16
Nov
10

The Origin of Life: Storytelling or Science?

The events and narratives which follow are mostly fictional. Those parts in bold are historical fiction while those in italics are mostly speculation. Sections which lack any embellishment are my explanations and descriptions.

We shall start from a few billion years after the beginning of time, so not the very beginning, but before anything we would call living (at least on this normal little planet orbiting a normal little start in a relatively quite part of a normal galaxy in a mostly empty portion of the universe). We begin when the planet has cooled enough to sustain standing water on the surface. When was this? Some time between 4.4 and 4.2 billion years ago. Approximately two hundred million years after the collapse of the nebula which formed the Sun. The oldest known fossils date to approximately 3.5 billion years ago. This is where our fictional narrative ends, and it shall be denoted as T=0, for dating purposes, we’ll pretend it is PRECISELY 3.5 billion years ago. This is not to say there is no evidence of biological activity before this time, since the oldest evidence for biological activity (in the form of biochemical markers of biological activity) date to 3.85 billion years ago.

T=-500,000,000
The first self-replicating form, only a few dozen molecules in size and having all the complexity of a single strand of RNA, shorter than the smallest genomes which sprung into existence from a random assemblage of molecules. One of millions of short sequences of RNA trapped in this particular little cavity of a rock. Because of its particular palindromic sequence, it attaches and binds to shorter sequences and free floating nucleotides and holds them at the correct orientation to yield a duplicate of itself, but because the bonds holding these two sequences together is so weak, they float apart to facilitate, each, additional copies. Alas, these copies aren’t always accurate, and looped segments are sometimes included which result in copies which cannot replicate. All is not lost, however, because all of these sequences break down, meaning those lineages which continue to replicate are the only ones which remain. Some of these, due to quirks of replication, are left with functional loops which form occasionally. These loops do interesting things, some twist and fold upon themselves leaving peculiar pits and dents in the structure, and while these do not remain for long, it is long enough to give these strands significantly longer lifespans. The folding and twisting does something else: the RNA now produces multiple different replicates, depending upon the state of the folding. Some of these smaller RNAs, while they last for only a brief period of time–far less than the parent RNA, aid in the survival of the parental RNA sequence by stabilizing the loops and hairpins as well as unfolding them at certain stages of the replication cycle.

T=+3,499,997,400
Where the idea of spontaneous generation (you didn’t think I would avoid this interesting bit, did you?) started. A man, a philosopher, about 40 years old, is standing beneath a stoa describing the origin of the world. He says “the Earth was formed when hot and cold first separated, it developed a hard shell which is partially cracked, it is through these cracks that we see the fires of the infinite. And now for the plants and animals, they and we arose from the water and the air. Some plants are born of the same type of parent while others grow from the surrounding materials. Those which come from parents had a first animal which sprung forth from one of the ethereal or aquatically appearing types.”

T=-400,000,000
Those little RNAs have changed since we last saw them, for one, they are now housed in a shell comprised of a phospholipid bilayer. They are much longer, with regulatory mechanisms to change which of those smaller alternative RNAs are produced. The “alternative RNAs” now have numerous functions, some poke through the phospholipids and bind to free floating RNAs, some bind other bilayers, while still others form structural components. Some of these protocells have alternative RNAs which facilitate the combining with other protocells. Others have components which add and remove portions of the bilayer while still others invade other pseudocells and use the contents as raw materials. A few of these pseudocells have combinations of DNA and RNA within them, the DNA functioning as a stable template for the shorter alternative RNAs. There is a vast diversity of these protocells, with a wide range of compositions.

While it certainly seems that cellular life must have existed long before the first microfossils, we must keep in mind that what we call “living” and what served as “primordial life” are two completely different things. Primordial life, conversely needs to fulfill four requirements: simple, self-replicating, selectable, and variable. Simple in that it is not so complex that its spontaneous arising is not highly improbable. Self-replicating in that it catalyzes its own reproduction. Selectable means that it must be subject to fairly rapid spontaneous degradation, so as to yield a persistence of only those which are effective at self-replication. Variability in sequence is very important to allow the integration of novel functional sequences. Auto-catalytic RNAs fulfill all four of these features, but we are left with a question: how do you get the basic components of the RNAs? Synthesis of all four ribonucleosides easily performed in a laboratory. DNA is slightly more difficult and requires the methylation of uracil at the fifth carbon. This can certainly be catalyzed by a ribozyme, and it’s absence in RNA lends support to the notion that RNA existed before proteins.

Book excerpt: T=+3,499,997,700

Now some animals come into being from the union of male and female, i.e. all those kinds of animal which possess the two sexes. This is not the case with all of them; though in the sanguinea with few exceptions the creature, when its growth is complete, is either male or female, and though some bloodless animals have sexes so that they generate offspring of the same kind, yet other bloodless animals generate indeed, but not offspring of the same kind; such are all that come into being not from a union of the sexes, but from decaying earth and excrements.

Some insects copulate and the offspring are produced from animals of the same name, just as with the sanguinea; such are the locusts, cicadae, spiders, wasps, and ants. Others unite indeed and generate; but the result is not a creature of the same kind, but only a scolex, and these insects do not come into being from animals but from putrefying matter, liquid or solid; such are fleas, flies, and cantharides. Others again are neither produced from animals nor unite with each other; such are gnats, ‘conopes’, and many similar kinds. In most of those which unite the female is larger than the male.

T=+3,499,998,500
It is around this time since the beginning of known life on this planet that Christians decided adopting the views of the leading Greek philosophers regarding the origins of specific organisms would probably be a good idea. If only the leaders of theses sects would pay attention to contemporary work as well rather than relying only upon ideas older than any modern country, I probably wouldn’t need to write this. Nevertheless, ideas within Aristotle’s and Plato’s works continue to confound honest inquiries into the very nature of life.

T=-300,000,000
We find protocells comprised of the more stable DNA with many ribozymes and a few proteins. These proteins are capable of only a select few reactions, namely those involved in DNA maintenance. This DNA isn’t like that seen in bacteria. It is linear but without histones, and free floating within the bilayer. This is still not the last universal ancestor, it is still based primarily upon ribozyme activity than proteins. It is an amalgam of DNA segments. It divides sporadically, not by fission, but by a process similar to budding. As the new bud grows, new copies are copied into the growing bud, finally pinching off to separate the growing bud.

Book excerpt: T=+3,499,999,090

In the creation, therefore, of the beings destined to inhabit the lower regions of the universe, the whole of which is frequently included in the term “earth,” it was fitting that living beings should first be produced from the waters and afterwards from the earth. For air is so akin to water that it thickens by being mixed with water in a vaporous state, it produces the storm blasts (the wind, I mean), it condenses the clouds, and it can support birds in flight. Now the pagan poet spoke truly when he said, “Olympus rises above the clouds” and “Lofty things are at peace,” for it is said that on the summit of Mount Olympus the atmosphere is so rarefied that no clouds overshadow it and no wind disturb it, no birds can fly there, nor can men who have scaled it find the denser air to breathe that they are used to below. Nevertheless, that atmosphere is air…

Oh, creation myths, why must you constantly ruin good inquiry?

T=-200,000,000
What we find could quite accurately be termed cells. While lacking a few rather important features of the last universal ancestor. They reproduce and grow in much the same way as L-form bacterial cells but lack many of the regulatory mechanisms and cell signaling pathways. They also lack any form of cell walls, but curiously, they do have cytoskeletal analogues. They are also occasionally infected with something similar to viruses, but these viruses aren’t like those we encounter today. These destroy the DNA within the cells and inject their own DNA, effectively taking over the cell completely. These particular “viruses” are a reproductive form of one type of cell while others are more similar to a dormant cell locked within a capsid, a kind of DNA time capsule.

T=+3,499,999,858
The man watched patiently as he brought the flasks to a boil, two years earlier, Louis Pasteur had claimed particles in the air were the cause of spoilage, but this did not convince Charles, though. Oh no, he was convinced that it would still spoil since everyone knew the little creatures that spoiled liquids grew from those liquids. Pasteur must have done something else to the liquids, the milk tasted sweeter, so perhaps he added sugar to it. Once the unusually shaped flasks were heated, he allowed them to cool and sit for several days. Strangely, they did not seem spoiled, the broth and beer remained clear. How could this be if the small creatures responsible for spoiling food came from the food itself?

T=-100,000,000
We now find free floating cells capable of sticking together in clumps. Perhaps “sticking” isn’t the appropriate word, more like “incompletely separating.” These small groups of cells exchange nutrients, some absorb carbon dioxide and produce sugars while others take nitrogen compounds and convert them to amino acids, exchanging the results in an early form of symbiosis. They do not form biofilms like the biotic forms of stromatolites, and are frequently degraded by other cells in the ancient oceans.

I now leave you to your own imaginations, we can explore the various hypotheses which actually resulted in living organisms, but the end result is the same. Every one of these hypotheses is quite plausible and may have very well lead to life somewhere in the universe. There is a lesson in that very fact. Whenever we think of “life,” we think of our lives, not “organized movement of molecules in such a way as to work against entropy.” We can, quite easily, describe death as the rapid increase in entropy within a previously organized and open system. What precisely life is may take far more time to discuss than how life may have begun. it could easily be argued that life never really began, but instead emerged as a function of the chemistry of the early planet which subsequently survived the destruction of the very conditions which brought it about.

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3 Responses to “The Origin of Life: Storytelling or Science?”


  1. 1 Plint the in Between
    November 16, 2010 at 1:26 pm

    Great – thanks for taking that on.

  2. 2 jaredcormier
    November 16, 2010 at 1:45 pm

    I was just trying to illustrate how abiogenesis and spontaneous generation are so very different. Hope it worked…

  3. 3 Pliny the in Between
    November 16, 2010 at 2:12 pm

    Yeah, there is a bit of difference between flies springing to life in old meat in a couple of days and a series of interwoven biochemical events stretched over half a billion years…


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