11. Origin and evolution of life (part I)
Geologists learn about the evolution of life on our planet by studying rock layers containing fossils
and other traces of biological activity. The task is difficult because the geological record isincomplete. Incompleteness comes from unconformities in the stratigraphic record (see chapter 9)
and processes destroying fossils (i.e. metamorphism, see chapter 8). An analogy can be madebetween the reconstruction of life history based on fossils and reading a book with missing pages.
The study of past life based on fossils is called paleontology. Paleontologists assign fossils totaxonomic groups (groups defined on the basis of shared morphological characteristics),
determine how and where fossil organisms lived (paleoecology), and study their evolutionary
relationships.
A look at the fossil record clearly shows that the biological landscape of our planet has gone
through considerable changes over time (think about the giant dragonflies of the Carboniferous or
the dinosaurs of the Jurassic!). The fossil record is punctuated by extinction events and theemergence of new species. Life is not static but evolves through time!
A breakthrough in our understanding of life history came in the 19th century when Charles Darwin
explained evolution in light of his theory of natural selection (a theory proposed independently by
the British naturalist Alfred Russel Wallace at roughly the same time). Evolution is the process bywhich organisms descend from other preexisting forms of life through modifications. Thesemodifications are the result of random genetic mutations affecting specific traits (e.g. morphology,physiology, behavior). If they are beneficial for the organism and increase the chance of survivaland reproduction, they will have a greater chance to be passed on from one generation to the next
(hence the term “natural selection”). Over many generations, these modifications can change thegenetic make-up of a population and lead to the emergence of a new species (speciation).
Advantageous traits that are inherited are called adaptations. Evolution by natural selection is aslow process. During rapid environmental changes, populations may not have time to adapt andentire species may face extinction. The biosphere has been affected several times by mass
extinctions which have wiped out a large proportion of species living on the planet. However,these major disturbances were followed each time by a phase of rapid diversification as we will see
in chapter 12.
In light of Darwin’s theory life can be represented by a tree, an evolutionary tree, in which eachbranch represents a group of organisms (Fig. 1). The branches at the very top of the tree represent
extant groups. Moving down these branches means traveling back in time. The junction between
two or more branches represents the time when new groups have evolved from a commonancestor. If we follow the branch of this common ancestor, we see that it too shares a commonancestor with another group. In this tree, we can find a common ancestor even for extant groups
that are very different from each other, such as eagles and slugs, if we travel back in time far
enough. Darwin himself surmised that there must exist at the base of the tree one “primordial lifeform” from which all the others have descended (Fig. 1).

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Figure 1: One of the very first illustrations of an evolutionary tree drawn by Darwin himself showing how life
diversity sprang from one single common ancestor (labeled ).

An evolutionary tree can be reconstructed on the basis of the morphological traits shared byorganisms. For example, we, humans, have a lot more characteristics in common withchimpanzees than with sea urchins. Therefore, our branch must be closer to that of chimpanzees
and the branch of our most recent common ancestor must be relatively close to the tree top. On
the other hand, the branch of sea urchins is far more distant from us and the most recent ancestor
we share with them must be found further back in time, thus farther from the tree top. Comparing
the morphological characteristics of extant groups of organisms does not tell us how theirancestors looked like, nor when they branched off to form new groups, and it says nothing about
their relationships with extinct species. To answer these questions, scientists turn to the fossil
record. For example, paleontologists have shown that the earliest birds probably emerged in theLate Jurassic and descended from dinosaurs.
Recently, molecular studies have provided new insight in the evolutionary relationships between
extant groups of organisms (a discipline called phylogenetics). The more similar two groups arefrom the viewpoint of their DNA or proteins, the closer they are in the evolutionary tree and themore recent their common ancestor is. Phylogenetic studies can even provide information on thetiming of divergence between two groups of organisms. In conclusion, data from fossils andmolecular studies are complementary and used together to unravel the evolutionary history of life.

11.1. The origin of life
11.1.1. What is life?
In order to answer the question of the origin of life, we must first define what life is. Whatdistinguish a living thing from a non-living thing? Let’s consider the most basic unit of life: the cell.
The simplest organisms are composed of a single cell devoid of nucleus: the prokaryotic cell.
Prokaryotes comprise two domains of life: bacteria and archaea. They share with all other formsof life a capacity of growth, reproduction, and evolution. They must take up matter from theirenvironment to grow (carbon and other elements, i.e. nutrients) and need a source of energy. Thecapacity of evolution is related to the transmission of genes from one generation to another. In allorganisms, DNA is the molecule carrying the genetic information. DNA must be able to makecopies of itself in order to pass on the genetic information to the next generation (DNA replication).
A living cell is also characterized by a permeable membrane which isolates and protects theDividing life in groups on the basis of shared characteristics is the job of taxonomists. The father of taxonomy is Carl Linnaeus(1707-1778) who laid down the foundation of the current system of naming and classifying organisms. The modern classification
comprises the following subdivisions: domain, kingdom, phylum, class, order, family, genus, and species.
The technique is referred to as “molecular clock”. The rate of modifications in DNA and proteins is roughly constant amonggroups of organisms. Therefore the differences between the DNA or proteins among distinct groups of organisms can be used toinfer the amount of time elapsed since they diverged from a common ancestor.

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genetic material and which helps maintain an internal equilibrium (i.e. homeostasis).
There are many ways to define life. For instance, the physicist Stephen Hawking proposes thefollowing definition: “One can define life to be an ordered system that can sustain itself against thetendency to disorder, and can reproduce itself”. From this perspective, even a computer virus turns
out to be alive!
Whatever the definition of life we choose, we should now ask ourselves how the origin of life canbe studied. The geological record can tell us a lot about primitive life forms but it cannot teach us
exactly how life came to be in the first place. To investigate the origin of life, we have to turn to lab
experiments.
11.1. 2. The lab approach
There are three basic ingredients needed for the emergence of life as we know it: (1) water, (2)organic molecules, and (3) energy. Water is an essential constituent of life. The body weight ofsome organisms is composed of 90% of water! Water is also an excellent solvent and cantransport elements involved in chemical reactions. Organic molecules are composed of a
backbone of carbon atoms linked to other elements, primarily H, O, N, P and S. Energy is needed
to build the large organic molecules needed to sustain life (e.g. proteins, RNA, DNA).
Here are three important steps toward the formation of a living cell:➀ Formation of simple organic molecules
The first breakthrough in our understanding of the origin of life came in 1953 with the Miller-Ureyexperiment (Fig. 2). Its aim was to reproduce the conditions existing on the early Earth and see
whether organic molecules could be produced. The experiment used water vapor and a mixture ofgases (CH4, NH3, H2, H2O) to simulate the primitive atmosphere and an electric arc as a sourceof energy to mimic the effect of lightning. Under these conditions, numerous organic molecules
could be synthesized, including a variety of amino acids. Other experiments using the same
approach but with different mixtures of chemical compounds succeeded in synthesizing
nucleotides, key components of RNA and DNA.
Another hypothesis suggests that organic compounds may have been carried to Earth bymeteorites and comets. A chemical analysis of the Murchinson meteorite showed that it contains
various organic molecules, including amino acids.
In conclusion, large amounts of organic molecules must have existed on the early Earth. However,
the absence of an ozone layer implies that they were exposed to intense UV radiations. Life musthave formed in an environment protected from these radiations, such as the underside of rocks or
at some depth under water.
C, H, O, N, P, S: the 6 elements essential for life are also among the most common elements in the universe!

Note that there was no free oxygen in the primitive atmosphere. Oxygen was produced later by photosynthesis.

Ozone (O3) is produced in the upper atmosphere by the reaction O2 + O  O3 in which O comes from the dissociation of O2 bysolar radiation

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Figure 2: The Miller-Urey experiment② Formation of complex organic molecules capable of self-replication (RNA, DNA)The next step toward the emergence of life is the formation of complex organic molecules(polymers like RNA consisting of a chain of nucleotides). RNA is similar to DNA but instead ofbeing double-stranded and helical, it is formed of a single strand of nucleotides. Biochemists haveshown that clay minerals can promote the assembly of nucleotides into strands of RNA. DNA is likea blueprint that carries the information needed for building proteins. However, DNA does notdirectly communicate with the protein factory. Instead, RNA is used to copy the information storedin DNA (transcription) and carry it to the protein factory (Fig. 3A). It is also involved in other tasks
like delivering the building units of proteins (i.e. amino acids). During cell division, DNA replicatesitself so that the genetic information is passed on to the daughter cells (Fig. 3B). DNA replication
requires protein enzymes to split the double-stranded DNA molecule and help connecting eachstrands with free nucleotides. The information for building these proteins is encoded in DNA. Lifeas we know it is therefore based on complex interactions between DNA, RNA and proteins. How tobridge the gap between the “prebiotic soup” and a complex DNA-based system? One possible
scenario involves RNA. RNA is a versatile molecule that can encode genetic information and bethe catalyst of its own replication. RNA could potentially have sustained a simple form of life before
evolving into the more complex DNA-based system. This hypothesis is referred to as theRNA-world hypothesis.

Figure 3: A. RNA transcription, B. DNA replication (source: Biology, Life on Earth, 9th ed.).

③ Formation of membrane-bound vesicles capable of self-reproduction
It has been shown that lipid vesicles can form abiotically and even divide spontaneously undercertain conditions (Fig. 4). The first protocell may have been composed of such lipid vesicles
enclosing an information-carrying molecule such as RNA. Spontaneous division of these vesicles
must have occurred in parallel with the self-replication of information-carrying molecules in order topass on the genetic code to the next generation of protocells. Many of these protocells must havefailed but those which bore advantageous modifications carried on their division and evolved bynatural selection toward life as we know it.

Figure 4: Lipid vesicles produced in the lab (sources: Deamer et al., 2002; Dworkin et al., 2001).

11.2.2. Evidence from the geological record
The geological record can provide information on the environmental conditions existing on theearly Earth. From the oldest Precambrian fossils, we can learn about the first primitive forms of life59and the timing of biological evolution.
The Earth is 4.56 Ga old. Life would have had a hard time to form before 3.9 Ga because of
repeated and violent meteorite impacts and a surface temperature above 100°C (remember theHeavy Bombardment in chapter 2). The first persistent oceans must have formed after this periodaround 3.8 Ga ago. The first evidence for the deposition of sediments under water comes from a
3.8 Ga rock formation in Greenland. Moreover, there was not or very little O2 in the atmosphereand the first cellular life forms must have been anaerobic prokaryotes. Volcanic eruptions released
gases such as CO2, H2S, SO2, and N2. Other gases that may have been present in the atmosphere
are CH4, NH3, and H2. The relative proportion of these gases is still debated.
Evidence for biological activity in the geological record can be classified in 4 categories:➀ Morphological evidence
Microfossils and microbial mats can be preserved in sedimentary rocks which have not been
metamorphosed.
② Biomineralization
There are two types of biomineralization: direct and indirect. An example of direct biomineralizationis the precipitation of CaCO3 by organisms to build a shell or skeleton (e.g. bivalves, reef corals).
Minerals can also be a byproduct of biological activity. An example of indirect biomineralization is
the precipitation of CaCO3 in relation with bacterial growth in Stromatolites (see section 7.6.2.). In
conclusion, the presence of specific minerals in rocks can indicate a possible link with biologicalactivity.
③ Stable isotope fractionation
Stable isotope fractionation is the process by which stable isotopes are segregated on the basis of
their mass during a physicochemical or biochemical process. For example, the evaporation ofwater involves the fractionation of the stable isotopes of oxygen. The ratio 18O/16O of the watermolecules in water vapor tends to be lower than in the liquid from which it evaporated. That isbecause the water molecules escaping from the liquid and turning into a gas tend to be enriched in16

O (the “light” isotope of oxygen). Similarly, biological processes produce isotope fractionation.

Photosynthesis, for example, produces organic compounds enriched in 12C relative to 13C.
Therefore, the isotopic analysis of sedimentary rocks can yield important clues regarding theoccurrence and nature of biological processes.
④ Biomarkers
Biomarkers are large organic molecules produced by living organisms (e.g. polypeptids,triterpenes, and steranes). Their presence in sedimentary rocks provides a strong evidence forGa stands for Giga Annum which means Billion of Years in Latin.

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biological activity. Moreover, biomarkers may also give an indication on the type of organisms fromwhich they derived. For example, the organic compound called algaenan is exclusively produced
by green algae.
Evidence provided by stable isotopes suggests that biological activity existed as early as 3.8 Ga.
The first morphological evidence comes from the remains of microbial mats (stromatolites)
discovered in Australia in a 3.5 Ga old rock formation (still somewhat controversial though). There
are multiple lines of evidence suggesting a diverse microbial life between 3.4-3.2 Ga.
In conclusion, we can infer from the geological record that life may have formed as early as 3.8 Ga
and was certainly present by 3.4 Ga.

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