Molecular Diversity Preservation International was founded and registered as a non-profit association (Verein) by Shu-Kun Lin and Benoit R. Turin in Basel in 1996 to enable the deposit and exchange of rare molecular and biomolecular research samples. The goal was to preserve the diversity of chemical compounds through the collection and storage of samples that could be made available to the scientific community for research purposes. This collection of samples was permanently transferred to the MDPI Sustainability Foundation in 2013, and Molecular Diversity Preservation International was dissolved. The collection of chemical samples is now operated by Molmall Sarl on behalf of the MDPI Sustainability Foundation.
The journal Molecules was established in 1996 in collaboration with Springer-Verlag (now Springer Science+Business Media) in order to document the chemical samples of the MDPI collection. Several other journals were established by the MDPI Verein, including Entropy (1999), the International Journal of Molecular Sciences (2000), Sensors (2001), Marine Drugs (2003), and the International Journal of Environmental Research and Public Health (2004). The publisher MDPI AG was spun off from MDPI Verein in 2010.
MDPI Verein co-organized several academic conferences, including the International Symposium on Frontiers in Molecular Science. It also runs virtual conferences, such as the Electronic Conference on Synthetic Organic Chemistry, which was started in 1997. In 2010 MDPI launched the platform Sciforum.net to host virtual conferences. In 2014, various virtual conferences were hosted in the areas of synthetic organic chemistry, material sciences, sensors, and sustainability. In 2015, MDPI co-organized two physical conferences with and at the University of Basel, the 4th Internationational Symposium on Sensor Science and the 5th World Sustainability Forum. Since 2015, scholars can organize their own conference for free on the Sciforum platform.
MDPI AG, a publisher of open-access scientific journals, was spun off from the Molecular Diversity Preservation International organization. It was formally registered by Shu-Kun Lin and Dietrich Rordorf in May 2010 in Basel, Switzerland, and maintains three offshore editorial offices in China. MDPI relies primarily on article processing charges to cover the costs of editorial quality control and production of articles. Over seventy universities and institutes have joined the MDPI Institutional Membership Program, set up in the fourth quarter of 2013; authors from these organizations pay reduced article processing charges. MDPI is a member of the Committee on Publication Ethics, the International Association of Scientific, Technical, and Medical Publishers, and the Open Access Scholarly Publishers Association (OASPA).
MDPI currently publishes over 150 peer-reviewed scientific journals. As of June 2016, 28 journals have been selected for coverage in the Science Citation Index Expanded, while 60 journals are indexed in other Thomson Reuters products, such as the Emerging Sources Citation Index, BIOSIS Previews, and The Zoological Record.
Thirty-two MDPI journals publishing in biomedicine, life sciences, and related areas are archived in PubMed Central. MDPI journals can also be found in other relevant indexing services, such as Scopus, which currently includes over 50 MDPI journals, and Ei Compendex, which covers 13 MDPI journals.
In line with OASPA's recommendation, all articles published by MDPI since 2008 are released under the CC-BY Creative Commons license and preserved with the Swiss National Library and CLOCKSS.
In December 2011, the MDPI journal Life published Erik D. Andrulis' theoretical paper, Theory of the Origin, Evolution, and Nature of Life, aiming at presenting a framework to explain life. It attracted coverage by the popular science and technology magazines Ars Technica and Popular Science, which characterized it as "crazy" and "hilarious". A member of the editorial board of Life resigned in response. Publisher Lin defended the journal's editorial process, saying that the paper had been revised following lengthy reviews by two faculty members from institutions different from the author's.
In 2013, another MDPI journal, Entropy, published a review paper claiming glyphosate may be the most important factor in the development of obesity, depression, attention deficit hyperactivity disorder, autism, Alzheimer's disease, Parkinson's disease, multiple sclerosis, cancer, and infertility. The paper itself does not contain any primary research results. It was criticized as pseudo-science by the popular science magazine Discover. With regard to the same controversial study, Jeffrey Beall has rhetorically asked, "Will MDPI publish anything for money?".
When publishers like MDPI disseminate research by science activists like Stephanie Seneff and her co-authors, I think it’s fair to question the credibility of all the research that MDPI publishes. Will MDPI publish anything for money?
A third instance of controversial publications is documented in the Australian paradox.
MDPI has published a statement in December 2013 as a response and defense on publishing controversial papers.
MDPI was included on Jeffrey Beall's list of predatory open access publishing companies as of February 2014, and removed in October 2015 following a successful appeal. Following Beall's criticism of MDPI, the Open Access Scholarly Publishers Association (OASPA) conducted an investigation in April 2014 and concluded that MDPI meets the OASPA Membership Criteria, stating that "Based on our findings we feel satisfied that MDPI continue to meet the OASPA Membership Criteria".
Jeffrey Beall concern was that "MDPI's warehouse journals contain hundreds of lightly-reviewed articles that are mainly written and published for promotion and tenure purposes rather than to communicate science." Beall also claimed that MDPI used email spam to solicit manuscripts.
MDPI characterized Beall's comments as "an incompetent general critique" and alleged that the inclusion of MDPI on his list was motivated by a hostility towards open access publishing in general, noting that he had recently published a commentary on that theme. Peter Murray-Rust, a chemist currently working at the University of Cambridge and an editorial board member of the-yet-to-be-started MDPI journal Data, criticized Beall's critique of MDPI as being "irresponsible" and lacking evidence. Nevertheless, Beall maintained MDPI on his list, criticizing the company for publishing obvious pseudoscience articles.
One of its journals had been targeted in the Who's Afraid of Peer Review? sting operation and rejected the fake paper. In 2014, MDPI's Life journal started featuring open peer review (optional, at the authors' discretion), which has been advocated as a transparency measure to combat predatory journals.
Further critique was raised by Martin Haspelmath who argues that the publication model employed by MDPI
"creates a strong incentive to create journals and book imprints that function like 'vanity presses,' allowing authors to publish their low-quality work without significant risk of rejection. [...] For example, I recently heard of two Chinese companies that are publishing a large number of open-access journals, some of them in my field of linguistics: Wuhan-based SCIRP ([...] over 250 journals) and Beijing-based MDPI ([...] over 120 journals). The business model here is to start a large number of new journals and to hope that some of them will succeed and bring profit. For example, MDPI's journal Languages
does not even have an editor yet. This is of course reminiscent of the business model of spam e-mail, and in fact, some observers have warned of the danger of 'predatory journals.'"
In response to Haspelmath, MDPI published a commentary in the same journal disputing a number of points.
Among the reasons Beall gave for adding MDPI to his list of questionable publishers was that the company "...claims that several Nobel Laureates serve on its editorial boards, but one investigation found that they didn’t realize they were listed." As evidence for this particular accusation, Beall pointed to a news story run by eCampus News. The original reporter later issued a correction and the article was modified and appended with the following notice:
An earlier version of this article stated that Nobel Prize-winning geneticist Mario Capecchi was not aware he was listed as a member of the editorial board for the MDPI journal Biomolecules. At the time, Capecchi's assistant, Lorene Stitzer, told eCampus News that "he was not aware of the fact that he had been included on the listing." After being contacted by MDPI, Stitzer now says Capecchi is in fact aware of being an honorary board member. eCampus News regrets the error.
With regard to Beall's accusation about Nobel laureate Mario Capecchi not being aware that he was on the editorial board of the journal Biomolecules, MDPI posted a response stating that "the Editor-in-Chief of Biomolecules obtained a written confirmation from Professor Cappechi that he was indeed aware of his membership"; copies of such correspondence have been posted as well. MDPI has compiled and posted emails claiming to document the acceptance by the following Nobelists as members of the board in MDPI journals: Robert F. Curl, Richard R. Ernst, Jerome Karle, Harold Kroto, Yuan-Tseh Lee, Rudolph A. Marcus, Eric S. Maskin, Steven Weinberg, Kurt Wüthrich and George Smoot.
The uncorrected story has been picked up other media outlets, such as Veja, a leading weekly news magazine in Brazil.