[Taxacom] Priorities in Funding

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Wed Mar 11 15:47:55 CDT 2020

 I reiterate that Donat seems to have a narrow (taxonomic) focus on a much broader issue. It could be argued that every (purely) taxonomic publication is a valuable piece of the overall biodiversity jigsaw. This is because (pure) taxonomy is descriptive, but most science (including stuff that usually gets included with taxonomy) is not descriptive. So, I would have fewer objections to making all (purely) taxonomic publications open, but not at the cost of making ALL scientific publications open. Having said that, Donat's vision of a comprehensive global taxonomic database does seem to me to be little more than a very expensive toy (a rubber duck that he can play with in the bath!) It isn't really going to be of much use for practical purposes outside of taxonomy. What we really need is some sort of meaningful cost-benefit analysis. Note that we already have a proliferation (mini-industry) of duplicated attempts to create global taxonomic databases of one kind or another. They only get so far, and it isn't clear to me that OA/OS will fundamentally change anything in that regard. I'm still suspicious that the main driver of OA/OS is corporate profit making.Stephen
    On Wednesday, 11 March 2020, 08:00:54 am UTC, Donat Agosti via Taxacom <taxacom at mailman.nhm.ku.edu> wrote:  
 The issue is not open science = open access = bad publishers. This is only one aspect.

What is at stake is that within open science we build an infrastructure that allows to provide access to the data from anywhere, be it from a taxonomic name, sequence, specimen, publication because everything is linked. Linked meaning a name, a sequence, a specimen is tagged with a standardized element, using in our domain for example TDWG vocabularies, and a link to the respective digital representation such as a digital specimen, if possible including a digital representation, a gene sequence (the sequence proper).

For that we need the respective standards and vocabularies, services and repositories that allow finding, access, reuse and curate, if necessary the respective data.

We need to understand how a particular research result has been calculated, on what data it is based and be able to reproduce it. For a new taxonomic name, we should be able to know, whether the name is available, on what data it is based (which specimens have been used, also the comparative material; what literature), how analyses have been performed.
To publish these results, we need publications that include all the structure, standards, we need mediators that provider services to create citable objects such as the figures and tables published in a publication and  disseminate these results, and we need aggregators that integrate these new results and again make sure that data is findable, accessible, interoperable and reusable.

Publications play only a part in this – but we are lucky in our domain, that we have publications that are either free or at a reasonable price that are open and provide these services.

Scientists, including taxonomists, increasingly create digital data, from images and other multimedia of specimens and their habitat in the field or afterwards in the lab, sequences, descriptions, use as much as possible digital copies of publications and GBIF as a resource to find specimens. These are all element of open science.

Currently, a major stumbling block, and in fact extremely time consuming, is to handle publications. First to know, that one exists, then to get a copy, then to extract the data and put it into a database. The goal has to be to minimize this dramatically. We have the means in our hand, open access, semantically enhanced publishing accessible through GBIF, including all the links in the publications.

Open Science is not  an empty shell as Steph points out https://twitter.com/stho002/status/1237503864607141888?s=09. In my little contribution I see it as a very concrete endeavor: Provide immediate open access to all taxonomic research results (e.g..new species) and data therein; liberate all the data imprisoned in our literature.

Open science is building an infrastructure by scientists for scientist that we control.


From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Sent: Tuesday, March 10, 2020 11:12 PM
To: taxacom at mailman.nhm.ku.edu; Donat Agosti <agosti at amnh.org>
Subject: Re: [Taxacom] Priorities in Funding


Your comments betray a narrow focus on a much broader issue. One could argue a certain case for open *taxonomic* literature, but Open Science is much broader that just taxonomy. It could be argued that each and every taxonomic publication is important, adding at least another small piece to the overall jigsaw. However, mandatory Open Science would effectively force the public to pay in advance for access to every piece of low grade, low interest scientific output including every inconclusive phylogenetic analysis lacking crucial taxa, every opinion on biogeography, every ecological study designed mainly to profit from external funding without producing anything useful, and goodness knows what else! The benefits simply aren't worth the costs. Furthermore, it is not as if everything is currently locked behind paywalls. Taxonomy may be a special case, in that the full article is more important than the abstract, but, for most other scientific publications, the abstract is more important than the full article, and abstracts are already open. We also have ResearchGate and other ways for making publications available (including Sci-Hub!). Taxonomic treatments are already being made available at Plazi by you. So we already have quite a lot of scope for information management (Zoological Record has been compiling new taxa for centuries, and much of it is available freely on the ION website). Mandatory Open Access/Open Science simply have minimal benefits for massive extra costs to the public purse. At the very least, it is misleadingly being sold as a "public good" issues, but the main beneficiaries are profit hungry publishers and externally funded institutions, with only minor benefits even for scientists. The public benefits not one whit! The economics involved can be summarised thus: journal subscriptions are paid for by externally funded institutions out of their overheads. This decreases their potential profit margins. Mandatory OA would shift the costs associated with publishing/literature access to the public purse. The public would be forced to pay in advance to free up every little bit of low grade scientific output. Although public money is wasted in many other ways, on a far bigger scale, it is nevertheless true that mandatory OA would, in the long run, divert even more trillions of dollars away from where it could be used for far more beneficial purposes to mankind. It is basically just the "establishment" sequestering even more public money for the benefit of its profit hungry shareholders, but to no benefit to the rest of mankind. This is how "the system" works! And they have the gall to try and spin it as a "public good" issue! Disgraceful!
Cheers, Stephen

On Tuesday, 10 March 2020, 08:34:18 am UTC, Donat Agosti via Taxacom <taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>> wrote:

Knowledge management is a reality, the best example being Google that helps - or better helped - us a lot to access content on the Internet that we would never have been able to discover. There is a big race to dominate this field, and there is a huge amount of money involved.

Rejecting Open Science because if siphons off money from are that deserve it more is like running against car, because horse carriages do it as well, and because some people might misuse it. Clearly, they will build tanks, but at the same time it allows to do certain things to his own advantage much more efficiently.

If you reject Open Science, then you essentially cement Google's position to dominate our knowledge, because they have the means to buy access to what they consider relevant to them (eg generating more revenues) which might not be what we as biodiversity scientists need.

What we need is to change statement such as "we are loosing one million species" IPBES to these are the one million species that we are going to lose, that we lost.

Clearly, the current way we do things is not delivering. Open Science has its flaws and could be misused. But already now, thanks to the tools and concepts the fledgling Open Science provides, 1154 new species or 87 new genera to science from 21 different journals (out of a total of 36) and 417 articles (650 articles) published in 2020 and duly cited have been added to GBIF as the sole deposit. This represents probably a third of all the new described animal species this year. This includes not just the names, but the taxonomic treatments, figures (5000 figures on BLR), in 837 cases also citation the holotype of which  445 have geo-coordinates. All of them have persistent identifiers so they can be cited, Wikidata could add a link and thus bridge the gap from the Wikimedia world to the facts in science. All of them are in a formats and repositories we scientists control and that can be adjusted with changing use cases and user requirements.

With maturing OS and acceptance by our community, I imagine a world in the very near future where we have a continuously updated catalogue of life with access to all the data (eg treatments, figures) in FAIR format, linked data based on the TDWG or other standards and including the persistent identifiers of the materials or gene sequences cited. This will allow on the other hand to link genes not only to an organism name but all the underlying currently implicit facts.

It will take a bit more to liberated all the data imprisoned in the current hundreds of millions of pages of biodiversity literature, of which a great stock in BHL is waiting to be dealt with.

Are there any other ways to remove the taxonomic impediment? Is it helpful to find all possible reasons to reject the new reality?


-----Original Message-----
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces at mailman.nhm.ku.edu>> On Behalf Of Stephen Thorpe via Taxacom
Sent: Monday, March 9, 2020 10:25 PM
To: Richard Pyle <deepreef at bishopmuseum.org<mailto:deepreef at bishopmuseum.org>>; taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>; Weakley, Alan <weakley at bio.unc.edu<mailto:weakley at bio.unc.edu>>
Subject: Re: [Taxacom] Priorities in Funding


Rich,I seems to me that you have missed the point. I'm all in favour of more funding for documenting biodiversity. My concern here is that OA/OS isn't going to result in more biodiversity being documented. Instead, it will either reduce the amount of biodiversity being documented, if funding isn't increased to cover OA costs. If funding is increased to cover OA costs, then the amount of biodiversity being documented will be the same, but extra public funding will be diverted from elsewhere just to make literature open to people who have no reason to want to read it. One might argue that all published taxonomy is intrinsically important, but OA/OS covers all science and there is an awful lot of non-taxonomic stuff that loses relevance quickly, and a fair bit that has little or no relevance to anything to begin with, being no more than a required output for a funded project. Mandatory OA/OS has the potential to boost profits of publishers and research institutions which operate on external (public) funding. Unless you own shares in either of those, I don't see any other benefits from mandatory OA/OS, other than being fractionally easier to access literature if you are one of the few people who needs to access large amounts of scientific literature on a regular basis. But at what cost? Trillions in the long run.Cheers,Stephen    On Monday, 9 March 2020, 09:03:30 pm UTC, Weakley, Alan via Taxacom <taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>> wrote:

Amen, Rich.

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Sent: Monday, March 9, 2020 4:57:05 PM
To: taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu> <taxacom at mailman.nhm.ku.edu<mailto:taxacom at mailman.nhm.ku.edu>>
Subject: [Taxacom] Priorities in Funding

I know I'm jumping in a bit late to this game (been travelling), but I did want to comment on a couple of things (and, perhaps, shift the direction of the conversation a bit; hence the new subject line).

John Wrote:

> And lets not forget the zillions spent on war, space exploration etc.

Consider this:
(the second half puts your point in perspective)

Stephen wrote:

> by way of diverting what in the long run will be $trillions away from
> healthcare, welfare, etc., thereby helping to keep much of the world
> locked in poverty.

That's a pretty LLLLOONNNGGGG run for the OA publishing price tag to add up to $trillions; but what the hell -- I'll bite.

Stephen:  you got it backwards, mate.  With just a *tiny fraction* of the $trillions already spent on healthcare, welfare, etc. (more like $quadrillions by the time OA costs add up to $trillions) -- which probably saves only a few tens of millions of lives --  we could make MAJOR progress on documenting, understanding and perpetuating global biodiversity -- something of profound importance to the entire future of humanity (i.e., many **billions** of lives).  And because we'd be siphoning only a *tiny fraction*, we'd *both* be able to save tens of millions of lives *and* give the future of humanity a fighting chance. Let's have our cake and eat it too!

Oh, and we don't even need to siphon a tiny fraction away from healthcare, welfare, etc. -- we can instead take a tiny fraction away from military, political campaigns, etc., who won't even notice that it's missing.

Donat clearly has the right of this, in my opinion. This may be a bit overly provocative, but entire civilizations have come and gone within the tiny window of time humans have roamed the planet, but global biodiversity is a nearly 4-billion-year old legacy that demands WAY more of our attention (compared to other luxuries we currently spend our time and resources on) than it has ever received. OA is an admittedly small(ish) part of this, but it is an important part nonetheless.

I know I'm preaching to the choir here, but our perpetual problem is that the choir of taxonomy/biodiversity has been *horribly* out of harmony, so there's no wonder hardly anyone has been listening.  It's great that the issue of Climate Change has reached the heights that it has, but it's inexcusable that the associated loss of biodiversity has been little more than a footnote on the large-scale global conversation about climate change. The loss of biodiversity wasn't even mentioned in the film "An Inconvenient Truth" (except in the extended features on the DVD).  I know we've been gradually getting better, and stories about the impact of climate change on biodiversity have been gradually making their way into the public consciousness.  But it's still a bit of the tail wagging the dog, in my opinion.  I think a STRONG case can be made that biodiversity loss should be **THE** major issue in the climate change conversation, because of it's potential impacts on the *entirety* of future human civilization (not just the measly few million years that we've been around so far, let alone the few decades of any particular human life, or more trivially, a political cycle).  We in the biodiversity community are WAY underselling both the value and the urgency of this issue.  The CBD and the like are all great steps in the right direction, but I fear those efforts are being seriously held back by our insatiable desire to bicker with each other about trivial issues.  The physicists and astronomers figured this out decades ago, which I think is largely why their funding levels are *five orders of magnitude* more than ours (reference the above-linked video).  Judging by the banality of what I often see on Taxacom and elsewhere, I'm not holding out a lot of hope.


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