Chatting with the Guardian Science Podcast – a Pod Delusion Special

September 12, 2017

pod delusion extra

Originally posted here September 9, 2011. The audio file no longer works. Thankfully, I found a copy on my hard drive, hence this post.

Ahead of last week’s Science Online conference in London, Graham Steel and James O’Malley sat down with Alok Jha, Mo Costandi and James Meikle from the Guardian to discuss science reporting and related issues.

Topics tackled include churnalism, linking to papers, and the changes in the landscape of science journalism over the last couple of years.

03:09 – 13:27 Discussion about the background of the Guardian’s Science Weekly Podcast
13:28 – 17:44 How much science literacy can you assume in your audience when reporting on science?
17:55 – 32:07 Churnalism.What is it and how common is it in terms of Journalism and Blogging?
32:10 – 36:10 Including links to Science Manuscripts in online news articles
36:11 – 42:15 George Monbiot’s Guardian article “Academic publishers make Murdoch look like a socialist”
42:16 – 52:01 The change in the landscape/ecosystem of science blogging over the last 12 months or so
52:07 – 52:44 The use of social media during the recent riots in London and elsewhere
52:50 – 58:37 World’s first clinical trial of stem cells to treat strokes is set to move to its next phase

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Talk on preprints at ReConEvent

August 28, 2017

At ReConEvent in June this year, we were very keen to attract a speaker to provide a talk for us on preprints. Of the three speakers we asked, all were keen to come (one from the USA, the others from the UK) but none of them were able to come on the day in question. Since this is a subject that I have been closely following for many years now, we decided a month before that I would deliver it myself. This event is now in it’s 5th year and I’ve never given a talk at it before so felt the time had come.

I chose the title as “Preprints: a journey though time(yes, this talk did contain a few Doctor Who gags) which I hope was self explanatory. I spent roughly 4 weeks (on and off) putting my slides together and rehearsed it several time in advance and timed it at 12 minutes. Twitter was a good venue to get ideas/feedback on the content.

preprint journey

We had a number of possible uncoference ideas (this was one of them) and it was delivered in the breakout room. As we had two cameramen this year, thankfully the talk was recorded and as matters stand, is the most viewed video from the event.

Preprints: a journey though time from Graham Steel

SLIDES

Last Slide – Further Reading

¨Preprint FAQ

¨The Rise of Preprints

¨The selfish scientist’s guide to preprint posting

¨Ahead of the curve: embracing preprints

¨The Role of Preprints in Journal Publishing

¨The Rise of Preprints in Physics, Mathematics, and Computer Sciences

¨The arXiv of the future will not look like the arXiv

//platform.twitter.com/widgets.js

Since this session had an allocated time of ~35 minutes, this meant there was time for a general discussion in the remaining time which was mostly preprint related.

 

“We’re Librarians”

July 16, 2017

RLC

When blogging, I tend to leave the title until last (as I did here). I chose this one as it reminded me of a title I used before but in a different setting – “We’re Scientists”

On July 15th 2017, Radical Librarians Collective (RLC) had a meet up here in Glasgow. These have been taking place annually around the UK since 2013, but this was the first one north of the border.

There is no central committee running RLC hierarchically. The Collective grew organically out of  conversations between like-minded library workers, and its membership continues to be fluid and evolving. You don’t have to be a library worker to be part of the Collective: RLC thrives on collaboration and open discussion so everyone is very welcome to contribute in whatever way and to whatever extent they are able.

The format of the event was an unconference setting, was free to attend and was held at the Glasgow Women’s Library in Bridgeton in the East End of Glasgow.

glasgow-womens-library-collective-architecture-scotland_dezeen_1568_2

This slideshow requires JavaScript.

Being a free to attend event, not all who signed up came along on the day, but most did, ~40 attendees. The format for the day was clear and informative. Being an unconference, a rough schedule was put in place in advance and several pitches were made.

The event began.

Bridgeton4

Having not been to an RLC event before, I was impressed at the level of detail that had been thought out in advance “to mitigate barriers to engagement within the group”. SOURCE

One thing that initially took me by surprise (but swiftly understood why) was that Chatham House Rule was in place for the meeting. One is aware of the rule but has only been to one event before (2010) where this applied.

The Cost of Open Access ?

In this instance however, tweeting was permitted providing that attendees did not associate things said to who said them. All complied with this. The # for the day was #radlib17 and here are all the related tweets.

The actual topics for the sessions unfolded.

After a welcome and introductions, the first main session was on trade unionism and putting the radical before the librarianship.

 

A week prior to the event, I put in a pitch myself:-

Maybe something about ‘Big Deals’ and how to get out of them ? There has an increasing movement against them of late.

Just a suggestion for a discussion.

I was pleasantly surprised that this was actually selected and a 30 minute discussion took place. This was kicked off (as informally agreed on the day) by a voluntary member of the group, Prof Charles Oppenheim, myself followed by a general discussion.

Some of the topics that may have come up (in no order):-

Recent cancellations of “Big Deals” in Europe and beyond.

FOI requests

Cost of journal subscriptions by Scottish Universities

Lawson S and Meghreblian B. Journal subscription expenditure of UK higher education institutions [version 3; referees: 4 approved]. F1000Research 2015, 3:274
(doi: 10.12688/f1000research.5706.3)

Sci-Hub

I think I am allowed to say that I made the closing remark, but I am not permitted to say what it was (Chatham House) but I may have pointed to some of the words on a t-shirt…

librarians

After a short lunch period, a workshop/cryptoparty session on internet security was had.

The event concluded at ~15:50 and as we had to vacate the building by 16:00, off we went having left our area in the same way in which we arrived.

Almost all of us then walked round to Bridgeton station and trained it back to Glasgow Central.

A somewhat brisk (was pishin’ it down at times) walk up Renfield Street to The Flying Duck for dinner/drinks etc.

flying-duck-optimised

I buggered off early but I understand there was some karaoke !!!!!!

Extracts of The Library of Alexandra

June 7, 2017

Carl1

On June 6th 2017, in a series of tweets, Carl Malamud @carlmalamud  unearthed a very interesting entity. Carl describes himself on Twitter as:-

Archivist. Usually Civil Servant. Founder of . Open Source America’s Operating System. It’s not just a good idea, it’s the law.

 

Carl Malamud is the President and Founder of Public.Resource.Org. The author of 8 books, Malamud was previously founder of the Internet Multicasting Service, a nonprofit that started the first radio station on the Internet and was responsible for making the SEC EDGAR database available. He is the recipient of the Berkman Award from Harvard, the Pioneer Award from the EFF, and the Bill Farr Award from the First Amendment Coalition.

SOURCE

And he concludes his thread with:-

In a subsequent tweet, he confirms that he will be taking this further:-

Carl1

I have since updated the Reception section of the Wikipedia page about Sci-Hub to reflect this.

 

Preprints – who to follow…

May 15, 2017

COS logo

I’ve touched upon the Center for Open Science previously on this blog. Looking back and ahead – Centre for Open Science

preprints

The following tweet from Brian Nosek @BrianNosek Executive Director at Center for Open Science @OSFramework was the conduit to this post.

A few tweets later

And thus, Preprint Explorers was created in real time. https://twitter.com/OSFramework/lists/preprint-explorers (now deleted) Another copy may follow 😉 (And indeed it did)

During this period, I thought about creating a list on here, and in no order (irrelevant)…

Conflict of Interest Statements (COIS) will now appear on PubMed Abstracts for all papers where indicated in publication.

April 20, 2017

pubmed image

New York University nutrition researcher Marion Nestle has been tracking industry-funded studies on her blog: 156 of 168 reported results that favored the funders’ interests. Annette Elizabeth Allen

This post was prompted by the following tweet:-

The link in the above tweet takes you to

Too many studies have hidden conflicts of interest. A new tool makes it easier to see them.

PubMed, the Google of scientific search, is now publishing funding information in its abstracts.

Great post by Julia Belluz @juliaoftoronto

My immediate response on Twitter

The screenshot in Julia’s post comes from….. PubMed PubMed Updates March 2017

Of the four changes mentioned, this is the most significant.

pm_update_fig1

The one example given by PubMed is from an Open Access (OA) paper indexed in PubMed Central (PMC) (additional arrow added).

PubMed COI

“PubMed will include conflict of interest statements below the abstract when these statements are supplied by the publisher”

Emphasis mine.

Generally speaking in terms of published research papers, COIs are largely hidden towards the end (if at all). They are vitally important IMO but this is the first time I’ve seen one indexed upfront in PubMed. Going back to a key point in Julia’s post:-

We strongly urge … all journals listed in PubMed to provide information about funding sources and other possible competing interests in all abstracts. To facilitate research, the “competing interest” section should be fully searchable. Thus, PubMed would advise users about the entity or entities that funded the study and whether (a) the authors reported no competing interests; (b) the authors reported the competing interests; (c) the article did not include a competing-interests disclosure statement; or (d) the journal did not provide disclosure of funding sources or the authors’ other competing interests.

pubmed pharma

SOURCE

In short my question is, will traditional/legacy/subscription based publishers make such important information freely available or remain hidden behind their paywalls ?

+++UPDATE 1+++

I asked my long term trusted contact at NCBI/NIH if they could confirm if these will appear widely or just on OA papers like the one mentioned.

They advised “I believe it’s on papers where indicated in publication”

+++UPDATE 2+++

I did a check on 22nd April to see if this change had been fully implemented. The following randomly picked papers were checked to see if COIs were mentioned in the Abstracts on PubMed. No mention made. Having read through the full texts of these, COIs appear in all of them. Clearly, still work to do for the PubMed team.

https://www.ncbi.nlm.nih.gov/pubmed/27249641
https://www.ncbi.nlm.nih.gov/pubmed/26631378
https://www.ncbi.nlm.nih.gov/pubmed/25246643

Extraordinary Everyday Lives #053 Open Science

April 16, 2017

ORIGINAL SOURCE c/o WAYBACK MACHINE

Update: A shorter and hopefully clearer version salvaged from Mikes analog backup recording has been posted and feds should now be getting this clearer file.

Update: Apologies for audio quality, some interference gremlins snuck in somewhere. We are looking at fixing it up somewhat and will republish the audio as soon as that’s done.

The Extraordinary Everyday Lives Show #053 Open Science
Thurs 24th July 2008

>>>>>>>>>>>> MP3 <<<<<<<<<<<<<<<<<<

This show is all about the intersection of Technology and Human desire. This year Dave and I have been focusing on deepening connections with those we subscribe to via RSS. Having a chat on a podcast is a remarkable way of doing that we have found. Agenda is loose guide only, we are very stream of consciousness, no edits, no script kinda guys.


New intro music this show. Courtesy of Graham, one of our guests. I remixed it a bit for the intro and play the full song, Wake Up Now, after the discussions.

Open Science

Rough chronological talking points:
-mike had nothing more than a vague idea such a movement would exist prior to starting work at a University in April.
-his RSS reader provided some clues to a trail which I followed Graham Steel was one of the first to respond to my thinking out loud
-how graham and mike hooked up
-richard discovered it after posting an experiment on his labrats blog, and people got in touch.
-two sides open scientific publication & open notebook scientists
-trust and sharing of unpublished latest work
-tension between competition and openness
-openness outwards facing and inclusionary of wider community sharing of scientific data
-paradigm shift involvement with and giving something back to community
-blogging science
-use of podcasts big uptake in unis
-richard is attending a Science Blogging event at the Royal Institute in London on Saturday 30th August
www.nature.com/natureconferences/sciblog2008/index.html. One of the science communications team at USyd interviewed me (richard) this morning about this conference. Very interesting: theyre really keen on the idea here. Im also going to an Open Science meet at Southampton two days after the London meeting, organized by Cameron Neylon.
-guys will try to record and live blog the london event
-whats this about? http://blog.openwetware.org/scienceintheopen/2008/07/21/the-full-web20-experience-my-talk-tomorrow-at-iwmw-in-aberdeen/
www.viddler.com/explore/CameronNeylon/videos/1/
-discussion about how to capture the esence of a event with blogging, podcasts etc. immediacy.
http://www.youtube.com/results?search_query=%22open+science%22&search_type=&aq=f
-going to use one of grahams songs for intro to this show http://www.macjams.com/song/34800 Wake Up Now
http://www.music20book.com/ Gerds book
-posters in 2nd Life http://www.flickr.com/photos/mikeblogs/195285627/
-mike talks about science in the sl community. specific uses of 3d environment.what are they good for in science? rf. mike crawling thru a molecule. [dnw]
-Knol somewhere between closed and open science use? http://knol.google.com/k/knol# (A knol is an authoritative article about a specific topic.)

Graham Steel http://twitter.com/McDawg

Networking between us public, science bloggers, scientists, researchers, physicians, Journals etc.

Nature Network http://network.nature.com/profile/steelgraham
Public Library of Science (PLoS) blog http://www.plos.org/cms/blog
Open Access Directory wiki http://oad.simmons.edu/
MacJams Music Blog http://blog.macjams.com/?p=223
Personal blog http://mcblawg.blogspot.com
Do Bloggers Add a New Dimension to Conferences? http://scienceblogs.com/clock/2008/01/science_blogging_conference_vi.php


Richard Grant (twitter: rpg_twit skype: rpg7sky AIM/iChat: rpg7aim)

Nature Network http://network.nature.com/blogs/user/rpg
University of Sydney http://blogs.usyd.edu.au/labrats/ Richards open science stuff
Personal blog http://rg-d.com/BioLOG/


LINKS and Random Stuff


The Royal Institution


http://www.science.usyd.edu.au/outreach/

http://www.oar2008.qut.edu.au/ Open access & research meeting in Brisbane towards the end of September. Some impressive names.
On the subject of technology and human desire, check out this presentation from Prof David Wishart in Canada. http://www.scribd.com/word/full/2159511?access_key=key-29c44pnl25896imfykd1 I mashed it a wee bit.

This just in:
http://dx.doi.org/10.1016/j.tree.2008.05.004
Over the past few years, blogging (‘web logging’) has become a major social movement, and as such includes blogs by scientists about science. Blogs are highly idiosyncratic, personal and ephemeral means of public expression, and yet they contribute to the current practice and reputation of science as much as, if not more than, any popular scientific work or visual presentation. It is important, therefore, to understand this phenomenon.

Acknowledgements

Intro music, Wake Up Now, by steck, via macjams.com.

Image: Culture Tubes, www.flickr.com/photos/10775233@N00/107326169

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Looking back and ahead – Centre for Open Science

March 13, 2017

COS logo

https://cos.io/

Follows a series of tweets from Brian Nosek @BrianNosek Executive Director at Center for Open Science @OSFramework

 

 

 

 

 

 

 

 

 

 

 

 

And finally….

nature or wikipedia

January 17, 2017

Would you rather be published in logo_nature

or cited in  wikipedia_logo_detail?

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!