Scientific Publication#

‣ Edito

Quick introduction

Plan

Introduction#

Science


Natural science is a branch of science concerned with the description, prediction, and understanding of natural phenomena. Those phenomena are divided into branches or fields like Physics, Astronomy, Chemistry, Biology and sub-fields (Organic Chemistry, Inorganic Chemistry, Astrochemistry, Quantum Chemistry …) that sometimes overlap between different branches. Scientific research rely on a systemic way of gathering and analysing data (empirical evidence) resulting from observation, experimentation and computation, aimed at increasing the global pool of humanity knowledge. Irrespective of their fields, scientists must employ the scientific method.


- you will have to communicate your research
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The various scientific fields
The scientific method
Mountains and fjords
The Woods
Cinque Terre
[Src](https://xkcd.com/1134/)

Communication

There is two main channels that scientists use to share their work


Conferences / Seminars

  • Talk



  • Poster

../../../_images/Jenny-2018.svg
../../../_images/Poster-ISIS2.svg
../../../_images/Poster_ASW.svg

Scientific paper

  • Example


History#

Note

Use this to subsection the history

1665 - 1940

From scholars to academics

Ressource: To Check


Scientific publication begin it’s journey in 1665 with the Philosophical Transactions of the Royal Society with contributions from Isaac Newton, Caroline Hershell, Benjamin Franklin, Charles Darwin… Publication of scientific work will remain in the hand of scientific society until the end of the second world war, a time when science publishers were notoriously inefficient and constantly broke, but science itself was about to enter a period of unprecedented growth resulting from government fundings.

Vocabulary

  • Scholars: A scholar is someone engaged in intellectual inquiry or intensive study. The term covers a wide range of career stages and types: advanced students, researchers employed at universities or hospitals or think tanks, people devoting their lives to religious study or writing, freelance or independent researchers. There are many awards, prizes, and fellowships whose title includes the word “scholar”; the recipient is generally supposed to be focused on intensive learning and/or research

  • Academics: An academic is a person employed to do teaching, research, or creative artistic work at an institution of higher education. The term is generally applied to someone who’s finished their postgraduate education and is pursuing a career in higher education. It isn’t used for undergraduates with part time university jobs; but it might sometimes be applied to advanced doctoral students.


../../../_images/Philosophical_Transactions_Volume_1_frontispiece.jpg

Fig. 17 Source#

Readings

  • [Fyfe, 2015]: Philosophical Transactions Finances

1950 -#

This is the time choosen by Robert Maxwell to enter the emerging business of scientific publication by creating the company Pergamon Press. As science was expanding, it become clear that it would need new journals to cover new areas of study, and while scientific societies argued about the boundaries of their fields, Pergamon just went to convince prominent academics that their particular fields required a new journal and install that person at the reins of it. They would then begin *selling subscriptions to university libraries which suddenly had a lot of government money to spend. From 40 journals in 1959, Pergamon was publishing 150 titles by 1965, scientific articles became the only way science was represented, and publishers were seen as a necessary partner in the advancement of science. Maxwell had transformed the business of publishing but science remained unchanged and scientist would published their work to whichever journal was the best fit for their research area. It is in the mid 70’s that publications became an inherent part of scientists career with the.

Scientific Journals#


Academic publishing is the subfield of publishing which distributes academic research and scholarship. Most academic work is published in academic journal articles, books or theses Scientific journals: periodical publication in which scholarship relating to a particular academic discipline is published Nowadays journals does not have a very good press as you can se from the articles listed on the right … Let’s try to understand why.

See also

Articles

  • Guardian Is the staggeringly profitable business of scientific publishing bad for science?

  • The Atlantic The Scientific Paper Is Obsolete, Here’s what’s next.

  • Works in progress The speed of science

  • Guardian The big idea: should we get rid of the scientific paper?

  • Huffpost Academic Journals: The Most Profitable Obsolete Technology in History

Podcast

» How it works#

‣ ‣ Missions #

Communicatig research

Editorial

Quality check

Recognition

Marketing

Disseminating

In Depth Explanation

The most obvious role of the journal is the selection of material. This is mainly subject based, Does this item fall within the remit of the journal and/or would it be of interest to our readers?.

This is the part played by the referees. A major part of the effort that sets the reputation of a journal is carried out by the referees.

The copy editing and general page design that make a journal look professional is carried out by copy editors and other non-academic professionals.

In terms of importance this ranks first from the point of view of many authors

Marketing of the journal to possible readers and other customers, e.g. libraries.

The delivery of the information (in the form of the physical item) to the purchaser or reader

Actors#

Now let’s have a look at the different actors of the publication sector

Publisher types

# Articles

1

2

3

Commercial

Government

Independant

Institute

Non-Profit

Society

Society or institution

University

University Press

taken from [Morrison et al., 2022]

Note

To keep exctracting (don’t forget to keep up to date)

E-Publishing#

Arxiv#

PhysicsE-print Archive, founded by Paul Ginsparg [Ginsparg, 1994]

This "e-print archive" began as an experimental means of circumventing recognized inadequacies of research journals

Note

Insert JSOTR

Others e-publishing models#

  • [Swinnerton-Dyer, 1992]: Publishing model heavily influenced bythe paper model in operation and based around a centralised server

  • to ref

  • [Odlyzko, 1995]: outline model based on the interactive and less formal possibilities of net-based publishing

  • to ref: concerned mainly with the pre-formal communication stage between researchers

  • to ref: elaborates the earlier model to include a mechanism for peer-review.

  • [Ginsparg, 1997]: describes theoperation of a real working e-publishingmodel. In this case the question is notwhether it works (use of the PhysicsE-prints Archive is currently running ataround 70,000 connections per day6) butwhether the implicit model it embodies isapplicable to other areas of research.

    • It does (give example of bioarxiv, psyarxiv etc)

» Today

Society vs Commercial publishers#

  • ACS: American Chemical Society Link

  • RAS: Royal Astronomical Society

  • …

Note

  • May be can create a table to keep a log of the main ones

Are all of those society non-for-profit organizations? the ACS is non-profit but it is also condidered predatory for high journal price etc …

An example: Elsevier

now RELX

Owned journal:

  • 1

  • 2

Note

Publication pipeline

  • Preliminary screening by journal editor

  • Anonymous and private review by a very small number of individuals (2-5)

retractionwatch

» What is right

Peer Review

Peer Review is necessary

Journal template ?

Very often publishing fees are justified by the employment of an army of editors that needs to be paid by the journal. Now sit down and think about it, you are actually doing the editorial job by using the journal latex template!

Good and bad:

  • You know what you are going to get but:

  • prevent creativity in sharing scientific content.

  • Reproducibility crisis in Science.

  • Lots of redundancy

Experiments are not described efficiently in scientific papers and hence are hardly reproducible, especially when dealing with metastable samples (like ASW)

  • Processing softwares not always shared

  • Data in databases is not efficiently described and hard to extract, reprocess (give example)

Overall, Scientific work is published in a Boring way, even though every piece of Science is interesting.

Oligarchy of scientific publishing#

more on economics from improve publication model: online article

How much does it cost#

» What is wrong

Monetisation of knowledge

for the benefits of Journals

  • You need to pay to publish (not always, OK, but most of the time)

  • You need to pay to have access to publications.

Of course those “fees” are not paid by scientist themseleves, but rather by their institutions or funding bodies.

to the detriment of Researchers

  • Loss of property rights over your work

Interstingly, while I am writing those lines along with wrapping up my PhD thesis, I am not paid by my institution - Pretty cruel system don’t you think ?

  • Increased poverty amoung PhD students

  • slavery …

Doesn’t really matt]er because we are passionate about what we do right ?

Well passion doesn’t bring food in the table.

A Monopoly#

What do they do with that money ?#

Surveillance#
Blog/Posts/Scientific_publication/Docs/science_tracking.png

Fig. 18 To modify#

Open Access

Yes, some journals offers Open Access, but very often it is a costly options as you need to pay Article Processing Charges (APC). For Nature they cost 9500 Euros !! (source: Here)

****: Directory of Open Access Journals

Journal Ranking#

Prestige, not quality

Tools#

  • Sherpa romeo: online resource that aggregates and analyses publisher open access policies

Also, for me, the problem is deeper.

  • Too many journal titles, enclose researcher into very narrow fields.

  • Astro thesaurus example, many subfields but is there a need for as many journal

Make comparaison:

List of all Asrto journals

The cost of Scientific publication

Promote competition vs collaboration

In the current atmosphere of highly competitive and uncertain research funding, publications are instrumental in determining how resources are distributed, who gets promoted, and in which directions research advances. This has cultivated a publish or perish mentalitywhere the focus is on maximizing the number of publications rather than on the validity and reproducibility of research findings as well as a decrease in the amount of information apportioned to each articles. ([Ghosh et al., 2012] copied from Intro)

Metrics
Impact Factor

Hierarchical stature of a journal is determined by the Impact factor metrics.

  • Have overtaken the review process as arbiters of quality and significance of research.

  • Astronomy papers ranked. - Sample size: 89

Are metrics a good indicator of paper quality#

H-index

Scientist are judged by their number of publication to climb the accademic ladder. This is measured using metrics.

Hence we all tend to publish quick and numerous papers, rather than well and low number

  • Puts scientist away from their main mission, understanding the bigger picture

The scatter problem#

Peer Review

Yes, I include the Peer Review process in this section as there is many flaws associated with it when performed in the context of commercial publications. [Ghosh et al., 2012] identified five of them:

  • Reviewers are expected to have comprehensive expertise

  • Reviewers do not have

Pressure to publish#

Poor reproducability#

Crisis ?#

Ok but journal put things in place, but is it effective

Reproducability vs replicability#

Alternatives#

Altmetrics#

Manifesto

Note

To explore

Actors of Scientific Publishing#

Clarivate#

Wikipedia

Own:

  • Web of Science

  • Endnote

  • Journal Citation Report (Responsible for Impact Factor of many publications) - cf 2022 report

Revenus : 1,254 billion USD

Can we do better ?#

I am not the first one that have been asking this question

Below is a selection of a few articles from this special issue

How ?#

Note

  • a sneak look at the open source software development workflow

  • Learning from open source software projects to improve scientific review [Ghosh et al., 2012]

Describe:

Proposed system#

Describe:

Describe:

Open Research#

Alternatives#

Publishing Cooperatives#

Open Journals#

Note

Ask Ross about volcanology publication (free)

Law Aspects#

To Add#

Wrong#

  • Existing Formats Are Not Tailored for Knowledge Transfer

The recent development of new media and communicative possibilities using information technology, and the need to communicate and comprehend increasing amounts of additional information such as numerical and multimedia data, make the traditional forms inadequate. Continued reliance on paper documents and their electronic shadows make it very difficult or impossible to incorporate massive amounts of data, moving images or software; there is simply no natural way to associate such ancillary information ‘into’ the traditional publication. Additionally, any software-based text mining or information extraction procedures require that paper-based information first be converted into machine-tractable form and made freely available for such mining.

  • The Ever-Increasing Problem of Information Overload

Scholars have experienced information overload for more than a century [VICKERY, 1999] and the problem is just getting worse. Online access provides much better knowledge discovery and aggregation tools, but these tools struggle with the fragmentation of research communication caused by the rapid proliferation of increasingly specialized and overlapping journals, some with decreasing quality of reviewing.

  • Verifying Claims and Re-using Results

Even in the rare cases where the data are part of the research communication, these are typically relegated to the status of supplementary material, whose format [Murray-Rust, 2008] and preservation (find citation) are inadequate. At present it is difficult for a scholar easily and sustainably to record the data on which the work is based in a form that others can absorb and use, and to maintain links to the associated textual publication.

Best solution is to be in charge during the whole precess!

Note

  • Give example of astronomical (telescope) data

Other Problems#

Papermills#

Solution#

The Deconstructed Journeal#

Note

Looks interesting, to read

More#

Scientific revolution#

Note

Interesting but bulky (to read though)

Alternatives#

  • [Priem, 2013]

  • Review: [Herman et al., 2020]: Propose that journal transition can be splitted into 3 categories:

    • Enhanced models of the traditional scholarly journal

    • Innovative models of the traditional scholarly journal

    • Alternative modes of knowledge dissemination

Important Peoples#

Aaron Swartz

Manifesto

Scihub

JSTOR#

Contraction of journal storage

Solution to the increasing number of academic journals in existence.

Preprints#

Definition#

Components

reproduced from [Chiarelli et al., 2019]

  • Keep checking to implement citations

The type of output that a preprint is meant to be

  • part of the scientific literature

A preprint is a complete scientific manuscript

Litterature

The position of a preprint in the knowledge production process

  • prior to formal publication

A ‘preprint’ is typically a version of a research paper that is shared on an online platform prior to, or during, a formal peer review process.

Litterature

Preprints as different versions of an output at different stages of the outputs’ lifecycle

  • before peer review

Preprints are made available “before, or in parallel to, submitting them to journals for traditional peer review.”

Litterature

The availability of preprints

  • preprints are openly available online

A preprint “can be viewed without charge on the Web.

Litterature

The individual(s) responsible for posting preprints

  • normally the author

A preprint “is uploaded by the authors to a public server.

Litterature

The usefulness of preprints to readers

  • preprints are considered valuable

“A preprint is a research output that has not completed a typical publication pipeline but is of value to the community and deserving of being easily discovered and accessed.

Litterature

Beyond#

Commenting#

  • [Marra, 2018]: check the commenting options from Arxiv

Electronic publishing#

Other Kinds of Scientific publication#

Research Compendiums

Note

To check for examples

Overlay Journals#

Wikipedia

Replacement#

Digital publishing#

Business Model#

cyberlibris

For me#

To include (alternatives)

Interesting Stuffs:

» Alternatives ?

Note

Quick paragraph to explain the need and the revolutionary movement in the US

  • Science for the people link

Include: openscholarlyinfrastructure

Internet#

Note

To insert: number of internet user worldwilde: Statistics

Other forms of scientific publication#

Blog#

Good one in French

Comments


Notes


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  • Author: Vincent Deguin;

  • Status: flag alt > 🔎

  • Reviewed: ❌

  • Updated: 28/05/2023

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