vendredi 1 septembre 2023

English translation of my article "Critical analysis of manuscripts and advice to authors on how to improve them. About publications : Klebel et al., 2020, Stern and O'Shea, 2019; Sarabipour et al., 2019; Inrae, 2016."


This H. 2020. L'analyse critique des manuscrits et les conseils d'amélioration donnés aux auteurs, Notes académiques de l'Académie d'agriculture de France / Academic Notes from the French Academy of Agriculture (N3AF), 9(2), 1-14.

Correspondance :

Groupe de gastronomie moléculaire, AgroParisTech, 16 rue Claude Bernard, Paris



The development of digital systems of information and the increase of the number of manuscripts submitted to scientific journals have been triggering major changes in scientific publishing, in particular about what is called ''peer review''. In this article, the circumstances that generated the old organisation of scientific publishing are recalled, the individual and collective interests of various features of the system are analyzed, and the principles that can lead to a modernization of the publication process are discussed. Changes in terminology, as well as of editorial practices, are proposed.


scientific publishing, manuscript, journal, access, free, peer review


For several years now, digital information processing techniques have been revolutionising scientific and technological publishing. In particular, researchers and their supervisory bodies have taken note of the reduction in the workload of private publishers to whom journals were entrusted, at a time when a movement was developing in favour of free access to publications (Inra, 2016). These changes have been widely discussed by scientists and institutions such as INRAE (Inra, 2016), the Académie des sciences (Bach and Jérome, 2014) and the Académie d'agriculture de France (N3AF, 2016; This, 2016).

More recently, various methods of publishing scientific work have been proposed, notably in the articles which are the subject of this review and which are discussed, with particular emphasis on the last one (Kleber et al., 2020).

Peer review?

Let us begin by examining the basis of the system that is still widely used today, associated with the terms 'peer review', 'peer expertise', 'peer evaluation' or 'peer validation', depending on countries (Bach and Jérome, 2014; Naegelen, 2016). First of all, it should be noted that these expressions are not all the same as 'peer review', which would rather be 'report by peers', but above all it should be noted that these designations, as well as the current common practice that accompanies them, are neither universal nor fixed. Less than a century ago (in 1936 to be precise), Albert Einstein (1879-1955) withdrew a manuscript from an American journal to which he had submitted it, because the journal had asked for an evaluation of his text (by a young researcher). He wrote to the journal: "We (Mr Rosen and I) had sent you our manuscript for publication and had not authorized you to show it to specialists before it is printed. I see no reason to address the -in any case erroneous- comments of your anonymous expert. On the basis of this incident I prefer to publish the paper elsewhere" (Kennefick, 2005). In fact, an author who produces a text assumes responsibility for it, and the reports requested by journals can amount to undue censorship.

Before analysing this very general practice of modern scientific journals, let us discuss the terms of the expression that designates it. On the one hand, with regard to the second member (the 'peers'), we understand that there can be hesitation and abuse in claiming to be Einstein's 'peer', for example, at least if the term is taken in its original sense (TLFi, 2019a). Furthermore, even if value does not wait for the number of years, the evaluation of a manuscript sent by a seasoned scientist can be shocking when it is done by a young scientist who is still imperfectly trained, even if the publisher who requested the report is capable of filtering the comments and arbitrating in the event of disagreement. However, the current influx of manuscripts in high-impact factor journals (Vesper, 2018) is leading publishers to solicit all those they identify in a field close to that of the manuscript, which can lead to inconsistencies: from experience, I know of at least two "quality" international scientific journals (according to the "impact factor", considered good or excellent by scientific institutions) which have sent manuscripts for evaluation to very young colleagues in my group (PhD students at the start of their thesis, who, moreover, have asked me to help them with the report). In short, perhaps we should abandon the term "peers" when referring to the procedure we are discussing here, and simply speak of "rapporteurs" when a report is requested by a member of the editorial board of a publication.

What are these reviewers asked to do, anyway? The word "evaluation", in one of the expressions we are discussing here, is questionable, because the objective is not to know whether an article is bad, fair, good or excellent, but to lead to the publication of quality articles. To this end, the reviewers must above all identify shortcomings or opportunities for improvement, so that the reports, forwarded to the authors, lead them to prepare manuscripts that are as irreproachable as possible from a scientific and literary point of view, from the conceptual discussion of the results to the spelling mistakes. Ultimately, authors should be responsible for their texts, with the publisher reserving the right to accompany certain publications with "Comments" or "Letters to the Editor", which would discuss points of disagreement, particularly in the interpretation of results.

Do journals need these reports? Can they stop at Einstein's personal point of view? This would be to forget that the publication of a scientific article is part of a collective effort, that scientists are most often paid by institutions, and that, as a result, they must place their work 'in relation' to the community. It would also be naïve to believe that all scientists are honest and perfectly conscientious, that all those who submit manuscripts have always properly examined previous work, that their validations are always sufficient, and that their work is literarily faultless. Moreover, even if we retain Einstein's point of view, it takes a powerful mind to assume sole responsibility for its scientific output, and no one loses anything in any case by having their manuscript read before publication, in order to benefit from advice on how to improve the text. Less experienced authors, on the other hand, have every interest in benefiting from the expertise of the 'reviewers' and the 'journal' that accepts their manuscript for publication.

The reason why we have placed the words "rewiewers" and "jounral" in inverted commas is as follows: we shall see later that the first term is historically justified, but we shall observe without delay that the word "journal" no longer applies to modern, digital, online publication systems (TLFi, 2019b); it would be more accurate to consider "scientific publications", terms that we shall retain for the remainder of this text.

Finally, it can be seen that, especially in recent decades, publishers of scientific publications have found it reassuring and helpful to call on the services of referees, not only to ensure the quality of their publications, but also to help them filter through the excessive number of submissions they receive. However, before discussing possible changes to the system for scientific publications, in the light of the developments that have led to the current system, it should be noted that it is constructive critical review, not evaluation, that the scientific community needs, and we understand the value of a positive process for improving manuscripts, with a view to publishing good quality articles. So it's not a question of "evaluation", but of critical analysis, or help with publication, or constructive examination. Since the reviewers' job is not to pass an examination, we propose the expression "critical analysis of manuscripts", which we will use in the remainder of this text.

The evolution of the system

With these terminological discussions out of the way, an examination of the history of scientific publishing provides a better understanding of the current situation, as well as possible developments in the system.

Ray Spier (2002) finds the origin of the system of reports in medicine: in the 9th century, Shap bin Ali Al Rawhi published a Physician's Ethics, in which he proposed that practitioners should keep notes of their consultations, in order to justify their practice if necessary (Al Kazi, 1997; Ajlouni and Al-Khalidi, 1997).

Then, after the Renaissance, when a greater number of individuals engaged in the practice of 'natural philosophy', according to a methodology that was gradually made explicit thanks to Francis Bacon, Galileo and others (Bacon, 1620; Galileo, 1640), scientists (the term did not yet exist, as will be shown below) communicated directly with each other, either orally or by post. For their correspondence, they were responsible for copying their manuscripts for distribution, or having them printed at their own expense. Marin Mersenne (1588-1648), in France (Taussig, 2010), and Henry Oldenburg (1619-1677), in England (Boas Hall, 1965), put scientists in touch with each other, but it was undoubtedly the Journal des Sçavans, created by Denis de Sallo (1629 -1669) in 1665 (Rémond, 2015), and then the Philosophical Transactions, later the same year, that were the first institutional scientific publications. Oldenburg, in particular, was secretary of the Royal Society of London, and the journal enabled him to simplify his correspondence (Cocheris, 1860). Neither of these journals had a system of referees. In France, they appeared the following year, when King Louis XIV commissioned the Royal Academy of Sciences to evaluate inventions and discoveries. The academicians were paid by the State, and the government took account of their reports, which took precedence over the opinions of the Censor.

Thanks to the minutes of the Royal Academy of Sciences, we know the tasks assigned to the academicians. First and foremost, they had to monitor scientific and technical developments by reporting on publications and research carried out in the provinces or in other countries. The Académie was also, and above all, a place where scientific and technical research was "validated": any scientist who was not a member of the Académie could submit his or her discoveries or inventions, which were validated by a committee made up of two or three academicians. A favourable report is a form of recognition designed to encourage scientific vocations and technical innovation; it may lead to publication, under the patronage of the Académie, in the Mémoires des savants étrangers or in the Recueil des machines et inventions approuvé par l'Académie royale des sciences. This was often a first step towards a scientific career or, for inventors, an opportunity to obtain an exploitation privilege, the forerunner of the patent, or to raise funds from patrons (Chabot, 2017).

At the time, the word "expert" existed in French, but not in English: it meant the author of reports. In practice, the academics in charge of the reports were not referred to as experts; they were "rapporteurs" who were required not only to validate or reject the work presented, as mentioned above, but also to discuss both the form (logic of the plan, coherence of the assertions made) and the substance (recognition of the knowledge, validity of the experiences described, interest of the work). Once the reports had been dated and signed, they were forwarded to the Académie for its "ordinary work". The rapporteurs proposed either that the dissertation be rejected or approved, and sometimes that it be printed in academic journals (Mafarette-Dayries, 2000).

In 1699, when the Académie royale des sciences was reformed, Bernard Le Bovier de Fontenelle (1657-1757) invented a new genre, with the series of volumes of the Histoire et Mémoires de l'Académie royale des sciences covering the period from 1699 to 1740, for publication between 1702 and 1742 (Seguin, 2012); this model was adopted by his successors, at least until 1786. Each volume of the Histoire de l'Académie royale des sciences consisted of two sections, bound into a single volume but recognisable by their individual pagination. The first part, known as the Histoire, was written by the Académie's secrétaire perpétuel and ended with the Éloges des académiciens décédés dans l'année. The second part was the Memoirs, which contained the works presented by the academicians or sent by foreign correspondents and approved by the company.

The Histoire de l'Académie royale des sciences itself provided an overview of the activities of scientists during a calendar year, giving the reader a general overview of the main discoveries made during that time and providing the memoirs themselves in the second part (Table 1).

When an author writes alone, as Denis de Sallo did, he is free and responsible for his choices, but when a journal publishes the manuscripts of several authors, it has to make decisions: in 1752, following criticism of the Philosophical Transactions, the Royal Society of London set up a committee to decide on publications and prevent its choices from being seen as arbitrary. However, it was not until the early 19th century that the first system of rapporteurs - quite different from that of the Royal Academy of Sciences - was introduced by English scientific societies (Csiszar, 2016).

Indeed, after the publication in 1830 of Reflections on the Decline of Science in England by the mathematician and engineer Charles Babbage (1791-1871), the Cambridge physicist William Whewell (1794-1866) persuaded the Royal Society of London to ask for reports on manuscripts submitted for publication in the Philosophical Transactions: written by eminent scientists, these reports could "often be more interesting than the memoirs themselves" and "be a source of publicity for science" (Whewell, 1831).

At the time, the Royal Society of London was creating the Proceedings of the Royal Society, a less expensive monthly than the Philosophical Transactions, to include papers presented to the Society, and Whewell was less concerned with 'bad' manuscripts than with promoting science (it was he who introduced the term scientist). He volunteered to write the first report with one of his former Cambridge students, the mathematician and astronomer John William Lubbock (1803-1865), who was also Treasurer of the Royal Society. They selected a manuscript entitled On an inequality of Long Period in the Motions of the Earth and Venus, in which the astronomer George Biddell Airy (1801-1892) proposed mathematical methods for calculating the orbits of the Earth and Venus.

However, Whewell and Lubbock disagreed about the quality of the paper: Whewell felt that the question studied was essential and the conclusions remarkable; Lubbock, on the other hand, was critical of Airy's mathematical presentation, so the joint report was difficult to prepare. Whewell wrote to Lubbock: "I don't think the job of the rapporteurs is to criticise particular parts of the paper; it is rather to show its place", and he proposed, if necessary, to warn the authors of possible errors. Lubbock, on the other hand, found it "hard to see how we could ignore important errors".

Airy was irritated to be asked to improve his text: "The article is as it is, and I take responsibility for it", he wrote to Whewell. In the end, Lubbock only agreed to sign the final report because it was the first of its kind (Lubbock, 1832). The report was read publicly and printed in the Proceedings, while Airy's article appeared in the Transactions.

Shortly afterwards, the Astronomical Society of London and the Geological Society of London followed suit. It was the geologist George Bellas Greenough (1778-1855) who introduced the word referee in 1817, bringing a legal term into science (Despeaux, 2011): at the time, the word referee meant an individual to whom one referred, particularly for a decision or judgement.

The practice of reports became widespread in England and Scotland. However, according to the President of the Royal Society, Augustus Frederick, the system of reporters only worked well with people "elevated by their character and reputation above the influence of personal feelings of competition or petty jealousy" (Despeaux, 2011).

In 1833, the reports ceased to be published: they became confidential and anonymous. Then, in 1836, Whewell came to consider that referees should be guarantors of the quality of publications. However, as the Royal Academy of Sciences was well aware, the rejections that resulted from negative assessments gave rise to criticism: the execution of Antoine-Laurent de Lavoisier (1743-1794) has even been partly attributed to the animosity that arose from criticism of a manuscript submitted by Jean-Paul Marat (1743-1793). In 1845, a London magazine portrayed the referees as "full of jealousy, hatred, malice, devoid of charity" (Wade, 1845).

In 1892, a movement (based on the text On the Organisation of Science) proposed standardising the selection and distribution of scientific articles. Then, at the beginning of the 20th century, the idea of editors and reporters began to be generalised, in order to avoid "the spreading of rubbish in the pure stream of science" (Foster, 1894).

In 1903, the Geological Society of London explicitly questioned the practice of reporting, which was sometimes severely criticised. At the time, the rapporteur system was mainly practised in Great Britain and North America, where rapporteurs were the "backbone of science" (Ziman, 1968). The different practice in Germany, for example, explains the reaction of Einstein, who until then had published in German in the Annalen der Physik, which had an acceptance rate of 95% (Spicer and Roulet, 2014).

However, as early as 1920, it was observed that the system of referees, which was more complex than direct publication under the authors' responsibility, was an obstacle to scientific progress. Some even considered that examining manuscripts was an outdated practice, "which was useful in the past, but which should be overcome" (Csiszar, 2016). Finally, from the 1960s onwards, the expression "scientific community" appeared, and the "systems of rapporteurs" became "peer review" or "peer evaluation". In 1973, review by scientists became the rule for the journal Nature (Baldwin, 2015).

The advent of the Internet turned the system upside down: in 1991, a digital service ( was set up to share "pre-prints" (or "author manuscripts"), i.e. manuscripts that had not been examined, in order to avoid delaying the publication of important results (CNRS, 2020). This platform will be relocated to (Cornell University) at a later date, and is at the heart of the discussions on the analysis by the rapporteurs (, 2019).

Then, in 2006, the Public Library of Science launched a free journal, PLoS ONE, which no longer took account of the "importance" of the work, provided that it was of academic quality; publication costs were then borne by the authors. In 2007, the EMBO Journal, the Frontiers series and BMJ Open experimented with a free journal, publishing the names of the referees and their grades.

Other innovations are gradually appearing, one of the most recent being Peers Communities In... (PCI, 2019): this involves creating communities made up of scientists in the same field who read manuscripts deposited in "digital archives" such as or and "recommend" them; the system is free and "transparent", and the - signed - reports and recommendations can be consulted.

Above all, the many innovations that have resulted from the widespread use of digital methods of information processing, with the disappearance of page layout and printing tasks in particular, have led to the view that the services of private publishers have become virtually useless, allowing the scientific community to structure itself to avoid spending considerable sums (Bach and Jérome, 2014; PCI, 2019). These developments are encouraged by research institutions, such as INRAE for the fields covered by the Notes académiques de l'Académie d'agriculture de France: food, agriculture and the environment.

More generally, and without being exhaustive (the list is too long), it can be observed - particularly by reading the texts that are the subject of this review - that the proposals are evolving towards a model where neither authors nor readers pay any more, with an operational transparency that remains to be improved, but that is increasing (Klebel et al., 2020). The fact that authors no longer pay may help to avoid the conflicts of interest mentioned above, while the fact that readers no longer pay may allow better dissemination of the knowledge produced by science.

As a reminder, here are some of the key proposals for understanding the renovation of scientific publications:

- l'Appel de Jussieu (Collectif, 2017): this is a document issued by a group of French scientists who want to develop new publication models, calling for the formation of an international consortium of players to federate initiatives. One of the objectives is to move rapidly towards the open access publication model, without the open access model delaying the process.

- the platforms of the French National Environmental Research Agency (AllEnvi, 2017): here, the main objective is to recognise the author's manuscript (pre-print) as an acceptable form of scientific communication, as is the case in certain communities (mathematics, for example).

- Inrae's Openscience blog (2018): this is an Inrae charter to promote open access to publications, including the provision of data, with the aim of transparency and evidence in support of publications, and also with a view to facilitating the reuse of data, in order to accelerate innovation.

- the Episcience model (2020): this involves both traditional publications and open archives: the organisation aims to combine two open access paths: the "golden" path, which involves running open access journals, and the "green" path, where articles are submitted for publication by deposit in an open archive.

- Peer Community In... (PCI, 2020): already mentioned, these communities are based on networks of specialists and recommenders who label manuscripts or texts.


In all recent discussions on scientific publication, there is a broad consensus in favour of the idea that published texts should be of high quality, which obviously requires explicit quality criteria. Some journals include such criteria in their "advice to authors" (AAS, 2019; Liumbruno et al., 2013). On the other hand, there is a list of defects to be corrected (Table 2) (Davies, 1974; Kamat et al., 2012; Kamat et al., 2014a; Kamat et al., 2014b). Obviously the list is long, but the bibliography compiled by Liumbruno et al. (2013) could be completed, in particular with Manske (2006) or Amrhein (2019).

This being the case, and even with good manuscripts, the question of the saturation of the current scientific publication system remains, which has led the scientific community to look for new publication methods. Various attempts have been made by different communities, which have in common that they want to benefit from new possibilities (IT) and no longer have to bear the costs of the old system (considered excessive), where the management of journals was often entrusted, or delegated, to private companies. Various groups, such as (in France) the Académie des sciences, Inrae, the CNRS and the Académie d'agriculture de France (Bach and Jérome, 2016; N3AF, 2016; Inra, 2016; CNRS, 2020) have discussed the possibilities and recommended solutions.

In the current discussions, some people are still afraid of exchanges with rapporteurs, and the excessive importance of the latter (Sarabipour, 2019), often because they continue to think in terms of "evaluation", but the proposal for critical review and advice to authors, with the aim of publishing texts when they are of sufficient quality, helps to dispel this fear. Moreover, the presence of these critical analyses certainly leads some authors to seek greater quality in their manuscripts than if they were assured of immediate, automatic publication.

In any case, Davies (1974) clearly explains the reasons why double anonymity (authors do not know who the referees are and vice versa) seems to be the rule, although this does not mean that anonymity cannot be lifted if the referees agree. The members of the editorial committees, on the other hand, must do a better job of identifying abuses by the referees, and of arbitrating.

Finally, while some have proposed open critical analysis, on the assumption that this would be the best way of avoiding malicious comments, putting an end to plagiarism, preventing reviewers from sticking solely to their analysis and encouraging honest and open scrutiny, the response has been that the analysis would be distorted, since politeness and fear of reprisals may lead reviewers to play down their criticisms.

Disputes over precedence, which have been raised in many discussions on the critical analysis of manuscripts, are at the origin of open archives, but it should be noted that the Académie des Sciences' system of sealed envelopes has existed for a very long time: the digital equivalent of this system is sufficient to establish precedence. What's more, just as publications now ask reviewers to avoid conflicts of interest that would lead to excessively complacent critical analyses (Elsevier, 2019), it is not difficult to propose that competition should be explicitly indicated (Rodman, 1970). Such a system would also have the added advantage of reducing the criticism sometimes levelled by authors at publications, concerning delays that would handicap them in international competition.

In reality, the experience of editorial boards shows that, often, authors demand rapid reactions while they themselves are slow to make the requested changes. On the other hand, scientific publishing knows well that, despite numerous rereadings, imperfections remain in the published texts: this is a reason not to publish hastily, especially if a manuscript deposit system is put in place.
Despite innovations, it is undoubtedly illusory to believe that we will be able to completely avoid the publication of bad articles, but the scientific community has every interest in the greatest vigilance regarding the analysis of manuscripts, and this is in By making editorial committees more active, there is a chance of improving the system. This improvement seems to involve better recognition of the work of the rapporteurs.
Finally, we see that our scientific communities have everything to gain from using digital methods to develop scientific publications. The work of critical analysis and advice given to authors, carried out in double anonymity, from officially submitted manuscripts, is more necessary than ever, and funding recovered from expensive subscriptions would benefit from being directed towards the development of renovated methods so that these analyzes are carried out under better conditions, reducing the work of rapporteurs who must be better recognized by research institutions.


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Edité par

Nadine Vivier, présidente de l'Académie d'agriculture de France.


Claude Debru est philosophe des sciences, professeur émérite à l'Ecole normale supérieure, membre de l'Académie des sciences, et membre de l'Académie d'agriculture de France.

Alain Pavé, biométricien, professeur émérite à l’Université Claude Bernard Lyon 1, membre de l’Académie des technologies et membre correspondant de l’Académie d'agriculture de France.


Cet article a été publié dans la rubrique « Notes de lecture » des Notes académiques de l'Académie d'agriculture de France.


9 décembre 2019


6 mars 2020


16 mars 2020

Hervé This est physico-chimiste dans l'UMR 0782 SayFood, directeur de l’Inrae-AgroParisTech International Centre for Molecular and Physical Gastronomy, professeur consultant à AgroParisTech, membre de l'Académie d'agriculture de France, membre correspondant de l'Académie royale des sciences, arts et lettres de Belgique et de l'Académie de Stanislas, membre de l'Académie d'Alsace, sciences, lettres et arts.

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