Archive for the ‘Open Access’ Category

At the Red Deer with the Founder of Xlear (pronounced Clear)

June 6, 2018

 

A memorable informal meeting from April 2007. Time to blog it. Having transferred from email to word to blog, this is McDawg’s longest post to date.

After downloading numerous maps about how to get from a railway station I had not been to before and walk about 1.5 miles to a travelodge that I had not been to before, I thought I was well equipped ahead of this meeting.

After getting off the train in no mans land, I only had one fellow passenger who got off the train with me to point me in the right direction. Getting from A to B on foot was obviously possible (they are both on land as far as I am aware) but would involve traversing motorways and the like. He pointed to a phone box and suggested I call a cab. Excellent idea but us Scottish are notoriously tight fisted. With no taxi numbers on me and none in the phone box (rare to even find a phone box these days) Hhmm.

After a few minutes, my taxi arrived from nowhere. £4 later – I was transported from A to B.

Not anticipating this 30 minute time warp into the future, I scoured the travelodge for Dr Lon Jones and his wife but the results came back negative. I went out for a smoke. 3 puffs in and a gentleman came round the corner. When I spoke with Lon on Tuesday, I told him that I had seen his picture on the web and as such, I would be able to recognise him. This gentleman certainly looked like him from a distance. As he came closer ……………. yep, that’s him. “Hi Lon” I said as he sailed by me. “Graham?” he said. “Your early” he said looking at his timepiece. I explained (pointing at map at the time) how I had just had a time warp experience in a mystery vehicle called a taxi (a little travelled in but handy vehicle used sparingly by Scotsmen unless blind drunk with no other option to get from B to A).

He left me to finish my cigarette but clearly was unaware that such an experience at a leisurely pace not uncommonly can take a few minutes. As I stubbed out the offending substance, he re-appeared at the door as I entered the Travelodge in no mans land.

He was quizzical about precisely where I had seen his photo. (Ed – from the Xlear website !!)


Dr Lon Jones and Jerry Bozeman

I said that I could not recall where I had seen it. Clearly, he and Mrs Jones had had a conversation vis a vis this issue whilst I had been puffing away outside. He said, “you probably wouldn’t have recognised my wife then (as I shook her hand) as she’s grown her hair.” Indeed this was a factually correct statement to make.

Chapter 1

We proceeded to move to a quiet table away from the burl of the current residents and visitors of the Red Deer Village, Innkeeper’s Lodge, Cumbernauld, Glasgow. Being situated (Ed – A80 actually) just 200m away from the busiest Motorway in Scotland, no deer were visible but they certainly would have been coated in red were they to roam around such a highway.

Mrs Jones was supping on the last drops of a pint of fine ale. After some brief opening pleasantries, Lon asked how I had become involved in CJD. I said that I thought he might ask that and had flung together the previous night some documentation that might be useful during our discussion. I responded with “what sort of music are you guys into?” and proceeded to ruffle through my rucksack for a CD that I thought would be a good closer but turned out to be a great ice-breaker. A copy of “Steck – The Best Bitz” (20 track compilation of work I recorded from 1985 – 2000). Took them both completely by surprise by this. Mrs Jones now known as Jerry mentioned that their hire car has a CD player but they have no CD’s. As such, whilst Lon’s musical taste in particular not in line with the content of the CD, at the very least, this will get listened to. They’re off to Iona the day after this discussion and after that, Eire and N Ireland.

Chapter 2

In contrast to previous face to face discussions with newish contacts, surprisingly, I took little notes – indeed, less than a page over the space of three hours intense conversation. Jerry I sensed was also a PhD. Indeed, she is a registered and practising psychotherapist. After revealing the nature of my day job, I jokingly suggested that maybe I could refer some of my clients to her. In part this was taken seriously until they both realised the irony of my remark. Both are clear thinkers.

Down to business and more ruffling of aforementioned rucksack or “rucky” as is referred to in this locale.

Now back home, the content of my rucky is much lighter and out of sync (content wise) than when it left these four walls this morning. I would add that I am pleased to still have four walls and a floor after my downstairs neighbour removed a large wall yesterday. Stewards’ enquiry is currently at stage two. Not as bad as initially suspected.

Dipping into sections 3 & 4 of rucky yielded the best documentation. In the meantime, “Pentosan Polysulphate by Linda Curreri” was eloquently passed over to Lon. This was my own personal copy as I was unable to locate the second copy that Linda sent to me which was originally destined for Ian Anderson from Jethro Tull who gets a mention in the foreword.

The “Timeline” of events document from 2000 to the current day was a great guider from time to time during the discussion. To answer Lon’s gambit, I briefly mentioned my brother and after a two year time lag, my band split up and it was maybe time (after 20 years in the semi-prof and amateur business) to try something else. I explained how I had been called a week after the band break up to consider being Vice-Chair of a (later to become Charity) CJD Support Group. I went onto explain that at the tender age of 32, to me, it seemed like an interesting but challenging role for me to consider, let alone accept. How right I was!!

Chapter 3

Lon intensely read Linda’s book and recalled that he had first heard from her (from memory) around 1999 – 2000. I remarked that I had not connected with Linda until 2003 but had remained in contact with her on a very regular basis right up to the current day. It became Xlear, sorry, clear that Lon had missed an opportunity to drop by and meet Linda face to face when he and Jerry were in New Zealand two years ago. They do however plan to return and most certainly will wish to meet this courageous and intensely interesting individual next time around. Not that it seemed to be required but the writer encouraged such an operchancity.

With Lon still engrossed in Linda’s book, I spoke at some length with Jerry about music and Church organs none the less. Personally, I had only played one about twice back in the Eighties when our, at the time Rev’d, was not in the building.

After a brief (but it ties in) relapse into the beginnings of my musical training at the piano and more importantly, keyboards etc etc, we went back to business and Jerry picked up again, her copy of today’s “The Independent” courtesy of the travelodge. Later on, I myself picked a free copy of this 70p ‘newspaper’, found little news but pages upon pages of advertisements. (These days, If I want news, I usually use the Internet.)

Chapter 4

My guests are both Vegetarians – I am not – omnivore. Having studied the menu, this was a vegetarian’s nightmare. Being polite (the cheeseburger option was most tempting), I went with the flow and three carrot/coriander/leek soups and crusty bread were swiftly delivered and quickly consumed. A second round could easily have been eaten up.

Unexpectedly, our (three hour) discussion transpired to be led namely by myself. It turned out that Lon was namely interested in anatomy related matters, but also very interested in issues namely such as preventative measures and how to rebalance internal human environments when faced with rogue bacterium and proteins.

I mentioned my contact with Dr Ellie Philips and how she had kindly sent me a shipload of Xylitol products and brought out some mints and gums. Lon quickly produced his own supply of Xylitol gum and an all round teeth cleansing moment took place. After all, in dental terms, this was one of the direct points of having this discussion. We practice what we “preach” type thing I suppose.

Lon knew a bit about ‘Prion disease’ but not much on the anatomy. The best way to respond was to describe the apparent misfolding of normal protein PrPc (of which little but some is known about) and the “misfolded” version until recently described as PrPsc. Now knee deep into scientific matters, Jerry walloped down a rather tasty looking Irish Coffee and went upstairs for a well earned rest judging from what I could gather.

With Lon now interested in “Prions” and the Nobel Prize Winner who coined a name for something that does not appear to actually exist (with certainty), he became more than interested on what we were trying to do to stop the relentless progression of the disease (PrPd) in humans specifically in Pentosan terms.

At this point, it was reasonable to re-dig my rucky and pull out further documentation. In the end, all “cards” were on the table (literally) and I told him to take away whatever he wanted. He did and thanked me for being so open.

Chapter 5 – The Book

My Xylitol contact list. This was and still is a working document, i.e., it is incomplete and subject to change. This was of immense interest to Lon. Lon (as I knew already) has a Patent on his Xlear Nasal Spray. Osmotically speaking, this is where everything made total and complete scientific sense. So, fighting bacterium is what mainly drives Lon. If I spin back to part of what he wrote to me if February, this now makes better sense.

“I am working on a book that deals with shifting our paradigm from the mechanical model to a complex one that honours the adaptations we and our evolutionary ancestors have made that helps us to deal more effectively with hostile agents in our environments. The billion dollars made by blocking such adaptations (fever, diarrhoea, rhinorrhea, to name just a few) is a large force that will not take this kindly”.

Around this time, Lon expanded upon his current book. This largely is complete pending a publisher that is sufficiently interested in making this widely available.

Currently dubbed “K C”, this book is about the Complex Adaptive System (previously dubbed CAS) When rogue bacterium enter their new “host”, they are extremely good at self replication and in certain terms millions of times over. Lon’s work deals with bringing internal environments back to their natural status and thus taming unwanted host particles. The rampant smart particles do not/never anticipate such a fight back and eventually go on to die. The system can therefore be restored back to normality not by fighting the bacterium, but by reinforcing the natural environment.

Does this work? It might do. Has this been tried? Yes. See here. Specifically, in relation to ear infection, a successful clinical trail (“n” of ~ 160 measured via similar “n” control) took place around 2005 but not accepted for publication. Since I am now aware that unpublished material can be less, equally and/or more interesting than published material, I look forward to viewing this section of the Author’s currently unpublished material. On the face of it, Xylitol as already very well documented in fighting off bacteria that causes dental decay is apparently effective when delivered intranasally.

Fully aware that Lon has patented this, this was not surprising. That said, in the commercial world that we live in, this was not surprising. Indeed, Lon mentioned a team in the US that cottoned on to “CAS” and intranasal Xylitol and carried out a clinical trial. Kind of handy for Lon when he found out and told them that he had the Patent.

Chapter 6

With the contents of my rucky pretty much now everywhere, but some still not on the table Lon looked at what was still in rucky. I told him to look through – no problem.

Around this time, we spoke about a number of issues but preventative measures came up several times. He mentioned a book that he and Jerry had just finished reading by a Dr Colin Campbell entitled “The China Study”. This I must check out.

My new friends seemed quite taken by their copy of handout “CJD Alliance Glasgow 2006” In particular; Lon was extremely interested in connecting with the Chair of that discussion, Dr Mark McClean. Moreover, Lon was I sense quite taken by Dr McClean’s summary from the Minutes of the discussion:-

“What have we achieved this afternoon?”

1. Three Medical Presentations. One on diagnostics, one on therapeutics and one on the problems inherent in tackling the different TSE strains. We asked today’s most important question – “what about systemic PrPd?”
2. The Legal Presentation – a vital branch in the past and present multidisciplinary approach to CJD/TSE. Mr Body’s success reflected his specialisation in the field – something our National Health Service should mirror.
3. Inevitable improvement of future research by our interested parties as they take away new knowledge acquired at this afternoon’s Discussion.
4. Further essential ‘networking’ between various interested parties – not to be underestimated.

Before closing this discussion, a number of points came to mind. Open Access in terms of medical research had been touched upon but I wanted to raise this again. Lon mentioned that he had received three requests for his first published Paper and zero for his second. We warmed superbly to the philosophy of Open Access via the Internet and asked how long I had been using the web. Six years. “Do you use Google to search for medical research?” Lon enquired. No, at the moment, PubMed but also now Open Access outlets and stressed the point that in Abstract form, it is impossible to fully evaluate a Paper. Having mentioned my recent conversation and contact with Peter Suber, Lon vigorously warmed to the OA philosophy and fully intends to make direct contact with him. Excellent news.

Having shared with Lon a copy of my Xylitol contact list, I sense he was a bit taken aback by this. Whilst he has a hard copy, I stressed that this was an e-document that contains many many active links. Copy now emailed to him.

Lon made mention of his Son Nathan and told me a bit about him. I asked if he had any other children. Thirteen. I thought he was being whimsical. No, he has fourteen kids via his first wife. Wow. For a period of around twenty odd years, he was certainly active. This man certainly has the largest family that I am personally aware of.

Chapter 7

As we closed up, I took stock. I had and indeed have a number of ‘action points’ that I will follow up. These were unexpected but much welcomed. Despite doing most of the talking, I had spent the afternoon with an extremely intelligent but somewhat reclusively mind mannered man. Whilst we may not meet again, we will certainly keep in touch – no question.

Would I require to conjure up another mystery taxi I was thinking? Thankfully no as Lon kindly offered to drive me back to the railway station in no mans land. As it happened, my main map came in rather handy after all and our direct route happened to be about twice as short at that of the one used by the mystery taxi driver !! This appears to be global phenomena. As such, the aforementioned comment about why Scotsmen only use such means of transportation sparingly. I rest my case.

As we arrived at my station, my twice an hour (I had no idea when) mystery train was there and just about to head off. A hasty goodbye and off I ran and JUST managed to board.

Goodbye Lon & Jerry

THE END

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“Open Access” at Bentham Science Publishers ?

January 2, 2018
0e1fe58

This caught my attention.

As did this.

Bentham1

So, having found an example of an “Open Access” (apparently CC-BY) paper at Bentham, as a reader, I have to comply with the following legalese when clicking on “Download”.
It gets worse.
When clicking on “Rights & Permisison” tab for this paper, more legalese….
Bentham2
Something fishy going on here.
Maybe something to do with a true source conflict.

And

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Copyright can be confusing. Please make it less confusing !

December 18, 2017

copyleftcopyright image CC logo

copyright 1

Just stumbled across a paper licensed under an Academic Free License (AFL) 3.0.

I don’t recall seeing such a license before. My gut reaction from the name suggested this might be similar to CC0/Public Domain.

The wording however is not as straightforward as one might think…

confused

Academic Free License (“AFL”) v. 3.0This Academic Free License (the “License”) applies to any original work of authorship (the “Original Work”) whose owner (the “Licensor”) has placed the following licensing notice adjacent to the copyright notice for the Original Work:

Licensed under the Academic Free License version 3.0

1) Grant of Copyright License. Licensor grants You a worldwide, royalty-free, non-exclusive, sublicensable license, for the duration of the copyright, to do the following:

a) to reproduce the Original Work in copies, either alone or as part of a collective work;

b) to translate, adapt, alter, transform, modify, or arrange the Original Work, thereby creating derivative works (“Derivative Works”) based upon the Original Work;

c) to distribute or communicate copies of the Original Work and Derivative Works to the public, under any license of your choice that does not contradict the terms and conditions, including Licensor’s reserved rights and remedies, in this Academic Free License;

d) to perform the Original Work publicly; and

e) to display the Original Work publicly.

2) Grant of Patent License. Licensor grants You a worldwide, royalty-free, non-exclusive, sublicensable license, under patent claims owned or controlled by the Licensor that are embodied in the Original Work as furnished by the Licensor, for the duration of the patents, to make, use, sell, offer for sale, have made, and import the Original Work and Derivative Works.

3) Grant of Source Code License. The term “Source Code” means the preferred form of the Original Work for making modifications to it and all available documentation describing how to modify the Original Work. Licensor agrees to provide a machine-readable copy of the Source Code of the Original Work along with each copy of the Original Work that Licensor distributes. Licensor reserves the right to satisfy this obligation by placing a machine-readable copy of the Source Code in an information repository reasonably calculated to permit inexpensive and convenient access by You for as long as Licensor continues to distribute the Original Work.

4) Exclusions From License Grant. Neither the names of Licensor, nor the names of any contributors to the Original Work, nor any of their trademarks or service marks, may be used to endorse or promote products derived from this Original Work without express prior permission of the Licensor. Except as expressly stated herein, nothing in this License grants any license to Licensor’s trademarks, copyrights, patents, trade secrets or any other intellectual property. No patent license is granted to make, use, sell, offer for sale, have made, or import embodiments of any patent claims other than the licensed claims defined in Section 2. No license is granted to the trademarks of Licensor even if such marks are included in the Original Work. Nothing in this License shall be interpreted to prohibit Licensor from licensing under terms different from this License any Original Work that Licensor otherwise would have a right to license.

5) External Deployment. The term “External Deployment” means the use, distribution, or communication of the Original Work or Derivative Works in any way such that the Original Work or Derivative Works may be used by anyone other than You, whether those works are distributed or communicated to those persons or made available as an application intended for use over a network. As an express condition for the grants of license hereunder, You must treat any External Deployment by You of the Original Work or a Derivative Work as a distribution under section 1(c).

6) Attribution Rights. You must retain, in the Source Code of any Derivative Works that You create, all copyright, patent, or trademark notices from the Source Code of the Original Work, as well as any notices of licensing and any descriptive text identified therein as an “Attribution Notice.” You must cause the Source Code for any Derivative Works that You create to carry a prominent Attribution Notice reasonably calculated to inform recipients that You have modified the Original Work.

7) Warranty of Provenance and Disclaimer of Warranty. Licensor warrants that the copyright in and to the Original Work and the patent rights granted herein by Licensor are owned by the Licensor or are sublicensed to You under the terms of this License with the permission of the contributor(s) of those copyrights and patent rights. Except as expressly stated in the immediately preceding sentence, the Original Work is provided under this License on an “AS IS” BASIS and WITHOUT WARRANTY, either express or implied, including, without limitation, the warranties of non-infringement, merchantability or fitness for a particular purpose. THE ENTIRE RISK AS TO THE QUALITY OF THE ORIGINAL WORK IS WITH YOU. This DISCLAIMER OF WARRANTY constitutes an essential part of this License. No license to the Original Work is granted by this License except under this disclaimer.

8) Limitation of Liability. Under no circumstances and under no legal theory, whether in tort (including negligence), contract, or otherwise, shall the Licensor be liable to anyone for any indirect, special, incidental, or consequential damages of any character arising as a result of this License or the use of the Original Work including, without limitation, damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses. This limitation of liability shall not apply to the extent applicable law prohibits such limitation.

9) Acceptance and Termination. If, at any time, You expressly assented to this License, that assent indicates your clear and irrevocable acceptance of this License and all of its terms and conditions. If You distribute or communicate copies of the Original Work or a Derivative Work, You must make a reasonable effort under the circumstances to obtain the express assent of recipients to the terms of this License. This License conditions your rights to undertake the activities listed in Section 1, including your right to create Derivative Works based upon the Original Work, and doing so without honoring these terms and conditions is prohibited by copyright law and international treaty. Nothing in this License is intended to affect copyright exceptions and limitations (including “fair use” or “fair dealing”). This License shall terminate immediately and You may no longer exercise any of the rights granted to You by this License upon your failure to honor the conditions in Section 1(c).

10) Termination for Patent Action. This License shall terminate automatically and You may no longer exercise any of the rights granted to You by this License as of the date You commence an action, including a cross-claim or counterclaim, against Licensor or any licensee alleging that the Original Work infringes a patent. This termination provision shall not apply for an action alleging patent infringement by combinations of the Original Work with other software or hardware.

11) Jurisdiction, Venue and Governing Law. Any action or suit relating to this License may be brought only in the courts of a jurisdiction wherein the Licensor resides or in which Licensor conducts its primary business, and under the laws of that jurisdiction excluding its conflict-of-law provisions. The application of the United Nations Convention on Contracts for the International Sale of Goods is expressly excluded. Any use of the Original Work outside the scope of this License or after its termination shall be subject to the requirements and penalties of copyright or patent law in the appropriate jurisdiction. This section shall survive the termination of this License.

12) Attorneys’ Fees. In any action to enforce the terms of this License or seeking damages relating thereto, the prevailing party shall be entitled to recover its costs and expenses, including, without limitation, reasonable attorneys’ fees and costs incurred in connection with such action, including any appeal of such action. This section shall survive the termination of this License.

13) Miscellaneous. If any provision of this License is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable.

14) Definition of “You” in This License. “You” throughout this License, whether in upper or lower case, means an individual or a legal entity exercising rights under, and complying with all of the terms of, this License. For legal entities, “You” includes any entity that controls, is controlled by, or is under common control with you. For purposes of this definition, “control” means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.

15) Right to Use. You may use the Original Work in all ways not otherwise restricted or conditioned by this License or by law, and Licensor promises not to interfere with or be responsible for such uses by You.

16) Modification of This License. This License is Copyright © 2005 Lawrence Rosen. Permission is granted to copy, distribute, or communicate this License without modification. Nothing in this License permits You to modify this License as applied to the Original Work or to Derivative Works. However, You may modify the text of this License and copy, distribute or communicate your modified version (the “Modified License”) and apply it to other original works of authorship subject to the following conditions: (i) You may not indicate in any way that your Modified License is the “Academic Free License” or “AFL” and you may not use those names in the name of your Modified License; (ii) You must replace the notice specified in the first paragraph above with the notice “Licensed under ” or with a notice of your own that is not confusingly similar to the notice in this License; and (iii) You may not claim that your original works are open source software unless your Modified License has been approved by Open Source Initiative (OSI) and You comply with its license review and certification process.

Quite a lot of text right ?

copyright

After a quick search, the AFL license dates back to 2002 and was released in the same era as the launch of the Creative Commons ones.

The wording (human-readable summary) as below of the Creative Commons CC0/Public Domain one is much more easier to understand.

public domain

“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

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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.

 

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!

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)

Open Science Enthusiast

April 22, 2016

@KLA2010 Just noted “Open science enthusiast” on your profile. Have used that term for myself a few times.

— ⓪ Grⓐhⓐm Steel (@McDawg) April 22, 2016

canScience

140 is too short, so …… I was going to use ‘TweetLonger’ but decided not to do so in the end.

As to who first came up with “Open Science Enthusiast”, we’ll never know and frankly, who cares…. To me, in short, it means “Citizen Scientist”.

I was present at Scotland’s 1st Open Knowledge (possibly 2nd) event (in Edinburgh back) in 2012. [2]

VLUU L200  / Samsung L200

At one point, those present were asked to describe themselves in just three words. Off the top of my head, I went for ‘Open Science Enthusiast’. I was the only one to do it in three words, so that was my starting point. – Since then, I’ve used it elsewhere even including peer reviewed papers such as:-

Buckland, A. et al., (2013). On the Mark? Responses to a Sting. Journal of Librarianship and Scholarly Communication. 2(1), p.eP1116. DOI: http://doi.org/10.7710/2162-3309.1116

The term has been used elsewhere, e.g. here by Dr Marcus Hanwell @mhanwell

best-of-science-2015

I predict that high on the list of many open science enthusiast’s new year’s resolutions will be the education of both established and future researchers on the importance of openness, licensing, sharing, and reproducibility.

Best of Opensource.com: Science  December 25th 2015

Marcus D. Hanwell | Marcus leads the Open Chemistry project, developing open source tools for chemistry, bioinformatics, and materials science research. He completed an experimental PhD in Physics at the University of Sheffield, a Google Summer of Code developing Avogadro and Kalzium, and a postdoctoral fellowship combining experimental and computational chemistry at the University of Pittsburgh before moving to Kitware

Also relevant if this lovely poignant quote from Dr Jennifer Molloy [1]

[1]Molloy quote

SOURCE

[2]

FULL REPORT of my experience in Edinburgh that day

Why Open Access ? Here’s my personal story

March 2, 2015
 (Re-posted from my now deceased blog, 13th October 2008) 

 

I did re-post this to my WP blog a couple of years ago but it was worthy of an update.

I decided to rewrite this post after receiving this tweet from Dr Martin Eve:-

I would very much encourage everybody to read his compelling post Open access in a time of illness

 

Why does Open Access matter to me?

I became involved in patient advocacy in September 2001 just under two years after I lost my brother Richard (who was aged 33 at that time) to a fatal, rare neurodegenerative disease (vCJD). At that time period, the prognosis of the disease was grim to say the least and with no treatment on or under the table, 9 months after the official diagnosis of his condition, it had gone downwards so much, we as a family were allowed under Scottish Law (with approval from his GP) to let him go.

The situation was so rapid, it didn’t occur to any of us to declare anything but defeat.

Richard & Graham

Graham & Richard Steel 1999

That was the history to the start of this post but not the point of writing it.

Two years later…

We (family) were approached to become more involved in a related support group. Dad declined, I agreed and took up the post of Vice-Chairman, a fairly daunting task at the age of 33.

During the early years of this work, I commenced the process of studying peer reviewed scientific, technical and medical (STM) research in detail for the first time.

One of the first questions I was asked  by the organizations Secretary was “Should we send scientific papers to family members, they’re quite complicated?” Me, “Well, I think we should give them the chance to look at relevant papers. Some might actually be interested in reading them, we should at least give them that opportunity rather than deny them”.

As Dr Eve touches upon in his post:-

Namely, that there isn’t a public for this material because it is specialized in both its wording and its content.

This is total nonsense and I really can’t stand it.

I completely agree.

This namely involved paper copies of Toll Access (TA) articles passed to the support group (which then became of Charitable status) I was involved with, by highly regarded UK researchers in the field in question. Whilst ‘we’ were able to share such research (with family members of the organization) by post using “fair use”, I knew that copyright restricted me from sharing any such material with a wider audience – the organizations website which I agreed to take over the handling of.

Despite this restriction, simply by placing as much information online in an open manner wherever possible, in the space of year, traffic had increased by over 4000%. As such, even before I knew what Open Access (OA) was, it was abundantly clear that being open was the main key to outreaching.

During this period, one of our three Scientific Advisors (Prof. Sarah Tabrizi) made me aware of PubMed.

After leaving that organization in 2005, I wanted to continue my patient advocacy work with broadened wings and become involved in other issues.

When did I become aware of OA?

Mid 2006. Up until the day in question, I had a pretty simple template email system in place to request PDFs of TA manuscripts directly from authors.

On the day in question, I noted from the Abstract of the Manuscript that I was looking for, there was a link to the full article. I had never seen a full paper online before. I had been of the view that all such content was locked behind an online paywall.

paywall

PLoS Pathogens
was the first OA Journal that I came across.

Not only could I access the Manuscript I was looking for and had requested, but the real eye opener was that I was able to access the entire Journal online for free! And not just that Journal, but I had stumbled upon something extremely significant.

open-access-logo

OA was a dream come true. Until then, I had sent out ~1000 requests directly to researchers for their paywalled PDFs. 90% of those requests were happily fulfilled. At say £30 a paper, that would have cost me £30,000.

I did on one occasion burn a substantial number of these to CD-r at say 1 pence a copy (only a handful of copies were made) and hand over to  CJD International Support Alliance (CJDISA) in my remit as their Information Resource Manager. I was subsequently advised by a Librarian that this was a breach of publisher copyright.

homesewing

As I said in this interview:-

One of my main eternal frustrations remains not being able to share my extensive library of papers due to Draconian copyright restrictions. Creative Commons is a dream come true….. Indeed, I’m wearing one of my PLOS t-shirts right now =) Prof Lawrence Lessig, you remain a STAR !!

Why should scientific and medical research be an open-access resource for the world?

To me, it makes so little sense* in this day and age to carry out and share STM research in a closed environment.

*Unless you are a traditional subscription based publisher of course.

May I quote in part, Associate Professor Bevin P. Engelward, the winner of the 1993 Nobel Prize for Physiology or Medicine from this 2007 PLoS Biology article:-

…In an age rife with the potential for infectious pandemics, bioterrorism, and toxic environmental calamity, and at a time when we need new ways to cure terrible illnesses, public access is our society’s compelling answer to accelerating the best science possible. This advance is much needed, both by researchers working in academic settings and in the private sector. Indeed, we should demand no less. We invite our fellow scientists to join in the demand for open access to biomedical literature.

Science, progress, societal benefits from that is a pretty concise focus.

Indeed, here’s a shot of Peter Murray-Rust and @McDawg discussing their forthcoming OA related Manuscript in London, August 2008.

(Image c/o Joe Dunckley’s sciblog Flickr stream)

What I do to support Open Access, and what can others do?

Simple. Spread the word.

My most blogged about post to date is precisely about this.

The blogosphere / and much more now, social media is an astonishingly great place to share and discover information. I’ve blogged fairly extensively about OA since I started blogging late 2007.

I’d like to close with this, again from Dr Eve.

What I’d like to close with here is that when worlds collide, interesting things happen. I remain dedicated to facilitating open access in the humanities disciplines, even when nobody needs this in a life-threatening circumstance, although I have argued that such circumstances do exist (in Open Access and the Humanities). But for me, the patronizing arguments that either everyone who needs it already has access or that there is no audience for OA can easily be countered by stories like this. We need open access. It makes the web a far better place, one where patients can turn to find high-quality material that can help them make sense of their conditions, one where others can turn to help them make sense of their worlds and cultures.

The musician in me cannot omit something poignant on this post. As such, here’s McDawg’s favourite mix of Peter Gabriel’s Shock The Monkey arising as a result of this competition. Such a mix was technically out of bounds for me at the time, but a friend in Portugal offered to assist on my behalf and did.

Peter Gabriel fully supports initiatives such as Creative Commons, The Open Society Institute, Students For Free Culture etc.