agriscience slides ian ferguson slides october 2012
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www.mpi.govt.nz
Ian FergusonDepartmental Science Advisor
The Scientist Who Came in from the Cold:Interfacing Science and Policy
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The New Zealand Institute for Plant & Food Research Limited
Plant & Food Research
Plant & Food Researchs mission is to provide theresearch that drives the growth, profitability andsustainability of plant and seafood-based food
industries in New Zealand
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The New Zealand Institute for Plant & Food Research Limited
Plant & Food Research
Auckland, NZ Head Office
Locations NZ (15 sites) Australia USA
Operate under the NZ Companies Act Corporate Structure Shareholders
New Zealand Government
Annual revenue $115 million~50% private contracts
and royalties~50% NZ Government
contracts andcore funding
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The New Zealand Institute for Plant & Food Research Limited
Breeding programmes
- kiwifruit- apples- pears
- blueberries- raspberry- hops- peaches & nectarines- apricots
- potatoes- forage crops- cereals- peas- ornamentals
...
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The New Zealand Institute for Plant & Food Research Limited
Booster Broccoli High levels of cancer fighting compounds Joint Australia-NZ project, launch in second half of 2009
Purple Heart potato Purple skin and purple flesh tones
High in antioxidants and loved by gourmets
Crop and fruit cultivars
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Crop and fruit cultivars
ZESPRI GOLD Kiwifruit Sweet, yellow-fleshed kiwifruit Annual returns predicted to reach NZ$1 billion by 2009
JAZZ apples Tangy, crunchy, juicy ap ples with flavour Rated by consumers in Europe and US as outstanding Excellent shelf life
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New crops grown internationallyunder licence
Kiwiberry (A. arguta)
Premium-priced, convenience, ready-to-eat, bite-sized fruit, appeals to consumers
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New Vegetable Crops - Potatoes
High fibre / low glycaemic potency
Diverse colour and shape range with excellent agronomiccharacters
Resistant to cold-sweetening
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New cultivars frommarket assisted
selectionThousands
o fgenes
Hundredso f
leads
Func t iontested
candida tes
Testing in plants
Genediscovery
Function discovery
Traitdiscovery
Product development
BioinformaticsDNA based homology
MicroarraysGene over-expression
High valueFunctional
Foods
The genomics pipeline
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Fruit gene databases available
Apple* genome 2010Kiwifruit* * genome 2012Grape genome 2007Papaya genome 2008Citrus genome 2012
Peach genome 2009Strawberry* genome 2011Tomato genome 2012Potato * genome 2011Pear** genome 2012Blueberry
Avocado
Genome sequences
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Actinidia chinensis x
A. melanandra
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The Whole Genome
The genome of apple ( Malus x dom est ica) has been described,and we can use its high quality draft sequence to explain theorigin of the crop.Draft genome sequence of the apple Golden Delicious Whole genome shotgun (WGS) approach was used
603.9 Mb covers about 81.3%, anchored 71.2 % of metacontigsusing a high quality genetic map with 1,643 markersTotal number of genes predicted is 57,524 - the highest reportedamong plants so far
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Pear diversity courtesy of J. Postman, USDA-NCGR-Corvallis
The pear genome
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The New Zealand Institute for Plant & Food Research Limited
The pear genome
Sequenced with collaborators in IASMA, Italy
600 million base pairs, 51,000 genes,
25% less DNA than apple
Apple and pear hada common ancestor35 million years ago
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Genome wide selection:
Whole genome sequence
Re-sequence (using next gen sequencing) specific cultivars andcompare against the whole genome sequence e.g. heritageagainst domesticated.
Provides thousands of sequence variants on every gene/locus.So we can compare two cvs with the same trait and look for whatis the same.
Provides an immediate marker or gene to select for doesnthave to be predetermined is an association.
The Genomics revolution and breeding andselectionThe genomics revolution and breedingand selection
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Have the human sequence.Re-sequence each SLT member. Lay the genomes of the SLTmembers on the reference human genomeGet an association of a particular gene across all SLT members.Even though not related, they have the same gene and we canthen look for that gene in the population and find people withthat gene.If SLT members related, wouldnt work, since they share toomay sequences.Because unrelated, the association is too powerful not to be a aa strong selective marker.
The genomics revolution and breedingand selection
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The New Zealand Institute for Plant & Food Research Limited
Sustainable Production
Protecting and restoring
the environment
while maintaining profitability
Q if i h i l i
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The New Zealand Institute for Plant & Food Research Limited
Quantifying the environmental impactof growing: Sustainable approaches
Transport
Transport
Transport
T r a n s p o r tGrape
Growing Harvest Juicing
Fermenting
Bottling/Packaging
Local &OverseasDrinking
Materials
Energy
Wastes
Emissions
Grapeto
Glass
Food milesCarbon costs
energyfertilisersrain
drainageleachateprunings
CO 2 consumption
CO 2 emission
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Where have we exceed our planets limits?
United Nations Department of Economic and Social
Affairs:Building a Sustainable and Desirable Economy-in-Society-in-Nature
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Natural Capital:
Our stocks of natural materials &energy
Ecosystem Services:
The beneficial flows of goodsbetween natural capital stocks, orstocks & humans
Natures Blessing: Capital & Interest
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Costanza et al.(Nature, 1997) - 17ecosystem servicesacross 16 biomes.
The 17 Ecosystem Services many involve soil
Gas regulation Climate regulation Disturbance regulation Water regulation Water supply Erosion control Soil formation
Nutrient cycling Waste treatment Pollination Biological control Refugia
Food production Raw material Genetic resources Recreation Cultural
Services
Stocks
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A global synthesis revealsbiodiversity loss as a majordriver of ecosystem change
Evidence is mounting that extinctions are alteringkey processes important to the productivity andsustainability of Earths ecosystems. Furtherspecies loss will accelerate change in ecosystemprocesses, but it is unclear how these effectscompare to the direct effects of other forms ofenvironmental change that are both drivingdiversity loss and altering ecosystem function.
7 JUNE 201 2 | VOL 486 | NATURE | 105
Biodiversity
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In April this year, the Intergovernmental Platform on Biodiversity andEcosystem Services (IPBES) was born in Panama City. It hopes to gain similarglobal scientific authority and policy influence for biodiversity to what theIntergovernmental Panel on Climate Change (IPCC) has for climate change although not the same opposition and controversies.454 | NATURE | VOL 488 | 23 AUGUST 2012
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Biodiversity mattersNot only in wild places
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but also on farms and inorchards
where biodiversity provides
Ecosystem servicesPollination
Pest controlDecomposition
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Orchardmanagement
practices
Exportmarkets
Compelling NZstory
Biodiversity
Decomposition& nutrient
release
Disease
control
Pestcontrol
Orchard ororchard
$ returnto
growers
Pollination
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The New Zealand Institute for Plant & Food Research Limited
Efficient and Innovative Crop Production
Canopy management
High Efficency Production
Better Cropping
Dwarfing
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The New Zealand Institute for Plant & Food Research Limited
Biosecurity
Protecting our borders
Controlling invasions
Ensuring market access
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The New Zealand Institute for Plant & Food Research Limited
Safety and Sustainability
Food Safety
Chemicals in food
High integrity food
Food research: Breeding & Biotechnology for
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The New Zealand Institute for Plant & Food Research Limited
Food research: Breeding & Biotechnology forHealthy Foods
Red-fleshed apples:
Anthocyanins for health
Consumer appeal
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The New Zealand Institute for Plant & Food Research Limited
Digestive Health Immune Function Mental Acuity and Brain Health Energy, Physical Performance
and Fitness Satiety and Weight Management
Foods for Health
Food products and functionality
G i bi d l f d
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Gut microbiota and plants.....- We are what we can digest and what our microbes can ferment...Phytochemicals and non-digestible carbohydrates both interact withthe microbial population in our colon and impact on our metabolism
It isnt justwho is there that is important...- what they produce
- how they produce it
Ability to proliferate and succeed in the colon is dependent on theflexibility and responsiveness of microbiota to diverse substrates
Gut microbiota and plant foods.....(Juliet Ansell)
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The GI tract and gut microbiotic environment arelinked
RNA sequencing advances means we can get
global snapshot of microbiome
Metagenomics means we can measure the globalhost response
Functional metabolomics (urine, faeces) means wecan understand the interface
Co-metabolismGut microbiota and plant foods.....
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Research with kiwifruit :in vitro and using an animal modelThen human clinical trials
In vitro kiwifruit fermentation
Specific beneficial bacteria and associated products increase
Gut microbiota and plant foods.....
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The New Zealand Institute for Plant & Food Research Limited
Human gene response to foods
Nutritional genomics and personalisednutrition and foods
Gastronomics: humangene differences toaromas
Consumer preference
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Ethylene receptor
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Kendrik & Chang,Curr Op Plant Biol 11, 479, 2008
Receptors are negativeregulators
active in repressing downstreamresponse
+ ethylene, receptor activityreduced
CTR1 negatively regulatesethylene response byrepressing EIN2
+ ethylene reduces CTR1activity leading to reduced
ubiquitin-based EIN3/EILprotein degradation
EIN2 relays ethyleneresponse through to TFs inEIN3/EIL family and theERFs
Ethylene receptorgenes in kiwifruit
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Ethylene receptor genes in kiwifruit
Thousandso f
genes
Hundredso f
leads
Func t iontested
candida tes
Gene
discovery
High valueFoods
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Thousandso f
genes
Hundredso f
leads
Func t iontested
candida tes
Gene
discovery
High valueFoods
Kiwifruitripening at20C
Receptor geneexpression
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The New Zealand Institute for Plant & Food Research Limited
Chinese Red Bayberry (Yangmei)
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UniGene expression profilesduring bayberry fruitripening. (A) Overallexpression profiles for theUniGenes expressed in fruitlibraries of three differentmaturity stages, (B) Fourexpression profiles areshown, with I and IVindicating UniGenes withup-regulated and down-regulated expression,
respectively, and II and IIIindicating those withirregular expression. Thelines with 10 different colorsfrom blue to red show theabsolute expressionmagnitude at 75 DAF, withthe RPKM values 0-10, 10-20, 20-40, 40-80, 80-160, 160-320, 320-640, 640-1280,1280-2560, and over 2560represented by colors 1 to10, respectively, (C) GOclassification for up-regulated and down-regulated UniGenes, with *and ** indicating significantdifference at 5% and 1%,respectively.
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0
15
30
45
MrCHS
0
10
20
R e l a t
i v e
i n t e n s i
t y
MrF3H
0
10
20
MrANS
0
1
2
MrCHI
0
40
80
120
MrF3'H
0
15
30
45
MrDFR1
SJ DK BQ0
2
4
MrUFGT
0
15
30
45
MrDFR2
SJ DK BQ0.00
0.01
0.02
MrMYB1
SJ DK BQ0
20
40
60
80
100
T o
t a l a n
t h o c y a n
i n s ( m g
/ 1 0 0 g
F W )
Fig. 1. (A) Difference in fruit color and anthocyanincontent in ripe SJ, DK and BQ fruit. (B) Expressionanalysis of anthocyanin biosynthesis genes as well as
MrMYB1 in ripe SJ, DK and BQ fruit by qPCR. MrACT gene was used to normalize expression of the genesunder identical conditions. The vertical bars representS.E. of three replicates.
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Old Crops but New Markets?
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Loquat Fruit
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Low temperature damage Succesful postharvest treatments
Postharvest science to ensurequality in the supply chain
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0 5 10 15 20 250
40
80
0.0
0.2
0.4
0.6
F i r m n e s s
( N )
Days in storage
E t h y l e n e p r o d u c
t i o n
( n l / g
. h )
0
1
2
3
DkERF1
0
1
2
0 5 8 16 20 220 5 8 16 20 220 5 8 16 20 22
DkERF2
0
1
2
DkERF3
0
1
2
3
DkERF4
0
1
2
DkERF5
0
1
2
DkERF6
0
1
2
DkERF7
0
6
12
18 R e
l a t i v e
i n t e n s i t y
R e
l a t i v e
i n t e n s i t y
R e
l a t i v e
i n t e n s i t y
Days in storageDays in storageDays in storage
R e
l a t i v e
i n t e n s i t y
Days in storage
DkERF8
0 5 8 16 20 22
0
1
2
3DkERS1
0
1
2
DkETR1
0
2
4
DkETR2
0
1
2
DkCTR1
0
1
2
DkEIL1
Expression of DkETRs , DkCTR1 , DkEIL1 and DkERF genesduring ripening of Yangfeng persimmon fruit at 20 oC. Fruitat day 0 was set as the calibrator (set as 1) for relativeexpression. Error bars on each column indicate S.E. fromthree biological replicates
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0 1 2 3 4 50.0
0.5
1.0
1.5
2.00
15
30
45
E t h y l e n e p r o d u c
t i o n
( n l
/ g . h
)
Days in storage
F i r m n e s s
( N )
Control
2d CO2
0.0
0.4
0.8
1.2
1.6
S o l u b
l e T a n n i n
( t a n n
i n a c
i d e q u i v a
l e n t
F W % )
0
2468
Days in storageDays in storageDays in storage
Days in storage
Control 2d CO
2
DkERF2
0
4
812
DkERF4
0
20
40
60DkERF5
0
5
10
15DkERF8
0
4
8
12
R e
l a t i v e
i n t e n s
i t y
R e
l a t i v e
i n t e n s
i t y
R e
l a t i v e
i n t e n s
i t y
0 1 2 3 4 50 1 2 3 4 50 1 2 3 4 5
0 1 2 3 4 5
R e
l a t i v e
i n t e
n s
i t y
DkERS1
0
1
23
DkETR1
0
20
40
60DkETR2
0
3
6DkCTR1
0
1
2
3DkEIL1
0
2
4
DkERF1
02468
DkERF3
0
4
8
12DkERF6
0
1
23
DkERF7
Effects of CO 2 treatment on DkERF gene expression in Mopanpersimmon fruit. CO 2 (~95%, v/v) was applied for 2 days. EightERF genes were choosen to analyze changes in transcripts levelin response to the CO 2 treatment. For the relative mRNAabundance, day 0 fruit was set as 1.
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All these data andinformation lead to theneed for:
A systems approach
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5 receptor genes in 2 subfamilies
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5 receptor genes in 2 subfamilies2 CTR genes4 EIL genes transcription factors14 ERF genes transcription factors
Xripening in air 20Cripening with ethylene at 20C1-MCP at 20Cripening at 0C plus 20C
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A systems approach
What do we require? Data
Ayroles et al Nature Genetics, 41, 299, 2009
Drosophila
6 phenotypes
10096 geneticallyvariable transcripts
intercorrelatedresulting in 241transcriptionalmodules
Modules ofbiologicallymeaningful correlatedtranscripts e.g.metabolic pathways,TF binding sites,tissue specificity etc
Transcriptionalconnectivity = geneticnetworks
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A systems approach
What do we need to develop? Predictivemodels
Most common approach for transcriptome analysis isreverse engineering: assumes that causality of
transcriptional regulation can be inferred fromchanges in mRNA expression profiles is the waywe routinely look at transcript patterns
Modelling of gene regulatory networks (GRN) uses
statistical models, neural networks, Bayesiannetworks
Aim is not to develop t rue models, but develop valid models which can be tested and
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A systems approach
Just thinking about this alerts us to: the deficiencies in our datasets
over-interpretation of transcript patterns
the need for models even at the most conceptual- to use for experimental testing by disruptiveapproaches
better ways of analysing large datasets
an appreciation that even if we cant measureeverything (and probably dont want to), we need tothink in terms of networks and connectivity, ratherthan very simplistic unidimensional flows of
information.
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The New Zealand Institute for Plant & Food Research Limited
The Scientist Who Went out from
the Warm: Interfacing Science andPolicy Ian Ferguson
The New Zealand Institute for Plant & Food Research Limited
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provide a source of independent challengewhich seeks to ensure that policy decisions areinformed by the best science advice andevidence available
ensuring the scientific evidence is at the coreof departmental decision making; scrutiny andchallenge of departmental resources to facilitatethis goal; advise on cross- departmental issues.
Report - House of Lords Select Committee on Science and Technology, 2012
What is a DSA?
Independence
Evidence atthe core
of decisionmaking
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they must have the skills to transcend disciplinaryboundaries and synthesise knowledge across severaldisciplines.
In that role they are not expected to be exper ts in a l l that theyconfer adv ice upon
mediating between the broader scientific community andpolicy formation, as well as providing public commentary.
provision of strategic scientific advice, ensuring the quality ofevidence to support policy formation, and participation inplanning, managing and supervising the purchase of agencyrequired research.
Towards better use of evidence in policy formation: a discussion paperOffice of the Prime Ministers Science Advisory Committee, April 2011
What is a DSA?
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Be an accom pl ish ed and wel l -respectedleader in sc ience and in no vat ion
Have a s t rong and b road und ers tand ingof the pr im ary sector and the sc iencerequired to sup po r t MPI's broad range of
responsibi l i t ies
Unders tand governm ent p rocesses andthe ro le of sc ience and sc iencei n n o v a ti o n i n i n f o r m i n g p o l i cy a n dregu la to ry s ys tems
Unders tand th e chal leng es of researchpr ior i t i sa t ion , de l ivery, qual i tyassurance , and know ledge /t echno logytransfer and up take
DSA for MPI
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DSA for MPI
Have s t rong co nnec t ions to theNew Zealand and in ternat ionalsc ience com mu ni ty asdem on st ra ted by extens ive
ne tworks
Be an excel lent wr i t ten andora l com mu nica to r wi th s t ronginterpersonal ski l l s
Be able to effec t ively m anagepo tent ia l con f l ic ts of in teres t
First thoughts: NZ Primary Production
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Science-based and s c ience dr iven biologic al econo m y- primary production raised to a very high international standard based on science andinnovation
Science base and s uc cess tends to get forgo t ten? - i s hard tom easu re imp act
Techno logical chal leng es to progress have w e s ta l led?-step changes may be technology-based which are difficult to implement or not attractive,or have regulatory or other constraints?
Envi ronmenta l con s t rain t s to p rodu c t ion regulatory such as biosecurity (bringing in new plant material), footprints (export marketdriven, environmental driven), greenhouse gas agreements, water quality/irrigation,landuse decisions need for high level of science input.
Need to make growth sustainable, not just have sustainability
First thoughts: NZ Primary Production,MPI and Science
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MPI is s c ience-based , but sc ienc e dr iven?MPI based on science but is it science driven? Not like a CRI, but by driven, meanable to access and evaluate latest and best science an end-user. How completeand effective is MPI as an enduser?
Breadth of ac t iv i t ies- a little overwhelming How do we ensure that there is an adequate science baseto this?
Four fo cus areas in s t ra tegy a l l sc ience-basedMaximise export opportunitiesImprove sector productivityIncrease sustainable resource useProtect from biological risk
First thoughts: Role of DSA in MPI
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MPI sc ience two m ajor aspec ts :1. Regulation and standards requires the most rigorous science information and
access and processes to stand up to challenge. This requires internal sciencequality assurance systems. We must ensure there is robustness andprocesses across the organisation.
2. MPI is a major science funder and should be driving research priorities, andalso have science evaluation processes at the highest level these should beco-ordinated across the organisation. So to this extent, MPI is a science leaderand innovator and major end-user. This needs robust strategy andprioritisation, evaluation of science, and of outcomes and impact are allthese in place at the same level?
If MPI funding at the implementation/applied end of the spectrum, how do theyknow that there the whole pipeline is being filled, and in the right way? So needsubstantial say in funding at the more fundamental/developmental end of thepipeline? Providers are faced with fragmented funding agencies
Role of DSA in MPI
Role of DSA in MPI
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We are making a fundamental shift in the way we work.
MPIs role is no longer the regulatory compliance role ofi t s p redecessor o rg an isa t ions . MPI i s n ow wo rk ing topar tner wi th and enable the pr imary ind ust r ies to ach ievethe maximum benefit for New Zealand
Wayne McneeMPI Annual report, 2011/ 2012
Role of DSA in MPI
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Some of the high level aspects:.Quality science used in MPI strategy development
Science quality - peer review, quality assurance, robust and consistentprocesses.
Links to research providers how good are the linkages re science? Patchyprobably?
Acting at the interface of MPI and science providers and stakeholders -partnership models
Profiling science culture internally and externally
Accessing external science advice external verification/audit?
International (plus MFAT, NZAid, MBIE)
Internal integration, co-ordination and consistency currently inconsistent?
Role of DSA in MPI
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The challenge is how to do better in two related domains:
the generation and application of knowledge toinform policy making,
And
the use of scientific approaches to themonitoring and evaluation of policy initiatives.
It is important to separate as far as possible the role ofexpert knowledge generation and evaluation fromthe role of those charged with policy formation.
Towards better use of evidence in policy formation: a discussion paperOffice of the Prime Ministers Science Advisory Committee, April 2011
Science and Policy
Separatingknowledge
andevaluation
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It is also important to note that there are limits toscientific knowledge and to the scientific approach;governments and their advisors must be aware of suchlimitations..
Towards better use of evidence in policy formation: a discussion paperOffice of the Prime Ministers Science Advisory Committee, April 2011
Hot off the press Scientists around the world have reacted with dismay toconviction of six Italian scientists and a former governmentofficial on manslaughter charges. The seven were convictedafter prosecutors successfully argued that public statementsthey had contributed to a false sense of security in the Italiancity of LAquila ahead of the 2009 earthquake that killed 309people
Science and Policy (2) We dont knoweverything
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Science and Policy
Knowledge
& evidence
Evaluation Policy
Science
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The New Zealand Institute for Plant & Food Research Limited
Thanks
PFR:Andy AllanBrent ClothierJuliet AnsallLouise Malone
Zhejiang University:Zhang Bo
Yin Xue RenChen Kun Song
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www.mpi.govt.nz
Ian Ferguson
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www.plantandfood.com
The New Zealand Institute for Plant & Food Research Limited