The Nature of Consciousness

Piero Scaruffi

(Copyright © 2013 Piero Scaruffi | Legal restrictions )
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These are excerpts and elaborations from my book "The Nature of Consciousness"

The Origin of Replication

The mystery of the origin of genes is particularly challenging because a gene is such a complicated structure and is unlikely to evolve spontaneously. 

The US biologist Walter Gilbert noted that most of a person's DNA does not code genes but what appears to be gibberish, and even the part that is code is distributed in fragments (or "exons") separated by useless pauses (or "introns").  In his opinion the first genetic material was made of exons, that symbiotically got together and formed new, more complex genetic material. Introns are not random leftovers, but sort of gluing elements from the original material. In a sense, his theory points to the possibility that the gene is not the ultimate unit, but exons are.

Attention has been focusing on RNA since RNA has been shown to be a self-replicating molecule that can act as its own catalyst. DNA cannot make copies of itself, and proteins cannot create themselves. They both depend on each other. But (some kind of) RNA can act as its own enzyme (i.e., its own catalyst). Therefore, RNA is capable of replicating itself without any need for proteins.

Stanley Miller proposed that the first living creatures may have been able to synthesize protein and reproduce without the help of the DNA, depending solely on RNA to catalyze their growth and reproduction. The US chemist Thomas Cech had already proven (in 1982) that RNA molecules alone can induce themselves to split up and splice themselves together in new arrangements. It is also chemically plausible that all four RNA nucleotide bases could have been created in nature by ordinary atmospheric, oceanic and geological processes.  Miller's theory, though, requires that life be born in lukewarm water, not the very high temperatures of thermophiles.

The German physicist Manfred Eigen induced RNA molecules to replicate by themselves, thereby lending credibility to the hypothesis that RNA came before DNA and that the first forms of life employed only RNA. Eigen's experiments with "autocatalytic cycles" involving RNA showed that, under suitable conditions, a solution of nucleotides gives rise spontaneously to a molecule that replicates, mutates and competes with its progeny for survival.  The replication of RNA could then be the fundamental event around which the rest of biology developed. Eigen speculates that the genetic code was created when lengths of RNA interacted with proteins in the "primordial soup". First genes were created, then proteins, then cells. Cells simply provide physical cohesion. Cells first learned to self-replicate and then to surround themselves with protective membranes.

The US physicist Freeman Dyson believes that one cannot consider life only as metabolism or only as replication. Both aspects must be present. Therefore, we must look not for the origin of life, but for the origin of replication and for the origin of metabolism. Since it is unlikely that both metabolism and replication occurred at the same time in one of the primitive organic molecules, Dyson thinks that life must have had a double origin. It is more reasonable to assume that life "began" twice, with organisms capable of reproduction but not of metabolism and with (separate) organisms capable of metabolism but not of reproduction, and only later there arose a mixture of the two by some kind of symbiosis: organisms capable of both reproduction and metabolism.

Dyson's idea is that organisms that could reproduce but not replicate came first. The most elementary form of reproduction is simply a cell division: two cells are created by dividing a cell into two. Replication implies that molecules are copied. Reproduction with replication implies that the new cells "inherit" the molecules of the mother cell. Replication became a parasite over metabolism, meaning that organisms capable of replication needed to use organisms capable of metabolism in order to replicate. First proteins were born and somehow began to metabolize. Then nucleic acids were born and somehow began to replicate using proteins as hosts.

The two organisms became one thanks to a form of symbiosis between host and parasite. Dyson borrows ideas taken from Manfred Eigen (who claims that RNA can appear spontaneously) and Lynn Margulis (who claims that cellular evolution was due to parasites). Basically, his theory is that RNA was the primeval parasite.

The French virologist Patrick Forterre (“A hypothesis for the origin of cellular domain”, 2006), instead, thinks that today’s living beings are descendants of three RNA viruses. These RNA viruses originally evolved the double-stranded DNA molecule to defend their RNA genes, and eventually this “shield” took on a life of its own and became the main mechanism for bacteria, archaea, and eukaryota. It is a fact, that the genes of viruses seem to date back in time to before the birth of cell-based life.

The genetic code is just a code that relates mRNA triples and protein's aminoacids.  The genetic code is the same for every being. It is just a code. It translates the instructions in the genotype into a phenotype. But it is an extremely sophisticated code. Did the genetic code itself evolve from a more primitive code? It is unlikely that the first self-replicating organisms were already using today's genetic code. How did the genetic code arise? And why don't we have any evidence of a pre-existing system of replication? Why is it that today there is only one code, rather than a few competing codes (just like there are a few competing genomes)?

The Origin of Proteins

Yet another theory is that perhaps the original living material was neither DNA nor RNA but proteins themselves. DNA and RNA carry the instructions for making proteins, and proteins make up bodies, and bodies make other bodies that carry new sets of instructions. This is a brief summary of how life works today. The question is who could have done it all by itself: which natural structure can be both a body and a program? RNA seems like the ideal candidate because it does both jobs: RNA transmits DNA's instructions on how to make proteins, but RNA can also fold up and catalyze reactions, i.e. the jobs of proteins. In 1985 the US physicist Ken Dill had developed a mathematical tool to solve the protein-folding problem ("Theory for the folding and stability of globular proteins", 1985). Later, using the same tool, Dill showed that foldable polymers ("foldamers") can originate an autocatalytic set, i.e. a loop in which they catalyze the formation of copies of themselves ("Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers", 2017).


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