By Vexen Crabtree 2008
It took 4.5 billion years of tumultuous history before Earth hit upon the right conditions for the creation of organic chemicals. Of the crystal replicators, it was DNA that was the most successful, becoming the prevalent and stable replicator, marshalling the available materials to endlessly copy itself. From then, it was a long time before single-cell life emerged, and then an even longer period before multicellular life finally burst upon the scene.
This page is old and poorly referenced especially in the details on biochemistry, despite my 2008 edit that improved the style of the page.
There are two main theories on abiogenesis1:
Hydrothermal vents "on the early Earth's deep ocean floor gave rise to conditions for life. The early Earth would be a prime place for such vents, as the thin crust had many more breaks than today's thicker crust"1. Primitive extreme heat-loving life has indeed found on such vents, which spew the correct chemicals suitable for the development of life.
Primordial soup: "In 1953, chemists Stanley Miller and Harold Urey developed a mixture of molecules thought to be similar to Earth's atmosphere about 4 billion years ago and subjected the mix to an event similar to lightening". They thusly produced a variety of organic chemicals1. Likewise, a more accurate replication of the conditions on the early Earth was used by John Sutherland from the University of Manchester, UK. He "seem[s] to have got it right. The recipe and conditions that they came up with to mix the five ingredients - including a good blast of UV light - produce ribonucleotides" - New Scientist (2009)2.
The hydrothermal vents origin generally has more evidence for it than the lightning-strike model, although, the evidence does not yet rule either theory out. The most ancient genes traced on Earth hint that extreme heat, radiation and pressure were the environmental conditions that early life endured3. Geologists inform us that in the preceding 4.5 billion years, the Earth has gone through many changes. Prof. Paul Davies quips that "Earth" is a most unsuitable name for our planet as life was forming:
Back four billion years [...] the whole world is almost completely submerged beneath a deep layer of hot water. No continents divide the scalding seas. Here and there the peak of a mighty volcano thrusts above the surface of the water and belches forth immense clouds of noxious gas. The atmosphere is crushingly dense and completely unbreathable. The sky, when free of cloud, is lit by a sun as deadly as a nuclear reactor, drenching the planet in ultra-violet rays. At night, bright meteors flash across the heavens. Occasionally a large meteorite penetrates the atmosphere and plunges into the ocean, raising gigantic tsunamis, kilometres high, which crash around the globe.
The seabed at the base of the global ocean is unlike the familiar rock of today. A Hadean furnace lies just beneath, still aglow with primeval heat. In places the thin crust ruptures, producing vast fissures from which molten lava erupts to invade the ocean depths. The seawater, prevented from boiling by the enormous pressure of the overlying layers, infuses the labyrinth fumaroles, creating a tumultuous chemical imbroglio that reaches deep into the heaving crust. And somewhere in those torrid depths, in the dark recesses of the seabed, something extraordinary is happening, something that is destined to reshape the planet and, eventually perhaps, the universe. Life is being born.”
The Earth used to be a highly radioactive place. It still is: the deeper you dig, the more radioactive the rocks are. Billions of years ago there was no ozone layer, so the Earth was bathed in deadly UV radiation, as mentioned by Prof. Davies above. He also charts the most ancient forms of life that still exist. We find that the oldest single-cell life copes incredibly well with radiation. It is also anaerobic and even anaerphobic, and thrives only in intense heat. It is clear that the oldest bacteria have such resilience and requirements because life itself evolved in an environment that had no oxygen, was heavily laden in radioactivity, and was at a high temperature. But even these primitive forms of life required organic molecules. Where did they come from? Experimenters have reconstructed several methods by which biological molecules would have arose, as we will see.
“Chemotrophs make biomass from carbon dioxide, which has always been readily available on Earth either as a gas or dissolved in water. Energy can be supplied by a variety of chemical reactions. [...] Among the 50 or so identified species of hyperthermophiles, the organisms with the highest growth temperatures include Pyrodictium and Pyrobaculum. They have no truck with oxygen at all, which accords well with the theory that these heat-loving archaea are living fossils from an oxygen-free era of long ago. These superbugs obtain their energy from sulphur by combining it with hydrogen to make hydrogen sulphide.
Sulphur is scattered widely among important biomolecules, a minor but important chemical in extant life. Sulphur-metabolizing bacteria include some of the most ancient hyperthermophiles. This points to a key role for sulphur in the formation of life. The old name for sulphur is brimstone, a devilish substance associated with fiery volcanoes and hell. [...] Not only was the real Eden most likely a Hadean inferno, it may also turn out that life was created from brimstone!”
“Chemists have tried to imitate the chemical conditions of the young earth. They have put these simple substances in a flask and supplied a source of energy such as ultraviolet light or electric sparks - artificial simulation of primordial lightning. After a few weeks of this, something interesting is usually found inside the flask: a weak brown soup containing a large number of molecules more complex than the ones originally put in. In particular, amino acids have been found - the building blocks of proteins, one of the two great classes of biological molecules. [...] Laboratory simulations of the chemical conditions of earth before the coming of life have yielded organic substances called purines and pyrimidines. These are building blocks of the genetic molecule, DNA itself.
Processes analogous to these must have given rise to the 'primeval soup' which biologists and chemists believe constituted the seas some three to four thousand millions years ago. [...] Under the further influence of energy such as ultraviolet light from the sun, they combined into larger molecules. [...]
This process could continue as a progressive stacking up, layer upon layer. This is how crystals are formed. On the other hand, the two chains might split apart, in which case we have two replicators, each of which can go on to make further copies. [...]
So we seem to arrive at a large population of identical replicas. But now we must mention an important property of any copying process: it is not perfect. Mistakes will happen. [...] Erratic copying in biological replicators can [...] give rise to improvement, and it was essential for the progressive evolution of life that some errors were made.”
The conditions on primitive Earth can be reconstructed in a laboratory, wielding the production of simple amino acids and other biochemicals. These rose to fame with the famous Miller and Urey experiments. In 1953 Stanley Miller subjected a mixture of methane, ammonia, hydrogen and water in a 3-part system (gas, vapour, liquid) to the action of an electric discharge. Oparin and Haldane had already predicted the results of this: A multitude of organic molecules, sugars and amino acids were formed. These reactions were more efficient if the system was held at a higher temperature. The organic material was found mostly in the water chamber. The vast majority of organic molecules are not stable in an oxidizing atmosphere - such as the one we now have, which is another clue that biogenesis occurred deep, and not on the surface.
We know more about the specific formation of organic material that we did fifty years ago, and all types of amino acid but one have been recreated using variations on the original experiments. Varying the temperature, ratios and methods of ionisation will lead to successful results - as long as the sphere remains reducing (not oxidizing). Katchalsky's group (Israel) first succeeded in forming polypeptides with Montmorillonite (a highly common clay) up to an efficiency of nearly one hundred percent. It is widely regarded that clay, with its ideal chemical properties and its abundance under most of the oceans and the Earth, is the likely candidate for the source of the main evolutionary steps that occurred from chemistry to biology. There are forms of crystal evolution that can be observed in clays, where different crystals cause the metabolism of different chemicals and forming patterns, of themselves, inside the clay. Many other experiments and variations of the Miller-Urey lines have resulted in the spontaneous production of organic molecules; many theorists have held that after millions of years of these processes, the Earth would have been covered in a primordial soup of organic compounds.
From these chemicals many types of sugars and bases can be (and are) formed. More experiments continue to produce evidence that most important biochemicals are formed with ease under prebiotic conditions. Continued reactions such as simply stirring formaldehyde with calk produce important molecules such as deoxyribose, a constituent of DNA. Over such a huge span of time the reactions would have produced a huge abundance of organic matter laid on the clays of the oceans.
Coincidentally some of our most ancient religions and philosophies have held that mankind was 'made' from clay. Although there some serious caveats to mention before the poor reader starts going all medieval: (1) they do not mean the precise substance as described by science, (2) life doesn't come "from" clay, some types of clay merely acted as a catalyst, and (3) we merely translate (quite a few) ancient words as 'clay' which were themselves used to describe a variety of materials. Nonetheless it is still nice that by luck some pre-science beliefs do actually hit on correct-sounding statements, even if for the wrong reasons. Finally, the use of clay as a building material of the gods makes sense in terms of human experience because after all, clay is what us Humans created models and figurines out of.
5000 years ago in Sumeria: It was said that the god Enki created humans by forming their shape in clay by laying in it7 and the goddess Aruru created the wild man Enkidu "from a piece of clay moistened with her own spittle"8. The Epic of Atrahasis records that humans are made from a mixture of clay and divine blood and saliva for the purpose of working the soil on the Earth (pictured on the right, from the British Museum).9
Greek science, 2500 years ago: Anaximander of Miletus (~610BCE-546BCE) was an early scientist from Ionia in ancient Greece. "He proposed the spontaneous origin of life in mud, the first animals being fish covered with spines. Some descendants of these fishes eventually abandoned the water and moved to dry land, where they evolved into other animals"10. A pleasing precursor to the theory of evolution!
The Hebrew Scriptures, 6th centuryBCE: "The LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul. [...] Out of the ground the LORD God formed every beast of the field, and every fowl of the air" (Genesis 2:7,19).
The pagan Stoics, from the 3rd centuryBCE, believed that "a human being is partly fire, partly made of lower clay; in so far as he is fire [...], he is part of God"11. Our earthly component came from clay.
Islam, 1300 years ago:
The Qur'an contains many clear statements that mankind was made from clay. These can be found in Qur'an 3:49 (a bird is made by clay by the power of God), 6:2, 7:12, 15:26, 17:61, 38:71,76. But that's not the whole story. In Qur'an 15:26 there are some strange additions; mankind was made in clay "that gives forth sound, of black mud fashioned in shape", or from a different translation, "from dry clay and black moulded loam" (Dawood). Clearly, this is not the wet Monmorillonite clay that may have played an important part in the history of the earth in helping in the formation of the first organic molecules. Unfortunately this "scientifically" correct statement in the Qur'an falls foul of technicalities: the role clay played in the ancient evolution of life was merely that of a catalyst, and life does not come "from" clay at all. And... the formation of life from organic chemicals involved so many steps over such a period of time, that almost any statement about creating life "from" something could be said to be true. See: Islam and Science: Errors in the Qur'an and Arab Education: 2. Biology Mistakes.
Even before the end of the period that produced the prebiotic soup chemicals would have been inter-reacting in increasingly complex ways. A polymer (a generic name) consists of a row of molecules attached end on end. An example would be a chain of people holding hands. The chemical reactions mean that the highest potential is at the end of these chains where the chain can gain length by reacting with more molecules. Many types of polymers only accept the same molecules of which it is itself comprised. We therefore have a chain of "people" that grow in length.
As the polymer becomes long it will eventually break into two. Physical forces, UV radiation, oxygen molecules, ionized particles can all cause this to happen and it is frequent. We therefore have a self-replicating polymer that duplicates, uses available resources and has potential to mutate when chemical reactions go astray. Any crystal that grows is a limited example of a type of life. So, here are a few quotes from experts in the first principles of evolution who both point out that this simple starting-point enabled evolution to start playing a part:
“This process could continue as a progressive stacking up, layer upon layer. This is how crystals are formed. On the other hand, the two chains might split apart, in which case we have two replicators, each of which can go on to make further copies. [...] So we seem to arrive at a large population of identical replicas. But now we must mention an important property of any copying process: it is not perfect. Mistakes will happen. [...] Erratic copying in biological replicators can [...] give rise to improvement, and it was essential for the progressive evolution of life that some errors were made.”
“...the law of natural selection takes a simple form: The organisms that reproduce most efficiently sooner or later dominate the population ... [this was] recognized long before Darwin developed his complete theory, for example by Malthus at the end of the 18th century”
L.E.Orgel "The Origins of Life" (1973)12
However, it is not the generic crystal we are interested in. Why is carbon the fundamental organic element? The simple answer is that if another chemical, maybe Silicon, was more appropriate then the chemical reactions would have favoured it and it would have dominated. Of all the elements, one of them was most efficient at these complex reactions. It was carbon. Perhaps on other planets it will be a different element, it depends on factors unknown; most likely temperature, the speed that the planet cooled, etc. Here, carbon was best. Because of that, other elements that bind easily to carbon became prominent, mainly the CHOMSP group.
It is obvious that if there are two similar strands which both require the same chemicals, that the most efficient one will eliminate the other one over time. Mutations and errors will create variants and we therefore have evolution, as attested to by our experts above.
Let us consider three types of mutation: One that is irrelevant and causes no noticeable change, one that causes the protein (or structure) to be unstable or "broken" and the third type - where it continues to function in the same way, with only a small difference.
In the second case, a major mutation could result in a radically different structure, but most the time it will result in failure. In the third case however we have possible evolution. If this mutation is more efficient or equally functional as the parent, it could result in a new type of crystal duplication. If the new variant uses the local chemical resources better than the parent with regards to self-duplication then it will proliferate.
We are considering a time before such things as cells and other highly macroscopic complex organisms. The same methods of competition apply at every level of chemistry - driven by the fact that chemical resources are limited.
Silicon is the same group as carbon. It is postulated that carbon, being -4 valency, is ideal to support complex molecules without making processing too difficult or unpredictable. Silicon is the most likely molecules, for most laymen, that can be considered a valid alternative for carbon as it can theoretically cover the same complexity range of molecules as carbon.
Silicon based life would require a higher energy metabolism. Indeed silicon life, although it would seem plausible, would be highly different from carbon-based life. All reactions would be at a much higher temperature in order to react with silicon atoms and therefore most of the structures and metabolic paths that we use would not be enough. Also at higher temperatures many of the chemicals we use are unstable.
It could be guessed that silicon life could only exist in a world where stronger and more consistent energy sources are available. A world closer to a sun, or with a heat-trapping atmosphere. However despite many attempts it has not been possible to build any accurate metabolic paths that could conceivably deal with a silicon-based organic system. Life based on silicon would be completely different (I mean it) from life as we know it.
Life evolved on Earth using all the materials available - carbon happened to be the most suitable carrier for organic methods on this planet due to this planets environment and conditions. We can therefore guess that life on planets that are similar to ours will also find carbon the most suitable base-element for organic molecules.
Towards the end of the abiogenesis era, masses of new biological compounds were being assimilated and used by replicating units that were once crystals, but which we now call by another name. DNA was produced very early on; it has existed for 3.5 billion years; Prof. Davies remarks that "[i]t makes nonsense of the phrase 'as old as the hills': DNA was here long before any surviving hills on Earth"13. For the following billions of years, DNA existed inside disconnected cells of protective material. Prof. Richard Dawkins succinctly describes the transformation from that state to the present day:
“Was there to be any end to the gradual improvement in the techniques and artifices used by the replicators to ensure their own continuation in the world? There would be plenty of time for improvement. [...] Four thousand million years on, what was to be the fate of the ancient replicators? They did not die out [...] but do not look for them floating in the sea. [...] Now they swarm in colonies, safe inside gigantic lumbering robots, sealed off from the outside world, communicating with it by tortuous indirect routes, manipulating it by remote control. They are in you and in me; they created us, body and mind; and their preservation is the ultimate rationale for our existence. They have come a long way, those replicators. Now they go by the name of genes, and we are their survival machines.”
How did these replicating chemicals evolve to collect such a massive quantity of material that their bodies contain uncountable billions of proteins and chemicals? The cell is the most important first stage. Macromolecules and such polypeptides would have survived better if they could retain molecules that they required for later use or for catalysts in reactions that they carry out during replication. Therefore, those that chemically retained some necessary chemicals survived more leading to the growth of species of 'things' that had thin membranes. Thick membranes, impermeable ones, would have held out too much, when the aim was simply to hold down some types of molecules/protein that is useful to the organism. The fossil records suggest that we had cells with membranes at least 3 billion years ago, but it was another two billion years from then until we had multicellular organisms appear in the fossil record.
Following on from the formation of the prebiotic soup there was another 2 billion year phase of oceanic anaerobic oxygen production which is believed to be the source of a lot of today's oxygen. This production meant that aerobic respiration became possible, leading to today's typical oxygen dependant cells.
There are many primitive types of cell-species known, but I will note one of the classes in particular because it is normally noted, within this context. It is hailed as one of the most important candidates of the ancestor of the cell as we know it. The class of Thermophilic Prokaryotic Bacteria (heat-loving with no nuclei) survive in non-boiling water over 100 degrees Celsius. They are endowed with a sulphur based metabolism.
The only place these could have existed is in highly pressurized areas of ocean, near natural sources of heat. It is precisely at these locations, at the thermic chimneys that are abundant on the bottom of the deepest oceans, that we find such bacteria. The combination of the hot energy source and the concentration of the prebiotic soup that would exist at that depth, 4 billion years ago, would be a dreamily rich location of polypeptide chemical evolution.
“Methanococcus jannaschii - a strange microbe that was recovered just recently by the deep sea vessel Alvin from a volcanic vent on the Pacific floor. This microbe lives at crushing pressures 245 times greater than at sea level and at scalding temperatures just a few degrees below the boiling point of water. The microbe belongs to an ancient kingdom of organisms known as the Archaea, often found in extreme environments, like hot springs or deep sea vents. Despite their obscurity, the Archaea constitute a third kingdom of life, alongside the Prokarya, cells like bacteria that have no nucleus, and the Eukarya, organisms with nucleated cells, which include all plants and animals.
The entire genome or genetic blueprint of the microbe has now been chemically sequenced indicating that the Archaea is neither plant nor animal, yet is related to both -- and likewise related to humans. Further study of these organisms may lead to further clarification of the path of evolution on Earth -- and the possibility of life on other planets.”
“Over the past two centuries scientists have painstakingly pieced together the history of life. The fossil record shows clearly that ancient life was very different from extant life. Generally speaking, the farther back in time you go, the simpler were the living things that inhabited the Earth. [...] This record of complexification and diversification is broadly explained by Darwin's theory of evolution.”
From the appearance of the cell in the fossil record, through to multicellular organisms and amoebas, etc, life is increasingly well documented.
Single-cell life has a very high rate of evolution and change16. Bacteria, therefore, adapt quickly (in evolutionary terms) to things like new antibacterial products. But the development from unicellular to multicellular life took a long time in history, as we will see below. The details are important, because analysing the timespans between major developments is one theoretical way to measure the likelihood that particular biochemical developments will be made on other planets similar to Earth, and, in general the greater insight we have into the genetic history of life, the greater our ability to combat problems such as disease and ageing.
“Geologists divide up the 4600 million years of the earth's geological history into major areas and periods. [...] The earliest era is called the Precambrian - a long, complex and poorly understood phase. During it there were periods of mountain-building and at least one ice age. It was a time when the lithosphere, atmosphere and hydrosphere first developed, and the first organisms appeared. Life was, however, essentially primitive, consisting of simple plants like algae.”
"The Nature of the Environment" by Prof. Andrew Goudie (1993)17
Some proteins that are produced by a cell's DNA protrude through the cell lipid wall, and actively retain chemicals from the local environment. These sensor molecules developed into the system of senses that single-cell organisms use to navigate their environment. In multicellular species, the same mechanisms "form the basis for chemical communication between cells and organs, using hormones and neurotransmitters"18. The mutation which caused multicellular plants to arise from replicating cells that do not divide properly had obtained by three billion years ago19. This and the arrival of sexual reproduction a billion years afterwards sped up the value and speed of evolution immensely, resulting in a rapidly expanding variety of life forms.
“For most of the four billion years since the origin of life, the dominant organisms were microscopic blue-green algae, which covered and filled the oceans. Then some 600 million years ago, the monopolizing grip of the algae was broken and an enormous proliferation of new life-forms emerged, an event called the Cambrian explosion. Life had arisen almost immediately after the origin of the Earth, which suggests that life may be an inevitable chemical process on an Earth-like planet. But life did not evolve much beyond blue-green algae for three billion years, which suggests that large life-forms with specialized organs are hard to evolve, harder even than the origin of life. Perhaps there are many other planets that today have abundant microbes but no big beasts and vegetables.”
“The oldest well-documented true animal fossils, [... in] Australia (in the Flinders Mountains north of Adelaide), are dated at 560 million years. Known as ediacara, they include creatures resembling jellyfish. Shortly after this epoch, about 545 million years ago, there began a veritable explosion of species, culminating in the colonization of the land by large plants and animals.”
The Bible (NIV). The NIV is the best translation for accuracy whilst maintaining readability. Multiple authors, a compendium of multiple previously published books. I prefer to take quotes from the NIV but where I quote the Bible en masse I must quote from the KJV because it is not copyrighted, whilst the NIV is. Book Review.
(1995, Ed.) New York Public Library Science Desk Reference. Paperback book. Published by The Stonesong Press Inc. and The New York Public Library, New York, USA.
Budge, E. A. Wallis. (1857-1934)
(1921) The Babylonian Legends of the Creation.
(2003) The Origin of Life. Paperback book. Originally published 1998 as The Fifth Miracle. Current version published by the Penguin Group.
Goudie, Prof. Andrew
(1993) The Nature of the Environment. Paperback book. 3rd edition. Originally published 1984. Current version published by Blackwell Publishers, Oxford, UK.
(2004, Ed.) Jealous Gods & Chosen People: The Mythology of the Middle East. Hardback book. Published by Oxford University Press.
Orgel, L. E.
"The Origins of Life" (1973).
(1995) Cosmos. Paperback book. Originally published 1981 by McDonald & Co. Current version published by Abacus.
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