being utilised.”

After this was confirmed, I thought I would revisit the issue of how easy or not it was to share content since the last time I had tried. Initially, I thought not much had changed as in you still had to manually download papers and upload to ReadCube.

No response to those tweets.

I was pleased? to note however that things have indeed changed….but….

without any announcement as how to do it ????

Personal communication:-

‘Even with the Nature implementation – there was no real education effort once it went live which was a shame. Unless you knew to click the “share” icon – you didn’t know it was there’.


Totally random Springer Nature papers accessed – October 20th 2016.

readcube1

springer2

springer3

The point being that sharable links are now there automatically, no longer any need to faff around with downloading and uploading papers to create them.


sn-scishare

As matters stand though, it would appear that Springer Nature don’t really want you to know how simple this now is.


On a lighter note to end with…

+++UPDATE+++

sharedit1

Since writing the above, Springer Nature have now * put out the following resources which provide the needed clarity !

* After I put in a request for this with folks from Springer Nature in person.

sharedit-email

 

Making Sense of Research Papers

October 21, 2016

This post was prompted by the following tweet on 20th October 2016:-

 blcomp-pic1CC-BY

BACKGROUND

This got me thinking again about this issue. I don’t think this issue relates solely to open access papers, but to any science/research papers. As such, let’s leave the open access issue aside (where possible) for the purposes of this post.

From a personal point of view, as a non academic, I started reading research papers back in 2001 during my time in the Charitable Sector. For the organization in question, we had three fully qualified Scientific Advisors (at any given time) who were always to hand to assist us Trustees and Members when it came to technical issues where we were out of our depth.

3scientiststaralongtravistaylor-anthonycarboni-m-0527-653x0_q80_crop-smartIMAGE SOURCE

Given the fact that we were producing monthly newsletters which always included information on the latest research in the field in question, their input was invaluable.

As matters progresses, I started to consume more and more information, especially after one of our Advisors made me aware of PubMed ! Several months in, I was requesting dozens of PDFs per month either for personal use or to pass on internally to my colleagues. At times, rather than pestering our Advisors on every occasion, if I couldn’t understand a paper, emailing the author (or calling them) usually did the trick.

I then built up a large database of researchers in various fields (in this case, namely Neuroscience and Glycobiology) and over time, I/we had an extensive field of expertise at our virtual fingertips.  This was all in a time period before social media I should add !

Moving on several years.

spinning-clock

On the internet there is a lot of information. Good, bad and ugly. In terms of the topic of this post, there are LOADS of Patient Forums online. Personally, I am only antiquated to a handful. Cue an earlier post, The International Gang of Four (IGF).

I recall I phrase I used from someone else in a comment I left on a PLOS paper which read:-

Articles in Science Journals do demand some effort from the reader; it’s not like reading the newspaper!

When I thought about that comment again, it sort of made me think of a partially related topic.

Patients would be confused if they were to have free access to the peer-reviewed medical literature on the web

Without being pejorative or elitist, I think that is an issue that we should think about very, very carefully, because there are very few members of the public, and very few people in this room, who would want to read some of this scientific information, and in fact draw wrong conclusions from it […] Speak to people in the medical profession, and they will say the last thing they want are people who may have illnesses reading this information, marching into surgeries and asking things. We need to be careful with this very, very high-level information.

Oral evidence to inquiry, March 1st 2004, John Jarvis (Managing Director, Wiley Europe)

Response

This position is extremely elitist. It also defies logic. There is already a vast amount of material on medical topics available on the Internet, much of which is junk. Can it really be beneficial for society as a whole that patients should have access to all the dubious medical information on the web, but should be denied access to the scientifically sound, peer-reviewed research articles?

In some cases, to be sure, comprehending a medical research study can be a demanding task, requiring additional background reading. But patients suffering from diseases are understandably motivated to put in the effort to learn more about their conditions, as the success of patient advocacy groups in the USA has shown. Patients absolutely should have the right to see the results of the medical research that their taxes have paid for.

SOURCE

In 2011 after giving an invited talk at the conclusion of a JISC funded project entitled Patients Participate!, I found out about the excellent Sense About Science.


I then put out the following tweets this morning:-

Responses thus far…

Going back to the opening tweet:-

Lay summaries, supplements, primers: Scientists (and journals) strive to make science accessible to public (and each other)

lay-summaries

Petition calls for lay summaries in ecology journals

Simplified synopses of research papers could help to bridge the gap between scientists and the public.

PLOS Medicine This Journal provides an Author Summary for all if not most papers.

Some other resources I found last night after a quick search:-

STM Digest will feature lay summaries of science papers with societal impact

Opinion: Lay summaries needed to enhance science communication

That last link takes you to the Access to Understanding homepage.

This slideshow requires JavaScript.

Access to Understanding is a collaboration uniting organisations that want to improve public understanding of the latest biomedical and health research findings.

Our mission is to bridge the gap between public access to biomedical research articles online, and the wider understanding of the findings described in those articles.

Although online, open access to current research is increasing, much of this information is only accessible to a niche audience, usually just other scientists, due to the use of highly technical language. Access to Understanding aims to make scientific knowledge truly accessible by championing clear, concise and balanced summaries of research findings making them understandable to non-specialists. We are doing this by:

  • Providing guidance for anyone who is planning to write about biomedical research for a non-specialist audience.
  • Promoting online resources that support the use of plain-English writing in biomedical and health research.
  • Encouraging early-career scientists to write about research in an accessible way through our Access to Understanding science writing competition and giving anyone the opportunity to vote in our People’s Choice Award.
  • Working with like-minded organisations and individuals who want to help us bridge the gap between access and understanding – find out more here.

If you would like to help us achieve these goals, please contact us and tell us how you can help.

Access to Understanding ran an annual Competition from 2013 – 2015.

Here you can find the winners and commended entries from each year of the Access to Understanding science writing competition.

It was an honour to have been asked to act as one of the judges over 2013 – 2014 competition. Here is a video summary this of at the British Library (BL) which I think summarizes all of the above in context.

A Review of MegaJournals

October 17, 2016

landscape-evolving

BACKGROUND

One issue that I’ve been following for a number of years is so called MegaJournals.

Mega journal as defined on Wikipedia.

Cue ‘Open Access and The Dramatic Growth of PLoS ONE‘ which I wrote for the figshare blog back in 2012. (As you will see, PLOS ONE started publishing papers in 2006).

The concept of OA “Megajournals” appears to have started around June 2011 as per this post by Mark Patterson (at that time with PLOS, now with eLife):

“Remarkably, PLoS ONE became the largest peer-reviewed journal in existence inside four years (and will publish as much as 1.5% of the articles indexed in PubMed in 2011), and over the past 12 months has been emulated by many other established publishers in various disciplines”.

plos-one-2012

doi:10.1371/journal.pbio.1001235.g001

A large part of the reason for the spike in the dramatic rise since Q1 & Q2 2011 is the fact that that was the time that PLoS ONE, received its first Impact Factor .That opened the floodgates in a big way (e.g. China) and it can clearly be seen from above that this fact has led to a significant effect.

Around the same time, Frank Norman posted a more broader and detailed post Megajournals which indeed was the conduit to my own post.

The trend towards Open Access has catalysed the creation of many new journals and new publishers. BioMedCentral, established in 2000, was a pioneer of open access publishing, launching a large number of journals. Public Library of Science (PLoS) initially established a small number of high-level journals, then in 2006 it launched PLoS ONE. This was the first of a new kind of journal, later dubbed mega-journal. PLoS ONE aimed to publish any article that met the test of scientific rigour, and eschewed any measure of importance or impact in its editorial and peer review process. In 2010, PLoS ONE published 6,749 articles, making it the largest journal in the world (by volume). Its success helped to persuade the mainstream publishing industry that fee-paid open access was a viable business model.

Recently I invited representatives from a number of open access publishers to discuss megajournals. Five of them gave presentations to an audience of scientists here, and one visited me subsequently to inform me about their operations.

I then revisited the output of PLOS ONE around a year later.

plosone

I was not alone in thinking that the exponential growth seemed unstoppable. With hindsight, such growth can equally be followed by exponential decay.

In May 2015, Mike Taylor posted Have we reached Peak Megajournal?

Bo-Christer Björk’s (2015) new paper in PeerJ asks the question “Have the “mega-journals” reached the limits to growth?”, and suggests that the answer may be yes. (Although, frustratingly, you can’t tell from the abstract that this is the conclusion.)

I was a bit disappointed that the paper didn’t include a graph showing its conclusion, and asked about this (thanks to PeerJ’s lightweight commenting system). Björk’s response acknowledged that a graph would have been helpful, and invited me to go ahead and make one, since the underlying data is freely available. So using OpenOffice’s cumbersome but adequate graphing facilities, I plotted the numbers from Björk’s table 3.

megajournal-volumes-2010-20151

As we can see, the result for total megajournal publications upholds the conclusion that megajournals have peaked and started to decline. But PLOS ONE (the dark blue line) enormously dominates all the other megajournals, with Nature’s Scientific Reports the only other publication to even be meaningfully visible on the graph. Since Scientific Reports seems to be still in the exponential phase of its growth and everything else is too low-volume to register, what we’re really seeing here is just a decline in PLOS ONE volume.

It’s interesting to think about what the fall-off in PLOS ONE volume means, but it’s certainly not the same thing as megajournals having topped out.

What do we see when we expand the lower part of the graph by taking out PLOS ONE and Scientific Reports?

megajournal-volumes-2010-2015-without-top2-recoloured2

So the establishment of new megajournals is very much a good thing, and their growth is to be encouraged. Many of the newer megajournals may well find (and I hate to admit this) that their submission rates increase when they’re handed their first impact factor, as happened with PLOS ONE.

Onward!

Touched upon in the posts by Norman and Taylor is Scientific Reports (SR). SR was launched in 2011 (with little fanfare) by Nature Publishing Group (now Springer Nature) and over the last couple of years has seen significant growth. Interestingly a few weeks after its launch, PLOS ran with the following post on their Official Blog:-

Welcome, Nature. Seriously.

welcome-nature1

We shall come back to SR shortly.

Whilst PLOS ONE has many supporters, it also has its critics, most notably, some of the individuals who blog for The Scholarly Kitchen:-

Is PLoS ONE Slowing Down?

The Rise and Fall of PLOS ONE’s Impact Factor (2012 = 3.730)

PLOS ONE Output Falls Following Impact Factor Decline

PLOS ONE Output Falls 25 Percent

PLOS ONE Shrinks by 11 Percent

As PLOS ONE Shrinks, 2015 Impact Factor Expected to Rise

What is clear however was that in terms of output, this seemed to have peaked around 2013/2014 and has subsequently been in decline ever since.

In August 2016, Scholarly Kitchen ran with a post:-

Scientific Reports On Track To Become Largest Journal In The World

scientific-reports-v-plos-one

An unpredictable publication flow and revenue stream through APCs will have very different effects on the two publishers. Springer Nature has an enormous, diversified stable of journals and revenue streams, which allows them to play a long-term strategy game with Scientific Reports. Annual revenue fluctuations with one journal are not going to put Springer Nature in financial trouble. In contrast, PLOS’ income is almost exclusively based on APC revenue, with 97% of their 2014 revenue coming from publication fees. More importantly, 91% of all 2015 papers published in PLOS journals were published in PLOS ONE, the remaining 9% split among six other journals. As revenue from PLOS ONE functions to subsidize the publication costs of these six other titles, downward pressure on PLOS ONE puts the entire organization at risk.

Over last weekend, I noted a very recent post on Times Higher Education:-

Mega-journals: the future, a stepping stone to it or a leap into the abyss?

Nature’s new kid on the block is now the biggest journal in the world. But while such giants are currently overturning the world of scholarly publishing, their long-term future is unclear, says Stephen Pinfield.

In September, Plos One was overtaken. Nature’s Scientific Reports published 1,940 research articles in that month, compared with Plos One’s 1,756. The figures for August were 1,691 and 1,735, respectively. Scientific Reports has grown rapidly since its launch in 2011, a rise that has coincided with (some have suggested, partly contributed to) a decline in Plos One. Like Plos One, Scientific Reports publishes across STEM, although in reality, the former has more papers in health and life sciences and the latter in physical sciences.

oamj

Pinfield’s projected figures for SR in 2016 are based on data from August and September 2016 alone. I them made the following graph based on data from here on SR.

scientific-reports-growth-1

After I tweeted details of Pinfield’s post and my own graph, things got rather interesting on Twitter. Here’s some of what I saw.

mj-post

mj-post1

mj-post2

Based upon available data, SR certainly appears to be on track to become the largest Journal in the world overtaking PLOS ONE but possibly not until early next year.

On the other hand however, whether megajournals are growing or shrinking might be seen as irrelevant. Put another way, a key question worth thinking about is whether there is a growing proportion of papers published (including as preprints, an increasingly popular way of dissemination information rapidly and freely) without being judged on ‘relevance’ or ‘expected citation potential’ or ‘perceived scientific quality’, but just on the basis of some basic objective criteria, e.g. the detail of the description of materials and methods, statistical robustness and logic of the conclusion in view of the data, etc.

Such objective criteria can, of course, also be applied by journals not known as Mega Journals. See Science (which needs communication) first, careers (which need selectivity) later, Velterop et al (2015).

I will conclude with the closing paragraph’s from Pinfield’s post:-

What remains to be seen is whether mega-journals, as currently constituted, will prove to be a major innovation that contribute to the reshaping of research publishing in an increasingly open access world, or whether their real importance will lie in being a stepping stone to even more radical forms of scholarly communication. This will partly depend on the extent to which the open access “wild animal” will be domesticated. Signs of that already abound, meaning that any change is more likely to be incremental rather than disruptive.

It is, of course, possible that mega-journals will sink without trace: that probably applies to some of the current smaller hopefuls. But there does now seem to be momentum behind some of larger titles, which means they, at least, are likely to continue to prosper. In the short term, though, what is clear is that the battle to publish the largest journal in the world seems to be swinging towards a new form of a very old journal, Nature.

Stephen Pinfield is professor of information services management at the University of Sheffield. He is currently principal investigator on an AHRC-funded project investigating mega-journals and the future of scholarly communication.

Steel, Graham (2016): A Review of MegaJournals. figshare.

https://dx.doi.org/10.6084/m9.figshare.4036410.v2

Retrieved: 12 55, Oct 17, 2016 (GMT)

Think Check Submit

September 26, 2016

thinkchecksubmit.org

Think. Check. Submit. from Think. Check. Submit. on Vimeo.

 

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Public Domain works by Charles Darwin are being legally sold online. Is this ethical ?

August 21, 2016

darwin manuscript

paywall

Early on Sunday morning (21st August 2016), I spotted the following (anonymized) #icanhazpdf request tweet:-

darwin tweet

After spotting this, I did indeed find that the publication of this Charles Darwin paper from 1858 is indeed sitting behind a paywall:-

darwin paywall

(Thankfully, the person who left the original #icanhazpdf request for the paper found a link to the free version).

darwin paywall1

Here’s some of the responses to my tweet:-

 

 

 

 

 

 

 

 

 

 

Thankfully, a quick online search threw up a number of open access copies of this work such as here on the Darwin Online website.

So, should works dating back to that era be out of copyright and sitting in the public domain ? YMMV it would seem.

Some tweets from Copyright Librarian Nancy Sims:-

 

 

 

 

 

 

So, after being initially surprised that this public domain work is being sold by a publisher (in this case Wiley), they are within their legal rights to do this.

Earlier this year, there was an interesting thread relating to such matters after I posted this tweet:-

This is also linked to this one:-

One person however is of the view that this is NOT legal:-

Others disagree with that view:-

Let’s see if Copyright expert Charles Oppenheim will comment:-

RESPONSE

 

 

Views of someone associated with a publisher:-

the_invisible_a @McDawg @HistGeekGirl it seems wrong in principle, even if it may technically be legal. Just shows how messed up laws are.

— Andrea Wiggins (@AndreaWiggins) August 21, 2016

(Jan Velterop implies that he is of the view that it’s legal to download this from Sci-Hub as the work itself is Public Domain)

 

Updated thoughts on live-streaming an event

July 19, 2016
This post is a re-assessment of a comment I left back in 2010 on the following blog post by Martin Fenner.
I shall leave the below intact from the original (other than some formatting). So as someone who regularly continues to follow Conferences/Events virtually, have my thoughts changed much since 2010 ? Essentially, not that much really.
Firstly, I’ve live-streamed many events since then having previously just briefly dabbled. One common misconception about live-streaming, is that if you do it, no-one will come to the event IRL. This came up in the discussion below with Mike & David. They have over two decades of first hand experience in the field. Essentially, they said “the opposite is true“.
In terms of the quality of live-streaming, this can vary massively. Some of the free applications that I used years ago either no longer exist or are now cluttered with adverts (unless you pay for a premium account). Now that there are many platforms that offer broadcasting/recording in HD, the quality of live-streaming had certainly improved, generally.
Over the last two years or so, a number of mobile APPs (e.g. Periscope, Meerkat & UStream etc.) have been released meaning that after a couple of taps, you can be live on the web. Again, the quality of these APPs can vary a lot. Archiving these recordings could be made easier (although I have limited experience in this particular area).
I still firmly believe that if you’re streaming from an event, getting a secure web connection remains important.
I also still firmly believe that post event, it’s really important to archive the recordings online ASAP before interest disappears.
Another entity to compliment live-streaming is live blogging.

 This is something I’ve dabbled with a couple of times. Firstly, briefly at Repository Fringe (Edinburgh) 2015 and also earlier for UKSG in 2014 e.g., here and here.  Being part of a team certainly helped given the size of this event.

One person I know who has much more experience than me (and most) in this is Nicola Osborne, Jisc MediaHub Manager / Digital Education Manager at EDINA. You can view her work here.

 All in all, live streaming/blogging is certainly here to stay and technology/software continues to revolutionize the possibilities for making events open to wide audiences online.
One caveat remains though. By not attending events IRL, you do miss out on face to face discussions/socializing/networking etc.

Interesting post Martin.

I’ll try to keep this as brief as possible. That wasn’t possible, so here goes.
From an general subjective Conference perspective namely focusing on the virtual attendee angle, I think one has to consider many variables such as:-

A) What subjects are you going to cover?
B) Who is your “target audience”?
C) How will you make them aware of the event?
D) Is it free or fee (#scio10 was $175 – #solo09 – £10 in person or £10 for Second Life)
E) How interactive do you wish to make it be for virtual attendees?
F) How does one tackle sessions that involve unpublished data?
etc.etc.

Now since we only appear to be able to use a max. of four url’s in the comments feed on NN at the moment, I’ll choose ’em sagaciously.
On Jan 10th, I posted this on my blog (sorry, link rot) before virtually attending last weekend’s events in North Carolina.

Based upon past experience(s), the thing that I was really looking forward to was the live-streaming/chat-room aspect of the Conference. Despite the much applauded wi-fi connection they had set up (extremely important these days and secured internet access to all present) c/o company SignalShare, it became clear fairly early on that there was -phlegm- a problem with the live-stream.

++ACTION POINT++ Must find out what went wrong so that we can learn from this for the future.

Each chunk (hourly sessions) of the event was split into five parallel sessions (Rooms A to E) and the aim was to live-stream content from all discussions in D & E. This meant that ahead of the event, virtual attendees could chose which sessions they wanted to attend. In the end alas, over the whole weekend, only about 1.5 hours worth was streamed and with very little notice.

I found this rather disappointing I have to say as discussed with Martin over the weekend (can a DM Twitter discussion be classed as a “personal communication”?) so time to follow events in other ways. I was pretty much glued to the #scio10 Twitter feed all weekend and I very much agree with AJCann’s comments above.
==
I like Martin’s Twitter suggestions !!

Richard Grant & I covered various aspects of Conference event coverage during a podcast we did with Mike Sefang & David Wallace (link rot, try here) in July 2008. (relevant section starts at 19’30”) As a result of that discussion and with the permission of NPGs Timo Hannay, Richard recorded audio of the Wrap-Up Panel: Embracing change: Taking online science into the future at Science Blogging 2008: London which was uploaded to web within a few hours. Cool….

As discussed with a few NN staffers, even though all sessions were video recorded, due to technical issues, none of the NN files ever appeared on the web. That said, Cameron Neylon recorded and from memory live-streamed (and also self archived) some of the sessions via his laptop. Also cool.

An observation from “Science Blogging 2008, North Carolina”:http://scienceblogs.com/clock/2008/01/science_blogging_conference_vi.php is as follows. Similar to what Cameron did in London, that year, a couple of individuals, Wayne Sutton and to a lessor extent, Deepak Singh, live-streamed events from their laptops. Within the space of a week (after that, little interest), their uploaded files had been viewed over 15,000 times which I think was pretty impressive. Observation from Science Online London: 2009. Video footage of 7 sessions were uploaded c/o NN’s Joanna Scott 2 weeks after the event. Total views ~ 500.

My take on this from this data is that if you are going to attract the attention of virtual attendees using video format, it needs to be instant ideally, or delayed by a day or two at the most, before interest fades. The same I guess applies to audio. As to Second Life, I personally have limited experience of this platform so am unable to comment. One for Lou & Jo to discuss as Lou has indicated earlier.

As Cameron Neylon has mentioned elsewhere on teh interwebs, as matters stand, livestreaming using a wi-fi connection is still very 50/50 in success terms. Whilst livestreaming from this years Science Online UK event shouldn’t be completely ruled out (we should at least try a secure [not wi-fi] web connection, IMO) all things considered, I have to say that I’m pretty much with Martin as per the last para of his post.

One final point. I really like the idea of Science Online 2010: London being a two day event, yay !! The meatspace socialising aspect of such events is a real draw and something that you miss by non physical presence. I can’t really add to Stephen’s comments above in this regard.

Oh waits, I still have a link final up my sleeve. Whilst I was unable to attend the pre Science Online 2009: London party in person, I did manage to fling together the following montage. Apols for re-posting here but I thought it was rather cool and in doing something like this, it gives virtual attendees a flavour of the social aspect of events, which I think is not “essential” but of general interest.

Oh bums, I appear to have have ran out of links so let’s see if I can post this without the “missing link”.

Oh sh*te, we can’t embed stuff from Vimeo here, so “el missing linky is here.”:http://vimeo.com/6306956

Essentials of Glycobiology

May 25, 2016
Originally posted on my now deceased blog on Friday, 17 October 2008

Essentials of Glycobiology – New Edition is freely available from the NLM/NCBI Bookshelf

As reported today on Open Access News (OAN):-

… Essentials of Glycobiology, the largest and most authoritative text in its field, will be freely available online beginning October 15, through collaboration between the Consortium of Glycobiology Editors, Cold Spring Harbor Laboratory Press, and the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). Fittingly, the release of the book follows soon after the October 14th celebration of International Open Access Day, which will highlight prior successes in providing such open access to research journals. …

Here is the book. The Foreword is a great place to start of course.

OAN Comments:

* Add this to the growing list of widely-used textbooks that are available OA.
* Who’s backing this is also noteworthy. It’s not an author who negotiated the right to self-archive a copy, or an OA startup publisher; it’s a scientific press and the National Library of Medicine.
* The first edition of the book has been OA since 2003. Apparently, the impact on sales of the print copy hasn’t been overwhelmingly negative, or it seems unlikely the publisher would support OA to the new edition.

My Comments:

Glycobiology is a most fascinating area that continues to gather interest over time.
I applaud all involved for contributing to and publishing this work to the widest audience on the planet.

Press Release: Novel publishing approach puts textbook in more hands

1 comment:

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Glycobiology – update

May 25, 2016

Originally posted on my now deceased blog on Saturday, 12 January 2008

Now that I’m blogging more often, I wish to expand further on one aspect of Glycobiology – 21st Century Style which I posted on this blog mid December.

Pentosan Polysulphate (or PPS for short)

PPS was something that I became interested in late 2002. As a result, this led me to become interested in the field of Glycobiology and making contact with at least two dozen leading Glycobiologists from around the world.

Since social networking is all the rage these days, I am currently co-admin of two Glycobiology related online groups, one on Facebook, the other, on Nature Network.

PPS may be a merely a drop in the Glycomics ocean, but it is the substance that I have the greatest knowledge and first hand experience of.

Since my email records only go back to Feb 2006 (I had to change computers and lost a lot of older emails), I cannot recall specifically when contact was made with a Linda Curreri based in Dunedin, New Zealand but it would have been during 2003. We still keep in touch.

Linda maintained a very well referenced and detailed website dedicated to Pentose Sugar. Linda like myself is a layperson but her general research knowledge was and remains sublime. A decision was taken last year by Linda to no longer maintain the site but I offered to come to the rescue if required.

A few months before then however, I had discovered the brilliant WayBackMachine c/o Archive.org

We then knew that despite the site being archived, it would be (and is) preserved perfectly as it was on the web.

I therefore for the first time am providing a link to archived website PENTOSE SUGAR

Further preservation was done in the form of book “Pentosan polysulphate : a medicine made from beech bark” by Linda Curreri early 2007. ISBN 9780473119720 (pbk.) : $12.00

—-

At the time of writing, there are 731 Papers about Pentosan archived in PubMed. Importantly however, only 98 are readable (open access) at full article level. That’s not a lot really.

When one considers the clinical usages and research areas of PPS, I find it quite staggering that so little research has been published thus far.

Let’s take arthritis for example. PubMed throws up over 175,000 Papers. When we add Pentosan to the search mix, the number falls to 32, and down further to only three at full article level.

For a condition that afflicts millions of patients, pretty much to date, only the non-human variety are allowed to receive PPS treatment.

But wait !!. Check out the ARTHOPHARM website in Australia and this page.

Go back, check and FULLY read through archived website PENTOSE SUGAR

Being a layperson and patient advocate with no loyalty to anyone other than patients, no patents pending (or ever likely) and no conflicts of interest to declare, I simply wrote this blog to place information in the public domain.

I will end with a Legal Precedent from 2002 and it’s wide ramifications. The following text is from the Pentose Sugar website.

“Law. Pentosan Polysulphate is not and cannot be patented. This places it in the public domain. However PPS is only available under patented trade names which appear on its packaging. This is a complete nonsense, because the brand name is not pentosan polusulphate and it is the trade name which is being marketed. The brand patenting merely protects the commercial property of the manufacturer. If a pharmaceutical company does not ‘develop’ PPS for specific indications and patent their brand name(s) this unique medicine does not become available as a treatment option. In effect legislation made up by law maker’s is blocking pentosan polysulphate’s availability for sick human’s. PPS is however readily available for scientific research.

In the London High Court in December 2002
, Dame Elizabeth Butler-Sloss ruled in favour of two teenagers with advanced vCJD to have pentosan polysulphate to treat this prion disease. The case had absolutely nothing to do with any patented brand name; it was about the right of two dying people to have a medicine that could save their lives .The medicine was the unpatented pentosan polysulphate. Dame Elizabeth’s decision set a precedent and it would seem that the legal constraints which surround this pentose medicine, though firmly in place are flimsy and could in fact be nul and void.

It could also be argued that due to the unique status of pentose sugar in human physiology that it is an absolute right of humans to source and assimilate pentose sugar whether it is a food sweetener or a medicine that has been compounded by a chemist, and neither medical specialists, government officials, man made laws or scientists and pharmaceutical companies ( both of which appear to claim the unpatented generic medicine PPS) have any right to prevent them. Whether by collusion or not, this is indeed happening….globally.

Scientists will always continue research even though principles have been proven, it is what they do, but this should not be used as an excuse to prevent pentosan polysulphate’s use in humans, because science has already proven the safety and worth of this medicine to the human organism.”

http://www.getgooglesearch.com/htmlcodes/search.html

5 comments:

Francis said…

Is the archived version of the pentosesugar website no longer available?
Also, I tried looking out for the book itself, but the only website reference for it doesn’t have any copies. Any working links would be appreciated. I dont mind paying directly to the author herself

Thank you,
Francis

McDawg said…

@ Francis. This link should work for the archived pentosesugar website:- http://web.archive.org/web/20041205094941/www.pentosesugar.com/toc.html

Shall email you the authors contact details.

Francis said…

Hey McDawg,

The webarchive is perfect. I haven’t received the author’s details though.
PS. I would like to know more about your expertise on Pentosan.

Thanks,
Francis

McDawg said…

@Francis.

If you would kindly drop me an email (steelgraham AT hotmail DOT com), I’ll see if I can assist you.

Kind regards,

Graham

McDawg said…

@ Francis. I tried to email you the information you were looking for but there is no email address in your profile. Overnight, I received the following message from Linda Curreri which she asked me to post on my blog.

HELLO FRANCIS,

TO PURCHASE A COPY OF THE BOOK PENTOSE SUGAR, A MEDICINE MADE FROM BEECH BARK, PLEASE EMAIL ME AT

lcurreri@xtra.co.nz

KIND REGARDS,

LINDA CURRERI [AUTHOR]

Glycobiology – 21st Century Style

May 25, 2016

Originally posted on my now deceased blog on Monday, 10 December 2007

Glycobiology – 21st Century Style


Glycobiology 21st Century Style

 

I’ve been thinking about an ‘appropriate’ image for this for quite some time, so here we go. All that I added was ’21st Century Style’.

SOURCE (C)

Follows some thoughts I had last year.

If accepted for publication, my co-authors and I will deliver something of substance in the New Year.

Complex sugar chains and glycosaminoglycan (GAG) side chains
make up an integral part of our mind and body.

It was an Albrecht Kossel who was awarded a Nobel back in 1910 as the first to recognize that nucleic acids contained a carbohydrate. Due to its 5 carbon molecular structure, he called it pentose “the stuff of genes”.

During the first half of the last Century, the chemical and biological structures of carbohydrates were very much a point of focus. Whilst this was to become an integral part of modern day molecular biology, at the time, they were not forerunners unlike other major classes of molecules. Largely, this was due to their (very) complex structures, difficulty in understanding their sequence(s), and the fact that their biosynthesis could not be directly predicted from the DNA template.

53 years ago Nature magazine published a scientific Paper by Maurice Wilkins and his two colleagues at King’s College, London, called “Molecular Structure of Deoxypentose Nucleic Acids” Wilkins M.H.F., A.R. Stokes A.R. & Wilson, H.R. Nature 171, 738-740 (1953)

Something called heparin was “discovered” by a second-year student at John Hopkins University in 1916. By the 1930’s, heparin came into use namely as an anti-coagulant. Essentially, this was made using animal ‘by products’ such as pig, dog and later, bovine gut material. By the early 1940’s, “purified” heparin was available for clinical and experimental use.

Post WW2, Germany was unable to import heparin and there was also a shortage of many basic resources such as sugar. A novel method of deriving synthesized heparin type substances led to the development of sulphanated pentose sugar made essentially from the bark of beechwood trees. The most commonly used term these days for this particular (Polyanion) substance is Pentosan Polysulphate or PPS. Its most common broad (oral) usage commenced in the 1960’s and continues in many countries (namely USA and mainland EU) in relation to the management of the common bladder complaint, internal cystitis (IC). SP54 (the purest form of PPS known continues to be manufactured by a small family run German company, Bene. Here is a page from the Bene website that lists it’s currently known broad usages.

Around the same time, Germany, Japan and the (former) Soviet Union also focused on Xylitol which is a five-carbon sugar alcohol, a natural carbohydrate which occurs freely in certain plant parts (for example, in fruits, and also in products made of them) and in the metabolism of humans. Xylitol has been known to organic chemistry at least from the 1890’s.

Where there is deficiency or excess of (Proteoglycans) PG’s this can play a lead role in the pathogenesis of a substantial range of common and rare conditions ranging from arthritis, diabetes, cancer, HIV/Aids through to protein folding neuro degenerative conditions such as Alzheimer’s disease (AD).

Semi synthesized HSPG’s (Heparan Sulphate Proteoglycans) over the last few years in particular are now referred to as Glycans. There are 14 Glycans in the family including Glypicans.

In 2005, Nature published a seminal Paper by Professor’s Fuster and Esko (5) entitled “The Sweet and Sour of Cancer: Glycans as Novel Therapeutic Targets” which reported on several significant developments.

In this Paper, Fuster and Esko et al demonstrated the potential use of Glycans in the treatment of many types of cancer/tumor and concluded the Paper with a “(this) might represent the ‘tip of an iceberg’ of therapeutic potential that awaits future discovery” type ending.

Have matters progressed since then?

Glycans have now been brought into real time Clinical usage, namely as surrogate markers in the treatment of a number of cancers.

How far are we from human trials of Glycan use for the likes of HIV, Cancers and Alzheimer’s disease?

Book, ‘Essentials of Glycobiology’ is available online and can be (Open Source)accessed via this book is currently being revised with an updated version was released this year via TA.

The Journal of Glycobiology published its first online Journal in September 1990.

Whilst there has been an increasing wider focus of attention in the Glycobiology field over the last few years in particular, some of the core principles from a cellular level stretch back over a Century.

In Australia and (limited extent) New Zealand in particular, Glycans continue to be used safely and successfully in the treatment of the arthritic joints (osteoarthritis) in both animal and man (1).

The latest reported commentary (2) from the most recent Global Conference on AD in Madrid is highly suggestive that diabetes, whilst certainly not the cause, has a degree of interlinkage with a number of neurodegenerative diseases.

With regards to Alzheimer’s (Amyloidosis generally) despite a substantial number of Peer reviewed published Papers showing Glycan promise in vitro and in vivo, there has been little/no interest from the Pharma Industry.

To sense the ‘sweet flavour’ of the future of Glycobiology in the 21st Century, the word Glycomics comes to mind (3,4).

Are such Generic based approaches deemed as potentially large threats to large Pharma?

(1) PMID:12014849PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12014849&itool=iconabstr&query_hl=5&itool=pubmed_docsum
(2) http://www.wilmingtonstar.com/apps/pbcs.dll/article?AID=/20060722/NEWS/607220330/-1/State
(3) http://www.functionalglycomics.org/static/consortium/main.shtml
(4) http://glycomics.scripps.edu/pub/NatMethodsEditorial2005.pdf
(5) PMID: 16069816 [PubMed – indexed for MEDLINE]http://www.nature.com/nrc/journal/v5/n7/abs/nrc1649.html

1 comment:

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