The Phenomenon Of Evolution

The theory of evolution developed out of earlier ideas, some clearly anticipating what Charles Darwin and Alfred Russel Wallace would introduce to the world in 1858. The important concept was that the diversity of life, present and past, was not static and produced by externally derived creation events but was the product of historical processes, operating since some origin time on Earth—and still operating. One can view these as the biological version of the prevalent idea of a universally applicable natural law. Darwin himself left open how the whole process may have started, but biologists almost uniformly assume it was a terrestrial, strictly chemical phenomenon (this, too, is an assumption that, while not necessitated by specific knowledge, reflects the purely materialistic working world view of most scientists). The theory of evolution is elegantly simple and requires only a few basic elements. Darwin and Wallace introduced a few, to which several additional broad generalizations about the phenomenon of life can be added.

Darwinian Fundamentals

The basic postulates of evolution are simple and well known, but it is worth listing them: (1) organisms vary, (2) some of that variation is heritable from parent to offspring, and (3) there is population pressure on resources related to survival and reproduction; that is, organisms produce far more offspring than the environment can support. From any system with these general properties, the fact of evolution could be predicted, so that once they were clearly stated, darwinian phenomena are neither surprising nor really open to doubt. But this doesn't mean we could deduce any particular life form, even simple ones.

These basic principles can be summarized in Darwin's own phrase: "descent with modification." He deduced the consequence of persistent population pressure on resources: the variation that is able to reproduce more prolifically will be more commonly represented in future generations. He extrapolated this over long time periods, assuming it worked more or less consistently and gradually, to hypothesize that this natural selection explained the adaptation of organisms to their environment and accounted for the origin of new species from previous species over long time periods.

We should be aware of what these evolutionary premises do not say. They do not specify the resources under stress nor what it is that is heritable (or how it is inherited). Darwin did not specify correctly where new variation comes from, and there are widespread ideas in biology that are based on tacit additions to the basic principles (for example, some aspects of strong genetic determinism). We will see the implications of these assumptions.

We also don't need to argue about whether darwinian processes happen, as they are rather obvious and make very little in the way of specific assumptions. They not only apply to life but to any system built up of multiple, changeable units with competitive inheritance. But at the heart of Darwin's contribution to science was the theory that this is the process responsible for the transformation of species. Surprisingly, nothing in Darwin's premises necessitates species formation, even if his process adequately explained the form and structure of life. The separation into distinct species—which is what he was trying to explain—does not follow. At least one additional postulate is needed. This is (4) sequestration.

Sequestration and Diversification

Sequestration is implicit in Darwin's postulates. Life forms are isolated from each other, so that differences can accumulate between individuals. Darwinian variation does not immediately blend away (ironically, Darwin's mistaken idea of blending heredity was a problem for his theory, a fact that bothered him greatly). We use mating barriers between organisms to define "species." Even assuming they are genetically based, such barriers can be established by genetic changes having nothing to do with response to environments. In fact, whether adaptive or even random processes per se lead to new species has never been adequately proved as a generalization, and partly depends on our definition of "species."

Darwin was trying to explain the diversification of life into many species. In fact, he felt, and it is often argued, that phylogeny, or branching (divergent) speciation, is predicted by his evolutionary postulates. He developed his theory with the species question in mind, but adaptation does not by itself imply speciation. A global primeval soup could in principle evolve by changes in its chemical composition, energy, or some other cyclical processes diffusing through it over time. This does not constitute divergence among the states of life, except in the sense that there would be variation, as there is among readers of this book.

Evolutionary thinking predicts branching because descent with modification produces variation, and if that variation does not freely mix, then eventually reproductive exchange between the different branches becomes no longer possible. This is the essence of "speciation." Variation is sequestered within lineages, which accumulate increasing divergence over time. Because this process never ends, each lineage in turn diversifies. The result is a nested phylogeny.

It would seem from a superficial consideration of the similar nature of all cells that the basic machinery of life had developed before cells began to diverge. This assumes there was once only one cell population. Cells effectively isolate very localized packets of living matter from each other and from the surrounding "soup." Internally, the cell maintains the special conditions for using DNA to code for protein, a system almost certainly already present when organized cells evolved. Higher-level organization of life into multicellular organisms depended on this so that even within an organism there is local isolation of material.

Sequestration of material into cells, however, can never be complete. Even the first cells had to evaluate their environment and interact selectively with it (bring in nutrients, release waste, control ion concentrations and pH, and so on). Multicellular organisms require interaction and hence exchange of "information" among cells. Elaborate mechanisms have evolved for this, including partially permeable cell membranes, with mechanisms for transporting material across them, signaling mechanisms that work across cell membranes, and mechanisms for direct contact or transfer between adjacent cells.

DNA sequences, which will be described specifically in Chapter 4, are inherited across generations and thus, by nature, retain a trace of the past. Indeed, the sequestration of DNA from direct modification by the cell is one of the cornerstones of modern evolutionary theory, as we will see. However, DNA replication is not perfect or evolution could not have occurred, and if we have some external means of calibrating species history, such as known points in the fossil record, we can compare sequences of fundamental genes in representatives of the major branches of organisms to make educated guesses about what the ancestral cell type and its

Bacteria Archaea Eucarya


Fungi Plants

Figure 1-2. Tree of the major branches of life, based on ribosomal RNA. Redrawn from (Woese 2000) with permission. Original figure copyright 2000 National Academy of Sciences, U.S.A.

mechanisms may have been like (e.g., see Doolittle 1998; Doolittle 1998; Woese 2002). The process of accumulation of errors in DNA copying is highly stochastic (probabilistic); therefore, not all genes give precisely the same picture, so we have to aggregate data from many genes simultaneously. By grouping sequences that are most similar and roughly equating the amount of difference with time since common ancestry, we can reconstruct a hierarchical, treelike, representation of the history of life (e.g., Banfield and Marshall 2000).

The idea is based on the assumption that life had a single ancestry, here on Earth, represented by the trunk of our metaphoric tree. The tree of life reconstructed by genes presumably really is the tree of cellular life because basic biochemical mechanisms had to precede cells. Given a single origin of life, the principle of sequestration then leads naturally to diversification. Again, sequestration cannot be complete or we would never have aggregates of essentially similar cells that we call organisms or of essentially similar organisms that we call species. We will see, however, that this, like so many things in life, has important exceptions.

In addition to sequestration, three other aspects of life are so ubiquitous and fundamental that they should be added as generalizations about life as it happens to have happened on Earth. These are (5) modularity, (6) duplication, and (7) chance. Biological evolution could occur without them, but they have nearly comparable ubiquity and predictive power to the other postulates.

Modularity and Duplication

New structures from molecular to morphological are built by evolution from preexisting foundations. One of the most important and fundamental aspects of this is modularity. From molecules to morphology, we see variations on similar themes. These comprise separate modules or units from which more complex structures have been constructed. And one of the most important ways this has taken place is by the duplication of structures,with subsequent differentiation.The pervasiveness of duplication of structure has been known since systematic biology began and has only been reinforced by the history of discovery in physiology and molecular biology.

Modularity and Duplication Below the Level of the Cell

The modular nature of most of the basic biological molecules can be seen in Figure 1-3, which shows the chemical structure of nucleic acids, amino acids, and steroids. Variation on core structures as found in nucleic and amino acids was probably to a great extent a natural given, whereas variation in other molecules like steroids is at least to some extent manufactured by organisms. This is certainly true of protein families, as will be seen throughout this book.

The system of life today has been built on the modular nature of a corresponding concatenation of nucleic and amino acids into DNA/RNA and proteins. The nature of its ultimate origins is debated, but at some point biological information came to be stored in the form of the specific sequences, not the chemical nature, of these components. In particular, genetic coding is based on the order of concatenation of nucleotides in DNA and RNA, which has no chemical bearing on the nature of the protein being coded.The code for a given amino acid (see Chapter 4) is essentially universally used and has no bearing on the chemical nature of that amino acid nor on what that amino acid will do in a final protein. So it is in that sense a true code.

Nucleic Acids sugars

PENTOSE a 5-carbon sugar


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