Evolution As A Defining Feature Of Life
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In Sullivan, W. T. and Baross, J. A. (eds.) (2006) Planets and Life: The Emerging Science of Astrobiology, Cambridge: Cambridge University Pr. (In press)
10 EVOLUTION: A DEFINING FEATURE OF LIFE
John A. Baross
University of Washington
In biology nothing makes sense except in the light of evolution. It is possible to describe living beings without asking questions about their origins. [But] the descriptions acquire meaning and coherence only when viewed in the perspective of evolutionary development
– Theodosius Dobzhansky (1970:6)
10.1 From Lamarck to Darwin to the Central Dogma The basic notion of evolution is that inherited changes in populations of organisms result in expressed differences over time – these differences are at the gene level (the genotype) and/or expression of the gene into an identifiable characteristic (the phenotype). The important underlying fact of evolution is that all organisms share a common inheritance, or, put more dramatically, all extant organisms on Earth evolved from a common ancestor. We see this in the universal
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nature of the genetic code and in the unity of biochemistry: (a) all organisms share the same biochemical tools to translate the universal information code from genes to proteins, (b) all proteins are composed of the same twenty essential amino acids, and (c) all organisms derive energy for metabolic, catalytic and biosynthetic processes from the same highenergy organic compounds such as adenosine triphosphate (ATP). In On the Origin of Species Charles Darwin (1859) (Fig. 10.1) built his theory of evolution using evidence that included an ancient Earth thought at the time by many geologists to have an age in millions of years. He also took the extinction of species to be a real phenomenon since fossils existed that were without living representatives. Since different species showed close phenotypic similarities, he argued that existing organisms descended from other organisms including extinct groups. The key to his evolutionary theory therefore was that inherited characteristics of organisms can change through time and that these changes occur gradually and without discontinuities. Jean Baptiste Lamarck (1809) had earlier recognized a similar principle of evolution and offered an explanation generally referred to as “inheritance of acquired characters.” By this Lamarck meant that the variations in characteristics or adaptations seen in organisms were acquired in response to the environment. Classic examples include the long neck of the giraffe as an adaptation for foraging tender foliage on treetops, or the use of long legs by some aquatic fowl to venture into deep waters in search of prey. While this is certainly how these phenotypic characteristics are utilized to the advantage
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of the organism, under Darwinian principles they were not acquired as a response to the needs of the environment. One of Darwin’s major contributions was his explanation of how and why organisms change over time and how they acquire characteristics useful for living in different environments. Darwin referred to the mechanism for character changes through time as natural selection. Natural selection is based on the idea of the struggle for existence (survival of the fittest) in populations where there are more individuals of each species than can survive. A variation in any characteristic of an individual that gives an advantage in surviving (and therefore reproducing) will be “naturally selected” since the new trait will be preferentially inherited by subsequent generations. Darwin differed from Lamarck by recognizing that character changes that offer a survival advantage and are “naturally selected” originate from a pool of randomly generated character changes that are not directed by environmental conditions. Note that Darwin proposed his theory without knowing the mechanism for the inheritance of acquired traits – not until forty years later would the field of genetics begin with the recognition that Gregor Mendel’s principle of discrete units of inheritance (genes) was correct. Mendelian genetics established that phenotypes are transmitted from one generation to another following statistical principles and that these phenotypes reside in simple heritable “characters.” The nature of these heritable characters were unknown to Mendel, but their location was confined to chromosomes by 1910 and then to DNA as the genetic material by Hershey and Chase (1952). This
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immediately led to the discovery by Watson and Crick (1953) of the doublehelix structure of DNA and shortly afterwards to the elucidation of the genetic code and to the understanding that a gene is primarily a sequence along a section of DNA that codes for a protein using an alphabet composed of the four bases that constitute DNA. The steps leading from DNA to a specific protein are referred to as the central dogma: a DNA gene is transcribed to make messenger RNA (mRNA), followed by translation of mRNA into a protein. The exceptions to the central dogma are those genes that specify not proteins, but instead the various classes of RNA that are involved in both transcription and translation, such as ribosomal RNA (rRNA) and transfer RNA (tRNA).
10.2 Evolution at the Molecular Level The Watson and Crick discovery also opened the doors to studies of evolution at the molecular level and helped develop classification schemes that allow for the evolutionary comparisons of all groups of extant organisms, as well as the construction of models for inferring the nature of Earth’s earliest microbial communities and the emergence of multicelled organisms (Hedges, 2002). Usually, ribosomal RNA genes and ribosomal protein genes are used for evolutionary studies because they have highly conserved sequences, meaning sequences that are found across all domains of life (Woese et al., 1990). Most
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functional RNA molecules have secondary structures that are associated with their function. The base sequence determines to a great extent the functional secondary structure. Mutations that change the secondary structure of RNA molecules will frequently render them inactive. These conserved sequences must have originated a long time ago in a common ancestor and be of fundamental importance to all species. They are especially associated with the cell’s ribosomes, where proteins are assembled, because this process is so fundamental to the functioning of all cells. A central concept in evolutionary theory is that a gene coding for a characteristic is subject to mutation (change) in a random fashion, which in some cases can lead to variability in that characteristic in the next generation. Mutations come about due to mistakes made during DNA replication, or through external factors such as ionizing radiation or toxic chemicals. Most mutations are moot, i.e., they have little or no effect on the protein product of the gene or (for ribosomal RNA genes) the function of the RNA. Others, particularly those involving deletions and insertions that can result in structural changes in the transcribed protein or in a ribosomal RNA, can render it inactive. The most lethal mutations are those that damage the genes involved in DNA replication, transcription of DNA into mRNA, or translation of mRNA into a protein – in particular, mutations involving deletions or insertions of bases can change the structure of the transcribed mRNA and protein. Changing environmental conditions can negatively affect growth and
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survival (inducing stresses), and depending on the degree and kind of stress, can result in death of the organism. To survive such a lethal stress the organism must have mutation rates sufficiently high to handle the stress, but not so high as to cause lethal damage to the genome (the entire set of genes defining the species). Moreover, all extant organisms have a set of conserved genes for repairing mutations or proteins affected by environmental stresses such as starvation, heat, radiation, changes in pH, etc. While these “stress” genes are not 100% effective, they greatly reduce the number of deleterious mutations. The same genes can also target other specific genes for an increased mutation rate under stress conditions – these are called “stressdirected adaptive mutations” (Wright, 2004). For example, this mechanism can be observed when bacteria are starving from lack of their usual nutrient, but then undergo increased evolutionary rates of specific genes involved in the metabolism of alternate nutrients for growth. There is debate about how random mutations lead to useful characters, and particularly about the mechanisms involved in adaptation that eventually results in useful complex structures such as enzymes, bacterial flagella motors, eyes and brains. In evolution, adaptation means more than simply being well suited to the environment; it also involves in any generation the selection of one particular genetic change (over many other possibilities) that results in maximum reproductive success. But since many incremental steps are involved in evolving complex structures and processes, it would seem that adaptation involves a sequence of coordinated (not random) steps. Until recently, there was no
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satisfactory mechanism that could account for the evolution of complex structures. Two kinds of evolutionary change are recognized. Microevolution results in changes at the species level and accounts for the shortterm variability observed in populations. The second process of macroevolution involves the more substantial changes that over long times result in the development of new higher taxa such as genera, families, orders, etc. Macroevolution affects the genotypes of individuals within populations and thus also involves microevolution. Macroevolution is also invoked as the mechanism that results in the gradual formation of novel complex structures that involve multiple genes. Development of the eye has provided a classic illustration for gradualism producing increasing complexity and function. There are more than forty different eye structures found in both invertebrates and vertebrates with a range of complexity from light sensitive patches to compound eyes (Parker, 2003). It was once thought that these photosensitive organs developed independently along several different branches of the Tree of Life, a classic example of convergent evolution (independent evolution of morphologically and/or functionally similar structures). Recent molecular data, however, show that in many cases macroevolution is not totally a gradual set of changes based on mutation and natural selection. There appears to be a common set of genes that instigated the evolution of the eye in as diverse a group as fruit fly, squid and humans. These genes are called “tool box” genes (Carroll, 2005), and are common to many diverse organisms, implying that they are inherited from a common ancestor. For example,
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one group of genes called HOX genes1 account for the incredibly high diversity found in animal body plans. The three principal anatomical plans for wings exemplified in birds, bats and pterosaur, were also thought to be the products of convergent evolution. The bird wing developed from the entire arm, the bat wing from a hand, and the pterosaur wing from a single finger. Similar HOX genes, acting on different sets of genes in birds, bats and pterosaurs, resulted in the evolution of different kinds of wings (Carroll, 2005). The profoundly important point is that the origin of diverse body forms of animals and their organs may have more to do with the way multiple genes are expressed and less to do with the number of different kinds of genes. We are learning that a basic set of genes is used in animals in different ways to produce the myriad different body forms, appendages and organs. “Genetic switches,” specific gene sequences that “instruct tool kit genes where to act and what to do” (Carroll, 2005), select which specific genes get expressed. This new combination of evolution with developmental biology is called EvoDevo and is revolutionizing our understanding of macroevolution and embryology. EvoDevo also offers an explanation for the rapid macroevolutionary changes (termed punctuated equilibrium by Eldredge and Gould (1972)) that appear in the fossil record and that cannot be explained by gradualism. An example of punctuated equilibrium is the sudden appearance of diverse animal forms during HOX comes from “homeo” (like), and “box,” from the fact that the DNA
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sequence is short enough to fit into a box drawn on paper.
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the Cambrian Explosion 550 Ma (Sec. 16.3.1). EvoDevo studies indicate that this sudden emergence of highly diverse animal forms was due to the evolution of key regulatory HOX genes in the common ancestor to all Cambrian animals (Carroll, 2005)
10.3 Mechanisms for Acquiring New Genes Besides mutation, other mechanisms can effect changes in genes that coordinate cell structures, metabolism or physiological trait, whether for sudden acquisition of new genes or incremental changes of individual genes or groups of genes. These mechanisms are:
• fusion of different cells, sometime called endosymbiosis • coevolution • lateral gene transfer
Symbiosis is any interaction between two organisms (occasionally more than two organisms are involved) in which at least one of the organisms benefits from the relationship. This broad definition includes parasitic associations in which the parasite benefits at the expense of the host, or mutualistic associations in which
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both organisms benefit. Some symbiotic associations are obligatory where either the host or symbiont (or both) is unable to live independently. For instance, a recent model based on whole genome sequences indicates that the first eukaryote cell may have formed by the fusion of Bacteria and Archaea, and that Bacteria contributed the operational genes while Archaea contributed the informational genes (Rivera and Lake, 2004).2 While there are other models for the origin of eukaryotes (Gupta, 1998; Martin and Müller, 1998), there is agreement about the bacterial and archaeal origin of informational and key operational genes in eukaryotes. Such a fusion would fall into the category of mutualistic symbiosis since both cells benefited from this association. Furthermore, we have evidence for ancient symbioses in eukaryote cells in that their mitochondria (involved in oxygen respiration) and chloroplasts (involved in photosynthesis) both first occurred in specific groups of bacteria (Sapp, 2005; Wakeford, 2002). The proposed fusion of an archaeum with a bacterium somehow resulted in conditions favorable for evolution to greater complexity, multicellularity, and sexual reproduction. Similarly, the later acquisition by early eukaryotes of the mitochondria and chloroplast from bacteria must have had a profound effect on eukaryote evolution and particularly on their adaptation into habitats bathed in light and oxygen. Unfortunately, most of the evolutionary steps from the proposed The Tree of Life divides all species into three Domains called Archaea
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(containing the archaea), Bacteria (containing the bacteria), and Eukarya (containing the eukaryotes). See Fig. 11.1.
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fusionbased “protoeukaryote” to singlecell eukaryotes (Chap. 13) are unknown since no known extant organism retains characteristics that can definitely be interpreted as intermediate to those of modernday eukaryotes. For example, we do not know the intermediate steps/structures involved in the transition from the generally circular, doublestranded DNA chromosome of bacteria and archaea to the complex linear DNAprotein chromosomes of eukaryotes. While the fusion of two cells is not believed to have been a common occurrence in the early life history of organisms, there are many examples of other forms of symbiosis that are widely distributed in eukaryotes, allowing them to live under conditions that otherwise would not be possible (Sapp, 1994). One of the first cases to be identified was the symbiosis of an alga and a fungus to form a lichen, researched in detail and recognized in the late 19th century by Beatrix Potter (better known as the author of Peter Rabbit) well before symbiosis was accepted by the British scientific community.3 Other examples of symbiosis include hydrothermal vent tubeworms and clams that utilize inorganic chemical energy sources, plants that assimilate nitrogen via nitrogen fixation by root hair bacteria, and the microbial communities in the guts of ruminants and insects that anaerobically digest complex polysaccharides such as cellulose (Sapp, 1994; Wakeford, 2001). Parasitism, another form of symbiosis, can result in radical Wakeford (2001) has an interesting account of Potter’s futile attempt to
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convince the British scientific community of the importance of her observations.
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changes in the physiology of the host that include mating and feeding behavior, and morphological changes. It has been suggested that other ancient symbiotic events involving bacteria and eukaryotes occurred that are not as obviously visible in the cell as are mitochondria and chloroplasts, but are nevertheless important in the early evolution of eukaryotes (Margulis, 1993; Margulis et al., 2000). Coevolution is a special kind of symbiosis in which two kinds of organisms interact in such a way that each exerts a selective pressure on the other. Classical examples include flowering plants and their insect pollinators, and predators and their prey. Less obvious examples may include whole ecosystems in which all trophic levels from bacteria to animals have coevolved. Understanding the nature of coevolving ecosystems is one of the most difficult and important challenges in ecology. Lateral gene transfer (also referred to as genetic exchange and horizontal gene transfer) is the transfer of DNA from one organism to another such that it effects a “permanent” change in the genetic composition of the recipient. Genetic exchange can be mediated by cellcell contact (conjugation), by viral infection (transduction), or by incorporation of DNA from the environment (transformation). The recent accumulation of complete genome sequences from representatives of all the domains of life have revealed a universal pattern of lateral gene transfer for acquiring genes or parts of genes. Woese et al. (1990, 2002) speculated that this mechanism was widespread in the early evolutionary stages of life and vital to producing the diversity reflected in the present three domains of
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life. Furthermore, we now know that viruses4 have played and continue to play a significant role in the evolution of life through lateral gene transfer (Canchaya et al., 2003). This is illustrated by the high abundance of bacterial viruses (bacteriophages or phages) in marine environments, exceeding the bacterial population by an order of magnitude. Viruses are the most abundant biological entity on Earth, yet poorly understood. It is presumed that the primary role of viruses in the environment is causing death in bacteria (or producing disease in eukaryotes), but their significance as vehicles for transmitting new genes to bacteria in situ is not well understood, although likely extensive. Jiand and Paul (1998) calculated that at the low rate of infection of 108 per infected bacterial population, viralmediated gene transfer takes place in Earth’s oceans at the rate of ~2 x 1016 per second. The characters transmitted by phage in the environment, their rate of transmission, and the environmental factors involved in the transfer of genes are generally unknown. However, recent evidence shows the presence of bacterial genes in marine phages, including genes that code for proteins necessary for photosynthesis (Hambly and Suttle, 2005). Similarly, a significant portion of eukaryote chromosomes (approximately 45% for humans and a much higher percentage for some plants and an amoeba species) is composed of remnants from RNA viruses (called retrotransposons, or mobile genetic elements that replicate by 4
A virus is defined as an intracellular parasite and is incapable of living without a host cell. While it shares many of the biochemical characteristics of a living cell including nucleic acids and proteins(although much smaller and simpler) except that it cannot reproduce independently, only by infecting a normal cell.
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reverse transcription: RNA to DNA rather than DNA to RNA) (Bushman, 2001). Most of these viral sequences in eukaryotes are not transcribed into proteins. But do they nevertheless serve some important function to the organism? And if not, why do organisms retain them anyway? Some retroviral sequences have been implicated in the evolution of vertebrate genes including the development of the human placenta and the regulation of the gene for starch hydrolysis, but most have no apparent function and along with other nonprotein coding regions on eukaryotic chromosomes, have been called “selfish DNA” (Bushman, 2001). How important is lateral gene transfer in evolution? Results from whole genome sequences of bacteria and archaea indicate that lateral gene transfer may be the most important mechanism for acquiring new genes, including those involved in complex and coordinated phenotypes. For example, ~16% of the genome of Escherichia coli K12 is viral genes. Microorganisms have evolved elaborate mechanisms for incorporating acquired genes into their chromosome at specific sites. These sites can serve as “pathogenicity islands” if all of the acquired genes are involved in disease production, such as for the choleraproducing bacterium Vibrio cholerae (Faruque and Mekalanos, 2003), or they may be “genetic islands,” which align acquired genes involved in key physiological activities such as magnetotaxis (Grünberg et al., 2001) or the dissimilatory reduction of sulfate (Mussmann et al., 2005). It is very unlikely that the formation of a genome with sufficient information to lead to freeliving (selfsufficient) cells could have originated without a
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mechanism for acquiring “functional” genes from other early cells or communities of interdependent cells or “precells” (Baross and Hoffman, 1985). This is certainly consistent with the fact that all life on Earth is derived from a common ancestral pool of genes based on a universal genetic code (Woese, 1998). Darwinian evolution would have played an important role in these early stages and selection would have favored specific biochemical and molecular structures and mechanisms over others. Could this imply that if we started over again by resetting the clock to 4 Ga, the resultant life would have the same biochemical and molecular properties, including the same genetic code, as presentday Earth life? If environmental conditions and the starting pool of organic compounds were the same, it is probable that a second genesis would result in biochemistry that would resemble or possibly be indistinguishable from presentday Earth life. The strong link between specific nucleotide bases and specific amino acids is one more example verifying that there are “rules of organic chemistry” that favor specific reactions or macromolecular structures (Copley et al., 2005). In such a second genesis, however, contingency in evolution could result in the selection of organisms and ecosystems significantly different from those found on Earth. Yet, compared to presentday organisms, they would share a similar biochemistry and evolve many or all of the same phenotypes (both structural and functional), albeit possibly with different genotypes. Further discussion of these points is found in Chap. 27.
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10.4 Could There Be Life Without Evolution?
Many of the definitions of life include the phrase “undergoes Darwinian evolution” (Chap. 5). The implication is that phenotypic changes and adaptation are necessary to exploit unstable environmental conditions, to function more optimally in the environment, and to provide a mechanism to increase biological complexity. Evolutionary changes have even been suggested for hypothesized “clay crystal life” of CairnsSmith (1982), referring to randomly occurring errors in crystal structure during crystal growth as analogous to mutations (Sec. 27.4.2). Would a selfreplicating chemical system capable of chemical transformations in the environment be considered life? If selfreplicating chemical compounds are not life, then replication by itself is not sufficient as a defining characteristic of life. Likewise, the ability to undergo Darwinian evolution, that is, a process that results in heritable changes in a population, is also not sufficient to define life if we consider minerals that are capable of reproducing errors in their crystal structure to be equivalent to evolution. Although this property of clays may have been vital in the origin of life and particularly in the prebiotic synthesis of organic macromolecules and as catalysts for metabolic reactions, can the perpetuation of “mistakes” in crystal structure result in the selection of a “more fit” crystal structure? It is important to emphasize that evolution is not simply reproducing mutations (mistakes in clays), but selecting those variants that are functionally morefit.
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The canonical characteristics of life are an inherent capacity to adapt to changing environmental conditions and to increase in complexity by multiple mechanisms, but particularly by interactions with other living organisms (and, at least on Earth, also with viruses). Natural selection is the key to evolution and the main reason why Darwinian evolution persists as a characteristic of many definitions of life. Clays could never evolve an eye or a nose, or adapt behavioral strategies to exclude clays with other crystal characteristics. Hmmm – would Michael Crichton’s Andromeda Strain (1969), a carbonbased crystal capable of using chemical and physical energy sources, be considered life? (Incidentally, the Andromeda Strain could also mutate, which was probably a necessity to reach a happy ending to the story.) The only alternative to evolution for producing diversity would be to have environmental conditions that continuously create different life forms, or similar life forms with random and frequent “mistakes” made in the synthesis of chemical templates used for replication or metabolism. These mistakes would be equivalent to mutations and could lead to traits that gave some selective advantage in an existing community or in exploiting new habitats. This could lead to life forms that undergo a form of evolution without a master information macromolecule such as DNA or RNA. It is difficult, however, to imagine such life forms being able to “evolve” into complex structures unless other mechanisms such as symbiosis or cell/cell fusion are available.
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10.5 Evolution and Extraterrestrial Life
We have seen that evolution is much more than mutation and natural selection. It is the key mechanism for heritable changes to occur in a population. Mutation is not the only mechanism for acquiring new genes. Lateral gene transfer appears to be one of the most important mechanisms and clearly one of the earliest mechanisms for creating diversity and possibly for building genomes with the requisite information to result in freeliving cells, as opposed to codependent communities of “precells” with insufficient genetic information to escape communal life (Baross and Hoffman, 1985). Lateral gene transfer is also one of the mechanisms to align genes from different sources into complex functional activities such as magnetotaxis and dissimilatory sulfate reduction. It is possible that this mechanism was important in the evolution of metabolic and biosynthetic pathways and other physiological traits that may have evolved only once even though they are present in a wide diversity of organisms. The coevolution between two or more species is also a hallmark of evolution manifested in many ways from insect/plant interactions to the hundreds of species of bacteria involved in the nutrition of ruminant animals. The organisms and the environment also coevolve depending on the dominant characteristics of the environment and the availability of carbon and energy sources. Even some of the most extreme environments on Earth, such as hydrothermal vent sulfide chimneys and the very acidic Rio Tinto River in Spain, have a remarkably high diversity of organisms (Kelley at al., 2002; Zettler et al.,
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2003). Diversity drops off, however, in environments with combinations of stressors such as high temperature and high pH, or high salt and high or low temperature (Chap. 14). If the ability to undergo Darwinian evolution is a canonical trait of life no matter how different that life form is from Earth life, then are there properties of evolving extraterrestrial organisms that would be detectable as positive signs of life? Evolution provides organisms the opportunity to exploit new and changing environments, and one piece of evidence for the probable cosmic ubiquity of evolution is that on Earth life occupies all available habitats and even creates new habitats as a consequence of its metabolisms. Another hallmark of evolution is the ability of organisms to coevolve with other organisms and to form permanent and obligatory associations. Also, it is highly probable that an inevitable consequence of evolution is the elimination of radically different biochemical lineages of life that may have formed during the earliest period of evolution of life. Extant Earth life is the result of either selection of the most fit lineage or homogenization of some or all of the different lineages into a common ancestral community that developed into the present three major lineages (domains). All have a common biochemistry based on presumably the most “fit” molecular information strategies and energy yielding pathways among a potpourri of possibilities. One caveat and perhaps a verification of the above statement is that genetic remnants of other lineages may still exist in some of the deeply rooted archaea as evidenced from the unique 16S rRNA found in Nanoarchaeum equitans and novel and presently
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undelineated metabolic pathways in some hyperthermophilic Crenarchaeota (Huber et al., 2003; Hügler et al., 2003). Thus, one of the apparent generalizations that can be made from extant Earth life, and the explanation for the development of a “unity of biochemistry” in all organisms, is that lateral gene transfer is both an ancient and an efficient mechanism for rapidly creating diversity and complexity. Lateral gene transfer is also an efficient mechanism for selecting the genes that are most “fit” for specific proteins and transferring them into diverse groups of organisms. The result is both the addition of new genes and the replacement of lessfit genes having a similar function. Natural selection based solely on mutation is not likely an adequate mechanism for evolving complexity. More importantly, lateral gene transfer and endosymbiosis are probably the most obvious mechanisms for creating complex genomes that can lead to freeliving cells and complex cellular communities in the short geological time available from life’s origin to the establishment of microbial communities more than 3.8 billion years ago (Sec. 12.3). An important implication of the existence of viruses or viruslike entities during the early evolution of cellular organisms is that their genomes may have been the source of most genetic innovations due to their rapid replication rates, high rates of mutation from replication errors, and gene insertions from diverse host cells. It is interesting that Darwin perceived evolution as random changes in individual species that could lead to selection of more fit traits, but he could not have known that some of these fit traits could be transferred to species that were not only not sexually compatible
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but belonged to separate domains. It is clear that both the individual organism and its community coevolve. In a sense, evolution is evolving, allowing cells to control their own evolution – accept or reject changes in genotypes from newly acquired foreign genes. While this has already been demonstrated in bacteria, the source of foreign genes and the kinds of genes most likely to be selected for permanence are largely not known. However, it is clear that the evolution of a useful trait by one organism frequently means that it is likely to be acquired by other organisms. It appears that the field of biology is beginning to break out of its molecularreductionist “egg” and emerging more focused on what Carl Woese (2004) terms “holistic biology,” where the emphasis, rather than just on genes, is on the cell, communities and ecosystems. This would also take evolution to a new level of inquiry with emphasis on coevolution, cellular complexity, and the reexamination of the concept of ecosystems as “super organisms.” The new science of EvoDevo integrates well with this new holistic approach while offering another lesson about evolution: chance mutations or microevolution create the panoply of gene variation, but it is key genes and combinations of key genes that “better meet the imperatives of ecological necessity, and they arise and are selected for repeatedly” (Carroll, 2005). Finally, what are the limits of evolution for Earth life? This is a complex question with many different components. On the one hand, it involves the different possible biochemistries from carbon chemistry that are not found in extant Earth organisms but could be better suited for environmental conditions that exist
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on other planets and moons (Chap. 27). The technology exists to design genes and groups of genes that could lead to novel phenotypes suited to exploit new habitats and novel energy sources. These kinds of studies would be important and perhaps essential in our quest to search for life elsewhere. Another component to the question of the limits of evolution is where we are going and what will Homo sapiens or its successors be like if it continues to evolve for tens of thousands or million of years? This is an integral part of our search for advanced extraterrestrial intelligence, which requires us to imagine our future portrait (Chap. 26). We cannot imagine all of the possible changes that will occur after millions of years of evolution but based on the just the tens of thousands of years of primate evolution, it is likely that one possible outcome will be an increasing ability to control our environment and all that is evolving. It is also likely that we will someday know if we are alone in the Universe.
10.6 Summary It is evident that cells are more than the information encoded in their genomes. They are part of a highly integrated biological and geochemical system in whose creation and maintenance they have participated. The unity of biochemistry among all of Earth’s organisms emphasizes the ability of organisms to interact with other organisms to form coevolving communities, to acquire and transmit new
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genes, to use old genes in new ways, to exploit new habitats, and most important to evolve mechanisms to help control their own evolution. It is expected that these characteristics are likely to be present in extraterrestrial life even if it has had a separate origin and a very different unified biochemistry from that of Earth life. Since evolution is an essential feature of Earth life and probably all life, the search for life elsewhere should include a search for evidence of evolution.
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Figure Caption
Figure 10.1. Charles Darwin (18091882), in his later years at Down House, his combined home, office and laboratory (see App. D). (photo courtesy John van Wyhe)
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General Reading and Surfing
Desmond, A. and Moore, J. (1991). Darwin: The Life of a Tormented Evolutionist. New York: Warner. This is an excellent and thoroughly researched biography of Darwin. As the title implies, Darwin struggled as to how to present the theory of evolution in a way that was acceptable to a community shackled by Victorian mores.
Judson, H. W. (1979). The Eighth Day of Creation: The Makers of Revolution in Biology. New York: Simon and Schuster. This is the definitive historical study of the mid20thcentury birth of molecular biology and a must read for anyone interested in how revolutions in science get started. It has been reprinted with an updated preface (New York: Cold Spring Harbor Laboratory Press, 1996).
Knoll, A. H. (2003). Life on a Young Planet: The First Three Billion Years of Evolution on Earth. Princeton: Princeton Univ. Pr. This is a “tour de force” portrait of life from Earth’s beginning to the Cambrian explosion. Knoll is masterful in blending geology, geochemistry and biology in the context of Earth history.
Lovelock, J. E. (1979). Gaia: A New Look at Life on Earth. Oxford: Oxford Univ.
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Pr. James Lovelock and Lynn Margulis first put forth the proposition that the composition and temperature of the atmosphere is an evolutionary product of interrelated activities in the biosphere, especially those of microorganisms, and that the entire biosphere behaves as a single selfregulating organism. The Gaia Hypothesis has been every bit as influential as it is controversial (see Sec. 10.5 for related thinking).
www.mendelweb.org An excellent website for learning the details of what Mendel actually did.
Conway Morris, S. (2003). Life’s Solution: Inevitable Humans in a Lonely Universe. Cambridge: Cambridge Univ. Pr. Conway Morris has a different perspective on evolution. He argues for determinism rather than contingency: Evolution has predictable and inevitable outcomes. His metaphysical arguments are interesting and certainly thought provoking and somewhat reminiscent of chapter 31 in Christian de Duve’s excellent book, Vital Dust: Life as a Cosmic Imperative (New York: Basic Books, 1995)
Ptashne, M. (1992, 2nd ed.). A Genetic Switch. Cambridge, Mass.: Blackwell Science.
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This classic work describes the basic molecular reactions underlying the regulation of gene transcription in all organisms and how the genes involved in these reactions, when combined, produce complex regulatory circuits. The regulatory circuits found in bacteria are the forerunners to the evolution of the more complex regulatory circuits involved in macroevolution and the emergence of EvoDevo (Carroll, 2005)
Ridley, M. (ed.) (1997). Evolution. Oxford: Oxford Univ. Pr. This is an excellent compilation of many of the classic papers on evolution. The list of authors is the “Who’s Who” of great evolution thinkers and includes Charles Darwin, Stephen J. Gould, Ernst Mayr, George Gaylord Simpson, Richard Dawkins, Francis Crick and many others. The topics covered include adaptation, macroevolution, molecular evolution, biodiversity, human evolution, and evolution and philosophy.
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References
Baross, J. A. and Hoffman, S. (1985). Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life. Origins of Life 15, 32745. Bushman, F. (2001). Lateral DNA Transfer, Mechanisms and Consequences. New York: Cold Spring harbor Laboratory Press CairnsSmith, A. G. (1982). Genetic Takeover and the Mineral Origins of Life. Cambridge: Cambridge University Press Canchaya, C., Fournous, G., ChibaniChennoufi, S., Dillmann, M.L. and Brüssow, H. (2003). Phage as agents of lateral gene transfer. Curr. Opin. Microbiol. 6, 41724. Carroll, S. B. (2005). Endless Forms Most Beautiful: The New Science of Evo Devo. New York: W. W. Norton & Co. Copley, S. D., Smith, E. and Morowitz, H. J. (2005). A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proceed. Natl. Acad. Sci., USA 102, 444247. Crichton, M. (1969). The Andromeda Strain. New York: Alfred A. Knopf. Darwin, C. (1859). On the Origin of Species. London: John Murray. Dobzhansky, T. (1970). Genetics of the Evolutionary Process. New York: Columbia University Press.
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Eldredge, N. and Gould, S. J. (1972). Punctuated equilibria: An alternative to phyletic gradualism. In T. J. M. Schopf and J. M. Thomas (eds.) Models in Paleobiology, pp. 82115. San Francisco: Freeman. Faruque, S. M., and Mekalanos, J. J. (2003). Pathogenicity islands and phage in Vibrio cholerae evolution. TRENDS in Microbiol. 11, 50510. Grünberg, K., Wawer, C., Tebo, B. M. and Schüler, D. (2001). A large gene cluster encoding several magnetosome proteins is conserved in different species of magnetotactic bacteria. Appl. Environ. Microbiol. 67, 457382. Gupta, R. S. (1998). Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among Archaebacteria, Eubacteria and Eukaryotes. Microbiol. Mol. Biol. Rev. 62, 143591. Hambly, E. and Suttle, C. A. (2005). The virosphere, diversity, and genetic exchange within phage communities. Curr. Opin. Microbiol. 8, 44450. Hedges, S. B. (2002). The origin and evolution of model organisms. Nature Reviews Genetics 3, 83849. Hershey, A. D. and Chase, M. (1952). Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen Physiol. 36, 3956. Huber, H., Hohn, H. J., Stetter, K. O. and Rachel, R. (2003). The phylum Nanoarchaeota: Present knowledge and future perspectives of a unique form of life. Res. Microbiol. 154, 16571. Hügler, M., Huber, H., Stetter, K. O. and Fuchs, F. (2003). Autotrophic CO2
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fixation pathways in archaea (Crenarchaeota). Arch. Microbiol. 179, 16073. Jiang, S. C. and Paul, J. H. (1998). Gene transfer by transduction in the marine environment. Appl. Environ. Microbiol. 64, 278087. Kelley, D. S., Baross, J. A. and Delaney, J. R. (2002). Volcanoes, fluids, and life at midocean ridge spreading centers. Ann. Rev. Earth Planet. Sci. 30, 385 491. Lamarck, J. B. (1809). Zoological Philosophy. Translated into English by H. Elliott, 1914. New York: Macmillan. Margulis, L. (1993). Symbiosis in Cell Evolution, 2nd edition, New York: W. H. Freeman. Margulis, L., Dolan, M. F. and Guerrero, R. (2000). The chimeric eukaryote: Origin of the nucleus from the Karyomastigont in amitochondriate protists. Proceed. Natl. Acad. Sci., USA 97, 695459. Martin, W. and Müller, M. (1998). The hydrogen hypothesis for the first eukaryote. Nature 392, 3741. Mussmann, M., Richter, M., Lombardot, T., Meyerdierks, A., Kuever, J., Kube, M., Glöckner, O. and Amann, R. (2005). Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer. J. Bacteriol. 187, 712637. Parker, A. (2003). In the Blink of an Eye. Cambridge, Maryland: Perseus Publishing. Rivera, M. C. and Lake, J. A. (2004). The ring of life provides evidence for a
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genome fusion origin of eukaryotes. Nature 431, 15255. Sapp, J. (2005). The bacterium’s place in nature. In J. Sapp (ed.) Microbial Phylogeny and Evolution, pp. 352, New York: Oxford University Press, Inc. Sapp, J. (1994). Evolution by Association. A History of Symbiosis. Oxford New York: University Press. Wakeford, T. (2001). Liaisons of Life. New York: John Wiley & Sons, Inc. Watson, J. D. and Crick, F. H. C. (1953). A structure for deoxyribose nucleic acid. Nature 171, 73738. Weight, B. E. (2004). Stressdirected adaptive mutations and evolution. Mol. Microbiol. 52, 64350. Woese, C. R. (2004). A new biology for a new century. Microbiol. Mol. Biol. Rev. 68, 17386. Woese, C. R. (2002). On the evolution of cells. Proc. Natl. Acad. Sci., USA 99, 874247. Woese, C. R. (1998). The universal ancestor. Proceed. Natl. Acad. Sci., USA 95, 685459. Woese, C. R., Kandler, O. and Wheelis, M. L. (1990). Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria and Eukarya. Proc. Natl. Acad Sci., USA 87, 457679. Zettler, C. A. A., Messerli, M. A., Laatsch, A. D., Smith, P. J. S. and Sogin, M. L. (2003). From genes to genomes: Beyond biodiversity in Spain’s Rio
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Tinto. Biol. Bull. 204, 20509.
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In Sullivan, W. T. and Baross, J. A. (eds.) (2006) Planets and Life: The Emerging Science of Astrobiology, Cambridge: Cambridge University Pr. (In press)
10 EVOLUTION: A DEFINING FEATURE OF LIFE
John A. Baross
University of Washington
In biology nothing makes sense except in the light of evolution. It is possible to describe living beings without asking questions about their origins. [But] the descriptions acquire meaning and coherence only when viewed in the perspective of evolutionary development
– Theodosius Dobzhansky (1970:6)
10.1 From Lamarck to Darwin to the Central Dogma The basic notion of evolution is that inherited changes in populations of organisms result in expressed differences over time – these differences are at the gene level (the genotype) and/or expression of the gene into an identifiable characteristic (the phenotype). The important underlying fact of evolution is that all organisms share a common inheritance, or, put more dramatically, all extant organisms on Earth evolved from a common ancestor. We see this in the universal
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nature of the genetic code and in the unity of biochemistry: (a) all organisms share the same biochemical tools to translate the universal information code from genes to proteins, (b) all proteins are composed of the same twenty essential amino acids, and (c) all organisms derive energy for metabolic, catalytic and biosynthetic processes from the same highenergy organic compounds such as adenosine triphosphate (ATP). In On the Origin of Species Charles Darwin (1859) (Fig. 10.1) built his theory of evolution using evidence that included an ancient Earth thought at the time by many geologists to have an age in millions of years. He also took the extinction of species to be a real phenomenon since fossils existed that were without living representatives. Since different species showed close phenotypic similarities, he argued that existing organisms descended from other organisms including extinct groups. The key to his evolutionary theory therefore was that inherited characteristics of organisms can change through time and that these changes occur gradually and without discontinuities. Jean Baptiste Lamarck (1809) had earlier recognized a similar principle of evolution and offered an explanation generally referred to as “inheritance of acquired characters.” By this Lamarck meant that the variations in characteristics or adaptations seen in organisms were acquired in response to the environment. Classic examples include the long neck of the giraffe as an adaptation for foraging tender foliage on treetops, or the use of long legs by some aquatic fowl to venture into deep waters in search of prey. While this is certainly how these phenotypic characteristics are utilized to the advantage
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of the organism, under Darwinian principles they were not acquired as a response to the needs of the environment. One of Darwin’s major contributions was his explanation of how and why organisms change over time and how they acquire characteristics useful for living in different environments. Darwin referred to the mechanism for character changes through time as natural selection. Natural selection is based on the idea of the struggle for existence (survival of the fittest) in populations where there are more individuals of each species than can survive. A variation in any characteristic of an individual that gives an advantage in surviving (and therefore reproducing) will be “naturally selected” since the new trait will be preferentially inherited by subsequent generations. Darwin differed from Lamarck by recognizing that character changes that offer a survival advantage and are “naturally selected” originate from a pool of randomly generated character changes that are not directed by environmental conditions. Note that Darwin proposed his theory without knowing the mechanism for the inheritance of acquired traits – not until forty years later would the field of genetics begin with the recognition that Gregor Mendel’s principle of discrete units of inheritance (genes) was correct. Mendelian genetics established that phenotypes are transmitted from one generation to another following statistical principles and that these phenotypes reside in simple heritable “characters.” The nature of these heritable characters were unknown to Mendel, but their location was confined to chromosomes by 1910 and then to DNA as the genetic material by Hershey and Chase (1952). This
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immediately led to the discovery by Watson and Crick (1953) of the doublehelix structure of DNA and shortly afterwards to the elucidation of the genetic code and to the understanding that a gene is primarily a sequence along a section of DNA that codes for a protein using an alphabet composed of the four bases that constitute DNA. The steps leading from DNA to a specific protein are referred to as the central dogma: a DNA gene is transcribed to make messenger RNA (mRNA), followed by translation of mRNA into a protein. The exceptions to the central dogma are those genes that specify not proteins, but instead the various classes of RNA that are involved in both transcription and translation, such as ribosomal RNA (rRNA) and transfer RNA (tRNA).
10.2 Evolution at the Molecular Level The Watson and Crick discovery also opened the doors to studies of evolution at the molecular level and helped develop classification schemes that allow for the evolutionary comparisons of all groups of extant organisms, as well as the construction of models for inferring the nature of Earth’s earliest microbial communities and the emergence of multicelled organisms (Hedges, 2002). Usually, ribosomal RNA genes and ribosomal protein genes are used for evolutionary studies because they have highly conserved sequences, meaning sequences that are found across all domains of life (Woese et al., 1990). Most
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functional RNA molecules have secondary structures that are associated with their function. The base sequence determines to a great extent the functional secondary structure. Mutations that change the secondary structure of RNA molecules will frequently render them inactive. These conserved sequences must have originated a long time ago in a common ancestor and be of fundamental importance to all species. They are especially associated with the cell’s ribosomes, where proteins are assembled, because this process is so fundamental to the functioning of all cells. A central concept in evolutionary theory is that a gene coding for a characteristic is subject to mutation (change) in a random fashion, which in some cases can lead to variability in that characteristic in the next generation. Mutations come about due to mistakes made during DNA replication, or through external factors such as ionizing radiation or toxic chemicals. Most mutations are moot, i.e., they have little or no effect on the protein product of the gene or (for ribosomal RNA genes) the function of the RNA. Others, particularly those involving deletions and insertions that can result in structural changes in the transcribed protein or in a ribosomal RNA, can render it inactive. The most lethal mutations are those that damage the genes involved in DNA replication, transcription of DNA into mRNA, or translation of mRNA into a protein – in particular, mutations involving deletions or insertions of bases can change the structure of the transcribed mRNA and protein. Changing environmental conditions can negatively affect growth and
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survival (inducing stresses), and depending on the degree and kind of stress, can result in death of the organism. To survive such a lethal stress the organism must have mutation rates sufficiently high to handle the stress, but not so high as to cause lethal damage to the genome (the entire set of genes defining the species). Moreover, all extant organisms have a set of conserved genes for repairing mutations or proteins affected by environmental stresses such as starvation, heat, radiation, changes in pH, etc. While these “stress” genes are not 100% effective, they greatly reduce the number of deleterious mutations. The same genes can also target other specific genes for an increased mutation rate under stress conditions – these are called “stressdirected adaptive mutations” (Wright, 2004). For example, this mechanism can be observed when bacteria are starving from lack of their usual nutrient, but then undergo increased evolutionary rates of specific genes involved in the metabolism of alternate nutrients for growth. There is debate about how random mutations lead to useful characters, and particularly about the mechanisms involved in adaptation that eventually results in useful complex structures such as enzymes, bacterial flagella motors, eyes and brains. In evolution, adaptation means more than simply being well suited to the environment; it also involves in any generation the selection of one particular genetic change (over many other possibilities) that results in maximum reproductive success. But since many incremental steps are involved in evolving complex structures and processes, it would seem that adaptation involves a sequence of coordinated (not random) steps. Until recently, there was no
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satisfactory mechanism that could account for the evolution of complex structures. Two kinds of evolutionary change are recognized. Microevolution results in changes at the species level and accounts for the shortterm variability observed in populations. The second process of macroevolution involves the more substantial changes that over long times result in the development of new higher taxa such as genera, families, orders, etc. Macroevolution affects the genotypes of individuals within populations and thus also involves microevolution. Macroevolution is also invoked as the mechanism that results in the gradual formation of novel complex structures that involve multiple genes. Development of the eye has provided a classic illustration for gradualism producing increasing complexity and function. There are more than forty different eye structures found in both invertebrates and vertebrates with a range of complexity from light sensitive patches to compound eyes (Parker, 2003). It was once thought that these photosensitive organs developed independently along several different branches of the Tree of Life, a classic example of convergent evolution (independent evolution of morphologically and/or functionally similar structures). Recent molecular data, however, show that in many cases macroevolution is not totally a gradual set of changes based on mutation and natural selection. There appears to be a common set of genes that instigated the evolution of the eye in as diverse a group as fruit fly, squid and humans. These genes are called “tool box” genes (Carroll, 2005), and are common to many diverse organisms, implying that they are inherited from a common ancestor. For example,
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one group of genes called HOX genes1 account for the incredibly high diversity found in animal body plans. The three principal anatomical plans for wings exemplified in birds, bats and pterosaur, were also thought to be the products of convergent evolution. The bird wing developed from the entire arm, the bat wing from a hand, and the pterosaur wing from a single finger. Similar HOX genes, acting on different sets of genes in birds, bats and pterosaurs, resulted in the evolution of different kinds of wings (Carroll, 2005). The profoundly important point is that the origin of diverse body forms of animals and their organs may have more to do with the way multiple genes are expressed and less to do with the number of different kinds of genes. We are learning that a basic set of genes is used in animals in different ways to produce the myriad different body forms, appendages and organs. “Genetic switches,” specific gene sequences that “instruct tool kit genes where to act and what to do” (Carroll, 2005), select which specific genes get expressed. This new combination of evolution with developmental biology is called EvoDevo and is revolutionizing our understanding of macroevolution and embryology. EvoDevo also offers an explanation for the rapid macroevolutionary changes (termed punctuated equilibrium by Eldredge and Gould (1972)) that appear in the fossil record and that cannot be explained by gradualism. An example of punctuated equilibrium is the sudden appearance of diverse animal forms during HOX comes from “homeo” (like), and “box,” from the fact that the DNA
1
sequence is short enough to fit into a box drawn on paper.
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the Cambrian Explosion 550 Ma (Sec. 16.3.1). EvoDevo studies indicate that this sudden emergence of highly diverse animal forms was due to the evolution of key regulatory HOX genes in the common ancestor to all Cambrian animals (Carroll, 2005)
10.3 Mechanisms for Acquiring New Genes Besides mutation, other mechanisms can effect changes in genes that coordinate cell structures, metabolism or physiological trait, whether for sudden acquisition of new genes or incremental changes of individual genes or groups of genes. These mechanisms are:
• fusion of different cells, sometime called endosymbiosis • coevolution • lateral gene transfer
Symbiosis is any interaction between two organisms (occasionally more than two organisms are involved) in which at least one of the organisms benefits from the relationship. This broad definition includes parasitic associations in which the parasite benefits at the expense of the host, or mutualistic associations in which
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both organisms benefit. Some symbiotic associations are obligatory where either the host or symbiont (or both) is unable to live independently. For instance, a recent model based on whole genome sequences indicates that the first eukaryote cell may have formed by the fusion of Bacteria and Archaea, and that Bacteria contributed the operational genes while Archaea contributed the informational genes (Rivera and Lake, 2004).2 While there are other models for the origin of eukaryotes (Gupta, 1998; Martin and Müller, 1998), there is agreement about the bacterial and archaeal origin of informational and key operational genes in eukaryotes. Such a fusion would fall into the category of mutualistic symbiosis since both cells benefited from this association. Furthermore, we have evidence for ancient symbioses in eukaryote cells in that their mitochondria (involved in oxygen respiration) and chloroplasts (involved in photosynthesis) both first occurred in specific groups of bacteria (Sapp, 2005; Wakeford, 2002). The proposed fusion of an archaeum with a bacterium somehow resulted in conditions favorable for evolution to greater complexity, multicellularity, and sexual reproduction. Similarly, the later acquisition by early eukaryotes of the mitochondria and chloroplast from bacteria must have had a profound effect on eukaryote evolution and particularly on their adaptation into habitats bathed in light and oxygen. Unfortunately, most of the evolutionary steps from the proposed The Tree of Life divides all species into three Domains called Archaea
2
(containing the archaea), Bacteria (containing the bacteria), and Eukarya (containing the eukaryotes). See Fig. 11.1.
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fusionbased “protoeukaryote” to singlecell eukaryotes (Chap. 13) are unknown since no known extant organism retains characteristics that can definitely be interpreted as intermediate to those of modernday eukaryotes. For example, we do not know the intermediate steps/structures involved in the transition from the generally circular, doublestranded DNA chromosome of bacteria and archaea to the complex linear DNAprotein chromosomes of eukaryotes. While the fusion of two cells is not believed to have been a common occurrence in the early life history of organisms, there are many examples of other forms of symbiosis that are widely distributed in eukaryotes, allowing them to live under conditions that otherwise would not be possible (Sapp, 1994). One of the first cases to be identified was the symbiosis of an alga and a fungus to form a lichen, researched in detail and recognized in the late 19th century by Beatrix Potter (better known as the author of Peter Rabbit) well before symbiosis was accepted by the British scientific community.3 Other examples of symbiosis include hydrothermal vent tubeworms and clams that utilize inorganic chemical energy sources, plants that assimilate nitrogen via nitrogen fixation by root hair bacteria, and the microbial communities in the guts of ruminants and insects that anaerobically digest complex polysaccharides such as cellulose (Sapp, 1994; Wakeford, 2001). Parasitism, another form of symbiosis, can result in radical Wakeford (2001) has an interesting account of Potter’s futile attempt to
3
convince the British scientific community of the importance of her observations.
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changes in the physiology of the host that include mating and feeding behavior, and morphological changes. It has been suggested that other ancient symbiotic events involving bacteria and eukaryotes occurred that are not as obviously visible in the cell as are mitochondria and chloroplasts, but are nevertheless important in the early evolution of eukaryotes (Margulis, 1993; Margulis et al., 2000). Coevolution is a special kind of symbiosis in which two kinds of organisms interact in such a way that each exerts a selective pressure on the other. Classical examples include flowering plants and their insect pollinators, and predators and their prey. Less obvious examples may include whole ecosystems in which all trophic levels from bacteria to animals have coevolved. Understanding the nature of coevolving ecosystems is one of the most difficult and important challenges in ecology. Lateral gene transfer (also referred to as genetic exchange and horizontal gene transfer) is the transfer of DNA from one organism to another such that it effects a “permanent” change in the genetic composition of the recipient. Genetic exchange can be mediated by cellcell contact (conjugation), by viral infection (transduction), or by incorporation of DNA from the environment (transformation). The recent accumulation of complete genome sequences from representatives of all the domains of life have revealed a universal pattern of lateral gene transfer for acquiring genes or parts of genes. Woese et al. (1990, 2002) speculated that this mechanism was widespread in the early evolutionary stages of life and vital to producing the diversity reflected in the present three domains of
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life. Furthermore, we now know that viruses4 have played and continue to play a significant role in the evolution of life through lateral gene transfer (Canchaya et al., 2003). This is illustrated by the high abundance of bacterial viruses (bacteriophages or phages) in marine environments, exceeding the bacterial population by an order of magnitude. Viruses are the most abundant biological entity on Earth, yet poorly understood. It is presumed that the primary role of viruses in the environment is causing death in bacteria (or producing disease in eukaryotes), but their significance as vehicles for transmitting new genes to bacteria in situ is not well understood, although likely extensive. Jiand and Paul (1998) calculated that at the low rate of infection of 108 per infected bacterial population, viralmediated gene transfer takes place in Earth’s oceans at the rate of ~2 x 1016 per second. The characters transmitted by phage in the environment, their rate of transmission, and the environmental factors involved in the transfer of genes are generally unknown. However, recent evidence shows the presence of bacterial genes in marine phages, including genes that code for proteins necessary for photosynthesis (Hambly and Suttle, 2005). Similarly, a significant portion of eukaryote chromosomes (approximately 45% for humans and a much higher percentage for some plants and an amoeba species) is composed of remnants from RNA viruses (called retrotransposons, or mobile genetic elements that replicate by 4
A virus is defined as an intracellular parasite and is incapable of living without a host cell. While it shares many of the biochemical characteristics of a living cell including nucleic acids and proteins(although much smaller and simpler) except that it cannot reproduce independently, only by infecting a normal cell.
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reverse transcription: RNA to DNA rather than DNA to RNA) (Bushman, 2001). Most of these viral sequences in eukaryotes are not transcribed into proteins. But do they nevertheless serve some important function to the organism? And if not, why do organisms retain them anyway? Some retroviral sequences have been implicated in the evolution of vertebrate genes including the development of the human placenta and the regulation of the gene for starch hydrolysis, but most have no apparent function and along with other nonprotein coding regions on eukaryotic chromosomes, have been called “selfish DNA” (Bushman, 2001). How important is lateral gene transfer in evolution? Results from whole genome sequences of bacteria and archaea indicate that lateral gene transfer may be the most important mechanism for acquiring new genes, including those involved in complex and coordinated phenotypes. For example, ~16% of the genome of Escherichia coli K12 is viral genes. Microorganisms have evolved elaborate mechanisms for incorporating acquired genes into their chromosome at specific sites. These sites can serve as “pathogenicity islands” if all of the acquired genes are involved in disease production, such as for the choleraproducing bacterium Vibrio cholerae (Faruque and Mekalanos, 2003), or they may be “genetic islands,” which align acquired genes involved in key physiological activities such as magnetotaxis (Grünberg et al., 2001) or the dissimilatory reduction of sulfate (Mussmann et al., 2005). It is very unlikely that the formation of a genome with sufficient information to lead to freeliving (selfsufficient) cells could have originated without a
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mechanism for acquiring “functional” genes from other early cells or communities of interdependent cells or “precells” (Baross and Hoffman, 1985). This is certainly consistent with the fact that all life on Earth is derived from a common ancestral pool of genes based on a universal genetic code (Woese, 1998). Darwinian evolution would have played an important role in these early stages and selection would have favored specific biochemical and molecular structures and mechanisms over others. Could this imply that if we started over again by resetting the clock to 4 Ga, the resultant life would have the same biochemical and molecular properties, including the same genetic code, as presentday Earth life? If environmental conditions and the starting pool of organic compounds were the same, it is probable that a second genesis would result in biochemistry that would resemble or possibly be indistinguishable from presentday Earth life. The strong link between specific nucleotide bases and specific amino acids is one more example verifying that there are “rules of organic chemistry” that favor specific reactions or macromolecular structures (Copley et al., 2005). In such a second genesis, however, contingency in evolution could result in the selection of organisms and ecosystems significantly different from those found on Earth. Yet, compared to presentday organisms, they would share a similar biochemistry and evolve many or all of the same phenotypes (both structural and functional), albeit possibly with different genotypes. Further discussion of these points is found in Chap. 27.
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10.4 Could There Be Life Without Evolution?
Many of the definitions of life include the phrase “undergoes Darwinian evolution” (Chap. 5). The implication is that phenotypic changes and adaptation are necessary to exploit unstable environmental conditions, to function more optimally in the environment, and to provide a mechanism to increase biological complexity. Evolutionary changes have even been suggested for hypothesized “clay crystal life” of CairnsSmith (1982), referring to randomly occurring errors in crystal structure during crystal growth as analogous to mutations (Sec. 27.4.2). Would a selfreplicating chemical system capable of chemical transformations in the environment be considered life? If selfreplicating chemical compounds are not life, then replication by itself is not sufficient as a defining characteristic of life. Likewise, the ability to undergo Darwinian evolution, that is, a process that results in heritable changes in a population, is also not sufficient to define life if we consider minerals that are capable of reproducing errors in their crystal structure to be equivalent to evolution. Although this property of clays may have been vital in the origin of life and particularly in the prebiotic synthesis of organic macromolecules and as catalysts for metabolic reactions, can the perpetuation of “mistakes” in crystal structure result in the selection of a “more fit” crystal structure? It is important to emphasize that evolution is not simply reproducing mutations (mistakes in clays), but selecting those variants that are functionally morefit.
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The canonical characteristics of life are an inherent capacity to adapt to changing environmental conditions and to increase in complexity by multiple mechanisms, but particularly by interactions with other living organisms (and, at least on Earth, also with viruses). Natural selection is the key to evolution and the main reason why Darwinian evolution persists as a characteristic of many definitions of life. Clays could never evolve an eye or a nose, or adapt behavioral strategies to exclude clays with other crystal characteristics. Hmmm – would Michael Crichton’s Andromeda Strain (1969), a carbonbased crystal capable of using chemical and physical energy sources, be considered life? (Incidentally, the Andromeda Strain could also mutate, which was probably a necessity to reach a happy ending to the story.) The only alternative to evolution for producing diversity would be to have environmental conditions that continuously create different life forms, or similar life forms with random and frequent “mistakes” made in the synthesis of chemical templates used for replication or metabolism. These mistakes would be equivalent to mutations and could lead to traits that gave some selective advantage in an existing community or in exploiting new habitats. This could lead to life forms that undergo a form of evolution without a master information macromolecule such as DNA or RNA. It is difficult, however, to imagine such life forms being able to “evolve” into complex structures unless other mechanisms such as symbiosis or cell/cell fusion are available.
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10.5 Evolution and Extraterrestrial Life
We have seen that evolution is much more than mutation and natural selection. It is the key mechanism for heritable changes to occur in a population. Mutation is not the only mechanism for acquiring new genes. Lateral gene transfer appears to be one of the most important mechanisms and clearly one of the earliest mechanisms for creating diversity and possibly for building genomes with the requisite information to result in freeliving cells, as opposed to codependent communities of “precells” with insufficient genetic information to escape communal life (Baross and Hoffman, 1985). Lateral gene transfer is also one of the mechanisms to align genes from different sources into complex functional activities such as magnetotaxis and dissimilatory sulfate reduction. It is possible that this mechanism was important in the evolution of metabolic and biosynthetic pathways and other physiological traits that may have evolved only once even though they are present in a wide diversity of organisms. The coevolution between two or more species is also a hallmark of evolution manifested in many ways from insect/plant interactions to the hundreds of species of bacteria involved in the nutrition of ruminant animals. The organisms and the environment also coevolve depending on the dominant characteristics of the environment and the availability of carbon and energy sources. Even some of the most extreme environments on Earth, such as hydrothermal vent sulfide chimneys and the very acidic Rio Tinto River in Spain, have a remarkably high diversity of organisms (Kelley at al., 2002; Zettler et al.,
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2003). Diversity drops off, however, in environments with combinations of stressors such as high temperature and high pH, or high salt and high or low temperature (Chap. 14). If the ability to undergo Darwinian evolution is a canonical trait of life no matter how different that life form is from Earth life, then are there properties of evolving extraterrestrial organisms that would be detectable as positive signs of life? Evolution provides organisms the opportunity to exploit new and changing environments, and one piece of evidence for the probable cosmic ubiquity of evolution is that on Earth life occupies all available habitats and even creates new habitats as a consequence of its metabolisms. Another hallmark of evolution is the ability of organisms to coevolve with other organisms and to form permanent and obligatory associations. Also, it is highly probable that an inevitable consequence of evolution is the elimination of radically different biochemical lineages of life that may have formed during the earliest period of evolution of life. Extant Earth life is the result of either selection of the most fit lineage or homogenization of some or all of the different lineages into a common ancestral community that developed into the present three major lineages (domains). All have a common biochemistry based on presumably the most “fit” molecular information strategies and energy yielding pathways among a potpourri of possibilities. One caveat and perhaps a verification of the above statement is that genetic remnants of other lineages may still exist in some of the deeply rooted archaea as evidenced from the unique 16S rRNA found in Nanoarchaeum equitans and novel and presently
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undelineated metabolic pathways in some hyperthermophilic Crenarchaeota (Huber et al., 2003; Hügler et al., 2003). Thus, one of the apparent generalizations that can be made from extant Earth life, and the explanation for the development of a “unity of biochemistry” in all organisms, is that lateral gene transfer is both an ancient and an efficient mechanism for rapidly creating diversity and complexity. Lateral gene transfer is also an efficient mechanism for selecting the genes that are most “fit” for specific proteins and transferring them into diverse groups of organisms. The result is both the addition of new genes and the replacement of lessfit genes having a similar function. Natural selection based solely on mutation is not likely an adequate mechanism for evolving complexity. More importantly, lateral gene transfer and endosymbiosis are probably the most obvious mechanisms for creating complex genomes that can lead to freeliving cells and complex cellular communities in the short geological time available from life’s origin to the establishment of microbial communities more than 3.8 billion years ago (Sec. 12.3). An important implication of the existence of viruses or viruslike entities during the early evolution of cellular organisms is that their genomes may have been the source of most genetic innovations due to their rapid replication rates, high rates of mutation from replication errors, and gene insertions from diverse host cells. It is interesting that Darwin perceived evolution as random changes in individual species that could lead to selection of more fit traits, but he could not have known that some of these fit traits could be transferred to species that were not only not sexually compatible
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but belonged to separate domains. It is clear that both the individual organism and its community coevolve. In a sense, evolution is evolving, allowing cells to control their own evolution – accept or reject changes in genotypes from newly acquired foreign genes. While this has already been demonstrated in bacteria, the source of foreign genes and the kinds of genes most likely to be selected for permanence are largely not known. However, it is clear that the evolution of a useful trait by one organism frequently means that it is likely to be acquired by other organisms. It appears that the field of biology is beginning to break out of its molecularreductionist “egg” and emerging more focused on what Carl Woese (2004) terms “holistic biology,” where the emphasis, rather than just on genes, is on the cell, communities and ecosystems. This would also take evolution to a new level of inquiry with emphasis on coevolution, cellular complexity, and the reexamination of the concept of ecosystems as “super organisms.” The new science of EvoDevo integrates well with this new holistic approach while offering another lesson about evolution: chance mutations or microevolution create the panoply of gene variation, but it is key genes and combinations of key genes that “better meet the imperatives of ecological necessity, and they arise and are selected for repeatedly” (Carroll, 2005). Finally, what are the limits of evolution for Earth life? This is a complex question with many different components. On the one hand, it involves the different possible biochemistries from carbon chemistry that are not found in extant Earth organisms but could be better suited for environmental conditions that exist
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on other planets and moons (Chap. 27). The technology exists to design genes and groups of genes that could lead to novel phenotypes suited to exploit new habitats and novel energy sources. These kinds of studies would be important and perhaps essential in our quest to search for life elsewhere. Another component to the question of the limits of evolution is where we are going and what will Homo sapiens or its successors be like if it continues to evolve for tens of thousands or million of years? This is an integral part of our search for advanced extraterrestrial intelligence, which requires us to imagine our future portrait (Chap. 26). We cannot imagine all of the possible changes that will occur after millions of years of evolution but based on the just the tens of thousands of years of primate evolution, it is likely that one possible outcome will be an increasing ability to control our environment and all that is evolving. It is also likely that we will someday know if we are alone in the Universe.
10.6 Summary It is evident that cells are more than the information encoded in their genomes. They are part of a highly integrated biological and geochemical system in whose creation and maintenance they have participated. The unity of biochemistry among all of Earth’s organisms emphasizes the ability of organisms to interact with other organisms to form coevolving communities, to acquire and transmit new
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genes, to use old genes in new ways, to exploit new habitats, and most important to evolve mechanisms to help control their own evolution. It is expected that these characteristics are likely to be present in extraterrestrial life even if it has had a separate origin and a very different unified biochemistry from that of Earth life. Since evolution is an essential feature of Earth life and probably all life, the search for life elsewhere should include a search for evidence of evolution.
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Figure Caption
Figure 10.1. Charles Darwin (18091882), in his later years at Down House, his combined home, office and laboratory (see App. D). (photo courtesy John van Wyhe)
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General Reading and Surfing
Desmond, A. and Moore, J. (1991). Darwin: The Life of a Tormented Evolutionist. New York: Warner. This is an excellent and thoroughly researched biography of Darwin. As the title implies, Darwin struggled as to how to present the theory of evolution in a way that was acceptable to a community shackled by Victorian mores.
Judson, H. W. (1979). The Eighth Day of Creation: The Makers of Revolution in Biology. New York: Simon and Schuster. This is the definitive historical study of the mid20thcentury birth of molecular biology and a must read for anyone interested in how revolutions in science get started. It has been reprinted with an updated preface (New York: Cold Spring Harbor Laboratory Press, 1996).
Knoll, A. H. (2003). Life on a Young Planet: The First Three Billion Years of Evolution on Earth. Princeton: Princeton Univ. Pr. This is a “tour de force” portrait of life from Earth’s beginning to the Cambrian explosion. Knoll is masterful in blending geology, geochemistry and biology in the context of Earth history.
Lovelock, J. E. (1979). Gaia: A New Look at Life on Earth. Oxford: Oxford Univ.
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Pr. James Lovelock and Lynn Margulis first put forth the proposition that the composition and temperature of the atmosphere is an evolutionary product of interrelated activities in the biosphere, especially those of microorganisms, and that the entire biosphere behaves as a single selfregulating organism. The Gaia Hypothesis has been every bit as influential as it is controversial (see Sec. 10.5 for related thinking).
www.mendelweb.org An excellent website for learning the details of what Mendel actually did.
Conway Morris, S. (2003). Life’s Solution: Inevitable Humans in a Lonely Universe. Cambridge: Cambridge Univ. Pr. Conway Morris has a different perspective on evolution. He argues for determinism rather than contingency: Evolution has predictable and inevitable outcomes. His metaphysical arguments are interesting and certainly thought provoking and somewhat reminiscent of chapter 31 in Christian de Duve’s excellent book, Vital Dust: Life as a Cosmic Imperative (New York: Basic Books, 1995)
Ptashne, M. (1992, 2nd ed.). A Genetic Switch. Cambridge, Mass.: Blackwell Science.
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This classic work describes the basic molecular reactions underlying the regulation of gene transcription in all organisms and how the genes involved in these reactions, when combined, produce complex regulatory circuits. The regulatory circuits found in bacteria are the forerunners to the evolution of the more complex regulatory circuits involved in macroevolution and the emergence of EvoDevo (Carroll, 2005)
Ridley, M. (ed.) (1997). Evolution. Oxford: Oxford Univ. Pr. This is an excellent compilation of many of the classic papers on evolution. The list of authors is the “Who’s Who” of great evolution thinkers and includes Charles Darwin, Stephen J. Gould, Ernst Mayr, George Gaylord Simpson, Richard Dawkins, Francis Crick and many others. The topics covered include adaptation, macroevolution, molecular evolution, biodiversity, human evolution, and evolution and philosophy.
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References
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