Robustness and Developmental Systems: A Workshop Overview
Beyond canalisation: robustness
in developmental systems
Paul E. Griffiths
12/09/2024
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.”
Waddington, ‘The Evolution
of Developmental Systems’
1952, p.155 & Fig 1
12/09/2024
2
Robustness workshop, Bordeaux
12/09/2024
Robustness workshop, Bordeaux
3
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
identity
•
Epigenetic 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
12/09/2024
Robustness workshop, Bordeaux
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.
12/09/2024
Robustness workshop, Bordeaux
5
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)
12/09/2024
6
Robustness workshop, Bordeaux
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
identity
•
Epigenetic 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
12/09/2024
Robustness workshop, Bordeaux
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)
12/09/2024
Robustness workshop, Bordeaux
8
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 graph
•
Their 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
12/09/2024
Robustness workshop, Bordeaux
9
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.
12/09/2024
Robustness workshop, Bordeaux
10
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.
12/09/2024
Robustness workshop, Bordeaux
11
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
12/09/2024
Robustness workshop, Bordeaux
12
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
12/09/2024
Robustness workshop, Bordeaux
13
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)
12/09/2024
Robustness workshop, Bordeaux
14
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
12/09/2024
Robustness workshop, Bordeaux
15
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
12/09/2024
16
2017
12/09/2024
Robustness workshop, Bordeaux
17
Delve into the intricate world of developmental systems and robustness with insights from Paul E. Griffiths. Discover the evolution of developmental processes, the significance of epigenetics, and the interplay between genotypes and phenotypes. Gain a deeper understanding of epigenetic inheritance and the role of genes in shaping developmental events. Join the discourse at the upcoming workshop in Bordeaux for a comprehensive exploration of these critical concepts.
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Presentation Transcript
Beyond canalisation: robustness in developmental systems Paul E. Griffiths 12/09/2024 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. Waddington, The Evolution of Developmental Systems 1952, p.155 & Fig 1 12/09/2024 Robustness workshop, Bordeaux 2
12/09/2024 Robustness workshop, Bordeaux 3
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 identity Epigenetic 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) 12/09/2024 Robustness workshop, Bordeaux 4
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. 12/09/2024 Robustness workshop, Bordeaux 5
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) 12/09/2024 Robustness workshop, Bordeaux 6
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 identity Epigenetic 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) 12/09/2024 Robustness workshop, Bordeaux 7
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) Meredith West image 12/09/2024 Robustness workshop, Bordeaux 8
Extending Waddingtons model Coding and non-coding regions of the genome, epigenetic and exogenetic factors can all be represented as variables in a causal graph Their 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 12/09/2024 Robustness workshop, Bordeaux 9
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. 12/09/2024 Robustness workshop, Bordeaux 10
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. 12/09/2024 Robustness workshop, Bordeaux 11
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 12/09/2024 Robustness workshop, Bordeaux 12
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 12/09/2024 Robustness workshop, Bordeaux 13
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) 12/09/2024 Robustness workshop, Bordeaux 14
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 12/09/2024 Robustness workshop, Bordeaux 15
Acknowledgments 2017 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) 12/09/2024 Robustness workshop, Bordeaux 16
12/09/2024 Robustness workshop, Bordeaux 17
