Pre-Biotic Synthesis and
the "primordial soup":
According to the modern science the collection of chemicals necessary for
life's natural origin is called the "primordial soup". The natural
questions regarding this statement are
1) Could the soup have ever been produced? and
2) Is there any geological evidence that it ever existed?
1. Could the soup have ever been produced?
When in 1950's Stanley Miller performed experiments of discharging
electrical spark into the mixture of H2, HCN, H2O, CH4, CHO, and NH3 gasses,
after many attempts he got a very small amount of amino acids upon which life
is built. Furthermore, it was discovered that comets and carbonaceous
asteroids contain a huge amounts of organic molecules, therefore, scientists
assumed that a lot of comets and asteroids were falling on the earth in its
early history. All together it seems that there were enough pre-biotic organic
In the last 5 decades researchers designed their pre-biotic synthesis
experiments in such a way as to get the sought-after organic molecules. They
used methane (CH4) and ammonia (NH3), only because they are essential to the
production of the proper amino acids giving the desired results and not
because they were convinced that these elements existed in the prebiotic
conditions. Even Stanley Miller admitted: "it is assumed that amino acids
more complex than glycene were required for the origin of life, then these
results indicate a need for CH4 (methane) in the atmosphere"7.
So, whether or not these gases were really there at the early condition of the
earth they didn't questioned at all. They just wanted to see if they could
produce the right molecules using various contrived mixtures of gasses. It
turns out that these experiments of synthesizing simple molecules were simply
exercises in organic chemistry still describing nothing about the chemical
origins of life.
"Miller-experiments" doesn't use free oxygen, however, in the
absence of oxygen the pre-biotic chemicals would get destroyed by UV
radiation, which is thought to have been 100 times stronger on the early earth
than it is today14. E.g. it is well known that the ozone in the atmosphere
which is composed of oxygen, protects life from harmful UV radiation. One more
reason Stanley Miller avoided to use oxygen is because it prevents the
synthesis of organic molecules like the ones obtained from the experiments!
Pre-biotic synthesis now finds itself in "damned if you do, damned if you
1. Pre-biotic synthesis can only take place in a reducing atmosphere (one with
gasses which tend to lose electrons during chemical reactions), but that very
fact would guarantee the destruction of highly sensitive pre-biotic chemicals
by UV rays.
2. You could protect the molecules with oxygen, but in doing so you'd
eliminate any chance of their production in the first place.8
Now, according to the assumption the primordial soup had to be rich with
organic molecules where many random chemical interactions could take place to
produce life. However, not only the UV radiation destroys molecules but their
life-spans are also limited. At 100 C the life-span of
Adenine and Guanine are 1 year,
Uracil is 12 years, and
Cytozine is 19 days8
Here we can just note that nucleic acids and other important proteins such as
chlorophyll and hemoglobin have never been synthesized in origins-of-life type
So, to solve the problem of short life-span of the molecules Miller proposed
that life originated at 0 C at which temperature the life-span of the
molecules jump about 1 million years. This proposal brought another problem.
At zero temperature
Ribose-a sugar which helps build DNA, has a half-life of 44 years 5 and
Cytozine a half life of 17,000 years8.
So, we can see how the temperature of prebiotic period is just an assumption
without knowing what actually was the case.
According to the one mathematical calculation, at the time of the earth's
formation the earth was extremely hot because of the intense meteorite
bombardment going on at that time.
This is defeating to the hypothesis of building of primordial cosmic soup by
comets and asteroids. Many authors explained that organic carbon could not be
delivered in large amounts to the early earth because it would be generally
superheated and destroyed during impact13.
[[[It is also estimated that every 10 million years there are devastating
bombardments of asteroids and comets on this earth planet. ]]]
Another problem facing the soup is the fact that all biological organic
molecules must somehow acquire the proper "handedness", known as
"chirality." Amino acids can either exist in a
"right-handed" form, or in the mirror image "left-handed"
form. From the standpoint of doing chemistry, left-handed molecules are no
different than right-handed ones. Yet, for some unknown reason, life uses only
left-handed molecules amino acids. At what point did life begin to
discriminate between right and left handed molecules? There is no known
chemical reaction which "weeds out" the "right" from the
"left" for all known chemical reactions produce more or less
"racmic mixtures," of 1/2 right and 1/2 left handed molecules. As
one scientist stated, "the basis for the origin of biomelecular chirality
still remains obscure9".
2. Is there any geo-chemical evidence that the soup ever existed?
Despite a lot of geological researches to find an evidence supporting the
presence of the primordial soup there was no high level of non-biological
carbon found - as expected - in the ancient sediments of Precambrian rocks.
Further, there were not rocks found containing "unusually large
proportion of carbon or organic chemicals"11 which would prove the
presence of the methane-ammonia atmosphere necessary for prebiotic synthesis.
In connection with this it must be mentioned that even a significant quantity
of ammonia in the primitive atmosphere would have been destroyed within 30,000
years by UV rays11 and methane within a few tens of years16.
Most amazingly according to geological evidence the presence of CO2 atmosphere
was very predominant. In the "Miller-experiments" using CO2 only a bit of
Glycinel was produced but no any amino acids.
There were ideas that the early atmosphere was created by magma of the
volcanoes, however magma contains N2, CO2 and H2 but no methane or ammonia16
by which elements supposed form the primordial soup.
Some scientists say that even if somehow the ammonia-methane atmosphere was
there, that would not produce a soup but rather an oil slick up to 10 m
thick12. Although there is no any evidence for this hypothesis, still some say
that it is because once life evolved, it consumed the entire prebiotic
storehouse of molecules and left no trace of its existence. However this is
also not a good argument because rocks would have been formed on the earth
during the time of the soup, but before the supposed origin of life, thus
preserving a record of the primodial organics. There is no evidence, however,
of these primordial organics.
So, now although there is no evidence that the primordial soup existed let's
assume that it was there so that we go further analyzing the chemical origins
of life, more specifically could the molecules undergo synthesis to form
larger, more complex molecules
When "monomers"-simple organic molecules form covalent bonds with
one another to produce "polymers"-bigger complex organic molecules,
that is called a process of polymerization.
Monomers in the pre-biotic soup are the amino acids, sugars, lipids, simple
carbohydrates, nucleic acids.
Polymers like fats, complex carbohydrates, phospholipids are chains--often
very long chains--of monomers.
For easy understanding here is an analogy:
monomers are like the letters,
polymers are the words,
biochemical pathways are the sentences,
cells are the paragraphs,
biological systems are the chapters, and
the organism is the whole book!
So, the polymers are like words which are thousands of letters long.
Most of the scientists proposed that life was generated in the prebiotic soup,
however according to the Le Chateliers Principle, one of the basic laws of
chemistry, the presence of a product (in this case, water) will slow down the
reaction. In the line of the same principle as the experiments also show,
trying to polymerize monomers into polymers where water is the solvent will be
futile. Conclusively, the polymerization in the chemical origins of life could
never take place.
To overcome this stumbling block some proposed that a heating and drying
process took place to remove the water and simultaneously to give energy to
the polymerization process. When this idea is questioned, how this heating and
drying didn't destroy the created polymers, some theorized locations for
this reaction have been intertidal pools where repeated cycles of heating and
drying can take place. However, in that case all the water had to be removed
just like in the laboratories, to produce even a small amount of polymers one
have to create perfect conditions carefully measuring the heating and drying
cycles. Such laboratory circumstances are cautiously designed and in no way
simulate possible natural conditions.
Pre-RNA World, RNA World, DNA/Protein World.
So, let's now assume, like many scientists do, that somehow at one point the
polymers were formed of which some came together and so formed the first
self-replicating molecules. Somehow, from these molecules the true origin of
(This is an interesting scenario, however, never demonstrated by experiments
in the laboratory. With other words polymers cannot form a self-replicating
After many carefully-designed experiments in the lab few self-replicating
molecules have been created called e.g. the PNA (phospho-nucleic acid) which
in its later development in the prebiotic condition supposed to turn into RNA.
But the scientists have no idea how did PNA turned into RNA and moreover how
PNA came into existence naturally in the first place.
When AATE (amino-adenosine triacid ester) was discovered to have an ability of
creating new AATE molecules the joy didn't last long that 'now the origins
of life was ultimately found'. To see why is that so, let's see the direct
words of Jonathan Safari: "This system [AATE] carries very little
information, in contrast to even the simplest cell. Mycoplasma gentalium has
the smallest known genome of any living organism, which contains 482 genes
comprising 580,000 bases. This organism is an obligate parasite. A free-living
organism would need many more genes."19 He additionally explained that
this molecule only replicates in chloroform solution, a highly natural
condition, and that when it does replicate, it happens so accurately that it
is opposing the idea of Darwinian mutation-selection mechanism.
Lastly, when the GCN4 self-replicating molecule was produced in the lab, which
does replicate in water, and does catalyze its own replication22, it was found
that that it replicates only under specific 15 or 17-unit peptid code of amino
acids. Although considered as precursor of life, still there are some strong
objections and unanswered questions to this. Given the existence of an aqueous
sea of amino acids which are somehow defying chemical laws to form long
chains, the chances of properly forming the proper 15-unit self-replicating
peptide in a given reaction are one in 3 X 109.19 When and how chirality's could
have been acquired and why this 20-amino-acid-based replicator could switch to
a completely different 4-nucleic-acid-based replicator, such as RNA or DNA,
are questions that also remains unanswered.
Further the theory explains that an unknown precursor of RNA somehow or other
turned into self-replicating RNA molecule from which life arose. The RNA which
has a complementary code to DNA is active when DNA breaks up to create
proteins or to replicate. So, because only few types of RNA have
auto-catalytic self-replicating abilities, the idea of the RNA existing
without DNA certainly meets a chicken and egg problem18.
When we speak about the self-replication which requires many enzymes and
genetic biochemical molecules they must be protected within the
cell-wall-structure. However, the problem is that the protective cell requires
replicating genetic machinery to be created. Thus we run into the chicken egg
problem - which was the first, the self-replicating machinery (which needs a
cell to operate), or the cell itself, which protects (and is created by) the
cellular machinery? The answer is: 'because the complex system of RNA cannot
function without other distinct components (as above described) and because
both are simultaneously necessary in the process of self-replication neither
of them came first'.
So, as the scientific fairytale goes on, at one point the RNA turned into DNA
- the main genetic molecule of all life. How? Let's see what does John
Maynard Smith an emeritus professor of biology at the University of Sussex
say, in his book, "The Major Transitions in Evolution":
"The origin of the [DNA based genetic] code is perhaps the most
perplexing problem in evolutionary biology. The existing translational
machinery is at the same time so complex, so universal) and so essential that
it is hard to see how it could have come into existences or how life could
have existed without it. The discovery of ribozymes has made it easier to
imagine an answer to the second of these questions, but the transformation of
an 'RNA world' into one in which catalysis is performed by proteins, and
nucleic acids specialize in the transmission of information [a "DNA
World"], remains a formidable problem."22
We can boldly declare that the theory of natural chemical origins of life has
very big problems. So lets once more, briefly, describe the locations where,
according to the scientists, life could originate.
1. Deep sea thermal vents
Although deep sea thermal vents give enough heat necessary for some reactions,
still the polymerization process through dehydration synthesis is impossible
in water. Furthermore, the high heat of deep sea thermal vents would quickly
decompose the organic compounds.
2. Tide pools (or somewhere in the intertidal zone)
This kind of places would be still exposed to minor amounts of water quitting
thus the dehydration synthesis. In the laboratories, in the imitation tide
pools where heating and drying conditions were provided it was possible to
create only small to modest polymers.
Let say that the polymers were created, but then in the water-safe place there
would be no high rate of random chemical reactions.
This discovery also nullifies the primordial soup theory in which it was
assumed that in the water a very high rate of random chemical interactions
took place due to the molecules constantly bumping in each other. But as
already mentioned polymerization cannot take place in water. Seeing that the
primordial soup theory doesn't work scientists proposed even a less probable
place of the life's origin a solid sticky place of the pool's itertidial
zone. However, in such place molecules could have almost no chance of finding
each other. Moreover, experimental evidence suggests that the types of large
polymers necessary for the origins of life would be difficult, if not
impossible to create under even perfect tide pool-like conditions.
As already discussed water prevents polymerization. Moreover, the
ocean would highly thicken the pre-biotic soup ultimately completely
dissolving it. And actually, that a viable primordial soup was created
in an ocean is almost unthinkable.
4. Volcanic Ridges
In the idea that the place of life's origin are the ridges there is no
problem for the heating and drying of the organic molecules. Still, the
unanswered question is how the molecules got there? Previously the monomers
were considered to be in the primeval soup. Therefore, in the same line, the
monomers had to be brought by water up to the ridges which, it seems, had to
be near the water. But if water could get to the ridges once, it could
certainly return second and third time ending thus the dehydration synthesis.
But let say that the water came up to the volcanic ridges only once, so that
later in the dry place the synthesis of polymers could occur. This case is
similar to the tide-pool hypothesis and so it has the same problem. According
to the experiments, synthesizing monomers in high concentration under perfect
temperature resulted in too small number of polymers what is not enough for
the next steps in the origins of life. Furthermore, volcanic ridges are
usually very hot so any organic molecules would be quickly destroyed by the
high amounts of heat.
5. Clay surfaces
As in the book of Genesis Moses speaks about God's creating a man from a
clay in the 20th century A. Graham Cairns-Smith came up with the theory that
that clay crystals could have acted as a template which could allow for the
continued creation and replication of organic material. Although this scenario
might happened, the problem with this idea is that there are no any
experimental proofs to make it acceptable.
6. Extra-terrestrial Origin
Because after many scientific researches some scientists concluded life could
not occur on the earth some of them begin to consider the idea of
extra-terrestrial origin of life.
For some time, they came up with the idea that the origin of life was the
Mars, but it is now considered improbable because on its travel from Mars to
the earth, life would certainly get destroyed. Other alternative was to
consider the comets because they have higher concentration of organic material
then the early earth planet. However, the extreme varieties of temperature
from very cold condition - when they travel in the cold areas of the universe;
to the very hot temperature - when they are accelerate close to the sun and
their richness in water are the greatest problems for polymerization.
Meteorites, similarly to the comets, have extremely hot temperatures
especially when they enter earth's atmosphere and therefore, the instant
destruction of any organic molecules would be inevitable.
Despite of many difficulties, nowadays the hypothesis of extra-terrestrial
origins of life are so expertly presented as they would be irrefutable.
An interesting question here we can ask is "why all these different
scientific theories started at all"? The cause is the desire for
naturalistic explanation of the world and the origins of life. With other
words, if the philosophy of naturalism would not be promoted these hypotheses
would not follow it. Another question is: 'if the scientific theory is
promoted because of a philosophy, is that theory fit to be called a science?
Are all the above discussed theories only meant to confirm the philosophy of
naturalism claiming that there must be natural explanations for everything'?
The answer is obviously-yes, and all the different theories were attempted to
be made undefeatable.
The last so-called undefeatable and unprovable naturalistic theory we would
like to mention is the "multi-verse' hypotheses which many scientists
don't even consider to be a scientific theory. This theory considers our
universe to be one of the many infinite universes and because it was friendly
to the existence of life, or with other words it happened to have the correct
formulas for life, this universe was naturally selected to contain life. To
this theory, obviously guided by naturalistic preconceptions, there is no
As a general conclusion, we can see that scientific theories are either
refutable by other scientific arguments or when irrefutable but also unproven
they are promoted because of philosophical prejudice. Still, scientists
maintain a great hope that "one day" they will know the real truth. Paid
by the government an astronomical amounts of money the scientists look in the
eye of common public to be very important. Despite of all their endeavors,
their researches always fail to prove the chemical origins of life. The
question is how long they will be able to cheat people? They cheated them for
the last 300 years, they might cheat them for 50 or more years, but they will
certainly not cheat them for ever. Already now, even the staunchest
evolutionists usually admit that no one is even close to explaining how
DNA-based life could arise from nonliving materials, and when strongly opposed
they don't force their views about the origins of life upon the nonbeliever.
So, the last question, which we will leave to the reader of this essay to
answer is: "Is the natural chemical origin of life really a scientific
1. Life Itself, by Francis Crick (New York: Simon and Schuster, 1981) and
Directed Panspermia by F. H. C Crick and L. E. Orgel, Icarus 19:341-346 (1973)
2. "it is the job of science to provide plausible natural explanations
for natural phenomena"
(Science and Creationism, a view from the National Academy of Sciences (2nd
edition), Nat Acad Press, 1999. Pg. 20. At "http://books.nap.edu/html/creationism/")
3. Information Theory and Molecular Biology. Hubert P. Yockey, 1992, Cambridge
University Press. The reader is encouraged to check out chapters 8-10 for a
good discussion of the problems with the natural chemical origins of life.
This book is available from the UCSD Libraries.
4. "Creationists have looked forward to the day when science may actually
create a "living" thing from simple chemicals. They claim, and
rightly so, that even if such a man-made life form could be created, this
would not prove that natural life forms were developed by a similar chemical
evolutionary process. The scientist understands this and plods on
(Stansfield, William D. [Professor of Biological Sciences, California
Polytechnic State University], "The Science of Evolution," ,
Macmillan: New York NY, 1983, Eighth Printing, pp10-11)
5. Statments made by Stanley Miller at a talk given by him for a UCSD Origins
of Life seminar class on January 19, 1999 (the talk was attended and notated
by the author of this article).
6. Overman, Dean L. "Case against Accident and Self-Organization" (Rowman
& Littlefield Publishers, 1997) The reader is encouraged to read Parts III
and IV for a good non-technical discussion of problems facing the natural
chemical origins of life.
7. Stanley Miller as quoted in Origins: A skeptics guide to the Creation of
Life on Earth by Robert Shapiro (New York: Sion and Schuster, Summit Books,
1986), pg. 112.
8. Denton, Michael. Evolution: A Theory in Crisis (Bethesda, Md.: Adler and
Adler, 1985), pg. 261).
8. Levy, Matthew and Stanley Miller. The Stability of the RNA bases:
Implications for the origin of life. Proceedings of National Academy of
Science, USA (Vol. 95, pg. 7933-7938).Darwin, Charles (1898). The Life and
Letters of Charles Darwin, Vol II, p. 202. New York: D. Appleton.
9. Bonner, William A. "Origin and Amplifications of Biomolecular
10. Schopf, J. William in Exobiology (edited by Cyril Ponnamperuma),
North-Holland Publishing Company: Amsterdam-London, 1972 in the Precambrian
paleobiology chapter, Pg. 27.
11. Abelson, Philip H. "Chemical Events on the Primitive Earth,"
from the Proceedings of the National Academy of Sciences, USA, Vol 55 Pg.
12. Lasaga, Antonio, H. D. Holland, M. J. Dwyer. "Primordial Oil
Slick". Science vol 174, Oct 4, 1971 pg. 53-55.
13. Anders, Edward. "Pre-biotic organic matter from comets and
asteroids." Nature, Vol 342, November 16, 1989 pg. 255-257.
14. Canuto V. M., Levine, J. S., Augustsson, T. R., Imhoff, C. L., Giampapa,
M. S. "The young Sun and the atmosphere and photochemistry of the early
Earth". Nature Vol 305, September 22, 1983, pg. 281-286.
15. Schlesinger, Gordon and Stanley. L Miller. "Prebiotic Synthesis in
Atmospheres Containing CH4, CO, and CO2." Journal of Molecular Evolution,
Vol 19 pg. 376-382 (1983).
16. The Search for Life's Origins. National Research Council Space tudies
Board, National Academy Press: Washington D.C., 1990, pg. 66, 67, 126)
17. Brooks J., "Origins of Life," Lion: Tring, Hertfordshire UK,
18. Vaneechoutte, M., The scientific origin of life. Considerations on the
evolution of information, leading to an alternative proposal for explaining
the origin of the cell, a semantically closed system. Annals of the New York
Academy of Sciences, 901, 139,2000.
19. Safarti, Jonathan. "Self-Replicating Enzymes?" Creation Ex
Nihilo Technical Journal 11(1):4-6, 997. Also available at fix this!!!
20. Tjivikua, T., Balester, P. and Rebek, J., Jr., 1990. A Self-Replicating
System. J. Amer. Chem. Soc., 112(3):1249-50.
21. Lee, D. H., Granja, J. R., Martinez, J. A., Severin, K., and Ghadiri, M.,
R., 1996. A self-replicating peptide. Nature 382:525-528 ...also see Nature
22. Maynard Smith, John [Emeritus Professor of Biology at the University of
Sussex] & Szathmary, Eors [Institute for Advanced Study, Budapest,
"The Major Transitions in Evolution," W.H. Freeman: Oxford UK, 1995,
23. Lazcano, A., 1997. The tempo and modes of prebiotic evolution. In:
Cosmovici, C.B., Bowyer, S., Wertheimer, D. Eds. , Astronomical and
Biochemical Origins and the Search for Life in the Universe. Editrice
Compositori, pp. 419430.
24. J. D. Watson, F. H. C. Crick, Molecular Structure of Nucleic Acids; A
Structure for Deoxyribose Nucleic Acid, Nature, 2 April 1953, VOL 171,
Note also: Crick
got the x-ray diffraction pattern of a double helix by shining x-rays through
crystallized DNA but even then very little was known about DNA. Crick wasn't
sure if the genetic information was carried in the DNA or in the proteins. DNA
seemed to be an unlikely candidate since it had only 4 nucleotides, but the
DNA was ubiquitously in every living cell, so they knew it meant something.
They also weren't sure if the nucleotides pointed outward or inward--or did
the did the phosphate backbone point inward or outward. They knew it was a
polynucleic acid, but didn't know exactly what exact structure of the full
chain was. They took got the x-ray pattern and knew that it was helical, and
therefore the bases had to point inward towards each other. But what's amazing
about Watson and Crick made all the right predictions--they predicted that DNA
would be the perfect genetic molecule, because they saw from the way the
nucleotides were oriented that you could easily replicate the DNA, carry
information, even allow for mutations, and do everything you would expect a
genetic molecule to do. On a personal note, Lyle Jensen, grandfather of IDEA
Club founder Kirk Jensen, is a creationist and a member of the AAAS. Kirk's
grandpa took the same x-ray pictures as Crick and Watson and made the exact
calculations to get the bonding angles, atom positions, and stacking positions
of the oligomeric nucleotide bases etc., and really nailed down the exact
structure of DNA. Lyle Jensen used something similar to the14 base-pair strand
that Crick used, but developed better mathematical techniques so he was able
to take diffraction patterns and bypass many of the mathematical problems
people had previously encountered regarding the exact structure of crystalline