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Evolution and Origin

of Cells
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Evolution and Origin
of Cells
A. Malcolm Campbell, PhD

Christopher J. Paradise, PhD
Evolution and Origin of Cells

Copyright © A. Malcolm Campbell and Christopher J. Paradise. 2016.
All rights reserved. No part of this publication may be reproduced, stored

in a retrieval system, or transmitted in any form or by any means—
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brief quotations, not to exceed 250 words, without the prior permission
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Abstract
It is easy to understand how cells are produced from preexisting cells. And
it is possible to imagine how space dust condensed to form inanimate
planets. But what stumps most people is how inanimate matter suddenly
formed the first living cell. This problem has vexed scientists and philoso-
phers over the millennia, but recent research has cracked open this black
box that is the origin of life. After formally defining evolution, this book
presents the modern classic experiments that show how abiotic molecules
can be formed from inorganic starting materials. Once biologically im-
portant molecules such as lipids and RNA were formed, they could self-
assemble into complex shapes that exhibit life-like traits such as growth,
reproduction, competition and energy storage. Biologists have produced
all these behaviors in non-living vesicles to the point it becomes difficult
to distinguish when to know if an object is living or not. In addition, this
book addresses the important question of how religion and science can
coexist without one threatening the other.
Keywords
evolution, theory, natural selection, selective advantage, genetic drift,
gene flow, emergent property, faith, science, proteins, nucleic acid, car-
bohydrates, lipids, hydrophilic, hydrophobic, cell theory, amphiphilic,
vesicles, RNA-world hypothesis, ribozymes, mRNA, directed evolution,
micelles
Contents
Preface...................................................................................................ix
Acknowledgments....................................................................................xi
Introduction.........................................................................................xiii
Chapter 1 Defining Evolution............................................................1
Ethical, Legal, Social Implications: Evolution
and Religion are Compatible..........................................5
Chapter 2 Abiotic Processes Can Generate Biologically
Important Molecules..........................................................9
Self-Organizing and Replicating Molecules......................15
Chapter 3 Non-Living Vesicles Can Compete and Grow..................23
Self-Organizing Vesicles...................................................23
Abiotic Vesicle Growth and Reproduction........................25
Chapter 4 Non-Living Vesicles Can Harvest and Store Energy.........33
Conclusion............................................................................................37
Glossary................................................................................................39
Index....................................................................................................41
Preface
This book covers the evolutionary origin of life and is part of a thirty book
series that collectively surveys all of the major themes in biology. Rather
than just present information as a collection of facts, the reader is treated
more like a scientist, which means the data behind the major themes are
presented. Reading any of the thirty books by Campbell and Paradise
provides readers with biological context and comprehensive perspective
so that readers can learn important information from a single book with
the potential to see how the major themes span all size scales: molecular,
cellular, organismal, population and ecologic systems. The major themes
of biology encapsulate the entire discipline: information, evolution, cells,
homeostasis and emergent properties.
In the twentieth century, biology was taught with a heavy emphasis
on long lists of terms and many specific details. All of these details were
presented in a way that obscured a more comprehensive understanding.
In this book, readers will discover compelling evidence that illuminates
how abiotic molecules, their chemical properties and natural selection
could have led to the natural production of the first cell on Earth. With
this information, readers will also see for themselves some of the support-
ing evidence behind our understanding of these important topics. The
historic and more recent experiments and data will be explored. Instead of
believing or simply accepting information, readers of this book will learn
about the evolution of life the same way professional scientists do–with
experimentation and data analysis. In short, data are put back into the
teaching of biological sciences.
Readers of this book who wish to see the textbook version of this
content can go to www.bio.davidson.edu/icb where they will find
pedagogically-designed and interactive Integrating Concepts in Biology
for introductory biology college courses or a high school AP Biology
course.
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Acknowledgments
Publishing this book would not have been possible without the generous
gift of Dr. David Botstein who shared some of his Breakthrough Prize
with AMC. David’s gift allowed us to hire talented artists (Tom Webster
and his staff at Lineworks, Inc.) and copyeditor Laura Loveall. Thanks go
to Kristen Mandava for project management and guidance on the pub-
lishing process. In particular, we are indebted to Katie Noble and Melissa
Hayban for their many hours of help and attention to detail.
Kristen Eshleman, Paul Brantley, Bill Hatfield and Olivia Booker
helped us with technology at Davidson College. We are grateful to ad-
ministrators Tom Ross, Clark Ross, Carol Quillen, Wendy Raymond,
Verna Case, and Barbara Lom who had confidence in us and encouraged
us to persist despite setbacks along the way.
These books were the product of the shared labor of my two vision-
ary coauthors Laurie Heyer and Chris Paradise. We shared the dream
and the hardships and developed this book from scratch. My family has
been very supportive and I thank Susan, Celeste and Paulina for their
support and patience. I also want to thank Jan Serie, my pedagogical
mentor, who taught me so much about the art and science of helping
students learn. I benefited from the support of the Howard Hughes
Medical Institute grant 52006292, the James G. Martin Genomics
Program, and Davidson College. This book would not have survived
its first draft without my students who endured the typos and the early
versions of this book. These undergraduates participated in a bold ex-
periment to see if beginners could construct their own knowledge, retain
what they learned, and transform the way they see themselves and the
discipline of biology. While many people said that beginning students
were not up to the task, my students proved them wrong.
Introduction
A vexing problem in biology is trying to use evidence to understand how
life first began. Today, all organisms come from preexisting organisms
so it is difficult to imagine how the first living cells came into existence.
How could abiotic (non-living) molecules coalesce to form a living
(biotic) cell? Just because it is hard to imagine, however, does not mean
this problem is beyond scientific investigation. A growing number of
scientists (biologists, chemists, biochemists, and biophysicists) have de-
signed very clever experiments to improve our understanding about the
origin of life. This book focuses on the molecular aspects of evolution
with special attention to the formation of complex living cells from sim-
pler abiotic components. After clearly defining evolution, the reader will
examine data that revealed how non-living chemicals can exhibit traits
resembling simple cells. The four chapters of this book divide the research
into discrete topics, but remember that the chapters are not intended
to represent a historical account of what happened. These four chapters
present what might have happened and more importantly, they provide
experimental evidence that the origin of life from abiotic processes is not
as difficult to imagine as it used to be.
CHAPTER 1
Defining Evolution
Although evolution began as a biological term, it has spread to many

areas of society. Most people have a general sense what the term means,
such as change over time, or survival of the fittest. However, the formal
definition of evolution is the change in allele frequency in a population
over time. Evolution is often referred to as a theory but the term theory
has two different meanings. The more casual use of theory is defined as a
guess, which is similar to a hypothesis; “I have a theory to explain why we
have not heard from Martians yet.” The scientific use of theory is defined
as a widely accepted concept that has been demonstrated many, many
times. For example, the theory of evolution has been supported by over
1,000,000 scholarly papers. Because of the dual use of the word theory,
many scientists now refer to the principle of evolution to help nonscien-
tists understand the widespread degree of confidence in evolution as the
only scientific explanation for the diversity of life.
Charles Darwin is often credited with the discovery of the primary
mechanism of evolution, natural selection (Figure 1), but the concept
of biological change over time had been around for a while. Darwin’s fa-
mous 1859 publication, On the Origin of Species, spelled out the essential
elements of evolution by natural selection as we understand it today.
To understand natural selection, it is important to know its five basic
tenets, which are evident in nature (Figure 1):
1. Overproduction: Each generation of an organism produces more

offspring than nature can support.
2. Variation: With each new generation, individuals have slight dif-
ferences in characteristics, which means they have slightly different
abilities.
2 EVOLUTION AND ORIGIN OF CELLS
sunlight
shade
from tree
A B C
Figure 1 Example of natural selection. A, Overproduction of a variety

of acorns leads to competition for the limited resource of light. B,
Faster germinating acorns grow first and shade out their competition.
C, Those with the selective advantage survive, reproduce, and
propagate the trait of fast germination in the next generation.
Source: Original art.
3. Competition: Overproduction of offspring results in competition

for limited resources, such as water, food, and shelter.
4. Selective advantage: Variation results in some individuals who have
an advantage over others, depending on the circumstances. Varia-
tions in strength, acquiring energy, stress resistance, and so on al-
lows a subset of individuals to out-compete others for the limited
resources. Those with the advantage continue living.
5. Reproduction: Those who survive the competition are able to repro-
duce and pass on to the next generation the genetic information that
enabled them to out-compete others. The next generation exhibits
additional variation based on the successful trait that they inherited
from their parents.
The five basic tenets of natural selection are all around—literally. Let’s
use grade point average (GPA) as an analogy for selective advantage. There
are many students in any given class—more students than the teacher
expects will earn a letter grade of A (overproduction). Each class is filled
with students of different types of intelligence and work ethic (variation).
Students who exhibit the most of these two traits earn the top GPA (com-
petition). Some students are super smart but uninterested; others work
hard but are not as smart. The best grades are earned by students who
have the right combination of work ethic and intelligence (selective ad-
vantage). At this point, the analogy of grades and natural selection weak-
ens but is still instructive. Students who earn the top grades can expect to
Defining Evolution 3
A evolution
B natural selection
C mutation
D gene flow
E genetic drift
Figure 2 Evolution and the four mechanisms of evolution. A,

Depiction of evolution where circles represent individuals in a
population with different alleles (gray shading). The frequency of
alleles changes over time. B, Natural selection favors circles that are
allowed to reproduce. C, Mutation is the appearance of a new allele
through DNA change. D, Gene flow is the arrival of a new allele from
a different population. E, Genetic drift is the arbitrary loss of an allele
through a process not related to natural selection.
be promoted to the next level and maybe even earn scholarships so that
they can become teachers. Becoming a teacher is not exactly analogous to
reproduction, but transmitting information and study habits to the next
generation is adequate for our purposes.
When the allele frequency of a population changes over time, evolu-
tion has occurred. Biologists have defined four distinct mechanisms that
cause evolution (Figure 2). Natural selection has been presented already,
but the other three mechanisms may be less familiar. Mutation can hap-
pen with erroneous replication of DNA by DNA polymerase. Gene flow
changes allele frequency when an individual from one population trans-
mits a new allele to one or more individuals in another population.
Genetic drift is different from natural selection because the loss of an
allele is due to random events, such as a large explosion that kills every-
thing within a given radius. Loss of an allele from a population through
genetic drift is more likely to occur for rare alleles or small populations.
Evolution helps us understand life as it exists today and continues to
change over time. We can look back into history to see earlier steps of
evolution, but don’t be fooled into thinking that evolution has an end
goal to accomplish. Evolution is shaped by random mutations—some of
which are beneficial. It is a common misconception that humans are the
pinnacle of evolution, but let’s consider a different world. Imagine that
200 years from now Earth has no oxygen, with only CO2 and nitrogen in
our atmosphere. Under these oxygen-deficient conditions, humans and
all other animals would go extinct. Microbes that can live in the absence
of oxygen would be rulers of the planet. Because environments change all
the time, a selective advantage today may not be beneficial tomorrow. It
is best to avoid the common misconception that adaptive evolution is a
series of steps toward an endpoint or goal. Instead, it is better to think of
natural selection as ongoing optimization for changing conditions. Adap-
tive evolution proceeds because of the process illustrated in the five basic
tenets as shown in Figure 1, in combination with the four mechanisms
illustrated in Figure 2.
In 1973, geneticist Theodosius Dobzhansky famously stated, “Noth-
ing in biology makes sense except in the light of evolution.” Dobzhansky
meant that the existence of viruses, the size of redwood trees, and the
smell of a skunk seem illogical unless they are seen through the lens of
natural selection. The world today makes sense with respect to natural
selection, but it is hard to imagine what Earth looked like before any
life had evolved. It has been difficult to collect experimental evidence
about the origin of life that took place approximately 3.5 billion years
ago. Of course, we cannot conduct traditional controlled experiments;
it is impossible to find a second planet Earth where we can manipulate
this second Earth to produce new life forms. However, the lack of a spare
Earth as an experimental system has not prevented some very clever inves-
tigators from conducting research on how life may have evolved.
Because biology is the study of life, it seems logical that biologists
should begin by defining the word life. Although life is a difficult term to
define, it satisfies three fundamental properties: life replicates itself; life
undergoes changes; and life occupies three-dimensional space big enough
to contain cargo. However, life is an emergent property that occurs
when certain molecules come together in very specific ways. Emergent
properties occur only when constituent parts are assembled appropri-
ately. A cell phone has many amazing properties, but its isolated parts of
individual electrons, plastic, and silicon wafers are not functional on their
own and lack valuable emergent properties. Like a cell phone, life is more
than the sum of its individual parts.
Ethical, Legal, Social Implications: Evolution and

Religion are Compatible
On October 18, 2004, the school board in Dover, Pennsylvania, voted
6 to 3 in favor of teaching intelligent design (ID) as an alternative to
evolution. Two months later, eleven parents whose children were affected
by the new education policy filed a lawsuit (Kitzmiller vs. Dover Area
School District) to prevent the teaching of religion as science. Five days
before Christmas in 2005, Judge John E. Jones III ruled in favor of the
parents and against the Dover School Board. In his ruling, Jones wrote a
139 page opinion explaining why ID cannot be used for science educa-
tion. He wrote, “The overwhelming evidence at trial established that ID
is a religious view, a mere re-labeling of creationism, and not a scientific
theory.” Jones continued by stating, “ID violates the centuries-old ground
rules of science by invoking and permitting supernatural causation. . . .”
When Darwin published his explanation of evolution, he experienced
a very negative response from society, because he challenged a widely held
religious belief of the late 1800s—life on Earth had not changed since di-
vine creation. Darwin’s science-based proposal of evolution explained the
natural world based on data. A popular political cartoon showed Darwin’s
head on a monkey because people misinterpreted “descent with modifica-
tion” to mean that we were direct descendants of monkeys. The essential
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problem was people felt like they were being forced to choose either reli-
gion or science. However, this choice was a false dichotomy. People may
choose to believe in the God of their religion and still accept the principle
of evolution. Religion and science are two different ways of trying to un-
derstand the world, but they cannot explain the same concepts.
Any time there is a misunderstanding, it usually begins with a break-
down in communication. To help clarify, let’s define some key terms.
According to Webster’s online dictionary, religion is “1) the service and
worship of God or the supernatural; 2) a cause, principle, or system of
beliefs held to with ardor and faith.” Faith is “complete trust” or a “firm
belief in something for which there is no proof.” Notice that religion and
faith do not require evidence. Instead, they are based on explanations
outside nature for ideas that cannot be experimentally demonstrated. We
cannot conduct experiments to demonstrate the existence of God or the
absence of God. People of faith have complete trust in something that is
beyond earthly matters.
Faith and religion stand in stark contrast with science, which is,
“knowledge or a system of knowledge. . . concerned with the physical
world and its phenomena. . . covering general truths or the operation of
general laws especially as obtained and tested through scientific method.”
The scientific method is based on personal observation, experimentation,
hypothesis testing, collecting and analyzing data, and reproducibility of
observations. Notice that terms, such as belief or faith, are not used
to describe science. That’s why it is inappropriate to ask someone, “Do
you believe in evolution?” Evolution is a scientific concept, and there-
fore it is not a matter of faith or religion. Belief is the wrong term
to describe evolution. Instead, it would be more appropriate to ask if
someone accepts evolution based on the available data. Scientists can
reject scientific conclusions and offer alternative explanations based on
different interpretations of the same data. Competing scientific ideas
must be founded on data, not faith, and must be testable without hav-
ing to invoke the supernatural. It is unscientific to say “I do not believe
in your scientific conclusion.” Not believing in evolution means the
person is refusing to consider the natural world in a scientific manner.
However, if one disgrees with the principle of evolution, then we can
discuss the evidence based on facts rather than faith.
Many famous biologists are deeply religious, though most of them

prefer to keep their religious convictions private. Biologists who are reli-
gious have no problem accepting evolution for the earthly explanations
and believing in God to explain their spiritual world and moral values.
Dr. Francis Collins, director of the National Institutes of Health (NIH)
in Washington, DC and a devout Christian, wrote a book to explain
how religion and science are not mutually exclusive for him and other
scientists, though the two fields are mutually exclusive in how they un-
derstand the world. He wrote, “Science is not threatened by God; it is
enhanced,” and “God is most certainly not threatened by science.” In
an interview, Collins elaborated by saying, “Don’t misunderstand me, it
is clear that the process of evolution by natural selection over hundreds
of millions of years is the ‘how’ that explains the marvelous diversity of
life. But that doesn’t provide the answer to ‘why.’ I think God provides
that answer.”
Parents in the Dover Area School District asked the US District
Court for the Middle District of Pennsylvania, to determine if ID was
religion or science. Judge Jones wrote, “We conclude that the reli-
gious nature of ID would be readily apparent to an objective observer,
adult or child.” Jones understood the significance of his opinion and
continued, “ID’s backers have sought to avoid the scientific scrutiny
which we have now determined that it cannot withstand by advocat-
ing that the controversy, but not ID itself, should be taught in science
class. . . . The goal of ID is not to encourage critical thought, but to
foment a revolution which would supplant evolutionary theory with
ID.” Note that Judge Jones is a self-described conservative Christian
and a George W. Bush appointee who was not trying to promote a
liberal agenda. Jones was basing his ruling on fact and a clear defini-
tion of science. The Judge did not rule on whether ID was correct or
not, because its validity was not on trial. What was being judged was
whether the religious belief in ID could be taught in a science class at
an equivalent level with the scientific principle of evolution. Jones em-
phatically ruled that science and religion are distinct, and faith cannot
be employed to formulate scientific conclusions. Therefore, this book
addresses how life evolved but do not consider the data to be a chal-
lenge to anyone’s personal beliefs or religion. Science, by definition,
cannot disprove anyone’s faith. Religion will always be distinct from

science and vice versa. The US government determined science and
religion are separate and should not be confused or substituted for one
another in a science class.
Bibliography
Collins FS. The language of God: a scientist presents evidence for belief.
New York, 2007, Free Press.
Darwin C. On the origin of species, Darwin Online (website): http://
darwin-online.org.uk/converted/pdf/1860_Origin_F376.pdf. Accessed
November 20, 2007.
Fisk MR, Giovannoni SJ, Thorseth IH. Alteration of oceanic volcanic
glass: textural evidence of microbial activity. Science 281(5379):
978–980, 1998.
Jones III, JE. Opinion from Tammy Kitzmiller, et al. (Plaintiffs) v. Dover
Area School District, et al. (Defendants). Case No. 04cv2688. US
District Court for the Middle District of Pennsylvania. December 20,
2005.
Murtas G. Question 7: construction of a semi-synthetic minimal cell: a
model for early living cells. Orig Life Evol Biosph 37(4–5):419–422,
2007.
Orgel LE. The implausibility of metabolic cycles on the prebiotic Earth.
PLoS Biol 6(1):e18. doi:10.1371/journal.pbio.0060018, 2008.
Shapiro R. Small molecule interactions were central to the origin of life.
Q Rev Biol 81(2):105–125, 2006.
Szostak JW, Bartel DP, Luisi PL. Synthesizing life. Nature 409(6818):
387–390, 2001.
Woese CR, Kandler O, Wheelis ML. Towards a natural system of
organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Proc Natl Acad Sci USA 87(12):4576–4579, 1990.
CHAPTER 2
Abiotic Processes Can

Generate Biologically
Important Molecules
Perhaps no other question has challenged humans more than the origin of
life. For many centuries, answers were based on religious perspectives and
lacked scientific foundations. As discussed in the Ethical, Legal, Social
Implications above, religion and science view the world in mutually ex-
clusive ways, but a person can believe in God and accept evolution. Over
time, scientists turned their attention to the fundamental question about
our existence. This chapter addresses how life could have evolved from
nonliving chemicals and molecules. The reader will examine original data
that make a compelling case for the origin of life that does not require
belief in the supernatural or God.
When life is examined closely, it becomes clear that life is composed
of four essential raw materials (Figure 3). Proteins provide shape to
cells and perform functions. Nucleic acids, such as DNA and RNA,
carry information from one place to the next and across generations.
Carbohydrates, in the form of sugars, provide structural support and
relay energy from one place to another, whereas lipids assemble into
double layered membranes around cells. From these four fundamental
classes of biological molecules, under the right circumstances and tim-
ing, the emergent property of life sprang from our abiotic planet.
The molecules at the center of this chapter are lipids. Lipids are often
diagramed as a circle with two long tails. The circle represents the hy-
drophilic “head group” that contains the acid and the 3-carbon glyc-
erol. Phospholipids also contain a phosphate that may or may not have
another molecule attached where to the PO4 shown in Figure 3D. The
OH –O O N C
HO C
OH C N+
C S C
O C O
HO OH C C C C C
O OH C C C C C O–
+N C N C N C N C N C
O O O O O
HO
O OH Thr Glu Ala Cys His
A carbohydrate B protein
O O
N
C H
O P O– 1 phosphate
O– C C H H O–
O N
P O O
N C
C
H C C C H 1 glycerol
C N O O H
O– C C
C
N H O C C O 2 acids
C H H2 C C H2
G O H2 C C H
H
H2 C C H
H H2 C C H2
N
H 1 lipid H C C H
O P
O C H C C H 2 fats 2 fatty
C
O– N H2 C C H2 acid tails
C O C H2 C C H2
C C C
N H2 C C H2
O
C C H C C H2
H
C O H
H C H2
H
H
H
N
N
C C D lipid
C
N
N C
O P C O C
C N
O C
O–
C C
A O H
H
H O
C
H
C C
H N H
C
O P C C
O N
O C O
O– C
C C
T H O
H
C nucleic acid
Figure 3 Complex biological molecules that form the building blocks

of life. A, The disaccharide lactose. B, Five amino acids connected
by peptide bonds. C, Four nucleotides connected by phosphodiester
bonds. D, A generic phospholipid drawn in chemical detail and as
simplified icon.
hydrophilic portion of a lipid interacts with the cytoplasm inside cells

and the watery outside world of a cell. The head group is recognizably
hydrophilic because it contains a phosphate with negative charges and
the acids contain oxygen, which is highly electronegative, or acts like
an electron “hog”. The elements N O P S tend to carry partial negative
charges, because when they covalently bind to other atoms, N O P S
ABIOTIC PROCESSES GENERATE BIOLOGICAL MOLECULES 11
tend to hold the electrons a little closer to themselves. When one or more
of these four elements is present, it is a good guess that portion of the
molecule is hydrophilic. The two hydrocarbon chains of a phospholipid’s
tails are composed completely of C and H, neither of which hog their
covalently shared electrons. Hydrocarbon chains are nonpolar, meaning
that none of the atoms have a partial charge. Water is polar, so it does not
interact well with nonpolar molecules, such as fats. The fats are attached
to the acids to make two fatty acids, which are hydrophobic. When lipids
are mixed together in the presence of water, the fatty tails stick together in
the middle with the hydrophilic head groups facing outward to the water.
Large amounts of lipids form what looks like a three-layered Oreo cookie
with hydrophilic cookie outsides and hydrophobic fat inside. These lipid
sheets can be planar, but they often circularize into spheres with an aque-
ous lumen trapped inside.
It is difficult to picture the universe as an expanding collection of
elements that coalesced into balls of fire and clay to form suns and plan-
ets. Imagine primitive Earth spinning on its axis and orbiting our sun.
Next, contemplate how proteins, nucleic acids, carbohydrates, and lipids
came into being before life evolved. These four building blocks of life are
produced by cells every second of every day now, but before life began,
how did these biological molecules appear on Earth and coalesce into a
living cell?
The universe is composed of the elements found on the periodic table
of the elements. These atoms do not self-assemble into complex biological
molecules when they are mixed in a test tube containing carbon, nitro-
gen, oxygen, and hydrogen. A fundamental principle of biology, which
is often referred to as the cell theory, states that all cells come from pre-
existing cells. Given the cell theory, how was the first cell produced? This
troubling question has been pondered by philosophers and scientists for
hundreds of years. In this chapter, data are presented will help explain
how a primitive cell may have assembled itself from complex abiotic
molecules.
Proteins, carbohydrates, and nucleic acids are typically hydrophilic,
whereas lipids are either hydrophobic or both. All four categories are
thought of as the products of living cells, and they fall into the category
of organic molecules, meaning that they contain carbon. Scientists looked
to reaction
vacuum chamber
access point water-cooled

side-arm condenser
boiler
trap
heat
Figure 4 Miller’s experiment to simulate primitive Earth. Modified
drawing from Miller showing the parts of his ancient world device.
Source: From Stanley L. Miller. 1953. Figure 1.
at these biological molecules and tried to determine how such complex

organic molecules could have been produced abiotically before life had
evolved. Thinking about the origin of organic molecules is similar to ask-
ing which came first, the chicken or the egg. It seems impossible to have
life without these complex molecules, and yet it seems impossible for
these complex molecules to be formed in the absence of life. Fortunately,
some very clever and persistent investigators have performed experiments
to determine if complex organic molecules could be formed in an abiotic
world.
In 1953, a graduate student at the University of Chicago named Stan-
ley Miller wanted to determine experimentally whether biologically rel-
evant organic molecules could be produced abiotically. Miller tried to
replicate primitive Earth environmental conditions for abiotic produc-
tion of amino acids, the basic subunits of proteins. Because no scientist
can wait a million years to let amino acids form naturally, Miller wanted
to speed up the process within a fabricated abiotic world (Figure 4). To
conduct his research, Miller needed a small, self-contained primitive
Earth, which he built out of glass. Geologists had already described which
simple, nonorganic molecules were present 3 billion years ago before life
evolved. Water and all the ingredients were poured into Miller’s side-arm
access point, which he later sealed shut. The “modern air” was removed by
connecting the apparatus to a vacuum pump, and then he filled the entire
device with hydrogen gas (H2) methane gas (CH4), and ammonia gas
(NH3). Miller applied heat to the flask; steam rose and moved to a reac-
tion chamber where Miller produced electrical sparks. Steam condensed
in a cooling chamber to form liquid that returned to the boiling flask to
repeat the cycle. The entire mixture moved in a clockwise direction, and
sparks of electricity flashed like prehistoric lightning storms in the reac-
tion chamber.
The electrical stimulation continued nonstop for an entire week. Dur-
ing the first day, the water became pink, and by the end of the week, the
water was deep red and turned cloudy. The access point side-arm was
cut one week later to remove the liquid for analysis. The red material
was dried and analyzed by two-dimensional thin layer chromatography
which is a process of physically separating molecules based on their chem-
ical properties. Once this two-step chromatography was completed, he
sprayed the entire paper with a stain to visualize what had been separated
from the red solution. He identified the complex organic molecules and
in the process discovered that at least three different amino acids were
formed abiotically under conditions similar to ancient Earth. The identi-
ties of the colored spots were later verified by Miller and others using a
variety of methods. Miller’s experiment confirmed that amino acids, the
subunits of proteins, could be synthesized in the absence of life. This
was the very first time biologically significant organic molecules had been
synthesized in the absence of living cells using only the abiotic materials
that resembled primitive Earth.
Miller stimulated others to think in new ways about abiotic forma-
tion of biological molecules and the origin of life. Since Miller’s ex-
periment, people have found multiple abiotic sources of lipids and the
subunits of nucleic acids. Scientists discovered lipids produced abioti-
cally in space when they examined a meteorite that landed in Australia
in 1969. In 2001, NASA chemists replicated the outer space synthesis of
lipids by shining ultraviolet (UV) light on a mixture of simple inorganic
gases. Interstellar ice is composed of the same four gases which are abun-
dant in space where UV light is abundant. NASA’s experiments synthe-
sized amphiphilic molecules that could assemble into membrane pieces
and even lipid bilayers in three-dimensional spheres of called vesicles
(Figure 5). All of these results increased the likelihood that primitive
hydrophilic
heads
lumen of
vesicle
aqueous
solution
hydrophobic
tails
Figure 5 Vesicles made of lipids similar to those formed in NASA’s

experiments. Line drawing of vesicles which are spheres made of two
lipid layers, or a bilayer. The center cavity of a vesicle is called its
lumen.
Earth could have produced the building blocks of life in the absence of
cells.
Based on a 2008 publication in the journal Science entitled “The
Miller Volcanic Spark Discharge Experiment,” scientists showed that
Miller’s primitive earth research had produced more than the three amino
acids he labeled by hand. Discovering that amino acids, nucleic acids and
lipids could be produced abiotically means that the first cells could be
composed of proteins, lipids, and a genetic material. Miller’s work dem-
onstrated that complex, biologically important molecules may have been
prevalent prior to the formation of the first cell. Now that it seems feasible
that biologically important molecules could have accumulated on Earth
before life evolved, we need to consider how these molecules could have
assembled into the very first living cell.
As defined previously in this book, life exhibits at least three
properties—change, replication, and existence as a three-dimensional
object big enough to contain cargo. Did all three properties emerge
simultaneously, or did one arise before the others? No one has data from
the first cell to answer this question directly, but perhaps the lack of an-
cient data is not an insurmountable barrier if modern data can simulate
ancient conditions as Miller did. Do abiotic, self-replicating molecules
exist today that can copy themselves, transferring information from
one “generation” to another? Can abiotic, membrane-bound vesicles
be produced that grow and divide? Could biochemists produce abiotic

complex molecular structures with the life-like properties of change, rep-
lication, and be big enough to carry cargo? This chapter presents some
of the original data so that the reader can determine for him or herself
if primitive life could have evolved from abiotically produced complex
molecules.
Self-Organizing and Replicating Molecules

Membranes and RNA molecules are not living objects, and yet they are
vital to the existence of life. If a living cell were dissected and all its parts
put in a pile, none of the parts would be living. Life is an emergent prop-
erty derived from a particular mixture of inanimate objects assembled
within cells. Ribosomes are self-organizing molecules in that they are not
assembled by a larger structure. Self-organizing ribosomes assemble them-
selves inside cells similar to the way a life raft self inflates when it touches
water. Large, multi-subunit molecules are critical to life. Is it possible to
devise a set of experiments that could demonstrate life-like properties in
nonliving objects?
In 1985, biologists proposed a radical hypothesis for the earliest en-
zymes: They were composed of RNA and not protein. This hypothesis,
called the RNA-world hypothesis, proposed that the earliest genomes
and enzymatic molecules were all made of RNA. In the 1980s, investiga-
tors had discovered a new class of RNA molecules called ribozymes; ribo-
because they were made of ribonucleic acids (RNA), and -zymes because
they functioned like protein-based enzymes. The discovery of ribozymes
defied what biologists thought was possible, and the lead investigator was
awarded a Nobel Prize. The RNA-world hypothesis is simple, but design-
ing experiments to test it has been challenging.
Sometimes politicians and other nonscientists consider researchers
to be out-of-touch when they study bizarre organisms that have no ob-
vious relevance to human existence. Such was the case with biologists
who studied the unicellular organism called Tetrahymena. This unicel-
lular, fuzzy creature was the origin for much of our understanding of
ribozymes, because a particular RNA intron has the capacity to excise
itself from the original mRNA. This self-splicing RNA intron was only
186 nucleotides long, and it spliced itself out of a larger RNA mole-
cule and then ligated the two severed RNA pieces back together. This
ribozyme intron molecule forms new covalent bonds between the two
loose ends of mRNA after excising itself. All eukaryotic cells have mixed
protein/RNA complexes that perform intron splicing and exon ligating,
but Tetrahymena could catalyze the splicing using only one RNA piece—
the first ribozyme discovered. From this offbeat organism came the be-
ginnings of the RNA-world hypothesis and much of the experimental
evidence supporting RNA as a key player in the origin of life.
The self-splicing RNA intron does its job in two steps; first it cuts the
RNA and the second step ligates the two loose ends. Ligation is chemi-
cally similar to the task performed by RNA polymerase. When given sub-
strates of two different RNA dinucleotides, CpU and GpN, the ribozymes
produced one trinucleotide and a single base without any phosphate:
CpU + GpN + ribozyme → CpUpN + G + ribozyme
The p represents the phosphodiester linkage between two individual

nucleotides, and N represents any of the four RNA bases.
Ligating one base to another is the first step in RNA polymerization,
and a pair of biochemists wanted to see how many bases could be polym-
erized by this self-splicing ribozyme. The motivation for their research
was to test the RNA world hypothesis. If life began with RNA enzymes,
then an RNA molecule should be able to polymerize more than one RNA
nucleotide. Before conducting their experiment, the investigators had to
design appropriate controls to perform in conjunction with the experi-
mental conditions. In this case, the investigators chose to include a nega-
tive control. The negative control tested whether in the absence of added
RNA nucleotides, the self-splicing intron could elongate a short piece of
starter RNA. The short piece of starter RNA, called pC5, was composed
of five RNA cytosine nucleotides in a row. They expected the negative
control not to extend the length of the pC5 RNA molecule because the
control lacked any RNA dinucleotides. In the experimental reactions, one
of four different RNA dinucleotides (GpC, GpU, GpA, or GpG) was
added to pC5 in four separate reactions. These five different polymeriza-
tion experiments (one negative control and four experimental conditions)
were analyzed by gel electrophoresis to separate each polymer based on

its size. Dark places on the gel indicated many copies of individual mol-
ecules of identical size; the darker the spot, the more molecules of that
size. Note that the pC5 starting RNA was labeled with radioactive 32P
so that only pC5 and any of its modified products could be detected by
exposing the x-ray film.
Every time experimental data are analyzed, it is best to begin with
the controls. For the negative control, the investigators observed that
pC5 was modified a little bit to produce shorter and longer fragments
at roughly the same rate. This indicated that the ribozyme had some
polymerase activity even in the absence of added RNA dinucleotides.
They also noted the new bands first appear after 30 minutes and were
more prominent after 1 hour. They examined the results for GpC and
saw from the intensity of the bands that the pC5 RNA polymers mostly
got bigger and not smaller. Furthermore, the bands of bigger RNA
polymers appeared within 10 minutes instead of 30. The ribozyme
added four new C RNA nucleotides to the starter pC5—nearly dou-
bling it’s original length in 1 hour. The investigators had discovered that
ribozymes did polymerize RNA by adding bases onto pC5. They also
realized that their ribozyme could not add a G to pC5 as demonstrated
by the preponderance of very short molecules in the GpG lanes of the
gel. This ribozyme polymerized only 3 of the 4 C bases onto the 39 end
of pC5. The investigators realized that elongating a polymer of nucleic
acid was equivalent to replicating biological information. However,
adding only four bases in 1 hour was not sufficient to be considered
a robust polymerase. For more compelling evidence of self-replicating
RNA molecules, the investigators wanted to see ribozymes that could
polymerize more bases at a faster rate.
Rather than searching organisms that contained more prolific RNA
polymerizing ribozymes, investigators decided to synthesize some in the
laboratory. These investigators used the tenets of natural selection in an
experimental process called directed evolution to isolate new molecules
that polymerize RNA faster (Figure 6). In their directed evolution experi-
ment, investigators generated many sequence variations of the Tetrahy-
mena ribozyme. From this bigger set, the scientists selected a subset of
the ribozymes that could polymerize RNA the fastest. They started with
Figure 6 One three-step cycle of directed evolution starting at the top

with ribozyme variants. In reality, each molecule would be present
many more times than shown here. The diagram emphasizes critical
steps (outlined below) and removes nonessential components for
clarity.
Source: Original Art.
trillions of ribozymes, each with slightly different sequences and func-

tional capacities. The hard part was devising a clever method for isolating
only those variants with improved RNA polymerase activity. They had to
conduct several rounds of directed evolution, and here are the three main
steps that constitute one round of directed evolution:
1. Start with a large population of ribozymes composed of sequence

variations of the Tetrahymena ribozyme (different shades of gray),
and isolate the ones with the fastest polymerase activity. A small
number of ribozymes were selected (box), but in the real experi-
ment, many first round winners would be selected from a much
larger starting population.
2. Replicate the winners (boxed ribozyme), and produce sequence vari-
ations of the winning ribozymes (various shades of gray) to form a
new mixed population of potential ribozymes.
3. Repeat the selection and replication processes as many times as de-
sired to isolate the fastest ribozyme.
The scientists constructed 1014 ribozyme variants derived from the

original Tetrahymena ribozyme. The investigators generated sequence
variation by randomly mutating a subset of the 186 nucleotides that con-
stituted the original ribozyme. Producing 10,000,000,000,000 variants
seems excessive until one calculates how many more variants they could
have made (4186, or approximately 10112 potential variants). By the end
of their directed evolution, the investigators had evolved and isolated 25
ribozymes with polymerase activity much faster than the original, natu-
rally isolated ribozyme. The 25 fastest ribozymes had many bases in com-
mon despite the potential for many differences in RNA bases. Some of
the original bases were not mutated by the investigators. Of the mutated
bases in all 25 selected sequences, some were exactly the same as in the
original ribozyme after the directed evolution indicating those particular
bases were important to the polymerase activity. A different subset of the
mutated bases either remained unchanged or were replaced by only one
of the other three possible bases.
The scientists conducted four cycles of directed evolution. Starting
with 1014 ribozyme variants, they selected the ribozymes that worked the
fastest at each round of directed evolution until they had the 25 best
RNA polymerases. The 25 best ribozymes polymerized RNA faster than
the original ribozymes from Tetrahymena. Many of the base pairings were
conserved in at least 24 of the 25 sequences whereas some others were con-
served in at least 22 of 25 sequences. These conserved bases are likely to
play an important role in the ribozymes’ improved function. After further
optimization of the 25 best evolved ribozyme sequences, the investigators
eventually built one ribozyme that could catalyze RNA polymerization
700 times faster than the biological one isolated from Tetrahymena.
The new ribozymes produced by directed evolution could polymerize
RNA at about 100 bases per minute. Remember that bases in the ribo-
zyme were unchanged after the directed evolution even though they had
been mutated. Using the multiplication rule for probability calculations,
the probability that one pair of bases would be conserved in all 25 vari-
ants by chance alone is 0.7125 ≈ 0.02%. Therefore, it seems likely that
the multiple conserved bases were critical for the ribozyme’s improved
function. Comparing the old and new ribozyme sequences helped the in-
vestigators determine which bases were critical for the enhanced function.
However, we know so little about ribozymes structure that it is impossible

to predict which bases catalyze the ligation reaction. No one has found
a naturally occurring ribozyme that exactly matched the one produced
by directed evolution even when BLAST is used search the NCBI da-
tabase because the database does not contain every sequence on Earth.
Any BLAST search will not survey the true diversity that exists in nature.
Therefore, it is possible that even faster naturally evolved ribozymes exist
in species that we have not sequenced. Since it is impossible to sequence
every individual organism on the planet, we are left with imperfect infor-
mation. All we can do now is continue to search through odd creatures
that may hold ancient clues about early ribozymes, which could represent
the earliest forms of transmitting genetic information from one genera-
tion to the next.
The purpose of Chapter 2 was to provide compelling evidence that
biologically relevant molecules could be produced abiotically. This
chapter showed that RNA-based enzymes were first hypothesized and
later found in nature. There is clear evidence that abiotic ribozymes are
capable of polymerizing RNA molecules very quickly. Through experi-
mentally controlled directed evolution, biologists were able to produce
a ribozyme with improved capacity to form RNA polymers. In short,
ribozyme RNA polymerases do exist and may have been the first genetic
information replicator. Ribozyme RNA polymerases satisfy two of the
criteria for the bare minimal requirements for the origin of life: replica-
tion and change over time. Chapter 3 presents information that will let
the reader decide if the data are compelling enough to support the hy-
pothesis that lipid membranes are capable of growing in the absence of
enzymes, and that living cells could form in the absence of life.
Bibliography
Been MD, Cech TR. RNA as an RNA polymerase: net elongation of
an RNA primer catalyzed by the Tetrahymena ribozyme. Science
239(4846):1412–1416, 1988.
Bergman NH, Johnston WK, Bartel DP. Kinetic framework for
ligation by an efficient RNA ligase ribozyme. Biochemistry 39(11):
3115–3123, 2000.
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Dworkin JP, Deamer DW, Sandford SA, et al. Self-assembling amphi-

philic molecules: synthesis in simulated interstellar/precometary ices.
Proc Natl Acad Sci USA 98(3):815–819, 2001.
Ekland EH, Bartel DP. The secondary structure and sequence
optimization of an RNA ligase ribozyme. Nucleic Acids Res 23(16):
3231–3238, 1995.
Ekland EH, Szostak JW, Bartel DP. Structurally complex and highly
active RNA ligases derived from random RNA sequences. Science
269(5222):364–370, 1995.
Johnson AP, Cleaves HJ, Dworkin JP, et al. The Miller volcanic spark
discharge experiment. Science 322(5900):404, 2008.
Miller SL. A production of amino acids under possible primitive earth
conditions. Science 117(3046):528–529, 1953.
Miller SL. Production of some organic compounds under possible primi-
tive earth conditions. J Am Chem Soc 77(9):2351–2361, 1955.
Miller SL. The mechanism of synthesis of amino acids by electric
discharges. Biochim Biophys Acta 23(3):480–489, 1957.
Ponnamperuma C, Woeller F. Alpha-aminonitriles formed by an electric
discharge through a mixture of anhydrous methane and ammonia.
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Tropsch-type synthesis over a temperature range of 100 to 400
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Walde P, Goto A, Monnard PA, et al. Oparin’s reactions revisited: enzy-
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chison carbonaceous meteorites. Nature 246:301–303, 1973.
CHAPTER 3
Non-Living Vesicles Can

Compete and Grow
Perhaps the most challenging aspect to understand about the origin of

life is how a cell membrane could form before cells existed. Scientists
had already learned about abiotic production of biologically important
organic molecules because organic molecules have been found on meteors
and Miller’s primitive earth experiment had produced them. Yet it might
seem implausible for abiotic forces to organize lipids into a sphere sur-
rounding some cargo and allow these spheres to grow and produce more
spheres. Could one or more lipids self-organize and replicate solely based
on the chemical properties determined by the composition of the mol-
ecules? If such lipids exist, are they capable of encapsulating cargo such as
self-replicating ribozymes? If a vesicle possessed all of these properties, it
would be possible to imagine how life evolved over a long period of time
through abiotic actions. The reader will evaluate the original data that has
supported an abiotic origin for primitive cells and their membranes.
Self-Organizing Vesicles
As described earlier, amphiphilic lipids and fatty acids have been synthe-
sized on meteors, on ice exposed to UV light, and near deep sea thermal
vents. But with Earth being so large, it is hard to imagine how enough
of these fatty acids could congregate in one place to coalesce into mem-
branes. One particular fatty acid called myristoleate (Figure 7A) does
congregate on a type of natural clay. To get a sense how chemicals can
cluster on particular surfaces, drop a small piece of food, such as a pretzel
or cracker crumb, into a soda and watch the bubbles form on the sur-
face of the food particle, causing it to rise and fall in the soda. Similarly,
O–
H
O H micelle vesicle
A B
Figure 7 Fatty acid structure and vesicle formation rates. A, Chemical

structure of a natural fatty acid, myristoleate. B, Fatty acid monolayer
forming a micelle and a bilayer forming a membrane vesicle.
myristoleate and other fatty acids can cluster onto the surface of clay
when both are immersed in a watery environment. Lipids and fatty
acids can form solid balls of lipids called micelles when mixed with water
(Figure 7B). Clay functions as a catalyst for micelles because it enhances
their formation, but the clay is not consumed in the process. The for-
mation of vesicles is experimentally detected by measuring the amount
of light absorbed by a solution of clay and lipids. Just as light cannot
shine through a glass of muddy water, vesicles prevent light from passing
through the solution. The amount of vesicles present is measured by the
amount of light absorbed by the sample. Vesicle formation from micelles
was tested with different solid surfaces, such as tiny plastic beads called
microspheres and different concentrations of clay. The investigators
tested clay, ceramic microspheres with a high density of negative charges,
ceramic microspheres with low density of negative charges, and buffer
alone as a negative control. They also plotted the initial rates of vesicle
formation using different amounts of clay from the data.
The investigators learned that many solids are capable of catalyzing
vesicle formation. During the cracker crumb and soda experiment, the
rate of bubble formation increased with the larger surface area of small
cracker crumbs. In other words, two small crumbs are more effective than
one larger crumb because of the increased surface area for bubble forma-
tion. As they expected, the higher concentrations of clay converted 100%
of the micelles into vesicles and the amount of light absorbed by the
solution stopped increasing after 10 minutes. Chemical reactions often
stop after a while, so it is best to use the initial slopes to examine rates of
Non-Living Vesicles Can Compete and Grow 25
reactions as a function of input. The slope from the first few time points
told investigators how fast a reaction was proceeding—not the final value.
When they added more lipids, more vesicles were formed.
What was not evident from the absorbance data was that bits of clay
and microspheres were becoming entrapped inside the growing vesicles.
Green-stained fatty acids were mixed with negatively charged ceramic
microspheres and viewed in different ways by microscopy to see the dif-
ferent components. This was the first time anyone had shown that self-
organizing vesicles could spontaneously trap cargo inside the lumen of
the vesicles, including smaller vesicles. The investigators wanted to deter-
mine whether the abiotic vesicles could entrap RNA molecules as well,
such as ribozymes that could polymerize RNA (see Chapter 2). When
mixed with red-stained RNA attached to clay or free floating RNA in
solution, the green-stained fatty acid vesicles were able to provide a three-
dimensional protective layer around the red RNA. The photographs of
these abiotic vesicles looked a lot like membrane-bound genomes seen in
prokaryotes today.
Abiotic Vesicle Growth and Reproduction

As was just shown, abiotic vesicles can spontaneously engulf RNA cargo
and that RNA ribozymes can function as RNA polymerases. However,
no one had produced evidence for abiotic vesicles exhibiting a key char-
acteristic of life—the ability to grow and reproduce. The first cell had to
grow and divide to produce two cells. To measure whether the experimen-
tally produced abiotic vesicles could grow spontaneously, the investigators
counted the number of vesicles and measured their size at different times
after the addition of more fatty acid micelles. To start the experiment,
investigators produced a narrow size distribution of starting vesicles by
pushing all of them through a type of paper similar to a coffee filter. The
entire population of uniformly sized vesicles got bigger after being “fed”
micelles. The growth of vesicles was linear over 4 hours in response to the
addition of micelles. It is as if the initial vesicles became “hungry” and
incorporated more and more fatty acid to increase their sizes.
In addition to growth, living cells have the ability to reproduce. Re-
production for abiotic vesicles would mean producing new smaller vesicles
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using abiotic processes. Since these lab-produced lipid vesicles lacked any
proteins or enzymes for cell division, investigators needed to determine
whether physical and chemical forces alone were sufficient to generate
new, and thus smaller, vesicles. The investigators pushed the larger vesicles
through the filter paper again to start the experiment with vesicles of a
uniform size (average radius of 62 nm). Pushing large vesicles through filter
paper holes is similar to the physical stress exerted on vesicles in shallow
pools that evaporate over time. The vesicles were essentially squeezed until
they produced two new vesicles (average radius of 45 nm) from a larger
parental vesicle similar to the way bacteria divide in half. The investiga-
tors repeated the cycle of growth through accumulation of more fatty acid
and vesicle reproduction by extrusion through a filter. The data revealed a
five-cycle alternating size pattern similar to the life cycle of organisms that
reproduce asexually. From these data, it is possible to apply logic and math-
ematics to understand the consequences of abiotic vesicle growth as dem-
onstrated in these experiments. These answers will affect the interpretations
of experimental data that are presented later in this chapter.
At this point, scientists have shown that abiotic lipids can assemble
spontaneously into membranes and form vesicles. Abiotic vesicle forma-
tion is catalyzed on the surfaces of clays found in nature today. They
also discovered that abiotic vesicles can grow in size through the accu-
mulation of more lipids. These vesicles can divide into smaller vesicles
as a consequence of passing through small holes. Furthermore, it was
shown that negatively charged RNA can catalyze vesicle formation and
become trapped inside abiotic vesicles. In Chapter 2, scientists showed
that abiotically produced ribozymes can polymerize RNA. Perhaps there
are ribozymes that can replicate themselves, although no one has found
self-replicating ribozymes yet. Abiotic vesicle formation with engulfed
self-replicating RNA genome sounds very similar to living cells. The ex-
perimental data were generated by abiotic molecules and their physical
and chemical processes driven by the shape and charge of nonliving mole-
cules. Is it still as difficult to imagine that given 1 billion years, cells could
have evolved from abiotic molecules under the influence of chemical and
physical properties?
Table 1 mathematically proved that when two new vesicles are formed
from one larger vesicle, they have a combined surface area approximately
Table 1 Comparison of abiotic vesicles before and after reproduction.

Radius Surface Volume Ratio (area/
Vesicle Size (nm) area (nm2) (nm3) volume)
large 62 48,281 997,800 0.05
small 45 25,434 381,510 0.07
percent change 27% shorter 47% less area 62% less volume
formulas: surface area of a sphere = 4π r2; volume of a sphere = 4/3 π r3
equal to the total surface area of the larger vesicle (each vesicle has about
50% of the original vesicle’s surface area). The calculations also proved
mathematically that the dividing vesicle volume decreased to less than
50% its original volume for each of the two new vesicles; each vesicle is
38% of the parental volume. By producing two vesicles with 38% the
original volume, only 76% (38 × 2 = 76) of the original volume is now
contained inside the two new vesicles. Therefore each abiotic vesicle divi-
sion causes about one-fourth of the larger vesicle’s cargo to be spilled to
the local environment. If the dividing vesicle contained a self-replicating
ribozyme, some of these molecules would be spilled into the surrounding
media. Earlier research demonstrated that RNA can be encapsulated in
newly formed vesicles, which means a variety of RNA genomes with dif-
ferent polymerase rates could become encapsulated inside newly forming
vesicles composed of different lipids. It is striking that with only two types
of abiotic molecules (RNA and lipids) these scientists have generated a
plausible mechanism to produce diversity within a population of growing
and dividing abiotic vesicles that contain RNA genomes. In short, they
discovered the first two tenets of natural selection using lipids, nucleic
acids, clay, and mathematics.
Three billion years ago when life was first evolving, the building blocks
of cells were present (abiotic lipids, amino acids, and nucleic acids) but in
limited concentrations, which means resources were limited. Limited re-
sources, variation in the population, and over production are the first three
tenets of natural selection. The only missing tenet is competition. Could
these RNA/lipid primitive cells “compete” for limited resources needed
to make more copies of themselves? In order for life to evolve, it would
be predicted that the earliest cells would have to compete with one an-
other for the available lipids. It would be very informative if abiotic vesicle
competition could be experimentally measured. If vesicles could compete,

then there would be a selective advantage for a subset of vesicles—the
fourth tenet of natural selection. With competition and reproduction, all
the components of natural selection could have been in place three billion
years ago when we know from fossil evidence that live cells first evolved.
To investigate the possibility that abiotic vesicle competition could
happen, the scientists produced two populations of lipid vesicles. One
population of “stressed vesicles” were filled with one molar (1 M) su-
crose sugar. It is well known that when a substance diffuses, it moves
down its concentration gradient to an area of lower concentration. In
this case, water would passively diffuse to areas of high sugar concentra-
tion inside the vesicle. Water would diffuse from outside to inside the
sugar-filled vesicles, causing the vesicle to swell and physically stress the
lipid membrane. When water is drawn across a membrane into areas of
concentrated dissolved particles, we use the term osmosis to describe
water’s passive movement. The investigators prepared a second population
of “relaxed vesicles” containing only buffer inside them so that there was
no osmotic pull for water to move into the relaxed vesicles. The investiga-
tors wanted to know if the sucrose-filled, osmotically “stressed” vesicles
would compete with the “relaxed,” buffer-filled vesicles.
The two populations of vesicles were labeled with different colored
dyes so that the investigators could distinguish which vesicles were
stressed and which ones were relaxed. After mixing the two types of vesi-
cles in a 1:1 ratio, they measured the surface area of both types of vesicles
independently. Relaxed vesicles were measured after adding additional
relaxed or stressed vesicles. Stressed vesicles were measured after adding
equally stressed or relaxed vesicles. When vesicles with the same osmotic
pressure were mixed together, their surface areas did not change. Mix-
ing stressed and relaxed vesicles produced rapid changes in vesicle surface
areas. Stressed vesicles grew and the relaxed vesicles got smaller. By fitting
exponential curves to the observed data, the investigators determined that
relaxed vesicles shrank at the same rate that stressed vesicles grew, sup-
porting their conclusion that fatty acids moved directly from the relaxed
vesicles to the stressed vesicles.
This elegant experiment was the first one to show that the abiotic
process of osmosis alone could lead to a lipid competition that was driven
by the cargo within an abiotic vesicle. Therefore, if any vesicle had higher
osmotic pressure, it would steal lipids away from vesicles with lower os-
motic pressure. This competition between abiotic vesicles happened in
the absence of life or proteins. These investigators demonstrated the exis-
tence of abiotic competition for limited resources—the remaining tenet
of natural selection that could have produced the first life forms.
The investigators recognized that 1 M sucrose inside vesicles was not
a biologically relevant cargo to generate osmotic pressure inside abiotic
vesicles. They decided to use transfer RNA (tRNA) cargo as a more bio-
logically relevant solute to generate osmotic pressure. tRNA is easy to
purchase and about the same size as the ribozymes described in Figure 6.
Once again, they measured the change in surface area of relaxed vesicles
and stressed vesicles containing tRNA when mixed with vesicles of similar
osmotic stress or the opposite osmotic stresses. Once again, the tRNA-
containing vesicles grew at the same rate that the relaxed vesicles shrank.
The biological relevance of this competitive experiment should be clear
because RNA molecules have already been show to become trapped inside
abiotically formed vesicles. This book has presented data showing that:
• Lipids can form through abiotic mechanisms.

• Abiotic vesicles can form spontaneously.
• Abiotic vesicles can trap RNA inside them.
• RNA ribozymes can polymerize RNA molecules.
• Abiotic vesicles can grow in area and volume by adding lipids.
• Abiotic vesicles can compete against each other for lipids.
• Abiotic vesicles can divide and leak their RNA cargo with
each division.
• Abiotic vesicles with RNA inside can outcompete vesicles
lacking RNA inside.
The data support the RNA-world hypothesis, which states abiotic fac-
tors and ribozymes could have led to the origin of life. This chapter has
shown that abiotically produced vesicles, similar to primitive cells, could
have experienced natural selection in ancient Earth. Therefore, the data
support the hypothesis that life originated through chemical and physi-
cal responses to abiotic conditions on Earth. This chapter presented the
experiments that demonstrated the five tenets of natural selections are

possible in the absence of life, which begs the question: How can a living
cell be defined? At what point is it appropriate to stop calling these objects
vesicles and refer to them as cells?
The experiments testing selective advantage used osmosis to stimulate
the competition for lipids between two populations of vesicles. As a re-
laxed vesicle shrank, the solute cargo was trapped inside. Stressed vesicles
grew as their cargo was diluted and relaxed vesicles shrank and increased
the concentration of their cargo. As sizes of the vesicles changed, the os-
motic pressure of the vesicles changed accordingly. Therefore, at some
point, the stressed vesicles would cease being stressed and the relaxed
vesicles would become stressed until they reached a balance among all
the vesicles. If the two populations converged to a common amount of
osmotic stress, it is reasonable to predict that adding a new population
of relaxed vesicles would cause all the old vesicles to grow at the expense
of the newly added vesicles. In short, this analysis of abiotic vesicle growth
and competition led to a proposal for the next round of experiments,
which is the heart of the scientific process when conducting evolutionary
research on the origins of life.
Science is a discipline of asking and answering questions. Chapters
2 and 3 presented the best data in the world trying to determine how
life could have evolved on Earth for the first time. Abiotic chemical and
physical properties are sufficient to explain many of the traits associated
with living cells and natural selection. Once the simplest cells were pres-
ent, reproduction would have led to an ever increasing diversity of life
forms. Keep in mind, evolution is an explanation of the natural world
(how) using data, whereas faith and religion explain spiritual and personal
beliefs (why), independent of data. Religion and science are not mutually
exclusive, and many people of faith believe that chemical and physical
properties were God’s creation and life evolved after the big bang that was
initiated by God.
Bibliography
Chen IA, Roberts RW, Szostak JW. The emergence of competition be-
tween model protocols. Science 305(5689):1474–1476, 2004.
www.Ebook777.com
Chen IA, Szostak JW. A kinetic study of the growth of fatty acid vesicles.
Biophys J 87(2):988–998, 2004b.
Chen IA, Salehi-Ashtiani K, Szostak JW. RNA catalysis in model proto-
cell vesicles. J Am Chem Soc 127(38):13213–13219, 2005.
Hanczyc MM, Fujikawa SM, Szostak JW. Experimental models of primi-
tive cellular compartments: encapsulation, growth, and division.
Science 302(5645):618–622, 2003.
Murtas G, Kuruma Y, Bianchini P, et al. Protein synthesis in liposomes
with a minimal set of enzymes. Biochem Biophys Res Commun
363(1):12–17, 2007.
CHAPTER 4
Non-Living Vesicles Can

Harvest and Store Energy
Chapter 2 demonstrated how RNA molecules can function as RNA poly-

merases. Chapter 3 showed how RNA molecules become entrapped in-
side abiotic vesicles and produce osmotic pressure to out-compete relaxed
vesicles for lipids. Life also requires energy, and so far this book has not
presented any data indicating that these primitive cells could harvest or
store energy. Is it possible for primitive, abiotic cells to store energy in an
abiotic world? Could growing vesicles sequester energy that could be used
to do work at a later time? Chapter 4 presents data that will help deter-
mine if energy storage is possible in an abiotic world.
The idea behind these experiments was pretty simple. Investigators
added lipids to vesicles capable of growing in size, and the added lipids
had a slight positive charge on them due to the low external pH of the so-
lution. They wanted to determine if the liquid inside the growing abiotic
vesicle would develop a lower pH as the vesicle grew. As shown in Chapter
3, newly added lipids will join the exterior of the bilayer in existing vesi-
cles. In this new experiment, the added lipids were synthesized to have a
negatively charged head group. Some of the lipid head groups would bind
a H+ ion from the buffered solution to maintain a neutral overall charge
on the outer layer of vesicle. As the outer layer of the vesicle accumulated
the new lipids, some of the new lipids would flip to the inner layer to
maintain mass balance in the bilayered membrane. The outer layer’s over-
all charge neutrality (mixture of positive and negative charges on lipids)
could act as a source of positive charges that would accumulate on the
inside of the vesicle. Inside the vesicle, some of the new lipid molecules
would release their H+ ions into the lumen. The arrival of new H+ ions
would lower the pH inside the vesicle. Accumulation of H+ ions inside
the vesicle would produce potential energy in the form of a proton gradi-
ent stored inside these primitive cells made of RNA and lipids. A proton
gradient is the energy source that generates ATP in mitochondria and
chloroplasts.
Remember that a H+ ion is the same thing as a proton, because H
atoms are composed of a proton and an electron. H+ ions have lost their
only electrons. pH is a negative log scale from 0 to 14 that describes how
many hydrogen ions, H+, are in a solution. A pH of 0 is a strong acid
with many H+ ions, whereas a pH of 14 is very basic with no H+ ions.
Neutral pH is 7 with an intermediate H+ ion concentration. Because
the volume of the vesicle is tiny compared to exterior buffer, the pH is
quickly lowered inside the vesicle, whereas the external pH is essentially
unchanged in the much larger volume of extracellular liquid. The chang-
ing vesicle pH is analogous to filling a boat with lake water; the water level
in the lake is essentially unaffected while the boat rapidly fills to the top.
Now that they had formulated testable hypotheses, the investigators
designed and performed their experiments. They added an amount of mi-
celles equivalent to the amount of lipids already in the vesicles with lu-
menal pH of the vesicles initially fabricated to be 8.2. They measured the
internal pH after adding the micelles and saw an initial rapid drop in pH
over the first 10 minutes and the pH drop continued slowly over several
hours. In their next experiment, they measured the internal pH over the
first few seconds after adding more micelles to some preexisting vesicles.
At the same time, they measured the change in surface area of the vesicles
as the micelles were incorporated into the vesicle membranes. The size of
the vesicles changed at the same rate as the pH dropped inside the vesicles.
Because pH is a negative log10 scale of H+ ions, one unit decrease in pH
represents a 101, or ten-fold, increase in H+ ions. The scientists measured a
decrease of 0.3 pH units in their experiments which represents a 100.3 ≈ 2,
or two-fold, increase in H+ ions. A 0.3 pH change equals a storage of
2.2 × 10−17 joules (unit of energy) for vesicles with an initial diameter
of 100 nm. The energy storage in the form of a pH gradient by abiotic
vesicles represents about 12% efficiency, which compares favorably to the
most famous energy pathway of photosynthesis (about 34% efficient).
The data generated by these experiments measuring the rate of change
was on a short time scale (seconds). If the goal was to demonstrate events
Non-Living Vesicles Can Harvest and Store Energy 35
that could lead to the formation of life, then these phenomena would
need to persist longer than a few seconds. Having the horizontal axis
in seconds helped them discern the rate of membrane growth and pH
gradient production. However, it seems unlikely that a gradient that
survives only a few seconds could be used as a biological power source.
Nevertheless, the investigators did conduct experiments to determine the
maximum pH gradient that they could produce that would be sustained
for hours. Since life consumes energy, showing that abiotic vesicles could
store energy was an important step in testing the possibility of abiotic
origin of life.
This book has presented a lot of data demonstrating that abiotic fac-
tors can lead to the formation of a vesicle composed of a lipid bilayer
capable of carrying cargo, growing, competing, reproducing, and gener-
ating potential energy in the form of a pH gradient. Abiotic vesicles can
carry nucleic acids that stress the vesicles, and some RNA molecules can
polymerize other RNA molecules. Proton gradients in chloroplasts and
mitochondria are used to produce new covalent bonds in adenosine tri-
phosphate (ATP), so the accumulation of a proton gradient is biologically
significant. In addition to trapping RNA inside abiotic vesicles, the inves-
tigators had discovered that vesicles can trap smaller vesicles within them-
selves. It might be possible to trap a pH gradient within the inner vesicle,
which would prevent the pH gradient from being lost during vesicle divi-
sion (see Table 1). A vesicle within a vesicle is analogous to mitochondria
and chloroplasts inside eukaryotic cells. Abiotic vesicles that can generate
proton gradients are one step closer to resembling living cells. As seen
often in biology, science makes progress by offering rational explanations
of natural phenomena that can be tested experimentally. The more times
a hypothesis is supported by additional experimentation, the more we
accept the hypothesis as the causal explanation. Eventually, a hypothesis
can be described as a theory if it has been supported so many times that
its status is considered secure, but never proven.
For skeptics who demand that a human be present to observe the
first cell’s formation or else they refuse to accept an abiotic origin of life,
they will never be satisfied by scientific evidence. But if an objective ob-
server would consider the data from this chapter, what initially sounded
outlandish can seem much more feasible—the formation of a living cell
www.Ebook777.com
from abiotic physical and chemical processes. With the competing ves-
icle experiments, the scientists demonstrated abiotic competition that
resembled natural selection. Interestingly, those who reject evolutionary
explanations for the origin of life on Earth cannot produce a witness for
alternative origins of life either: It is a logical impossibility. How could a
multi-cellular human record the creation of the first cells when humans
did not exist, much less know how to write? As a scientist, it is important
to rely upon observable facts today and extrapolate the simplest natural
way to explain the origin of life on Earth. Once the first cell exists, all
subsequent cells are easier to explain. Other challenges remain to be ad-
dressed. If the first cell was a prokaryote, how did the first nucleus evolve?
There are equally compelling experiments that have revealed how eukary-
otes came into being about 1.5 billion years ago.
Bibliography
Chen IA, Szostak JW. Membrane growth can generate a transmem-
brane pH gradient in fatty acid vesicles. Proc Natl Acad Sci USA
101(21):7965–7970, 2004a.
Chen IA, Szostak JW. A kinetic study of the growth of fatty acid vesicles.
Biophys J 87(2):988–998, 2004b.
Hanczyc MM, Fujikawa SM, Szostak JW. Experimental models of primi-
tive cellular compartments: encapsulation, growth, and division.
Science 302(5645):618–622, 2003.
Conclusion
The definition of life at the beginning of this chapter focused on three
properties: 1) passing information from one generation to the next; 2)
occupying three-dimensional space; and 3) changing over time. By defini-
tion, humans did not record the origin of life on Earth, so we must de-
duce which physical and chemical properties contributed to that amazing
first cell. RNA is the most widely accepted molecule that provided both
the genetic information and the enzymatic capacity to replicate. Lipids
spontaneously form membranes that can grow, divide, and store energy.
Science is driven by data, and scientists interpret nature after obser-
vation and experimentation. This book provided the data necessary to
understand how the first cell could have evolved from abiotic origins.
Simply noting that some data are missing is insufficient to refute our un-
derstanding of evolution. All data were missing until a scientist discovered
them. To reject a hypothesis, someone needs data that directly contradict
current understanding. The data need to be reproducible and founded
on scientific standards of credibility. Hearsay and secondhand accounts
are unacceptable to be considered scientific data. So far, the origin of life
experiments presented in this book have been replicated and continue to
support the RNA world hypothesis. With repeated validation, the hy-
pothesis is becoming a scientific theory similar to gravity, relativity, and
evolution. In science, it is okay to be wrong as long as a person submits
his or her ideas to peer review for others to test the claims. Even Nobel
laureates have been wrong more times than right. We will never prove
with mathematical certainty how life evolved on Earth the first time, but
we can offer plausible explanations that are supported by data.
Glossary
abiotic. something that is not alive.
amphiphilic. molecules are part hydrophobic and part hydrophilic.
carbohydrates. energy-rich molecules typically composed of sugars, which
include carbon, hydrogen, and oxygen.
catalyst. a component of a reaction that is not consumed by the reaction but
accelerates the reaction rate.
cell theory. universally accepted and states that all cells come from preexisting
cells.
directed evolution. it improves a known function through multiple rounds of
variation and selecting optimal function.
electrophoresis. the process in which large molecules can be separated according
to size and electrical charge by applying an electric current to them in a gel.
emergent property. an emergent property is an unexpected consequence appar-
ent only when examining combined systems.
evolution. the scientific explanation for the origin of life and its continual change
over time.
gene flow. gene flow is the movement and incorporation of alleles from one pop-
ulation to another.
genetic drift. the loss of alleles by random causes and not natural selection.
hydrophilic. water loving, means a chemical will dissolve in water.
hydrophobic. water hating, means a chemical will not dissolve in water.
ligation. the formation of covalent bonds joining two pieces of DNA or RNA.
lipids. fats and oils that do not dissolve in water and are a critical component of
cell membranes.
lumen. lumen is the inner open space or cavity of a tubular organ.
micelles. non-hollow spheres of lipids where the fatty tails fill the interior of
the ball while the hydrophilic portions form the outer layer that interacts with
the water.
microspheres. microscopically small round beads used by scientists.
mRNA. messenger RNA that was transcribed from a gene and is translated by the
ribosome into a protein.
mutation. a change in DNA sequence.
myristoleate. fatty acid that self-organizes on clay surfaces and can form larger
lipid molecules.
natural selection. one mechanism by which evolution takes place and is often
summarized as survival of the fittest.
40 GLOSSARY
natural selection. one of the four mechanisms of evolution and consists of five
parts: overproduction, variation, competition, selective advantage and reproduc-
tion of those who survive.
nucleic acid. the building blocks of RNA and DNA and are formed by the
assembly of sugars, bases, and phosphate.
osmosis. the passive movement of water drawn by a concentrated solution.
pH. a negative log scale from 0 to 14 that describes how many hydrogen ions are
in a solution.
phosphodiester. series of two covalent bonds linking an oxygen to a phosphorous
to another oxygen; connects DNA and RNA nucleotides.
proteins. they have shapes that determine their function and are formed by the
assembly amino acids.
ribozymes. function like protein enzymes but are composed completely of RNA.
RNA-world hypothesis. it proposes that the first life forms on Earth used RNA
as genetic material and enzymes.
selective advantage. variation results in some individuals who have an advantage
over others, depending on the circumstances. Variations in strength, acquiring
energy, stress resistance, and so on allows a subset of individuals to out-compete
others for the limited resources. Those with the advantage continue living.
theory. in a science context means a widely accepted concept that has been
demonstrated many, many times.
vesicles. small spheres composed of membranes and engulfing a small space
inside.
Index
Abiotic processes, 9–15 Faith, definition of, 6
self-organizing and replicating Fatty acid structure, 24
molecules, 15–20
Abiotic vesicle, 33–35 Gene flow, 4
growth, 25–30 Genetic drift, 4
competition, 27–28 Grade point average (GPA), 2
experiments testing selective Green-stained fatty acids, 25
advantage, 30
formation of, 26–27 H+ ion, 33, 34
1 M sucrose inside, 29 Hydrophilic, 10–11
osmosis, abiotic process of, 28–29 Hydrophobic, 11
reproduction for, 25–26
RNA world hypothesis, 29–30 Intelligent design (ID), 5–8
self-replicating RNA genome, 26 Interstellar ice, 13
two populations of, 28
energy storage in, 33–36 Life, properties of, 14
trapping RNA inside, 35 Ligation, 16
Adenosine triphosphate (ATP), 34, 35 Lipids, 9
Amphiphilic molecules, 13 bilayer, 35
Lumen, 33
BLAST, 20
Micelles, 24
Carbohydrates, 9 Microspheres, 24
Cell theory, 11 Miller Volcanic Spark Discharge
Chloroplasts, 35 Experiment, 14
Collins, Francis, 7 Mitochondria, 35
Myristoleate, 23
Darwin, Charles, 1
Directed evolution, 17–18 Natural selection, five basic
four cycles of, 19 tenets, 1–2
one three-step cycle of, 18 Non-living vesicles
Dobzhansky, Theodosius, 4 abiotic vesicle growth and
reproduction, 25–30
Earth, simulation of primitive, 12–14 self-organizing vesicles, 23–25
Electrophoresis, 17 Nucleic acids, 9
Enzymes, radical hypothesis for, 15
Evolution Osmosis, abiotic process of, 28–29
definition of, 1
ethical, legal, social implications pC5, 16–17
of, 5–8 pH, 33–35
theory, definition of, 1 Phosphodiester linkage, 16
42 INDEX
Proteins, 9 Scientific method, operation of

Proton gradients, 35 general laws, 6
Self-organizing ribosomes, 15
Religion, definition of, 6 Self-organizing vesicles, 23–25
Ribosomes, 15
self-organizing, 15 Tetrahymena ribozyme, 15
polymerase activity in, 17 Theory, definition of, 1
RNA, 35 Two-dimensional thin layer
trapping inside abiotic chromatography, 13
vesicles, 35
intron, 15–16 Vesicles, 13, 14
-world hypothesis, 15 self-organizing, 23–25
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Evolution and Origin

A. Malcolm Campbell, PhD

Evolution and Origin of Cells

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Although evolution began as a biological term, it has spread to many

1. Overproduction: Each generation of an organism produces more

Figure 1 Example of natural selection. A, Overproduction of a variety

3. Competition: Overproduction of offspring results in competition

Figure 2 Evolution and the four mechanisms of evolution. A,

Ethical, Legal, Social Implications: Evolution and

Many famous biologists are deeply religious, though most of them

cannot disprove anyone’s faith. Religion will always be distinct from

Abiotic Processes Can

Figure 3 Complex biological molecules that form the building blocks

hydrophilic portion of a lipid interacts with the cytoplasm inside cells

access point water-cooled

at these biological molecules and tried to determine how such complex

Figure 5 Vesicles made of lipids similar to those formed in NASA’s

be produced that grow and divide? Could biochemists produce abiotic

Self-Organizing and Replicating Molecules

CpU + GpN + ribozyme → CpUpN + G + ribozyme

The p represents the phosphodiester linkage between two individual

were analyzed by gel electrophoresis to separate each polymer based on

Figure 6 One three-step cycle of directed evolution starting at the top

trillions of ribozymes, each with slightly different sequences and func-

1. Start with a large population of ribozymes composed of sequence

The scientists constructed 1014 ribozyme variants derived from the

20 EVOLUTION AND ORIGIN OF CELLS

However, we know so little about ribozymes structure that it is impossible

Dworkin JP, Deamer DW, Sandford SA, et al. Self-assembling amphi-

Non-Living Vesicles Can

Perhaps the most challenging aspect to understand about the origin of

Figure 7 Fatty acid structure and vesicle formation rates. A, Chemical

Non-Living Vesicles Can Compete and Grow 25

Abiotic Vesicle Growth and Reproduction

Table 1 Comparison of abiotic vesicles before and after reproduction.

competition could be experimentally measured. If vesicles could compete,

• Lipids can form through abiotic mechanisms.

30 EVOLUTION AND ORIGIN OF CELLS

experiments that demonstrated the five tenets of natural selections are

Non-Living Vesicles Can

Chapter 2 demonstrated how RNA molecules can function as RNA poly-

Non-Living Vesicles Can Harvest and Store Energy 35

Proteins, 9 Scientific method, operation of

• Cellular Structure and Function by A. Malcolm Campbell and Christopher J. Paradise

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