Transcript Explaining diversity through evolution

Explaining diversity through
evolution: branching and clustering
Philippe Huneman
IHPST (CNRS/Université Paris I
Sorbonne)
« Challenges to evolutionary theory » ? ->
EXTENDED evolutionary theory.
Dawkins 1982; Turner 2001; Sterelny et al. 1996;
Odling-Smee et al. 2003; Pigliucci 2007; Gould
2002 (« expansion »)
I. THE EXPLANANDA OF
EVOLUTIONARY THEORY
Evolutionary theory explains (Lewontin) :
Adaptation
Diversity
Evolution
Modern Synthesis evolutionary theory explains (Lewontin) :
Adaptation
-> explained (defined ?) by natural selection
Diversity
Adaptive radiation, « principle of divergence »
Evolution
-> several causes, the major one being natural selection
The two explanada are related:
Adaptation -> competitive exclusion -> diversity
(Darwin’s finches beaks)
Diversity
• There are different ways of being different
• The diversity issue = why is difference occurring in the way
it occurs ??
• Variety, but not much novelty (Darwin)
-> unity through diversity
Alike, though difference : The concepts of homology (and
analogy)
The wing of bats and the fins of fish as the same thing, though
different – or different instances of the same thing
•
Finally, then, although in many cases it is most difficult even to conjecture by what
transitions organs could have arrived at their present state; yet, considering how
small the proportion of living and known forms is to the extinct and unknown, I
have been astonished how rarely an organ can be named, towards which no
transitional grade is known to lead. It is certainly true, that new organs appearing
as if created for some special purpose rarely or never appear in any being; as
indeed is shown by that old, but somewhat exaggerated, canon in natural history
of "Natura non facit saltum." We meet with this admission in the writings of
almost every experienced naturalist; or, as Milne Edwards has well expressed it,
"Nature is prodigal in variety, but niggard in innovation." Why, on the theory of
Creation, should there be so much variety and so little real novelty? Why should all
the parts and organs of many independent beings, each supposed to have been
separately created for its own proper place in nature, be so commonly linked
together by graduated steps? Why should not Nature take a sudden leap from
structure to structure? On the theory of natural selection, we can clearly
understand why she should not; for natural selection acts only by taking advantage
of slight successive variations; she can never take a great and sudden leap, but
must advance by the short and sure, though slow steps.
Origin of species (6th ed.) ch. 6.
Diversity, 1
Idea of a morphospace
Generalised morphospace
Issue : The clustering within the morphospace
Why is there such fact ?
Diversity, 2
The pattern of branching
• A, B, C, D, E
Possible comparisons : (Ab) (CDE)), (abc (de)), (a
(bcde)) (ab ((cd)e)) etc.
(A (BC)D)
(A (D (CB)))
(A(CB)D)
(A (D (BC)))
• (A (D (BC))
• (A (CB) D)
• (A (BC) D)
• (A (D (BC)) = (A (DBC)) + (A D (BC))
• Suppose you have (A (DB) C) also … : then no
possible branching pattern
• The fact is that we have something like a tree !
Why ??
-> Darwin’s answer : Common descent.
Notice : Kant’s problem (Critique of judgment)
was the same
His answer = transcendantal presuppositions of
the reflective power of judgment…***
• Evolution = answers two questions about rare
facts in spaces of possible spaces
• Are there equal ?
• No equivalence : you can have branching with
no clustering
• And clustering with no branching
x
xxxxxx xxx xxxxxx xxxxxx xxxxxxxx xxxx xxxxxxxxxx xxxxxx
X xxxxx xxxxxxxx
xxxx xxxx
xxxxx xxx xxxxxxxxxxxxxxxx
• Or is an answer to the Clustering question not
enough to answer the Branching question ?
And does an answer to the Branching question
entails a clustering ? Not necessarily, but it
may be teh case.
- > What process can be likely to answer the two
questions ?
II. DARWINIAN EVOLUTIONARY
THEORY EXPLAINING DIVERSITY
Darwin’s view
Unity through diversity ?
The « Conditions of existence » and the « Unity
of type »
(E.S. Russell Form and function, 1916; Cuvier vs.
Geoffroy St Hilaire 1830)
Forme
(Function)
Geoffroy St Hilaire
Unity of type
Cuvier
Conditions of existence
Common descent
Natural selection
• It is generally acknowledged that all organic beings have been formed on
two great laws Unity of Type, and the Conditions of Existence. By unity of
type is meant that fundamental agreement in structure, which we see in
organic beings of the same class, and which is quite independent of their
habits of life. On my theory, unity of type is explained by unity of descent.
The expression of conditions of existence, so often insisted on by the
illustrious Cuvier, is fully embraced by the principle of natural selection.
For natural selection acts by either now adapting the varying parts of each
being to its organic and inorganic conditions of life; or by having adapted
them during long-past periods of time: the adaptations being aided in
some cases by use and disuse, being slightly affected by the direct action
of the external conditions of life, and being in all cases subjected to the
several laws of growth. Hence, in fact, the law of the Conditions of
Existence is the higher law; as it includes, through the inheritance of
former adaptations, that of Unity of Type.
• Chapter VI. Origin of species
• Darwin’s thesis : « unity of type » is subsumed
under natural selection
• What is « common descent » for two traits at
a same phylogenetic level
….resorts to « natural selection » when
considering the first stages (plesiomorphic
states) of the trait…
• Thus, we can hardly believe that the webbed feet of the upland goose or
of the frigate-bird are of special use to these birds; we cannot believe that
the same bones in the arm of the monkey, in the fore leg of the horse, in
the wing of the bat, and in the flipper of the seal, are of special use to
these animals. We may safely attribute these structures to inheritance.
But to the progenitor of the upland goose and of the frigate-bird, webbed
feet no doubt were as useful as they now are to the most aquatic of
existing birds. So we may believe that the progenitor of the seal had not a
flipper, but a foot with five toes fitted for walking or grasping; and we may
further venture to believe that the several bones in the limbs of the
monkey, horse, and bat, which have been inherited from a common
progenitor, were formerly of more special use to that progenitor, or its
progenitors, than they now are to these animals having such widely
diversified habits. Therefore we may infer that these several bones might
have been acquired through natural selection, subjected formerly, as now,
to the several laws of inheritance, reversion, correlation of growth, &c.
• Consequences : micro and macroevolution
• Darwin’s gradualism
• The scale-free diagram – zoom in (processes)
and zoom out (branching pattern, homologies)
The Modern Synthesis view
Change in allelic frequencies as the core of
evolution
« Population thinking » (Mayr) and population
genetics: genes and (alleles) populations are the
two main explanatory levels.
Natural selection is the main cause of the
departures from gene frequencies equilibria
About processes: macroevolution as
extrapolation from microevolution (Mayr,
Simpson)
About patterns : Gradualism
III. WHAT WOULD BE AN
ALTERNATIVE VIEW ?
Population thinking and typology
• Amundson’s classification (« Homology and
homoplasy : a philosophical perspective » 2004):
typology = homology more important than
natural selection
« Typologists were united not by metaphysical or anti-evolutionary
commitments, but by a belief in the importance of homology over
adaptation”
- > Micro vs macro evolution = is adaptation
different than « novelty »? (Muller and Newman
2003) Should novelty need another explanans ?
Form
Function
Geoffroy St Hilaire
Unity of type
Cuvier
Conditions of existence
Common descent
Natural selection
Homology
Unity
Typological thinking
Adaptive radiation
Diversity
Population thinking
The alternative in explaining unity-indiversity
• MS : explains diversity through adaptation
(radiations…)
& explains unity by common descent (and in fine
natural selection…)
• Typologist : explains unity (in diversity) by
commonalities of structure; explains diversity by
novelties + homology
MS explanation of diversity issues
• Branching: d (A,B) < d (A,C) = there is a
common ancestor A’ of A and B, and A’’ of A’,
A, B and C
• Clustering : a restricted number of (coarse
grained) selective pressures + common
descent
-> attractors in design space (as « good tricks »)
Typologists answer
Clustering: some forms are attractors in design
space – ie whatever the genetic structure, the
environmental structure, etc., the same form
will appear (at all levels **)
The clustered forms are not living in the same
environment at all, hence natural selection
can not be the explanation (fins/wings)
Typologists answer, 2
Branching = explained by common descent
& Common descent can not be traced back to
natural selection & Natural selection is just noise on pure
branching (homoplasies); it does not explain
branching
Clustering: not all combinations of
parts/traits/molecules/cells are equiprobable
• D’Arcy Thompson : morphologies – effects of
changing scale; conservation laws etc. -> a few
forms will be realized
• Stuart – combining toolkit molecules
A nice example: Modularity in cell
metabolism networks
Intuitive idea : you have many nodes – non
modular (non clustered) graphs are the most
probable networks; selection will pick up the
most modular ones (because of advantages of
modularity)
• BUT: « Modularity is known to be one of the most relevant
characteristics of biological systems and appears to be
present at multiple scales. Given its adaptive potential, it is
often assumed to be the target of selective pressures.
Under such interpretation, selection would be actively
favouring the formation of modular structures, which
would specialize in different functions. Here we show
that, within the context of cellular networks, no such
selection pressure is needed to obtain modularity. Instead,
the intrinsic dynamics of network growth by duplication
and diversification is able to generate it for free and
explain the statistical features exhibited by small
subgraphs.” (Sole and Valverde 2010)
Dissymetry in the alternative
• MS view : natural selection explains the
branching (through common descent) and
(through both homologies and analogies) the
clustering
• Typologist view : clustering explained by common
dynamics/topological properties etc. *** ;
branching explained by common descent not tied
to natural selection
-> less unified than MS : reasons for homology;
reasons for attractors in design space
• Pb. The unity of typologist program is less
straightforwardly visible !!!
Role of development
• Network dynamics : development is what
explains the clustering
-> (Developmental) typologist view : Common
developmental processes underpin
homologies (hence the branching) and
clustering
TYPOLOGIZING THE ALTERNATIVES
TO MS
Several cleavages
• Genes / epigenetics (Gilbert; Kirschner & Gerhardt 2005)
• Genes / developmental systems (DST)
• Genes / Genomics (Fox Keller 2000, Stolz, etc.): what if
« genes » don’t exist any more in molecular genetics ?
• Genes / organisms (West Eberhardt 2003; Walsh 2008;
Odling Smee et al. (2003))
(Gould & Lewontin 1979 Bauplan)
• Forms / Genes (Pigliucci 2007)
• Structure/ Function (adaptation) (Amundson 2005)
• Externalism vs. Internalism (Godfrey Smith 1996)
What may be the targets of criticism ?
The 2 controversial gene-related theses in the Modern
Synthesis :
Darwinism (natural selection as causing evolution, adaptation
and diversity)
Mendelism (Particular inheritance)
-> genes are the substrate of inheritance
Weissmanism (germen soma distinction)
-> development does not impinge on evolution
(p)
(q)
Genes are:
THE Units of inheritance
Causes of development
Genes are:
Units of inheritance
Some other channels are found : methylation
patterns; parental imprinting (narrow
epigenetic level) ;
cultural units (bird songs, nests, language, etc.)
Causes of development
Genes are:
Units of inheritance
Some other units are found : methylation patterns; parental imprinting (narrow epigenetic level) ;
cultural units (bird songs, nests, language, etc.)
Causes of development
Phenotype as non additive outcome of genotype and
(intra & extra cell) environment
(see Norms of reaction, from Woltereck to Lewontin)
« Causal parity thesis »
Stochastic gene expression
-> critique of the notion of« genetic programme »
Suppose that methylation patterns are
inherited:
Does it change anything for the relationship
between development and evolution ? (thesis
q)
Not if they are not reliably affected by
development
Those two trends of critiques are not logically
related
They will challenge (p)
But not necessarily (q)
Challenging q
Possibly : very sophisticated developmental
phenomena (involving genes, epigenetics etc.)
without making development relevant for
evolution
-> see genotype phenotype maps
Gspace, Dspace
a. Gspace, Pspace, with Dspace
Dspace is evolutionary irrelevant
Genotype space
Phenotype
space
Developmental
space
b. Gspace, Pspace, with Dspace
Dspace is evolutionary relevant
• Is the actual (set of) GP maps of type a or b ?
It’s an empirical issue
• But (some conceptual points): This explains
the macro-microevolution controversy : small
and large scale view of the graphs
• The smaller the zone in Gspace, the higher the
chances that the map will be well behaved
(type a)
• If you consider macroevolution
• If it’s a type b case (which is likely)
• Then you must consider developmental
processes (against q) as relevant for evolution
•
•
•
•
If you ask the diversity questions
Then you consider macroevolution
If it’s a type b case (which is likely)
Then you must consider developmental
processes (against q) as relevant for evolution
• Then you may have to consider the
developmental - typologist view