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The problem of evolutionary "novelties"

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1 The problem of evolutionary "novelties" on Sun Jan 24, 2016 10:27 am

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The problem of evolutionary "novelties"

http://reasonandscience.heavenforum.org/t2283-the-problem-of-evolutionary-novelties

Gerd B. Muller and Stuart Newman argue that what they call the 
"origination of organismal form" remains an unsolved problem.

French biologist Jean Rostand, for example, wrote ["A Biologist's View," Wm. Heinemann Ltd. 1956] 1
Even among biologists, the idea that new organs, and thus higher categories, could develop gradually through tiny improvements has often been challenged. How could the "survival of the fittest" guide the development of new organs through their initial useless stages, during which they obviously present no selective advantage? (This is often referred to as the "problem of novelties".) Or guide the development of entire new systems, such as nervous, circulatory, digestive, respiratory and reproductive systems, which would require the simultaneous development of several new interdependent organs, none of which is useful, or provides any selective advantage, by itself? 

Evolutionary geneticist Wallace Arthur wrote in 1997 that "current evolutionary theory, based on natural selection and adaptation in present-day lineages is, at the very least, incomplete," hence "the feelings of dissatisfaction that many evolutionary developmental biologists have with neo-Darwinism." 4

Massimo Pigliucci writes: 
The immediate obstacle that arises once we consider novelties as “qualitatively distinct” from existing traits is that the MS tells us how traits spread in natural populations (by natural selection, drift, etc.) but is silent on how they arise—except in the trivial case of quantitative variants of already existing features.
To put it simply, the question is not, say, how different species of turtles get different colors or shapes of their shells; the problem is how do we account for the transition between reptiles without and with shells in the first place?
 http://philpapers.org/archive/PIGWIA/

Popper famously wrote that 
“[Darwinian theory] never gives us a full explanation of anything’s coming into being in the course of evolution,” because it is a theory that assumes variation and “therefore . . . cannot really explain it. . . . It is strictly a theory of genes, yet the phenomenon that has to be explained in evolution is that of the transmutation of form” 
(Popper and Eccles 1977, 560, note 1, in Platnick and Rosen 1987, 13).


Ernst Mayr, a major figure of the MS, defined novelties as “any newly acquired structure or property that permits the performance of a new function, which, in turn, will open a new adaptive zone” (Mayr 1963, 602).2

Neo-Darwinism's Unsolved Problem of the Origin of Morphological Novelty3

Meyer argues that the origin of body plans (and other morphological novelties) during the history of life is increasingly recognized as a fundamental and unsolved problem in theoretical and evolutionary biology. He also argues that there is a good reason for this. In particular, he notes that neo-Darwinism attempts to account for the origin of novel form as the result natural selection acting solely on genetic variations of different kinds. Yet the construction of novel body plans depends upon new sources of epigenetic (as opposed to just genetic) information, and genes alone do not generate this higher-level information and structure.

LeConte also candidly acknowledged this problem, which was called the "problem of novelties" then; today it is the problem of "irreducible complexity":

... neither can it [natural selection] explain the first steps of advance toward usefulness. An organ must be already useful before natural selection can take hold of it to improve on it. evolution is an axiom, and axioms do not need supporting evidence. Given the spectacular success of naturalism in other areas, it may seem a quite reasonable axiom. But wouldn't it be nice if modern evolutionists were as honest as LeConte, and recognized that their confidence in Darwinian evolution is also based on an axiom rather than on evidence?

Evolutionary novelties 5

How novel traits arise in organisms has long been a major problem in biology. Indeed, the sharpest critiques of Darwin's theory of evolution by natural selection often centered on explaining how novel body parts arose.

The numerous definitions of evolutionary novelties can generally be divided into two categories. One emphasizes function, essentially focusing on the origin of novel functional capabilities, such as flight or vision, while the other definitions are structural, emphasizing the developmental origin of novel body parts. We prefer the latter definition because it more specifically highlights the developmental genetic problems with the origin of novelties.

Genomic processes and the origin of novelties

There is broad agreement that the vast majority of the genetic changes responsible for the evolution of morphology occur at pre-existing cis-regulatory elements. In addition, protein changes in enzymes and receptors in various pigment pathways have been found to be important for changes in coat color in mammals and flower color in plants. While there is ample evidence for the importance of cis-regulatory elements in the evolution of morphology, it's questionable whether the amount and the kind of genetic change involved in the origin of novelties has been achieved by these small-scale changes. Furthermore, the evolution of novelties requires the integration of external signals into a new, stereotyped and cell-type-specific pattern of gene expression. There is increasing evidence that the evolution of novel characters involves genetic mechanisms other than mutations at existing cis-regulatory elements. Thus, the genetic mechanisms responsible for character origination may be different from the mechanics of character modification.

Most important among them is how did the gene regulatory network arise that endows a structure with the developmental individuality required to form a unique body part? Downstream of this general question are many other detailed ones: How do novel cis-regulatory elements arise? How is the cohesion of gene-expression output achieved? Is the mechanism of network innovation the same as divergence? And, are different kinds of phenotypic change biased so that they are realized more often through cis-regulatory or protein evolution? It is likely that the origination of novelties occurs through multiple genetic routes, but an important emerging theme is that large-scale network rewiring requires genome-wide changes, including transposable element invasion and transcription factor evolution.

Resumed : many questions, but no answers.

What, if anything, Is an Evolutionary Novelty? 6

The idea of phenotypic novelty appears throughout the evolutionary literature. Novelties have been defined so broadly as to make the term meaningless and so narrowly as to apply only to a limited number of spectacular structures. Here I examine some of the available definitions of phenotypic novelty and argue that the modern synthesis is ill equipped at explaining novelties. I then discuss three frameworks that may help biologists get a better insight of how novelties arise during evolution but warn that these frameworks should be considered in addition to, and not as potential substitutes of, the modern synthesis.


1. Introduction. 
“Evolutionary novelty” has been a recurring term in the evolutionary biology literature (Nitecki 1990). There is a palpable tension among biologists whenever evolutionary novelties are considered for discussion, with a common fear that the concept will be used as a wedge to undermine the modern synthesis (MS) constituting the currently accepted view of evolutionary theory. Ever since Goldschmidt (1940) professed dissatisfaction with the MS’s ability to explain variation across species, his “hopeful monsters” have repeatedly reared their ugly heads and have consistently been beaten back by defenders of the orthodoxy. Yet, evolutionary novelties persist as a fascinating problem for theorists and experimentalists alike, a problem that has been taken seriously enough to become a major stated goal of a whole field of investigation, known as “evo-devo” (for evolution and/of development). Despite great progress over the past decade at finally incorporating development in the modern synthesis, however, the uneasiness when the subject of evolutionary novelties is brought up remains. Why?


2. Evolutionary Novelties: Examples versus Concepts. 

What is an evolutionary novelty? A list of most-often cited examples include the shell of turtles (Cebra-Thomas et al. 2005), flight (Prum 2005), flowers (Albert, Oppenheimer, and Lindqvist 2002), the ability of great tits to open bottles of milk (Kothbauerhellmann 1990), the transition from the jaw to the ear of some bones during the evolution of mammals from reptiles (Brazeau and Ahlberg 2006), eyes (Fernald 2006), hearts (Olson 2006), bipedalism (Richmond and Strait 2000), and the origin of Hox genes (Wagner, Amemiya, and Ruddle 2003).

Depending on who one asks, less spectacular examples of novelties are also cited: new patterns of wing colors in butterflies (Beldade and Brake- field 2002), variations in jaw morphology of cichlid fish (Meyer 1993), or the sexually dimorphic horns of horned beetles (Emlen 1994). It is difficult to see what all of these features have in common, partly because they span all levels of biological organization, from morphological to behavioral to molecular traits. So, is the concept of “evolutionary novelty” a cluster concept (Wittgenstein [1953] 1973, Section 66) that does not admit of precise boundaries, but is nonetheless meaningful, or are we facing a disjointed set of examples whose only loose commonality is that they are interesting to biologists? 
   One way to approach the question is to examine how biologists have variously defined evolutionary novelties and then to ask which of the commonly cited empirical examples do square with the proposed definitions. Ernst Mayr, a major figure of the MS, defined novelties as “any newly acquired structure or property that permits the performance of a new function, which, in turn, will open a new adaptive zone” (Mayr 1963, 602). This links novelties directly to the ecology of the organism, imposing the stringent criterion that a novelty be connected to the adaptive radiation of a whole group. While some of the empirical examples listed above fit the bill (e.g., bird wings), there are also examples of clear evolutionary novelties—such as the transition from the jaw to the ear of some bones during early mammalian evolution—that are difficult to connect to a radiation (mammals did not radiate until the extinction of the dinosaurs). Moreover, while the various jaws of African cichlids are clearly linked to this group’s radiations, it is questionable in what sense variations of a preexisting structure (the jaw) can be considered a “novelty.” Indeed, the latter case would in fact fail to meet Mayr’s own definition. Major new features can evolve without being causally linked to adaptive radiations, while some features may play a role in radiations despite not being novelties in an interesting sense of the word.

Next, let us consider Arthur’s (2000, 811) definition of novelty: “Novelties and apomorphies are essentially the same.” Apomorphies are unique derived characters of a taxon, which carry no phylogenetic information. The problem here is that this is so broad that any new character or variation, no matter how trivial, becomes an evolutionary novelty. This is certainly not the kind of puzzle that has made some biologists question the explanatory power of the MS. If Mayr’s definition can be set aside because of its coupling of novelties and evolutionary radiations, Arthur’s can be discarded as uninformative with respect to the big questions that have fueled the debate about novelties. The two remaining definitions I wish to consider are best treated together because of their conceptual similarities and the light they shed on what I think is most interesting about novelties. Muller and Wagner (1991, 243) conceptualized a novelty as “a structure that is neither homologous to any structure in the ancestral species nor homonomous to any other structure of the same organism,” while West-Eberhard (2003, 198) thought of it as “a novel trait [based on] a qualitatively distinct developmental variant.” The interesting thing about these two definitions is that they are explicitly developmental in nature (unlike Mayr’s), do not refer directly to any specific ecological role of the novelty (again, contra Mayr), and are implicitly evolutionary but not trivially so (unlike Arthur’s). Muller and Wagner’s and West-Eberhard’s concepts are best understood within the goal of evo-devo: to explicitly include development in the MS (Love 2003). The immediate obstacle that arises once we consider novelties as “qualitatively distinct” from existing traits is that the MS tells us how traits spread in natural populations (by natural selection, drift, etc.) but is silent on how they arise—except in the trivial case of quantitative variants of already existing features.

It is this conceptual distinction that led Muller and Newman (2005) to separate what they call “variation” from “innovation”: the problem of variation has been addressed by the MS, while the problem of innovation remains elusive. Analogously, Muller and Newman also separate the concept of novelty from that of adaptation (unlike Mayr), noting that the MS provides us with explanatory tools to understand adaptations (natural selection) but falls short when it comes to the question of novelties. The second aspect of both Muller and Wagner’s and West-Eberhard’s definitions is the implied statements they make about evolution. Because of their emphasis on nonhomology, these authors rule out broad conceptions of novelties such as Arthur’s. Indeed, as Muller and Newman (2005) point out, while discussing Arthur (2000), “some apomorphies are rooted in novelties, others are not,” so that the concept of apomorphy is entirely perpendicular to that of evolutionary novelty. Yet, there are remaining issues even with Muller and Wagner’s and West-Eberhard’s conceptualizations. On the one hand, they do not include any reference at all to ecology, turning the problem almost exclusively into one pertaining to developmental biology. Second, they may err on the side of stressing discontinuity too much, ignoring conceptualizations of evolution as using previously existing structures in novel ways, what Jacob (1977) famously referred to as “tinkering.” I do not put a high premium on precise definitions; indeed, I think that evolutionary novelties are a necessarily fuzzy concept, like that of biological species (Pigliucci 2003). Nonetheless, it seems to me that these two deficiencies need to be addressed, which is why I venture to propose an amended definition of evolutionary novelties: Evolutionary novelties are new traits or behaviors, or novel combinations of previously existing traits or behaviors, arising during the evolution of a lineage, and that perform a new function within the ecology of that lineage. This definition does not imply any specific mechanism or long-term evolutionary effect, since the first one is precisely the objective of empirical research in this area and the second one is a matter to be settled based on the historical record. However, my definition (1) makes explicit the fact that often novelties are not absolute discontinuities but can be built on previously existing parts, (2) indicates that they are a phenomenon that affects the evolution of certain lineages without implying that all derived characters are in fact novelties, and (3) requires some kind of ecological function to eventually be coupled with the novelty, although it does not imply a necessary link between novelties and adaptive radiations.

3. Why Is the Modern Synthesis Insufficient? “Describing a single individual is as theoretically peripheral to a populationist as describing the motion of a single molecule is to the kinetic theory of gases. In this important sense, population thinking involves ignoring individuals” (Sober 1980, 370). As mentioned above, several authors have hinted at the fact that the modern synthesis is not sufficient to account for evolutionary novelties, implying more or less forcefully that the MS is incomplete in some major respect (Schlichting and Pigliucci 1998; Gould 2002). This has in turn led to unnecessarily defensive reactions by supporters of the MS, who apparently often confuse the possibility of an expansion of the MS with an outright rejection of it. The MS arose out of a necessity to reconcile classic Darwinian ideas and the new fields of Mendelian and statistical genetics (Mayr and Provine 1980). It achieved an account of how variation and heredity come about and effectively unified natural history, Mendelian genetics, population biology, and paleontology. Famously, what was left out of the synthesis was development, despite the large amount of work on the embryology of both plants and animals that had been done up to that point. Equally famously, the synthesis did not address what some biologists perceived as a different kind of phenotypic variation, the one differentiating species and higher taxa and, in particular, what we now refer to as evolutionary novelties. This culminated in Goldschmidt’s (1940) bold attempt at expansion (again, not rejection) of the MS, an attempt that led to vehement dismissal by the synthesists, especially Mayr. It is this conceptual history that allows us to make sense of the enthusiasm that has greeted the onset of evo-devo in the 1990s: on the one hand, here finally was a chance to put development back into the MS, made possible by the advances in understanding and the technical possibilities of molecular biology; on the other hand, perhaps we were finally going to come up with a reasonable explanation for the hidden problem of innovation and definitively put to rest the specter of hopeful monsters. It is still early to say what evo-devo will or will not be able to accomplish, but some things are clear enough to illuminate this discussion. First, much evo-devo research so far is more about “devo” than about “evo” and has little at all to do with ecology (in turn, a strangely unnoticed additional missing piece from the MS). Therefore, despite some spectacular discoveries (such as the evolutionary conservation of Hox genes [Lemon and McGinnis 2006]), there is little reason to expect this line of inquiry to offer a fresh way of looking at the problem of novelties. Second, to the extent that evo-devo has expressly attempted to link up with the MS and its population-level approach, this has been through the study of the molecular-developmental underpinnings of quantitative variation, which means that evo-devo still addresses primarily the problem that has already been dealt with by the MS (Pigliucci and Kaplan 2006). To put it simply, the question is not, say, how different species of turtles get different colors or shapes of their shells; the problem is how do we account for the transition between reptiles without and with shells in the first place?

4. What Other Explanatory Frameworks? 
Well, then, are there any additional (not “alternative”) explanatory principles the use of which biologists may profitably explore to extend the modern synthesis and account for evolutionary novelties? There are at least three promising candidates, each of which has received some attention over the years and that may need to be combined to some extent in order to satisfactorily expand the synthesis: complexity theory, phenotypic/genetic accommodation, and epigenetic inheritance systems. 

4.1. Complexity Theory. 
Complexity theory is a vast and heterogeneous field of mathematical research (Bak and Chen 1991). It has been explicitly applied to evolutionary theory (Sneppen et al. 1995) and even to the specific question of evolutionary novelties (Toquenaga and Wade 1996). The idea is that certain kinds of systems, those characterized by an intermediate level of connectivity among their components (like a limited degree of epistasis in genetic networks), exhibit surprisingly complex behaviors that are emergent properties of the interactions among the system’s components. Some complex systems exhibit a number of stable states between which the system rapidly transitions, spending little time in intermediate states. These “attractors” open up the tantalizing possibility that shifts in phenotype (say, from nonshelled to shelled reptiles) may occur rapidly because the beginning and ending states are stable islands in phenotypic space, while the intermediate forms are not. In this sense, biological systems may share formal commonalities with a large number of natural (e.g., hurricanes) and artificial (e.g., economies) systems that would make the evolution of phenotypes in biology partly (although not entirely) a matter of generalizable laws of form, a project that goes back at least to D’Arcy Thompson ([1917] 1942). The problem with complexity theory, at least as perceived by most biologists, resides precisely in its focus on the formal similarities among different kinds of systems, so much so that it is often regarded as little more than a metaphor. Equally important, and related to the same issue, is the fact that complexity theory seems to be able to come up “only” with qualitative descriptions, significantly deviating from the ideal of quantitative mathematics established in physics and consciously imported into the MS by people like Fisher, and which eventually gave us the statistical treatments of evolutionary quantitative genetics. This sense of apparent limitation of complexity theory may have resulted in its approach having already peaked in biology during the 1990s, a fate similar to a predecessor of the theory that similarly promised a mathematical treatment of qualitative phenomena: Thom’s (1977) “catastrophe theory.” The latter also enjoyed a brief period of application in biology and was invoked by Waddington (1979) as a way to expand the MS. Thom’s attempt suffered from the fact that, while the math allowed for enticing graphical descriptions of sudden state transitions, it was so general that it was difficult to go beyond its use as a metaphor in any specific scientific context. Then again, recently Gavrilets (1999) has remarked that in evolutionary biology models should be thought of as playing the part of useful metaphors, rather than of providing specific predictions. There is some recent evidence that the idea of phenotypic attractors may as yet generate empirically parametrized models that are close enough to “real” biology to be palatable to biologists. For example, work by Salazar-Ciudad and Jernvall (2005) on the genotype-phenotype mapping of teeth morphology in mammals indicates that while simple phenotypes follow the pattern expected by the MS (small genetic changes correspond to small phenotypic changes), complex phenotypes are characterized by rapid evolutionary transitions without intermediate forms.

4.2. Phenotypic and Genetic Accommodation. 
Phenotypic and genetic accommodation are phenomena highlighted by West-Eberhard (2003) that relate to Waddington’s idea of genetic assimilation (Pigliucci and Murren 2003) and to the concept of phenotypic plasticity (Pigliucci 2001). Phenotypic accommodation is a well-documented phenomenon by which the inherent plasticity of developmental systems extends to the changes in the environment internal to the organism, triggering a concerted series of accommodations. A classic—and surprisingly understudied—example is the spontaneous appearance of bipedalism in a variety of vertebrates (West-Eberhard 2003). The initial impetus may be due to a mutation or an environmental accident (e.g., a viral infection) that impairs the use of the forelimbs in the newborn. Subsequently, the developmental trajectory of bones, cartilage, muscles, and tendons is altered to plastically “accommodate” the new situation. The adult animal displays a host of complex morphological alterations that, if found in the fossil record, would “clearly” point to a long process of “mosaic” evolution (the MS explanatory principle for such cases). Moreover, the behavior of the animal is also altered and may indeed channel said morphological changes. But how can this sort of accident be of evolutionary importance? It can because the change can eventually become fixed by genetic mutations, if the new phenotype is advantageous and/or if the conditions that generated it (e.g., an environmental or behavioral change) are persistent enough to allow the standard process of mutation and natural selection to “assimilate” the novelty. Again, it is remarkable, in this context, that very little serious attention has been paid to the possible origin of bipedalism through behaviorally or environmentally induced phenotypic accommodation.The key point of phenotypic-genetic accommodation is that the genetic change follows, rather than precedes, the phenotypic change. Moreover, because the initial stimulus is environmental or behavioral, it can simultaneously affect several individuals in a given population, which bypasses another infamous problem faced by the standard MS account: even beneficial genetic changes are initially at low frequency, and they are predicted to often disappear from the population via drift before becoming common enough that natural selection can fix them.


4.3. Epigenetic Inheritance Systems. 
Epigenetic inheritance systems (EIS) comprise a broad category of phenomena that have been under recent intense study in molecular developmental biology and are beginning to be taken seriously by evolutionary biologists (Jablonka and Lamb 2005). The basic idea is that there is more than genetics to the study of inheritance, as behaviors, cultural attributes, and nongenetic modifications of gene expres​sion(e.g., via DNA methylation) can all be passed to the next generation without any change in DNA sequence. In a sense, EIS is an example of scientific application of the broader philosophical framework known as developmental systems theory (Oyama, Griffiths, and Gray 2001), the idea that inheritance comprises the whole set of developmental resources, including genes, epigenetic effects, and environmental resources necessary to recreate an organismal system. There are several molecular mechanisms that make epigenetic inheritance possible, including histone modification, small interfering RNAs, and DNA methylation patterns, though the latter are by far the best understood. For example, methyl groups attached to certain regions of the DNA strand of a chromosome alter the expression of the genes comprised in those regions of DNA. Sometimes these patterns of methylation are reset in the germ line, and their modifications are therefore not heritable, but we now know of cases in both plants and animals were there is no reset, or the reset is only partial. Moreover, epigenetic systems can be affected by environmental signals, such as a variety of stresses. This, one should hasten to say, does not have anything to do with Lamackiantype inheritance of “acquired” characteristics, because the environmentally induced changes are still random with respect to adaptation. What makes EIS relevant to evolutionary theory is that they may represent a reservoir of heritable variation above and beyond the classic one residing in DNA sequences. Furthermore, EIS have been implicated in macroevolutionary phenomena such as interspecific hybridization and polyploidy (Salmon, Ainouche, and Wendel 2005). Even more fascinatingly, EIS interact in complex fashion with standard genetic inheritance, not only because EIS alter gene expression but because genes themselves encode the proteins necessary for the very existence of EIS. The combinatorial possibilities are mind-boggling, and it seems likely that some of this hitherto unexpected variation may help us understand the problem of innovation that underlies the evolution of phenotypic novelties.


5. Conclusion: Where To Next?
 Popper famously wrote that “[Darwinian theory] never gives us a full explanation of anything’s coming into being in the course of evolution,” because it is a theory that assumes variation and “therefore . . . cannot really explain it. . . . It is strictly a theory of genes, yet the phenomenon that has to be explained in evolution is that of the transmutation of form” (Popper and Eccles 1977, 560, note 1, in Platnick and Rosen 1987, 13). It is because the modern synthesis is a theory of genes, not of phenotypes, that it is incomplete. Of course, being incomplete is not the same as being wrong, which is why I argue—with Gould (2002)—that we are still building on the foundations laid out by Darwin almost 150 years ago and that no earth-shattering paradigm shift is in the works. Yet, “defenders” of the synthesis have been busy over the past several decades denying that we need anything more than the conceptual tools that the MS already affords us (Stebbins and Ayala 1981). Let me put it clearly: while the MS has been very successful at expanding Darwinism to account for genetics and population biology, it has failed to sensibly incorporate both developmental biology and ecology; while the MS has given us an account of genetic variation and of how it changes in populations over time, it has reached an impasse on the question of the origin and evolution of phenotypic novelties and organismal body plans. Since the MS has had several decades to try, it seems sensible to seriously explore some of the potential additions and see where they might lead us. I have outlined three promising venues of theoretical and empirical research that have the potential of providing new insights into the question of evolutionary novelties. These may or may not pan out, of course, but it seems that they—especially in combination—provide evolutionary biologists with enough food for thought to be taken seriously and to force us to go beyond the standard hand-waving argument of MS supporters that “this is already adequately explained by the synthesis.” From a practical standpoint, I suggest that biologists concentrate on a limited number of “model systems” to understand phenotypic novelties. The use of model systems in biology has a long, and sometimes controversial, history. Fruit flies, rats, and Arabidopsis plants have been adopted as model systems in genetics, behavioral biology, and developmental biology, respectively. The success of this approach is based on the idea that by concentrating efforts on a small number of organisms one can learn much more about them than by spreading efforts on a larger, albeit more representative, group. As an example, I put together Table 1 to list a number of potential model systems for the understanding of evolutionary novelties. It seems to me that to understand an evolutionary novelty, by and large, means to be able to provide an account of four components, listed in the Table: its history (in terms of fossil record or in the sense of sequence of events on independently reconstructed phylogenies); why it came to be frequent in a population (i.e., its functional ecology); how is it made possible at the developmental level; and what sort of genetic underpinning helps instantiate it. Notice from the Table that it is hard to find systems where all these questions have been answered to a reasonable degree of satisfaction, but the point is that this is the sort of thing we would like to know in order to understand evolutionary novelties. From a theoretical and philosophical standpoint, what we need to articulate is how precisely the additional conceptual elements I have briefly sketched above (as well as possibly others, such as niche construction; Odling-Smee et al. 2003) exactly fit with each other and with the already existing MS framework. This is a research program that obviously is beyond the scope of this essay but that nevertheless seems ripe for pursuit and should unfold over the foreseeable future.



1) http://www.math.utep.edu/Faculty/sewell/articles/mathint.html
2) http://philpapers.org/archive/PIGWIA/
3) http://www.discovery.org/a/2248
4) http://www.evolutionnews.org/2014/03/evolution_is_an083301.html
5) http://www.sciencedirect.com/science/article/pii/S0960982209019459
6) http://philpapers.org/archive/PIGWIA/

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2 Re: The problem of evolutionary "novelties" on Sun Jun 12, 2016 6:30 am

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Morphological novelties abound in the history of animals and have been essential to the diversification of animal forms. The scope of novelties encompasses many familiar structures, from antlers to ear bones, from whale tails to panda thumbs. New structures and pattern elements are often key features that distinguish animal groups. For example,
the vertebrates are characterized by an elaborate forebrain, the neural crest, and cartilageaall novelties that were critical to the success of the vertebrate lineage and that allowed the evolution of further innovations such as teeth and jaws. Structural novelties (or “key innovations”) are associated with adaptive radiations into new ecological territories. The movement of vertebrates onto land is tied to the evolution of the tetrapod limb; the escape of insects into the air required the evolution of wings. The distinctive molar tooth shape has evolved independently several times in association with herbivory. Other novelties such as feathers and butterfly scales permit the display of colors and color patterns used for communication or predator avoidance. New structures require the evolution of new developmental programs. To understand the origin of morphological novelties, we must look again to the genetic control of development. Have new developmental regulatory genes evolved to sculpt novel body parts? Or are “old” genes recruited for new patterning roles? And, if regulatory genes are reused, are they co-opted individually or as part of larger, preexisting circuits? This chapter uses case studies to examine various ways in which new structures and pattern elements evolved through changes in developmental gene regulation. In several instances, shared aspects of development and regulatory gene expression reflect the evolution of novelties from preexisting ancestral structures. Such novelties evolved through downstream regulatory changes in developmental programs. In other cases, “old” developmental regulatory genes evolved a new role in the formation of novel pattern elements. In the best-documented examples, groups of genes or entire genetic circuits were recruited to carry out a new developmental function.

WHAT IS MORPHOLOGICAL NOVELTY?
The history of evolutionary biology is replete with operational definitions of novelty. For our purposes, which are primarily to understand the developmental and genetic basis of the evolution of novel animal forms and patterns, a “novelty” is defined as a structure or pattern element, or even an entire body plan, that has a new adaptive function. This chapter focuses on the best examples of morphological novelty for which developmental genetic knowledge has been elucidated. We do not address other forms of innovation, though they are fascinating in their own right, such as the evolution of physiological adaptations through protein evolution (for example, antifreeze proteins, lens crystallins, keratins, lactose synthesis, immune systems), because they do not concern morphological evolution per se. Quantitative morphological variation, even when extreme, is not considered novel unless it encompasses a fundamental functional shift. Thus most homologous body parts are not considered novelties, even when the range of a vertebrate forelimb, for example, extends from the gigantic size of a whale flipper to the tiny arm of a tree shrew. Certainly, a gray area exists in terms of the degree of functional change considered sufficient to warrant classification as a novelty. Here, we limit our discussion to cases where a functional shift is accompanied by fundamental changes in development. These examples include the evolution of feathers, the origin of the insect wing and the spider spinneret, and the evolution of lepidopteran pigmented wing scales. Other examples of novelty represent the evolution of a new structure, cell layer, or pattern element with no clear morphological antecedent. The cryptic origins of these innovations make them particularly interesting to evolutionary biologists. Several key innovations evolved in the chordate lineage, including the notochord, cranial placodes, the neural crest, and paired limbs. The wealth of developmental genetic knowledge about higher vertebrates and a few key outgroups, such as the cephalochordate amphioxus and urochordate ascidians, allows us to trace the evolution of some chordate novelties through comparisons of these taxa.
  Some ascidians have evolved direct development that eliminates the notochord, the defining structure of the chordate lineage. Snakes are “limbless tetrapods,” having an extended axial skeleton associated with a novel mode of locomotion. Although the loss of ancestral characters typically is not considered to be a novelty, in these examples key morphological characters disappear in the context of a new ontogeny. Other examples of body plan changes include turtles, which have an armored shell resulting from rearrangements of tetrapod characters combined with redeployment of specific cell types, and cephalopods and echinoderms, which exhibit novel body plans that are characterized by new structural components as well as reorganization of ancestral features. The origins of most novelties have long puzzled biologists. Observing an anatomically and developmentally complex structure such as a bird feather, a butterfly wing, or the vertebrate brain does not provide insight into the means by which that structure evolved. Nevertheless, taking a comparative approachaintegrating the study of paleobiology, comparative embryology, and developmental geneticsaprovides a window into the history of some important morphological novelties. The evolution of these novelties involves changes in the regulation of transcription factors, signaling molecules, and structural proteins.



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A Systems Approach to Generating Functional Novelties 1

How do functional new adaptations arise in evolution ?  Partial answers come from the knowledge of molecular networks and genome organization accumulated over the past half century. In that period,  we have witnessed a paradigm shift in scientific thinking from an atomistic, mechanical, reductionist viewpoint to a systems perspective that incorporates cell circuitry and molecular networks into a more integrated view of cellular and organismal activities, based in large measure on information processing. Current “systems” thinking  attributes primary functional significance to the collective properties of molecular networks rather than to the individual properties of component molecules .
How does our knowledge of heritable variation fit into this new perspective? The most basic answer is that hereditary change results from processes carried out by dedicated cell functions subject to regulatory architectures. Our view of genome change has become one that describes active cell processes rather than a series of random accidents. Today we think in molecular and cellular terms about change processes at all levels:

• Localized point mutations result from untemplated incorporations by mutagenic DNA polymerases.
• Organisms acquire new biochemical routines through horizontal DNA transfers.
• Major genome rearrangements result from repair of DS breaks or from the action of mobile genetic elements.
• Whole genome mergers are the products of phagocytosis or cell invasions leading to endosymbiosis.

The various natural genetic engineering operators  are the molecular agents of active genome change. What characteristics do these operators display that fit them into the new systems perspective? The brief answer is that they have the capacities needed for a process similar to the kind of engineering humans undertake when we want to develop novel products or carry out established functions in a more efficient or responsive manner. We do not continually reinvent the wheel or randomly tweak individual system components, as the traditional evolutionary theory postulates. Instead, we reassemble known system or circuit elements in novel ways and, when technological advance or human imagination makes them available, we introduce novel components to a system. The long route from the transistor and integrated circuits to smart phones is a relevant example. Accordingly, let us adopt systems engineering as a theoretical metaphor for evolutionary change. To justify this metaphor, we will list some empirically well-documented biological analogies to systems engineering capacities. Then we will move on to
consider more speculative ideas about what additional capacities might be uncovered by further research.

Reorganizing Established Functions to Generate Novelty


When an electronic or microchip engineer sets out to design a new circuit or chip architecture, she bases it on existing components that can be assembled by available technology. This is analogous to utilizing existing evolutionary inventions as the basis for a novel genomic architecture: coding sequences (exons), regulatory signals, chromatin formatting signals, and higher-order constructs such as centromeres, telomeres, and Hox complexes.  Cells possess the molecular apparatus to amplify the corresponding sequence components as either DNA or RNA and then place them in new locations and new arrangements in the genome. As described earlier for protein evolution by domain swapping, this combinatorial process has a far greater probability of success than trying to modify each element in the genome one nucleotide at a time. The genomic assembly mechanisms have sufficient flexibility that they can operate hierarchically to rearrange all types of successful evolutionary inventions. These DNA inventions can range in size and intricacy from a single exon encoding a protein domain to a complex enhancer element executing a sophisticated regulatory algorithm to a complete genetic locus encoding one or several alternative RNA and protein products and even to megabase-sized conserved (syntenic)
chromosome segments.

Retention, Duplication, and Diversification of Evolutionary Inventions


There is a clear trend in the fossil record toward increasing size and structural complexity of organisms over time. The earliest cells have left no discernable trace. Early fossilized communities of prokaryotes, such as stromatolites, can sometimes be sizable , but we know that the appearance of eukaryotes marked a quantum leap in cell and, ultimately, organism complexity. The early multicellular fossils of marine animals from the Ediacaran are smaller and have simpler organizations than their Cambrian successors, and the successful colonization of land by plants and animals has led to the appearance of even larger and more intricately organized forms. Rather than attribute this apparent pattern of increase in size and complexity to some undefined innate drive, as Lamarck did (www.ucl. ac.uk/taxome/jim/Mim/lamarck_contents.html), we can understand
the succession of larger and more intricately organized forms over time to illustrate the tendency of living organisms to retain, amplify, diversify, and reuse their evolutionary inventions. This growth in complexity occurs not so differently from the way that human engineers continually find new ways to build upon and add to technological innovations. We can list (in increasing order of complexity) just some of the evolutionary inventions  that have been subject to widespread reuse and readaptation

It requires great faith to believe that a process of random, accidental genome change could serve this function. Indeed, as many biologists have argued since the 19th Century, random changes would overwhelmingly tend to degrade intricately organized systems rather than adapt them to new functions.





1) Evolution, a view from the 21th century

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