The Role of Theory in Advancing 21st-Century Biology Catalyzing Transformative Research (2008) / Chapter Skim
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3 Are There Still New Life Forms to Be Discovered? The Diversity of Life - Why It Exists and Why It's Important
3 Are There Still New Life Forms to Be Discovered? The Diversity of Life - Why It Exists and Why It's Important
Pages 38-66
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From page 38... ...
The fantastic creatures that populate the ocean's hydrothermal vents are just one example of situations where discoveries have triggered an expansion of biology's theoretical framework. Our views of where life can exist have been regularly revisited; organisms are being discovered in 38
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From page 39... ...
. The vast numbers of new genes are not necessarily mere variations on known themes; the potential functional diversity -- in other words, proteins and synthetic pathways that carry out currently unknown reactions -- to be found in microbial communities is enormous (e.g., Venter et al., 2004; Zhang et al., 2006; Gill et al., 2006)
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From page 40... ...
Clearly, the living world will continue to evolve in response to environmental change, but from the human perspective the time scale of that adaptation is crucial. Understanding the role of biological diversity and how it is generated, maintained, and lost is a critical goal for 21st-century biology.
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From page 41... ...
In particular, DNA sequences provide data that can be treated quantitatively and are more broadly comparable across the diversity of life than the type of data that predated the molecular revolution (Kim, 2001a)
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From page 42... ...
Second, while evolution is driven by general rules of natural selection, there is also an element of chance. Many possible genotypes may have the same phenotype and fitness, so that the eventual descendant whose sequence is studied today could have many equally possible ancestors.
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From page 43... ...
For example, it is very difficult to resolve the branching order among lineages that diverged either very recently or very long ago. Solutions to these problems will likely require statistical models of molecular processes other than simple single base-pair DNA mutations as employed now.
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From page 44... ...
Closely associated microbial communities appear to be a common, if not universal, fea ture of the physiology of multicellular organisms. These communities contribute to a variety of functions, from digestion to defense against pathogens.
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From page 45... ...
What ecological and evolutionary role do viruses play? Viruses are important not only as pathogens but as agents of lateral gene transfer and catalysts that generate tremendous genetic variation in their specific hosts. Viral activity also has important consequences for turnover of the elements, for example, in carbon cycling in aquatic systems. It has only recently been recognized that virus particle numbers are enor mous, often exceeding those of co-occurring cellular life. For example, seawater contains 10 times more bacteriophage than cellular microbes. Estimates suggest the biosphere harbors perhaps as many as 1031 viral particles (Edwards and Rohwer, 2005)
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From page 46... ...
Defining the role of horizontal gene transfer is only one of several fundamental theoretical issues raised by the study of microbial communities (Box 3-2)
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From page 47... ...
(2001) have estimated that random pairs of homologous DNA sequences from humans would differ in about 1 out of every 1,000 base pairs, meaning that one human differs from another at an average of 3 million sites.
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From page 48... ...
Thus, the protein electrophoresis era helped to resolve the theoretical debate about estimates of genetic variability and shifted the debate from the amount of genetic variability to its causes. The "balance" school argued that genetic variation was the outcome of natural selection (in the jargon of population genetics, of superiority of heterozygotes, frequency-dependent selection, and variation in fitness among habitats)
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From page 49... ...
However, current molecular data conclusively confirm that dominant molecular variation in populations must be neutral. The theory of natural selection is not thereby overturned -- it is clear that many DNA sequences have experienced natural selection.
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From page 50... ...
. The availability of extensive sequence data has led theoreticians to develop an arsenal of statistical techniques to deduce the prob able action of natural selection on DNA sequences (Ford, 2002)
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From page 51... ...
One nice example is the genes that code for the red- and green-sensitive opsins in humans, which were generated by the du plication of a sex-linked gene in hominoids and Old World monkeys, and which give us trichromatic vision. Howler monkeys, a group of New World monkeys, evolved trichromatism independently through a duplication of the same gene in the x chromosome.
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From page 52... ...
How much of this diversity contributes to function is still unknown, but results deriving from comparative genomics and high-throughput methods to examine genome-wide expression patterns combined with functional genetic analyses in fungi, plants, and animals challenge our previous conceptions and suggest much remains to be learned about how genome diversity dictates functional diversity. The discussion below is not meant to be comprehensive but serves to illustrate that while the "central dogma" is broadly correct for protein-coding genes, it is apparent that our theoretical framework explaining how genomes function requires expansion.
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From page 53... ...
However, the observation that many of these sequences are transcribed, sometimes on both strands, combined with the discovery of a number of RNA-mediated gene-silencing mechanisms involving double-stranded RNA, raises the possibility that in some instances these gene fragments contribute to diversity of gene expression patterns by targeting functional genes containing the same sequence. RNA interference, RNAi, is an evolutionarily conserved mechanism in fungi, plants, and animals that generates short 21-23 nucleotide RNAs (siRNA)
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From page 54... ...
. From studies done to date, it is clear that noncoding DNA sequences can have significant effect on phenotype and are subject to natural selection (reviewed in Bird et al., 2006)
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From page 55... ...
Therefore, improving our ability to predict computationally the function of gene products, or to understand the functional consequences of mutation, is an important challenge. Since the mid-1990s, the increasing availability of genomic sequences and molecular diversity data has stimulated interest in the fields of bioinformatics and computational biology.
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From page 56... ...
Instead, Darwin hypothesized that such traits find their evolutionary value in how they promote mating. The process that causes traits to evolve because of how they contribute to mating is called "sexual selection," which Darwin contrasted with "natural selection," the process causing traits to evolve that promote survival.
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From page 57... ...
Such a situation contradicts the traditional assumption that the cheapness of sperm invites passionate male promiscuity and the expensiveness of eggs necessitates female coyness during their careful choice of good gene-bearing males. But male seahorses make tiny sperm just as male peacocks do, and female seahorses make large eggs just as peahens do; nonetheless, male seahorses care for the young and female seahorses entrust their eggs to a male's pouch.
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From page 58... ...
This is the context in which evolution plays out, where all the different kinds of variation at the genetic level provide, or fail to provide, a selective advantage and where external changes in an environment eventually lead to the adaptation, migration, or extinction of local species. The field of ecology has a long history of theoretical approaches to the understanding and prediction of what governs species diversity in different environments, the role of species diversity in ecosystem stability, and the impact of environmental change.
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From page 59... ...
, each specific to a different prey species, may hold each prey species at a low enough density to enable other species to persist. For instance, specialized consumers of seeds or seedlings may contribute to maintenance of tree species diversity in forests (Janzen, 1970; Connell, 1971)
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From page 60... ...
The challenge may be epitomized by the latitudinal gradient in species diversity: In most higher taxa of plants and animals, diversity is highest in tropical regions and declines toward both poles. On land, diversity declines from warm, wet environments (such as those that harbor tropical wet forest)
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From page 61... ...
may support this hypothesis (which parts from the traditional supposition of population geneticists that genetic variation is so plentiful that phenotypic evolution is seldom limited by the rate of origin of adaptive mutations)
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From page 62... ...
If biodiversity depends on evolutionary processes acting on the available genetic reservoir over geological time scales, the loss of species due to rapid, human-caused environmental change has profound consequences on the stock of genetic possibilities for the future. Philosophically, if biodiversity is largely the consequence of natural selection acting on random genetic events in specific communities and environments over very long time periods, the search for underlying, quantifiable, predictable order in the origin, maintenance, and loss of species is made vastly more difficult.
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From page 63... ...
The population genetic theory of microevolution should, ideally, enable us to predict population survival versus extinction, but doing so will require both significant theoretical advances and far more information than is currently available. The first question is whether or not the environmental change is one that would be expected to trigger an adaptive response.
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From page 64... ...
. What aspects of a species' environment will change, what characteristics might, by evolving, provide adaptation to these alterations, and what levels of selectable genetic variation might enable adaptive change in these features are all major unknowns.
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From page 65... ...
In evolutionary biology, a deeper understanding is required of the causes of niche conservatism, the dimensionality of genetic variation, the factors that determine variability (the capacity of characters to vary) , and the nature of and linkages between genetic and demographic processes in changing environments.
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From page 66... ...
At all levels, general theories to explain and predict diversity would be a great advance: from defining the evolutionary relationship of species, to predicting the function of proteins from gene sequence, to relating the form and functions of organisms to their genomes, to predicting the stability of ecosystems from their constituent species. The vastness of the diversity and the important, but as yet undefined, role of chance and history in biological systems make the development of such theories a grand challenge indeed.
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