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.
Department of Clinical Chemistry, Microbiology
& Immunology,
Faculty of Medicine & Health Sciences
University Ghent, B 9000
Presented at the Closure
Symposium, Gent,
Revised version published
in the Annals
of the New York Academy of Sciences 901: 139-147.
March 2000.
See also: "The replicator, a
misnomer. Conceptual implications for genetics and memetics.",
representing an earlier version of related ideas, presented at the First Symposium on Memetics,
Abstract
The hypothesis is put
forward that the origin of life, i.e. the origin of the first cell, cannot be
explained by natural selection among self replicating molecules, as is done by
the RNA-world hypothesis. To get around the chicken and egg problem of the
semantic closure of the cell - no replication of informational molecules
(nucleotide strands) without functional enzymes, no functional enzymes without
encoding in informational molecules - a prebiotic evolutionary process is
proposed that - from the informational 'point of view' - somehow must have
resembled the current scientific process. The cell was the outcome of the interactions
of i) a complex premetabolic community with ii) informational molecules which
were devoid of self replicative properties. Comparably scientific progress is
possible essentially because of i) interaction between a complex cultural
society with ii) permanent information carriers like printed matter, and may
eventually lead to self replicating technology whereby semantic closure occurs
anew.
Explaining the origin of
life as a scientific process might provide a unifying theory for the evolution
of information, whereby at two events symbolisation/encoding of interactions
into permanent information occurred - once of chemical interaction, once of
animal behavioural interaction - and whereby at one occasion this encoding has
led to autonomously duplicating chemistry (the cell). From this it is arguable
that the development of autonomously replicating entities may be one of the
outcomes of current scientific progress.
1. Introduction
The cell is defined here as
a semantically closed system (or a system closed to efficient cause (1)). It is
the only such system existing on Earth thus far and it is generally agreed that
it has originated only once. With a semantically closed system it is meant that
the system contains all the information and functionality to duplicate itself.
Put differently, semantic closure means here that the information (nucleotide
strands) to produce processors (enzymes) which are able to replicate this
information depends on the functioning of these processors, whereby the
functioning of these processors depends on the content of the information they
replicate.
The hypothesis put forward
here states that it is virtually impossible that the highly complicated system
'cell' developed gradually around some simple self replicating molecules
(RNA-hypercycles, autocatalytic peptide networks) by means of natural
selection, as is proposed by e.g. the RNA-world hypothesis (2-7). Instead I
propose that the cell was the result of prebiotic events which - from an
informational point of view - are comparable to the current scientific process.
Science is possible because of the interaction of a behavioural community
(culture) with permanent information carriers having unlimited informational
content (printed texts). Comparably, I argue that it was the interaction
between a chemical metabolic community (prebiotic chemistry) with newly
developed nucleotide strands as carriers having unlimited informational
content, which led to the cell (the origin of life). Just as printed texts do
not self replicate but rely on the existence of an underlying metabolism to be
replicated, nucleotide strands were replicated by a prebiotic metabolic complex
network of interactions. The first cell, some 4 billion years ago, represented
a completely new concept, that of autonomous duplication, which compared to
nothing in the society from which it was born.
Present day culture
(cultural selection) then is considered to be in an earlier developmental stage
than biology (natural selection), a stage which is best compared with prebiotic
chemical interaction at the time when informational molecules (nucleotides)
were developed. Natural selection (as in biological evolution) however is about
selection among variations on the theme of autonomous duplication, a theme not
yet developed in culture/science/technology.
Still, it is possible that
cultural semantic closure can develop, for example in the form of self
replicating machines. As was the case for the first cell compared to the
prebiotic community from which it arose, these machines will compare to nothing
of the cultural/scientific society from which they may arise. Like the cell
left its native pond and took off to conquer every corner on Earth, as was
possible by exponential growth due to autonomous duplication, the putative autoreplicative
properties of these machines might enable them to leave native Earth and to
conquer every corner of the Universe. As the prebiotic metabolic chemical
interaction led to autonomously duplicating chemistry - once nucleotides were
available as permanent carriers of information, cultural behavioural
interaction may lead to autonomously replicating technology. Indeed, the
availability of printed texts since 500 years has increased complexity
(scientific knowledge and technology) exponentially and may lead to
autonomously replicating technology.
2. Background
The author is well aware
that the ideas developed here are highly unusual. They were developed i) by
considering evolutionary events (prebiotic, biological and cultural) as the
evolution of information and interaction - from the detached "point of
view" of information, ii) by trying to find formal analogies between
biology and culture and iii) by studying critically the presently available
hypotheses concerning the origin of life.
3. Definitions
Since the words we use most
often lead to confusion, because the same word may have different connotations
to different people, it is necessary to first explain how I define the most
important concepts used in this paper.
Information. An elegant and highly applicable
description of the concept "information" is Gregory Bateson's "A
difference which makes a difference." (8). Of all the molecules with
surround molecule A, only those which can interact with A can be said to
contain information. There are many different molecules surrounding A, but only
a few are able to make a difference, i.e. to influence the chemical 'behaviour'
of A. Comparably, of all the noises and visual signals reaching an animals'
perception system only some will influence its behaviour and can be said to be
informational. This definition implicitly represents the contextual dependance
of information. In the above example, those signals not influencing the
behaviour of animal A, may be informational to animal B.
Biology and culture. Biology is basically the study of
autonomously duplicating chemistry. Chemistry requires direct physical/material
contact to make a difference, i.e. to let informational interaction occur. The
interactions (information exchange) between organic molecules and cells are
material/chemical. Culture became possible when animals started to influence
each others behaviour by means of sonic and visual signals, which do not
require direct contact and can be exchanged over long distances. This is a profoundly
new manner of making a difference - of transmitting information.
Transient information. During behavioural interaction
(chemical and cultural) information is transient, since the difference which
can make a difference does no longer exist after the interaction. During
chemical behavioural interaction molecules are transformed (reappearing later
in the chain of interactions as the consequence of ongoing interactions).
During cultural behavioural interaction, sonic and visual signals exist during
a limited time and mental processes are required to make signals with a
comparable informational content reappear later in the interconnected chain of
behavioural interactions.
Permanent information. While nucleotides enabled to encode
chemical behavioural interaction, symbolic language enabled to encode cultural
behavioural interaction. From an informational point of view, written (to a
lesser extent), printed and electronic texts compare best to nucleotide
strands. They represent permanent differences which continue to exist whether
or not interaction is going on. They have the potential to make differences at
many instances (nucleotides when translated, texts when read, interpreted, ..).
Also, because they are symbolic, they have unlimited informational content (7),
which means that a limited set of conventions (symbols, syntax) enables to
represent many differences. Another important characteristic is that permanent
information can be recombined (at random), increasing exponentially the
informational space that can be searched. While it is impossible to mix
processes, interactions, processors, their encoded representations can be
recombined endlessly. It is impossible to mix processes: One can't mix the
activity of enzyme x with that of enzyme y, one can't take the bacterium Escherichia
coli and mix it with a piece of human tissue, while keeping a functional
process, one can't mix the ideas of two people by mixing their brain processes.
But we can mix a functional
E. coli cell with human enzymes, by inserting into its genome the code
for such a human enzyme. Evolution itself created a lot of new enzymes by the
same process. In culture, having printed texts, many different lineages of
information can continuously come together, with copy true backups of the
original ideas existing for proofreading.
Processors. Processors are entities which can
repeat the same activity several times without being changed by the
interaction. Processors (enzymes, transistors) are digital catalysts. Analog
catalysts like some co-enzymes, ribozymes and thioesters are transformed during
the process of interaction. Polypeptidic enzymes and transistors still exist
after the interaction.
Life cannot be understood by studying a
single living organism. Since all currently living cells are the descendants of
the ancestor cell - the first and still only autonomously duplicating system
that ever was developed, life is to be considered as a single 4 billion year
old billion-billion cellular organism, consisting of all the descendants of the
first cell. Cooperation and competition between these cells and between
temporary colonies of cells (multicellular organisms) happen continuously as is
also the case for cells within multicellular organisms. Because of the
possibility of exponential growth, as a consequence of autonomous duplication,
the organism "Life" continuously changes its environment and has to
adapt to these self-induced changes. Eventually the environment (biosphere) can
be understood as a creation of this organism and as a part of it (consistent
with the modern version of the Gaia hypothesis (9)). The question 'What is
life' cannot be answered by studying a single living organism, because all
extant creatures can be understood only in the context of the relations with
other extant organisms and by considering the past evolutionary interactions
and events.
Evolution and
complexity.
The most general and
straightforward definition of evolution is "change over time". We
observe that more interactions and different pathways become possible with
time. This increased flexibility can be considered as complexity (a concept
closely related to or synonymous with "intelligence"). The increase
of complexity is not a necessity, but is almost inevitably as a consequence of
competition and cooperation between the descendants of the autonomous
duplicator. This follows from the fact that evolution is open ended towards
more complexity: more complex systems are able to exploit new niches which were
beyond reach before this level of complexity was reached. For example,
multicellular animals can feed on complete unicellulars, but not vice versa
(remark: also parasitic unicellulars do not ingest their hosts). This open
niche explains for instance the tremendous radiation observed, once the concept
of a multicellular animal had evolved.
Selection, cultural
selection and natural selection
Selection is a general
principle. It occurs when variations on a theme exist. None, one, more or all
variations will be able to exist in the given environment. Radioactive decay is
an example of selection among variations on the theme of physically stable
atomic configurations in a universe (environment) with certain parameters for
fundamental laws. The difference with cultural and natural selection is that
there is no amplification/replication of the fit variations.
In cultural selection,
different answers to a problem (variations on a theme) may be valued
differently by the environment (in casu the scientific community). The most
valued hypothesis will be amplified, other hypotheses may disappear. The
difference with natural selection is that the amplification efficiency of
hypotheses is not encoded in these hypotheses: hypotheses do not self
replicate, but are replicated by scientists, presses, computers.
In natural selection, the
only theme is amplification efficiency itself and selection among the different
variations on the theme of autonomous replication automatically leads to
amplification. At first sight this is a powerful principle, but with respect to
developing more complexity, biology is hampered because of limitations in
searching information space: only those variations which do not diminish
autonomous duplication efficiency can exist. To the contrary, the evolution of
cultural information does not depend on its ability to replicate autonomously.
Therefore any idea or recombination of ideas imaginable is possible. Hence, the
difference between cultural selection and natural selection: if science were to
proceed by natural selection, this would mean that the texts produced by
science also should contain all the necessary information on how to make a new
text. Any changes to these texts which would undermine the ability to self
reproduce would disable the text to spread any further.
Remark: in defining these
generally used, but difficult concepts, not a single neologism has been used.
All that has been done is rethinking the concepts we use, broadening their
content where needed (like the concept of behaviour), narrowing it elsewhere.
4. The origin of life:
problems with the RNA-world model
The discovery of catalytic
activity of RNA-molecules (ribozymes)(2) has led to the revival of the idea
uttered in 1968 by Francis Crick that a single biopolymer, like RNA, might have
served both informational and catalytic roles and thus have propelled the
evolution towards the first cell by means of natural selection (10). To the
contrary, the hypothesis put forward here states that no such autonomous
duplication existed before the first cell and thus that natural selection
started only with the first cell.
Despite searching
quadrillions of molecules, it becomes clear that such a spontaneous
RNA-replicator is unlikely to be found (11). Reports of self replication of
nucleotides (2, 4, 6) and peptides (12) still depend upon human intervenience
(for instance by changing the environmental conditions between two rounds of
replicaton or by denaturing the double strands). The problem of how to denature
the double nucleotide-strand in a nonenzymatical manner has been overlooked and
has contributed to the failure to establish molecular self-replication.
Even if these practical
problems could be overcome, the RNA-world puts the burden of both replication
and variable informational content on the same molecule, so that the
COSMIC-LOPER (Capability of Searching Mutation Space Independent of Concern
over Loss Of Properties Essential of Replicaton)(11) will be very limited.
Indeed, as explained above (see the difference between natural and cultural
selection), introducing natural selection too early is a limitation rather than
a gain. I propose that the original role of nucleotides was not self
replicative so that high recombinatorial freedom of the information they
carried existed, as is the case in current human culture, using printed texts.
It should be stressed here that many of the important findings of RNA-world
research (e.g. 13) need not to be dismissed, as long as the catalytic role of
ribozymes is restricted to metabolic and translational functions.
One consequence of this
model is that evolution could try out an exponentially larger number of
possibilities (high COSMIC-LOPER) and could proceed much faster than natural
selection. Comparably cultural selection since the introduction of printed
texts some 500 years ago has increased complexity (scientific knowledge and
technology) exponentially, while it took natural selection roughly 2 billion
years to go from prokaryote to eukaryote, 1 billion years to proceed to the
first multicellular animals and 1 billion years to the first symbol using
animal (humans), some half a million years ago only.
Another problem with the
RNA-world hypothesis is known as Eigen's paradox (7): the simplest cell known
today contains a chromosome with 2000 genes, most of these encoding for very
different functionalities and with none of these genes by theirselves
containing sufficient information to cover the complex process of autonomous
duplication. Eigen realized that a society of self replicating competing RNA-hypercycles
will outcompete each other when brought together in a cell, instead of merging
into a chromosome. (Eigen's paradox is solved (?) only by the rather artificial
stochastic corrector model (7)).
5. Hypothesis: The
possible congruence between culture after the introduction of printed texts
with prebiotic chemistry after the development of nucleotide strands.
Christian de Duve (3) has
argued convincingly how the enzymatically driven metabolism of biology is
functionally congruent with the prebiotic catalysis driven by for example
thioesters. Although enzymes are very different from thioesters, they fulfill
the same functional role. I argue that this congruence can be found back in
current society where metabolic and informational functions of living beings
are being conveyed to technological counterparts: computation, pattern
recognition, speech, vision (all by computers and robots), locomotion (cars,
airplanes, missiles, ..., robots), energy provision (steam engines, nuclear
plants, ..., photovoltaic cells).
Another congruence, is the
observation that the rate of current transformations exponentially increased
after the introduction of permanent information carriers ((written), printed
and electronic texts) which are copyable in high numbers with high fidelity,
which have unlimited informational content and which can be recombined
endlessly. Congruently, it is generally agreed that the complex enzymes
(digital catalysts) could have been developed only after nucleotide strands
existed, whereafter enzymes gradually replaced the original (analog) catalysts.
Congruently, science is
possible because of the interaction of scientists and permanent information
carriers, and this interaction of scientists and printed matter depends on the
ongoing activities of a lot of other people, farmers in the first place.
Farmers in turn exploit plants and animals to produce food, animals and plants
can thrive only because of bacterial metabolism. This is just to say that
scientific activity and knowledge is only possible because it thrives on a
complex underlying network of chemical, biological and cultural interactions.
Congruently, I propose that certain elements of a complex premetabolic network
(as proposed to have existed by de Duve (3)) started to develop symbolic language
in the form of nucleotide strands (think of humans as their counterpart) and
that this may have started a process comparable to the scientific process.
6. Brief proposal of a
model for the development of the first cell by means of a 'scientific' process.
The following is intended
only to draw a possible picture of the course of events.
Imagine a large membrane
irregularly making contact with a solid substrate, creating a microcosmos in
between membrane and substrate while the presence of gaps allows for interaction
with the environment outside of the membrane. Prebiotic metabolism (3) develops
in this microcosmos. At some moment, some of the constituents of this network
enable the production of nucleotide strands, possibly connected to the outside
of the membrane. Initially RNA nucleotides fulfilled this function (in
combination with some catalytic functions), and enabled the development of some
enzymes like RNA-DNA polymerases (reverse transcriptases) leading to DNA
strands. (Polymerases are indeed supposed to be among the earliest enzymes
(14)). These strands played a role comparable to that of the printed texts
representing scientific hypotheses in the present day world, e.g. hypotheses on
how to construct more efficient technology (enzymes). Billions of these
DNA-proto-genes were produced, most without any functionality. Comparably, many
of our hypotheses do not lead to more technological functionality. Those
strands which encoded for enzymes with higher efficiency increased the
efficiency of the local society as a whole, which resulted in a higher
probability that these 'genes' were reproduced more successfully. Comparably,
the technologically most advanced societies gain most economic advantages,
without necessarily destroying other societies, upon which they keep relying
for more basic, metabolic needs and which eventually may profit from this
knowledge. In the end, many informationally different large protochromosomes -
formed by ligation/combination of proto-genes and containing an assembly of
genes encoding for very different functions, were attached to the membrane,
surrounded by enzymes (free and membrane-attached) which were encoded by
neighbouring and/or other chromosomes. Occasionally, blebbing (somehow
comparable to obcell formation (15, 16)) occurred, i.e. splitting of and
circularizing of a piece of the membrane - a phenomenon still observed in
present day bacteria like the meningococcus). It can be imagined that at
several of these occasions the closing membrane internalized a protochromosome and
some enzymes. At one of billions of such occasions the protochromosome that was
enclosed, can have been composed of the essential genes carrying the
information on how to duplicate the whole system, while (essentially!) some of
the active enzymes and ribozymes enclosed (DNA-RNA polymerases, ribosomes) were
capable of translation of the chromosomal information into enzymes with
metabolic (e.g. pyrophosphate synthase) and replicative (DNA-DNA polymerase)
functions. Reverse transcriptase, not much needed anymore at that time and
therefore probably rare, was not included - a possibly likely outcome. The
first cell, life, was born and natural selection, selection among variations on
the theme of autonomous duplication, started. Because of functional self replication
constraints on the kind of information that can be contained, the evolution
towards higher complexity - which had been extremely fast since the
introduction of nucleotides as permanent carriers of information - slowed down
drastically. On the other hand, competition between autonomously duplicating
systems now was possible and (bio)diversity increased.
7. Discongruences?
One might argue that the
scientific process cannot be compared to simple chemistry because science is
not random and science is done by goal directed beings (humans), unlike
molecules. First, it can be easily argued that science can be considered as a
largely random process. Second, it is clear that humans are goal directed
beings unlike molecules. But if we, for the sake of the argument, imagine that
self replicating technology will result from our activities, it becomes clear
that this was never - and still isn't - our goal. Such is true for most of our
inventions. The invention of writing some 5000 years ago was not to make scientific
activity possible, but was goal directed towards facilitating the inventory of
life stock and property. The introduction of the press in
8. Conclusion. The
possibility for a grand unifying theory of the evolution of information
Explaining the origin of life
as a scientific process might provide a unifying theory for the evolution of
information, whereby at two events symbolisation/encoding of interactions into
permanent information occurred - once of chemical interaction, once of animal
behavioural interaction - and whereby at one occasion this encoding has led to
autonomously duplicating chemistry (the cell). From this it is arguable that
the development of autonomously replicating entities may be one of the outcomes
of current scientific progress.
9. References
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itself. A comprehensive enquiry into the nature, origin and fabrication of
life.
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3. de Duve, C. 1995. Vital Dust. Life as a Cosmic Imperative. Basic
Books.
4. Ferris, J. 1994.
Chemical replication. Nature 369: 184-185.
5. Joyce, G. F. 1989. RNA
evolution and the origins of life. Nature 338: 217-224.
6. Orgel, L. E. 1992.
Molecular replication. Nature 358: 203-209.
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Szathmary. 1995. The major transitions in evolution. W.H. Freeman.
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and Nature.
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Homage to Earth. Nature 391: 550-551.
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views of ancient events. Nature 283: 2026.
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Anchor.
See also: self replicating
nanotechnology:
http://www.foresight.org/Conferences/MNT6/Abstracts/Hall/
http://www.zyvex.com/nanotech/selfRepNATO.html
Cavalier-Smith, T. 2002.
The neomuran origin of archaebacteria, the negibacterial root of the universal
tree and bacterial megaclassification. Int J Syst Evol Microbiol. 52:7-76.
Cavalier-Smith, T.2002. The
phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol. 52:297-354.
Woese, C.: http://www.eurekalert.org/pub_releases/2002-06/uoia-nce061402.php PNAS. 18 June 2002.
Woese, C. 1998. The
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Woese, C.R. 2000.
Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. USA 97: 8392-8396.
ADDITIONAL THOUGHTS
This view implicitly holds
that viruses and other mobile genetic elements are older than the first cell.
When stating that bacteria cannot
feed on multicellular organisms, I mean that bacterial cells cannot engulf
other cells, while eukaryotic cells can. In fact, C. de Duve considers this as
one of the breakthroughs of the eukaryotic cell: by throwing off the external
skeleton (bacterial cell wall) and developing an endoskeleton (actine tubules)
eukaryotic cells became the first predators on Earth, able to ‘eat’ other
cells.