Complex Phenotypes Arise Out Of A Few Basic Processes

Even the most complex of phenotypes are produced to a great extent by a few basic developmental principles, a fact that makes it easier to understand the evolution of the diverse complexities of life. Not surprisingly, this directly reflects the underlying modular genetic toolkit and shares many of its organizational properties.

Complexity is an illusive term, but getting big is one kind of complexity. Size can be achieved simply by mitosis of adherent cells that function together as a physical entity. Spatially varied scaling (allometry) or temporally varying growth rates (heterochrony) among the parts of an organism are simple kinds of processes repeatedly used in different ways among organisms. But to be more than a structureless lump, such growth needs to be regionally differentiated, and temporal or spatial asymmetries that locate function are vital to many complex phenomena. We see this even in single-celled organisms, the classic example being the syncytium of a fly egg that establishes polarity via the interaction of factors with different concentration gradients within the cell.

Given the redundancy and diversity of function occurring even within a single cell, there would perhaps be too much chaotic cross-reaction had internal organization not already evolved early in the history of cells (and there is plenty of molecular chaos in cells as it is!). For example, cell membranes are loaded with ion channels and signal receptors responding to a host of different conditions, but they use similar sets of internal mechanisms such as protein kinase reactions. Intracellu-lar membranes, lipid molecules, organelles, cytostructural molecules, transport and packaging proteins, nuclear membrane structures, and chromosome modification produce extensive intracellular sequestration.

As noted earlier, morphological and physiological systems are typically characterized by repetition of modular units and/or segmentation. Rather than gene-for-unit specification, quantitative patterning processes bring repetitive structures about and as we have seen in several chapters, such processes may only require a modest number of interacting critical factors.

In some of the most well-understood examples, the factors are diffusible signals and their receptors that activate or inhibit selective gene expression. In principle, a two-component reaction-diffusion-like process can generate complex periodic patterning. We do not yet know how many factors are critical for the kinds of repetitive patterning we have described, from ommatidia in flies to hair to the arrangement of regions in vomeronasal or olfactory epithelia and the like. We know that there are some simple components, such as interactions between Bmps and Fgfs, or the Delta-Notch system, but we know that many if not most of the systems studied so far have redundancy or alternative pathways, that organisms can compensate for missing components, or, as revealed by many mouse knockout experiments, that the effects of a pathway are variable depending on naturally occurring variation even within a species.

Simple patterning processes can work because of the partial sequestration among the cells in a tissue field, which enables each cell to interpret and respond to the relative concentration of diffusing signaling factors in its particular extracellular environment. This allows repetitions of the same structure to occur, surrounded by inhibition zones. Making this even easier to understand is that these patterning processes are nested from the first stage of an organism. One process sets up fields, for example, basic polarity, anatomic axes, or organizing centers, which provide partial isolation or differentiation that can initiate subsequent more regionalized patterning, generating a hierarchy of ever more localized differentiation. This seems at least in part to be how limbs, vertebral columns, and invertebrate segmentation work. Because of the evolution of families of signaling and transcription factors, and their receptors and enhancers, initial pathways can diversify by specializing the various gene family members, another aspect of sequestration (that is often only partial because there can be cross-reactions).

Morphological modularity is facilitated by, but also facilitates, the reusable nature of regulatory and signaling genes. Because these genes can be used in different combinations at different times or contexts in the same organism; prior stages in which a gene has been used lead to sequestered, differentiated descendant cells that then can respond to the same signaling factor in a different way. Some signaling path ways are used multiple times in different ways, even during the development of a single structure; an example is Fgf and Hedgehog signaling in dental patterning and tooth development (Jernvall and Thesleff 2000). It is the cis-regulation of gene expression that makes this combinatorial phenomenon possible, and these ubiquitous facts constitute another major fundamental commitment to a particular way of life that was made billions of years ago.

With the use of this set of mechanisms, complex traits develop via a few simple processes in addition to periodic patterning. Budding out or invaginating inward is brought about by local asymmetric cell growth, a signaled process. Branching is another simple process that is widespread in nature and can be repeated to generate a nested hierarchy of components. Among the widespread examples of complexity produced by such processes are the lung and bronchial trees of animals, the distribution of blood vessels, and, of course, real branches on plants. Plants avoid the need for layered repetitive patterning by retaining the potential for generating diversified structures that can be repetitively invoked in the sequestered environments produced by branching.

Differentiation by combinatorial expression of regulatory genes also applies to physiological traits and sometimes involves related or identical genes. This is the case, for example, for ion channel function, cell adhesion genes in neural development, the control of neuronal firing, osmotic function, lipid transport, the differentiation of cells from common precursors in the blood system, and many others.

We haven't covered all biological systems in this book by any means. We've concentrated on particular phenomena that are important to understanding how complex organisms work and how they got that way. The principles and often even the specific genetic phenomena are, however, similar for systems that we have not mentioned. For example, digestion involves the breakdown, absorption, and so on of proteins, fats, sugars, and other carbohydrates, using gene products just like the other systems (e.g., proteases, binding factors). Kidney filtration rests on ion channels and similar structures. Many of these are pure "chemical" processes; that is, they involve genes to the extent of synthesizing chemicals (e.g., HCl, pancreatic enzymes) and secreting them from cells but are mainly not "informational" in the sense of most systems and phenomena in which we have been interested here.

We can illustrate the kind of evolution that leads to diverse complex traits via a single set of mechanisms by an example from ^JP'^i'M}^ our own work. Among the most important characteristics of vertebrates are their mineralized tissues. As vertebrates evolved, the initial calcified tissue of external scales expanded to include teeth and bones (actually, it is not entirely clear which of these came first or whether the pattern was the same in all early vertebrate lineages). A class of secretory calcium-binding phosphoprotein (SCPP) genes, almost all still linked in a single chromosomal cluster (and that appear to have evolved through a series of gene duplication events in ray-finned and tetrapod lineages), is involved in the formation of different mineralized tissues in different species (Kawasaki and Weiss 2003). Some of these genes are expressed in bone development, others in forming the mineralized parts of teeth, and still others in lactation and salivary secretion (calcium binding in saliva can secure the mineral and probably has antibacterial function), tissues that arise from different parts of the embryo's developmental tree. Most or all of these tissues involve epithelial-mesenchymal interaction of the type described in Chapter 9.

These SCPP genes are physiological and not informational; they directly serve a final structural function rather than a developmental or patterning one. But the nature and arrangement of the gene family shows how step-by-step a diversity of complex traits can evolve through or taking advantage of gene duplication. The first SCPP gene was present before vertebrates, serving calcium-related metabolic func-tion(s). In vertebrates, this trait could be used in the evolution of anterior feeding mechanisms (teeth), body protection (scales), and internal body support (bone). Subsequently, new functions took advantage of these genes and their epithelial expression pattern in the evolution of salivary and lactational functions that are basically unrelated to bones (except perhaps in the indirect sense like the use of casein to make calcium available to mammalian infants). Thus, metabolic function evolves through the same kind of gene duplication and subsequent divergence, resulting in the modular function "strategies" that we see in complex morphological structures.

Branching: A Common Metaphor with Differences

This is a point to note that some of the same metaphors apply at many different levels, as a reflection of correlated effects of the basic nature of evolution as revealed by the principles we have been describing. The idea of branching and nested hierarchy is a prime example. This is indicated in Figure 17-3. Karl Ernst von Baer was one of the 19th century founders of modern embryology. In pre-evolutionary times, he noted the way the embryos of collections of species, like vertebrates, begin life looking very similar. But as the embryos age, they diverge in form in the various species, ending up with adult variations on the theme of their shared overall body plan.

Figure 17-3A shows an attempt by Charles Darwin to understand von Baer's notions. Evolution in its original sense of developmental "unfolding" from a shared body plan might be due to a Creator's design, but Darwin saw that the embryolog-ical data were highly relevant to the problem of the evolution of species. He was among the first to use a similar branching metaphor for the divergence of species from a common ancestor (Figure 17-3B). Again there was a shared form, but that reflected the state of the ancestor. Development and evolution relate morphological similarities to very different time scales. There was both confusion and connection between the two, accounting for the famous Biogenic Law of Ernst Haeckel (shared to some extent by Darwin) that during embryogenesis (ontology) species sequentially recapitulate their ancestral forms (phylogeny).

Figure 17-3C schematically shows the somatic divergence of organ systems within the body of a vertebrate, starting from a single cell, the fertilized egg at the top, and ending up with the shedding of another single cell to form the next generation (sperm cells at the bottom). Finally, Figure 17-3D shows a fractal simulation of branching that, as we saw in Chapter 9, has been likened schematically to the structure within organs like the lung.

Metaphors are only so useful, and the phenomena in Figure 17-3 are different in important ways. But to a very real extent they are all the same, and for similar reasons: they all relate to the descent with modification, by duplication with variation, of partially sequestered lineages of genetically differentiated modules of cells. We have tried to show in this book how parallels like these are found throughout the living world, from genomes to species.

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