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Beyond canalisation: robustness in developmental systems Beyond canalisation: robustness in developmental systems

Beyond canalisation: robustness in developmental systems - PowerPoint Presentation

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Beyond canalisation: robustness in developmental systems - PPT Presentation

Paul E Griffiths 19618 Robustness workshop Bordeaux 1 Developmental systems An animal is in fact a developmental system and it is these systems not the mere adult forms which we conventionally take as typical of the species which becomes modified during the course of evolution ID: 932532

workshop robustness development bordeaux robustness workshop bordeaux development inheritance causal sense griffiths developmental theory cell information study 2017 waddington

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Slide1

Beyond canalisation: robustness in developmental systems

Paul E. Griffiths

19/6/18

Robustness workshop, Bordeaux

1

Slide2

Developmental systems

“An animal is, in fact, a developmental system, and it is these systems, not the mere adult forms which we conventionally take as typical of the species, which becomes modified during the course of evolution.”

Waddington, ‘The Evolution of Developmental Systems’ 1952, p.155 & Fig 1

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Robustness workshop, Bordeaux

Slide3

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Slide4

Senses of ‘Epigenetic’

Epigenesis: the idea that the outcomes of development are created in the process of development, not preformed in the inputs to development; ‘epigenetic’ can be used in this sense

Epigenetics (broad sense – Waddington 1942): the study of the causal mechanisms by which genotypes give rise to phenotypes; the integration of the effects of individual genes in development to produce the ‘

epigenotype’Epigenetics (narrow sense – Nanney 1958): the study of the mechanisms that determine which genome sequences will be expressed in the cell; the control of cell differentiation and of mitotically and sometimes

meiotically heritable cell identityEpigenetic inheritance (narrow sense): the inheritance of genome expression patterns across generations (e.g. through meiosis) in the absence of a continuing stimulus

Epigenetic inheritance (broad sense): the inheritance of phenotypic features via causal pathways other than the inheritance of nuclear DNA. We refer to this as ‘

exogenetic

inheritance’ (West and King 1987)

(from Griffiths and

Stotz

2013)

4

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Slide5

The Epigenotype

"For the purpose of a study of inheritance, the relation between phenotypes and genotypes can be left comparatively uninvestigated; we need merely to assume that changes in the genotype produce correlated changes in the adult phenotype, but the mechanism of this correlation need not concern us. Yet this question is, from a wider biological point of view, of crucial importance, since it is the kernel of the whole problem of development"

Waddington, ‘The Epigenotype’ 2012 [1942], 10.

"…the genotype is [in] continual and unremitting control of every phase of development. Genes are not interlopers, which intrude from time to time to upset the orderly course of a process which is essentially independent of them; on the contrary, there are no developmental events which they do not regulate and guide"

Waddington, 2012 [1942], 12.

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Robustness workshop, Bordeaux

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Slide6

Beyond the epigenotype

Once nurturing -- that is, development -- is accepted as an

ineliminable and integral part of

“biological” nature, it can no longer be contrasted with nature. It cannot represent, for instance, an environmental "outside" to an inherited "inside

Susan

Oyama

,

The Nurturing of Natures

(2002)

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6

Robustness workshop, Bordeaux

Slide7

Senses of ‘Epigenetic’

Epigenesis: the idea that the outcomes of development are created in the process of development, not preformed in the inputs to development; ‘epigenetic’ can be used in this sense

Epigenetics (broad sense – Waddington 1942): the study of the causal mechanisms by which genotypes give rise to phenotypes; the integration of the effects of individual genes in development to produce the ‘epigenotype

’Epigenetics (narrow sense – Nanney 1958): the study of the mechanisms that determine which genome sequences will be expressed in the cell; the control of cell differentiation and of mitotically and sometimes

meiotically heritable cell identityEpigenetic inheritance (narrow sense): the inheritance of genome expression patterns across generations (e.g. through meiosis) in the absence of a continuing stimulus

Epigenetic inheritance

(broad sense): the inheritance of phenotypic features via causal pathways other than the inheritance of nuclear DNA. We refer to this as ‘

exogenetic

inheritance’ (West and King 1987)

(from Griffiths and

Stotz

2013)

7

19/6/18

Robustness workshop, Bordeaux

Slide8

The ontogenetic niche

“genes inherit a rich and supportive environment… The niche is a legacy bequeathed to progeny and responsible for the diverse but dependable influences on the developing organism.”

West, M. J., & King, A. P. (1987).

Brown-headed cowbird

(

Molothrus Ater)

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Robustness workshop, Bordeaux

8

Slide9

Extending Waddington’s model

Coding and non-coding regions of the genome, epigenetic and

exogenetic

factors can all be represented as variables in a causal graphTheir influence on phenotypic outcomes can be measured using causal information theory measures such as ‘specificity’ (Griffiths et al 2015,

Pocheville et al 2017) or ‘information flow’ (Ay and Polani 2008)

Brett

Calcott

has presented Waddington’s ideas using this formalism

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Robustness workshop, Bordeaux

9

Slide10

Causal information theory can be used to quantify

Waddingon’s ideas

Calcott

, Brett. “Causal Specificity and the Instructive-Permissive Distinction.”

Biology and Philosophy

32, no. 4 (July 2017): 481–505.

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Robustness workshop, Bordeaux

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Slide11

Causal information theory can be used to quantify

Waddingon’s ideas

Calcott

, Brett. “Causal Specificity and the Instructive-Permissive Distinction.” Biology and Philosophy

32, no. 4 (July 2017): 481–505.

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Robustness workshop, Bordeaux

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Slide12

Is the extended model useful?

Problems

Need to represent all causes as discrete variables to use information theory – highly artificial

Features of low dimensional landscapes can’t be generalised to high-dimensional

But these concerns probably apply as much to Waddington’s original model

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Slide13

Reservations about

canalisation

“[learnt/innate] does have some value in placing behaviors on a lability continuum, with some behaviors more ‘nurture dependent,’ more changeable and variable, and others more ‘nature dependent,’ more stereotyped and resistant to change.” (

Marler, 2004, 31)

Why assume that dimension reduction like this is possible?Song sparrows and cowbirds – a cautionary tale

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Robustness workshop, Bordeaux

13

Slide14

Reservations about

canalisation

Showing that a trait is insensitive to changes in one or a few parameters (‘pegs’ in Waddington’s diagram) is very far from showing that it is canalized in a high-dimensional model

There is no general evolutionary rationale for extrapolating canalization-relative-to-a-parameter from one dimension to others

Classifying two different traits as both ‘canalized’ because they fail to respond to different environmental manipulations

is hardly better than classifying them together because one is not very large, another is not very rigid, and a third is not very heavily pigmented

(Griffiths and

Machery

2008)

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Robustness workshop, Bordeaux

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Slide15

Conclusion

Arguably, the assumption that extrapolating canalization-relative-to-a-parameter from one dimension to others is a reasonable inference is an expression of ‘psychological essentialism’ about biological kinds

We should not trust our intuitions about canalization based on Waddington’s attractive image of the developmental landscape

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Robustness workshop, Bordeaux

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Slide16

Acknowledgments

Theory and Methods in Bioscience Group

Charles Perkins Centre

www.griffithslab.org Griffiths, P. E. and J. G.

Tabery (2013) Developmental Systems Theory: What Does it Explain, and How Does It Explain It? In R. M. Lerner and J. B. Benson(Eds),

Embodiment and Epigenesis: Advances in Child Development and behavior Vol. 45.

Griffiths, Paul E. “Genetic, Epigenetic and

Exogenetic

Information in Development and Evolution.”

Interface Focus

7 (2017).

Griffiths, Paul E, and Edouard

Machery

. “Innateness, Canalisation and ‘

Biologicizing

the Mind.’”

Philosophical Psychology

21 (2008)

Robustness workshop, Bordeaux

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16

2017

Slide17

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