Once life formed on Earth, over time it became more complex…eventually leading to humans capable of pondering their own existence. All life on Earth descends from the very first instance of life. Natural selection drove species to form and adapt to new environments and ecological niches. The rise of oxygen in the atmosphere about 2.5 billion years ago caused a proliferation of new life forms that had more efficient metabolic pathways. We will look at some of the milestones in the formation of more complex life throughout Earth’s 4.5 billion year history.

The Last Universal Common Ancestor

The Last Universal Common Ancestor (LUCA) on Earth is a concept, rather than an actual organism. Any universal characteristics of life on Earth are universal either because they are inherited or because they are truly fundamental to life in general. Without a second example of life we are unable to understand how common these features will be on other worlds.

LUCA represents the earliest shared qualities of ancestral life and likely appeared on Earth between 3.5 to 4 Gya and seeded our planet with life. All of the features of life today would have been inherited from LUCA. From what we know about terrestrial biology, this means that LUCA would have been carbon-based, dependent on water, incorporated left-handed amino acids, and used ATP for energy transport. LUCA would have used DNA or RNA to encode genes and translate them into proteins. Significantly, the codons that translate for specific amino acids are the same in every known organism. This code must have been passed down from a common ancestor from which every other species has since evolved. LUCA might not have even been as sophisticated as a single celled organism.

The Tree of Life

The first instance of life was likely very simple and single-celled. Today, life is fantastically varied and complex. We separate the life we see today into three domains based on shared cellular structure and genetic material. The three domains of life, archaea, bacteria, and eukaryotes, are a diversification of the Last Universal Common Ancestor (LUCA).

• Bacteria make up the largest domain with both the greatest number of individual species and a biomass that exceeds the combined biomass of all plants and animals. Bacteria were one of the earliest forms of life on our planet and they are found in most habitats. Bacteria can rapidly recombine their genes with other bacteria to allow for genetic innovations, such as resistance to antibiotics.
• Archaea are genetically distinct from bacteria with their own, separate domain. Archaea are known to generate energy in a variety of ways and have been found in some of the most extreme environments on Earth. Halophiles, for example, exist in extremely salty conditions.
• Eukaryotes are distinct from prokaryotes in containing a central nucleus enclosed in a membrane and also contain other membrane-bound organelles. Examples of eukaryote organelles include chloroplast, the site of photosynthesis in plants and some algae, and mitochondria, where energy is generated in a cell. Eukaryotes can be uni- or multi-cellular, allowing for larger and more complex organisms.

Both bacteria and archaea are prokaryotes: single-celled microbes that do not contain membrane-bound organelles. However, the membranes in archaea incorporate a different type of lipid than either bacteria or eukaryotes. Genetic analysis reveals that archaea are closer to eukaryotes in an evolutionary sense than they are to bacteria. Archaea and eukaryotes use many of the same enzymes for DNA translation.

The Diversification of Life

Endosymbiosis

Eukaryotic cells have gained membrane-bound organelles and increased complexity through the process of endosymbiosis. Endosymbiosis is a process whereby primitive organisms benefited by living inside other organisms. Chloroplasts and mitochondria are examples of highly complicated organelles in eukaryotes that have their own membrane. They retained the DNA, messenger RNA, transfer RNA, and ribosomes of their bacterial ancestors before they were symbiotically incorporated into larger eukaryotic cells. The larger cell presumably provided protection and easy access to organic molecules while the chloroplast and mitochondria provided energy to the larger cell. This beneficial relationship led to the creation of larger, more efficient cells.

Cyanobacteria

The rise of oxygen likely began with organisms known as cyanobacteria, an early type of photosynthetic bacteria thought to be the first organism to produce oxygen as a byproduct. Photosynthesis is the process by which organisms can harness the energy of the sun to generate energy for their own use. Cyanobacteria are the only know prokaryotes to produce oxygen, and this adaptation brought about the destruction of many other organisms.

The rise in atmospheric oxygen was far from smooth and steady (see Figure 3 below). Cyanobacteria slowly became more abundant, but there was still a significant delay in the build up of oxygen. There are several processes that would have hindered the rise in oxygen. Oxygen would have reacted with various chemicals, mainly iron, in the oceans, and these reactions would trap oxygen, prevent it from building up the atmosphere.

Oxygen may also have been taken up by microbes in metabolic pathways that generate energy. Organisms that used the oxygen to oxidize ammonia appear to have been plentiful at the time and could have been effective in the reduction of free-floating oxygen.

Other organisms produced methane as a byproduct that could have acted as a sink for atmospheric oxygen. However, organisms that are known to produce methane require nickel to carry out the necessary reactions, and concentrations of nickel were dropping. The decrease of nickel would mean less excreted methane, and would allow oxygen to begin accumulating.

The increase of oxygen in the atmosphere was poisonous for anaerobic organisms. Most life before the Great Oxidation Event was anaerobic, so the rise of atmospheric oxygen surely resulted in one of the most significant extinction events in Earth’s history. The fossil record shows a mass extinction of anaerobic life around 2.4-1.6 billion years ago, coincident with the rise of aerobic life.

Anaerobic vs Aerobic Life

The rise of atmospheric oxygen coincided with the appearance of far more complicated life forms. There is every reason to believe that the rise in oxygen would have been responsible since aerobic metabolisms are more efficient.

Respiration, in biological terms, describes the process by which organisms convert nutrients into usable energy by forming ATP bonds. Respiration begins with glycolysis, wherein glucose, a sugar, is broken down to form two molecules of a compound called pyruvate along with two molecules of ATP. Without oxygen, organisms have no choice but to undergo anaerobic respiration, or fermentation. Anaerobic respiration of yeast is what makes bread rise and beer bubbly. In this scenario, pyruvate is shuttled down a pathway which produces just two molecules of ATP.

In the presence of oxygen, aerobic respiration becomes possible. With the help of oxygen, pyruvate can be broken down and enters a more complicated pathway known as the Krebs cycle or the citric acid cycle (note that organisms exhibit an enormous variety of metabolic pathways; the citric acid cycle merely represents one of the more common and well understood pathways). Through the citric acid cycle, organisms can produce from 30–36 ATP from just one molecule of glucose. Though more complicated to assemble, and therefore likely taking longer to evolve, this process can be up to 18-fold more efficient than anaerobic respiration. With more energy, it is possible to carry out more biochemical processes. This may have allowed cells to become increasingly complex and trend towards the more varied, multicellular life we see today.

Want to know more: Viruses

Viruses are even more abundant than bacteria. A virus consists of three functional parts: (1) genetic material, (2) protein coat, and typically (3) an envelope of lipids outside the protein coat. For genetic material, viruses have been discovered to use both DNA and RNA. The protein coat, also known as the capsid, encases and protects this genetic material. The envelope of lipids adds an additional layer of protection.

However, the question of whether viruses can be considered life is hotly debated. Viruses have their own genetic material and are even capable of evolving through natural selection. Viruses survive and replicate by infecting a host cell. After attaching to a cell, the virus injects its DNA into the host cell. Now, the virus is capable of taking over the host cell’s replication mechanisms. In doing so, the virus can now create copies of itself until it has exhausted the cell’s resources. Millions of viruses can be made in this period before the cell dies and viruses escape to infect new host cells. Because viruses require the metabolism of a host cell to produce energy and reproduce, they can not be called self-sustaining. In this way, viruses fail the NASA definition of life.

Despite their differences, evidence of viruses appear wherever life does, suggesting that viruses and life evolved together.  The history of viruses is traced through their DNA or RNA and has given rise to three theories on how viruses came to be.

Regressive evolution theory proposes that viruses were once components of small, parasitic cells. Similar to the idea of endosymbiosis, viruses may have begun as small structures within larger cells that over time became separated. In fact, there exist today some bacteria that, like viruses, can only reproduce in a host cell. As they evolved, these small parasitic structures regressed further from cell-like characteristics, becoming the viruses we see today. However, there is no evidence of types of cells today that could serve as an intermediary between early and present day viruses. Even the smallest cellular parasites fail to really resemble viruses at all.

Another theory is the escaped gene theory, which proposes that viruses got their start as DNA or RNA that escaped from the genome of a larger organism. Surprisingly mobile DNA has recently come to play a large role in biology. Plasmids (Figure below) are circular units of DNA and separate from the genome of an organism. They are most commonly found in bacteria and have been known to move between cells. Scientists have also recently discovered transposons, or “jumping genes,” which are large segments of DNA that can move around within a cell’s genome. While either of these mechanisms could have provided the genetic material for viruses, it remains unclear where the complicated capsids enclosing these genes arose from.

The pre-cellular origin theory proposes that viruses formed from complex proteins that spontaneously arose even before RNA. Viruses could have evolved alongside the first cells or even before. However, this fails to account for the dependency viruses have on host cells. If viruses need the mechanism of a host cell to survive, how did they manage before cells even evolved?

The exact origin of viruses, much like the origin of life, remains an open question. This vein of research is being pushed forward through analysis of viral and host DNA sequences. What we can say is that genetic comparisons show that the origins of viruses may have predated life splitting into the three different domains. Perhaps the precursors to viruses evolved from the self-replicating molecules that dominated the RNA world. Similar to RNA, viruses are capable of self-assembling in host cells.

Viruses are now well enough understood to be used as tools in biomedical research. In a process called gene therapy, researchers use viruses to inserting genes into specific cells, offering possible treatments for diseases like cystic fibrosis. Some viruses will seek out and destroy cancer cells, while leaving healthy cells alone, allowing for a highly targeted and effective treatments.

Review Questions

1. What are the three domains on the tree of life and how do scientists distinguish between them?
2. What are the main differences between prokaryotes and eukaryotes?
3. Give an example of endosymbiosis and explain what advantages and disadvantages were gained by organisms that evolved from such situations.
4. How did cyanobacteria cause one of Earth’s mass extinctions?
5. What causes aerobic metabolism to be more efficient than anaerobic metabolism?

Exercises

1. Four examples of eukaryotic organelles that evolved from endosymbiosis include (1) choloroplasts, (2) mitochondria, (3) nitroplasts, and (4) diazoplasts. Conduct the necessary research to construct a table that compares these four examples in separate rows with three different columns: (1) the kinds of organisms that contains these organelles, (2) the approximate timeframes for when the incorporation of these organelles occurred, and (3) explanations of the function of these organelles.