POSSIBLE PATHWAYS BEFORE AND AFTER THE RNA WORLD ON THE BASIS OF
EXPERIMENTAL AND THEORETICAL EVIDENCES
Kunio Kawamura
Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
Gakuen-cho 1-1, Sakai, Osaka 599-8531, Japan.
kawamura@chem.osakafu-u.ac.jp(Received October 31 2005 Accepted December 5 2005)

Abstract
Although the RNA world hypothesis is important as a model of the emergence of life-like systems, thishypothesis has some drawbacks. This hypothesis was already evaluated from the hydrothermal origin of life
hypothesis in our recent paper. On the other hand, a unified theory for the origin and evolution of life has been
attempted to develop on the basis of our recent investigations concerning the subjectivity of life and themolecular machinery of assigning genotype and phenotype. In the present paper, the RNA world hypothesis isfurther evaluated on the basis of the unified theory as well as the experimental evidences concerning thechemical evolution under hydrothermal environments.

Keywords
hydrothermal reactions, RNA, RNA world, a unified theory of origin and evolution of life, enzyme

1. Introduction

simulation experiments have been carried out at low

Although the RNA world hypothesis is important

temperatures. In addition, there have been no[1,2], it has some drawbacks (Fig. 1 (A)). The RNA

practical techniques for the investigations of chemical

world hypothesis appears to be inconsistent with theevolution of RNA under hydrothermal conditions. In

hypothesis that life originated under hydrothermal

our group, (1) monitoring techniques of hydrothermal

environments(thereactions [6-9], (2) the stability of RNA molecules

hydrothermal origin of life hypothesis) [3]. RNA[8,10-14], (3) prebiotic formation of RNA at highmolecules are regularly supposed (1) to be less stabletemperatures [15-17], (4) tertiary structures of nucleic

than DNA and proteins and (2) to be difficult toacids under hydrothermal conditions [18], have been

maintainstudied.

intertiarytheprimitive

structures

since

ocean

biologicallyimportant interactions, such as hydrogen bonding and

If a life-like system entirely consisting of RNA

hydrophobic interaction, become weak at highmolecules have emerged on primitive earth, naturally

temperatures (Fig. 1 (B)) [4,5]. However, most of thethe system would be more labile than the present cell

Viva Origino 33 (2005) 258-268© 2005 by SSOEL Japan- 258 -

Viva Origino 33 (2005) 258-268

catalytic RNA moleculesAin vitro selection of functional RNA molecules
prebiotic simulations at low temperatures

RNA worldhydrothermal environmentsB

C a unified theory of origin
and evolution of lifestability of RNA at high temperatures
prebiotic simulations at high temperatures
tertiary structures at high temperatures

attributes of life
minimum life-like system

Figure 1. Evaluation of the RNA world hypothesis from different aspects. While the RNA world hypothesis is supportedby the viewpoint A, some drawbacks remain from the viewpoints B and C.

type systems because of the low stability of RNA. In

2. 1. Monitoring methods of hydrothermal reactions

addition, an essential point of view of the RNA world

While hydrothermal reactions were normally

hypothesis is that RNA molecules could have playedinvestigated using batch reactors, it was difficult toimportant or central roles for the emergence of life.

monitorThus, this hypothesis is not in conflict with themillisecond time scale. To monitor such rapid

speculation that other prebiotic materials would havereactions, the flow reactor monitoring systems are

facilitated the RNA world. However, there have been

becoming practical techniques [23-25]. We havefew systematic investigations on the roles of suchinventedmaterials for the chemical evolution of RNA.

hydrothermal reactions using a micro-flow reactor

hydrothermalareal-time

reactionsmonitoring

withinmethodtheofIn our previous paper we have discussed thesystem assembled with fused-silica capillary tubing,possibility of an RNA world from the standpoint of

which enables the monitoring reactions at 0.002 - 150

the stability of RNA and the prebiotic simulations ofs at temperatures over 300 oC [6-8]. Furthermore, thisRNA formation (Fig. 1 (B)) [19]. In this paper,technique was applied to conduct in situ monitoring

additional discussions are attempted on the basis of

UV-visible absorption spectra under hydrothermal

the experimental evidences and a unified theory on

conditions [9]. These methods have facilitated thethe origin and evolution of living organisms, whichinvestigation

was deduced from our continuous investigations on

millisecond – second time scale (Fig. 2).

of hydrothermal

reactionsatthethe origin and evolution of life (Fig. 1 (C)) [20-22].
2. 2. The degradation and the prebiotic formation of2.

Chemicalevolution

of

RNA

under

RNA
The

hydrothermal systems- 259 -

stabilityofRNA

monomers,

dimers,Viva Origino 33 (2005) 258-268

fused-silica capillary tubing
inner diameter: 0.015 - 0.25 mm
residence time: 0.002 - 150 s
flow

heatingquenching

Figure 2. Monitoring system of hydrothermal reactions. Samples are immediately heated up in a fused-silica capillarytubing with inner diameter 0.015 – 0.25 mm and immediately quenched by cooling. This principle enables monitoringhydrothermal reactions within 0.002 - 150 s.

*pN → pN (deactivation of activated monomer)

oligomers, and polymers has been investigated using(3)

the flow reactor system. The half-lives of thesewhere pN, *pN, and oligoN indicate nucleotide

molecules are in the time ranges 2 - 70 s at 200 oC

monomer,and 0.01 - 0.9 s at 300 oC [8,10-14]. These reactions

oligonucleotide. The accumulation of oligoN is

appeared to be so fast under hydrothermal conditions

determined by the relative magnitude of the processes.

that RNA molecules could not have survived for a

In general, the oligomerization in the prebiotic RNA

geological time scale [19].

formation models can be desicribed by the following

activated

On the other hand, simulation reactions for theequations (4,5).

formation of RNA oligomers on the primitive earth

oligoNi + *pN(association of monomers)
oligoNi…pN

the phosphorimidazolides of nucleotide monomers[26-31]. However, most of the studies were carriedomonomer,→andoligoNi…pN→

conditions have been extensively investigated using

out at 25 oC and no investigations were performed atnucleotide(4)

oligoNi+1(phosphodiester bond formation)(5)

where Kass is the association constant in equation (4)C [31]. We have carried out kinetic

and kphos is the formation rate constant in equation

investigations at temperatures up to 80 oC on (1) the(5). The over all rate constant of oligomerization

template-directed formation of oligoguanylate on a

(kform) is expressed in equation (6).

over 37

kform = Kass . kphos

polycytidylic acid template [15], (2) the cyclizationofoligonucleotides

theAll three different prebiotic formation reactions ofoligocytidylate formation in the presence of Pb2+ [32].

oligonucleotides proceeded at 75 - 80 oC although theIt was confirmed that these reactions proceed at 75 -efficiency of the reactions decreases with increasing

80 oC. The reactions are expressed by the following

temperature [15-17,32]. This fact indicates that theequations [15,33],

magnitude of kform could be greater than that ofpN + *pN → oligoN[16,17],

and

(3)

(6)

(oligomerization)

oligoN → (Np) (decomposition of oligoN)(1)degradation under hydrothermal conditions if the(2)

magnitude of Kass is sufficiently large under- 260 -

Viva Origino 33 (2005) 258-268

hydrothermal environments. For instance, the kinetic

following

analysis of the template-directed reaction suggested

degradation rates of RNA are so fast is determined onthat the low efficiency of oligoN formation at 80 oC

the basis of our perception and it does not seem to be

is due to the weak association between activatedbased on a scientific viewpoint. For instance, thenucleotide monomer (*pN) and oligoN because

metabolism of RNA molecules in modern organisms

hydrogeninteraction

is normally controlled at the millisecond time range

decrease with increasing temperature. Thus, the[11,19]. Based on our considerations on the stability

template-directed formationof RNA could beof RNA, the following viewpoints were proposed on

possible under hydrothermal conditions, if thethe accumulation of RNA under hydrothermal

association between activated nucleotide monomer

environments [11,19]. First, the stability of RNA(*pN) and oligoN is facilitated at high temperatures.

should be evaluated on the basis of the relative rates

bondingandhydrophobic

standpoint.

Theevaluation

that

the

It is normally assumed that the degradation ratesof the prebiotic formation and decomposition. Ourof RNA are so fast that the accumulation of RNA

data suggested that the rate of prebiotic formation

under hydrothermal conditions could not have beenreactions of RNA could have been greater than that ofdifficult. The temperature of the primitive ocean isdegradation of RNA under hydrothermal conditions

still speculative so that the possibility to consider theat around 300 oC. Thus, oligonuleotides could havecold origin of life is also important. In addition,

formed at high temperatures if a sufficient amount ofexperiments on simulated hydrothermal vent systems

the activated monomer have been supplied. Second,in deep ocean might suggest that prebiotic molecular

the comparison of the reaction rates concerning thesystems could have survived by the circulation

formation and degradation of RNA with and without

betweenvents.

prebiotic enzymes is necessary since enzymes are

Nevertheless, it is indispensable to examine whether

essential for controlling biochemical reactions in

RNA systems could have emerged and survived atorganisms (Fig. 3). In addition, it has been pointed

high temperatures. In this paper, the relationshipout that large differences are essential between the

between the stability of RNA and the prebiotic

reaction rate constants with enzymes (kcat) and thoseformation of RNA should be discussed from thewithout enzymes and the enzymatic reaction rates are

cold

water

and

hydrothermal

primtive enzymatic

formationprimitive enzymatic

RNA accumulation

degradation

non-enzymatic

non-enzymatic

Figure 3. The accumulation of RNA under hydrothermal conditions should be evaluatedfrom two different viewpoints. First, the accumulation should be evaluated by both therates of the prebiotic formation and degradation of RNA. Second, the accumulation
should be evaluated by both the rates with and without prebiotic enzymes.

- 261 -

Viva Origino 33 (2005) 258-268

in a narrow range for controlling biochemicalof EB as a function of temperature were substantiallyreactions [33]. We have attempted the comparison of

consistent with the Tm values which were determined

a number of reaction rate constants with and without

using a differential scanning calorimeter (DSC).

enzymes including thermophilic enzymes [19]. First,

Nevertheless, the change in absorbance at 100 - 130

this trend was possible to extend to temperatures asohigh as thermophilic enzymes survive. Second, it was

detectable by DSC, and this finding indicates that an

found that there is a large difference between theunknown weak interaction exists between EB andenzymatic reaction rates and the reaction rates

DNA at 100 - 130 oC. Since the measurements by

without enzymes at high temperatures 200 – 300 oC.

DSC or conventional spectrophotometer are difficult

This fact implies that a sufficient difference between

or impossible at over 100

the reaction rates with and without primitive enzymes

phenomenon are currently investigated using the new

could have been developed under hydrothermal

method.

C was observed by the flow system, which was notoC, details on thisenvironments. In other words, primitive enzymes

Although the values of Tm for DNA and RNA are

could have emerged at such high temperatures.

normally lower than 100 oC, the double helix and a

Primitive RNA and/or other molecules could bevariety of tertiary structures of nucleic acids should

considered as candidates of primitive enzymes [19].

be maintained in hyperthermophilic organisms atover 100 oC. Thus, we are currently investigating

2. 3. Tertiary structures of RNA at high temperatures.

what prebiotic environments and materials could

The weak interactions, such as hydrogen bonding

have facilitated the formation of such tertiary

and hydrophobic interaction, play important roles instructures of nucleic acids at high temperatures. In

biochemical reactions. Tertiary structures of RNA

addition, it would be important to focus the role ofmolecules, such as Watson-Crick double helix,

electrostatic

several structures of tRNA, rRNA, and ribozymes areorganisms and primitive life-like system underparticularly important. However, these structureshydrothermal conditions since hydrogen bonding anddisappear with increasing temperature since thehydrophobic interaction are weak.

interaction

forhyperthermophilicinteractions become weak at high temperatures.

Conclusively, for instance, the reason that RNA is

However, there have been no practical techniques to

not easily accumulated under simulated hydrothermal

measure the strength of the interactions at highconditions does not seem to be due to thetemperatures over 100 oC. Thus, we have attempted

decomposition of RNA formed by the prebiotic

to detect such interactions using our in situ UV-

pathways. The decrease of biologically important

visible spectrophotometric system [9]. The UV-interactions at high temperatures is critical for thevisible absorbance changes for the intercalation ofprebiotic formation model reactions. In other words,

ethidium bromide (EB) into double-helical DNA

RNA molecules could not have accumulated underwere measured in the presence of different salts athydrothermal environments unless some additives

481 nm at 25 - 200 oC [18]. The absorbance changes

have facilitated the weak interactions. In addition,- 262 -

Viva Origino 33 (2005) 258-268

one should consider that the life-like systems havehumans because of consciousness. Later, the term

emerged in thermodynamically open systems (Fig. 3).

was extended to use as a term indicating an attribute

Since our investigations have been carried out forof organisms beyond the nature of humans by

RNA systems entirely consisting of RNA molecules,

IMANISHI Kinji for the first time. Imanishi has

we have attempted to search whether prebiotic

pointed out that organisms cause subjective actions

protein-like molecules could have facilitated thetowards environments for their survival althoughprebioticRNA

organisms do not have naturally consciousness. In

molecules. It was found that the thermal condensation

addition, Imanishi argued that subjective actions of

products of amino acids as protein-like molecules

organisms

possess both catalytic and inhibitory activities for thecontribute to evolution. Such nature of organisms

formation and degradation or RNA, while themay not be easily accepted on the basis of theactivities were indeed weak [34-38].

conventional

formation

anddegradationof

towards

views

environmentsofextensively

biologicalscience.

Nevertheless, it was necessary to construct a unified
3. An attempt to develop a unified theory for thetheory to describe behaviors of life-like systems at

description of chemical evolution and biologicaldifferent hierarchies on the basis of the definition ofevolution.

life [20-22]. To develop such a theory, it was

3. 1. The definition of life and the hypothesis on theattempted to find the correlation between themechanism of evolution

subjectivity of organisms and the assignment method

In this paper and a previous paper [19], the RNA

between genotype and phenotype. Life-like systems

world hypothesis has been evaluated from empiricalon the earth were classified into three categories, thatdata concerning the hydrothermal origin of life.

is, the cell type system (Class I), the virus type

These analyses suggest that RNA systems would

system (Class II), and other systems (Class III) on thehave been possible under hydrothermal environments

basis of both the subjectivity and the assignment

if facilitated with effective adjuncts. Naturally, themethods between genotype and phenotype for theseexperimental analyses of the RNA world hypothesis

systems,

are important, but theoretical analyses would be also

subjectivity

indispensable. Here, the evaluation of the RNA

observed. The principle of the assignment method

hypothesis is attempted on the basis of a unified

between genotype and phenotype was extended to thetheory of origin and evolution of biosystems on theassignment between information and function at

earth. Attempts to define “life” would provide insighthigher hierarchies of life-like systems and theinto the origin of life problem. A few years ago, I

correlation between the subjectivity of life-likehave proposed a definition of life that “Life is thesystems and the assignment methods was investigated.

system that has subjectivity” [20-22]. The term

Conclusively, it was hypothesized that the assignment“subjectivity” was originally adopted as a term of

methods between information and function byphilosophy, where one supposes subjectivity oforganisms contribute to the evolution of organisms,- 263 -

where
and

the

correlation

betweenthethe

assignment

methodswasViva Origino 33 (2005) 258-268

Higher level ofsubjectivity

Naturalselection

Basicsubjectivity
Modification of
the system

Mutation(a)

Cognition

Assignment ofgenotype and phenotype
Assignment of
information and function(b)

Figure 4. A proposed mechanism of evolution of biosystems. (A) indicates Darwinian evolution
using a cyclical relationship between natural selection and mutation. (B) indicates the proposedmechanism using a cyclical relationship between “the subjectivity of life” and “the assignment
between information and function”. The principle of “the assignment between genotype andphenotype” at the molecular level is extended to higher hierarchies of organisms, where the term
is generalized as “the assignment between information and function”.

in which the assignments are caused by the subjective

system entirely consisting of RNA molecules could

actions of organisms towards environments (Fig. 4).

hardly have possessed such functions. Presumably,
the adsorption of the RNA molecular system on a

3. 2. A problem of RNA systemmineral surface or with protein-like molecules might

According to the proposed theory, a life-likehave enabled to keep the continuity as a single

system that is regarded as alive should havebiosystem (Fig. 5). Naturally, the essence of the RNA

possessed a nature that the system can subjectively

world hypothesis is that RNA molecules could haveintroduce the environment as a part of the organisms

played important roles. Thus, it does not deny theand can adapt itself to the environmental changes forcontribution of other molecules. However, there havesurvival. In other words, it can be assumed that the

been few studies on the roles of other molecules forlife-like system should have held capability to keep

RNA systems. From this viewpoint, the role of somecontinuity (individuality) and stability as aA

single system [39]. Question is whether RNA
world type systems could have possessed sucha nature or not under the primitive earth
conditions. However, RNA molecules arenormally

unstablecompared

with

DNA

B

RNA molecule

protein-likemolecules

molecules and proteins. Although the closed
mineralsurfacevessels in the cell type organisms would be
obviously important to expedite the continuity
and stability as single biosystems, an RNA

Figure 5. The continuity of life-like systems can be preservedby cells (A), but also it might be maintained by minerals orprotein-like molecules (B).

- 264 -

Viva Origino 33 (2005) 258-268

additional molecules should be evaluated as well as

could have survived within the surrounding cold

the viewpoint of the behavior of RNA under

ocean are important. Nevertheless, the scenariohydrothermal

systematic

described in this paper intimates that first life-likeinvestigations are necessary to search the roles ofsystems could have emerged, survived, and evolved

such molecules of maintaining RNA systems under

under hydrothermal environments.

conditions.

Thus,

the primitive earth conditions.
On the other hand, a catalytic network consisting

4. Conclusions.

of protein-like molecules, in which its reproduction is

In this paper, the RNA world has been evaluatedweakly catalyzed by other protein-like molecules inon the basis of the experimental analysis concerning

the network, can be categorized as a system thatthe hydrothermal origin of life and a unified theory ofpreserve information concerning the structure of thethe origin and evolution of biosystems on the earth.

catalysts. This type of protein-like molecules can be

These analyses imply that an RNA world entirely

regarded as a candidate of primitive enzymes. Such aconsisting of RNA molecules is unlikely to occur andcatalytic network system could be stable andsome adjuncts could have facilitated the emergence

efficiently preserve the continuity as a single system.

of RNA systems under primitive earth conditions.

As mentioned above, weak inhibitory and/or catalytic

RNA systems possessing functions to preserve

activities of thermal condensation products of amino

information and enzymatic abilities seem to be fairly

acids as protein-like molecules have been detectedadvanced systems and it is important to find more

for both the formation and degradation of RNA

primitive systems, such as a system consisting ofmolecules [34-38]. Naturally, these activities areprotein-like molecules, which could have preservedmuch weaker than those of real enzymes. Presumably,

ambiguous information and weak catalytic abilities.

the enzymatic activities would have been evolved insynchrony with the development of the coding
systems and the synthesis of primitive enzymes. In

Acknowledgments

addition, this type of protein-like molecules might
have enhanced

the weak interactions

The author greatly appreciates the financial

for thesupport from the local government of Osaka

formation and replication of RNA molecules as

Prefecture for attendance to the ISOLAB’05 meeting.

mentioned above. While plausible materials andenvironments to facilitate the accumulation of RNA

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