Some Additional General Principles

The foregoing attempted to give a general, if superficial, picture of the basic patterns of animal and plant development and form, stressing the processes or phenomena that are repeatedly observed among species or within individuals during their development. So brief a catalog gives a poor reflection of the diversity of mechanisms, and we have to be careful about how we interpret the data, perhaps especially in regard to what appears to be widely conserved developmental characteristics because they often are quite different when examined in detail. This is clear when multiple species (sometimes even closely related species) are compared.

Not Everything We See Is "Necessary"

Simpler organisms have no clear-cut body plan, some can develop a whole new organism from any cell or at least from cells located throughout their body, and some have no clear-cut "embryo" stage. Plants have an organizational "plan" and have essentially totipotent cells throughout their bodies. In the case of animals with classic body plans, the hierarchy of development and phylogenetic similarities led biologists to form a general idea of how development works, and this then became intimately related to the study of evolution (Richards 1992). Going back to the leading embryologist Karl Ernst von Baer in the early 1800s, it had been shown that there is typically less phenotypic divergence early and more divergence later in development, consistent with a hierarchical dependency of later structures upon earlier foundations. Before the discovery of evolution, the idea was that similar animals developed their adult forms by modification of a largely identical early form. Around Darwin's time, the changes among species were widely considered to have come about by sequential building of new structures upon existing adult stages over the generations, a process called "terminal addition." This explained how complexity arose or evolved. Essentially, natural selection was treated as if it worked only on adults.

The famous and classic example has to do with the stage of vertebrate embryos known as the pharyngula, at which gill arches, somites (prevertebral segments), dorsal nerve cord, and early limb buds were present. Ernst Haeckel (see Figure 87), Darwin's energetic and prolific defendant and science-popularizer in Germany, developed his well-known recapitulation theory of morphological evolution and called it the Biogenetic Law, that Ontogeny (development) Recapitulates Phy-logeny. This theory held that in development an organism passes through the adult stages of its ancestral species, adding on later stages leading to its current more advanced form.

Ernst Haeckel Theory
Figure 8-7. Ernst Haeckel. 1899 drawing by F. von Leubach, in Haeckel 1906.

In Haeckel's famous figure, diverse vertebrates are shown passing through pharyngula stages, which are essentially the same, presumably representing their ancestral state as a kind of primitive gilled fish (Figure 8-8B).An "hourglass" model developed over the years in which the different forms of vertebrate cleavage had been canalized to produce a stereotypical pharyngula common to vertebrates, which then diversified later in development to the varying adult morphologies. We know now (and in truth it was known to Haeckel) that the pharyngula stages are not as identical as depicted; even more importantly, however, the earliest stages from cleavage onward are in fact quite diverse among vertebrates, and indeed the supposed stereotypical traits vary in their timing of appearance (Bininda-Emonds et al. 2003; Raff 1996; Richardson et al. 1997; Richardson and Keuck 2001; 2002). Nonetheless, there are similarities, even if they were exaggerated, and they provide important evidence for shared ancestry.

As a digression, historians and philosophers of science have many times remarked on the ubiquitous, perhaps even necessary, element of public advocacy (or even propaganda) that is necessary for a controversial view to gain acceptance. One can go further and note that one of the problems in science is that there is, and always has been, a whole lot of "fudging" going on: theory is routinely defended by selective use, presentation, collection, and manipulation of the evidence, ignoring some facts and stressing others, redefining terms, and retrospectively and conveniently reinterpreting data. This cannot be justified formally, but it in many classic cases was necessary, in the face of imperfect data or measurement (or understanding), in order to reach a general understanding of things. Gregor Mendel's supposed cheating in his analysis of pea plants is a famous example (Weiss 2002b), and so it was with the classical Copernican revolution in astronomy that occurred despite many totally wrong inferences and facts incompatible with the theory as proposed at the time. Many theories are wrong, but even correct theories typically require commitment to a framework even in the face of such evidence. Darwin's wrong ideas about inheritance and the problem of the age of the Earth did not prevent recognition of the overall truth of common ancestry.

Even in related animals that end up with similar adult morphology, developmental stages subsequent to the pharyngula can vary greatly (Raff 1996). There are several well-studied examples of this: sea urchins, anurans (frogs), and ascidians (primitive chordates including tunicates, or sea squirts). From genetic phylogenies of contemporary species, among closely related species with similar adult forms, some are found to pass through an intermediate juvenile or larval stage, whereas others do not. Furthermore, the similarity of larval stages across the phylogeny suggests that it probably was the ancestral state (at least, it is an ancient state). However, a larval stage has been dispensed with in several subsets of the descendant lineages. Figure 8-9 shows the "pluteus" larval stage in sea urchins. Several frog lineages have subsets of species that pass through an immature, tadpole stage. The converse situation also appears to be true: among sea urchins, there are genetic differences in how similar developmental stages are achieved (Kissinger and Raff 1998; Nielsen et al. 2003; Raff 1996; Raff 1999). Comparable statements appear to apply to the development of flowers among angiosperm species (Kramer and Irish 1999; Ma and dePamphilis 2000).

It is clear that there has not been an absolute, or clear-cut, advantage to going through one or the other form of development—a ladder of developmental sophis

B fertilization maturity

Figure 8-8. (A) Ernst Haeckel's famous figure showing divergent adult stages from similar pharyngula stages; (B) developmental constraint notion, that divergent blastula stages among vertebrates all pass through a common pharyngula stage and then diverge again to the adult form. (A) photograph courtesy Michael Richardson; (B) modified after Richardson, Hanken et al. 1997 with permission.

B fertilization maturity

Figure 8-8. (A) Ernst Haeckel's famous figure showing divergent adult stages from similar pharyngula stages; (B) developmental constraint notion, that divergent blastula stages among vertebrates all pass through a common pharyngula stage and then diverge again to the adult form. (A) photograph courtesy Michael Richardson; (B) modified after Richardson, Hanken et al. 1997 with permission.

tication or improvement is not evident. Direct and indirect developers with very similar morphology are doing well today. A larval stage is not a necessary aspect of a frog's solving the "problem" of becoming an adult; some do, some don't, and axolotls stop at the larval stage. If the idea of evolution by natural selection is correct, then it must be that under some local environmental conditions, when the l arva adult l arva

Figure 8-9. Variation in sea urchin development showing the repeated evolution (or repeated loss) of the pluteus larval form in different branches. Modified from (Wray et al. 2003), reprinted with permission.


Figure 8-9. Variation in sea urchin development showing the repeated evolution (or repeated loss) of the pluteus larval form in different branches. Modified from (Wray et al. 2003), reprinted with permission.

appropriate mutations were present, one route of development provided an advantage of some sort.

Repeated evolution of a structure is plausible if the mechanism is not too intricate. A potential alternative compatible with modern theory is that the structure was present in the common ancestor, and was repeatedly lost. A variation on this theme would be that the changes occurred by phenotypic drift: that both developmental strategies existed in a population because of some tractably simple genetic mechanism, and one variant replaced the other by chance (or, was not needed and its loss was tolerated by the screen of natural selection). When we see something spotted throughout a phylogeny, such as wings in some insect clades, tadpoles and optic cups in some amphibians, pluteal stages in some sea urchins, and some aspects of olfaction or color vision we face these explanatory possibilities.

Growth, Heterochrony, and Allometry

One of the persistent questions in the evolution of morphology or development is how what appear to be complex changes can be brought about in a practicable way in the time available and by the simple process of natural selection. It has long seemed—correctly, it appears—that it can't be that each variation on a theme is due to the arrival of a new gene specific to the purpose. For example, it would seem to be impractical for every stripe on a tiger, or vertebra, or cusp on a tooth to come about by the action of a new gene.

Discussion of this topic goes far back in the history of biological thought (Schlichting and Pigliucci 1998), but the best-known systematic attempt to explain the phenomenon of changes in shape in modern scientific terms belongs to D'Arcy Thompson (Thompson 1917), who stressed concepts of allometry (size differences in the same structure that may or may not be linear in all dimensions), heterochrony (changes in timing of the same structure), and heterotopy (changes in the placement of a structure in an organism) during development. His idea was to explain the structures in organisms in terms of the universal laws or properties of physics, rather than invoking biology-specific explanations. Whatever the proximate mechanism (which we would attribute to genes, cell characteristics, structure proteins, and the like), biological structures achieve their variation due to physical constraints and temporal aspects of their growth. A number of authors have recently dealt with these general topics (e.g., Calder 1984; Gould 1977; Hall 1999; Raff 1996; Schlichting and Pigliucci 1998; Wilkins 2002; Wolpert, Beddington et al. 1998). The close study of developmental timing has shown this to be a source of variation in vertebrate body plan, in contrast to the notion of a conserved pharyngula stage in vertebrates mentioned earlier. Timing seems to be simple to change, but can have what appear to be complex effects: a powerful tool for evolution.

In modern genetic terms, we seek to identify molecular mechanisms that will bring about these ends and to understand their relative importance. The appeal of an allometric or heterochronic approach is that in principle it can provide a means by which rather simple molecular processes can account for a wide and otherwise perplexingly complex diversity of shape or other higher-level complexity. Shape can be substantially changed simply by changes in the speed of or the differential timing of developmental processes like tissue growth, the onset of segment-formation, and so forth. This can be achieved by mutations in the dynamics of gene expression or the interaction of products of the same genes, without a need for new genes or mechanisms to arise. This may be a major means of morphological evolution (e.g., Carroll et al. 2001).

In fact, there are many examples of substantial differences in the timing and pattern of growth and development among related species, showing how variable this can be or how weakly correlated it is with phylogeny (e.g., Chipman et al. 2000). However, neither heterochrony nor allometry explains all morphological variation. For many changes, even among closely related species, more profound genetic mechanisms seem to be responsible (e.g., Raff 1996).

A famous example of the work of such mechanisms in evolution is the idea that humans are an example of neoteny; that is, we retain juvenile morphological proportions, particularly in brain size, as adults; this enables us to have relatively large heads compared with our closely related primate ancestors or contemporaries. Of course, we aren't really just grown-up babies (even if we act that way), but the differential shape and growth history resembles that of an arrested maturity.

Many aspects of development within a generation are responsive to environmental conditions, and some may be somewhat heritable genetically (e.g., mating type in yeast) or epigenetically (a well-nourished mother may produce a larger egg), a point that cannot be stressed enough (Lewontin 2000; Schlichting and Pigliucci 1998). If the environment persists, the effect is effectively heritable, even though not in genetic terms (Chapter 3). Many such factors, including effects on chromosome packaging (akin to genetic imprinting, e.g.), may remain to be discovered. Removal of the relevant environment may lead to a reversion of the organisms to their former state, but it may be that successful survival or mating will come to depend on the "environmental" trait. If so then if mutations arise and are favored by selection, genetic assimilation can occur (Hall 1999; Waddington 1953; 1956; 1957; Wagner 2000;Wagner and Misof 1993).Then the trait becomes inherited in the genetic sense. For example, by being bigger, an animal might be able to utilize a different food source, which could lead to selective favoring of other traits related to that change: animal gets bigger because the egg was larger because climate was favorable for its parents; because of larger size, animal can eat larger seeds than rivals from less favorable parental environment; genes for eating larger seeds hitchhike to high frequency as a result.

From Cells, to Organisms, to Communities, to ... "Gaia"?

There are numerous ways in which cells aggregate to form organisms, or organisms aggregate for common purposes, or ways that cells are connected physically, logically, or temporally or by social aggregation. This suggests that an appropriate notion of an "organism" should be broader than is usually considered. As human organisms that sequester a germ line, we tend to think that the "individual" in our usual sense is the essential unit of evolution, the very definition of a living being. But this is rather arbitrary (e.g., see Buss 1987).

The nature of association among cells carrying genotypes within a "species," defined as those that can potentially reproduce together, is variable. Cells within our bodies aggregate necessarily, and only the germ line connects us cellularly to other humans. But trees and sponges do not sequester a germ line, and the reproductive cells of species like some annelids change during the individual's life. Is there a major distinction in regard to the logic of evolution between the cells in our various organs and the ants in a hive? Bees can be viewed as having a restricted, sequestered, specialized germ line, in the form of the reproductive cells of the queen. This differentiation is induced, for example, by royal jelly, but is that conceptually different from the induction of our germ line by diffusible hormones? Our limbs develop more or less autonomously relative to other parts of our body, but is this so different from the "limbs" of a hive—its individual bees—relative to each other?

Sexually reproducing organisms are not completely separate units of evolution (except hermaphrodites). But how completely separate are the different humans in a population? We are cellularly connected internally by the tree of our developmental life histories and externally by our reproductive history. We communicate among disconnected cells in our own bodies by use of circulating free cells or signaling molecules and to others by the air using pheromones and their receptors and through transmitted vibrations (sound) received by a different kind of receptor, and so on. As we will see, the mechanisms are very much the same even at the fundamental level of genes. We have cellular dependence in our bodies, but the bodies (and hence cell aggregates) of our offspring depend on others in their population, certainly until they reach maturity. It is possible to take a more seamless view of biological connectivity, all through the common phenomenon of cell division. This is much the notion Bateson was trying to express long ago (Bateson 1894; 1913) in the sense of different individuals being extensions of a single organism.

Some of the subtleties, and perhaps the reasonableness of our suggestion that the notion of the individual organism is not so clear as is usually thought, can be seen in plants (Halle 1999). Because of the relative independence of the different shoot meristems, plants can shed gametes from different locations rather than having a single sequestered genome. Somatic mutation can lead these different reproductive units to become genetically variable over the many stems and long life of a tree. Further, the individual units compete with each other during the life of the plant. The individual stems draw sustenance from a common root system (which, however, has its own independent repetitive units), but they act in other ways as individuals.

We can extend the same ideas even more broadly to include the self-reproducing, homeostatic communities we call ecosystems. They have "organic" behavior, and even the very diverse species that make up an ecosystem have common ancestry, if very ancient. There is also complex communication among the organisms (e.g., via sounds, smells, and in many other ways). They eat each other, but how different is that from apoptosis or other aspects of degrading and recycling of its constituents that routinely occurs in complex organisms?

Notions of these sorts have been taken to their global extreme by a few investigators (Lovelock 1979; 1988; Lovelock and Margulis 1974). They suggest that it is productive to consider the entire global biosphere as a single homeostatic, self-evolving superorganism. This idea has been called Gaia, after the Greek goddess who drew the living world forth from Chaos. The Gaia idea has sometimes been used to argue that the Earth is an almost self-aware system that tries to maintain harmonious balance, resisting the pressure toward disorder from the forces of entropy (e.g., discussed by Turner 2000). Actually, within the confines of modern empirical science, roots of the Gaia hypothesis can be found in the work of a founder of modern geology, James Hutton (Hutton 1788), who viewed the world as a closed physical system subject to the physical laws of nature.

The basic idea is simply that, through various feedback mechanisms, the diverse forms of life maintain on Earth a stable physicochemical environment that would not be possible were the planet inert and life-free. Unlike passive physical structures, living forms are homeostatic, and their interactions depend on their evolutionary connectedness (for example, species consume each other in part because the prey is made of constituents similar to the predator's and hence reflect what the latter needs). In evolutionary terms, an excess of some resource can stimulate the evolution of organisms to fill it, and extinction can be viewed in some senses as a way to remove imbalance. At least, any multicomponent system with inputs, outputs, and interactions can achieve regularities of structure or various states of home-ostasis or equilibrium (or can spin out of control, but that has not yet happened to the biosphere). No mystic or conscious component need be invoked in considering the biosphere as a single interacting system.

Indeed, because evidence suggests that all life is cellularly connected through evolution, and currently interconnected in numerous ways, the question is whether we gain scientific insight by thinking of the biosphere as a unit. Certainly, we do this in reconstructing phylogenetic trees from DNA sequences or in using the biochemical pathways found in common to try to infer the origins of life. And many ecologists have thought about the overall energenetic aspects of life, such as its relationship to the conservation of energy and thermodynamic efficiency, as a criterion for selection and for the evolution or balance of ecosystems, food chains, and the like. It is valuable, at least, to remove conceptual constraints in trying to understand how organisms manage to get through life.

CONCLUSION: MANY WAYS OF "LIVING THE DREAM" The great biologist Francois Jacob supposedly said that the "dream" of every cell is to become two cells (so said his friend Jacques Monod) (Monod 1971)) (if DNA can dream, would it be of the ecstasy of base pairing?). In his classic book written shortly after the DNA coding system had been worked out, in which he had a major role, Monod considered that all of life is about the single "project" of reproduction. He refers to this as teleonomy to try, perhaps only partly convincingly, to avoid invoking teleology. The driving dream of reproduction is fulfilled in many ways; but rather than the project of life being to reproduce, it may be more accurate to say that a core characteristic of life is that it reproduces.

What is done to be big or complex are but different aspects of the same processes of basic cell biology and replication and of differentiation that started when they were small and simpler. The three to four billion-year-old unbroken membrane and its contents continually ooze off buds that, when they stick more or less together we call the "development" of an organism, when they separate we call the "reproduction" of a new organism, and when they no longer join cells during their life history we call "speciation." But these are all forms of variation on one, long, connected largely branching process. This is a remarkable fact, and it makes the evolution of life as we see it much more believable.

The single phenomenon "make more of life" has been a conserved trait of all the lineages of life forms that have survived to the present. But how making more is done varies tremendously. There are many ways to become long, large, mobile, complex, or to make progeny. We presume that the growth, development, and reproductive phenomena we have discussed at so many levels came about through the agency of random genetic change and natural selection. In modern biology, we are not satisfied that we understand a phenomenon until we understand it at the genetic level. This is but one way, and perhaps not even the best way to understand life and its development (Keller 2002). But our major purpose in this book is to understand the role of genes in the nature and evolution of life, and we now turn to what is known about the genetic basis of these phenomena, as they relate to development. We will see that genetic mechanisms, like the phenotypes to which they are related, may be conserved for long time periods, but are also quite fluid.

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