The hand of the Creator

 biodiversity informatics, Electronic resources, Pseudoscience  Kommentarer inaktiverade för The hand of the Creator
Mar 022016
 

Designed by MichaelangeloIn a post not long ago on SCI-HUB and its importance for communicating science, I also made some remarks on the quality of topnotch journals. Don’t expect quality because it is expensive or has a so-called Impact Factor of significance. And now it rains gold on my modest point. PLOS ONE (reads Public Library of Science)  is a well renowned Open Access Journal (authors pay), with the following statement:

PLOS ONE upholds rigorous standards for quality. Every article we publish undergoes peer review led by one of approximately 6,000 PLOS ONE Academic Editors.

On 5 January, the journal published a long article about human hand biomechanics. An eye-opener for many on how wrong things can go, but there was some latency before the article became widely known. Already the abstract got the scientific society to turn to twitter #HandOfGod, blogs and other social media for exclamations (this is just one):

The explicit functional link indicates that the biomechanical characteristic of tendinous connective architecture between muscles and articulations is the proper design by the Creator to perform a multitude of daily tasks in a comfortable way

It is actually quite funny. A long text on the intelligent and purposeful design of the human hand and – blasphemically – how it can be model for robot hands:

The clear link between the structure and the function of the human hand also suggests that the design of a multifunctional robotic hand should be able to better imitate such basic architecture.

Obviously there was no editing or review of this contribution, and it was probably hit by a wholly inadvertent blunder somewhere along the way. S happens. It is surprising, however,  that PLOS ONE do not retract the paper . Retraction Watch has already set out the net.

Could it happen with fish papers? Sure, worse stuff gets published all the time but you are not likely to read much about it here because I am of the opinion that I should not comment on particular fish research here, but only in scientific peer reviewed publications. But papers on intelligent design are not scientific, and it is really amusing when they slip into  respectable journals.

Has something like this happened before?  Yes, creationsists are bragging about it here, but note that most journals publishing their pseudoscience are of lesseer quality. A major scandal was a paper in the well-renowned Proceedings of the Biological Society of Washington in 2004. Do we have to be afraid that pseudoscience takes over? No, only real science can provide reliable explanations of the world and its history. LOL!

Only today, PLOS editors have reacted to their own temporary demise:

PLOS ONE editors apologize that language wasn’t addressed pre-publication. We’re looking into concerns w/ priority.

As if language were the problem …Where were the reviewers, the editors?

Heroine of science

 biodiversity informatics, Electronic resources, Fish  Kommentarer inaktiverade för Heroine of science
Feb 182016
 

I am one of those among many thousands, millions even, with privileged access to paywall-protected scientific publications through my affiliation with academic institutions.

I am not one among millions of students and scientists who are locked out from an enormous amount of scientific publications and consequently unable to fully develop their potential to reshape the world into a better place for all of us.

I am even privileged to support Open Access by paying for removing the paywall from my publications (occasionally it gets too expensive).

But what happens when I retire? Will I have to go back to the 20th Century procedures of tedious search for relevant literature and writing one after the other of reprint requests mailed to busy people which may or may not grant me the mercy of honoring my request (actually, nearly nobody declines a reprint request)? Not likely, things changed, irreversibly. But I may get locked out from information.

Before the Portable Document Format scientific publications were strictly published on paper, either by a scientific entity (university, museum, society) or by a commercial publisher. In taxonomy, Journal of Natural History, society journals such as Copeia, and museum bulletins like those of the American Museum of Natural History or the British Museum (Natural History) could thrive on subscriptions or exchange. Everything animalish was indexed in Zoological Record which also was affordable. Authors would be given or could buy reprints of their articles for further distribution. Old and antique books were available from academic libraries. From the 1970s on photocopying techniques enabled one to build up complete libraries of everything written about a taxonomic group (e.g., all cichlid papers) at very low cost. It was not ideal, but life was flowing more slowly in the old days. You could do time-consuming quality work. You didn’t have to publish in Nature at all cost. ”Impact factor” was unknown, everything had 100% impact.

With digital publishing and PDFs all that changed. Particularly publication metrics has inflated publishing, and science administration is no longer by experienced scientists but by anyone able to count impact points (don’t have to be able to count more than the total number of digits on two hands, however). On top of that, scientific publishing has gone commerical to an extent really unexpected for academics. The simple equation in science is idea->research->communication=>education->democracy and well-being. For any democracy full insight into scientific research and full free access to the results and communication of research must be a sine qua non. Instead patenting is bigger business than ever and ”copyright” laws become more and more idiotic.

While research as such has not changed at all since we got out of the Dark Ages, the last 20 years has seen an increase in publications and particularly commerical publications, as well as scientists. One study suggests a doubling of scientific papers every 8 or 9 years (Bornmann & Mutz, 2015) Publications are not necessarily less available today than in the Paper Age, but they are more numerous, and and more people need to be informed. This causes furstration over inequality between those that can pay for the information and those who can’t and there is no logical reason for this discrimination.

UNESCO statistics shows an increase in number of researchers globally from 3,954,280 in 1997 t0 4,908,293 in 2013, that is nearly one  million more researchers, but the reporting is incomplete. In Sweden there was an increase from 36,878 in 1997 to 62,994 in 2013, and China nearly tripled in scientists, from 548,000 in 1996 to 1,484,040 in 2013. So I think we can conclude that both researches and students are on the rise. This means more papers and more needs for reads.

The oligopoly consisting in only about four publishing companies publishes half of the scientific research and paywalls it (Larivière et al., 2015). A random scientific paper published by a commercial publisher may cost say 30 USD for downloading. Any scientist will read (at least skim through) between 100 and 1000 new papers annually. That means that a single article is supposed to bring in from China alone if only commercial papers are considered, 1,484,040*30*100= 42,120,000 USD. Every year. From that the publishing scientist gets exactly 0 (zero) USD, the funding agency gets exactly 0 (zero) USD, the reviewers get exactly 0 (zero) USD, and whoever funded the funding agency gets 0 (zero) USD. I must be exaggerating, of course, because universities pay large amounts for online journal packages so the individual article pricing only applies to those who cannot afford to pay; or authors pay 3,000 USD to make an article Open Access, which means 3,000 less for research and I suppose it is not discounted from the package subscription.

Profits in the leading commercial science publishers are over 30%, close to 40%, and profits over 2 billion USD have been reported for just one publisher (Larivière et al., 2015).

Why does this madness go on? And on? Actually it is only about vanity and sloppiness, chasing High Impact figures invented by the same publishers. Would you believe that you get 2 billion USD of real value each year? End of all disease, end of all wars, all species on Earth named, cars running on water as fuel… No, no, you get mostly words, words, words, powerpoints, and figures, mostly trivial stuff, , some of it not even edited or peer reviewed; nothing that could not be published by a small society for nearly nothing (but worth 2 billion USD). But perhaps it doesn’t matter because most people cannot afford the subscriptions anyway.

Lead author of Larivière et al. (2015), Vincent Larivière, is quoted by CBCNEWS:

”We need journals because of their prestige. Journals give discoveries and researchers a hierarchy.”

No no; we need journals to publish results of scientific research. When we let journals ”guide” us to ”correct” or ”best” or ”most relevant” (i.e., most expensive subscription) research and grade us according to how we fit their standards (i.e., how much they can charge), it is corruption and manipulation.

Enter as a heroine of science Alexandra Elbakyan and SCI-HUB ”…to remove all barriers in the way of science”. SCI-HUB is repository of research papers culling Open Access as well as paywalled papers and making them available at zero cost to humanity. Some say this is illegal, but that remains to be demonstrated. It is not illegal to read, download or store a PDF file that you find on the web. It is not illegal to search for paywalled publications on the web. It may be illegal to re-publish such publications, what do I know. SCI-HUB is not publishing anything, it only helps you find stuff. I like The Pirate Bay too. I have no need for it, but I believe it does miracles for people in small circumstances. The Pirate Bay, however re-publishes artistic material, so I guess it is not quite OK in many cases.  SCI-HUB is different, it enables recovering the information that scientists and the society have already paid for.

 

Sci-hub_dayanisma

SCI-HUB is apparently operated by using the LibGen repository of paywalled scientific articles; and on top of that adding (also to LibGen) paywalled articles accessed from subscription codes. In my trials it works well with major publishers, but will not open lesser independent journals, and it will not open articles immediately upon publication. At the time of writing the SCI-HUB website reports that it has 47 million scientific papers.

In practice, if you stumble on a paywalled article that you need for your research or studies, you paste the DOI code in the search field in SCI-HUB, click on the button with an arrow on it, and if the publication date is not too close, the PDF file will be delivered to you. You may have to learn some cyrillic text to understand more, but do you really need to know more?

SCI-HUB is a research tool created by Kazakhstanian software developer and neurologist, and consequently heroine of science Alexandra Elbakyan in frustration over the pricing of scientific articles. She has been quoted (source not found) to refer to the Human Rights Declaration:

”Everyone has the right freely to participate in the cultural life of the community, to enjoy the arts and to share in scientific advancement and its benefits.”

Others have likened her to Robin Hood; or called her a hero, which testifies to masculinocentrism in the digital sphere,.. but we know what you mean. Alexandra’s story is told at length, and partly with her own words, in Simon Oxenham’s blog post.

Certainly, publishing is not free of costs. It takes time and or money to process a manuscript, and print it, but in science most of the work of producing a scientific paper is done without cost for the publisher. The overpricing of scientific journals, aimed to be charged to the producers of the content of scientific journals, is definitely worth concern and opposition. There must be other models of dissemination of scientific information. There must be a way also for researchers outside rich universitites to share information on the same conditions as institutionalized colleagues.

I do not see that SCI-Hub is doing anything that researchers do not do anyway, except removing the time-consuming work of asking people for pdf reprints, and the equally time consuming work of sending pdfs around by e-mail. Many of us have also scanned our earlier publication and distribute the scans instead of sending paper reprints.

Indeed, social networks such as Academia and ResearchGate are also used as vehicles for distributing publications in a free way. Those are equivalents of closed societies, for which reason at least some legislation must permit exchange of publications between members; but of course, Academia and ResearchGate do not provide the same amount of information.

Interesting as pirating may be, SCI-HUB signals something deeper: the need to reform copyright laws. Copyright on knowledge (scientific and educational communication) is an anachronistic phenomenon in a society that has gone beserk in control of profit. To start with, copyright must be lifted from scientific and educational papers, including technical drawings and background data. At some point we must also look over copyright on artwork. It makes no sense to prohibit use of whatever artefact for 70, 90 or 100 years after the author died. I really don’t understand what makes so valuable out-of-focus or otherwise inferior fish pictures on the web with a big copyright sign on them [Example][Example 2]. That’s an indication that copyright must be reformed or die.

An alternative to paywalled profit publishing and SCI-HUB is of course to publish and support by subscriptions to other, academically sound journals, like, in ichthyology, Copeia, Journal of Fish Biology, Neotropical Ichthyology (Open Access), Ichthyological Research, Ichthyological Exploration of Freshwaters … Not necessarily free, but a start away from the overpriced.

Support an ichthyological society:

American Society of Ichthyologists and Herpetologists (journal: Copeia)

Sociedade Brasileira de Ictiologia (journal: Neotropical Ichthyology)

Société Française d’Ichtyologie (journal: Cybium)

European Ichthyological Society (no journal)

Sveriges Fiskforskares Förening (no journal)

Ichthyological Society of Japan (journal: Ichthyological Research)

Fisheries Society of the British Isles (journal: Journal of Fish Biology)

References

Bornmann, L. & R. Mutz. 2015. Growth rates of modern science: a bibliometric analysis based on the number of publications and cited references. Journal of the Association for Information Science and Technology, 66 11: 2215–2222.

Larivière, V., S. Haustein & P. Mongeon. 2015. The Oligopoly of Academic Publishers in the Digital Era. PLoS ONE 10(6): e0127502. doi:10.1371/journal.pone.0127502

 

Aug 082009
 

Roger Hyam’s blog post Calling time on biological nomenclature and the comments it received, also on Taxacom, makes me wonder if not biodiversity informatics is the enemy rather than the servant of science. What some of my colleagues argue for are empty name lists, including also artificial constructs like barcode species. Then erecting the haplotype as the focal point of taxonomy is apparently to be expected lying in ambush.

For taxonomists, names are abstractions of scientific knowledge, and cannot, consequently, be managed in a formalised top-down system. To call for science to be published in only certain journals, to advocate that certain kinds of ”species” should be the only ones permitted, are not friendly proposals to rationalise information flows, but denials of the process of free information gathering. It is plain denying that taxonomic papers are primarily contributions to science in the first place, and name machines only secondarily. Taxonomy must remain a scientific exercise, and cannot be a mechanical process.

The idol project brought forth is the International Code of Nomenclature of Bacteria, where there is a Committee to decide, a single place to register names, and — most importantly, forgotten by the supporters — less than 10 000 diagnosable units are included. Since bacteria are so different from other organisms, and the named units so few (at least that have been admitted by this Committee …) the ICNB is simply not possible to use as a model for the several million species of multicellular organisms, most of which have not been named yet.

Whereas I am a friend of registration of names, and advocating that scientific names as defined in the Botanical and Zoological Codes are as good markers as can be (human-friendly they are) of scientific processes of elucidating the characteristics, whereabouts, and history of pieces of biodiversity, I cannot be positive to registration replacing the scientific procedure of testing hypotheses of phylogenetic distinctness labelled with scientific names. No committee should certainly be involved here. And whereas barcodes can probably be an interesting tool for the food industry and similar, I don’t see much use for it in taxonomy where we have species concepts based on evolutionary theory, type specimens, and diagnoses that are compatible with scientific theory and hypotheses. In taxonomy, contrast to the barcode shop, we also have flexible systems to classify biological units other than ”species”.

Whereas taxonomists must be more collaborative with biodiversity informatics in, e.g., voluntary registration in ZooBank, and show more effort to make their work and naming visible, it is the task of biodiversity informatics to find the methods to discover, assemble, and present the objects of biodiversity. We must not adapt science to fit the index.

The concerted effort of GBIF and Encyclopedia of Life to build a Global Names Architecture (GNA), providing a Global Names Index (GNI), seems to me to be a way out of the dilemma that biodiversity informatics is entangled in: information about biodiversity cannot be extracted because there are too many names (with misspellings, synonyms, homonyms, etc.) out there and the approximate (can never be exact) meaning of a name may vary from one mention to another. Certain related efforts, such as transparently tagging names with identifiers, as is being done in Zootaxa and ZooKeys, are bridging the gap between computerified and human-mediated names. Thus the technology is there, it is evolving, and taxonomy should be able to continue as a science.

The real difference between the mega-name-consumers and taxonomy is that mega-name-consumers wish to have all in one place, which is probably of zero interest to taxonomy. They are also not interested in metadata such as diagnosis, type specimens, etc., and they do not want taxon concepts to change, which they inevitably must do in science. In taxonomy, only small sets of taxa (and names) are handled at any given time, and of these, all have a definite function in the particular study, may be a revision, a field guide, a phylogeny, or a classification. In such contexts, the name domain is self-contained, and all named units are related to each other by the hypothesis or scope of the study. Everything else is of zero interest. For a study of cichlid fishes, it is of no interest whatsoever if New Zealand Lepidoptera exist. Enter mega-name-consumers, who will need both in the same list because those lists are not based on any scientific criterion and it is absolutely not known what the list is for. If consumers could define their precise needs from study to study, it might be easier to design the tools to extract the names and concepts actually needed. To maintain lists of millions of names, even in a database, for no specific purpose does not make much sense. Indeed, most checklists of smaller scale as well, especially when produced by non-specialists are equally meaningless anachronisms of apparently undefeatable listmania.

So, we must ask from biodiversity informatics:

  1. Proper specification of what their taxonomic units (text-names or LSIDs) are going to be used for. Map species occurrences, make phylogenetic hypotheses, sort out homonyms, …?
  2. Design systems that can effectively detect, maintain, and trace name usage and relevant metadata, compatible with taxonomic objectives and procedures.
  3. Provide voluntary registration systems, and other tools facilitating the exchange of names and metadata between taxonomists and consumers.

Whereas 2 and 3 may be underway, I am beginning to doubt that anyone can give a good answer to 1…

For those who cannot embrace taxonomy fully, I recommend stamp collecting. It has all the flavors of registration, codes, hybridisation, phylogeography, central committees, misidentifications, rare haplotypes, identical reissues, fakes, top-down standards, and stasis. It is a totally unscientific enterprise with no limits to organisational options suitable for old frustrated men obsessed with control. Ooops, does it sound like DNA barcoding …?

Image: Wikimedia Commons, public domain

New toy in town – GNI

 biodiversity informatics, zoological nomenclature  Kommentarer inaktiverade för New toy in town – GNI
Maj 112009
 

Some days ago – well, maybe weeks then – I touched on the usefulness of ZooBank, Catalog of Fishes, and friends. The bigger of them all is, however, GNI, a pronounceable acronym, a component of the GNA (The Global Names Architecture), but unrelated to GNU (GNU’s Not Unix). The Global Names Index is a name […]

From fishes to ZooBank

 biodiversity informatics, Ichthyology  Kommentarer inaktiverade för From fishes to ZooBank
Apr 172009
 

Fishes are among the most informatized organisms that I know. There may be a number of reasons for that, but reasons aside, the fact is that Daniel Pauly and Rainer Froese created FishBase independently of Bill Eschmeyer’s Catalog of Fishes, and ichthyologist Julian Humphries created the museum collection database with the collection management system MUSE […]

In the beginning …

 biodiversity informatics, Ichthyology  Kommentarer inaktiverade för In the beginning …
Apr 122009
 

This is a fast start blog to introduce myself (only a glimpse) and what possible kind of writings can be expected here. As an ichthyologist, I will write mainly about fish. I manage two e-mail lists, my twitter, and blogs for two projects. Let’s see if there is more to say. As a biodiversity informatician, […]

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