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.

 

Mario Vaneechoutte

Department of Clinical Chemistry, Microbiology & Immunology,

University Hospital, B 9000 Ghent, Belgium

 

Presented at the Closure Symposium, Gent, Belgium, May 3-5th 1999.

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, Namur, Belgium, August 1998. 

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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 Western Europe was intendend partially to spread the Bible, while its impact on scientific activity was not foreseen. Computers were invented to increase computation speed, and not to result in robots or the internet, etc. Still, each of these goals enabled new knowledge and insights which made other applications and goals emerge. While none of these goals intended to develop self replicating technology, it is conceivable that in the near future, some people may find some applications for such technology (see e.g. 17) and may try to develop this. The fact that at present we are conveying rapidly many functionalities to machines, indicates that this difficult enterprise becomes less and less unthinkable.

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

1. Rosen, R. 1991. Life itself. A comprehensive enquiry into the nature, origin and fabrication of life. Columbia Univ. Press. New York, NY.

2. Cech, T. R. 1986. A model for the RNA-catalyzed replication of RNA. Proc. Natl. Acad. Sci. USA 83: 4360-4363.

3. de Duve, C. 1995. Vital Dust. Life as a Cosmic Imperative. Basic Books. New York, NY.

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.

7. Smith, J. M. & E. Szathmary. 1995. The major transitions in evolution. W.H. Freeman. Oxford, UK.

8. Bateson, G. 1979. Mind and Nature.

9. Westbroek, P. 1998. Homage to Earth. Nature 391: 550-551.

10. Watson, J. D. 1993. Prologue: Early speculations and facts about RNA templates. In The RNA world. R. F. Gesteland & J. F. Atkins, Eds.: xv-xxiii. Cold Spring Harbour Laboratory Press.

11. Benner, S. 1999. Old views of ancient events. Nature 283: 2026.

12. Yao, S., I. Ghosh, R. Zutshi & J. Chmielewski. 1998. Selective amplification by auto- and cross-catalysis in a replicating peptide system. Nature 396: 447-450.

13. Zhang, B. & T. R. Cech. 1997. Peptide bond formation by in vitro selected ribozymes. Nature 390: 96-99.

14. Steitz, T. A. 1998. A mechanism for all polymerases. Nature 391: 231-232.

15. Blobel, G. 1980. Intracellular membrane topogenesis. Proc. Natl. Acad. Sci. USA 77: 1496.

16. Cavalier-Smith, T. 1987. The origin of cells: a symbiosis between genes, catalysts, and membranes. Cold Spring Harbour Symp. Quant. Biol. 52: 805-824.

17. Tipler, F. 1995. The physics of immortality: modern cosmology, God and the resurrection of the dead. 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 universal ancestor. Proc. Natl. Acad. Sci. USA 95: 6854-6859. 

Woese, C.R. 2000. Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. USA 97: 8392-8396.

 

ADDITIONAL THOUGHTS

14 October 2004.

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.

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