The Observation Deck » Open source confronts its midlife crisis

“So it seemed like only a matter of time before the companies built around open source software would have to confront their own crisis of confidence: open source business models are really tough, selling software-as-a-service is one of the most natural of them, the cloud service providers are really good at it — and their commercial appetites seem boundless. And, like a new cherry red two-seater sports car next to a minivan in a suburban driveway, some open source companies are dealing with this crisis exceptionally poorly: they are trying to restrict the way that their open source software can be used. These companies want it both ways: they want the advantages of open source — the community, the positivity, the energy, the adoption, the downloads — but they also want to enjoy the fruits of proprietary software companies in software lock-in and its concomitant monopolistic rents. If this were entirely transparent (that is, if some bits were merely being made explicitly proprietary), it would be fine: we could accept these companies as essentially proprietary software companies, albeit with an open source loss-leader. But instead, these companies are trying to license their way into this self-contradictory world: continuing to claim to be entirely open source, but perverting the license under which portions of that source are available. Most gallingly, they are doing this by hijacking open source nomenclature. Of these, the laughably named commons clause is the worst offender (it is plainly designed to be confused with the purely virtuous creative commons), but others (including CockroachDB’s Community License, MongoDB’s Server Side Public License, and Confluent’s Community License) are little better. And in particular, as it apparently needs to be said: no, “community” is not the opposite of “open source” — please stop sullying its good name by attaching it to licenses that are deliberately not open source! But even if they were more aptly named (e.g. “the restricted clause” or “the controlled use license” or — perhaps most honest of all — “the please-don’t-put-me-out-of-business-during-the-next-reInvent-keynote clause”), these licenses suffer from a serious problem: they are almost certainly asserting rights that the copyright holder doesn’t in fact have….”

Academic Paywalls Harm National Security – Defense One

“If Harvard University cannot afford access, then it is certainly too pricy for defense consultants, businesses (especially small ones), and think tanks. A previous employer of mine, a consultancy that supports senior national security leaders, gave up its academic journal subscriptions in the wake of price hikes. Some military research centers simply make do with minimal access. The high cost of academic articles has even dissuaded defense companies, from time to time, from turning concepts into reality.

But perhaps you doubt that scholarly journals offer extensive benefits to national security. To illustrate these benefits, I will focus on three: informing policy, skill and capability building, and technological insight….”

The International Tree?Ring Data Bank (ITRDB) revisited: Data availability and global ecological representativity – Zhao – – Journal of Biogeography – Wiley Online Library

Abstract:  Aim. The International Tree?Ring Data Bank (ITRDB) is the most comprehensive database of tree growth. To evaluate its usefulness and improve its accessibility to the broad scientific community, we aimed to: (a) quantify its biases, (b) assess how well it represents global forests, (c) develop tools to identify priority areas to improve its representativity, and (d) make available the corrected database….

Methods. We identified and corrected formatting issues in all individual datasets of the ITRDB. We then calculated the representativity of the ITRDB with respect to species, spatial coverage, climatic regions, elevations, need for data update, climatic limitations on growth, vascular plant diversity, and associated animal diversity. We combined these metrics into a global Priority Sampling Index (PSI) to highlight ways to improve ITRDB representativity.

Results. Our refined dataset provides access to a network of >52 million growth data points worldwide. We found, however, that the database is dominated by trees from forests with low diversity, in semi?arid climates, coniferous species, and in western North America. Conifers represented 81% of the ITRDB and even in well?sampled areas, broadleaves were poorly represented. Our PSI stressed the need to increase the database diversity in terms of broadleaf species and identified poorly represented regions that require scientific attention. Great gains will be made by increasing research and data sharing in African, Asian, and South American forests.

Main conclusions. The extensive data and coverage of the ITRDB show great promise to address macroecological questions. To achieve this, however, we have to overcome the significant gaps in the representativity of the ITRDB. A strategic and organized group effort is required, and we hope the tools and data provided here can guide the efforts to improve this invaluable database….”

New study makes 52 million tree stories more accessible to science

“The world’s primary archive of tree ring data, which holds more than 52 million cost-free records spanning 8,000 years of history, has gotten a makeover by scientists from four countries committed to making science more accessible.


The co-authors report in the Journal of Biogeography that the International Tree Ring Data Bank, developed in 1974 and populated by hundreds of contributing scientists and agencies, had only been used for a handful of studies at a global scale due to inconsistent data accessibility and formatting.

The team corrected thousands of formatting issues that prevented files from being read, requiring scientists to either manually correct errors or omit large portions of available data. “The data correction took weeks of intensive work,” says Manzanedo. “In the sample records, any misplaced character or erroneous empty space would make a whole file unreadable. Finding those was sometimes like finding a needle in a haystack. We kept a log with our decisions to ensure the future traceability of the process.” …”

Open access and academic imperialism

“Recently, major scientific funding bodies in several European countries agreed to mandate that researchers they fund (approximately €7.6 billion annually) should publish their results in open-access journals, intending to penalize authors who publish in journals that use a paywall for some or all of their articles (Enserink 2018). We think this policy is a mistake….”


Academic publishing empires need to go [PeerJ Preprints]

Abstract:  In response to the editorial “Open access and academic imperialism” by Burgman (2018) and signed by a large group of editors, we wish to express our disappointment with such a narrow and misleading interpretations of the recent attempts to make academic publishing more open, and what consequences this might have for the global conservation community. We highlight that the current guidelines of Plan S are open for comment until Feb 1st 2019 (see Instead of calling for a more nuanced approach – something that has been done for the past 20 years – we encourage everyone to actively participate in factoring in the nuances.

EPA to pursue final ‘science transparency’ rule in 2019 | TheHill

The Environmental Protection Agency (EPA) plans to pursue next year a final version of its much-criticized rule that would restrict the scientific studies it can use to justify regulations.

In a Friday interview with The Hill, acting EPA chief Andrew Wheeler dismissed the idea that the science transparency regulation was on the “back burner” since the administration recently listed it as a “long-term” regulatory action.

“It is not a back-burner issue. I feel strongly about that,” Wheeler said. “And we will move forward to finalize that next year.” …

Wheeler rejected the main criticism from opponents of the rule, that it is meant to restrict the agency’s ability to regulate by putting out of reach large bodies of valuable science, such as many epidemiological studies that by their nature cannot be reproduced.

“I don’t think it’s designed to restrict what we use. It’s designed to get the information out to the public. The critics look at it as ‘oh, you’re trying to get rid of a lot of the studies, you’re trying to restrict what the agency can use.’ No,” he said. …

California Attorney General Xavier Becerra, who has sued the Trump administration’s EPA numerous times — frequently with success — said if the science rule moves forward, he’ll fight it….”

Gold Open Access Journals: From scientists’ “publish or perish” to publishers’ “publish to get rich” – Mapping Ignorance

This situation is clearly not sustainable. Scientists, workers of science, receive pressure from multiple agents. On the one hand, we need to publish (publish or perish is still a valid leitmotif for us). But now we need to publish Q1 journals if we want to promote and get funds to keep doing research. And we should do this not just for ourselves (I’m at the end of my career, I can’t promote further than being a full professor with six sexenios6), but especially for keeping our labs alive for the future of our people, PhD students and junior associate professors. And now, we are also pressed to publish open access. This is indeed promoted and required by the national 2011 “Ley de la Ciencia, la Tecnología y la Innovación” (Science, Technology and Innovation Act) if your research has been produced with public funding. And Spain is not an isolated case. This is happening everywhere. Open access philosophy apparently promotes a democratic, solidary and transparent science system, so that governments and public funding agencies are demanding the researchers to acquire the compromise of publishing OA as a sine qua non requisite just to apply for funds. We keep this compromise thanks to Green Open Access, publishing our pre-prints in public, free-access repositories of our institutions. I wonder why we don’t skip the journal and just publish our manuscripts in the repository without the need for journal submission and peer review. I sincerely think that the quality of my papers would be more or less the same (I’m very perfectionist and know how to do my job after 30 years of experience), and the publication time would be substantially reduced….

This is the problem. Is there a solution? I think the answer is YES. Scientists have, logically, a leading role in scientific publication and the solution to this unbearable situation is in our hands. We cannot be working for the benefit of private companies anymore. Moreover, measures of governments and funding agencies designed to promote open access policy (enforcing researchers to publish in OA journals; reaching millionaire agreements with publishing oligopolistic companies) have failed because they were inadequate. The solution is that, once again, science workers (scientists) start leading and commanding the publication of our results. Scientific societies, national and international, were promoters of classical journals….”

ALLEA Response to Plan S

“ALLEA [All European Academies] supports open access as a major step towards realising the universality of science and welcomes the ambition of Plan S in this regard. Implementation will however require extensive consultation and dialogue with all parties, in particular the research performing communities represented through ALLEA and other scientific stakeholders….

In summary, ALLEA broadly welcomes Plan S but with major caveats. The time scale envisaged for such a complex transformation is clearly unrealistic if the preconditions identified by ALLEA in its earlier statements are to be implemented prior to Plan S becoming operational; the funding agencies have to provide the necessary funds in their budgets for paying the publications fees, resolve the question of promotion of early career researchers, consider the special circumstances of minority disciplines, address the IP issues, and the like. To do this it will be essential to engage the full spectrum of affected parties and policy makers. Scholarly communication is the life-blood of research and it is in all our interest to make this as reliable, efficient, sustainable, trustworthy and open as possible. In particular, critical peer review and community evaluation is crucial and must be properly incentivised, enabled and rewarded. ALLEA looks forward to working with the initiators of Plan S, endorsing organisations, as well as other stakeholders in facilitating this necessary transformation of not just academic publishing, but the whole system of research evaluation, accreditation and validation. We note also that the universality of science requires that this be a global transformation of the research ecosystem, but one which can be initiated and led by Europe.”

University of California in subscription showdown with Elsevier | Times Higher Education (THE)

The long-running battle to oust high-cost subscription journals from the world of research is at a showdown moment, with a leading US university system set to break from the globe’s biggest academic publisher.

The University of California system is down to the final weeks of its $11 million (£8.8 million) per year contract with Elsevier and, with negotiations stalled, it has begun telling its faculty to brace for impact….”