Memorandum submitted by the EDIT Consortium
EXECUTIVE SUMMARY
1. Given the Government's reaction to the
last report `What on earth? The threat to the science underpinning
conservation', it is unlikely that significant new funding
can be expected as a result of the current enquiry. It is the
view of the EDIT consortium that a sensible strategy would be
to seek to establish clear responsibility for a number of infrastructural
issues, viz:
2.
put the funding for taxonomic collections, including
living materials, into a long-term strategic plan with clear lines
of responsibility;
3.
identify which science funding body should be responsible
for the development an effective means to map between alternative
systems (specifically DNA and morphological) so that we keep the
best elements of the existing knowledge base while embracing new
approaches;
4.
identify which science funding body should lead the
development of infrastructure to move taxonomy from an artisanal
to an industrial structure;
5.
identify which science funding body should be responsible
for developing a metric to assess contributions published directly
to the web, which will measure significance of taxonomic work
independently of the print publications in which the material
appears and influence science managers to use the metric in assessing
staff output;
6.
Support for open access publications, by whatever
means are necessary;
8.
Stop the loss of taxonomic expertise, and ideally,
reverse this negative trend reversed over 5-10 years. This must
involve examining the policies that have driven taxonomy out of
UK Universities.
BACKGROUND
2. The European Distributed Institute of
Taxonomy (EDIT) consortium consists of 27 partner institutes supported
by the European Union. The consortium has six operational and
structural objectives : to reduce fragmentation and to transform
taxonomy into an integrated science; to strengthen the scientific,
technological and information capacities needed for Europe to
understand how biodiversity is modified through Global change;
to progress toward a transnational entity by encouraging durable
integration of the most important European taxonomic institutions,
forming the nucleus of excellence around and from which institutions
and taxonomists can integrate their activities; to promote the
undertaking of collaborative research developing, improving and
utilising the bio-informatics technologies needed; to create a
forum for stakeholders and end-users for taxonomy in biodiversity
and ecosystem research; and to promote the spreading of excellence
to fulfil the needs of biodiversity and ecosystem research for
taxonomy based information. Further information can be found at
http://www.e-taxonomy.eu
THE STATE
OF SYSTEMATICS
AND TAXONOMY
RESEARCH
3. The number of described species globally
has increased linearly over the past 50 years, whereas the estimated
number of living species has increased tenfold. With the advent
of climate change, the destructive potential of Invasive Species,
the increasing anthropogenic mobility of some species and the
global interests of many European countries, any country has potential
interests in the global biota. The motivation to create the EDIT
consortium was to integrate the pool of taxonomic expertise such
that expertise would be available within an European context,
if unavailable within any particular state. Furthermore, integration
of European taxonomic institutions is expected to allow recruitment
to fill gaps in coverage.
4. Estimates for the total number species
varies between 4 and 10 times the number already described (1.8
M) and at current rates, preliminary descriptions and names could
be completed by 2050 for the lower bound and effectively never
for the upper bound.
5. The majority of taxa to be discovered
are very small (<1 mm), including microbial. The current balance
of expertise is estimated to be 4,000-6,000 professional taxonomists
and 30,000-40,000 amateur taxonomists across the world (http://tinyurl.com/yw82xx).
For a discussion of the term `taxonomist' see Enghoff & Seberg
(2006)1. There are few data available on the spread of taxonomic
expertise of the amateur community, but amateur microscopical
societies, eg the Quekett Society http://www.quekett.org, lists
only 17 others worldwide of which 5 are British. This implies
that much of the recent productivity will not translate into very
small organisms. It is difficult to see how one could manage and
direct such an amateur workforce and particularly how to maintain
taxonomic standards.
6. Taxonomic science of the highest international
quality, specifically descriptive and nomenclatural studies, can
be conducted by individuals with quite basic equipment: indeed
there are numerous self-funded amateurs in this category. Lacking
an intrinsic dependence on large or expensive equipment, there
is no natural driver to establish fora in which the taxonomic
community can debate priority and no obvious purpose for such
a priority list. Priority is therefore normally established locally.
One objective of the EDIT project is to establish a level of managerial
collaboration between major taxonomic institutions which may develop
a mechanism to determine Institutional priorities for research.
7. The advent of DNA-based methods requires
a source of reliably identified specimens from which DNA can be
extracted. Consequently the morphologically best-represented and
most-studied groups will inevitably be best represented in sequence
databases. Groups with poorly developed basic taxonomy or poorly
represented in Museum collections will not necessarily benefit
from this new technology, although DNA-based methods can increase
descriptive productivity by assisting in the characterisation
of species and the establishment of relationships. There is also
a danger that DNA-based taxonomies will de-couple from morphologically-derived
taxa, of which there are vastly more presently defined. There
is a particular risk that mapping of species concepts between
the two definition types will increase levels of confusion and
noise in the databases.
8. EDIT was conceived on the premise that
taxonomy cannot address the shortcoming described in paragraph
3 if we continue with current practices, essentially independent
of the amount of funding applied to the problem. It is essential
that we develop better ways of working and the strategy being
followed by EDIT is to use Web technology to facilitate collaborative
working and by more efficient exposition of the results of taxonomic
effort. There is not yet evidence that teams of taxonomists work
faster than the same number of individual taxonomists, but multidisciplinary
teams including taxonomists can more effectively focus taxonomic
effort. Nevertheless, EDIT views it as essential to move taxonomy
from an artisanal to an industrial basis which will mean that
the process needs to be broken down into steps to increase throughput
efficiency (see the report "Taxonomy in Europe in the 21st
century" attached as an appendix). Critical to the development
of this vision will be mechanisms to deliver credit, ie the means
for career advancement, to those undertaking the work (see paragraph
25).
9. EDIT is predicated on facilitating taxonomy
(nomenclature, identification and systematics1) as it is currently
practised. Although we recognise the need for a fundamental change
in taxonomic practice, it is not clear that new approaches will
deliver the required properties of stability and accessibility.
Should we choose to abandon description and Linnean nomenclature
in favour of identifiers, while it may increase throughput, it
is not certain to meet the needs of the bioscience community,
policy makers, environmental management, education and the public
in general. What is needed is an effective means to map between
alternative systems so that we keep the best elements of the existing
knowledge base while embracing new approaches.
10. In order to change taxonomic practice,
an EDIT goal, we consider it essential to accommodate the methods
used by taxonomists now, including publication vehicles. This
is in large part to avoid jeopardising perceived career progression
based on established mechanisms.
Data collection, management, maintenance and
dissemination
11. In 2006 the United Kingdom Taxonomic
Needs Assessment, conducted by the Global Taxonomic initiative,
determined that "In the UK the following types of information,
listed in order of importance, were identified as important for
biodiversity conservation but not sufficiently accessible;
In the Overseas Territories the following types
of information, listed in order of importance, were identified
as important for biodiversity conservation but not sufficiently
accessible;
12. Data access is undoubtedly a major bottleneck
both to taxonomists and to users of taxonomy. It is here that
we expect Web technologies to have the most significant impact.
It is essential that we unlock the store of information currently
held on paper in libraries, even the best of which cannot be comprehensive.
These data need to be re-structured to give access to names, descriptive
information, linked to specimen and collection information and
mapped onto other digital resources, such as molecular databases.
The key barrier to this is cost, especially the tyranny of publisher
charging access fees to old, obscure material that they no longer
sell on paper, but also the cost of extracting and structuring
text-based material to make it amenable to data mining.
13. Taxonomic publications characteristically
have low initial impact but are accessed and cited over many decades.
Consequently primary taxonomic output, especially the larger monographs,
is marginalised from the high-impact journals. The NHM (London)
published 2222 papers in the financial years 2003-2007 in 649
journals: 39 per cent of journals (23 per cent of papers) were
not included in the Science Citation Index and consequently did
not have impact factors. The pressure on editors to drive their
Impact Factor ever upward is driving descriptive taxonomy into
more obscure journals that are less effectively accessible to
internet search (eg Web of Science) and thus more difficult to
find. Furthermore, the pool of referees available to such journals
is often more restricted, so it is hard to manage issues of data
quality.
14. EDIT considers that data access is central
to improving efficiency, so is developing a "cyber-platform"
(http://www.editwebrevisions.info/content/work-plan) that will
capture data in a structured manner and make it available to users.
We have adopted the design developed by the CATE project (http://www.cate-project.org)
and have offered community web sites (scratchpads; http://www.editwebrevisions.info/scratchpads)
that have gathered 237 users from 28 countries, creating 53 sites
with 102,000 pages since their launch in March 2007. The principle
is to allow users to deposit data in any form, but to encourage
building structure into the data which can be garnered into a
common data resource (Common Data Model) and made available through
a program interface to other applications.
15. It is usually the case that funding
for infrastructure can be secured to built data structures (eg
EDIT) but it is rarely the case that funding can be found to populate
those structures. Since it does not lead to funding, the population
of databases does not earn any credit for the data generator in
terms of career progression. Populating databases is consequently
often opportunistic: the data are often not optimally structured
and even more rarely compliant with current standards and ontologies.
Perhaps even worse, there is rarely funding for long-term maintenance
of these data sets which too often become `orphaned' when their
creators retire or move on. It would benefit the enterprise to
establish a data centre to have responsibility for curating data
in a manner similar to the care of specimens.
16. A common request to taxonomists from
other communities is for identification guides, ideally keys,
but at least monographic treatments to facilitate accurate identification.
A related EU project, Key2Nature (http://www.key2nature.eu/en/index.html)
plans to build identification keys to specific geographical regions.
To do this they need standardised descriptive data presented in
a matrix fashion. These data will not be generated within Key2Nature
itself; the project is predicated on the assumption that they
will be generated by the taxonomic community. The project's goals
are to give access to eLearning tools for identifying biodiversity.
17. DNA-based methods, while falling in
price rapidly, are still comparatively expensive for the most
commonly studied groups in environmental impact assessments. Whereas
there is no doubt that these techniques will be invaluable in
the future, current efforts to build the barcode databases necessary
to support them are limited by the availability of authoritatively
identified organisms from which to extract DNA.
18. Ultimately taxonomic authority rests
on the ability to compare an unknown with a standard held in a
recognised collection. It is imperative that these collections,
which taken collectively constitute a very large-scale distributed
research infrastructure, be maintained. The most expensive (in
terms of cost per collection item) are under most threat and are
the collections of living cultures that underpin microbial systematics.
We note with concern the current situation at RGB Kew resulting
from the funding difficulties in which Defra finds itself.
19. The current Rules of Nomenclature require
new taxa be described and named, or any other taxonomic act, in
paper publication. This is currently being addressed by parallel
paper and web publication. It is likely that the Zoological community
will move to accepting web-based publication in the moderately
near future. To allay the major concern it is urgent that a central
archive strategy be put in place, independent of the publishers
themselves, to fulfil the role that repository libraries have
traditionally played. It is obviously desirable that we move to
an open-access model for taxonomic literature and away from the
current models which often requires data generators to pay substantial
fees to publishers.
SKILLS BASE
20. The only survey of UK taxonomists of
which we are aware (http://tinyurl.com/2z3nl8) can be summarised
as follows.
| | |
| |
| Age | Total |
per cent | Male |
Female |
| | |
| |
| <20 | 2 | 0
| 1 | 0 |
| 21-30 | 14 | 2
| 8 | 2 |
| 31-40 | 155 | 19
| 120 | 32 |
| 41-50 | 230 | 29
| 184 | 47 |
| 51-60 | 235 | 29
| 206 | 26 |
| >60 | 169 | 21
| 152 | 20 |
| Not given | 56 |
| 31 | 16 |
| Total | 861 |
| 702 | 143 |
| | |
| |
| | |
| |
21. These taxonomists were reported from 176 institutions
and had expertise in 192 taxonomic groups, detailed at <http://tinyurl.com/ywhsuv>.
It is of course not possible to infer trends from a single sample
point, but it is of concern that close to 60 per cent are between
40 and 60, with a further 20 per cent past normal retirement age.
22. European science is facing a tremendous loss of taxonomic
expertise. Despite the availability of a well developed taxonomic
infrastructure, European taxonomic research, including its collection
management aspects, increasingly relies on an aging taxonomic
community, with permanent staff often over 50 years old and with
a significant input by retired researchers and skilled amateurs
who frequently have to self-fund their research. <http://tinyurl.com/2yb82j>
23. Efforts to find enthusiastic young people with an
interest in becoming qualified taxonomists are thwarted by insufficient
training opportunities and a lack of long-term professional prospects.
To address this problem, education is an essential component of
EDIT. The main challenge is to stop the loss of taxonomic expertise,
and have this negative trend reversed in 5-10 years from now.
EDIT will strive to achieve this by increasing the transfer of
knowledge and by establishing an integrated European training
programme for taxonomy. In parallel, public education will increase
the awareness of the vital contribution that taxonomy can make
to biodiversity and ecosystem research, and consistent lobbying
will contribute to enhance interest of decision-makers and funding
agencies.
24. UK University education in whole organism biology,
and consequentially systematics, seems to be in sharp decline
judging by the educational records of those appointed to the Natural
History Museum and Royal Botanical Gardens, Kew & Edinburgh.
Increasingly appointees are recruited from other countries. It
is noteworthy that many of the UK-trained taxonomists employed
by these Institutions come from the pool of graduates trained
on courses in which the Institution staff are heavily involved
in teaching (Reading and Edinburgh Universities; Imperial College,
London). This increased involvement helps to disguise the decline
in University staff equipped to teach taxonomy.
25. A key barrier to change is the mechanism by which
scientific productivity is now measured. Such is the weight placed
on impact factors and citation rates that it is difficult to produce
the large coherent works required for taxon identification while
getting employer's recognition, or worse, getting tenure. EDIT
seeks to develop a metric to assess web-based usage and assign
credit to data creators as an alternative to the Citation Index.
26. It is relevant to note the State of Emergency declared
by the EPPO Council (http://tinyurl.com/2hwj3a):
"The work of National Plant Protection Organizations
(NPPOs) relies on scientific expertise, but the services providing
this expertise increasingly lack staff, funds and training.
On the one hand, the whole scientific basis of the phytosanitary
field is quickly eroding. Taxonomy, classical plant pathology
and other scientific fields which are vital for sustaining sound
public policy are threatened with extinction, because they are
no longer in the forefront of science priorities.
On the other hand, the need for phytosanitary expertise, training
and research is substantially and continuously increasing. The
number and complexity of plant pest problems increases every year.
New developments and new technology have to be mastered, going
far beyond existing expertise.
Unless urgent action is taken, indispensable expertise and
scientific disciplines will irreversibly disappear, and NPPOs
will be unable to do their duty."
REFERENCES
1. Enghoff, H. & Seberg, O. (2006). A Taxonomy of
Taxonomy and Taxonomists. The Systematist 27, 13-15.
2. Cowan, S. T. (1955) The principles of microbial classification.
Introduction: the philosophy of classification. The Journal
of General Microbiology 12, 314-319.
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