Investigator interference will now be
summarized. As mentioned earlier, investigators do not have 5 billion years to conduct
origin of life experiments, so some interference is necessary.
Interference Strategy #1: Eliminate the Undesirable Chemicals
If chemical A and chemical B react to form chemical P, then this chemical reaction can be
written as A+B—> P. Suppose that Miller’s water trap contains 3 chemicals, A,
B and C. The possible reactions involving the chemicals are as follows: A + B–>P
and A +C->D.
Unfortunately, the second reaction is favored. So after a few days all of the
chemicals in the flask are D, but the researcher desires chemical P. So instead of using
the contents of the flask to create P, he orders A and B from his chemical supplier. He
mixes these two chemicals while applying heat, and the product is P. This process is how
organic chemists make chemicals. They control the chemicals that they start with, and this
influences the products that they get. Applying this technique to origin of life scenarios
is questionable because it is not clear how nature can exclude the undesirable chemicals.
In chapter 7, figure 7.1 shows that one of the functions that enzymes perform
is to eliminate undesired reactions. They accomplish this by speeding up the desired
reactions. When investigators manipulate the chemicals in their system to create a desired
product, they are mimicking this particular mode of enzyme action. They are using their
knowledge of chemistry because the required molecular knowledge is not present in the
system.
Examples of cross reaction elimination:
• Fox’s thermal proteins. He did not include carboxylic acids
or other organic components (like aldehydes) that might terminate a growing protein chain.
• The most extreme examples of cross reaction elimination involve
RNA. The reason is that ribose is included freely, but no amino acids are included. This
is not a plausible condition. Amino acids react very quickly with sugars like ribose to
create very long chain polymers. Anyone who has baked cookies or toasted a piece of bread
is familiar with this reaction. Browning is caused when amino acids (especially lysine)
react with sugar. This reaction would make any sugar present in the primordial soup
unavailable for RNA formation.11,12
Interference Strategy #2: Concentrating Volatile Chemicals
Concentrated formaldehyde is critical for the synthesis of ribose. Concentrated hydrogen
cyanide and ammonia are critical for the synthesis of adenine. It is not clear how these
chemicals could ever be present in high concentrations on the early earth.13
How does one concentrate a chemical that boils at sub-freezing temperatures in a small
puddle? This is a difficult problem.
Interference Strategy #3: The Use of Condensation Agents or
Activated Monomers
Condensation agents help form all of the bonds that are necessary in biological
precursors, whether RNA or protein. Condensation agents remove water and by doing so
promote the formation of large biological molecules. Condensation agents were discussed
for proteins, but they have also been used to successfully join RNA nucleotides into short
chains. RNA synthesis usually just skips this step, and instead researchers usually just
add an activated monomer like impA, impG, impC, or impU.
There are no plausible synthesis mechanisms for the condensation agents or
the activated monomers. If they are created in Miller’s spark experiment or if they
exist in meteorites, then the amount present is minuscule. How some investigators can add
these chemicals in abundance to reactions, and still think that they are modeling
plausible prebiotic conditions is certainly not clear.
Nevertheless, the motivation for using these techniques is clear. Without
these techniques, the biological precursors are limited to a size that is too small to be
biologically active.16 Given that condensation agents and activated monomers are often
coupled with carefully timed washes designed to grow the protein or RNA molecule, the
analogy to blowing up the door in figure 9.4 definitely applies.
Interference Strategy #4: Controlling the Energy Sources
In most experiments, destructive energy sources are eliminated by the investigator. For
example, if the trap in Miller’s spark chamber is illuminated with UV light, many of
the products will be destroyed.4
Interference Strategy #5: Substituting Human Knowledge
This is the most subtle form of interference, and the most common. In systems that lack
the required molecular knowledge, it is very easy for researchers to unintentionally add
knowledge to the system through the design of their experiment.
The carefully controlled sequential washes that accompany many RNA and
protein chain elongation experiments are a perfect example. Often a growing RNA or protein
molecule is attached to a stationary substrate, activated nucleotides or amino acids are
added, and a rinse is applied after the desired chemical bond forms. This form of
interference is present in most prebiotic experiments, and sometimes it goes unnoticed.
Conclusion:
The goal of this chapter was to show that the precursors to life whether RNA or proteins
are extremely difficult to create. Maybe one or two such molecules are expected given
optimal conditions and 5 billion years. The design inference based on this conclusion
alone is very strong. The inference will be strengthened in the next chapter. The next
chapter will show that the knowledge required for self replication is very large. If the
entire ocean is packed tight with either proteins or RNA, then the odds that one of the
molecules can self replicate is still zero. Several thousand bits of knowledge are
required, and zero tries (or almost zero) will never allow chance to create this much
knowledge.
Many investigators researching the origin of life are disappointed with their
progress, and this shows in the scientific literature. Today, it is acceptable to publish
an article that is critical of the origin of life paradigm as such articles do get
published.
Any publication suggesting the possibility of design is either rejected or
starts a witch hunt in which the editor who approves the article is the target. The first
step in any scientific revolution is to realize that there is a problem with the current
theory, and for many scientists this realization has already taken place. Joyce and Orgel
summarize the situation as follows:
“In our initial discussion of the RNA World
we will accept The Molecular Biologist’s Dream: “Once upon a time there was a
prebiotic pool of Beta-D-nucelotides . . . We will now consider what would have to happen
to make the dream come true. This discussion triggers the Prebiotic Chemist’s
Nightmare: how to make any kind of self replication system form the intractable mixtures
that are formed in the experiments designed to simulate the chemistry of the primitive
earth.”20
References:
1) Temussi, et al., “Structural Characterization of Thermal Prebiotic
Polypeptides,” Journal of Molecular Evolution, p105-110, 1976.
2) Miller, Orgel, The Origins of Life on Earth, Prentice Hall, 1974.
3) Shapiro, “The Prebiotic Role of Adenine: A Critical Analyis,” Origins of Life
and the Evolution of the Biosphere,” 25:83-98, 1995.
4) Thaxton, Bradley, Olsen, The Mystery of Life’s Origin: Reassessing Current
Theories, Philosophical Library, 1984.
5) Levy, Miller, “The Stability of the RNA bases: Implications for the Origin of
Life,” PNAS, 95: 7933-7937, 1998.
6) Shapiro, “Prebiotic Cytosine Synthesis: A Critical Analysis and Implications for
the Origin of Life,” PNAS, 96: 4396-4401, 1999.
7) Larralde, Robertson, Miller, “Rates of decomposition of Ribose and other Sugars:
Implications for chemical Evolution,” PNAS, 92: 8158-8160, 1995.
8) Joyce, Schwartz, Miller, Orgel, “The Case for an Ancestral Genetic System
Involving Simple Analogues of the Nucleotides,” PNAS, 84: 4398-4401.1989.
9) Joyce, Visser, Boeckel, Boom, Orgel, Westrenen “Chiral Selection in Poly (C)
Directed Synthesis of Oligo (G),” Letters to Nature, 310: 602-604,1984.
10) Fuller, Sanchez, Orgel, “Studies in Prebiotic Synthesis. V11 Solid State Synthsis
of Purine Nucleosides,” Journal of Molecular Evolution, 1:249-257, 1972.
11) Nissenbaum, Kenyon, Oro, “On the Possible Role of Organic Melanoidin Polymers as
Matrices for Prebiotic Activity,” Journal of Molecular Evolution. 6:253-270, 1975.
12) Thaxton, Bradley, Olsen, The Mystery of Life’s Origin: Reassessing Current
Theories, Philosophical Library, pp 60-61,1984.
13) Thaxton, Bradley, Olsen, The Mystery of Life’s Origin: Reassessing Current
Theories, Philosophical Library, p 64,1984.
14) Ferris, “Prebiotic Synthesis: Problems and Challenges,” Cold Spring Harbor
on Quantitative Biology, Vol L11: 29-34, 1987.
15) Thaxton, Bradley, Olsen, The Mystery of Life’s Origin: Reassessing Current
Theories, Philosophical Library, pp 43-44,1984.
16) Ferris, “Montmorillonite Catalysis of 30-50 Mer Oligonucleotides: Laboratory
Demonstartion of the Potential Steps in the Origins of the RNA world,” Origins of
Life and Evolution of the Biosphere, 32:311-332, 2002.
17) Osterberg, Orgel, Lohrmann, “Further Studies of Urea Catalyzed Phosphorylation
Reactions,” Journal of Molecular Evolution, 2:231-234, 1973.
18) Fox, Dose, Molecular Evolution and the origin of Life, Freeman and Co., 1972.
19) Thaxton, Bradley, Olsen, The Mystery of Life’s Origin: Reassessing Current
Theories, Philosophical Library, pp 66,1984.
20) Joyce and Orgel, The RNA World, Gesteland, Cech, Atkins, Cold Spring Harbor,
“Prospects for Understanding the Origins of the RNA World,” p50, 1999.
21) Mojzsis, Krishnamurthy, Arrhenius, The RNA World, Gesteland, Cech, Atkins, Cold Spring
Harbor, “Constraints on Molecular Evolution,” p20-21, 1999.
21) Fox, Dose, Molecular Evolution and the origin of Life, Freeman and Company, p37, 1972.
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