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An Unresolved Puzzle: The origins of Life.

14 February 2013, 07:50

                                 An Unresolved puzzle: the Origins of Life.

Where the earth, the moon, the stars and living beings, including ourselves, come from are ancient questions which are addressed in the opening verses of the book of Genesis.

Early civilization, including the authors of Genesis, however, lacked the understanding of nature on which to base a realistic theory of the origins of the Universe or of life on our planet.   Thus Anaximander of  Miletus  (610 – 546 BC), an early Greek  philosopher, considered that “ from warmed up water and earth emerged either fish or entirely fishlike animals. Inside these animals, men took form and embryos were held prisoners until puberty; only then, after these animals burst open, could men and women come out, now able to feed themselves.”  He claimed that, when acted upon by the Sun, spontaneous generation of  living  creatures in a moist environment continued ‘to this day’, that being in the 6th century BC,  with aquatic forms being produced directly from lifeless matter.  

Aristotle (384 – 322 BC) believed that new plants and animals can spring not  only  from  kindred  ancestry , but also spontaneously, using whatever nutrients are available to them.  As regards sexual reproduction Aristotle’s views were somewhat unflattering of  the  female  contribution .  He argued that the male parent provided the “form,” or “soul” in the form of semen, and the female parent contributed unorganized matter, allowing the embryo to grow.

A sequence of ground baking discoveries, however,  demonstrated conclusively that the idea of spontaneous generation of life, abiogenesis, was not in line with the available scientific evidence.  The presence of microbes in the environment was demonstrated by Antonie van Leewenhoek in 1676, but the significance of his discovery was slow to be understood.  During the 19th century, however, microorganisms were shown to be  the causative agents of several diseases  and then, in 1861, Louis Pasteur demonstrated that organisms such as bacteria and fungi do not spontaneously appear in sterile, nutrient-rich media.  Instead, every living thing came from a previously living thing, a process called biogenesis.  But where then did the very first living thing come from? 

Günter Wächtershauser proposed the iron-sulfur world theory and suggested that life might have originated at deep-ocean hydrothermal vents at the mid ocean ridge.  Wächtershauser proposed that an early form of metabolism predated genetics. By metabolism he meant a cycle of chemical reactions that release energy in a form that can be harnessed by other processes. The volcanic exhalations in deep ocean vents are rich in the different oxidation states of carbon, ranging from methane to carbon dioxide, ammonia and hydrogen sulfide whereas the solid substructure contains transition metals  such as iron and nickel, which catalyze the conversion of the former to simple organic molecules as the building blocks of the more complex molecules found in living organisms. As a consequence there are thriving communities of various types of oceanic life, ranging from archaebacteria to fish in the vicinity of deep sea vents,  while the surrounding ocean floor is sparsely inhabited. Volcanic vents are inhabited by extremophiles that can survive boiling temperatures. The DNA polymerase used in recombinant research and forensic science derives from Pyrococcus furiosus, an organism isolated from such vents and remains fully active at 100º C.

It has been proposed that amino-acid synthesis could have occurred deep in the Earth’s crust and that these amino-acids were subsequently shot up along with hydrothermal fluids into cooler waters, where lower temperatures and the presence of clay minerals would have fostered the formation of peptides and primitive cells. This is an attractive hypothesis because of the abundance of CH4 (methane) and NH3 (ammonia) present in hydrothermal vent regions, a condition that was not provided by the Earth’s primitive atmosphere. A major limitation to this hypothesis is the lack of stability of organic molecules at high temperatures, but some have suggested that life would have originated outside of the zones of highest temperature. There are numerous species of organisms that can survive under extreme conditions and other organisms currently living immediately around deep-sea vents, suggesting that this is indeed a possible scenario.

Any scientific theory, however, needs to be supported by the scientific method of investigation.  The scientific method involves the collection of data, the formulation of a hypothesis consistent with this data,  making predictions that are consistent with the hypothesis  and then testing whether  the predictions can be verified. 

In trying to comply with this requirement  we are faced with  problems that  appear insurmountable. The earth is thought to have come into being 4.5 billion years ago and the first evidence for life appeared  0.7 billion years later, by which time oceans had already formed. The scientific method seems  almost impossible to apply when looking at things through the mists of time, even with the benefit of hindsight. One approach may be to try and recreate artificially, on  a laboratory scale, conditions that are thought to have existed in the vicinity of volcanic vents, but even if we could do this we may need to sit around for a few million years to verify our thesis. On the other hand, if indeed volcanic vents are the cradle of life, then why would they stop to be so and perhaps the creation of new life is ongoing.  But it will be impossible to perform an experiment such as done by Pasteur, to establish whether life can spring forth around a sterile hydrothermal vent.

Looking at the problem from an entirely different perspective, a relevant question seems to be whether recent death be reversed, since all the biochemical components required for such a reversal are likely to still be present.  Algae exposed to intense sunlight at low tide in the  intertidal  zones, where land meets the sea, may indeed appear dried out and “dead”, but such marine algae have tolerance to frequent water deprivation built into their  biochemical makeup and are quickly revitalized when the tide returns. Seeds are able to tolerate very low moisture levels due to specific changes in their enzymes and in the composition of  solutes  inside their cells, such as to compensate for hydrogen bonding interactions that were lost due to the decreased availability of intracellular water.  Similar patterns of adaptation have been found in a group of plants known as “resurrection” plants that can tolerate very low moisture levels. ( A pertinent question is whether such adaptive traits can be conferred onto economically important crops by specific modifications in their genomes.  This would then make it possible for such genetically modified crops to survive extreme droughts). 

The simple answer, therefore, seems to be that stresses can be survived by a series of adaptive responses in seeds, algae and resurrection plants, such as to avoid death, but we have no evidence that death itself  can be reversed, however recently death had occurred.

At times it is as though the hand of a super intelligent tinkerer can be discerned in the progress of evolution to produce more efficient organisms. It was first proposed by Carl Woese in his RNA world hypothesis that ribonucleic acids (RNA) played a  very important role in early life forms, in that all genetic information was carried in RNA. RNA can also perform certain catalytic functions as ribozymes, a property that has been retained in the catalytic site of ribosomes, which are the seat of protein synthesis in all organisms.  To switch from RNA to DNA as the carrier of genetic information held definite advantages since the lack of a 2’-hydroxyl group in the ribose moieties of DNA molecules confers enhanced stability on DNA relative to RNA. But to achieve this it is necessary to produce an enzyme, ribonucleotide reductase, that can reduce ribonucleotides to deoxyribonucleotides. And to produce the ribonucleotide reductase we would need a gene that encodes it.  But could there have been a RNA encoded gene within this RNA world that coded for an enzyme which  produces the deoxyribonucleotides needed to switch all genetic information to DNA?  This would certainly be a weird example of foresight in an early form of life. To replicate genetic information  held in RNA would also have required a DNA polymerase with reverse transcriptase* ability to be able to use RNA strands as template.

Perhaps our intelligent tinkerer thought about all of this.

*(Reverse transcriptase is an enzyme that can produce DNA strands from a RNA template and is also the means by which the AIDS virus RNA is converted into DNA in infected cells).

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