Search This Blog

Wednesday, April 16, 2025

Academic publishing

From Wikipedia, the free encyclopedia
Scientific and technical journal publications per million residents of the world as of 2020

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. The part of academic written output that is not formally published but merely printed up or posted on the Internet is often called "grey literature". Most scientific and scholarly journals, and many academic and scholarly books, though not all, are based on some form of peer review or editorial refereeing to qualify texts for publication. Peer review quality and selectivity standards vary greatly from journal to journal, publisher to publisher, and field to field.

Most established academic disciplines have their own journals and other outlets for publication, although many academic journals are somewhat interdisciplinary, and publish work from several distinct fields or subfields. There is also a tendency for existing journals to divide into specialized sections as the field itself becomes more specialized. Along with the variation in review and publication procedures, the kinds of publications that are accepted as contributions to knowledge or research differ greatly among fields and subfields. In the sciences, the desire for statistically significant results leads to publication bias.

Academic publishing is undergoing major changes as it makes the transition from the print to the electronic format. Business models are different in the electronic environment. Since the early 1990s, licensing of electronic resources, particularly journals, has been very common. An important trend, particularly with respect to journals in the sciences, is open access via the Internet. In open access publishing, a journal article is made available free for all on the web by the publisher at the time of publication.

Both open and closed journals are sometimes funded by the author paying an article processing charge, thereby shifting some fees from the reader to the researcher or their funder. Many open or closed journals fund their operations without such fees and others use them in predatory publishing. The Internet has facilitated open access self-archiving, in which authors themselves make a copy of their published articles available free for all on the web. Some important results in mathematics have been published only on arXiv.

History

The Journal des sçavans (later spelled Journal des savants), established by Denis de Sallo, was the earliest academic journal published in Europe. Its content included obituaries of famous men, church history, and legal reports. The first issue appeared as a twelve-page quarto pamphlet on Monday, 5 January 1665, shortly before the first appearance of the Philosophical Transactions of the Royal Society, on 6 March 1665.

The publishing of academic journals has started in the 17th century, and expanded greatly in the 19th. At that time, the act of publishing academic inquiry was controversial and widely ridiculed. It was not at all unusual for a new discovery to be announced as a monograph, reserving priority for the discoverer, but indecipherable for anyone not in on the secret: both Isaac Newton and Leibniz used this approach. However, this method did not work well. Robert K. Merton, a sociologist, found that 92% of cases of simultaneous discovery in the 17th century ended in dispute. The number of disputes dropped to 72% in the 18th century, 59% by the latter half of the 19th century, and 33% by the first half of the 20th century. The decline in contested claims for priority in research discoveries can be credited to the increasing acceptance of the publication of papers in modern academic journals, with estimates suggesting that around 50 million journal articles have been published since the first appearance of the Philosophical Transactions. The Royal Society was steadfast in its not-yet-popular belief that science could only move forward through a transparent and open exchange of ideas backed by experimental evidence.

Early scientific journals embraced several models: some were run by a single individual who exerted editorial control over the contents, often simply publishing extracts from colleagues' letters, while others employed a group decision-making process, more closely aligned to modern peer review. It was not until the middle of the 20th century that peer review became the standard.

The COVID-19 pandemic hijacked the entire world of basic and clinical science, with unprecedented shifts in funding priorities worldwide and a boom in medical publishing, accompanied by an unprecedented increase in the number of publications. Preprints servers become much popular during the pandemic, the Covid situation has an impact also on traditional peer-review. The pandemic has also deepened the western monopoly of science-publishing, "by August 2021, at least 210,000 new papers on covid-19 had been published, according to a Royal Society study. Of the 720,000-odd authors of these papers, nearly 270,000 were from the US, the UK, Italy or Spain."

Publishers and business aspects

In the 1960s and 1970s, commercial publishers began to selectively acquire "top-quality" journals that were previously published by nonprofit academic societies. When the commercial publishers raised the subscription prices significantly, they lost little of the market, due to the inelastic demand for these journals. Although there are over 2,000 publishers, five for-profit companies (Reed Elsevier, Springer Science+Business Media, Wiley-Blackwell, Taylor & Francis, and SAGE) accounted for 50% of articles published in 2013. (Since 2013, Springer Science+Business Media has undergone a merger to form an even bigger company named Springer Nature.) Available data indicate that these companies have profit margins of around 40% making it one of the most profitable industries, especially compared to the smaller publishers, which likely operate with low margins. These factors have contributed to the "serials crisis" – total expenditures on serials increased 7.6% per year from 1986 to 2005, yet the number of serials purchased increased an average of only 1.9% per year.

Unlike most industries, in academic publishing the two most important inputs are provided "virtually free of charge". These are the articles and the peer review process. Publishers argue that they add value to the publishing process through support to the peer review group, including stipends, as well as through typesetting, printing, and web publishing. Investment analysts, however, have been skeptical of the value added by for-profit publishers, as exemplified by a 2005 Deutsche Bank analysis which stated that "we believe the publisher adds relatively little value to the publishing process... We are simply observing that if the process really were as complex, costly and value-added as the publishers protest that it is, 40% margins wouldn't be available."

Crisis

A crisis in academic publishing is "widely perceived"; the apparent crisis has to do with the combined pressure of budget cuts at universities and increased costs for journals (the serials crisis). The university budget cuts have reduced library budgets and reduced subsidies to university-affiliated publishers. The humanities have been particularly affected by the pressure on university publishers, which are less able to publish monographs when libraries can not afford to purchase them. For example, the ARL found that in "1986, libraries spent 44% of their budgets on books compared with 56% on journals; twelve years later, the ratio had skewed to 28% and 72%." Meanwhile, monographs are increasingly expected for tenure in the humanities. In 2002 the Modern Language Association expressed hope that electronic publishing would solve the issue.

In 2009 and 2010, surveys and reports found that libraries faced continuing budget cuts, with one survey in 2009 finding that 36% of UK libraries had their budgets cut by 10% or more, compared to 29% with increased budgets. In the 2010s, libraries began more aggressive cost cutting with the leverage of open access and open data. Data analysis with open source tools like Unpaywall Journals empowered library systems in reducing their subscription costs by 70% with the cancellation of the big deal with publishers like Elsevier.

Academic journal publishing reform

Several models are being investigated, such as open publication models or adding community-oriented features. It is also considered that "Online scientific interaction outside the traditional journal space is becoming more and more important to academic communication". In addition, experts have suggested measures to make the publication process more efficient in disseminating new and important findings by evaluating the worthiness of publication on the basis of the significance and novelty of the research finding.

Scholarly paper

In academic publishing, a paper is an academic work that is usually published in an academic journal. It contains original research results or reviews existing results. Such a paper, also called an article, will only be considered valid if it undergoes a process of peer review by one or more referees (who are academics in the same field) who check that the content of the paper is suitable for publication in the journal. A paper may undergo a series of reviews, revisions, and re-submissions before finally being accepted or rejected for publication. This process typically takes several months. Next, there is often a delay of many months (or in some fields, over a year) before an accepted manuscript appears. This is particularly true for the most popular journals where the number of accepted articles often outnumbers the space for printing. Due to this, many academics self-archive a 'preprint' or 'postprint' copy of their paper for free download from their personal or institutional website.

Some journals, particularly newer ones, are now published in electronic form only. Paper journals are now generally made available in electronic form as well, both to individual subscribers, and to libraries. Almost always these electronic versions are available to subscribers immediately upon publication of the paper version, or even before; sometimes they are also made available to non-subscribers, either immediately (by open access journals) or after an embargo of anywhere from two to twenty-four months or more, in order to protect against loss of subscriptions. Journals having this delayed availability are sometimes called delayed open access journals. Ellison in 2011 reported that in economics the dramatic increase in opportunities to publish results online has led to a decline in the use of peer-reviewed articles.

Categories of papers

An academic paper typically belongs to some particular category such as:

Note: Law review is the generic term for a journal of legal scholarship in the United States, often operating by rules radically different from those for most other academic journals.

Peer review

Peer review is a central concept for most academic publishing; other scholars in a field must find a work sufficiently high in quality for it to merit publication. A secondary benefit of the process is an indirect guard against plagiarism since reviewers are usually familiar with the sources consulted by the author(s). The origins of routine peer review for submissions dates to 1752 when the Royal Society of London took over official responsibility for Philosophical Transactions. However, there were some earlier examples.

While journal editors largely agree the system is essential to quality control in terms of rejecting poor quality work, there have been examples of important results that are turned down by one journal before being taken to others. Rena Steinzor wrote:

Perhaps the most widely recognized failing of peer review is its inability to ensure the identification of high-quality work. The list of important scientific papers that were initially rejected by peer-reviewed journals goes back at least as far as the editor of Philosophical Transaction's 1796 rejection of Edward Jenner's report of the first vaccination against smallpox.

"Confirmatory bias" is the unconscious tendency to accept reports which support the reviewer's views and to downplay those which do not. Experimental studies show the problem exists in peer reviewing.

There are various types of peer review feedback that may be given prior to publication, including but not limited to:

  • Single-blind peer review
  • Double-blind peer review
  • Open peer review

Rejection rate

The possibility of rejections of papers is an important aspect in peer review. The evaluation of quality of journals is based also on rejection rate. The best journals have the highest rejection rates (around 90–95%). American Psychological Association journals' rejection rates ranged "from a low of 35 per cent to a high of 85 per cent." The complement is called "acceptance rate".

Publishing process

The process of academic publishing, which begins when authors submit a manuscript to a publisher, is divided into two distinct phases: peer review and production.

The process of peer review is organized by the journal editor and is complete when the content of the article, together with any associated images, data, and supplementary material are accepted for publication. The peer review process is increasingly managed online, through the use of proprietary systems, commercial software packages, or open source and free software. A manuscript undergoes one or more rounds of review; after each round, the author(s) of the article modify their submission in line with the reviewers' comments; this process is repeated until the editor is satisfied and the work is accepted.

The production process, controlled by a production editor or publisher, then takes an article through copy editing, typesetting, inclusion in a specific issue of a journal, and then printing and online publication. Academic copy editing seeks to ensure that an article conforms to the journal's house style, that all of the referencing and labelling is correct, and that the text is consistent and legible; often this work involves substantive editing and negotiating with the authors. Because the work of academic copy editors can overlap with that of authors' editors, editors employed by journal publishers often refer to themselves as "manuscript editors". During this process, copyright is often transferred from the author to the publisher.

In the late 20th century author-produced camera-ready copy has been replaced by electronic formats such as PDF. The author will review and correct proofs at one or more stages in the production process. The proof correction cycle has historically been labour-intensive as handwritten comments by authors and editors are manually transcribed by a proof reader onto a clean version of the proof. In the early 21st century, this process was streamlined by the introduction of e-annotations in Microsoft Word, Adobe Acrobat, and other programs, but it still remained a time-consuming and error-prone process. The full automation of the proof correction cycles has only become possible with the onset of online collaborative writing platforms, such as Authorea, Google Docs, Overleaf, and various others, where a remote service oversees the copy-editing interactions of multiple authors and exposes them as explicit, actionable historic events. At the end of this process, a final version of record is published.

From time to time some published journal articles have been retracted for different reasons, including research misconduct.

Citations

Academic authors cite sources they have used, in order to support their assertions and arguments and to help readers find more information on the subject. It also gives credit to authors whose work they use and helps avoid plagiarism. The topic of dual publication (also known as self-plagiarism) has been addressed by the Committee on Publication Ethics (COPE), as well as in the research literature itself.

Each scholarly journal uses a specific format for citations (also known as references). Among the most common formats used in research papers are the APA, CMS, and MLA styles.

The American Psychological Association (APA) style is often used in the social sciences. The Chicago Manual of Style (CMS) is used in business, communications, economics, and social sciences. The CMS style uses footnotes at the bottom of page to help readers locate the sources. The Modern Language Association (MLA) style is widely used in the humanities.

Publishing by discipline

Natural sciences

Shares of the top five STM publishers in 2010 and 2020

Scientific, technical, and medical (STM) literature is a large industry which generated $23.5 billion in revenue in 2011; $9.4 billion of that was specifically from the publication of English-language scholarly journals. The overall number of journals contained in the WOS database increased from around 8,500 in 2010 to around 9,400 in 2020, while the number of articles published increased from around 1.1 million in 2010 to 1.8 million in 2020.

Most scientific research is initially published in scientific journals and considered to be a primary source. Technical reports, for minor research results and engineering and design work (including computer software), round out the primary literature. Secondary sources in the sciences include articles in review journals (which provide a synthesis of research articles on a topic to highlight advances and new lines of research), and books for large projects, broad arguments, or compilations of articles. Tertiary sources might include encyclopedias and similar works intended for broad public consumption or academic libraries.

A partial exception to scientific publication practices is in many fields of applied science, particularly that of U.S. computer science research. An equally prestigious site of publication within U.S. computer science are some academic conferences. Reasons for this departure include a large number of such conferences, the quick pace of research progress, and computer science professional society support for the distribution and archiving of conference proceedings.

Since 2022, the Belgian web portal Cairn.info is open to STM.

Social sciences

Publishing in the social sciences is very different in different fields. Some fields, like economics, may have very "hard" or highly quantitative standards for publication, much like the natural sciences. Others, like anthropology or sociology, emphasize field work and reporting on first-hand observation as well as quantitative work. Some social science fields, such as public health or demography, have significant shared interests with professions like law and medicine, and scholars in these fields often also publish in professional magazines.

Humanities

Publishing in the humanities is in principle similar to publishing elsewhere in the academy; a range of journals, from general to extremely specialized, are available, and university presses issue many new humanities books every year. The arrival of online publishing opportunities has radically transformed the economics of the field and the shape of the future is controversial. Unlike science, where timeliness is critically important, humanities publications often take years to write and years more to publish. Unlike the sciences, research is most often an individual process and is seldom supported by large grants. Journals rarely make profits and are typically run by university departments.

The following describes the situation in the United States. In many fields, such as literature and history, several published articles are typically required for a first tenure-track job, and a published or forthcoming book is now often required before tenure. Some critics complain that this de facto system has emerged without thought to its consequences; they claim that the predictable result is the publication of much shoddy work, as well as unreasonable demands on the already limited research time of young scholars. To make matters worse, the circulation of many humanities journals in the 1990s declined to almost untenable levels, as many libraries cancelled subscriptions, leaving fewer and fewer peer-reviewed outlets for publication; and many humanities professors' first books sell only a few hundred copies, which often does not pay for the cost of their printing. Some scholars have called for a publication subvention of a few thousand dollars to be associated with each graduate student fellowship or new tenure-track hire, in order to alleviate the financial pressure on journals.

Open access journals

Under Open Access, the content can be freely accessed and reused by anyone in the world using an Internet connection. The terminology going back to Budapest Open Access Initiative, Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities, and Bethesda Statement on Open Access Publishing. The impact of the work available as Open Access is maximised because, quoting the Library of Trinity College Dublin:

  • Potential readership of Open Access material is far greater than that for publications where the full-text is restricted to subscribers.
  • Details of contents can be read by specialised web harvesters.
  • Details of contents also appear in normal search engines like Google, Google Scholar, Yahoo, etc.

Open Access is often confused with specific funding models such as Article Processing Charges (APC) being paid by authors or their funders, sometimes misleadingly called "open access model". The reason this term is misleading is due to the existence of many other models, including funding sources listed in the original the Budapest Open Access Initiative Declaration: "the foundations and governments that fund research, the universities and laboratories that employ researchers, endowments set up by discipline or institution, friends of the cause of open access, profits from the sale of add-ons to the basic texts, funds freed up by the demise or cancellation of journals charging traditional subscription or access fees, or even contributions from the researchers themselves". For more recent open public discussion of open access funding models, see Flexible membership funding model for Open Access publishing with no author-facing charges.

Prestige journals using the APC model often charge several thousand dollars. Oxford University Press, with over 300 journals, has fees ranging from £1000-£2500, with discounts of 50% to 100% to authors from developing countries. Wiley Blackwell has 700 journals available, and they charge different amounts for each journal. Springer, with over 2600 journals, charges US$3000 or EUR 2200 (excluding VAT). A study found that the average APC (ensuring open access) was between $1,418 and US$2,727.

The online distribution of individual articles and academic journals then takes place without charge to readers and libraries. Most open access journals remove all the financial, technical, and legal barriers Archived 2021-05-06 at the Wayback Machine that limit access to academic materials to paying customers. The Public Library of Science and BioMed Central are prominent examples of this model.

Fee-based open access publishing has been criticized on quality grounds, as the desire to maximize publishing fees could cause some journals to relax the standard of peer review. Although, similar desire is also present in the subscription model, where publishers increase numbers or published articles in order to justify raising their fees. It may be criticized on financial grounds as well because the necessary publication or subscription fees have proven to be higher than originally expected. Open access advocates generally reply that because open access is as much based on peer reviewing as traditional publishing, the quality should be the same (recognizing that both traditional and open access journals have a range of quality). In several regions, including the Arab world, the majority of university academics prefer open access publishing without author fees, as it promotes equal access to information and enhances scientific advancement, a previously unexplored but crucial topic for the region's higher education. It has also been argued that good science done by academic institutions who cannot afford to pay for open access might not get published at all, but most open access journals permit the waiver of the fee for financial hardship or authors in underdeveloped countries. In any case, all authors have the option of self-archiving their articles in their institutional repositories or disciplinary repositories in order to make them open access, whether or not they publish them in a journal.

If they publish in a Hybrid open access journal, authors or their funders pay a subscription journal a publication fee to make their individual article open access. The other articles in such hybrid journals are either made available after a delay or remain available only by subscription. Most traditional publishers (including Wiley-Blackwell, Oxford University Press, and Springer Science+Business Media) have already introduced such a hybrid option, and more are following. The fraction of the authors of a hybrid open access journal that makes use of its open access option can, however, be small. It also remains unclear whether this is practical in fields outside the sciences, where there is much less availability of outside funding. In 2006, several funding agencies, including the Wellcome Trust and several divisions of the Research Councils in the UK announced the availability of extra funding to their grantees for such open access journal publication fees.

In May 2016, the Council for the European Union agreed that from 2020 all scientific publications as a result of publicly funded research must be freely available. It also must be able to optimally reuse research data. To achieve that, the data must be made accessible, unless there are well-founded reasons for not doing so, for example, intellectual property rights or security or privacy issues.

Growth

In recent decades there has been a growth in academic publishing in developing countries as they become more advanced in science and technology. Although the large majority of scientific output and academic documents are produced in developed countries, the rate of growth in these countries has stabilized and is much smaller than the growth rate in some of the developing countries. The fastest scientific output growth rate over the last two decades has been in the Middle East and Asia with Iran leading with an 11-fold increase followed by the Republic of Korea, Turkey, Cyprus, China, and Oman. In comparison, the only G8 countries in top 20 ranking with fastest performance improvement are, Italy which stands at tenth and Canada at 13th globally.[

By 2004, it was noted that the output of scientific papers originating from the European Union had a larger share of the world's total from 36.6% to 39.3% and from 32.8% to 37.5% of the "top one per cent of highly cited scientific papers". However, the United States' output dropped from 52.3% to 49.4% of the world's total, and its portion of the top one percent dropped from 65.6% to 62.8%.

Iran, China, India, Brazil, and South Africa were the only developing countries among the 31 nations that produced 97.5% of the most cited scientific articles in a study published in 2004. The remaining 162 countries contributed less than 2.5%. The Royal Society in a 2011 report stated that in share of English scientific research papers the United States was first followed by China, the UK, Germany, Japan, France, and Canada. The report predicted that China would overtake the United States sometime before 2020, possibly as early as 2013. China's scientific impact, as measured by other scientists citing the published papers the next year, is smaller although also increasing. Developing countries continue to find ways to improve their share, given research budget constraints and limited resources.

Role for publishers in scholarly communication

There is increasing frustration amongst OA advocates, with what is perceived as resistance to change on the part of many of the established academic publishers. Publishers are often accused of capturing and monetising publicly funded research, using free academic labour for peer review, and then selling the resulting publications back to academia at inflated profits. Such frustrations sometimes spill over into hyperbole, of which "publishers add no value" is one of the most common examples.

However, scholarly publishing is not a simple process, and publishers do add value to scholarly communication as it is currently designed. Kent Anderson maintains a list of things that journal publishers do which currently contains 102 items and has yet to be formally contested from anyone who challenges the value of publishers. Many items on the list could be argued to be of value primarily to the publishers themselves, e.g. "Make money and remain a constant in the system of scholarly output". However, others provide direct value to researchers and research in steering the academic literature. This includes arbitrating disputes (e.g. over ethics, authorship), stewarding the scholarly record, copy-editing, proofreading, type-setting, styling of materials, linking the articles to open and accessible datasets, and (perhaps most importantly) arranging and managing scholarly peer review. The latter is a task that should not be underestimated as it effectively entails coercing busy people into giving their time to improve someone else's work and maintain the quality of the literature. Not to mention the standard management processes for large enterprises, including infrastructure, people, security, and marketing. All of these factors contribute in one way or another to maintaining the scholarly record.

It could be questioned though, whether these functions are actually necessary to the core aim of scholarly communication, namely, dissemination of research to researchers and other stakeholders such as policy makers, economic, biomedical and industrial practitioners as well as the general public. Above, for example, we question the necessity of the current infrastructure for peer review, and if a scholar-led crowdsourced alternative may be preferable. In addition, one of the biggest tensions in this space is associated with the question if for-profit companies (or the private sector) should be allowed to be in charge of the management and dissemination of academic output and execute their powers while serving, for the most part, their own interests. This is often considered alongside the value added by such companies, and therefore the two are closely linked as part of broader questions on appropriate expenditure of public funds, the role of commercial entities in the public sector, and issues around the privatisation of scholarly knowledge.

Publishing could certainly be done at a lower cost than common at present. There are significant researcher-facing inefficiencies in the system including the common scenario of multiple rounds of rejection and resubmission to various venues as well as the fact that some publishers profit beyond reasonable scale. What is missing most from the current publishing market, is transparency about the nature and the quality of the services publishers offer. This would allow authors to make informed choices, rather than decisions based on indicators that are unrelated to research quality, such as the JIF. All the above questions are being investigated and alternatives could be considered and explored. Yet, in the current system, publishers still play a role in managing processes of quality assurance, interlinking and findability of research. As the role of scholarly publishers within the knowledge communication industry continues to evolve, it is seen as necessary that they can justify their operation based on the intrinsic value that they add, and combat the perception that they add no value to the process.

Peer review

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Peer_review
A reviewer at the American National Institutes of Health evaluating a grant proposal

Peer review is the evaluation of work by one or more people with similar competencies as the producers of the work (peers). It functions as a form of self-regulation by qualified members of a profession within the relevant field. Peer review methods are used to maintain quality standards, improve performance, and provide credibility. In academia, scholarly peer review is often used to determine an academic paper's suitability for publication. Peer review can be categorized by the type of activity and by the field or profession in which the activity occurs, e.g., medical peer review. It can also be used as a teaching tool to help students improve writing assignments.

Henry Oldenburg (1619–1677) was a German-born British philosopher who is seen as the 'father' of modern scientific peer review. It developed over the following centuries with, for example, the journal Nature making it standard practice in 1973. The term "peer review" was first used in the early 1970s. A monument to peer review has been at the Higher School of Economics in Moscow since 2017.

Professional

Professional peer review focuses on the performance of professionals, with a view to improving quality, upholding standards, or providing certification. In academia, peer review is used to inform decisions related to faculty advancement and tenure.

A prototype professional peer review process was recommended in the Ethics of the Physician written by Ishāq ibn ʻAlī al-Ruhāwī (854–931). He stated that a visiting physician had to make duplicate notes of a patient's condition on every visit. When the patient was cured or had died, the notes of the physician were examined by a local medical council of other physicians, who would decide whether the treatment had met the required standards of medical care.

Professional peer review is common in the field of health care, where it is usually called clinical peer review. Further, since peer review activity is commonly segmented by clinical discipline, there is also physician peer review, nursing peer review, dentistry peer review, etc. Many other professional fields have some level of peer review process: accounting, law, engineering (e.g., software peer review, technical peer review), aviation, and even forest fire management.

Peer review is used in education to achieve certain learning objectives, particularly as a tool to reach higher order processes in the affective and cognitive domains as defined by Bloom's taxonomy. This may take a variety of forms, including closely mimicking the scholarly peer review processes used in science and medicine.

Scholarly

Scholarly peer review or academic peer review (also known as refereeing) is the process of having a draft version of a researcher's methods and findings reviewed (usually anonymously) by experts (or "peers") in the same field. Peer review is widely used for helping the academic publisher (that is, the editor-in-chief, the editorial board or the program committee) decide whether the work should be accepted, considered acceptable with revisions, or rejected for official publication in an academic journal, a monograph or in the proceedings of an academic conference. If the identities of authors are not revealed to each other, the procedure is called dual-anonymous peer review.

Academic peer review requires a community of experts in a given (and often narrowly defined) academic field, who are qualified and able to perform reasonably impartial review. Impartial review, especially of work in less narrowly defined or inter-disciplinary fields, may be difficult to accomplish, and the significance (good or bad) of an idea may never be widely appreciated among its contemporaries. Peer review is generally considered necessary to academic quality and is used in most major scholarly journals. However, peer review does not prevent publication of invalid research, and as experimentally controlled studies of this process are difficult to arrange, direct evidence that peer review improves the quality of published papers is scarce.

Medical

Medical peer review may be distinguished in four classifications:

  1. Clinical peer review is a procedure for assessing a patient's involvement with experiences of care. It is a piece of progressing proficient practice assessment and centered proficient practice assessment—significant supporters of supplier credentialing and privileging.
  2. Peer evaluation of clinical teaching skills for both physicians and nurses.
  3. Scientific peer review of journal articles.
  4. A secondary round of peer review for the clinical value of articles concurrently published in medical journals.

Additionally, "medical peer review" has been used by the American Medical Association to refer not only to the process of improving quality and safety in health care organizations, but also to the process of rating clinical behavior or compliance with professional society membership standards. The clinical network believes it to be the most ideal method of guaranteeing that distributed exploration is dependable and that any clinical medicines that it advocates are protected and viable for individuals. Thus, the terminology has poor standardization and specificity, particularly as a database search term.

Technical

In engineering, technical peer review is a type of engineering review. Technical peer reviews are a well-defined review process for finding and fixing defects, conducted by a team of peers with assigned roles. Technical peer reviews are carried out by peers representing areas of life cycle affected by material being reviewed (usually limited to 6 or fewer people). Technical peer reviews are held within development phases, between milestone reviews, on completed products or completed portions of products.

Government policy

The European Union has been using peer review in the "Open Method of Co-ordination" of policies in the fields of active labour market policy since 1999. In 2004, a program of peer reviews started in social inclusion. Each program sponsors about eight peer review meetings in each year, in which a "host country" lays a given policy or initiative open to examination by half a dozen other countries and the relevant European-level NGOs. These usually meet over two days and include visits to local sites where the policy can be seen in operation. The meeting is preceded by the compilation of an expert report on which participating "peer countries" submit comments. The results are published on the web.

The United Nations Economic Commission for Europe, through UNECE Environmental Performance Reviews, uses peer review, referred to as "peer learning", to evaluate progress made by its member countries in improving their environmental policies.

The State of California is the only U.S. state to mandate scientific peer review. In 1997, the Governor of California signed into law Senate Bill 1320 (Sher), Chapter 295, statutes of 1997, which mandates that, before any CalEPA Board, Department, or Office adopts a final version of a rule-making, the scientific findings, conclusions, and assumptions on which the proposed rule are based must be submitted for independent external scientific peer review. This requirement is incorporated into the California Health and Safety Code Section 57004.

Pedagogical

Peer review, or student peer assessment, is the method by which editors and writers work together in hopes of helping the author establish and further flesh out and develop their own writing. Peer review is widely used in secondary and post-secondary education as part of the writing process. This collaborative learning tool involves groups of students reviewing each other's work and providing feedback and suggestions for revision. Rather than a means of critiquing each other's work, peer review is often framed as a way to build connection between students and help develop writers' identity. While widely used in English and composition classrooms, peer review has gained popularity in other disciplines that require writing as part of the curriculum including the social and natural sciences.

Peer review in classrooms helps students become more invested in their work, and the classroom environment at large. Understanding how their work is read by a diverse readership before it is graded by the teacher may also help students clarify ideas and understand how to persuasively reach different audience members via their writing. It also gives students professional experience that they might draw on later when asked to review the work of a colleague prior to publication. The process can also bolster the confidence of students on both sides of the process. It has been found that students are more positive than negative when reviewing their classmates' writing. Peer review can help students not get discouraged but rather feel determined to improve their writing.

Critics of peer review in classrooms say that it can be ineffective due to students' lack of practice giving constructive criticism, or lack of expertise in the writing craft at large. Peer review can be problematic for developmental writers, particularly if students view their writing as inferior to others in the class as they may be unwilling to offer suggestions or ask other writers for help. Peer review can impact a student's opinion of themselves as well as others as sometimes students feel a personal connection to the work they have produced, which can also make them feel reluctant to receive or offer criticism. Teachers using peer review as an assignment can lead to rushed-through feedback by peers, using incorrect praise or criticism, thus not allowing the writer or the editor to get much out of the activity. As a response to these concerns, instructors may provide examples, model peer review with the class, or focus on specific areas of feedback during the peer review process. Instructors may also experiment with in-class peer review vs. peer review as homework, or peer review using technologies afforded by learning management systems online. Students that are older can give better feedback to their peers, getting more out of peer review, but it is still a method used in classrooms to help students young and old learn how to revise. With evolving and changing technology, peer review will develop as well. New tools could help alter the process of peer review.

Peer seminar

Peer seminar is a method that involves a speaker that presents ideas to an audience that also acts as a "contest". To further elaborate, there are multiple speakers that are called out one at a time and given an amount of time to present the topic that they have researched. Each speaker may or may not talk about the same topic but each speaker has something to gain or lose which can foster a competitive atmosphere. This approach allows speakers to present in a more personal tone while trying to appeal to the audience while explaining their topic.

Peer seminars may be somewhat similar to what conference speakers do, however, there is more time to present their points, and speakers can be interrupted by audience members to provide questions and feedback upon the topic or how well the speaker did in presenting their topic.

Peer review in writing

Professional peer review focuses on the performance of professionals, with a view to improving quality, upholding standards, or providing certification. Peer review in writing is a pivotal component among various peer review mechanisms, often spearheaded by educators and involving student participation, particularly in academic settings. It constitutes a fundamental process in academic and professional writing, serving as a systematic means to ensure the quality, effectiveness, and credibility of scholarly work. However, despite its widespread use, it is one of the most scattered, inconsistent, and ambiguous practices associated with writing instruction. Many scholars questioning its effectiveness and specific methodologies. Critics of peer review in classrooms express concerns about its ineffectiveness due to students' lack of practice in giving constructive criticism or their limited expertise in the writing craft overall.

Critiques of peer review

Academic peer review has faced considerable criticism, with many studies highlighting inherent issues in the peer review process.

The editorial peer review process has been found to be strongly biased against 'negative studies,' i.e. studies that do not work. This then biases the information base of medicine. Journals become biased against negative studies when values come into play. "Who wants to read something that doesn't work?" asks Richard Smith in the Journal of the Royal Society of Medicine. "That's boring."

This is also particularly evident in university classrooms, where the most common source of writing feedback during student years often comes from teachers, whose comments are often highly valued. Students may become influenced to provide research in line with the professor's viewpoints, because of the teacher's position of high authority. The effectiveness of feedback largely stems from its high authority. Benjamin Keating, in his article "A Good Development Thing: A Longitudinal Analysis of Peer Review and Authority in Undergraduate Writing," conducted a longitudinal study comparing two groups of students (one majoring in writing and one not) to explore students' perceptions of authority. This research, involving extensive analysis of student texts, concludes that students majoring in non-writing fields tend to undervalue mandatory peer review in class, while those majoring in writing value classmates' comments more. This reflects that peer review feedback has a certain threshold, and effective peer review requires a certain level of expertise. For non-professional writers, peer review feedback may be overlooked, thereby affecting its effectiveness.

Elizabeth Ellis Miller, Cameron Mozafari, Justin Lohr and Jessica Enoch state, "While peer review is an integral part of writing classrooms, students often struggle to effectively engage in it." The authors illustrate some reasons for the inefficiency of peer review based on research conducted during peer review sessions in university classrooms:

  1. Lack of Training: Students and even some faculty members may not have received sufficient training to provide constructive feedback. Without proper guidance on what to look for and how to provide helpful comments, peer reviewers may find it challenging to offer meaningful insights.
  2. Limited Engagement: Students may participate in peer review sessions with minimal enthusiasm or involvement, viewing them as obligatory tasks rather than valuable learning opportunities. This lack of investment can result in superficial feedback that fails to address underlying issues in the writing.
  3. Time Constraints: Instructors often allocate limited time for peer review activities during class sessions, which may not be adequate for thorough reviews of peers' work. Consequently, feedback may be rushed or superficial, lacking the depth required for meaningful improvement.

This research demonstrates that besides issues related to expertise, numerous objective factors contribute to students' poor performance in peer review sessions, resulting in feedback from peer reviewers that may not effectively assist authors. Additionally, this study highlights the influence of emotions in peer review sessions, suggesting that both peer reviewers and authors cannot completely eliminate emotions when providing and receiving feedback. This can lead to peer reviewers and authors approaching the feedback with either positive or negative attitudes towards the text, resulting in selective or biased feedback and review, further impacting their ability to objectively evaluate the article. It implies that subjective emotions may also affect the effectiveness of peer review feedback.

Pamela Bedore and Brian O'Sullivan also hold a skeptical view of peer review in most writing contexts. The authors conclude, based on comparing different forms of peer review after systematic training at two universities, that "the crux is that peer review is not just about improving writing but about helping authors achieve their writing vision." Feedback from the majority of non-professional writers during peer review sessions often tends to be superficial, such as simple grammar corrections and questions. This precisely reflects the implication in the conclusion that the focus is only on improving writing skills. Meaningful peer review involves understanding the author's writing intent, posing valuable questions and perspectives, and guiding the author to achieve their writing goals.

Alternatives

Various alternatives to peer review have been suggested (such as, in the context of science funding, funding-by-lottery).

Comparison and improvement

Magda Tigchelaar compares peer review with self-assessment through an experiment that divided students into three groups: self-assessment, peer review, and no review. Across four writing projects, she observed changes in each group, with surprising results showing significant improvement only in the self-assessment group. The author's analysis suggests that self-assessment allows individuals to clearly understand the revision goals at each stage, as the author is the most familiar with their writing. Thus, self-checking naturally follows a systematic and planned approach to revision. In contrast, the effectiveness of peer review is often limited due to the lack of structured feedback, characterized by scattered, meaningless summaries and evaluations that fail to meet the author's expectations for revising their work.

Stephanie Conner and Jennifer Gray highlight the value of most students' feedback during peer review. They argue that many peer review sessions fail to meet students' expectations, as students, even as reviewers themselves, feel uncertain about providing constructive feedback due to their lack of confidence in their writing. The authors offer numerous improvement strategies. For instance, the peer review process can be segmented into groups, where students present the papers to be reviewed while other group members take notes and analyze them. Then, the review scope can be expanded to the entire class. This widens the review sources and further enhances the level of professionalism.

With evolving technology, peer review is also expected to evolve. New tools have the potential to transform the peer review process. Mimi Li discusses the effectiveness and feedback of an online peer review software used in their freshman writing class. Unlike traditional peer review methods commonly used in classrooms, the online peer review software offers many tools for editing articles and comprehensive guidance. For instance, it lists numerous questions peer reviewers can ask and allows various comments to be added to the selected text. Based on observations over a semester, students showed varying degrees of improvement in their writing skills and grades after using the online peer review software. Additionally, they highly praised the technology of online peer review.

Tuesday, April 15, 2025

Fermentation

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Fermentation
Phylogenetic tree of bacteria and archaea, highlighting those that carry out fermentation. Their end products are also highlighted. Figure modified from Hackmann (2024).

Fermentation is a type of redox metabolism carried out in the absence of oxygen. During fermentation, organic molecules (e.g., glucose) are catabolized and donate electrons to other organic molecules. In the process, ATP and organic end products (e.g., lactate) are formed.

Because oxygen is not required, it is an alternative to aerobic respiration. Over 25% of bacteria and archaea carry out fermentation. They live in the gut, sediments, food, and other environments. Eukaryotes, including humans and other animals, also carry out fermentation.

Fermentation is important in several areas of human society. Humans have used fermentation in production of food for 13,000 years. Humans and their livestock have microbes in the gut that carry out fermentation, releasing products used by the host for energy. Fermentation is used at an industrial level to produce commodity chemicals, such as ethanol and lactate. In total, fermentation forms more than 50 metabolic end products. This process highlights the power of microbial activity.

Definition

The definition of fermentation has evolved over the years. The most modern definition is catabolism, where organic compounds are both the electron donor and acceptor. A common electron donor is glucose, and pyruvate is a common electron acceptor. This definition distinguishes fermentation from aerobic respiration, where oxygen is the acceptor and types of anaerobic respiration, where an inorganic species is the acceptor.

Fermentation had been defined differently in the past. In 1876, Louis Pasteur described it as "la vie sans air" (life without air). This definition came before the discovery of anaerobic respiration. Later, it had been defined as catabolism that forms ATP through only substrate-level phosphorylation. However, several pathways of fermentation have been discovered to form ATP through an electron transport chain and ATP synthase, also.

Some sources define fermentation loosely as any large-scale biological manufacturing process. See Industrial fermentation. This definition focuses on the process of manufacturing rather than metabolic details.

Biological role and prevalence

Fermentation is used by organisms to generate ATP energy for metabolism. One advantage is that it requires no oxygen or other external electron acceptors, and thus it can be carried out when those electron acceptors are absent. A disadvantage is that it produces relatively little ATP, yielding only between 2 and 4.5 per glucose compared to 32 for aerobic respiration.

Over 25% of bacteria and archaea carry out fermentation. This type of metabolism is most common in the phylum Bacillota, and it is least common in Actinomycetota. Their most common habitat is host-associated ones, such as the gut.

Animals, including humans, also carry out fermentation. The product of fermentation in humans is lactate, and it is formed during anaerobic exercise or in cancerous cells. No animal is known to survive on fermentation alone, even as one parasitic animal (Henneguya zschokkei) is known to survive without oxygen.

Substrates and products of fermentation

The most common substrates and products of fermentation. Figure modified from Hackmann (2024).

Fermentation uses a range of substrates and forms a variety of metabolic end products. Of the 55 end products formed, the most common are acetate and lactate. Of the 46 chemically-defined substrates that have been reported, the most common are glucose and other sugars.

Biochemical overview

Overview of the biochemical pathways for fermentation of glucose. Figure modified from Hackmann (2024).

When an organic compound is fermented, it is broken down to a simpler molecule and releases electrons. The electrons are transferred to a redox cofactor, which in turn transfers them to an organic compound. ATP is generated in the process, and it can be formed by substrate-level phosphorylation or by ATP synthase.

When glucose is fermented, it enters glycolysis or the pentose phosphate pathway and is converted to pyruvate. From pyruvate, pathways branch out to form a number of end products (e.g. lactate). At several points, electrons are released and accepted by redox cofactors (NAD and ferredoxin). At later points, these cofactors donate electrons to their final acceptor and become oxidized. ATP is also formed at several points in the pathway.

The biochemical pathways of fermentation of glucose in poster format. Figure modified from Hackmann (2024).

While fermentation is simple in overview, its details are more complex. Across organisms, fermentation of glucose involves over 120 different biochemical reactions. Further, multiple pathways can be responsible for forming the same product. For forming acetate from its immediate precursor (pyruvate or acetyl-CoA), six separate pathways have been found.

Biochemistry of individual products

Ethanol

In ethanol fermentation, one glucose molecule is converted into two ethanol molecules and two carbon dioxide (CO2) molecules. It is used to make bread dough rise: the carbon dioxide forms bubbles, expanding the dough into a foam. The ethanol is the intoxicating agent in alcoholic beverages such as wine, beer and liquor. Fermentation of feedstocks, including sugarcane, maize, and sugar beets, produces ethanol that is added to gasoline. In some species of fish, including goldfish and carp, it provides energy when oxygen is scarce (along with lactic acid fermentation).

Before fermentation, a glucose molecule breaks down into two pyruvate molecules (glycolysis). The energy from this exothermic reaction is used to bind inorganic phosphates to ADP, which converts it to ATP, and convert NAD+ to NADH. The pyruvates break down into two acetaldehyde molecules and give off two carbon dioxide molecules as waste products. The acetaldehyde is reduced into ethanol using the energy and hydrogen from NADH, and the NADH is oxidized into NAD+ so that the cycle may repeat. The reaction is catalyzed by the enzymes pyruvate decarboxylase and alcohol dehydrogenase.

History of bioethanol fermentation

The history of ethanol as a fuel spans several centuries and is marked by a series of significant milestones. Samuel Morey, an American inventor, was the first to produce ethanol by fermenting corn in 1826. However, it was not until the California Gold Rush in the 1850s that ethanol was first used as a fuel in the United States. Rudolf Diesel demonstrated his engine, which could run on vegetable oils and ethanol, in 1895, but the widespread use of petroleum-based diesel engines made ethanol less popular as a fuel. In the 1970s, the oil crisis reignited interest in ethanol, and Brazil became a leader in ethanol production and use. The United States began producing ethanol on a large scale in the 1980s and 1990s as a fuel additive to gasoline, due to government regulations. Today, ethanol continues to be explored as a sustainable and renewable fuel source, with researchers developing new technologies and biomass sources for its production.

  • 1826: Samuel Morey, an American inventor, was the first to produce ethanol by fermenting corn. However, ethanol was not widely used as a fuel until many years later. (1)
  • 1850s: Ethanol was first used as a fuel in the United States during the California gold rush. Miners used ethanol as a fuel for lamps and stoves because it was cheaper than whale oil. (2)
  • 1895: German engineer Rudolf Diesel demonstrated his engine, which was designed to run on vegetable oils, including ethanol. However, the widespread use of diesel engines fueled by petroleum made ethanol less popular as a fuel. (3)
  • 1970s: The oil crisis of the 1970s led to renewed interest in ethanol as a fuel. Brazil became a leader in ethanol production and use, due in part to government policies that encouraged the use of biofuels. (4)
  • 1980s–1990s: The United States began to produce ethanol on a large scale as a fuel additive to gasoline. This was due to the passage of the Clean Air Act in 1990, which required the use of oxygenates, such as ethanol, to reduce emissions. (5)
  • 2000s–present: There has been continued interest in ethanol as a renewable and sustainable fuel. Researchers are exploring new sources of biomass for ethanol production, such as switchgrass and algae, and developing new technologies to improve the efficiency of the fermentation process. (6)

Lactic acid

Homolactic fermentation (producing only lactic acid) is the simplest type of fermentation. Pyruvate from glycolysis undergoes a simple redox reaction, forming lactic acid. Overall, one molecule of glucose (or any six-carbon sugar) is converted to two molecules of lactic acid:

C6H12O6 → 2 CH3CHOHCOOH

It occurs in the muscles of animals when they need energy faster than the blood can supply oxygen. It also occurs in some kinds of bacteria (such as lactobacilli) and some fungi. It is the type of bacteria that convert lactose into lactic acid in yogurt, giving it its sour taste. These lactic acid bacteria can carry out either homolactic fermentation, where the end-product is mostly lactic acid, or heterolactic fermentation, where some lactate is further metabolized to ethanol and carbon dioxide (via the phosphoketolase pathway), acetate, or other metabolic products, e.g.:

C6H12O6 → CH3CHOHCOOH + C2H5OH + CO2

If lactose is fermented (as in yogurts and cheeses), it is first converted into glucose and galactose (both six-carbon sugars with the same atomic formula):

C12H22O11 + H2O → 2 C6H12O6

Heterolactic fermentation is in a sense intermediate between lactic acid fermentation and other types, e.g. alcoholic fermentation. Reasons to go further and convert lactic acid into something else include:

  • The acidity of lactic acid impedes biological processes. This can be beneficial to the fermenting organism as it drives out competitors that are unadapted to the acidity. As a result, the food will have a longer shelf life (one reason foods are purposely fermented in the first place); however, beyond a certain point, the acidity starts affecting the organism that produces it.
  • The high concentration of lactic acid (the final product of fermentation) drives the equilibrium backwards (Le Chatelier's principle), decreasing the rate at which fermentation can occur and slowing down growth.
  • Ethanol, into which lactic acid can be easily converted, is volatile and will readily escape, allowing the reaction to proceed easily. CO2 is also produced, but it is only weakly acidic and even more volatile than ethanol.
  • Acetic acid (another conversion product) is acidic and not as volatile as ethanol; however, in the presence of limited oxygen, its creation from lactic acid releases additional energy. It is a lighter molecule than lactic acid, forming fewer hydrogen bonds with its surroundings (due to having fewer groups that can form such bonds), thus is more volatile and will also allow the reaction to proceed more quickly.
  • If propionic acid, butyric acid, and longer monocarboxylic acids are produced, the amount of acidity produced per glucose consumed will decrease, as with ethanol, allowing faster growth.

Hydrogen gas

Hydrogen gas is produced in many types of fermentation as a way to regenerate NAD+ from NADH. Electrons are transferred to ferredoxin, which in turn is oxidized by hydrogenase, producing H2. Hydrogen gas is a substrate for methanogens and sulfate reducers, which keep the concentration of hydrogen low and favor the production of such an energy-rich compound, but hydrogen gas at a fairly high concentration can nevertheless be formed, as in flatus.

For example, Clostridium pasteurianum ferments glucose to butyrate, acetate, carbon dioxide, and hydrogen gas: The reaction leading to acetate is:

C6H12O6 + 4 H2O → 2 CH3COO + 2 HCO3 + 4 H+ + 4 H2

Glyoxylate

Glyoxylate fermentation is a type of fermentation used by microbes that are able to utilize glyoxylate as a nitrogen source.

Other

Other types of fermentation include mixed acid fermentation, butanediol fermentation, butyrate fermentation, caproate fermentation, and acetone–butanol–ethanol fermentation.

In the broader sense

In food and industrial contexts, any chemical modification performed by a living being in a controlled container can be termed "fermentation". The following do not fall into the biochemical sense, but are called fermentation in the larger sense:

Alternative protein

Fermentation is used to produce the heme protein found in the Impossible Burger.

Fermentation can be used to make alternative protein sources. It is commonly used to modify existing protein foods, including plant-based ones such as soy, into more flavorful forms such as tempeh and fermented tofu.

More modern "fermentation" makes recombinant protein to help produce meat analogue, milk substitute, cheese analogues, and egg substitutes. Some examples are:

Heme proteins such as myoglobin and hemoglobin give meat its characteristic texture, flavor, color, and aroma. The myoglobin and leghemoglobin ingredients can be used to replicate this property, despite them coming from a vat instead of meat.

Enzymes

Industrial fermentation can be used for enzyme production, where proteins with catalytic activity are produced and secreted by microorganisms. The development of fermentation processes, microbial strain engineering and recombinant gene technologies has enabled the commercialization of a wide range of enzymes. Enzymes are used in all kinds of industrial segments, such as food (lactose removal, cheese flavor), beverage (juice treatment), baking (bread softness, dough conditioning), animal feed, detergents (protein, starch and lipid stain removal), textile, personal care and pulp and paper industries.

Modes of industrial operation

Most industrial fermentation uses batch or fed-batch procedures, although continuous fermentation can be more economical if various challenges, particularly the difficulty of maintaining sterility, can be met.

Batch

In a batch process, all the ingredients are combined and the reactions proceed without any further input. Batch fermentation has been used for millennia to make bread and alcoholic beverages, and it is still a common method, especially when the process is not well understood. However, it can be expensive because the fermentor must be sterilized using high pressure steam between batches. Strictly speaking, there is often addition of small quantities of chemicals to control the pH or suppress foaming.

Batch fermentation goes through a series of phases. There is a lag phase in which cells adjust to their environment; then a phase in which exponential growth occurs. Once many of the nutrients have been consumed, the growth slows and becomes non-exponential, but production of secondary metabolites (including commercially important antibiotics and enzymes) accelerates. This continues through a stationary phase after most of the nutrients have been consumed, and then the cells die.

Fed-batch

Fed-batch fermentation is a variation of batch fermentation where some of the ingredients are added during the fermentation. This allows greater control over the stages of the process. In particular, production of secondary metabolites can be increased by adding a limited quantity of nutrients during the non-exponential growth phase. Fed-batch operations are often sandwiched between batch operations.

Open

The high cost of sterilizing the fermentor between batches can be avoided using various open fermentation approaches that are able to resist contamination. One is to use a naturally evolved mixed culture. This is particularly favored in wastewater treatment, since mixed populations can adapt to a wide variety of wastes. Thermophilic bacteria can produce lactic acid at temperatures of around 50 °Celsius, sufficient to discourage microbial contamination; and ethanol has been produced at a temperature of 70 °C. This is just below its boiling point (78 °C), making it easy to extract. Halophilic bacteria can produce bioplastics in hypersaline conditions. Solid-state fermentation adds a small amount of water to a solid substrate; it is widely used in the food industry to produce flavors, enzymes and organic acids.

Continuous

In continuous fermentation, substrates are added and final products removed continuously. There are three varieties: chemostats, which hold nutrient levels constant; turbidostats, which keep cell mass constant; and plug flow reactors in which the culture medium flows steadily through a tube while the cells are recycled from the outlet to the inlet. If the process works well, there is a steady flow of feed and effluent and the costs of repeatedly setting up a batch are avoided. Also, it can prolong the exponential growth phase and avoid byproducts that inhibit the reactions by continuously removing them. However, it is difficult to maintain a steady state and avoid contamination, and the design tends to be complex. Typically the fermentor must run for over 500 hours to be more economical than batch processors.

History of the use of fermentation

The use of fermentation, particularly for beverages, has existed since the Neolithic and has been documented dating from 7000 to 6600 BCE in Jiahu, China, 5000 BCE in India, Ayurveda mentions many Medicated Wines, 6000 BCE in Georgia, 3150 BCE in ancient Egypt, 3000 BCE in Babylon, 2000 BCE in pre-Hispanic Mexico, and 1500 BC in Sudan. Fermented foods have a religious significance in Judaism and Christianity. The Baltic god Rugutis was worshiped as the agent of fermentation. In alchemy, fermentation ("putrefaction") was symbolized by Capricorn ♑︎.

Louis Pasteur in his laboratory

In 1837, Charles Cagniard de la Tour, Theodor Schwann and Friedrich Traugott Kützing independently published papers concluding, as a result of microscopic investigations, that yeast is a living organism that reproduces by budding. Schwann boiled grape juice to kill the yeast and found that no fermentation would occur until new yeast was added. However, a lot of chemists, including Antoine Lavoisier, continued to view fermentation as a simple chemical reaction and rejected the notion that living organisms could be involved. This was seen as a reversion to vitalism and was lampooned in an anonymous publication by Justus von Liebig and Friedrich Wöhler.

The turning point came when Louis Pasteur (1822–1895), during the 1850s and 1860s, repeated Schwann's experiments and showed fermentation is initiated by living organisms in a series of investigations. In 1857, Pasteur showed lactic acid fermentation is caused by living organisms. In 1860, he demonstrated how bacteria cause souring in milk, a process formerly thought to be merely a chemical change. His work in identifying the role of microorganisms in food spoilage led to the process of pasteurization.

In 1877, working to improve the French brewing industry, Pasteur published his famous paper on fermentation, "Etudes sur la Bière", which was translated into English in 1879 as "Studies on fermentation". He defined fermentation (incorrectly) as "Life without air", yet he correctly showed how specific types of microorganisms cause specific types of fermentations and specific end-products.

Although showing fermentation resulted from the action of living microorganisms was a breakthrough, it did not explain the basic nature of fermentation; nor did it prove it is caused by microorganisms which appear to be always present. Many scientists, including Pasteur, had unsuccessfully attempted to extract the fermentation enzyme from yeast.

Success came in 1897 when the German chemist Eduard Buechner ground up yeast, extracted a juice from them, then found to his amazement this "dead" liquid would ferment a sugar solution, forming carbon dioxide and alcohol much like living yeasts.

Buechner's results are considered to mark the birth of biochemistry. The "unorganized ferments" behaved just like the organized ones. From that time on, the term enzyme came to be applied to all ferments. It was then understood fermentation is caused by enzymes produced by microorganisms. In 1907, Buechner won the Nobel Prize in chemistry for his work.

Advances in microbiology and fermentation technology have continued steadily up until the present. For example, in the 1930s, it was discovered microorganisms could be mutated with physical and chemical treatments to be higher-yielding, faster-growing, tolerant of less oxygen, and able to use a more concentrated medium. Strain selection and hybridization developed as well, affecting most modern food fermentations.

Post 1930s

The field of fermentation has been critical to producing a wide range of consumer goods, from food and drink to industrial chemicals and pharmaceuticals. Since its early beginnings in ancient civilizations, fermentation has continued to evolve and expand, with new techniques and technologies driving advances in product quality, yield, and efficiency. The period from the 1930s onward saw a number of significant advancements in fermentation technology, including the development of new processes for producing high-value products like antibiotics and enzymes, the increasing importance of fermentation in the production of bulk chemicals, and a growing interest in the use of fermentation for the production of functional foods and nutraceuticals.

The 1950s and 1960s saw the development of new fermentation technologies, such as immobilized cells and enzymes, which allowed for more precise control over fermentation processes and increased the production of high-value products like antibiotics and enzymes. In the 1970s and 1980s, fermentation became increasingly important in producing bulk chemicals like ethanol, lactic acid, and citric acid. This led to developing new fermentation techniques and genetically engineered microorganisms to improve yields and reduce production costs. In the 1990s and 2000s, there was a growing interest in fermentation to produce functional foods and nutraceuticals, which have potential health benefits beyond basic nutrition. This led to new fermentation processes, probiotics, and other functional ingredients.

Overall, the period from 1930 onward saw significant advancements in the use of fermentation for industrial purposes, leading to the production of a wide range of fermented products that are now consumed worldwide.

Science fiction magazine

From Wikipedia, the free encyclopedia https://en.wikipedia.org/wiki/Science_fi...