agriscience slides ian ferguson slides october 2012

8/13/2019 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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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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Breeding programmes

- kiwifruit- apples- pears

- blueberries- raspberry- hops- peaches & nectarines- apricots

- potatoes- forage crops- cereals- peas- ornamentals

...


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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


7/80The New Zealand Institute for Plant & Food Research Limited

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



New crops grown internationallyunder licence

Kiwiberry (A. arguta)

Premium-priced, convenience, ready-to-eat, bite-sized fruit, appeals to consumers



New Vegetable Crops - Potatoes

High fibre / low glycaemic potency

Diverse colour and shape range with excellent agronomiccharacters

Resistant to cold-sweetening



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



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 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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Sustainable Production

Protecting and restoring

the environment

while maintaining profitability

Q if i h i l i


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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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Efficient and Innovative Crop Production

Canopy management

High Efficency Production

Better Cropping

Dwarfing


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Biosecurity

Protecting our borders

Controlling invasions

Ensuring market access


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Safety and Sustainability

Food Safety

Chemicals in food

High integrity food

Food research: Breeding & Biotechnology for


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Food research: Breeding & Biotechnology forHealthy Foods

Red-fleshed apples:

Anthocyanins for health

Consumer appeal


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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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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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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

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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

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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 Scientist Who Went out from

the Warm: Interfacing Science andPolicy Ian Ferguson



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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.


Science and Policy

Separatingknowledge

andevaluation


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S i d P li


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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..


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

d l


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Science and Policy

Knowledge

& evidence

Evaluation Policy

Science

h k


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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


agriscience slides ian ferguson slides october 2012

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