Module 5 The History of Life

GIOVANNE G. TAMPOS
BS BIOLOGY PROGRAM
Module No. and Title Module 5 The History of Life
Module Objectives/Outcomes
Lessons in the Module Lesson 1 The Origin and Evolution of Early Life and the Major
Transitions
Lesson 2 Evolution and Development
Lesson 1 The Origin and Evolution of Early Life and the Major
Transmissions
Learning Outcomes a. A Describe the origin and evolution of early life.
b. Discuss the mechanism of major transmission of the
evolution to multicellularity and individuality.
INTRODUCTION
One of the most interesting but difficult to fathom is
to determine how life started on Earth. Many theories
are trying to explain the origin of the first life but only
a few theories. It was even unfathomable to estimate
the creation of the Earth, some have predicted that it
was formed within a thousand years and a million
years. But now because of fossil evidence, it was
estimated to be billions of years, around 4.5 billion
years. To imagine the physical appearance of the
Earth at this point is as hard as identifying the events
that led to the creation of the precursors of life up
until it came to a life that recognizes organisms and
how these early organisms evolved under natural
selection.

Life has the following properties:

1) can attain homeostasis, can adjust the internal
environment to maintain a stable equilibrium;
2) with structural organization, the ability to maintain
distinct parts and the connections between them;
3) metabolism, the control of chemical reactions,
growth, and reproduction; and
4) response to environmental conditions or stimuli.

In general, it is the total chemical phenomenon of a

living organism. It is also common that all life evolved
under the process of natural selection.

In this chapter, we will discuss the origin of life on

Earth (Fig. 1). This includes determining the physical
properties of Earth at the pre-life formation and what
were the events that led to the organization of
chemicals as a precursor of organic compounds. We
Figure 1. Early events in the history of life on will discuss also the nature of how it become
Earth. Dates are in billions of years or gigaannum organized and formed as prokaryotes and how it
(Ga) before the present time. Cited by Bergstrom yielded to become multicellular and eventually
and Dugatkin (2016) adapted from Joyce (2002). formed individuality. These events happened over
some time and they occurred via various major
transitions. These ideas are presented based on fossil evidence which leads to the formulation of
hypotheses and is eventually tested by various experiments.

ABSTRACTION
A. EVIDENCE OF EARLY LIFE
 Fossil evidence provides historical tales of the events in the past geological history of the Earth.
These were commonly found embedded in sedimentary rocks including sandstones, siltstones,
and limestones. Usually, the rocks were formed by the accumulation of particles of sediment
with the skeletal remains of organisms. In this manner, past activities of life about 3.5 billion
years ago were at least determined.
Some areas that held most fossils with
exceptionally well-preserved soft
tissues called “Lagersta¨tten” were
excavated in Burgess Shale in the
Canadian Rockies, fossils that showed
the community during the Middle
Cambrian period; the Messel Oil Shale
in Frankfurt, Germany which
preserves animals and plants from an
Eocene lake including the numerous
fish, birds, mammals; the Hunsruck
Slate in Germany showing the trilobite
limbs and other soft parts in the
Devonian period; and some localities
in China with feathered dinosaurs and
early flowering plants of Cretaceous
Period. In the Agnes gold mine in
South Africa, remarkable microfossils
Figure 2. Microfossils of organisms from 3.2 billion years 3.2 billion years old were discovered
ago. (A, B) Examples of microfossils from the approximately by Emmanuelle Javaux (Fig. 2).
3.2-billion-year-old sample from South Africa. Detailed analysis of microfossils
revealed that microorganisms possessed a cell-wall-like structure at this point.

Even if there were already much meaningful fossil evidence recorded to approximately estimate
the origin of life, information is still limited to making a concrete phylogenetic reconstruction. It
is unknown until now the organisms at the base of the tree of life- this is referred to as the Last
Universal Common Ancestor (LUCA). This is the starting point where different life forms
emerged. LUCA is not a single organism but a population of organisms.

B. HYPOTHESES AND THEORIES OF THE ORIGIN OF LIFE

There have been several proposed ideas on the physical properties of the Earth which becomes
the precursor leading to the steps in the formation of life. Desmond Bernal and Graham Cairns-
Smith have thought that clay adsorbed organic compounds led to genetic takeover. Gunther
Wächtershäuser proposed the Iron-Sulfur World where life could begin in a special mineral
surface known as pyrite, a crystalline mineral of iron sulfide. He explained that chemical
reactions that occurred on the flat surface of the minerals have resulted in metabolism. After the
initiation of metabolic processes, the reaction pathways are then encapsulated by a membrane
similar to cellular life forms. Jeffrey Bada and Stanley Miller also proposed that chemical
reactions necessary for life to proceed were initiated upon the melting of organic compounds
within the ice sheet.

However, all these proposed ideas are based on the initiation of simple compounds. Cellular
formation deals with complex interacting polymer molecules encapsulated by a membranous
material. None of the ideas above completely adhere to the complex process.

One hypothesis that details the simple reaction to complex processes that might have resulted in
the formation of life is the prebiotic soup hypothesis for the origin of life. In this hypothesis, a
prebiotic soup is a pool of organic molecules suspended in water before life arose. These organic
molecules become diverse because of the matter from extraterrestrial objects such as carbon-
rich meteorites and comets which are known to carry amino acids, purines, and pyrimidines.
Through the process of abiogenesis—the chemical formation of life from nonliving material—the
earliest life forms that emerged from the such prebiotic soup may even have used various parts
of this soup as a source of energy and nutrients. Extra-terrestrial objects also carry amphiphilic
molecules (molecules with both hydrophilic and hydrophobic ends) that can self-assemble into
vesicles—small, fluid-filled spaces enclosed by a lipid membrane.

Complex molecules may have risen from deep in the ocean also. Hydrothermal vents on the
ocean floor leaked sulfide-rich compounds from giant “black smokers” rising as high as 20
meters above their bases. These sulfide-rich compounds
interacting with iron-rich waters on the ocean floor under
high pressure and temperature would lead to the
production of compounds that may have played a role in
the early formation of life.

Aleksandr Oparin and J. B. S. Haldane in the 1920s

hypothesized the emergence of the earliest life forms from
the prebiotic soup. In the 1950s, Stanley Miller and Harold
Urey experimented to validate the hypothesis of Oparin
and Haldane by simulating the prebiotic soup in a
laboratory. They added common amino acids like glycine,
alanine, and valine into the interaction of methane (CH4),
hydrogen (H2), ammonia (NH3), and water (H2O) with an
energy source, an electric current. The experiment
produced the building blocks of life which are complex
molecules. But how do these organic molecules assemble
into complex structures: lipid membranes, nucleotide
chains, and proteins? The assembly of these structures
Figure 3. Miller and Urey experiment.
might occur on surfaces. The microscopic spaces between
clay layers may concentrate the reagents and binding to
the clay surface may align molecules so that they readily polymerize. A similar process may
happen when a solution freezes: Complex molecules such as nucleotides can be concentrated in
the spaces between growing ice crystals, facilitating reactions involving these reagents. In this
case complex organic molecules self-assembled into the replicating vesicles that would evolve to
become protocells.

Figure 4. Early stages in the origin of

life. To understand how life evolved,
we need to know how small inorganic
molecules gave rise to the organic
compounds critical to life; how the
organic compounds were assembled
into structures such as vesicles, RNA,
and peptides; and how these
structures came together to form
early protocells. Adapted from
iBiology.org cited by Bergstrom and
Dugatkin (2016).

In 1986, Walter Gilbert hypothesized that complex molecules of life-based forms, RNA, can be
produced in a prebiotic soup environment. He referred to this time as RNA World. These RNAs
were found to self-replicate based on laboratory experiments and variations could occur on self-
replicating ribozymes or the RNA. The RNA serves as catalysts (enzymes) in the reactions and
carries genetic material. In this manner, natural selection is already achieved, replication as a
form of reproduction and the transmission of heredity through the observed replications of
various mutations under laboratory conditions.

C. The Evolution of Protocells

Protocells are simple cell-like entities that predated cellular life forms in the history of life. They
are formed from the aggregation of abiotic (non-living) components abundantly present on the
early earth. They display certain characteristics similar to living cells which are self-organized,
endogenously ordered, and are a spherical collection of lipids. How did this self-organized
structure evolve which eventually contain not just lipids but also RNAs?

Organic molecules aggregates (prebiotic-

soup hypothesis) form fatty acid vesicles,
RNAs, and peptides accordingly on solid
surfaces and at the deep of the ocean
due to hydrothermal vents. This evolves
and units eventually become protocells.
Modern cells have complex structures of
phospholipid bilayers embedded with
numerous transmembrane proteins that
ferry molecules from one side to the
other and transduce signals across the
membrane. Early membranes on the
other hand have been assembled from
simple organic molecules in the
environment, and thus have a simpler structure. It is composed of molecules that spontaneously
self-assemble into lipid bilayers and form enclosed vesicles. In the presence of micelles—small
spherical assemblages of fatty acid molecules with hydrophobic tails inside and hydrophilic
heads outside—these vesicles can grow as they incorporate the micelles into their walls. With
further growth, the vesicle would take on the form of a thin, elongated strand. Strands of this
sort are fragile and can be broken up even by gentle motion, forming a set of new “daughter”
vesicles. Additionally, the presence of phospholipids in the walls or membrane slowed down the
moving out of fatty acids from the vesicle’s bilipid layer. Because this is advantageous in terms of
the growth of the cell, selection favors vesicles that contain the acyltransferase machinery to
synthesize phospholipids. Eventually, membranes would be dominated by phospholipids—and
selection would favor the evolution of transport structures to move metabolites across the
membrane. The protocells most likely lead to the first prokaryotic cells.

The evolution of encapsulated cells from pools of replicating biotic molecules was developed due
to mutualistic interaction or mutualism. Two or more molecular substrates each contribute
in a positive way to the replication of the others referred to as molecular mutualism. Molecular
mutualisms may have been important among replicators—entities that can replicate themselves.
 D. FROM RNA TO DNA
DNA and RNA encode the information used to make proteins, but the enzymatic activity of
proteins is necessary to replicate DNA and transcribe it into RNA. Proteins are needed to make
nucleic acids likewise; nucleic acids are needed to make proteins. But which comes first? It was
proposed that RNA played both roles: information carrier and enzymatic molecule. It was
supported by in1980s research led by Thomas Cech and Sidney Altman which discovered that
enzymes need not be proteins. RNA can act as an enzyme called ribozyme. These are
documented in small virus-like particles known as viroids code for one class of ribozymes, which
cause damage to commercial plants such as chrysanthemums.

RNA world was coined by Walter Gilbert to capture the idea that early life—from about 4 billion
to 3.5 billion years ago—may have been RNA-based. Evidence are supporting the hypothesis like
many present-day protein-based enzymes have cofactors—nonprotein components needed for
enzymatic function—that are RNA nucleotides or based on such nucleotides. Eventually, DNA
evolved as a replacement for an earlier system in which RNA was the informational molecule.
RNA forms an efficient transmission system and is favored under natural selection in early life.
But DNA evolved because it is more chemically stable than RNA, primarily because DNA’s
deoxyribose sugar is less reactive than RNA’s ribose. The structure of DNA also reduces the
potential for outside molecules to interact and disrupt the nitrogenous bases that encode
sequence information. It also acts as genetic storage system. DNA replication systems also have
“proofreading” capabilities or repair mechanisms that are not present in RNA replication. So if
there are errors in one strand of the helix structure, the other complementary strand can be
used by the cell to correct the error. And because of the selective advantage of DNA from RNA,
evolutionary biologists were thinking what are the possibilities that lead to the development and
selection of DNA. Although much work still needed to be undertaken, some experts
hypothesized that the formaldehyde (CH2O) that Earth generally produced at that time had a
role in the formation of DNA. In an experiment, Michael Robertson and Stanley Miller mixed
formaldehyde with the RNA nucleotide uracil. The resulting chemical reactions provided an
indirect link between the RNA world and the proteins that are so critical in DNA-based genetic
transmission.

E. EVOLUTION OF SINGLE-CELLED ORGANISMS

It is difficult to reconstruct a phylogenetic history up until the LUCA. But based on the fossil
evidence and the many ideas relating to the appearance of RNA and the evolution and selection
of DNA, it is interesting to make inferences and generate hypotheses about how the first cells
have arisen and their structural forms.

Before the details of knowing the evolution of single cells, first, let’s review the basic types of
cells. Prokaryotic cells are structurally simpler and evolved much earlier than eukaryotic cells.
Typically, the cell lacks membrane-bound organelles, and their DNA is not contained in a nucleus.

Figure 5. Tree of Life

It is ancient, having originated on the order of 3 billion years ago. Eukaryotic cells have
membrane-bound organelles and a distinct nucleus containing DNA.

Prokaryotic cells may have evolved from simpler RNA-based life forms. Mutualistic interaction at
the molecular level is thought to be important in this evolution. This type of evolution from RNA-
based life forms known as replicators (entities that can replicate themselves) was suggested to
form following the hypercycles model. The model was proposed in 1977 by Manfred Eigen and
Peter Schuster. The model generally suggests that replicators (RNA-based) were dependently
replicating with other close replicators. This type of relationship is also known as molecular
mutualism, the replicators affect each other’s reproduction positively. Over time, the replicators
will be encased in a membrane made of fatty acids. These membrane-encased replicators are
known as protocells. In this manner, natural selection operates and favored the mutualistic
relationship of replicators and also encapsulation. Eventually, these protocells replicate similarly
to their replicators. The replication, a cellular reproduction, is eventually favored by natural
selection because of the physical properties of the Earth at this time.

F. MAJOR TRANSMISSIONS

Several major occurrences in the history of life led to the eventual evolution of organisms. As
summarized by John Maynard Smith and Eors Szathmary, the following are the major events of
life on Earth:

➢ The origin of self-replicating molecules capable of heredity.

➢ The transition from RNA as both catalyst and genetic material to a division of labor with
protein as catalyst and DNA as genetic material.
➢ The origin of the first cells.
➢ The emergence of eukaryotic cells.
➢ The evolution of sexual reproduction.
➢ The evolution of multicellular organisms from single-celled ancestors.
➢ The evolution of developmental complexity within multicellular organisms.
➢ The evolution of individuality, including the evolution of germ cells, a specialized line of
cells that became gametes.
➢ The evolution of groups, including complex societies.
➢ The evolution of eusocial societies, like those seen in some species of bees, ants, and
wasps, with a division of labor and sterile workers.

The major transitions above cover some processes if not most of them according to Smith
Szathmary. These processes are :
a) Individuals give up the ability to reproduce independently, and they join together to form
a larger grouping that shares reproduction;
b) Once individuals aggregate into higher-level groupings, they can take advantage of
economies of scale and efficiencies of specialization. An economy of scale arises when a
group can perform a task more efficiently than a single individual or when a group can do
things that a lone individual cannot do at all. For example, groups of social insects such as
 ants and bees can acquire food in ways that individuals working alone cannot. Efficiencies
of specialization arise because once groups are collectively engaged in a task, they can
benefit not only from larger numbers but also from a division of labor, allowing different
individuals to specialize in different tasks.
c) Aggregation and specialization facilitate changes in information technologies. Organisms
develop new and increasingly efficient ways to acquire, process, transmit, and store
information. If you would recall from the above topic, replicators are aggregating after
dependently replicating from one another and eventually forming groups to seemingly
become higher-level. At this point, individual replicators give up their ability and
properties to share properties with the group. The higher-level individuals get “locked-in”
and cannot easily revert to their previous states.

G. MAJOR TRANSITION: THE EVOLUTION OF THE EUKARYOTIC CELL

Figure 6. Endosymbiosis and the evolution of mitochondria and plastids.

Eukaryotic cells evolved between 1 and 2 billion years after prokaryotes. There are six major
groups of eukaryotes now recognized by evolutionary biologists. The RNA, enzymes, and
ribosome analysis showed a strong phylogenetic link between prokaryotic and eukaryotic cells.
Some suggested that eukaryotic cells shared a common ancestor with species in the prokaryotic
domain Archaea while others suggested another prokaryotic domain, Bacteria (Eubacteria). But
phylogenetic analyses indicate that eukaryotic “informational” genes—genes associated with
transcription and translation—are most closely related to archaeal genes, whereas “operational”
genes are associated with metabolic processes, cell membrane formation, and amino acid
production are most closely related to bacterial genes. Another working hypothesis on the
analysis of the ancient eukaryotes reveals that it emerged from the fusion of an archaeal cell
probably under phylum Eocyta and a bacterium. The evolution of eukaryotes is probably a
product of endosymbiosis of archaeal and bacterial cells.

In 1970, Lynn Margulis proposed the endosymbiotic theory to explain the origin and evolution of
two eukaryotic organelles: the mitochondria and chloroplasts. Margulis argued that bacterial
species capable of energy production and photosynthesis began to reside within early eukaryotic
cells forming endosymbiosis. Bacterial species such as endosymbionts provided the most critical
resources such as energy and food and which in return are protected from various dangers in the
environment. Over time, a facultative symbiotic relationship became an obligate relationship
wherein one can no longer survive without the other. Margulis’s endosymbiosis hypothesis was
further supported by the phylogenetic analysis of the chloroplast and mitochondria. It reveals
that chloroplast’s RNA is closely related to cyanobacteria and mitochondrial genes of eukaryotes
are closely related to proteobacteria.

H. MAJOR TRANSITION: THE EVOLUTION TO MULTICELLULARITY

Our previous topic focuses on the evolution of single-celled organisms. Now let us understand
also how multicelled organisms are formed. We might think that multicellularity is an obligate
condition but in the early evolution of multicellularity, cells joined together may still be
disbanded. Early multicellularity is temporary rather than a fixed condition. Single-celled
organisms evolved to form multicellular and are eventually favored under natural selection
because of the advantages they can provide to the organism.

Let us take a look at how slime molds

Dictyostelium discoideum use
multicellularity to its advantage.
Slug—composed of cells of slime
molds that were completely
independent before its formation—
responds to environmental cues
before they aggregate. The cells are
communicating in the environment
via a chemical called cAMP (cyclic
adenosine monophosphate). At the
point of the densest section of cells in
the soil, cAMP is released, and this
signals cells “downstream” at the
point from which the cAMP was
emitted. Individual cells arrive at the
point and adhere to form
multicellular slugs. The signaling
system allows the slug to orient to
ambient environmental cues such as
light, temperature, ammonia, and
oxygen gradients that it uses to move
up toward the surface of the soil,
where reproduction will occur. The
benefits of multicellularity in slugs are
not limited to orienting to stimuli and
migrating to the surface for
reproduction. The slug is also able to
form a slime “sheath” around itself
that helps protect it from nematode
predators. By aggregating to form a
slug and coordinating their behaviors,
Figure 7. Slug forming a slime. the slime mold cells were able to
benefit from an economy of scale, the
ability to move more efficiently in a large, coordinated group. It also provided an advantage
during reproduction. When a slug reaches the soil surface, it forms into two-part, a fruiting body
which is a stalk (non-reproductive cells), and spores (reproductive cells). The fruiting bodies
elevate and raise the spores, an advantageous behavior of increasing the chances of dispersal of
the spores. However, the division of labor as to what cells become the fruiting body and the
spores is still a mystery. So far the idea was, cells that are rich in resources generally become
spore cells, and those that are less well-nourished become stalk cells.

I. MAJOR TRANSITION: THE EVOLUTION OF INDIVIDUALITY

As I have said, the early evolution of multicellular
organisms is not obligate. So how does
individuality was achieved in evolution?
Individuals as defined as “integrated and
indivisible wholes” that can reproduce and pass
on to their offspring heritable variations. Natural
selection facilitates transitions from one level of
individuality to another, by the same sort of
gradual process with incremental improvements
that Darwin proposed for the evolution of other
complex traits. This transition involves one critical
component of the transfer of
fitness from lower to higher levels of the
organization, the differentiation of cell lines into
those specialized in reproduction (germ cells),
and those specialized in maintenance and growth
of the organism (somatic cells, or soma).

Let us take a look at the evolution of volvocine algae. It evolved into multicellular about 230
million years ago into the evolution of individuality. One of the species of this algae, the Volvox
carteri, its individual is typically made up of about 2000 small somatic cells and as many as 16
large reproductive cells. Each somatic cell has two flagella, which are long, hair-like projections
from a cell that produces the motion, necessary to get nutrients. The fate of a cell—large germ
or small soma cell—is determined by the expression of a gene known as regA. When this gene is
expressed, it suppresses several nuclear genes that code for chloroplast proteins. Since
cell growth is dependent on these chloroplast proteins, and cell division depends on cells
reaching a critical size, cells in which regA is expressed remain small and produce flagella,
becoming the soma cells. If cells are above a critical size, regA is not expressed, and these cells
photosynthesize, grow larger, and lose the ability to produce flagella. These larger cells go on to
form the germ line.

J. MAJOR TRANSITION: SOLITARY TO GROUP LIVING

Living in groups requires a degree of sociality that is not required for solitary living, and this also
often entails new levels of coordination and communication between individuals to obtain such
benefits. Living in a group provides several advantages: foraging-related benefits of living in
groups (economies of scale) and increase protection from predators. Group living typically
imposes costs in addition to providing benefits also. One disadvantage is parasite transmission.

The evolution follows the economies of scale, an evolution that provides advantages to the
survival or natural selection of the organisms.
Application

1. Describe the early conditions of the earth before the start of life.
2. Describe how organic molecules aggregate to form protocells.
3. Discuss the transition from prokaryotes to eukaryotic cells.

Rubric for Scoring

Scoring 8 - 10 pts 5 - 7 pts 2 - 4 pts

clear presentation of ideas but
1. Clarity (10 Very clear with few vague/confusing
pts) presentation of ideas statements Vague; confusing
Place your score
in the box.
Writing is very clear;
strong evidence is Writing is somewhat clear;
presented; extensive some evidence is presented;
2. Voice (10 knowledge of the topic knowledge of the topic is
pts) is evident evident Writing is unclear
Place your score
in the box.
3. highly disorganized;
Organization Thoughts/ideas flow thoughts/ideas do not flow repetitive information
(10 pts) smoothly smoothly presentation
Place your score
in the box.
Using vivid words and
phrases; the choice Communicate clearly but Limited vocabulary;
4. Word and placement of writing lacks variety; choice jargon and cliché’ are
choice words are accurate, and placement of words are present and detract
(10pts) natural, and not forced inaccurate and overdone from the meaning.
Place your score
in the box.
Sentences sound
Sentences are well awkward, distractingly
5. Sentence constructed and have Most sentences are well repetitive; difficult to
structure and varied structure and constructed and have varied understand, make
grammar (10 length; no errors in structures; make few errors in numerous errors in
pts) grammar, and spelling grammar and spelling. grammar and spelling
Place your score
in the box.

Sources:
Bergstrom, C. and L.A. Dugatkin (2016). Evolution, 1st edition, W. W. Norton & Company, United
States of America.
Jonathan B. Losos (2014). The Princeton guide to evolution, Princeton University Press, United
States of America.