Examination of Witnesses (Questions 20-39)
Professor Stephen Hopper, Dr Eimear Nic Lughadha,
Professor Mary Gibby, Dr Michael Dixon and Professor Richard Lane
19 FEBRUARY 2008
Q20 Lord Krebs: Is it that mycology
is the most important under-represented area in taxonomy, or is
it just that mycology happens to be what we are talking about
now? Could I, if I were a microbiologist working on bacteria,
make the same kind of pitch about bacterial taxonomy? Or if I
were working on soil invertebrates, could I make the same pitch
about collembola or something like that? How important are fungi
compared with other groups that might be understudied?
Professor Lane: There will be a number of organisms
that would be candidates for particular care and study. Most of
them would be very small organisms; most of them would be protists,
single-celled organisms. There will, of course, be the extremely
primitive organisms, bacteria and viruses, which we would take
on board. Why? Because technology has recently given us an opportunity
to investigate them in a way that we could never do before. No
longer do we have to worry about, if we can cultivate it, we can
describe the species of bacterium, if we can cultivate it, we
can generally describe a protozoan. Now, increasingly, we have
technology and informatics techniques, which allow us to explore
the world that we do not have to culture. That is where, interestingly
enough, the debate extends beyond the organisations represented
here. Our organisations are built around having objects and for
many of these organisms there is not an object that is easy to
retain so, historically, we have not done much about them. But
now we can, they have come onto the agenda and they have become
much more tractable. It is the ability to do that in a way that
you could not before. "Metagenomics" is going to allow
us to look at whole communities of organisms that it was not possible
to investigate, even 10 years ago. That is going to accelerate.
In answer to your question, a number of groups of organisms are
under-represented, most of them will be small, physically. So
if I was interested in soil mites, I probably would not want to
start looking at the morphology of mites; I would take what we
already know as the skeleton of knowledge and then fill in the
extraordinarily large number of spaces with new technology, such
as DNA approaches.
Q21 Lord Colwyn: Perhaps we can move
on now to discussing the relationship between systematics and
taxonomy and the web. We had an excellent presentation from Charles
Godfray a couple of weeks ago, when he talked about the current
uses of the web and how it might be used. We also heard of the
proliferation of non-professional taxonomy on taxonomy sites,
which sounded very interesting. We also heard that there is a
relatively slow progress in bringing data from the major UK taxonomic
collections on line. If the UK systematics community is perhaps
not doing so well, and we heard how it occupies a unique position
with two of the top five world biodiversity institutes. Who and
where are the users of these data? Is retrospective data capture
justified and how should it be funded?
Professor Hopper: I came from Perth in Western
Australia before I joined Kew. If I can give you an example there,
the herbarium is fully digitised—the historical data collection
was completed about 10 years ago. This is a rather applied example
but that State is in the midst of an incredible mineral boom and
has stringent environmental legislation requiring miners to report
on the environmental impacts of their activities, and repair and
restore if they get granted approval. Ten years ago, it would
have been impossible to advise them as to the likelihood of them
encountering a threatened species in the areas of interest to
their lease. With the historical collection now databased, it
is possible to say for the whole flora based on the information
in the collections; there are areas of intense biodiversity richness,
where the alarm bells should go off if your mineral interest happens
to coincide with it. We can develop predictive models about what
would have been in mines sites, if they are into repair and restoration,
from the database that is available. The short answer to your
question is that getting the historical information that can be
located in geographical space is an incredibly powerful tool for
an example like that. There are all sorts of intrinsic scientific
questions that become possible when you have a grip on the collections
that are available. I said in my opening remarks that I believe
that taxonomy is hypothesis driven and every name is a hypothesis
about the features of an organism, its geographical distribution
and its ecology. The historical collections are part of the database
that go into formulating that hypothesis and as incoming collections
arrive we get more and more precise. Ultimately, we are able to
be much better custodians of the global biodiversity that is our
heritage if we have both the historical and the incoming new information
digitised in this way.
Q22 Lord Colwyn: Would you believe
that the UK taxonomists are up with the rest of the world?
Professor Hopper: By no means; way behind. The
scale of the enterprise is much larger because the UK has these
tremendous historical collections—the Kew collection has
about 7 million specimens; the Western Australian herbarium collection
I am talking about has 600,000. The task is formidable but the
pay-offs and benefits of dealing with this very tractable question
are not what I would regard as an expensive way forward at all.
It is a relatively small investment for significant paths for
all kinds of applications of biodiversity knowledge. The UK has
a long way to go, but with a modest investment of funds, the job
could be done and done well.
Professor Lane: There are two different issues
wrapped up in Charles Godfray's comments. One was about primary
data, which come from specimens, what they are and where they
were found. The second is information—a database on legumes
or a group of other organisms—and whereas the latter are
mushrooming in all sorts of places, and different groups are now
able to do that, it is the primary data points that are lagging
behind, so I think we should distinguish between these. We should
also be aware that there are initiatives like the Biodiversity
Heritage Library, which is putting the biodiversity literature
on the web.
Q23 Chairman: May I ask who is paying
for that?
Professor Lane: Currently, the Biodiversity
Heritage Library is paid for by US money.
Q24 Chairman: Government money or
charitable trusts?
Professor Lane: US foundations; much in the
same way that Dr Nic Lughadha referred to for the African Plants
Initiative. So, getting those geo-reference data properly on the
web is extremely important. The challenge we face is how to prioritise.
Our organisation has 70 million objects; you cannot start in A
and go through to Z. We have to look at particular groups of organisms
where we believe the information that they generate will be valuable.
We cannot do it on our own, because we also need to look at specimens
in other organisations. For example, we have been talking to some
major museums in North America about putting all the vertebrates
from three or four major museums on the web. The general belief
is that because they are data in space and time, they will generate
lots of hypotheses in their own right, as a genome sequence does,
for example, as well as answering fairly focused questions on
what has changed and where is it now. It is the need to focus
and do some of them first and mine those data which is our biggest
challenge.
Q25 Lord Colwyn: Who and where are
the users of this data?
Professor Gibby: It is significant that the
Mexican Government has invested in getting access to data on Mexican
specimens that are across the world; sending people out to capture
that data to take back to Mexico because they need it. The users
are all over the world because, of course, our collections are
all over the world. Prioritising could be prioritising for individual
countries, like the African Plants Initiative for providing information
for Africa. That government realised the importance of the historical
data and put the money behind it.
Q26 Earl of Selborne: A recent NERC
science theme report on biodiversity highlights, amongst other
things, the challenge of "providing increased human capacity
to reverse declining taxonomic expertise". We have heard
from Dr Dixon that, in fact, it is up to all of the three institutions
represented here today to determine how their grant-in-aid from
the three different funding streams is spent. If you did somehow
manage to increase human capacity in terms of increased taxonomic
expertise, would you choose to spend your money in that way, or
would there be other areas on which you would wish to spend instead?
Dr Dixon: The first thing to say is that taxonomy
is becoming a bigger and bigger science. It has been referred
to already as a big science, but what technology enables us to
do has expanded dramatically over the years, so it is probably
true that we spend a smaller proportion of our overall expenditure
on descriptive taxonomy but not on taxonomy and systematics overall.
We develop capacity where we can; we are not a higher education
institution but we do work with Imperial College; we teach an
MSC course on advanced taxonomy and systematics. Over the last
decade about 200[39]
students have gone through that course. As an institution—I
am sure it is the same in Kew and Edinburgh—we host a number
of PhD students registered in a range of universities across the
UK, in our case, about 90[40]
at any one time in the Museum. Although the science theme report
points to diminishing proportion of resource spent on taxonomy
in some of our institutions, I would not agree with the statement.
What we are very adept at doing is looking at external funding
streams and using those to pursue our own mission. We have heard
about American trust and foundation funding for big projects such
as the Biodiversity Heritage Library, the African Plants Initiative,
and the Latin American Plants Initiative. DEFRA's own Darwin Initiative
is effectively a capacity-building project. The Natural History
Museum has probably been one of the biggest recipients of grants
from the Darwin Initiative, which is great in that it builds capacity
in developing countries, helps our scientists develop new ideas,
new lines of inquiry, as well as producing application tools that
are relevant for those communities.
Dr Nic Lughadha: I should like to add to what
Dr Dixon said by saying that the numbers of PhD students being
trained in taxonomy and systematics in the broad sense might give
a misleading view on the next generation coming up who might do
descriptive taxonomy. At Kew, we have about 80 PhD students registered
and if you look at what is going to be in those doctoral theses,
only about 15 of those theses will have a substantive portion
of descriptive taxonomy. We have become adept, as Dr Dixon said,
at identifying sources of funding through which we could fund
a PhD student, but usually the topic is outside the standard descriptive
taxonomy field. Of those 15 students of our 80, the 15 who will
have descriptive taxonomy in their theses, 10 are registered overseas;
only five are registered in the British Isles. So the proportion
of our students that are learning to be descriptive taxonomists
is very limited. I suspect that the same might be true—perhaps
the proportion is different—at the Natural History Museum.
Dr Dixon: Another point to mention is that each
of our institutions engages with amateur scientists and other
communities in developing taxonomic expertise. The Museum, for
example, undertook a project with fly fishermen across the UK,
which enabled them to identify flies of particular interest to
them in pursuit of their hobby, and in developing that expertise
they were able to provide useful data on the health of water courses
in the UK. Building that capacity, as we plan to do as part of
our centre for UK biodiversity in the next phase of our Darwin
Centre Project, is also a useful way of building capacity, although
not necessarily in the professional sense.
Q27 Earl of Selborne: But there is
a limit to what you can do with amateurs, is there not? If you
come to succession planning in your institutions, you are going
to have a problem if you run out of suitably qualified taxonomists?
Dr Dixon: Yes, that is true.
Professor Gibby: It is a challenge to find people
to appoint to positions because if you are advertising for a lichenologist
or someone in mycology, you are not going to find them in the
UK; we would have to look abroad. We are trying to get some succession
planning, so that with one or two extra posts you can have someone
more junior working with the senior taxonomists and perhaps doing
more molecular work or more conservation applied work, but learning
from the taxonomist at the same time, otherwise those skills are
not going to be passed on easily to PhDs. We need to have partnerships
with people working alongside as part of a team to pick up those
skills.
Q28 Lord Warner: Could I understand
something on which I am not altogether clear. Is it the universities'
inability to produce taxonomists for you that is a constraint,
or if there was money available could you follow the example of
some other fields in science and quasi--science—like medicine—where
it has been employers who have developed the capacity to bring
new people into the fields. They have not relied on the universities;
they may have used validation processes in the universities but
it is the employers who have driven the agenda because, in some
cases, they got fed up with waiting for the universities to do
something. I am trying to understand where the real blockage is.
Professor Gibby: We have to drive that agenda
and make sure that we are getting people trained to do the jobs
now. That is the situation. We cannot rely on the universities
to do it. We can for other aspects of the skills that are useful
to the taxonomist now, but the taxonomy has to be something that
we teach because we are the only places that hold that expertise.
Professor Lane: I want to make two points. One
is that partnership is possible; if you look at the NERC initiative
in taxonomy, which was a good few years ago, which sought to link
universities and major taxonomic institutions together, it is
very clear to see the remaining imprint of that initiative a decade
later, with lots of students and a connection between institutions.
That is a very good example of a way of working together. The
second point is that in our experience, it has not been difficult
to hire taxonomists. If we take the broader view—and I defer
to the point that was made earlier on about descriptive taxonomists—just
to give an example, when we recently looked for senior researchers,
professorial level; we advertised and had over 200 applications,
87 per cent from outside the UK. In the event, we hired predominantly
people originating from outside the UK. Even if we specify a particular
taxonomic group, as we recently did in our entomology department,
two of the three people we hired are from outside the UK—from
Germany as it happens.
Dr Nic Lughadha: To follow up from Professor
Gibby's point. We have completely changed our recruitment model
in the past 20 years. Twenty years ago we were advertising for
plant taxonomists, entry level graduates. Now we advertise the
same level of position as a trainee botanist, so that we make
the assumption that we are going to get in somebody who is reasonably
bright, has some aptitude and we train them in-house. We no longer
expect to recruit taxonomists from the universities at entry level.
At a more senior level, and that tends to be where succession
planning gets explicit, we have had extreme difficulties in filling
gaps at senior level. For instance, in mycology but also in grasses,
we have advertised positions and failed to fill them despite extensive
searches in the UK and overseas.
Q29 Lord Krebs: We have already heard
some comments about DNA technology from Professor Lane and its
role in taxonomy. At the time of the last inquiry of the Sub-Committee,
we heard about DNA barcoding as an emerging tool in taxonomy and
it would be interesting to hear from you what has happened in
the last few years, who is routinely barcoding plants and animals,
what proportion of the UK flora and fauna have been barcoded and
how is that all being used?
Professor Lane: There was an initiative started
in Cold Spring Harbour Laboratory about five years ago on DNA
barcoding,[41]
and then we hosted at the Natural History Museum the first scientific
conference on DNA barcoding which many felt was a risky thing
to do for an emerging technology in a museum, but I am glad to
see that it has come to life. DNA barcoding has begun to expand
hugely in the scope of what it covers by engaging a very much
wider group of researchers and users of systematics than other
technologies have done. It is very important to say that its primary
role is in diagnostics and it is an important aid in species discovery,
but it relies on us having an established taxonomic framework
in which these diagnostics can be slotted, and that is absolutely
crucial. A number of organisations are taking the lead, so that
there is an all-birds biodiversity initiative, an all-fish biodiversity
initiative, where there is a small sequence for every group—I
will leave my colleagues to talk about the plant ones—and
we are currently running one based in London on mosquitoes, where
we aim to barcode 80 per cent of the world's known mosquitoes;
we are certainly on track to do that within the next two years;
interestingly enough, funded from an extraordinary diversity of
sources, including, again, American foundations.
Professor Gibby: Plants are a little more difficult
to work with because the mitochondrial DNA is not changing enough
for it to be the right tool. There is an international plant working
group to barcode plants and a member of staff at RBG is currently
chairing that group. That has had funding from the Consortium
for the Barcode of Life, but it is getting funding partly from
the consortium on barcoding plants but also with input from the
Garden to help fund that work. There is progress: at the Garden,
for example, one of things we are doing is making sure that when
we are making collections now we are also making DNA collections
so that material is collected in the right way. We have a pilot
project to barcode the liverwort flora of the UK, because it is
relatively small—about 350 taxa—and at the current
rate of progress it will be completed in about five years. We
are discovering species along the way and are using a group of
organisms that are quite difficult to identify, so it is a good
technique for trying to see how effective it is as a diagnostic
tool in plants. We are also part of an international tree barcoding
initiative, working with people around the world on barcoding
particular groups of trees. That is in collaboration with people
in botany at the Natural History Museum as well as at Kew and
many other laboratories.
Q30 Lord Krebs: I would like to ask
one follow-up question for clarification in response to Professor
Lane's comment about the need for some framework of taxonomic
identification within which the barcoding operates. As you know,
at the seminar we heard from Professor Bland Findlay a rather
sceptical set of comments about molecular typing of micro -organisms.
I quote from one of his paragraphs, "molecular markers have
the potential to sew confusion with the almost infinite variety
of genotypes from a vast global gene pool". I wanted to be
clear in my mind whether, when it comes particularly to under-studied
and under-identified micro-organisms, whether molecular typing
and barcoding is of limited value. When we hear about Craig Venter
going around the world identifying many new species of marine
microbes, is that of limited value in taxonomic terms?
Professor Lane: We need to distinguish between
micro-organisms[42]
and larger organisms; the species concept is quite different.
The metagenomics approach that people such as Craig Venter are
using, where you retrospectively assemble what you believe to
be the number of the species in that habitat. The advantage is
that is the only technique you can use currently to find out what
is there. The disadvantage is that there is no alternative and
independent method to assess whether that is a true estimate of
life, so it is experimental. Their approaches were taken on much
larger genome scans than the DNA barcoding, which is hoping to
use relatively small segments and very few of them—the plants
use four and in animals, we are trying to use one—eventually,
I cannot see us using one, it does not discriminate consistently
and we have now got good experiment evidence to show where it
does and does not discriminate. The concept whether there is a
standard set of short sequences that you could use, I think is
showing increasingly to be a very valid diagnostic. Like anything
in biology, it is not universal, but we are beginning to understand
exactly where its limits are.
Professor Gibby: In the case of diatoms, which
are single celled organisms, we have a NERC fellow working at
the Garden at the moment in collaboration with a diatom systematist,
trying to address the question of whether diatoms are universal
or whether there is bio-geographic patterning in those organisms.
They are ahead of the game in developing barcoding for diatoms
and it is proving a very useful tool to address that question.
Q31 Baroness Walmsley: It is always
tempting to assume that it is better overseas and indeed there
are some shining examples like the National Science Foundation
work on little known taxonomic groups, and the Canadian Barcode
of Life, and we heard from Kew in their evidence about the investment
that is going on in China into taxonomic infrastructure. Indeed,
I saw that last year when I went to Wuhan Botanic Garden and the
facilities there would have made your mouth water. So, the question
about that is, why do you think the UK might be slow in responding
to the gaps that everybody knows exist in taxonomic capacity?
Professor Hopper: I will be brave and venture
an opinion. If you look at the countries where taxonomy is funded,
and the contribution to global taxonomy is now in the top two
or three, they have a concerted funding campaign and institutions
set up to sponsor taxonomic research. There are various institutions
and organisations that support some taxonomic research in the
UK, but not one single place where you could say that there is
the equivalent of the Australian Biological Resources Study, for
example, or the NSF in the USA, where they have set up a dedicated
systematics programme.
Q32 Baroness Walmsley: Does it need
to be a place, or a virtual place?
Professor Hopper: It could be either; it needs
responsibility and a budget.
Q33 Chairman: In the case of China,
could it be because of the perceived power of traditional Chinese
medicine and its links in the case of the Wuhan Garden? Is there
a force pushing it forward there?
Professor Gibby: It is linked in, because all
the botanic gardens in China that have research institutes alongside
are very much pursuing the economic aspects of botany, at the
same time as doing the classical taxonomy and systematics and
the digitisation and databasing of the collections. They all have
that applied focus.
Q34 Baroness Walmsley: What they
do not know about kiwi fruit is not worth knowing! They call it
Chinese gooseberry, of course.
Professor Lane: It is about scale and many of
the big initiatives we are seeing in other countries are about
doing large-scale science, or large-scale infrastructure. It has
been interesting that our ability to raise funds for systematics
collections, as a science infrastructure, has been very successful
in Europe—the institutions at this table are part of a consortium
to integrate the research collections of Europe; 20 different
organisations, funded by the European Commission[43]—and
that was the highest rated integrated infrastructure, which is
quite something. So, integration is a key driver, but it is also
about seeing infrastructure as large-scale enterprises. It is
difficult to see which part of the science structure in the UK
where it would be easy to go and make a case for a basic infrastructure
that cuts across so many different research councils or government
departments.
Q35 Lord Methuen: Local and regional
recording schemes provide valuable data for conservation assessments.
These smaller organisations express their need for support for
managing databases, as well as for training and access to voucher
collections. How do the professional taxonomists from the large
institutions interact with and support these small organisations,
including local museums?
Professor Gibby: All of those organisations
get support through specialists in all of our institutions who
are working with the amateur community through specialist societies.
There is a wide range of specialist societies in which most of
the leaders of those societies—and they are a mixture of
professionals and amateurs, coming from within the communities
such as those sitting around this table—leading, training
and helping to take that forward. The Museum is obviously a major
player in NBN; all the specialist societies are contributing data
to the NBN, but they need the help of the professionals in our
organisations to come up with the correct names and synonyms.
I know that the conservation agencies have been very supportive,
at least in Scotland, SNH has been very supportive, in providing
those local recording organisations with the capacity to digitise
their paper records and get them linked in with the NBN. It is
our organisations, but also the conservation agencies, which are
helping support them.
Dr Nic Lughadha: The type of support we provide
extends from physically giving them a base—the British Mycological
Society, for instance, is headquartered at Kew and uses the Kew
address, and the staff there interact with our mycologists continuously—through
to support for publication. Perhaps the single most important
type of support is identification, being able to provide those
specialist identifications through access to the reference collections,
and that is what the amateur community most urgently looks for
from Kew.
Q36 Lord Krebs: My question relates
to your last point. I wondered what role the national institutions
have in standard setting for the amateur clubs and societies around
the country. If we are relying on amateur input for national data,
which is incredibly important, it is equally important that we
have the right standards and perhaps your point about identification
is part of that. Could you say a few words more generally about
that?
Dr Nic Lughadha: While we call these people
amateurs, many of them are very professional indeed and have professional
levels of experience. Certainly in mycology in the UK, that interaction
is essential. The professionals rely very heavily on the amateurs
providing material which fills gaps in distribution and often
adds new records of species that are new to the UK, or sometimes
even new to science. It is a very productive and close relationship.
Professor Lane: It is fair to say that the relationship
is pretty intimate. In our department of entomology, 15 members
of staff are national recorders, so they have this "other
life" where they can closely interact with the community.
Very often the national collections are the reference points where
people come for identifications and sometimes our staff provide
those, but very often—and that was the point just made—many
amateurs are extraordinarily knowledgeable and sometimes we will
use those as the authority rather than from inside our organisations.
Often the national collections then become the favoured repository
for vouchers, in due course, which is how the flow of knowledge
comes into our organisations, as well as the earlier flow-out
in helping them develop. All three institutions have quite an
intimate relationship with either the subject societies or recording
groups. There are an extraordinary number of recording groups
and we give them house room, as we do other organisations. Our
new centre for UK biodiversity is specifically designed to allow
many other organisations to come and use our facilities so that
they can ramp up the rate at which this work can be done.
Q37 Chairman: What is the take up
like? Are you finding other organisations coming to use these
facilities?
Professor Lane: The facility is not open yet,
it is just being developed. The interest is extraordinary. When
we have gone out and said that we intend to build this, is it
something that you could use and how would you use it? there has
been much enthusiasm.
Professor Gibby: The conservation agencies are
funding posts within the specialist societies to train people
and take them forward. We are hosting one of those posts in the
Botanical Society of the British Isles—a special Scottish
officer, hosted within the Garden—so that makes the networking
and communication very effective.
Q38 Lord Krebs: You obviously represent
the three major national institutions of taxonomic collections.
There are, of course, a number of other important regional institutions,
such as the National Museum of Wales, and some of the big civic
museums in Manchester and Liverpool, not to mention Oxford and
Cambridge. I wondered how your work integrates with the work of
these regional collections; is there sufficient integration, should
more be done, how closely to you work together?
Professor Gibby: From the plants point of view,
there are some plant specialists in these organisations whose
primary responsibilities are curation, local work and identification.
They are linked in with our contacts through the specialist societies,
so there are no other links because the plant people are not actively
undertaking research, they are either looking after the collections
or communicating with the public and trying to increase visitor
numbers to their museums.
Dr Nic Lughadha: The National Museum of Wales
might be the most research active of the institutions mentioned,
and Kew has active collaborations there, primarily focused on
UK or western European endemic species, and we are working with
both population genetics and conservation biology approaches,
so that the joint research informs conservation management decisions
on species such as whitebeams, hawkweeds, etc. To expand the definition
of regional nationals, we wondered whether here we should also
be looking at the UK overseas territories, which have very high
concentrations of UK biodiversity; There is very significant scope
for integration between the work of our institutions and that
of the overseas territories and it is an area that is often omitted
when considering the UK biodiversity. It is an area where we at
Kew are actively working and where we think there is further scope
for integration limited, as ever, only by resources.
Q39 Chairman: That came up in the
seminar that we had. It might be useful, if there are additional
things to say, if you could drop us a line giving us a list of
the obvious things.
Dr Nic Lughadha: Yes, of course.
Dr Dixon: From the Natural History Museum's
point of view, we welcome collaborative projects. We work quite
actively with regional museums but it tends to be very project
based and across the whole spectrum of what we do. There are real
opportunities for further collaboration and we would welcome ways
of taking that forward.
Chairman: You might welcome being "urged"
to do so by us!
39 This should be corrected to read "over 250". Back
40
This should be corrected to read "150". Back
41
The Consortium for the Barcode of Life. Back
42
Especially bacteria. Back
43
And managed by the Natural History Museum. Back
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