1.6: The Origins, Evolution, Speciation, Diversity and Unity of Life

The question of how life began has been with us since the beginnings or recorded history. It is now accepted that there was a time, however brief or long, when the Earth was a lifeless (prebiotic) planet. Life’s origins on Earth date to about 4 billion years ago under conditions that favored the formation of the first cell, the first entity with all of the properties of life. But couldn’t those same conditions have spawned multiple cells independently, each with all of the properties of life? If so, from which of these did life, as we know it today, descend? Whether there were one or more different “first cells”, evolution(a property of life) could only begin with ‘that or those’ cells.

115 Properties of Life

The progenote has been defined as the first cell from which all life then descended. This implies that the origin of a cell was a unique, one-time only event. The fact that there is no evidence of multiple, independent origins of cellular life might be evidence (albeit negative evidence) that life originated only once, to produce a progenote as defined, and that multiple first cells (or potential progenotes) never existed. Alternatively, we can propose that the cell we call our ancestral progenitor originally had company, but that this progenote was evolutionarily successful at the expense of other early life forms, which thus became extinct.

Whatever our progenote may have looked like, one of its descendants later evolved the solutions to living that we see in force in all cells and organisms alive today, including a common (universal) genetic code to store life’s information, as well as a common mechanism for retrieving the encoded information, what Francis Crick called the Central Dogma of biology. That ancestral cell is called our Last Universal Common Ancestor, or LUCA. We will consider ideas about life’s origins, progenotes, and universal ancestors in the last chapter of this book. For now, feel free to check out the links below for more information.

116 The Universal Genetic Code

117 Origins of Life

118 Life Origins vs Evolution

For the moment, our focus is on evolution, the property of life that is the basis of speciation and life’s diversity. Charles Darwin’s theory of evolution was an explanation of the structural diversity of species. A naturalist, Darwin lived at a time of ferment where scientific discovery was challenging religion. But by 1839, Charles Darwin had published his Narrative of the Surveying Voyages of His Majesty's Ships Adventure and Beagle. This was the first of many reports of his careful observations of nature, with the seeds of what was to become his theory of natural selection. He published his more fully formed theory of evolution by natural selection in 1859 in The Origin of Species. There, he finally acknowledged his evidence-based belief that that new species arise when beneficial traits are selected from random genetic differences in individuals in a population. At the same time, less fit individuals would be culled from the population. If natural selection acts on individuals, the emergence of new species (evolution) results from the persistence and spread of selected, heritable changes through successive generations in a population. In this way, evolution results in an increase in biological diversity and complexity at all levels of biological organization, from species to individual organisms and all the way down to biomolecules.

Darwin recognized that his theory would generate discord between science and biblical accounts of purposeful creation. He addressed the issue with great tact in introducing The Origin of Species: “Although much remains obscure, and will long remain obscure, I can entertain no doubt, after the most deliberate study and dispassionate judgement of which I am capable, that the view which most naturalists entertain, and which I formerly entertained–namely, that each species has been independently created–is erroneous.” Yet today, according to creationists, our exquisite eyes could only have formed by the intelligent design of a creator.

For the evolutionary perspective,see the article in National Geographic by E. Yong(Feb., 2016, with photography by D. Littschwager). Over time science favored Darwin. With the rediscovery of Mendel’s genetic experiments at the turn of the twentieth century, it became increasingly clear that the genes of an organism are the basis of an organism’s inherited physical and chemical traits, those traits that are passed down through the generations. It also became clear that Mendel had found the genetic basis for Darwin’s theory and that the evolution even of miraculous eyes can be explained. Science and religion found ways to co-exist but, the controversy persists.

Repeated speciation occurs with the continual divergence of life forms from an ancestral cell through natural selection and evolution. Our shared cellular structures, nucleic acid, protein, and metabolic chemistries (the ‘unity’ of life) are testimony to our common ancestry with all life, dating back to our LUCA! Living things even share some early behaviors,governed at least in part by genes.

Take as an example the fact that our biological clock is an evolutionary adaptation to our planet’s 24-hour daily cycles of light and dark. Day and night have been around since the origins of life, and all organisms studied so far seem to have a biological clock! The discovery of the genetic and molecular underpinnings of circadian rhythms (those daily cycles) earned Jeffrey C. Hall, Michael Rosbash and Michael W. Young the 2017 Nobel Prize in Medicine or Physiology (check out Circadian Rhythms Win Nobel Prize to learn more)!

The molecular relationships common to all living things largely confirm what we have learned from the species represented in the fossil record. Morphological, biochemical, and genetic traits that are shared across species are defined as homologous and can be used to reconstruct evolutionary histories. The biodiversity that scientists (in particular, environmentalists) try to protect is the result of millions of years of adaptation (natural selection), speciation, and extinction. Biodiversity needs protection from the unwanted acceleration of evolution arising from human activity, including blatant extinctions (think passenger pigeon), and near extinctions (think American bison by the late 1800s). Think also of the consequences of the introduction of invasive aquatic and terrestrial species and the looming effects of climate change.

Let’s look at the biochemical and genetic unity among livings things. We’ve already considered what happens when cells get larger when we tried to explain how larger cells divide their labors among smaller intracellular structures and organelles. When eukaryotic cells evolved further into multicellular organisms, it became necessary for the different cells to communicate with each other and to respond to environmental cues. Some cells evolved mechanisms to “talk” directly to adjacent cells and others evolved to transmit electrical (neural) signals to other cells and tissues. Still other cells produced hormones to communicate with cells far away, to which they had no physical attachment.

As species diversified to live in very different habitats, they also evolved very different nutritional requirements, along with more extensive and elaborate biochemical pathways to digest their nutrients and capture their chemical energy. Nevertheless, through billions of years of evolution and astonishing diversification, the underlying genetics and biochemistry of living things on this planet is remarkably unchanged. Early in the twentieth century, Albert Kluyver first recognized that cells and organisms vary in form appearance in spite of an essential biochemical unity of all organisms (see Albert Kluyver). This unity amidst the diversity is a life paradox that we examine in this course.

1.6.1. Random Acts of Genetic Variation, the Basis of Natural Selection

DNA contains the genetic instructions for the structure and function of cells and organisms. When and where a cell’s or organism’s genetic instructions are used (i.e., to make RNA and proteins) are highly regulated. Genetic variation results from random mutation. Genetic diversity arising from random mutations is in turn, the basis of natural selection during evolution.

119 The Random Basis of Evolution

1.6.2. The Genome: An Organism's Complete Genetic Instructions

Recall that every cell of an organism carries the same genome as every other cell. The genome of an organism is the entirety of its genetic material (DNA, or for some viruses, RNA), including genes and other kinds of DNA sequences. The genome of a common experimental strain of E. coli was sequenced by 1997 (Blattner FR et al. 1997, The complete genome sequence of Escherichia coli K-12. Science 277:1452-1474). Sequencing of the human genome was completed (more or less!) by 2001, well ahead of schedule (Venter JC 2001, The sequence of the human genome. Science 291:1304-1351). Recall also that the analysis of rRNA gene sequences resulted in the dramatic re-classification of life from five kingdoms into three domains. Thus, comparisons of specific gene or other DNA sequences can tell us a great deal about evolution. We now know that evolution depends not only on individual gene sequences, but on a much grander scale, on the structure of genomes. Genome sequencing has confirmed not only genetic variation between species, but also much variation between individuals of the same species. It is the genetic variation within species that is the raw material of evolution. It is clear from genomic studies that genomes have been shaped and modeled (or remodeled) in evolution. We’ll consider genome remodeling in more detail elsewhere.

1.6.3. Genomic 'Fossils' Can Confirm Evolutionary Relationships

We have been looking to gene and protein sequencing to find evolutionary relationships and even, familial relationships. You can read about an early demonstration of such relationships based on amino acid sequence comparisons across evolutionary time in Zuckerk and lE and PaulingL. (1965) Molecules as documents of evolutionary theory. J. Theor. Biol. 8:357-366. In addition, it has been possible for some time now, to extract DNA from fossil bones and teeth, allowing comparisons of extant and extinct species. DNA has been extracted from the fossil remains of humans, other hominids, and many animals. DNA sequencing reveals our relationship to animals (from bugs to frogs to mice to chimps...) and to Neanderthals (with whom we share some genes!) and our other hominid ancestors. Unfortunately, DNA from organisms much older than 10,000 years is typically so damaged or simply absent, that relationship building beyond that time is impossible.

Using what we know from gene sequences of species alive today, investigators have recently ‘reconstructed’ a genetic phylogeny suggesting the sequences of genes of some of our long-gone progenitors, including bacteria (to learn more, check out: Deciphering Genomic Fossils).The comparison of these ‘reconstructed’ ancestral DNA sequences suggests when photosynthetic organisms diversified and when our oxygenic planet became a reality. Closer to home, many remains of ancestral humans have been discovered in the Americas. These promise to unlock the mysteries of human settlement of the continents, though not without controversy. Indian tribal cultures treat their ancestors as sacred and argue against sampling such remains for DNA Analysis. In one example, a well-preserved mummified body was discovered in the Nevada desert in the 1940s. Tests of clothing fragments and hair revealed that this Spirit Cave mummy was over 10,000 years old. DNA sequence analysis was proposed to confirm the origins of the mummy. But then the Fallon Paiute-Shoshone tribe, which lives near the burial site, asserted a cultural relationship to the body and requested the right of its return in compliance with the Native American Graves Protection and Repatriation Act. Anthropologists then counter-asserted a need for further study of the body to learn more about its origins and about native American origins in general. The dispute ended only after 20 years, when the time the tribe consented DNA tests were allowed. When the DNA sequence analysis results established that the remains were indeed that of an ancestor to the tribe, the Spirit Cave mummy was returned to the Fallon Paiute-Shoshone to be reburied with full tribal rites in 2018. To read more, see Resolving American Indian Ancestry or Ice Age Mummy DNA Analysis Unlocks Tribal Secrets.

120-2 Genomic Fossils-Molecular Evolution

CHALLENGE

Tracing ancient remains to tribal descendants continues to cause culture/science tension. See the 42,000 year-old Australian aboriginal Mungo Man,(Perrotet, T. & Smith, D.M. 2019, The Homecoming; Smithsonian 50: 38-49), and then reflect on what the discovery can tell us and how the conflict was resolved.