Explaining diversity through evolution: branching and clustering

Philippe HunemanIHPST (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

DiversityAdaptive 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(CB)D)

(A (D (CB)))(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

Xxxx 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 HilaireUnity of type

Common descent

CuvierConditions of existence

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 HilaireUnity of type

Common descent

HomologyUnity Typological thinking

CuvierConditions of existence

Natural selection

Adaptive radiationDiversityPopulation thinking

The alternative in explaining unity-in-diversity

• 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 (p)Weissmanism (germen soma distinction)-> development does not impinge on evolution (q)

Genes are:THE Units of inheritance

Causes of development

Genes are:Units of inheritanceSome 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 inheritanceSome other units are found : methylation patterns; parental imprinting (narrow epigenetic level) ; cultural units (bird songs, nests, language, etc.)

Causes of developmentPhenotype 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 DspaceDspace is evolutionary irrelevant

Genotype spaceDevelopmental space

Phenotype space

b. Gspace, Pspace, with DspaceDspace 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