Explaining diversity through evolution : branching and clustering

1. Explainingdiversitythroughevolution: branching and clustering Philippe Huneman IHPST (CNRS/Université Paris I Sorbonne)

2. « 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 »)

3. I. The explananda of evolutionary theory

4. Evolutionarytheoryexplains (Lewontin) : Adaptation Diversity Evolution

5. Modern Synthesis evolutionary theoryexplains (Lewontin) : Adaptation -> explained (defined ?) by naturalselection Diversity Adaptive radiation, « principle of divergence » Evolution -> several causes, the major one beingnaturalselection

6. The twoexplanada are related: Adaptation -> competitive exclusion -> diversity (Darwin’sfinchesbeaks)

7. Diversity • There are differentways of beingdifferent • The diversity issue = why is differenceoccurring in the wayitoccurs ?? • Variety, but not muchnovelty(Darwin) -> unitythroughdiversity Alike, thoughdifference : The concepts of homology (and analogy) The wing of bats and the fins of fish as the samething, thoughdifferent – or different instances of the samething

8. 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 facitsaltum." 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.

9. Diversity, 1 Idea of a morphospace Generalisedmorphospace Issue : The clusteringwithin the morphospace Why is theresuchfact ?

12. Diversity, 2 The pattern of branching

13. A, B, C, D, E Possible comparisons : (Ab) (CDE)), (abc (de)), (a (bcde)) (ab ((cd)e)) etc.

14. (A (BC)D) (A(CB)D) (A (D (CB))) (A (D (BC)))

15. (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

20. The fact is thatwe have somethinglike a tree ! Why ?? -> Darwin’sanswer : Common descent. Notice : Kant’sproblem (Critique of judgment) wasthe same Hisanswer = transcendantal presuppositions of the reflective power of judgment…***

21. Evolution = answerstwo questions about rare facts in spaces of possible spaces • Are thereequal ? • No equivalence : you can have branchingwith no clustering • And clusteringwith no branching

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23. 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 itmay be teh case. - > Whatprocess can be likely to answer the two questions ?

24. II. Darwinianevolutionarytheoryexplainingdiversity

25. Darwin’sview Unitythroughdiversity ? The « Conditions of existence » and the « Unity of type » (E.S. Russell Form and function, 1916; Cuvier vs. Geoffroy St Hilaire 1830)

27. 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

28. Darwin’sthesis : « unity of type » is subsumedundernaturalselection • What is « commondescent » for two traits at a samephylogeneticlevel ….resorts to « naturalselection » whenconsidering the first stages (plesiomorphic states) of the trait…

29. 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.

30. Consequences : micro and macroevolution • Darwin’sgradualism • The scale-free diagram – zoom in (processes) and zoom out (branching pattern, homologies)

32. The Modern Synthesisview Change in allelicfrequencies as the core of evolution « Population thinking » (Mayr) and population genetics: genes and (alleles) populations are the two main explanatorylevels. Natural selection is the main cause of the departuresfromgenefrequenciesequilibria

33. About processes: macroevolution as extrapolation frommicroevolution (Mayr, Simpson) About patterns : Gradualism

34. III. Whatwouldbe an alternative view ?

35. Population thinking and typology • Amundson’s classification (« Homology and homoplasy : a philosophical perspective » 2004): typology = homology more important thannaturalselection « Typologistswereunited not by metaphysical or anti-evolutionary commitments, but by a belief in the importance of homology over adaptation” - > Micro vs macro evolution = is adaptation differentthan « novelty »? (Muller and Newman 2003) Shouldnoveltyneedanother explanans ?

37. The alternative in explainingunity-in-diversity • MS : explainsdiversitythrough adaptation (radiations…) & explainsunity by commondescent (and in fine natural selection…) • Typologist : explainsunity (in diversity) by commonalities of structure; explainsdiversity by novelties + homology

38. MS explanation of diversity issues • Branching: d (A,B) < d (A,C) = there is a commonancestor A’ of A and B, and A’’ of A’, A, B and C • Clustering : a restrictednumber of (coarsegrained) selective pressures + commondescent -> attractors in design space (as « good tricks »)

40. Typologistsanswer Clustering: someforms are attractors in design space – ie whatever the genetic structure, the environmental structure, etc., the sameformwillappear (at all levels**) The clusteredforms are not living in the sameenvironmentat all, hence natural selection can not be the explanation (fins/wings)

41. Typologistsanswer, 2 Branching= explained by commondescent & Common descent can not be traced back to natural selection - & Natural selection is just noise on pure branching (homoplasies); itdoes not explainbranching

42. Clustering: not all combinations of parts/traits/molecules/cells are equiprobable • D’Arcy Thompson : morphologies – effects of changingscale; conservation laws etc. -> a few formswill be realized • Stuart – combiningtoolkitmolecules

43. A niceexample: Modularity in cellmetabolismnetworks Intuitive idea : you have manynodes – non modular (non clustered) graphs are the mostprobable networks; selection willpick up the mostmodularones (because of advantages of modularity)

44. 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)

46. Dissymetry in the alternative • MS view : naturalselectionexplains the branching (throughcommondescent) and (throughboth homologies and analogies) the clustering • Typologistview : clusteringexplained by common dynamics/topological properties etc. *** ; branchingexplained by commondescent not tied to natural selection -> lessunifiedthan MS : reasons for homology; reasons for attractors in design space

47. Pb. The unity of typologist program is lessstraightforwardly visible !!!

48. Role of development • Network dynamics : development is whatexplains the clustering -> (Developmental) typologistview : Common developmentalprocessesunderpin homologies (hence the branching) and clustering

49. Typologizingthe alternatives to MS

50. Severalcleavages • Genes / epigenetics (Gilbert; Kirschner & Gerhardt 2005) • Genes / developmentalsystems (DST) • Genes / Genomics (Fox Keller 2000, Stolz, etc.): what if « genes » don’texistany more in moleculargenetics ? • 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)