Origins 25(1):2-48 (1998).
CONTENTS
Foreword
Introduction
Chapter 1: Is There Such a Thing as Life?
Chapter 2: The Matter of Life and Death
Chapter 3: What Makes a Cell Tick?
Chapter 4: Once Upon a Time There was a Molecule
Chapter 5: Message of the Molecules
FOREWORD
PROVING GOD?
Does life have a purpose, or are we here merely by chance? Everyone
has probably been confronted with that question at some point in life. Many of us have
concluded that life does have a purpose, that there is a Creator who had us in mind. But
just when we think we are sure of the answer, some unexpected crisis may bring the
question back to haunt us. Is there anything in nature itself that points to an
intelligent Designer?
In this special issue, Dr. Javor suggests that life itself provides
evidence that there must be a Designer. That evidence can be divided into four arguments.
Dr. Javor's first argument is that living matter is organized into
interdependent systems, arranged hierarchically. A large number of interdependent
components must all be in place in order for the living system to function. The term
"irreducible complexity" has been applied to such systems, with the inference
that such systems require intelligent design to come into existence. An intelligent
Creator is the best explanation for the interdependent systems of living organisms.
A second argument is that the disequilibrium of living systems could
not arise spontaneously. Life is based on many series of interacting chemical reactions,
none of which must be allowed to reach chemical equilibrium. All chemical reactions tend
toward equilibrium, but chemical equilibrium in living cells means death. How, then, could
non-equilibrium conditions originate in a nonliving system? There seems to be no
naturalistic answer to this question. An intelligent Creator provides the best available
explanation for the origins of the chemical disequilibrium that is responsible for making
cells alive.
The third argument is also chemical in nature. What is the source for
the biomolecules required for life? These biomolecules apparently require highly
improbable conditions for their origins. Conditions to produce one essential type of
molecule may prohibit formation of another type of molecule equally necessary for life.
Chance seems unable to produce any of the complex biopolymers needed for life. Molecular
sequences with informational content for specific functions are vital for life processes.
The potential number of different sequences is exceedingly vast, and it seems
inconceivable that the small set of sequences appropriate for life could be preferentially
created by random processes. Again, chance seems an implausible explanation for the
specific informational content of biopolymers. The best available explanation for the
existence of the biomolecules of life is an intelligent Creator.
Dr. Javor's fourth argument is that complex functions, such as seen in
living cells, are highly unlikely to arise by chance. Random aggregations of components
are highly unlikely to produce any useful function. Functionality of complex systems
typically depends on components which are pre-designed. But pre-design implies an
intelligent designer and therefore a purpose. Thus, the complex functions of the living
cell point to an intelligent Creator as the best explanation for their existence.
These are strong arguments for a Creator. However, they should not be
mistaken for absolute proof. God's existence cannot be proved by science. Many intelligent
people have chosen to reject arguments such as those presented here. The point of this
presentation is not to claim that we have no other choice than to accept the existence of
a Creator, but to show that we do have the choice to accept His existence. Not only is it
reasonable to do so, but, in view of the properties of living organisms, it is the best
choice available.
L. James Gibson
The explosion of biological knowledge continues unabated as we enter
the third millennium of the modern era. Highlighting the numerous milestones of
achievement are the successful cloning of "Dolly" from the nucleus of a sheep
udder cell and the accession of complete genomic nucleotide sequences from over twenty
organisms. But our knowledge of life will never be complete until an answer is found to
the question, "How did life originate on Earth"?
It is certain that not too many scientists spend sleepless nights over
this question. Most concern themselves with detailed studies of particular biological
systems, which usually demand their full attention. Whatever the origin of life is, more
practical concerns have to do with understanding the "here and now". In
addition, there is very little funding for scientists to ponder the origin of life on a
full-time basis.
In terms of philosophical interest, life's origin ranks with the most
profound questions ever raised. Wrapped within this problem are far-ranging implications
about the nature of the Universe and our place in it, the meaning and purpose of life, and
predictions about the future course of life on Earth. Our model of life's origin also
impacts our worldview and religious beliefs.
Thinking about life's origin, we can walk on one of two mutually
exclusive paths. Life on Earth could have been created by an extraterrestrial Creator, or
it could have come into existence by a fortunate interplay of nature's forces. Information
about the history of Earth would be helpful in deciding between the two options. If Earth
and the other planets of the Solar System were indeed born out of a spinning cloud of gas
over an extended period of time, as is asserted by many, then it would be easier to
suppose that the natural development of life is a continuation of some mysterious ongoing
process in the Universe. The opinion of the majority of scientists and philosophers
certainly leans in this direction.
It is not difficult to appreciate why this is so. Scientists are
trained to believe that science can explain and solve any problem. This intrinsic optimism
is essential to motivate scientists to wrestle new knowledge from the Unknown. With regard
to cosmic questions, if one supposes a universe without a Creator, the green light is on
to discover the nature of the mindless mechanisms that were responsible for the existence
of everything about us. Furthermore, if natural forces were able to accomplish so much
creative work, then it is incumbent on scientists to learn more about these forces and
possibly harness them.
But here a problem arises. Scientists are at their best when they study
repeatable phenomena. At present, no solar system is forming before our eyes. Even worse,
we do not see natural forces producing living organisms from solely nonliving matter. Yet
the millions of different life forms we see around us had to originate from somewhere! The
scientist, working on the assumption that there has to be a natural explanation for the
origin of life, becomes a detective. He is looking for clues to show how Mother Nature
brought life to Earth. Experiments are done to test which primordial scenario could more
likely bring life into existence.
Most scientists regard the postulate that our world is here as a result
of a Creation event as resorting to "magic" instead of a logical explanation
— an abandonment of science. It does not help matters that the story of Earth's
creation by a Creator comes from a manuscript that is over three-thousand years old. Since
then much has been learned about living things, our world and the Universe. Is it not
possible that if the ancients had our scientific knowledge, they would have reported the
story of the creation of Earth differently?
We do not know the answer. What the ancient biblical record reports is
that Earth and its biosphere were brought into existence in a creation event that took six
days for the Creator to accomplish. To most scientists, this sounds incredible. However, a
close look at what is occurring in the biosphere reveals many incredible facts.
This brief monograph was written to champion the views of a minority in
the scientific community. This minority holds that it is possible to accept this ancient
report of Earth's creation at face value — and still be a true scientist. But the
main purpose is to go a step further. It will be argued that a close examination of life
can lead observers to the logical conclusion that life itself is an actual evidence
for creation.
This subject is presented from a biochemical perspective, that is,
looking at living matter at the level of atoms and molecules. Although the use of
technical terms could not be avoided, they were kept to a minimum. The intent was to
communicate as clearly as possible the important molecular concepts undergirding life. It
is this writer's conviction that these may be understood without possessing a formal
education in chemistry or biochemistry. The biochemical concepts presented here should be
useful to all readers, regardless of their philosophical orientation, even if they cannot
accept this writer's conclusions.
ACKNOWLEDGMENT
The author would like to express appreciation for the insightful comments and helpful suggestions from the reviewers of this manuscript. Any remaining errors are this writer's responsibility.
CHAPTER 1
IS THERE SUCH A THING AS LIFE?
"Life is a spiritual pickle which keeps the body from decay".
A. Bierce
It was Dr. Albert Szent-Gyorgyi, a Nobel prize-winning biochemist,
who wrote: "Life, as such, does not exist".1 Most of us would quickly
disagree with him, Nobel prize notwithstanding, because we know that life is all around us
in the forms of people, animals, and plants.
We may not have noticed that he did not actually write "life does
not exist", but rather "life as such" does not exist.
"What we can see and measure are material systems", continued Dr. Szent-Gyorgyi,
"which have the wonderful quality of 'being alive'".1 That is, one
cannot put "life" in a test tube. There is no freestanding entity called
"life". The Hungarian-born scientist did not deny the concept of life, only that
it can exist autonomously, apart from material systems.2,3
Living organisms blanket the Earth so extensively that a typical gram
of soil will contain at least ten thousand microbes. Spores (inert forms of
microorganisms) swarm in the air, and specimens of marine life have been seen in the
deepest recesses of the oceans, several kilometers in the deep rocks, where hydrostatic
pressures approach 1000 atmospheres.
Not only are living organisms everywhere, they come in an astonishing
array of forms. It is estimated that the number of diverse species on our globe runs into
the millions!4 Their combined activities make Earth's surface a throbbing web
of constant change.
An important aspect of the biosphere is that diverse orders of
organisms support the existence of each other. A prime example is the work of
nitrogen-fixing bacteria, without which plants could not access the abundant nitrogen
available in the air. Soil microorganisms and bacteria living in the roots of certain
legumes in symbiotic relationship convert the nitrogen gas in air to water-soluble
nitrates and nitrites. Plants then use these for their growth.
Plants also utilize carbon dioxide from the air to manufacture
carbohydrates, harnessing solar energy. This process, photosynthesis, liberates oxygen.
Non-plant organisms use oxygen in generating energy by burning up plant material and by
releasing carbon dioxide as waste. This relationship between plants and non-plants is
illustrated in Figure 1.1.
FIGURE 1.1. Photosynthesis and the carbon-oxygen cycle throughout the biosphere.
The mutual interdependence of organisms, as seen in the biosphere
today, brings into question whether there ever was a time when only a single form
of life existed. While evolutionists have always insisted that this indeed was
the case, recently there is a reluctance to become specific about the nature of the
putative precursor organism(s) of modern life forms. This happened partly because of the
discovery that the chemical makeup of heat-tolerant microorganisms seems to be more
similar to eukaryotes (cells with nuclei), than to other forms of bacteria. Thus the
previously perceived, clearly defined, relative positions in the hierarchy of eukaryotes
over bacteria became bluffed.
An older pictorial representation of how different organisms were
supposed to have evolved from each other is shown in Figure 1.2. All life forms were
believed to have originated from ancient "prokaryotic cells".
FIGURE 1.2. An earlier version of the postulated evolutionary relations of the major life forms.5
This evolutionary bias is seen in the commonly used term "prokaryote", meaning "before kernel" in Greek, to designate any bacterium. (The term "kernel" represents the more commonly used word "nucleus".) The latest evolutionary scheme, shown in Figure 1.3, features a phylogenetic tree, where the trunk and the branch-points are unidentified and it is no longer clear whether the putative evolutionary ancestor was with or without a true nucleus.
FIGURE 1.3. Phylogenic relationships among life forms based on ribosomal RNA sequences.6
The great variety and abundance of living organisms on Earth is in stark contrast to the apparent sterility of our cosmic neighborhood. Based on several decades of probing, there is no hard evidence to suppose that any extraterrestrial life forms exist in the solar system.7 Furthermore, in the past few years very intensive "listening" has been underway for intelligent extraterrestrial radio signals,8 again, so far with no results. The apparent uniqueness makes the study of life all the more exciting.
GRAPPLING WITH THE DEFINITION OF LIFE
Entire fields of knowledge are connected with studies of living
organisms, i.e., biology, microbiology, biochemistry and biophysics. Yet after two
centuries of dedicated study we still do not have a very satisfactory definition of life.
For example, one dictionary defines life as "the property or quality that
distinguishes living organisms from dead organisms and inanimate matter, manifested in
functions such as metabolism, growth, response to stimuli and reproduction".9
This definition accurately describes in a general way the most recognizable features of
living organisms, but it does not illuminate the core concept of life. It leaves
unspecified what "that property or quality" is, which enables matter to behave
in such a unique manner that the term "life" is required to describe it.
Many forms of living matter exist as hierarchies of increasingly
complex structures. Cells join to form tissues, tissues interact to fashion organs, and
organs compose organisms. The term "life" has different technical meanings,
depending on whether it refers to cells, organs or organisms. This concept may be seen
when upon the unfortunate death of an accident victim, his or her organs (which are still
"alive") may be transplanted into another person. Under appropriate conditions
the new organ will continue to "live" because its individual cells are alive and
they interact with each other harmoniously to carry out the organ's functions. It is the
cells of the organs that are the smallest units of life. When they die, life disappears.
Thus a good place to begin the study of life is the cell.
Deciphering the composition and workings of cells on the molecular
level started in earnest at the beginning of the twentieth century when scientists reached
a sophisticated understanding of organic chemistry. Knowledge of the operation of living
cells continues to grow to this day at a dizzying pace. As of the middle of 1999 the
complete genomic structures of twenty-three organisms are available.10 With the
help of computer analysis it has been possible to parse the chromosomes of these organisms
into genes. Furthermore, utilizing the concept that genes with similar nucleotide
sequences often code for proteins with similar functions, educated guesses are made about
the roles of newly found genes. Within a few years we may have a complete understanding of
the internal workings of some bacterial cells.
Beyond achieving an ever-clearer grasp of life-processes, scientists
are now able to alter organisms by placing new genes into them. Optimism is rampant that
soon we will understand the molecular secrets of cellular differentiation, the formation
of diverse daughter cells from one parent cell. Currently a worldwide effort is underway,
with the leadership of the United States, to determine the nucleotide sequence of the
entire human genome, some 3 to 4 billion nucleotides long. Such knowledge, it is claimed,
will enable us to find out how cancer develops and how its spread may be arrested. We may
also gain a better understanding of a host of other diseases which are caused by
aberrations in the genetic material. Doubtless, we live in the golden age of biology, and
we may eagerly anticipate many existing discoveries in the near future! As comprehension
of the unique properties of living matter reaches unprecedented heights, we are
positioning ourselves to answer the age-old question, What is the origin of life
on Earth?
SUMMARY OF CHAPTER 1
REFERENCES AND NOTES ON CHAPTER 1
CHAPTER 2
THE MATTER OF LIFE AND DEATH
"Material things I touch and taste and see, all other things are immaterial to me".
A. Bierce
What is the difference between living and inanimate matter?
Intuitively, we are confident that we can easily tell the difference between them. But,
with the rapid increase in computer technology, could it happen that artificial
intelligence one day will effectively mimic aspects of human reasoning and behavior? Such
scenarios have already been presented in science fiction, where humans had to deal with a
supercomputer "Hal" in 2001, a Space Odyssey, or with lifelike robots
in the tale The Stepford Wives. What criteria would we use in deciding that those
moving and talking mannequins were lifeless after all?
Paul Weiss, a well-known biologist, wrote a tongue-in-cheek piece
entitled "Life on Earth (by a Martian)".1 In this story, some
Martians came to visit Earth in search of life. After lengthy and careful observation of
our planet, they concluded that life did indeed exist here, and furthermore, one life form
was predominant. They named it the "Earthian" and faithfully chronicled its
every particular. Apparently the Earthians had intricate symmetrical bodies; they moved,
emitted heat and sounds, and ate (mostly liquid food). Sometimes they divided, and they
eventually died. Which organism did the Martians observe and describe? Automobiles, of
course! (The Martians also noticed some rather unimpressive structures associated with the
Earthians, and they concluded that these were some sort of parasites, unworthy of further
study.)
Our capacity to determine whether or not an entity is alive is limited
by our previous experiences with living organisms. If we landed on a new planet, we could
find it difficult to decide whether or not life was present.
LOOKING FOR LIFE ON MARS
In the 1970s the United States sent two automated laboratories to Mars to determine if living organisms existed there. The results of the biology experiments strongly suggested some kind of biological activity on Mars. Carbon dioxide was released when a nutrient-rich liquid mixture was incubated with a scoop of Martian soil. In an Earth-based laboratory, the results would have constituted compelling evidence for the presence of life. Yet scientists interpreting the data which was radioed back from Mars were forced to conclude that in all likelihood Mars was sterile. The reason was that chemical analyses of the Martian surface indicated the complete lack of carbon-containing substances, other than the gas carbon dioxide.2 Now we know that the iron-rich surface, activated by ultraviolet radiation, degraded the radioactive test substances, resulting in false chemical signals. This is an example of carefully designed experiments, aimed at distinguishing between the presence or absence of life on the red planet, that were not quite equal to the task.
IS THERE A DIFFERENCE BETWEEN LIVING AND NONLIVING MATTER?
There are those who see an unbroken continuum between living and
nonliving matter. If this is so, the question of life's origin becomes a moot point.
Viruses, prions, mycoplasmas, rickettsiae and chlamidiae are offered as examples of
organisms that bridge the chasm between living and nonliving. But the differences between
living and nonliving matter are in fact so great that this chasm cannot be spanned.
Although viruses and prions are made from biopolymers, they are no more
alive than the enzyme additives in some detergents. Viruses are lifeless complexes of
proteins and nucleic acids. The biological activity of viruses, including their
replication, is completely dependent on the metabolic activity of the infected cell.
Prions are unique proteins that alter the structure of certain other proteins. The newly
changed proteins in turn acquire prion-type activity, creating a domino effect of protein
alteration. This property of prions renders them infectious. For reproduction, prions,
like viruses, are wholly dependent on live cells.
Rickettsiae, chlamidiae and mycoplasmas, on the other hand, are among
the smallest known living organisms, and are very much alive. The fact that chlamidiae and
rickettsiae are obligate intracellular parasites only means that they have serious
metabolic deficiencies. A clear distinction between living entities and nonliving
substances is essential for a consideration of whether it is possible to go from one state
to the other. For this reason we need to descend into the submicroscopic world of matter.
The elemental compositions of living and nonliving matter differ
greatly.4 The actual chemical determination of living matter is done on
"once-living matter". Before chemists can analyze living matter, they have to
take it apart to isolate its individual components, thereby killing it. Thus the actual
phenomenon of "life" is not amenable to detailed chemical scrutiny. In the very
process of laying hold of isolated "purified" components of living matter,
"life" slips out between the chemists' fingers, and what remains is an inert,
"lifeless" substance. This is so because living cells are composed of
lifeless, nonliving components. The implication is that the difference between
life and death is a question of how biomatter is organized. Therefore, it should be
possible to reverse the killing of cells by restoring them to their pre-disruption state.
Why this has not yet been done in the laboratory will be discussed in the next chapter.
The chemical evolutionary issue can be reduced to answering a two-part
question: 1) Is it conceivable that appropriate types of biomatter could have emerged on a
hypothetical primordial earth; and 2) If these substances existed, could they have
combined to form living matter?
Chemists have obtained valuable information regarding the differences
in the composition of "once-living" matter and of "never-living"
substances. Never-living matter — rocks, minerals, air, water, etc. — consists
of small molecules, often with high oxygen content. These "oxides" are sturdy
substances, stable under heat and mechanical stress. A good example is silicon dioxide
— sand, a most abundant gritty stuff.
Living and once-living organic matter, in contrast, is predominantly
constituted from large molecules which contain thousands, or even millions, of atoms. The
oxygen content in these substances is low, but if oxygen is allowed to interact freely
with these molecules, they lose biological activity. Surrounded by a sea of oxygen, living
matter continually fights the inroads of this element with oxygen-neutralizing mechanisms.
Fragile biomolecules are easily degraded or deformed by heat or mechanical stress.
The large qualitative differences between living and inanimate matter
have been recognized for hundreds of years. Scientists initially thought that biological
material could be produced only by living organisms, so they called these
"organic". But in 1828 the German chemist Frederich Wohler accidentally produced
urea by heating potassium cyanate with ammonium sulfate. Urea was at that time already
recognized as an animal waste product, definitely "organic" in nature.
Scientists quickly realized the implications of this breakthrough discovery. The
production of biological matter did not, after all, depend on "life forces". The
term "organic" was retained to designate all compounds that contain carbon, with
a few exceptions such as carbon monoxide, carbon dioxide, carbides, carbonates, cyanides
and isocyanates.
Although the types of life-forms run into the millions, their general
chemical compositions have important similarities. The gross chemical composition of the
well-studied colon organism Escherichia coli represents the "typical
cell" (see Table 2.1).
TABLE 2.1. Components of Escherichia coli Cells3
Component Percent of Total Weight Molecules Per Cell Number of Different Kinds of Molecules Water 70 24.3 billion 1 Proteins 15 2.4 million approx. 4,000 Nucleic acids 7 255 thousand 660 Polysaccharides 3 1.4 million 3 Lipids 2 22 million 50-100 Metabolic intermediates 2 many millions 800 Minerals 1 many millions 10-30
The high water content of living matter prompted Dr. Szent-Gyorgyi
to write: "we are a walking aquarium".5 We need all that water to
enable most chemical transformations of life to take place.
The importance of water for life-processes can be demonstrated quite
dramatically with freeze-dried microorganisms. We can collect bacteria from growth in a
liquid medium in the form of a wet paste. Rapidly freezing this material and placing it
under vacuum causes the frozen water to leave the bacteria unobtrusively, and the former
wet paste turns into powder. The dried microscopic cells are now in a state of suspended
animation. They are neither alive, nor are they dead. They can be stored indefinitely in
the dried state, without any change in their status. However, by simply mixing the powder
with water and the appropriate nutrients, the dormant cells spring into life once again.
In this procedure we manipulate life on the cellular level by withdrawing an all-important
cellular component. The most remarkable aspect of this process is the reversibility of the
life-processes by manipulating only the water content of the cells!
HOW BIOPOLYMERS ARE PUT TOGETHER
The bulk of dry matter in all organisms (more than 90%) is composed of the biopolymers: proteins, nucleic acids, polysaccharides and lipids. A common feature of these four classes of substances is that they contain many repeats of small building-block substances. Very significantly, all chemical linkages between the building blocks are created by dehydration. That is, the building blocks of all biopolymers are linked by splitting out water between them. This information is summarized in Table 2.2.
TABLE 2.2. How the Biopolymers Are Put Together
BIOPOLYMER BUILDING BLOCK CHEMICAL LINKAGE Protein Amino acid Peptide bond Nucleic acid Nucleotide N-glycosidic and phosphodiester bonds Polysaccharides Monosaccharide (simple sugar) Glycosidic bonds Lipids* Glycerol, fatty acids Ester bonds *Lipids are not true biopolymers, but they often aggregate to form large structures, such as membranes. Also, only a single type of lipid is listed here. In reality, there are many different kinds of lipids, with diverse compositions.
One of the challenges of chemical evolutionary postulates is to explain how these biopolymers could arise in a world assumed to be covered with water. It is a most difficult task to form new chemical bonds by eliminating water in an aqueous environment!
HOW CAN WE HAVE SO MANY DIFFERENT KINDS OF PROTEINS?
The bulk of biomatter is made from proteins. These are a most
interesting and versatile class of materials. In each cell there are hundreds to thousands
of different types of proteins, each with different chemical and physical characteristics.
Such diversity is due to both their great size (they are composed typically of long
strings of amino acids) and to the fact that any amino acid may be one of twenty different
kinds.7 What each protein is capable of doing depends a great deal on the
actual order in which the amino acids are linked. This feature of biology is similar to a
written language.
A word's meaning depends on the sequence of its letters. We choose from
26 letters of the English alphabet to make words. An estimated 500,000 different
combinations of letters in our language are recognized as meaningful. With some effort, we
could come up with many more sets of 500,000 combinations of letters that would be
nonsensical (Dr. Seuss started a nice collection of these). Similarly, the millions of
proteins represent only a tiny fraction of all possible combinations of amino acids.
Misspelling words jeopardizes their meaning. Likewise, for proteins to
function properly their amino acids must follow each other in a correct order.8
For example, the oxygen-carrying component in our blood — hemoglobin — is built
from 4 separate protein chains, each of which is a string of 142-146 amino acids. In an
inherited illness called "sickle-cell anemia", the gene for one of the protein
chains of hemoglobin sends out incorrect information to the protein-making complex. This
results in placing a wrong amino acid in the sixth position of a specific sequence of the
146. This alteration is enough to lead to distortion of the red blood cell, to anemia, to
many other problems, and, sadly, to death in many cases. While not all changes in
amino-acid sequences have such drastic consequences, this somewhat extreme example
underscores the importance of the correct order of amino acids for proteins.
The amino-acid sequences of proteins are crucial components of the
biological information content of cells. Proteins themselves are considered informational
biomolecules. But how does the protein-building apparatus know the correct
amino-acid sequence for each of the thousands of different proteins found in the cell?
The answer is that the genes of each cell are
libraries containing just such information. When the cell needs to make a certain type of
protein, it sends a copy of its amino-acid sequence information to the
protein-synthesizing complex. Bacteria, with a thousand different proteins, have a minimum
of a thousand genes. The recent triumph of obtaining the complete nucleotide sequence of
organisms has enabled us to count their genes and even to assign a function to many of
them. Table 2.3 shows a compilation for three microorganisms: Haemophilus influenzae
(1743 genes), Mycoplasma genitalium (471 genes) and Escherichia coli
(4288 genes). The first two organisms grow only inside humans in a nutritionally rich
environment. Escherichia coli, on the other hand, can proliferate independently
and may be considered a free-living organism.
TABLE 2.3. Distribution of Genes by Their Functions in Three Bacterial Cells9
Function H. influenzae U. genitalium E. coli Amino acid metabolism 68 1 131 Biosynthesis of cofactors, prosthetic groups and carriers 54 5 103 Cell envelope 84 17 195 Cellular processes 53 21 188 Central intermediary metabolism 30 6 188 Energy metabolism 105 31 243 Fatty acid and phospholipid metabolism 26 6 48 Purines, pyrimidines, nucleosides and nucleotides 53 19 58 Regulatory functions 64 7 45 Replication 87 32 115 Transcription 27 12 55 Translation 141 101 182
From this table it is seen that E. coli requires more than
1500 different proteins for growth. Most of these proteins are biocatalysts —
"enzymes" — that promote specific chemical conversions.
As for the biological functions of the other three classes of
biopolymers, nucleic acids are the repositories and transmitters of the genetic
information; lipids segregate the interior of the cell from its environment and, along
with polysaccharides, serve as energy reserves. In microorganisms, polysaccharides also
constitute part of the cell's outer envelope.
The non-polymeric, small metabolites are only a small portion of the
cell by weight, but their presence is absolutely essential for life-processes. In fact, it
is the chemical transformations of these compounds that make life possible. (This topic is
explored further in the next chapter.) Metabolic intermediates represent transitional
substances between precursors and building blocks. Building blocks are used, of course, to
make the all-important biopolymers. These in turn are assembled into more complex
supramolecular assemblies and organelles.
Matter is organized into successively more complex hierarchies in
cells. The logical interdependency among cellular components in the vertical hierarchy
parallels nicely the logical ties that connect letters with words, words with sentences,
sentences with paragraphs, etc., all the way to the level of a completed manuscript. This
concept is illustrated in Figure 2.1.
FIGURE 2.1. Organization of matter in the cell.
A crucial difference between biomatter and written material,
however, is that the degree of tolerance for error is much smaller in biology. If words
are misspelled, sentences are garbled, paragraphs do not hang together, or even if entire
chapters are missing from a manuscript, the document may still be partially useful. But
given the tight functional interdependence of its components from precursors and
biopolymers, cells are in trouble with less than a full complement of all their parts.
Each living cell contains thousands of different kinds of substances, present in multiple
copies, and sequestered, in the case of a bacterium, in a volume of a few cubic
micrometers (see Table 2.1).
At the level of supramolecular assemblies and above, the various
strands in Figure 2.1, which represent classes of biopolymers, are intertwined into
increasingly complex entities. The biological information in the genetic material and in
the many protein molecules becomes a coherent whole somewhat the way paragraphs support
each other in a good story. The "story" in this case is the life of the cell.
Besides vertical interdependence, there is also a horizontal
complementation among the components. One illustration of this interdependence is that the
manufacture of proteins requires nucleic acids and, conversely, nucleic acids cannot be
made without proteins. This circular relationship between proteins and nucleic acids from
a chemical evolutionary viewpoint resembles the classic "chicken and egg"
problem.
SUMMARY OF CHAPTER 2
REFERENCES AND NOTES ON CHAPTER 2
CHAPTER 3
WHAT MAKES A CELL TICK?
"Old chemists never die, they just reach equilibrium".
In presenting a case for a tight logical link between analyzing the
molecular aspects of life and the creationist paradigm, it is not enough to enumerate the
components of living matter. Simply knowing the components of living matter is not enough
to account for its biological activity. Living matter behaves differently than its
isolated components. Living cells incorporate selected substances and utilize
them either for energy or as building blocks for growth. They also secrete metabolic
waste. Living cells grow and divide into daughter cells. Lastly, when cells recognize
unfavorable environmental conditions, they make metabolic adjustments to preserve their
existence.1 Living matter gives every indication that it "wants" to
stay alive. This is a property of the complex network of components in living matter. The
whole seems to be more than the sum of its parts. If we collect all of the ingredients
from live cells, lace them in a membrane-enclosed vesicle, we have an inert,
"lifeless" assembly of biomatter. This bag may be stored indefinitely in an
environment hospitable for life, without the actual emergence of life. If we periodically
analyzed the contents of this artificial "cell", we would find little change in
its chemical composition. Such an arrangement of matter is called equilibrium.2
If we sampled the composition of life cells growing in a defined
laboratory setting, surprisingly, the results would be similar, that is, we would find the
chemical composition of live cells quite constant. But instead of the term
"equilibrium", we say that matter in live cells is in a "steady
state system". The significant difference between the two is the dynamic flux
of matter through live cells.
A mechanical illustration of this difference is shown in Figure 3.1.
Here, the contents of both vessels remain unchanged over time, but there is constant
movement of liquid through vessel A. The flow of molecules through cells is an
essential feature of life. (In contrast, the liquid in container B is stagnant.) The
movement of water through a compartment, representing the flux of matter through the cell,
is an oversimplification of what actually occurs. In reality matter changes as it travels
through the cell. The incoming precursors (biomonomers) are simple substances which are
gradually built up to successively more complex structures. In Figure 3.2 this is
represented by the arrows on the right, marked "biosynthesis" and
"assembly".
FIGURE 3.1. A comparison of the concept of steady state (A) and equilibrium (B).3
FIGURE 3.2. Movement of matter through the cell.
To complete the circuit, the biosynthetic flow of matter is balanced
by a set of degradative pathways. The very existence of degradative pathways in the cell
is remarkable, in view of the fact that biopolymers and the successively more complex
structures are made at prodigious expenditure of energy. Their constant degradation and
remodeling would seem a phenomenal waste. But we now know that in the course of
metabolism, components sustain oxidative damage with time. Accumulation of damaged
metabolites would clog the cell's machinery. The constant turnover of biomatter preempts
such a scenario.
However, since both biosynthesis and degradation are occurring in the
same cell, the two processes need to balance. An excess rate of degradation over
biosynthesis would be particularly disastrous. Thus, the rates of all metabolic processes
have to be coordinated for this tightrope act of metabolic symmetry (steady state). Figure
3.2 also shows the linkage between energy usage and biosynthesis. The substance
abbreviated as "ATP" is the chief carrier of chemical energy in the cell. Most
frequently, when chemical change requires input of energy, ATP (adenosine
triphosphate) is degraded to ADP (adenosine
diphosphate). The sum total of the chemical changes in
the cell equals the essence of life.
WHAT ARE CHEMICAL REACTIONS, ANYWAY?
Chemical reactions are nothing more than the movement of bonding
electrons around and between atoms. These electrons hold groups of atoms in clusters
called molecules. The fascinating property of matter is that these clusters behave very
differently than their constituent atoms.4 For example, clusters of oxygen
atoms and clusters of hydrogen atoms by themselves are gases. Hydrogen is very flammable,
even explosive. But when an oxygen and two hydrogen atoms are combined into a cluster,
water forms. The conversion of a mixture of oxygen gas and hydrogen gas to water is a
chemical reaction.
In chemical reactions, atoms and their bonding electrons leave an old
cluster and join a new one. As a result of changes in their atomic compositions, the
chemical properties of clusters change. By "chemical property" we mean the
tendency of molecules to acquire or give up atoms.
Why would atoms and their bonding electrons jump from one atomic
cluster to another? This is equivalent to asking why chemical reactions occur at all.
Chemists tell us that the driving force behind chemical changes is the intrinsic tendency
of all matter to exist in the lowest possible state of energy. This is why balls roll
downhill spontaneously, electricity flows from the negative to the positive pole, and hot
objects tend to cool down to the temperature of their environment.
Chemical reactions can be compared to a market transaction where
molecules trade atoms in order to shed some of their energy content. Just as in business
there are sellers and buyers, in chemical reactions there are atom clusters that can
achieve lower energy states by rearranging or giving up some of their atoms. These are the
"sellers". Other clusters — the "buyers" — receive new
atoms, and their energy levels increase. The important consideration for such chemical
transactions to occur is that when all the energy gains and losses are totaled, there
should be a net lowering of the overall energy content of the system.
Chemical changes take a finite amount of time. Some rearrangements are
faster than others. Chemists have found that if the vibrations of atoms are speeded up by
raising the temperature, the chemical change is more rapid. There are also helper agents
— catalysts — which facilitate reactions. Remarkably, almost every chemical
change in the cell has a facilitator catalyst — an "enzyme". Enzymes are
very large protein molecules, often hundreds of times larger than the atomic groups they
manage.
WHY ENZYMES?
The role of catalysts is the speeding up of chemical conversions. In
the case of living matter, why are catalysts necessary? Why must there be an increase in
reaction rate? If all chemical changes in the cell would slow down due to lack of
catalysts, what would happen? The answer is: chaos. Without specific catalysts guiding
molecules through precise paths of chemical changes, numerous "unauthorized"
chemical side-reactions would occur. This is due to the propensity of substances to
interact with each other in more than one way. Only those chemical changes which
contribute to the economy of the whole cell are useful.
This is a significant point. Individual chemical changes in the
cell (even dozens or hundreds of them) have little utility, unless their end products
belong in the closely knit network of substances needed by the cell. The meaning
of each chemical reaction and of each reaction product is derived from the fact that the
reaction products contribute to the functions of the living cell. All other chemical
conversions are wasteful and detrimental to the cell.
A reaction always runs its course, whether catalyzed or not, by
producing a characteristic ratio of reaction products and starting materials. When this
ratio is achieved, no further net chemical change happens under the
conditions of the reaction, and the substances are said to be in a state of chemical
equilibrium (Box 3.1).
BOX 3.1. TIME COURSE OF A CHEMICAL REACTION
In a typical chemical reaction between substances A and B, two new substances form, C and D:
A + B ®
¬C + D At the beginning of the reaction there are only the starting substances A and B.
During the reaction the amounts of A and B diminish and the amounts of products C and D increase. The products C and D react to re-form A and B. This is the reverse reaction.
At the end of the reaction there will be a constant amount of all four substances A, B, C, and D, because forward and reverse reactions balance each other. This state is called chemical equilibrium.
For every reaction there is an "equilibrium constant" Keq, a term which combines the characteristic ratios of reaction products and reactants at equilibrium. Reactions at equilibrium are of little use to the cell because it is the chemical changes that drive the phenomenon of life. In fact, when all of the reactions in the cell reach their equilibria, death occurs. This makes the roles of the enzymes paradoxical. They are required to keep the flow of materials on useful tracks preventing side-reactions, but the enzymes push the chemical conversions rapidly toward equilibria which, if achieved, doom the cell. To avoid disaster, the chemical conversions are organized into what amounts to "assembly lines" on the cell. The product of one reaction becomes the starting material for the next. This arrangement prevents the accumulation of products (Box 3.2).
BOX 3.2. THE LOGIC BEHIND CHEMICAL PATHWAYS
Catalyst #1
Reaction #1:
Glucose + ATP ®
¬Glucose-6-phosphate + ADP By itself, this reaction stops at equilibrium.
But a second reaction occurs in the cells:Catalyst #2
Reaction #2:
Glucose-6-phosphate ®
¬Fructose-6-phosphate uses up one of the products of the first reaction, preventing the formation of equilibrium. These two are the first two reactions in a ten-step biochemical pathway called "glycolysis".4
In the hundreds of chemical assembly lines, also called
"biochemical pathways", there are multiple chemical conversions. Some of these
build larger and larger molecules, while other pathways degrade substances to smaller
pieces. Degradation of energy-rich matter is coupled to the efficient capture of chemical
energy. This energy drives the growth and movement of the cell. Figure 3.2 is an attempt
to summarize the work of the metabolic paths in the interacting networks.
The metabolic fabric of the cells is seamless; there are no loose ends.
All biosynthetic paths lead to the production of more biomatter and growth, and all
degradative processes result in the harness of useful chemical energy and in the secretion
of waste. Each biochemical pathway has a single "rate limiting" step which
governs the rate for output of that chemical "assembly line." The enzyme
catalyzing this regulatory reaction is able to speed up, slow down, or even arrest the
output of that pathway, depending on the amount of product already available to the cell.
Thus, wasteful oversupply of metabolic components is prevented. This is one of the kinds
of sensing mechanisms which monitor the composition of the intracellular environment. As
excesses or shortages of biochemical intermediates develop, appropriate regulatory
adjustments are made in order to preserve the "steady state" of the cell. In a
well-functioning cell, the amounts of each of hundreds or thousands of substances remain
close to constant during a steady flux of material through the system. This
steady, non-equilibrium state of matter is an absolute prerequisite for the phenomenon of
life.
CHEMICAL DIFFERENCE BETWEEN LIFE AND DEATH
If a single reaction within a metabolic pathway were to reach
equilibrium in the cell, it would constitute a metabolic block, because (by definition of
what equilibrium is) there would be no net conversion of matter past that point. Some
metabolic blocks would not be fatal when alternative pathways could compensate the cell.
But when all the reactions in the cell reach their equilibria, life processes cease, and
the cell dies. Such a state can be achieved in a bacterial cell such as E. coli,
by using an organic solvent to poke holes in its membrane. When the membrane is opened the
cell is no longer capable of generating energy (an intact membrane is essential for this
process). The chemical conversions cease, and soon every reaction will reach its
equilibrium. The difference between non-equilibrium and equilibrium is nothing
less than the difference between life and death.5
The equilibrium status of a single chemical reaction can be converted
into a non-equilibrium state temporarily by either adding more reactants or by removing
one or more reaction products. The non-equilibrium state will last only as long as one of
these measures continues. The same considerations apply to biochemical chain reactions
(pathways) that have reached equilibrium. The equilibrium of each pathway may be
eliminated if it is provided with additional starting material and if the final product is
removed. This concept is illustrated in Box 3.3.
BOX 3.3. HOW TO UNDO THE EQUILIBRIUM OF AN ENTIRE PATHWAY
Consider a pathway
A E1
®
¬B E2
®
¬C E3
®
¬D E4
®
¬E E5
®
¬F E6
®
¬G at equilibrium. A through G are metabolites; E1 through E6 are enzymes.
The equilibrium constant for the pathway
Kpathway = *K1 *K2 *K3 *K4 *K5 *K6,
where K1 through K6 are the equilibrium constants of the individual reactions.
Simplification of this expression yields:
Kpathway = [G]/[A]
It is possible to undo the equilibrium status of this pathway by supplying more substance A and removing substance G. In the cell this would be possible only if the pathways supplying A and removing G were at non-equilibrium.
Thus, if the non-equilibrium steady states of all reactions could be
restored, the dead cells would live again. In theory this could be accomplished by
restoring each of the hundreds of interconnected biochemical pathways to its
non-equilibrium condition (Box 3.3). First any breach of the integrity of the cell's
membranes would have to be repaired, and a continuous supply of starting substrates of the
first reactions of every pathway would have to be supplied in order to launch all of the
chemical processes, more or less simultaneously. Such a procedure would begin turning the
metabolic wheels of the organisms, and it would live again.
While we can transfer any substance across a cell membrane by
"electroportation" (a short pulse of high voltage),6 the continuous
delivery into cells of large numbers of different metabolites for which there are no
built-in transport mechanisms is beyond our current technical capabilities. Herein lies
the reason why we cannot reverse death on the cellular level.
Closely akin to this is the problem of generating life from an inert
collection of biomolecules. To accomplish this, one would need to bring all of the needed
substances into a membrane-enclosed space (enzymes, substrates, genetic material, various
subcellular organelles) and then create a state of non-equilibrium among the hundreds of
substrates of the enzymes. The difficulty in accomplishing this rests with the propensity
of enzymes to establish equilibrium rapidly among their substrates. Thus far it has not
been possible to overcome this challenge even in the most sophisticated modern laboratory.
What would be required here is to be able to manipulate selected molecules
in the manner of "Maxwell's Demon."
HOW MAXWELL'S DEMON WORKS
This theoretical creature occupied space between two interconnected
compartments which were filled with gas molecules, and the demon could keep the
slow-moving molecules in one compartment and send the fast-moving ones into the other.
Such action would result in one compartment becoming warm and the other cold. In other
words, Maxwell's Demon could take a system at equilibrium and manipulate it into a
non-equilibrium state.
Whether this feat can be accomplished in the future by scientists is
not known. Manipulation of individual atoms and molecules is now becoming possible, using
"atomic force" microscopy.7 It is certain, however, that a
state of non-equilibrium cannot arise from an equilibrium state spontaneously.
But this is precisely what would be required if a live cell were to emerge from a dead
cell (Box 3.4).
BOX 3.4. MINIMUM REQUIREMENTS FOR CELLULAR LIFE
- Appropriate types and quantity of biomolecules plus water (Table 2.1).
- The capacity to accomplish the metabolic and regulatory tasks, outlined in Table 2.2
- A steady state non-equilibrium status among the chemical reactions.
The discussion of life in these three chapters emphasized both the complexity and the dynamics of the chemistry undergirding this amazing process. The minimum requirements for cellular life are summarized in Box 3.4. With these facts in the background we now turn to the current postulates of primordial abiogenesis that attempt to explain how life arose on Earth from nonliving matter.
SUMMARY OF CHAPTER 3
REFERENCES AND NOTES ON CHAPTER 3
CHAPTER 4
ONCE UPON A TIME THERE WAS A MOLECULE ...
"Primordial soup again?"
— caveman to wife in a Gary Larson cartoon"I have made it my rule not to read this literature on prebiotic evolution until someone comes up with a recipe that says 'Do this and do that, and in three months things will crawl in there'".
Max Delbruck1
The explosive increase in understanding living matter directs our
attention forward, toward the utilization of this great body of knowledge for curing
mankind's illnesses. At times, though, scientists glance backwards to gain a perspective
on the present, and to ask, "How did this rich ecosystem of Earth come into
existence?" The technical details of the answer vary from year to year, but the big
picture has not changed for many decades. It is basically as follows.
The Earth formed from a spinning mass of gaseous matter — the
"solar nebula" — by a process of accretion. Once this primitive, lifeless
planet cooled down it was largely covered by an ocean. Its atmosphere contained nitrogen
and carbon-containing substances, but was devoid of oxygen. Then a process called chemical
evolution began on this primordial Earth. It resulted in the emergence of the first living
cell and initiated biological evolution.
A recent text of biochemistry states these concepts succinctly:
The origin of life probably occurred in three overlapping phases: Phase I, chemical evolution, involved the non-instructed synthesis of biological macromolecules. In phase II, biological macromolecules self-organized into systems that could reproduce. In phase III, organisms evolved from simple genetic systems to complex multicellular organisms.2
Undergirding this scenario of life's origin is an unstated, but very
firm, conviction that under conditions where living organisms can exist, nature will bring
life into existence. This notion arises from two indisputable facts: 1) on planet Earth
conditions are favorable for life, and 2) our planet is teeming with a multitude of living
organisms. Despite the circularity of this argument, if one a priori discounts
the possible existence of a supernatural Creator, all that remain are naturalistic
scenarios for the origin of life.3 What follows here is a look at laboratory
experiments and theoretical considerations that have been produced in support of
evolutionary models.
Scientists are at their best when they study matter under well-defined
conditions. While it is true that the time scope of chemical evolutionary postulates
covers thousands or even millions of years (time segments unavailable for individuals), the
only function of time in these postulates is to increase the number of opportunities for
interaction between substances. Scientists can accomplish this in the laboratory
by various means that compress the time scale of the chemical evolutionary events to
manageable size.
We ought to be thankful for the efforts of stalwart chemists who have
dared to test the validity of their postulates in the laboratory. Their work gives us a
feel for the experimental challenges that confront chemical evolutionists. They are
following standard practice in science, in contrast to some in a field of chemical
evolution who appear content issuing theories, without a scintilla of experimental
evidence.4
During the 1960s and 1970s, considerable experimental work was done on
the behavior of matter under postulated primordial conditions.5 These
conditions were very diverse because a "primordial world" could be anything that
was sterile and devoid of oxygen. The experiments were conceived to test the validity of
the following theoretical transformation of matter on the primordial Earth:6
Stage 1 (early Earth atmosphere) ® Stage 2 (hot dilute soup) ® Stage 3 (polymerization) ® Stage 4 (protocell formation) ® Stage 5 (true cell formation).
CONSIDERATIONS OF THE EARLY EARTH'S ATMOSPHERE AND THE FORMATION OF THE PRIMORDIAL SOUP
Reduced atmospheric carbon dioxide is the only potential source for
the production of biologically relevant organic substances. The current atmosphere, which
contains 20% oxygen, is very oxidizing. Under synthetic conditions with oxygen present,
carbon dioxide yields only biologically irrelevant materials. Moreover, in the presence of
oxygen biologically relevant substances degrade.
Therefore it is axiomatic to any chemical evolutionary scenario that
the primordial atmosphere was free of oxygen. Experiments with gaseous mixtures have
varied from methane-ammonia-water (most reduced) to carbon dioxide-nitrogen-water (most
oxidized).
The classic experiments of Stanley L. Miller, in the laboratory of
Harold C. Urey,7 circulated the gases methane, ammonia, and hydrogen in a
closed system. The apparatus also included boiling a mixture of water and electrodes for
spark discharge that simulated lightning. After a week, four of the twenty amino acids
found in proteins were produced, along with other organic substances. Later this
experiment was repeated using nitrogen and a trace amount of ammonia. With this gas
combination, ten different amino acids were made along with other nonbiological amino
acids and organic substances.
The Miller experiment was modified by other investigators, who used
heat, ultraviolet radiation, and acoustic shock waves in place of sparks as an energy
source. Additional gases — such as ethane, hydrogen sulfide, carbon monoxide, or
hydrogen cyanide — were added. These efforts resulted in the production of most of
the amino acids, except histidine, arginine and lysine.8
The synthesis of adenine, one of two purine components of nucleic acids
(DNA, RNA), was reported from high concentrations of hydrogen cyanide in the presence of
large amounts of ammonia.9 Prebiotic scenarios that contain large
concentrations of ammonia and hydrogen cyanide are difficult to postulate. Adenine can be
formed from hydrogen cyanide, without ammonia, in the presence of sunlight.10
The production of guanine — the second purine — under prebiotic conditions is
less well-studied. However, it is known that guanine can be produced by reacting one of
the intermediates of adenine synthesis with cyanogen, a substance derived from hydrogen
cyanide.11 The three pyrimidines needed for nucleic acid synthesis —
uracil,12 cytosine13 and thymine — were synthesized by reacting
selected substances (which could have been potentially available) under prebiotic
conditions.
Another important class of ingredients — sugars — could have
been produced in a primordial environment by the reaction of formaldehyde with alkaline
substances.15 Two types of sugars, ribose and 2-deoxyribose, are essential for
building nucleic acids. These substances link up with purines or pyrimidines and a
phosphate to form nucleotides, which are the building blocks of nucleic acids (Table 2.2).
The chemical linkage between sugars and a purine or pyrimidine occurs with the loss of two
hydrogen and an oxygen, the equivalent of water. This process may not appear improbable,
but thus far it has not been possible to achieve in a simulated primordial environment.16
In addition to amino acids, there has been successful laboratory
synthesis of purines and sugars, short chain fatty acids, fatty alcohols and di- and
tricarboxylic acids under simulated primordial earth conditions.17 These
achievements supported the postulate that necessary organic substances were collected in a
primitive ocean, forming a "primordial broth". Initially scientists estimated
that about 3% of the primordial ocean by weight could have consisted of organic
substances.18 This estimate was made before the realization that on a prebiotic
earth several factors would reduce the amounts of organic matter in the ocean. The very
sources of energy that created organic compounds would also destroy some. In addition,
other chemical interactions including water's destructive effect would have diminished the
amounts of organics in the primordial ocean by a factor of ten thousand less than
originally proposed. This is the level we actually find today in the North Atlantic Ocean!19
There is no geological evidence available for the existence of a primordial soup either
worldwide or in smaller locations.20
Oxygen has been excluded from all prebiotic experiments, because its
presence precludes the production of biologically useful substances. Yet no prebiotic
scenario can rule out the presence of oxygen. High-energy ultraviolet light, which is now
filtered out by a layer of ozone (a very reactive form of oxygen gas) high in the
atmosphere, is capable of degrading water to oxygen and hydrogen. Hydrogen escapes from
the atmosphere, whereas oxygen remains. On ultraviolet photographs of Earth taken from the
Moon during the Apollo-16 mission, there is a large cloud of atomic hydrogen enveloping
our planet, extending outward some 40,000 miles. The only conceivable source of this
hydrogen is the extensive photodissociation of water vapor above the ozone layer.21
Thus laboratory simulations of the primordial production of biomonomers
leave substantial unresolved problems that in any other field of science would result in
the dismissal of the underlying theory. In this case, however, the attitude is:
"since we know that chemical evolution is true (we are here after all!), we just have
to keep on looking for answers".
An ingenious solution to a seemingly impossible predicament is the
notion that many of the required biomonomers were delivered to Earth by interstellar dust,
meteorites and comets.22 This mechanism provides, in theory, unlimited amounts
of starting material for chemical evolution to proceed.
POLYMERIZATION
Although there are some positive laboratory results showing how
biomonomers may have arisen in a primordial setting, there is an almost complete meltdown
in experimental efforts to show how biopolymers may be formed. If one stipulates the
availability of an unlimited supply of primordial biomonomers, three major obstacles
surface on the way toward producing proteins and nucleic acids. (The other two classes of
biopolymers — polysaccharides and lipids — are not considered here, because they
could be formed enzymatically if the correct proteins were available.)
The obstacles to forming proteins and nucleic acids are:
Our biotechnology is at such a level now that we can manufacture
protein and nucleic-acid fragments at will in the laboratory. These processes involve
chemical activation of the linkage groups of the building-block substances, meanwhile
protecting the rest of the molecule from participating in the linkup. The joining of these
modified building blocks occurs in the total absence of water.24 The order of
amino acids and nucleotides is determined by the experimenter.
Formation of a peptide bond (see Table 2.2) between two amino acids is
not favored thermodynamically. [It has been calculated that if one started with a very
concentrated solution of amino acids (a concentration of "one mole per liter"),
it would be necessary to have a volume 1050 times the Earth, in order to form
spontaneously a single protein molecule, 100 amino acids long25]!
Therefore it is not reasonable to suppose that amino acids would ever
link up into chains while in the primordial soup. Heating pure solutions of amino acids to
200°C for 6-7 hours has led to the formation of random protein-like polymers.26
But many of the peptide bonds between amino acids were unnatural in these
"proteinoids", and the sequence of amino acids reflected the composition of the
initial mixture. Moreover, no suggestion exists to explain how a catalytically active
proteinoid could be reproduced. Most recently it was shown that up to six residues of the
amino acid glycine could be linked under high pressure in a simulated thermal vent.27
The authors offer a reasonable theory that the chain elongation occurs through a cyclic
intermediate (diketopiperazine). However, this mechanism implies that other amino acids
may not be able to elongate, because their structures prevent the formation of this cyclic
intermediate.
Biomonomers (amino acids or nucleotides) may be linked to each other in
the presence of a chemical condensing agent which traps the water molecules that are split
out between the monomers. But in an aqueous environment these agents will interact
preferentially with the large amount of water in the environment. Thus, condensing
materials work only in nonaqueous environments.
The other two grave difficulties with primordial polymer formation
— the exclusive use of only "left-handed" or "right-handed"
monomers for protein or nucleic-acid synthesis, and the source of information that resides
in the sequences of biomonomers in proteins and nucleic acids — have not been
satisfactorily addressed.
The synthesis of either proteins or nucleic acids under prebiotic
conditions has yet to be accomplished. These necessary processes can be considered the end
of the chemical evolutionary road paved only in scattered patches with experimental
results. If one wishes to proceed beyond, it is necessary to traverse on the rocky terrain
which consists mostly of speculations.
PROTO CELL AND TRUE CELL FORMATION
Using Zubay's terminology, it is envisioned that the first phase of
chemical evolution consisted of the "non-instructed" phase,2 where
the emphasis was on the synthesis of random polymers of either proteins or nucleic acids,
or both. Current thinking is leaning toward a random synthesis of ribonucleic acid,
because it was discovered recently that some ribonucleic acids have catalytic activity.28
This discovery led to the speculation that the first biopolymers had both catalytic and
genetic capacities.
The second phase of chemical evolution is the "instructional
phase", where macromolecules would self-organize into autocatalytic systems. That is,
self-replicating systems would form from mixtures of random RNA or protein molecules.
Somehow such systems would be wrapped into protective membranes, forming
"protocells", the precursors of true cells.
Experimental models of protocells include coacervates (microscopic
droplets) of proteins and nucleic acids,29 proteinaceous microspheres,30
and lipid vesicles.31 These structures have been synthesized in the laboratory
from preformed biopolymers, or from protein-like substances that were obtained by heating
pure amino acids at high temperatures. Without entering into detailed considerations of
each, it can be said that none of these complexes manifest the essential qualities of
living cells. They were aggregates of polymers, predictably held together by physical
forces. As such, they represent experimental dead-ends, without any promise of shedding
light on the mysteries of abiogenesis.
But having come this far in our hypothetical journey on a primordial
Earth, it seems a pity to stop. If self-replicating systems of proteins and nucleic acids
could be found, could these serve as precursors to modern cells? Evolutionary
theoreticians posit that the Darwinian "descent with modification", along with
"survival of the fittest", concept of biological evolution may have been at work
even during chemical evolution.32,33 Thus, through a process of continual
modification, different biopolymers would have been formed, and those with useful
properties would have been retained.
There is an enormous amount of information stored in the structures of
nucleic acids and proteins in modern cells. It has been estimated that one cubic
micrometer (one thousand billionth of a cubic centimeter) of deoxyribonucleic acid (DNA)
encodes 150 megabytes of information. This is more than an order of magnitude greater than
the current CD-ROM optical storage density.34 The complete nucleotide sequence
of the genetic material of Escherichia coli, printed in a standard book form,
takes up about 1,100 pages. A similar effort for the human genome would fill one thousand
volumes of 1,100 pages each.
The rules of grammar define the correct spelling of words and the
proper usage of each word in a sentence. They do not determine the choices of
words. Similarly, although the rules of chemistry determine how biomonomers may
be linked into polymers, they are silent on the order in which these should be linked so
as to have biological significance.
The question is, by what processes would self-replicating systems of
proteins and nucleic acids select for and accumulate biologically valuable polymers? In
abiotic systems no selection pressure exists in favor of biologically useful
polymers! The potential usefulness of biopolymers is manifested only in living
cells. In nonliving matter the biological potential of molecules is of no consequence.
This point is generally ignored by chemical evolutionary theoreticians. A salient example
is the "obcell" hypothesis by T. Cavalier-Smith. He proposes that in the
prebiotic era, membrane-protein complexes known as "inside-out cells" (or
"obcells") formed as precursors of true cells. These structures contained
transport proteins, as well as nucleic-acid replication machinery and ribosomes,35
and somehow had the ability to harness light energy. He gives no indications whether his
"obcell" is alive or dead.
Albert Lehninger, however, clearly states that the hypothetical
protocells should have been alive:
... the first structure possessing 'life' was not necessarily a modern cell, complete with a membrane, a chromosome, ribosomes, enzymes, a metabolism, and the property of self-replication. The minimum requirement is that it could potentially evolve into a complete cell.36
If a cell possessed life, then its molecular components had to be in
steady state non-equilibria. Such a state could be maintained only if the individual
chemical reactions in the protocell were kept from reaching equilibrium. In modern cells
this is accomplished by the linkages of chemical reactions into biochemical pathways and
by coordinating the chemical activities of pathways through regulation of key enzymes. Since
protocells were supposed to have risen from random encapsulation of compounds and their
catalysts, it would follow that their chemical reactions were neither linked into pathways
nor regulated. Thus, chemical reactions in protocells would have been expected to
reach equilibria some time after encapsulation, resulting in dead protocells.
These considerations apply to all postulates of chemical evolution,
regardless whether they approach modern life from the inorganic37 or from the
organic world,4 whether the first postulated biopolymers were RNA38
or proteins,30 and whether life supposedly evolved on this planet or somewhere
in outer space.
SUMMARY OF CHAPTER 4
REFERENCES AND NOTES ON CHAPTER 4
CHAPTER 5
MESSAGE OF THE MOLECULES
Question: When is the whole greater than the sum of its parts?
Answer: When one buys a doughnut.
As a child I routinely destroyed my mechanical toys: windup
airplanes, automobiles, railroad engines, many of which emitted sparks and sounds, and
moved. I just had to see what was inside these marvelous devices. After peeling away the
thin layers of metal, I was invariably confronted with jumbles of springs, gears and many
unrecognizable objects. My toys lay in ruin, and I was no wiser.
Many useful objects lose their function when they are dismantled. This
is true of cars, radios, airplanes, refrigerators, pianos and essentially all manufactured
goods. Obviously, appliances function only when completely assembled. The creation of
these devices requires planning and execution. Piling microchips, capacitors and resistors
into a heap usually yields only a garbage dump instead of some useful electronic
equipment.
ACQUISITION OF NEW FUNCTION WITH ORGANIZATION IS THE WAY OUR WORLD IS PUT TOGETHER
The world is made from approximately one hundred different elements,
such as carbon, iron and oxygen. The differences among elements are due to the number and
arrangement of the protons and neutrons in the nucleus, and electrons in the outer regions
of the atom. Although the properties of individual electrons are identical in every
element, their differing combinations give a variety of chemical properties to the
elements. But, as elements combine to form compounds, their unique properties frequently
give way to new characteristics. For instance, inert white table salt emerges from
combining the greenish corrosive gas chlorine with the soft metallic, highly reactive
sodium.
Linking hundreds of left-handed amino acids into polypeptide chains
results in a most impressive variety of proteins. Thousands of different proteins function
as molecular machines, each promoting a unique chemical change. Other proteins support
biological structures, forming such diverse substances as tooth dentin or muscle fibers.
Living matter consists of a mix of molecular machines that propel
synchronized chain reactions. These enable life processes to occur in the cells. In
multicellular organisms the work of one cell complements others. Living organisms interact
in various ecosystems to form the biosphere that covers the globe. The Earth receives its
energy supply from the sun, and solar energy drives most biological systems directly or
indirectly. When the lowly E. coli utilizes the energy of glucose molecules, this
energy originates from an atomic furnace, millions of degrees hot, some 93 million miles
away.
The layers of our reality are successively more complex domains (Figure
5.1). A logical way to account for the appearance of new functions at each level of
increased complexity is to suppose that the Universe is here by design. Living organisms
fit remarkably well into this hierarchical order of reality. It is tempting to adopt a
"biocentric" view which would propose that reality was designed for the sake of
living organisms.
FIGURE 5.1. Reality is organized into increased levels of complexity.
LEVELS OF REALITY NEW FUNCTION Energy ———— ¯ Subatomic particles Stabilization of energy ¯ Atoms Shape, substance, chemical properties ¯ Molecules Novel chemical properties ¯ Cells Life ¯ Organs Specialized tasks needed by multicellular organisms ¯ Organisms Complex life forms ¯ Ecosystems Localized interaction among life forms ¯ Biosphere of Earth Global interaction among life forms ¯ Solar System (relationships are not clear) ¯ Universe
(relationships are not clear)
We attempted to show that living matter cannot possibly spring into
existence spontaneously under any circumstance. This is not an argument from ignorance.
Theoretically we know what would be required for living processes to commence. Chemical
evolution requires random processes to accomplish that which we are unable to do in the
laboratory! Since there are no selection processes to favor components of a
"future" biological system, any appeal to random processes, even if an infinite
amount of time were available, is futile.
As matters stand, rejection of the concept of the Creator leaves the
naturalistic scientist with the alternative of not knowing where life came from. Usually
scientists are comfortable living with uncertainty. In fact, curiosity of the unknown is a
chief motivator of scientists. When research uncovers an explanation for a scientific
problem, the scientist frequently moves to another area of work, looking for new
challenges.
But the question of life's origin is not just another scientific
problem. It undergirds all other human enterprise. If we do not know how life originated,
we do not know whether there is a purpose to existence, or whether we are all just
participating in an interesting fluke of nature. While scientists have a high tolerance
for the unknown, they have low tolerance for meaninglessness. Science is, after all,
foremost a search for meaning in nature. It would seem incongruent that so much meaning
can be found in nature at the levels on which scientists operate, but the sum total of
existence turns out to be meaningless!
Perhaps it is insulting to designate as meaningless the faith of those
who believe in the evolution of matter from gaseous nebulae into highly structured
biological entities. These evolutionists are awed by the sophistication seen in the
biological world and continue to be challenged to gain a better understanding of it. They
also take comfort in the apparent kinship between different forms of living matter, and
they work diligently toward understanding their phylogenetic relationships. Perhaps it is
more accurate to recognize naturalistic scientists as worshipers of nature, modern
descendants of the worshipers of objects and of natural manifestations of ancient times.
For these students of nature, science represents rational, logical
thinking; and the notion of Supernatural represents the opposite — irrationality,
magic and a return to the pre-scientific age. Indeed, much intellectual mischief has been
committed in the past under the guise of religion. However, as was seen in the previous
discussion, the phenomenon of life on Earth cannot be convincingly explained
without invoking the work of a supernatural Creator. The necessity of a Creator
is not a plea for a God of the gaps. It is our understanding of how living matter
functions that drives the argument for not only a Designer but for also an Implementor who
can fashion biomolecules into living matter. This view suggests that the laws of nature
have been ordained by the Creator to sustain an orderly Universe. These laws are to be
discovered and utilized by us. Belief in a supernatural Creator stimulates students of
nature to discover the Creator's thoughts. Contrary to the pronouncements of some1
that biology is meaningless without evolution, the study of nature draws the student
closer to its Author. For the creationist, religion and science are not mutually exclusive
domains. Rather, they are different avenues toward the same Source.
SUMMARY OF CHAPTER 5
REFERENCES AND NOTES ON CHAPTER 5
This collage represents a variety of plant and animal life. The layout was created by
Clyde L. Webster, who provided all but two of the photographs. The remaining two
photographs were provided by Katherine Ching.
All contents copyright
Geoscience Research Institute. All rights reserved.
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